Primo Congresso Nazionale della Divisione di
Chimica Teorica e Computazionale della società
Chimica Italiana
Atti del Congresso
22-23 Febbraio 2012
Area della Ricerca del CNR,
Pisa
Si ringraziano Antonio Romero e Francisco Avila per l’immagine di copertina
Primo Congresso Nazionale della Divisione
di Chimica Teorica e Computazionale della
Società Chimica Italiana
Atti del Congresso
I
II
r
Primo Congresso Nazionale della Divisione di Chimica
Teorica e Computazionale della società Chimica Italiana
Pisa, Area della Ricerca CNR
22-23 Febbraio 2012
Comitato
scientifico
Comitato
organizzatore
Gianfranco Pacchioni
Orlando Crescenzi
Dario Duca
Luciana Marinelli
Antonino Polimeno
Fabrizio Santoro
Mauro Stener
Maurizio Casarin
Fabrizio Santoro
Mauro Stener
Francisco Avila
Alberto Coduti
III
IV
Sponsors
Si ringrazia la Provincia di Pisa per aver gentilmente fornito le
cartine della città di Pisa
V
VI
La Divisione di Chimica Teorica e Computazionale della Società Chimica
Italiana, nata ufficialmente il 1 gennaio 2011, si avvia a concludere il suo
primo anno di attività, consistita soprattutto nell’organizzazione dei lavori
della Divisione nell’ambito del Congresso Nazionale SCI di Lecce dello scorso
settembre e nella istituzione del Premio “Medaglia Roetti” per ricercatori al di
sotto dei 40 anni. Il 1° Congresso della Divisione, in programma a Pisa il 22 e
23 Febbraio 2012, rappresenta un' importante occasione di incontro tra chi
opera in ambito teorico-modellistico chimico. E’ anche un momento per fare il
punto sulle ricerche e sulle eccellenze nel settore a livello nazionale nonché un
passo importante verso la creazione di una forte comunità di riferimento che
possa portare a positive sinergie sul piano di iniziative culturali e progettuali
comuni.
GIanfranco Pacchioni
Presidente della Divisione di Chimica Teorica e Computazionale della SCI
VII
VIII
Indice:
Keynote Lectures
KN01
KN02
KN03
KN04
KN05
KN06
KN07
KN08
KN09
KN10
C. Zannoni
Simulating molecular organisations of liquid crystals and other
functional materials in the bulk and close to interfaces
F. De Angelis
Modeling dye-sensitized solar cells: Understanding the
mechanism, improving the efficiency
B. Mennucci
How to model environment effects in electronic energy
transfer (EET) processes in light-harvesting systems
S. Moro
Targeting Membrane receptors: from virtual to real world
Conferenza Medaglia Pisani – R. Dovesi
1970-2012. Past and future of simulation in solid state
Chemistry and Physics at the Theoretical Chemistry Group in
Torino
F. Zerbetto
A bridge over chemical timescales
M. Olivucci
Using Trajectories to Probe the Mechanism of Ultrafast
Biological Photoisomerizations and Internal Conversions
C. Di Valentin
Engineering semiconductors band gap for visible light
activation
A. Painelli
Unconventional inhomogeneous broadening from polar
alvation: an essential state description of symmetry breaking in
charge-transfer chromophores
A. Rizzo
Non-linear spectroscopies and chirality
3
4
5
6
7
8
9
10
11
12
IX
Oral Contributions
OR01
OR02
OR03
OR04
OR05
OR06
G. Raos
Non-equilibrium simulations of polymeric materials:
applications to rubber reinforcement and polymer friction
R. Chelli
Exploiting configurational freezing in nonequilibrium Monte
Carlo simulations
G. Parisio
Flip-flop of steroids through lipid membranes: a rototranslational diffusion mechanism for crossing free energy
barriers
F. Negri
Modeling electronic and charge transport properties of
ambipolar and n-type organic semiconductors
A. Amadei
Theoretical Modeling of physico-chemical observables in
complex environments
G. Graziano
A statistical thermodynamic model for micelle formation
15
16
17
18
19
20
OR07
OR08
OR09
OR10
OR11
OR12
OR13
X
M. Visciarelli
Single molecule diodes based on etero – binuclear transition
metal complexes
G. Barone
DFT-D calculations of the structure of DNA oligomers
S. Alcaro
Molecular Modelling of DNA G-quadruplex complexes
G. Milano
Lipid-Based Nanostructures for Drug Delivery: Development
of Hybrid Particle-Field Molecular Models
I. Daidone
On the origin of infrared spectral changes upon conformational
transitions in proteins
G. Fronzoni
DFT simulation of NEXAFS spectra of molecules adsorbed on
surfaces: C2H4 on Si (100) case study
C. Gatti
Revealing Electron Delocalization through the Source
Function
21
22
23
24
25
26
27
OR14
OR15
OR16
OR17
OR18
OR19
OR20
OR21
OR22
OR23
OR24
OR25
OR26
OR27
F. Pazzona
The Central Cell Model: a cellular automata-based tool to
model molecular adsorption and diffusion in microporous
materials
G. La Penna
Modeling interactions between peptides and metal ions
S. Pipolo
Simulating azobenzenes Self Assembled Monolayers:
structural properties and a new classical force field
F. Gianturco
The chemistry of early universe models from quantum
simulations
C. S. Pomelli
Specific solvent effects in ionic liquid. From reactivity to
solvatochromism
L. Muccioli
Growth of pentacene on C60 from vapor deposition
simulations
B. Civalleri
Assessing the performance of global, range-separated and
double hybrid functionals for crystalline systems
F. Costanzo
Physisorption, diffusion and chemisorbed pathways of H2
molecule on Graphene and Single Walled Nanotube by first
principle calculations
M. Cossi
Ab Initio Modeling of PbSe Quantum Dots for Appications in
Dye-Sensitized Solar Cells
L. Maschio
Post-Hartree-Fock treatment of crystalline periodic systems:
the CRYSCOR code
G. Moro
Typicality of the response by quantum pure states - Barbara
Fresch, Giorgio J. Moro
G. Granucci
On the fly modeling of the photodynamics of spin changing
processes in organic molecules
A. Bagno
Prediction of NMR spectra of paramagnetic species
F. Lipparini
Towards a fully polarizable QM/MM/PCM approach
28
29
30
31
33
34
35
36
37
38
39
40
41
42
XI
OR28
OR29
OR30
OR31
XII
C. Petrongolo
Nonadiabatic Quantum Reactive Collisions on Three Coupled
PESs
D. Skouteris
Dynamics of the N+O → NO+ + e- process by a timedependent method
M. Rutigliano
Collision dynamics for the interaction of oxygen atoms and
molecules on a silica surface
D. Ceresoli
Ab-initio g-tensor of transition-metal complexes from the
orbital magnetization
43
44
45
46
Posters
P01
P02
P03
P04
P05
P06
P07
P08
P09
Elisa Albanese , Bartolomeo Civalleri
Mg/Zn
MIXED-METAL
BOROHYDRIDE
FOR
HYDROGEN
STORAGE:
AB-INITIO
PERIODIC
COMPUTATIONAL STUDY OF THE PHASE STABILITY
AND DECOMPOSITION
Ambra Irene Angioni , Stefano Corni, Benedetta Mennucci
COMPUTATIONAL MODELLING OF THE EFFECT OF
METAL NANOPARTICLES ON THE EXTENT OF
ELECTRONIC
ENERGY
TRANSFER
BETWEEN
ORGANIC CHROMOPHORES
Nerina Armata , Remedios Cortese, Dario Duca, Roberto
Triolo
MOF DERIVATIVES AS MOLECULAR TOOLS TO TRAP
METAL AZIDES
Martina Audagnotto , Anna Maria Ferrari
GLYCINE ADSORPTION ON ANATASE SURFACE: A
DFT PERIODIC STUDY
Francisco Avila , Fabrizio Santoro
COMPARISON OF VERTICAL AND ADIABATIC
HARMONIC APPROACHES FOR THE CALCULATION
OF THE VIBRATIONAL STRUCTURE OF ELECTRONIC
SPECTRA
Francisco Avila , Maria Grazia Lobello, Filippo De Angelis,
Fabrizio Santoro
PHOTOPHYSICAL PROPERTIES OF RUTHENIUM DYES
FOR
APPLICATIONS
IN
SOLAR
CELLS.
A
COMPUTATIONAL STUDY ON N3 DYE
Caterina Bernini , Rebecca Pogni, Riccardo Basosi, Adalgisa
Sinicropi
QM/MM CHARACTERIZATION OF REDOX-ACTIVE TRP
RADICALS IN LIP AND LIP-LIKE SYSTEMS
Alessandro Biancardi , Tarita Biver, Benedetta Mennucci,
Fernando Secco
MODELLING FLUORESCENCE OF INTERCALATING
AND MINOR GROOVE-BINDING MOLECULAR PROBES
FOR NUCLEIC ACIDS: A COMBINED QUANTUMMECHANICAL AND SPECTROSCOPIC STUDY
Enrico Bodo
THEORETICAL DESCRIPTION OF IONIC LIQUIDS:
HIGHLIGHTS FROM RECENT CALCULATIONS
49
50
51
52
53
54
55
56
57
XIII
P10
P11
P12
P13
P14
P15
P16
P17
P18
P19
XIV
Marco Bortoluzzi , Gino Paolucci, Francesco Enrichi, Mattia
Gatto, Stefania Roppa
EXCITED STATES OF N- AND O-DONOR LIGANDS
COORDINATED TO YF3 COMPARED TO THE
RESONANCE LEVELS OF VISIBLE AND NIR-EMITTING
LANTHANIDE IONS
Giuseppe Brancato , Costantino Zazza, Vincenzo Barone
TOWARDS
AN
EFFICIENT
PARALLEL
IMPLEMENTATION OF THE GLOB MODEL
Valentina Cantatore , Giovanni Granucci, Maurizio Persico
TRANSFERABILITY OF NONADIABATIC TRANSITION
RATES: A KEY TO FAST EXCITED STATE DYNAMICS?
Stefano Caprasecca , Ambra Irene Angioni, Benedetta
Mennucci
INCLUDING
ENVIRONMENT
EFFECTS
ON
ELECTRONIC ENERGY TRANSFER PROCESSES: A
FULLY POLARISABLE QM/DISCRETE/CONTINUUM
APPROACH
Silvia Carlotto , Laura Orian, Marilena Di Valentin, Antonino
Polimeno
CHARGE TRANSFER IN MODEL BIO-INSPIRED
PORPHYRIN-CAROTENE DYADS
Alessandro Erba, Luana Lambiase, Andrea Molino, Lorenzo
Maschio, Silvia Casassa
A FIRST-PRINCIPLE PERIODIC APPROACH TO THE
STUDY OF ICE CLATHRATES
Paolo Nicolini, Riccardo Chelli
FREE ENERGY ESTIMATES USING MOLECULAR
DYNAMICS
SIMULATIONS
WITH
DYNAMICAL
FREEZING
Bartolomeo Civalleri , Roberto Orlando, Michel Rerat, Mauro
Ferrero, Radovan Bast
LINEAR AND NON-LINEAR OPTICAL PROPERTIES OF
MOLECULAR CRYSTALS: AN AB-INITIO PERIODIC
COMPUTATIONAL STUDY
Andrea Correa , Luigi Cavallo
DYNAMIC
MODELING
OF
HETEROGENEOUS
ZIEGLER-NATTA CATALYTIC SYSTEMS
Francesco Ferrante, Nerina Armata, Remedios Cortese ,
Fabrizio Lo Celso, Antonio Prestianni, Dario Duca
COMPUTATIONAL APPROACHES USED IN THE
POLYCAT EU PROJECT
58
59
60
61
62
64
66
67
68
69
P20
P21
P22
P23
P24
P25
P26
P27
P28
Ugo Cosentino , Giorgio Moro
COMPUTATIONAL
INVESTIGATION
ON
THE
SPECTROSCOPIC PROPERTIES OF THIOPHENE BASED
EUROPIUM β-DIKETONATE COMPLEXES
Ph. D’Arco, Marco De La Pierre , M. Ferrabone, S.
Mustapha, Y. Noël, R. Dovesi
USE OF SYMMETRY IN THE CONFIGURATIONAL
ANALYSIS FOR THE SIMULATION OF DISORDERED
SOLIDS
Franco Egidi , Vincenzo Barone, Julien Bloino, Chiara
Cappelli
CALCULATING OPTICAL ROTATIONS OF ORGANIC
MOLECULES IN SOLUTION: COUPLING SOLVENT
EFFECTS TO THE ANHARMONIC VIBRATIONAL
CONTRIBUTIONS
Wagner Brandeburgo, Grisell Diaz Leines, Siri van Keulen,
Evert Jan Meijer, Jocelyne Vreede, Peter Bolhuis, Bernd
Ensing
AB INITIO MOLECULAR DYNAMIC SIMULATION OF
PHOTOACTIVE PROTEINS IN ACTION
Cesare Pisani, Alessandro Erba , Matteo Ferrabone, Roberto
Dovesi
NUCLEAR MOTION (TEMPERATURE) EFFECTS ON
THE DENSITY MATRIX OF CRYSTALS: AN AB INITIO
MONTE CARLO HARMONIC APPROACH
Matteo Ferrabone , Michel Rèrat, Fabien Pascale, Jacopo
Baima, Roberto Dovesi
PHONONS WITH THE CRYSTAL CODE
Anna Maria Ferrari , Yves Noel, Marco Delapierre, Ph.
D'Arco, Roberto Dovesi
ON THE USE OF SYMMETRY IN SCF CALCULATIONS
OF FINITE AND INFINITE SYSTEMS: THE CASE OF
FULLERENES AND CARBON NANOTUBES
Daniel Forrer , Michele Pavone, Maurizio Casarin, Vincenzo
Barone
SEMI-EMPIRICAL DISPERSION CORRECTION AT THE
METAL/ORGANIC
INTERFACE:
ACCURATE
DESCRIPTION OF MOLECULAR ADSORPTION ON
AG(111)
Alberto Fraccarollo , Angiolina Comotti, Maurizio Cossi,
Leonardo Marchese
ADSORPTION OF GASES IN NANOPOROUS DIPEPTIDEBASED MATERIALS. COMPUTER SIMULATION AND
EXPERIMENTAL STUDY
70
72
73
74
75
76
77
78
79
XV
P29
P30
P31
P32
P33
P34
P35
P36
P37
XVI
Elisa Frezza , Alberta Ferrarini
MODELING THE CHIRAL NEMATIC PHASE OF
OLIGONUCLEOTIDES: PHASE CHIRALITY AS A
REPORTER
OF
CHANGES
IN
DNA-DNA
INTERACTIONS?
Elisa Gambuzzi , Alfonso Pedone, Gianluca Malavasi, M.
Cristina Menziani
CMD AND DFT CALCULATIONS AS A CHALLENGE
FOR MAS-NMR SPECTRA INTERPRETATION: A ROUTE
TOWARD THE ELUCIDATION OF SILICATE GLASS
STRUCTURES
Fabio Grassi , Maurizio Cossi, Mario Argeri, Caterina Benzi,
Alberto Fraccarollo, Leonardo Marchese
DFT-TDDFT STUDY OF SQUARAINE ADSORPTION ON
PbSe SURFACES
Cristina Greco , Ronald Y. Dong, Alberto Marini, Elisa
Frezza, Alberta Ferrarini
AN INTEGRATED COMPUTATIONAL METHODOLOGY
TO BRIDGE THE MOLECULAR AND ELASTIC
PROPERTIES OF A BENT-CORE LIQUID CRYSTAL
Emiliano Stendardo, Francisco Avila, Fabrizio Santoro,
Roberto Improta
VIBRATIONALLY RESOLVED ABSORPTION AND
EMISSION SPECTRA OF OLIGOTHIOPHENES IN GAS
PHASE AND SOLUTION BY FIRST PRINCIPLE
CALCULATIONS
Sandro Jurinovich , Ilaria Degano, Benedetta Mennucci
COMPUTATIONAL STUDY OF THE INTERACTIONS
BETWEEN IRON-GALL DYES AND WOOL FIBERS
Valentina Lacivita , Michel Rérat, Roberto Orlando, Mauro
Ferrero, Roberto Dovesi
CALCULATION OF LONGITUDINAL POLARIZABILITY
AND
SECOND
HYPERPOLARIZABILITY
OF
POLYACETYLENE WITH THE COUPLED PERTURBED
HARTREE-FOCK/KOHN-SHAM SCHEME. WHERE IT IS
SHOWN HOW FINITE OLIGOMER CHAINS TEND TO
THE INFINITE PERIODIC POLYMER.
Anna M. Ferrari, Martina Lessio , Michel Rérat
ELECTRONIC AND DIELECTRIC PROPERTIES OF TIO2
NANOTUBES
Andrea Lombardi , A. Laganà, F. Pirani, M. Bartolomei
ENERGY BALANCE IN CO2 + CO2 HIGH TEMPERATURE
COLLISIONS
80
81
82
83
84
85
86
88
89
P38
P39
P40
P41
P42
P43
P44
P45
P46
Andrea Lombardi , A. Laganà, F. Pirani, M. Bartolomei, V.
Aquilanti
HYPERSPHERICAL SEPARATION OF THE INTERNAL
DEGREES OF FREEDOM IN TRIATOMIC MOLECULES:
X-A-X LINEAR SYMMETRIC CASE
Lorenzo Maschio , Michel Rèrat, Roberto Orlando, Roberto
Dovesi
AB INITIO ANALYTICAL INFRARED AND RAMAN
INTENSITIES FOR PERIODIC SYSTEMS THROUGH A
CPHF METHOD
Gloria Mazzone , Nino Russo, Emilia Sicilia
HOMOGENEOUS GOLD CATALYSIS: HYDRATION OF
1,2-DIPHENYLACETYLENE WITH METHANOL IN
AQUEOUS MEDIA. A THEORETICAL VIEWPOINT
Federico Melaccio , Igor Schapiro, Massimo Olivucci
ELECTROSTATIC EFFECTS INDUCED BY THE LIGHTDRIVEN RETINAL CHROMOPHORE ISOMERIZATION
IN BOVINE RHODOPSIN
Francesca De Rienzo, Marta del Cadia, Maria J. Ramos,
Maria C. Menziani
CHARACTERIZATION OF THE EXTRACELLULAR
SUBUNIT-SUBUNIT INTERFACE OF THE 5-HT3
RECEPTORS BY MEANS OF COMPUTATIONAL
ALANINE
SCANNING
MUTAGENESIS
AND
MOLECULAR DYNAMICS
Giorgio Moro , A. Arrigoni, L. De Gioia, U. Cosentino, R.
Brambilla
PROTEIN-PROTEIN INTERACTIONS IN THE COMPLEX
ERK2-KIM PEPTIDE AND IDENTIFICATION OF
PUTATIVE HIGH AFFINITY MUTANT KIM PEPTIDES: A
COMPUTATIONAL INVESTIGATION
Leonardo Pacifici , Antonio Lagana
QUANTUM REACTIVE SCATTERING CALCULATIONS
ON GRAPHIC PROCESSING UNITS
Daniele Padula , Lorenzo Di Bari, Gennaro Pescitelli,
Alessandro Lami, Antonio Rizzo, Fabrizio Santoro
ADIABATIC
AND
NONADIABATIC
VIBRONIC
APPROACHES TO THE SIMULATION OF ELECTRONIC
CIRCULAR DICHROISM SPECTRA
Alfonso Pedone , Thibault Charpentier, Maria Cristina
Menziani
FLUORINE ENVIRONMENT IN BIOACTIVE GLASSES:
FIRST-PRINCIPLES CALCULATIONS AND 19F, 29Si AND
23
Na SOLID STATE NMR SPECTROSCOPY.
90
91
92
93
94
95
96
97
99
XVII
P47
P48
P49
P50
P51
P52
P53
P54
P55
XVIII
David Picconi , Alessandro Lami, Fabrizio Santoro
EFFECTIVE
COORDINATES
FOR
QUANTUM
DYNAMICS
ON
CONICALLY
INTERSECTING
QUADRATIC
POTENTIAL
ENERGY
SURFACES.
INVESTIGATING THE ROLE OF DUSCHINSKY
EFFECTS
Vincenzo Barone, Corentin Boilleau, Ivo Cacelli, Alessandro
Ferretti, Susanna Monti, Giacomo Prampolini
ACCURATE
AND
RELIABLE
MODELING
OF
MAGNETIC INTERACTIONS IN ORGANIC DIRADICALS
Alberto Baggioli, Orlando Crescenzi, Martin J. Field, Franca
Castiglione, Guido Raos
COMPUTATIONAL 17O-NMR SPECTROSCOPY OF
ORGANIC ACIDS AND PERACIDS: COMPARISON OF
SOLVATION MODELS
Rinaldi Silvia Alice Carpini, Federico Melaccio, Massimo
Olivucci
A QM/MM STUDY ON HUMAN MELANOPSIN, A NEW
AND ATYPICAL NON-VISUAL PHOTORECEPTOR
Giacomo Saielli , Alessandro Bagno
RELATIVISTIC DFT CALCULATIONS OF THE NMR
PROPERTIES AND REACTIVITY OF TRANSITION
METAL METHANE σ-COMPLEXES: INSIGHTS ON C–H
BOND ACTIVATION
Giacomo Saielli
COARSE-GRAINED MD SIMULATIONS OF IONIC
LIQUID CRYSTALS
Caterina Bernini, Tadeus Andruniów, Massimo Olivucci,
Rebecca Pogni, Riccardo Basosi, Adalgisa Sinicropi
EPR, UV-VIS AND RR SPECTRAL PARAMETER SHIFTS
OF TRYPTOPHAN RADICALS EMBEDDED IN
CONTRASTING HYDROPHOBIC AND HYDROPHILIC
ENVIRONMENTS COMPUTED FROM QM/MM MODELS
OF PSEUDOMONAS AERUGINOSA AZURIN
Cristina Sissa , Francesca Terenziani, Anna Painelli, Arun K.
Manna, Swapan K. Pati
ESSENTIAL-STATE DESCRIPTION OF RESONANCE
ENERGY TRANSFER
Emiliano Stendardo , Francisco Avila, Fabrizio Santoro,
Roberto Improta
THE ABSORPTION AND EMISSION SPECTRA OF
OLIGO-THIOPHENE BASED BIOMARKERS: A PCM/TDDFT STUDY
100
102
103
104
105
106
107
108
109
P56
P57
P58
P59
Mauro Stener , D. Catone, P. Decleva, G. Contini, N. Zema,
T. Prosperi, V. Feyer, K. C. Prince, S. Turchini
RESONANT CIRCULAR DICHROISM OF CHIRAL
METAL-ORGANIC COMPLEX
Rosario G. Viglione , Orlando Crescenzi
A
THEORETICAL
PROTOCOL
FOR
THE
DETERMINATION OF THE METAL-SITE STRUCTURE
IN METALLOPROTEIN SUPERFAMILIES
Sara Zaccaron , Renzo Ganzerla, Marco Bortoluzzi
COMPUTATIONAL
STUDIES
ON
IRON-BASED
COORDINATION POLYMERS OF INTEREST IN
CULTURAL HERITAGE
Mirco Zerbetto , Dmytro Kotsyubynskyy, Maria Soltesova,
Jozef Kowalewski, Eva Meirovitchc, Goran Widmalm,
Antonino Polimeno
INTEGRATED
APPROACHES
TO
NMR
SPIN
RELAXATION
IN
FLEXIBLE
BIOMELECULES:
APPLICATION TO POLYSACCHARIDES
110
111
112
113
XIX
XX
Keynote Lectures
KN01
Simulating molecular organisations of liquid crystals
and other functional materials in the bulk and close to interfaces
Claudio Zannoni
Dipartimento di Chimica Fisica e Inorganica, Università di Bologna, Viale
Risorgimento 4, 40136 Bologna, Italy
E-mail: [email protected]
Many practical applications of liquid crystals (LC) and organic semiconductors, as
well as many fundamental physics problems deal with molecular organizations
close to interfaces [1]. Here we plan to show results for the simulation of these
organizations at molecular and atomistic resolution. While coarse grained,
molecular level, models have an important role in studying trends and simple
devices [2], atomistic molecular dynamics simulations [3] can in principle predict
actual morphologies and properties at various temperatures and working conditions
from a specific molecular structure. In the talk we present some recent examples of
atomistic simulations for various systems [4-6] trying to show the range and
applicability of the results for liquid crystals and organic electronics.
Support from
acknowledged.
[1]
[2]
[3]
[4]
[5]
[6]
EU
project
MINOTOR
(CP-FP228424-2)
is
gratefully
Beljonne, D.; Cornil, J.; Muccioli, L.; Zannoni, C.; Brédas, J.-L.; Castet, F.,
Chem. Mater., 2011, 23, 591.
Ricci, M.; Mazzeo, M.; Berardi, R.; Pasini, P.; Zannoni, C., Faraday
Discuss. 2010, 144, 171
Tiberio, G.; Muccioli, L.; Berardi, R.; Zannoni, C., ChemPhysChem
2009,10, 125.
Pizzirusso, A.; Berardi, R; Muccioli , L.; Ricci, M.; Zannoni , C., Chem.
Sci., 2012, 3, 573.
Papadopoulos, T.A.; Muccioli, L.; Athanasopoulos, S. ; Walker, A.B.;
Zannoni, C.; Beljonne, D. Chem. Sci., 2011, 2, 1025.
Muccioli, L. ; D'Avino, G.; Zannoni , C. , Adv. Mater. 2011, 23, 4532.
3
KN02
Modeling Dye-Sensitized Solar Cells: Understanding
the Mechanism, Improving the Efficiency
Filippo De Angelis,a
a
CNR-Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie
Molecolari (CNR-ISTM), Via Elce di Sotto 8, Perugia, Italy.
E-mail: [email protected]
We present computer simulations on the fundamental constituents of Dyesensitized solar cells (DSCs) and their interactions at the respective
molecular/solid/liquid interfaces. Predictive dye design and modeling of realistic
semiconductor (TiO2, ZnO) nanostructures enables us to investigate the structural,
electronic and optical properties of dyes adsorbed onto semiconductor surfaces by
means of DFT and TDDFT calculations. Thus, the alignment of ground and excited
state energy levels for the interacting DSC constituents is presented and discussed
in relation to experimental photovoltaic performances. Modeling of the combined
dye / semiconductor / electrolyte heterointerfaces is then achieved by performing
ab initio molecular dynamics simulations of semiconductor adsorbed dyes in the
solution and electrolyte environments. In particular, we present the case of Ru(II)dyes on TiO2 and their interaction with a Cobalt-based electrolytes. The nature and
localization of the electronic states at the dye/semiconductor/electrolyte interface is
discussed in relation to the device efficiency parameters. The mechanistic details of
dye regeneration and the recombination pathways with the oxidized dye and with
TiO2-injected electrons are finally presented, Figure 1.
References:
Figure 1. Ru-dye on TiO2 and Co(bpy)3.
4
[1] M. Pastore, F. De Angelis ACS
Nano 2010, 4, 556.
[2] F. De Angelis, S. Fantacci, R.
Gebauer J. Phys. Chem. Lett. 2011, 2,
813.
[3] F. De Angelis, S. Fantacci, E.
Mosconi, M. K. Nazeeruddin, M.
Grätzel J. Phys. Chem. C 2011, 115,
8825.
[4] P. Chen, J.H. Yum, F. De Angelis,
M. Grätzel et al. Nano Lett. 2009, 9,
2487.
[5] F. De Angelis, S. Fantacci, M.
Grätzel et al. J .Am. Chem. Soc. 2007,
129, 14156.
KN03
How to model environment effects in electronic energy
transfer (EET) processes in light-harvesting systems
Benedetta Mennucci
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via
Risorgimento 35, 56126 Pisa, Italy
E-mail: [email protected]
Photon absorption and energy transfer (EET) represent the first processes in both
natural and artificial light-harvesting systems. In the pursuit of mimicking the
optimal design of natural light-harvesting antennae it is of fundamental importance
to achieve a molecular-level explanation of these processes and the way they are
affected by the environment [1]. Such a goal is formidably challenging due to the
large network of interactions that couple all the parts of the system and the different
time and length scales involved. However, a possible strategy exists and it is
represented by the coupling of quantum chemical methods to classical approaches
that account for the environment response in all the steps of the process. Two
alternative classical approaches are here presented and discussed, namely a
continuum model [2] and a MM force field [3]. In both cases explicit treatment of
the environment polarization is introduced.
[1]
[2]
[3]
B. Mennucci, C. Curutchet, Phys. Chem. Chem. Phys., 13 (2011) 11538.
M.F. Iozzi, B. Mennucci, J. Tomasi, R. Cammi, J. Chem. Phys., 120 (2004)
7029.
C. Curutchet, A. Mu~noz-Losa, S. Monti, J. Kongsted, G. D. Scholes, B.
Mennucci, J. Chem. Theory Comput., 5, (2009) 1838.
5
KN04
world
Targeting membrane receptors: from virtual to real
Davide Sabbadin, Silvia Paoletta, Stefano Moro
Molecular Modeling Section (MMS); Department of Pharmaceutical and
Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova,
Italy
E-mail: [email protected]
G protein-coupled receptors (GPCRs) form a large membrane-protein family that
plays an important role in many physiological and pathological processes. Since the
sequencing of the human genome has revealed several hundred new members of
this receptor family, many new opportunities for developing novel therapeutics
have emerged. The increasing knowledge of GPCRs (biological space) and their
ligands (chemical space) enables novel drug design strategies to accelerate the
finding and optimization of GPCR leads [1]. From biophysics and pharmacological
perspective, structural information of GPCRs has been sought as a powerful tool to
better understand the evolutionary path of this fundamental signaling system as
well to clarify their pharmacological profiles. However, despite the common
transmembrane organization of these receptors key differences do exit between
them. Using adenosine receptors as a key-study, we would like to summarize how
computational methodologies, in particular membrane molecular dynamics, helped
us in understanding better their pharmacological behavior and in design novel drug
candidates [2].
[1]
[2]
6
Paoletta S, Federico S, Spalluto G, Moro S. Methods Enzymol. 2010, 485,
225.
(a) Poli D, Catarzi D, Colotta V, Varano F, Filacchioni G, Daniele S,
Trincavelli L, Martini C, Paoletta S, Moro S. J Med Chem. 2011, 54, 2102.
(b) Federico S, Paoletta S, Cheong SL, Pastorin G, Cacciari B, Stragliotto S,
Klotz KN, Siegel J, Gao ZG, Jacobson KA, Moro S, Spalluto G. J Med
Chem. 2011, 54, 877.
KN05
Medaglia “Cesare Pisani” della Società Chimica
Italiana
1970-2012. Past and future of simulation in solid state Chemistry
and Physics at the Theoretical Chemistry Group in Torino.
Roberto Dovesi
Dipartimento di Chimica, Università di Torino, and NIS –
Nanostructured Interfaces and Surfaces –Centre of Excellence,
http://www.nis.unito.it, Via P. Giuria 7, 10125 Torino, Italy.
E-mail: [email protected]
The scientific activity of the Theoretical Chemistry Group (TCG) of the
Torino University started when Cesare Pisani was called by Prof. Franco Ricca
from Milano to Torino in 1970 (he was working for a company). For more than
fourty years TCG, under Cesare’s guide, introduced tens of students to linear
algebra, group theory, theoretical chemistry, FORTRAN programming, simulation
in different areas.
Our challenge in those years (“will we be able to implement ab initio codes for the
study of the ground state properties of crystalline compounds? General, robust,
transferable codes?”) has been the guideline of the study, teaching and coding
activity during these decades and has generated CRYSTAL ( perfect crystalline
solids, Hartree-Fock and DFT), EMBED (defects, studied by “embedding” the
local perturbation in the infinite solid) and, more recently, CRYSCOR (MP2
treatment of crystalline solids with a local approach). CRYSTAL (born in 1976!
see www.crystal.unito.it) and CRYSCOR (born in2000; see www.cryscor.unito.it )
are publicly distributed (the last release is available since march 2010) and in use
in hundreds of laboratories, mostly abroad.
The original “core” of TCG (Cesare Pisani, Carla Roetti and Roberto Dovesi) grew
during the years (it is worth mentioning here the enormous contribution to the
development of CRYSTAL by V.R. Saunders, Daresbury, UK) and at the moment
includes at least 20 “stable” collaborators at the Torino University and from
several universities over the world.
In the present workshop 3 oral presentations and 10 posters based on CRYSTAL
and CRYSCOR, most of which devoted to new algorithms and implementations,
document that TCG has been able to overcome the severe, hard difficulties caused
by the sudden death of Cesare Pisani, preceded by Carla Roetti’s early passing
away just by one year . A summary of recent and in-progress developments in the
area of simulation of perfect and crystalline solids at TCG will conclude the
presentation.
7
KN06
A bridge over chemical timescales
Francesco Zerbetto
Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2,
40126 Bologna, Italy
Atomic and molecular processes occur on an incredibly wide range of time-scales.
Bonds can be formed in a few femtoseconds (or even faster), morphological
modifications can take microseconds to seconds, self-assembly of supra-molecular
structures can take days or longer. Even the movements of electrons, atoms, and
molecules belong to time-scales that are very far apart. Physicists, chemists, and
materials scientists have developed a variety of computational models that cover all
these times and are connected (loosely or strongly) to one another.
Here I will attempt to bridge these timescales by presenting a few examples of
recent work carried out in my group. Snapshots will be provided from several
examples such as the motion of molecules on metal surfaces and their selfassembly into ordered structures, the morphological transition that occurs when a
drop meets a gradient in the potential energy, the propensity of graphite to form
sp3-sp3 bonds upon laser irradiation, and other applications. Differences and
similarities of the models used will also be discussed.
8
KN07
Using Trajectories to Probe the Molecular Mechanism
of Ultrafast Biological Photoisomerization and Internal Conversion
Igor Schapiro‡, Mikhail Nikolaevich Ryazantsev‡, Luis Manuel Frutos‡‡,
Nicolas Ferré §, Roland Lindh¶, Massimo Olivucci‡,§§
‡Chemistry Department, Bowling Green State University, Bowling Green OH
43403, USA, ‡‡Departamento de Química Física, Universidad de Alcalá, 28871
Alcalá de Henares (Madrid), Spai, § Laboratoire de Chimie Théorique et de
Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 –
Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20,
France, ¶Department of Quantum Chemistry, Ångströmlab, Lägerhyddsv. 1, Box
518, 751 20 Uppsala University, Sweden, §§Dipartimento di Chimica, Università
degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy.
Quantum-mechanics/molecular-mechanics models of the visual pigment Rhodopsin
(Rh) based on an ab initio multiconfigurational wavefunctions are employed to
look at the light induced π-bond breaking and reconstitution occurring during the
Rh→bathoRh isomerizations and Rh→Rh internal conversion. More specifically,
semiclassical
trajectory
computations are used to
compare the excited (S1)
and ground (S0) state
dynamics characterizing
the opposite steps of the
Rh/bathoRh photochromic
cycle during the first 200
fs
following
photoexcitation. We show
that
the
information
contained in these data
provide an insight into the
sub-picosecond
π-bond
reconstitution process which is at the basis of the reactivity of the protein
embedded 11-cis and all-trans retinal chromophores. More specifically, the data
point to the phase and amplitude of the skeletal bond length alternation stretching
mode as the key factor switching the chromophore to a bonding state. It is also
confirmed/found that the phase and amplitude of the hydrogen-out-of-plane mode
controls the stereochemical outcome of the forward and reverse
photoisomerizations.
(1)
Schapiro, I.; Ryazantsev, M. N.; Frutos, L. M.; Ferré, N.; Lindh, R.; and
Olivucci, M. J. Am. Chem. Soc. 2011, 133, 3354–3364.
9
KN08
Engineering semiconductors band gap for vis-light
activation
Cristiana Di Valentin
Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Milano, Italy
E-mail: [email protected]
In this presentation different approaches for semiconductors activation in the vislight spectrum will be discussed on the basis of hybrid functional calculations:
doping, controlled defectivity and mixed solid solutions.
Periodic calculation have been performed with hybrid functional methods and an
atomic basis set approach, as implemented in the CRYSTAL code. Hybrid
functionals provide a more accurate description of semiconductors electronic
structure (band gap values, spin localization) with respect to standard LDA or GGA
functionals.
Doped TiO2 is worldwide prepared in order to lower the threshold energy for band
gap electron-hole excitation or to improve the surface photochemistry. In this talk
we review [1] some recent results focusing on the role of defects [2] and on the codoping [3] effect which is currently highlighted in the literature as a promising
approach.
GaN:ZnO solid solutions have been identified as a successful system for
photocatalytic or photoelectrochemical water splitting under visible-light
irradiation. However, the origin of their activity at longer wavelength with respect
to the parent materials (GaN and ZnO) absorbing in the UV spectrum is still a
matter of debate [4].
Electrochromic effect in WO3 is still an open issue. We propose [5] a
rationalization which is based on a charge state variation of oxygen vacancy defects
and show that these present rather anisotropic properties.
Hybrid functional calculations are precious tools to unravel the microscopic origin
of visible-light activation of semiconducting materials for a variety of applications.
[1]
[2]
[3]
[4]
[5]
10
C. Di Valentin, G. Pacchioni, Cat. Today. 2012, j.cattod.2011.11.030.
C. Di Valentin, G. Pacchioni, A. Selloni J. Phys. Chem. C 2009, 113,
20543.
C. Di Valentin, G. Pacchioni, H. Onishi, A. Kudo, Chem. Phys. Lett. 2009,
469, 166.
C. Di Valentin, J. Phys. Chem. C 2010, 114, 7054.
F. Wang, C. Di Valentin, G. Pacchioni, Phys. Rev. B 2011, 84, 073103.
KN09
Unconventional inhomogeneous broadening from polar
solvation: an essential state description of symmetry breaking in
charge-transfer chromophores
Anna Painelli, Cristina Sissa, Francesca Terenziani
Dip. Chimica GIAF, Università di Parma, & INSTM UdR-Parma, Parco Area delle
Scienze 17/A,43124 Parma, Italy
E-mail: [email protected]
Functional organic chromophores are based on extended π-conjugated structures
decorated with electron-donor and acceptor groups. Delocalized electrons coupled
with low-lying charge-transfer degrees of
freedom
are
extremely
responsive
to
perturbations driven by molecular vibrations and
by the interaction with the surrounding medium.
The complex interplay among the different
degrees of freedom is well captured by a family
of parametric Hamiltonians known as essential
state models. A minimal valence-bond basis is
chosen to describe the electronic structure. The
coupling between delocalized electrons and a
few effective vibrations is treated in a fully nonadiabatic approach. Polar solvation enters the
model as an overdamped boson field, opening the way to investigate both static and
dynamic disorder. Linear and non-linear optical spectra of several families of
chromophores and their complex evolution with solvent polarity are quantitatively
described based on a handful of adjustable model parameters. Here we discuss
static disorder induced by polar solvation, focusing attention on inhomogeneous
broadening that affects in a qualitatively different way linear and non-linear optical
spectra [1]. A couple of case studies will be presented, together with a detailed
discussion of symmetry-lowering and symmetry-breaking effects in polymethine
dyes [2].
[1]
[2]
J. Campo, A. Painelli, F. Terenziani, T. V. Regemorter, D. Beljonne, E.
Goovaerts, W. Wenseleers, J. Am. Chem. Soc. 2010, 132; C. Sissa, A.
Painelli, M. Blanchard-Desce, F. Terenziani, J. Phys. Chem. B 2011 115,
7009-7020.
F. Terenziani, O. V. Przhonska, S. Webster, L. A. Padilha, Y. L.
Slominsky, I. G. Davydenko, A. O. Gerasov, Y. P. Kovtun, M. P. Shandura,
A. D. Kachkovski, D. J. Hagan, E. W. Van Stryland, A. Painelli, J. Phys.
Chem. Lett. 2010, 1, 1800; C. Sissa, P. Mohamadzadeh Jahani, Z. G. Soos,
A. Painelli, ChemPhysChem, submitted.
11
KN10
Non-linear spectroscopies and chirality
Antonio Rizzo
CNR-Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici
(IPCF-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa,
Italy
E-mail: [email protected]
The application of linear chiroptical spectroscopies is very often restricted to the far
and near-UV region in highly absorbing and scattering biological systems. A novel,
non linear, low-scatter, long-wavelength CD spectroscopic tool, the two-photon
circular dichroism (TPCD), based on the theoretical intuition made more than thirty
five years ago by Ignacio Tinoco, Jr. [1], helps in bypassing this limitation. TPCD
has been recently proposed as a new tool for
the study of chiral molecules, after the
development of both a new experimental
technique - the double L-scan technique,
using pulsed lasers and devised by the group
of Hernández and co-workers [2] – and of a The TPCD stick spectrum of
solid computational approach, based on BINOL
modern analytical response theory, within a
Time-Dependent Density Functional Theory (TD-DFT) approach [3]. Examples of
applications of combined experimental and theoretical studies of TPCD in axially
chiral by-aryls, as R - (+) - 1,1' - bi(2-naphthol), R-BINOL [4,5], (R) - 3,3′ Diphenyl - 2,2′ - bi – 1 - naphthol, R-VANOL, and (R) - 2,2′ - Diphenyl - 3,3′ - (4biphenanthrol), R-VAPOL [6], will be presented. Also, the new perspectives
yielded by the recent development of a damped two-photon absorption (DTPA)
approach within response theory are discussed [7].
Other nonlinear optical properties exhibited by chiral assemblies and which are
currently under computational analysis, as excited state circular dichroism [8] and
other circular intensity difference phenomena arising also in pump-probe
spectroscopies [9], will also be discussed.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
12
I. Tinoco, J. Chem. Phys., 1975, 62, 1006.
L. De Boni, C. Toro and F. E. Hernández, Opt. Lett., 2008, 33, 2958.
B. Jansík, A. Rizzo and H. Ågren, Chem. Phys. Lett., 2005, 414, 461.
C. Toro, L. De Boni, N. Lin, F. Santoro, A. Rizzo, F. E. Hernández, Chem. Eur. J.
2010, 16, 3504.
N. Lin, F. Santoro, X. Zhao, C. Toro, L. De Boni, F. E. Hernández, A. Rizzo, J.
Phys. Chem B 2011, 115, 211.
A. Rizzo, F. E. Hernández, Molecules, 2011, 16, 3315.
K. Kristensen, J. Kauczor, A. J. Thorvaldsen, P. Jorgensen, T. Kjaergaard and A.
Rizzo, J. Chem. Phys., 2011, 134, 214104.
A. Rizzo, O. Vahtras, H. Ågren, J. Chem. Phys., 2011, 134, 244109.
A. Baranowska, A. Rizzo, B, Jansik, S. Coriani, J. Chem. Phys. 2006, 125, 054107.
Oral Contributions
OR01
Non-equilibrium simulations of polymeric materials:
applications to rubber reinforcement and polymer friction
Guido Raosa, Giuseppe Allegraa and Timothy J. Sluckinb
a
Dipartimento di Chimica, Materiali e Ing. Chimica “G. Natta”, Politecnico di
Milano, via Mancinelli 7, I-20131 Milano, Italy.
b
Faculty of Mathematical Studies, Highfield, Southampton SO17 1BJ, UK
E-mail: [email protected]
The rheology and the tribology of polymers and other complex materials (“soft
solids”, “structured fluids”) are interesting from both fundamental and applicative
viewpoints. Due to their long characteristic relaxation times — sometimes, as in
the case of glasses, exceeding the experimental time scale — and to their large
deformability — rubber is easily stretched to 300% of its length — their
mechanical response has to be probed and understood in a non-equilibrium, nonlinear regime. From a computational point of view, this requires explicit nonequilibrium simulations under a driving field or a set of pulling forces. We will
first describe our work on non-equilibrium Dissipative Particle Dynamics (DPD) of
polymer networks incorporating solid nanoparticles,[1] which has provided insights
into the phenomenon of “rubber reinforcement”.[2] We will then discuss our
preliminary work on the Molecular Dynamics (MD) of polymer chains absorbed on
solid surfaces, in order to understand the effect of surface heterogeneity on their
friction properties.[3]
Left: DPD simulation of a rubbery nanocomposite under oscillatory shear. Left:
MD simulation of a polymer chain diffusing on a random heterogeneous surface
(two snapshots taken at different times).
[1]
[2]
[3]
(a) G. Raos, M. Moreno, S. Elli, Macromolecules 2006, 39, 6744; (b) G.
Raos, M. Casalegno, J. Chem. Phys. 2011, 134, 054902.
G. Allegra, G. Raos, M. Vacatello, Prog. Polym. Sci. 2008, 33, 683.
G. Raos, G. Allegra, T. J. Sluckin, in preparation.
15
OR02
Exploiting Configurational Freezing in
Nonequilibrium Monte Carlo Simulations1
Paolo Nicolini,a Diego Frezzato,b Riccardo Chelli,a
a
Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
b
Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, I-35131
Padova, Italy
E-mail: [email protected]
To achieve acceptable accuracy in fast-switching free energy estimates by
Jarzynski equality2 or Crooks fluctuation theorem3, it is often necessary to realize a
large number of externally driven trajectories. This is basically due to inefficient
calculation of path-ensemble averages arising from the work dissipated during the
nonequilibrium realizations. We propose a computational technique, addressed to
Monte Carlo simulations, to improve free energy estimates by lowering the
dissipated work. The method is inspired by the dynamical freezing approach,
developed in the context of molecular dynamics simulations4. The idea is to limit
the configurational sampling to particles of a well-established region of the sample
(namely, the region where dissipation is supposed to occur), while leaving fixed
(frozen) the other particles. Therefore, the method, called configurational freezing,
is based on the reasonable assumption that dissipation is a local phenomenon in
single-molecule nonequilibrium processes, a statement which is satisfied by most
processes, including folding of biopolymers, molecular docking, alchemical
transformations, etc. At variance with standard simulations, in configurational
freezing simulations the computational cost is not correlated with the size of the
whole system, but rather with that of the reaction site. The method is illustrated
with two examples: (1) the calculation of the water to methane relative hydration
free energy and (2) the calculation of the potential of mean force of two methane
molecules in water solution as a function of their distance.
[1]
[2]
[3]
[4]
16
Nicolini, P.; Frezzato, D.; Chelli, R. J. Chem. Theory Comput. 2011, 7, 582.
Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690.
Crooks, G. E. J. Stat. Phys. 1998, 90, 1481.
Nicolini, P.; Chelli, R. Phys. Rev. E 2009, 80, 041124.
OR03
Flip-flop of steroids through lipid membranes: a rototranslational diffusion mechanism for crossing free energy barriers
Giulia Parisio, Alberta Ferrarini
Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via F.
Marzolo 1, 35131 Padova, Italy
E-mail: [email protected]
The spontaneous translocation (flip-flop) of lipids from one leaflet to the other of a
bilayer represents a putative mechanism for their transmembrane transport.
However the role of this process in lipid trafficking within the cell is still debated,
due to the limitations of the experimental techniques which have been used to
measure its rate [1]. Passive flip-flop is a challenge also for Molecular Dynamics
simulations, since it cannot be directly observed and sampled, due to its long
timescale. We report here a theoretical study of the transbilayer translocation of
steroids. The free energy surface of a steroid as a function of its position and
orientation in the lipid bilayer is calculated by an implicit membrane model, where
the anisotropy and the non-uniformity of the environment are taken into account, in
terms of the gradients of density, dielectric permittivity, acyl chain order
parameters and lateral pressure across the lipid bilayer [2]. The analysis of the
minima and saddle points of the free energy surface allows us to identify the
mechanism of flip-flop and to define a kinetic model for this process. The flip-flop
rate is calculated by solving the Master Equation governing the transitions between
free energy minima, with transition rates evaluated according to Kramers theory
[3], extended to multidimensional diffusion [4]. We will present this methodology
and the results obtained for steroids of different shape and polarity, including
cholesterol, which point to the role of polar substituents and to the importance of
their position in the molecular skeleton for transport through the membrane.
[1]
[2]
[3]
[4]
Garg, S.; Porcar, L.; Woodka, A.C.; Butler, P.D.; Perez-Salas, U. Biophys.
J. 2011, 101, 370.
Parisio, G.; Ferrarini, A. J. Chem. Theory Comput. 2010, 6, 2267.
Kramers, H.A. Physica 1940, 7, 284.
a) Langer, J.S. Ann. Phys. 1969, 54, 258. b) Moro, G.J.; Ferrarini, A.;
Polimeno, A.; Nordio, P.L. in Reactive and flexible molecules in liquids,
Th. Dorfmuller ed., Kluwer Academic Publishers: Dordrecht, 1989; p. 107.
17
OR04
Modeling electronic and charge transport properties of
ambipolar and n-type organic semiconductors
Fabrizia Negri,a Simone Di Mottaa
a
Università degli Studi di Bologna, Dipartimento di Chimica "G. Ciamician",
Via F. Selmi, 2 and INSTM, UdR Bologna, I - 40126 Bologna - Italy
E-mail: [email protected]
Recently synthesized quinoidal oligothiophenes have been shown to be promising
materials for their proved amphoteric properties[1] and their near infrared (NIR)
absorption features. Here we present evidence[2] for the biradicaloid and polyenic
character of quinoidal oligothiophenes. The identification of a doubly exciton state
offers a unified view of the low lying electronic states for quinoidal
oligothiophenes and polyenes. Among n-type organic semiconductors perylene
bisimide (PBI) have been shown to display promising electron mobilities. The solid
state packing and functional properties of PBIs can be tailored by the introduction
of appropriate substituents in the imide position or in the bay region.[3] We have
modeled their charge transport properties by propagating the charge carriers in
planar-core and core-twisted PBIs (see Figure 2), with a kinetic Monte Carlo
scheme.[4] Thermally induced dynamical effects were investigated by means of
molecular dynamics simulations coupled to quantum-chemical evaluation of
electronic couplings Vij.
Figure 1
Figure 2
[1]
Ortiz, R. P., Casado, J., Hernandez, V., Navarrete, J. T. L., Orti, E., Viruela,
P. M., Milian, B., Hotta, S., Zotti, G., Zecchin, S.et al. Adv. Func. Mat. 2006, 16,
531-536.
[2] S. Di Motta, F. Negri, D. Fazzi, C. Castiglioni, E. V. Canesi J. Phys. Chem.
Lett. 2010, 1, 3334.
[3] Schmidt, R.; Oh, J. H.; Sun, Y. S.; Deppisch, M.; Krause, A. M.; Radacki, K.;
Braunschweig, H.; Konemann, M.; Erk, P.; Bao, Z. A.; Wurthner, F. J. Am. Chem.
Soc. 2009, 131, 6215-6228.
[4] S. Di Motta, M. Siracusa, F. Negri, J. Phys. Chem. C 2011, 115, 20754.
18
OR05
Theoretical Modeling of physico-chemical observables
in complex environments
Andrea Amadei,a Isabella Daidone,b Massimiliano Aschib
a
Dipartimento di Scienze e Tecnologie chimiche, Universita’ di Roma Tor
Vergata. E-mail: [email protected]
b
Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita’ di l’Aquila
The ultimate goal of theoretical-computational chemistry is to provide rigorous
models and hence valid tools for interpreting and predicting real phenomena. The
validity and the strictness of a chemical theory is then measured by its ability of
reproducing the result of whatever experimental measurements. Unfortunately most
of the observables of interest for a chemist concern phenomena taking place in very
complex environments such as liquid solutions or interfaces. A model should then
address a problem in the whole complexity. For this reason one of the most crucial
aspects that a theoretician should address is not only to provide a sound model but
also to critically evaluate the approximations to be considered for its
implementation and application. In our laboratory, in the last decade, we have been
working essentially in this direction with the final aim of describing different
phenomena ranging from the spectroscopic signals to the mechanisms of chemical
and biochemical reactions in solution utilizing theoretical-computational tool
essentially working at electronic-atomistic level. In this presentation some of the
results obtained by our group in the last few years will be presented and
commented.
19
OR06
A statistical thermodynamic model for micelle
formation
Giuseppe Graziano
Dipartimento di Scienze per la Biologia, la Geologia e l’Ambiente, Università del
Sannio, via Port’Arsa 11, 82100 Benevento
E-mail: [email protected]
The process of micelle formation in water is considered to be a paradigmatic
manifestation of the hydrophobic effect [1]. Since there is no agreement on the
molecular-level origin of the latter, a satisfactory identification of the micellization
driving force is still lacking. I have developed a general approach to rationalize the
conformational stability of globular proteins as a function of temperature [2], and
concentration of stabilizing and destabilizing co-solutes in water [3]. Extending this
approach, I have devised a statistical thermodynamic model to rationalize the
process of micelle formation at different temperatures. Three fundamental
ingredients have to be considered when non-charged amphiphilic molecules
aggregate to form a micelle. First, there is a marked decrease in the solventexcluded volume (i.e., the shell region surrounding every solute molecule where
the center of solvent molecules cannot penetrate), that leads to a large gain in
configurational-translational entropy of water molecules. Second, there is a large
loss in translational entropy of non-charged amphiphilic molecules. Third, the
energetic attractions between the hydrocarbon tails in the micelle interior and those
of polar heads on micelle surface with surrounding water molecules are assumed to
balance the energetic attractions between amphiphilic molecules and surrounding
water molecules, so that there is no effect on the Gibbs energy change upon
micellization. The first contribution has been estimated by means of a suitable
application of classic scaled particle theory: the amphiphilic molecules are modeled
as spherocylinders and the micelle as a sphere. The second contribution has been
estimated by means of the Sackur-Tetrode equation and a correction term that takes
into account the effect of the volume packing density of water on the translational
entropy [4]. The situation of perfect balance of these two entropic contributions
corresponds to the critical micelle concentration.
[1]
[2]
[3]
[4]
20
Tanford, C. Science 1978, 200, 1012.
(a) Graziano, G.; Phys.Chem.Chem.Phys. 2010, 12, 14245. (b) Riccio, A.;
Graziano, G. Proteins 2011, 79, 1739. (c) Graziano, G.;
Phys.Chem.Chem.Phys. 2012, 14, in press.
(a) Graziano, G.; Phys.Chem.Chem.Phys. 2011, 13, 12008. (b) Graziano,
G.; Phys.Chem.Chem.Phys. 2011, 13, 17689. Graziano, G.
Int.J.Biol.Macromol. 2012, 50, 230.
Graziano G. Chem.Phys.Lett. 2008, 459, 105.
Single molecule diodes based on hetero–
binuclear transition metal complexes
OR07
Vincenzo Barone‡,Ivo Cacelli*, Alessandro Ferretti†, Michele Visciarelli‡
‡Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
*Dip.di Chimica e Chimica Indutriale Univ. Pisa, Via Risorgimento 35, 56100
Pisa, Italy
†Istituto di Chimica dei Composti Organo – Metallici del CNR, UOS di Pisa, Via
G. Moruzzi 1, Pisa
We present the results of our study on the charge transport properties of binuclear
pyrazine–bridged transition metal complexes with porphyrazine as ancillary ligand
[1]. We have considered non–symmetric species of the metals of the eighth group,
e.g. Fe, Ru and Os and we have applied non-equilibrium Green’s function and
Landauer–Buttiker transport theory, as implemented in the domestic FOXY code
[2]. We show that these systems exhibit rectifying behaviour and we propose some
possible improvement that may enhance the rectification ratio.
[1]
[2]
Hanack, M. and M. Lang (1994) Adv. Mater. 6(11): 819.
Cacelli, I., A. Ferretti, et al. (2007). Chem. Phys. 333: 26-36. 21
OR08
The interaction of DNA with metal complexes:
computational investigations
Giampaolo Barone, Riccardo Bonsignore, Angelo Spinello, Alessio Terenzi
Dipartimento di Chimica “S. Cannizzaro”, Università di Palermo, Viale delle
Scienze, Parco d'Orleans II, Edificio 17, 90128 Palermo, Italy
E-mail: [email protected]
We have recently reported on the synthesis and characterization of novel first row
transition metal complexes and the study of their DNA binding properties [1]. In
this context, we are also making use of computational methods as supporting tool
for the structural interpretation of the experimental spectra. For example, TD-DFT
calculations have been employed to rationalize the electronic transitions of the
absorption and emission spectra of a DNA-intercalating zinc(II) Schiff base
complex [2]. Moreover, DFT [3] and QM/MM [4] methods have been applied to
simulate the interaction of intercalators and DNA models. Such computational
approach has been at present extended by the use of classical MD simulations of
the metal complex-DNA systems, by explicitly including counterions and the water
solvent. The MD simulations are preliminary to the application of the QM/MM
calculations and are performed i) to obtain a DNA conformation relaxed at the
experimental conditions and ii) to explore a wider conformational space of the
DNA-molecule system. In this presentation few examples of the application of our
combined experimental/computational approaches to study the interaction of DNA
with heteroleptic transition metal complexes will be shown.
[1]
[2]
[3]
[4]
22
(a) Terenzi, A.; Fanelli, M.; Ambrosi, G.; Amatori, S.; Fusi, V.; Giorgi, L.;
Turco Liveri,V.; Barone, G. Dalton Trans. 2012, DOI:10.1039/C2DT11759B.
(b) Terenzi, A.; Barone, G.; Palumbo Piccionello, A.; Giorgi, G.; Guarcello,
A.; Portanova, P.; Calvaruso, G.; Buscemi, S.; Vivona, N.; Pace, A. Dalton
Trans. 2010, 39, 9140. (c) Barone, G.; Gambino, N.; Ruggirello, A.;
Silvestri, A.; Terenzi, A.; Turco Liveri, V. J. Inorg. Biochem. 2009, 103,
731. (d) Terenzi, A.; Barone, G.; Silvestri, A.; Giuliani, A.M.; Ruggirello,
A.; Turco Liveri, V. J. Inorg. Biochem. 2009, 103, 1. (e) Barone, G.; Longo,
A.; Ruggirello, A.;Silvestri, A.;Terenzi, A.; Turco Liveri, V. Dalton Trans.
2008, 4172.
Barone, G.; Ruggirello, A.; Silvestri, A.; Terenzi, A.; Turco Liveri, V. J.
Inorg. Biochem. 2010, 104, 765.
Barone, G.; Fonseca Guerra, C.; Gambino, N.; Silvestri, A.; Lauria, A.;
Almerico, A.M.; Bickelhaupt, F.M. J. Biomol. Struct. Dyn. 2008, 26, 115.
Ruiz, R.; García, B.; Ruisi, G.; Silvestri, A.; Barone, G. J. Mol. Struct.
(Theochem) 2009, 915, 86.
OR09
Molecular Modelling of DNA G-quadruplex complexes
Stefano Alcaro
Dipartimento di Scienze della Salute, Università degli Studi Magna Græcia di
Catanzaro, Edificio delle Bioscienze, Viale Europa, 88100 Catanzaro
E-mail: [email protected]
DNA and RNA can assume the G-quadruplex
fold, an unusual conformation adopted in some
physiological and pathological conditions [1].
The hyper-elongation of the human repeated
telomeric sequence folding into this conformation
is related to the hyper-proliferation of neoplastic
cells [2]. Recently the rationale of blocking the
elongation process has been proposed as new and
selective mechanism to develop antitumor agents
[3].
Docking experiments of selective ligands against
this special DNA are complicated by the target
polymorphism that prompts to take into account
multiple conformations [4]. Moreover, the lack of
Figure 1
a unique binding region suggested to develop
descriptors for a quick analysis of ligands [5] and the poses, such as the angle DU1DU2-DU3 reported in Figure 1 [6]. In this communication our recent
computational experiences carried out in an integrated drug design project are
reported and discussed with respect to experimental results.
This research work is supported by FIRB_IDEAS (RBID082ATK) and
PRIN (2009MFRKZ8) grants from the Italian Ministry of Education.
[1]
[2]
[3]
[4]
[5]
[5]
Burge, S.; Parkinson, G.N.; Hazel, P.; Todd, A.K.; Neidle, S. Nucleic Acids
Res, 2006, 34, 5402-5415.
Harley, C.B.; Futcher, A.B.; Greider, C.W. Nature, 1990, 345: 458-460.
Olaussen, K.A.; Dubrana, K.; Domont, J.; Spano, J-P.; Sabatier, L.; Soria. JC. Crit Rev Oncol Hematol, 2006, 57, 191-214.
Alcaro, S.; Artese, A.; Iley, J. N.; Missailidis, S.; Ortuso, F.; Parrotta, L.;
Pasceri, R.; Paduano, F.; Sissi, C.; Trapasso, F.; Vigorita, M. G.
ChemMedChem, 2010, 5, 575-583.
Alcaro, S.; Artese, A.; Costa, G.; Distinto, S.; Ortuso, F.; Parrotta, L.
Biochimie, 2011, 93, 1267-1274.
Alcaro, S.; Costa, G.; Distinto, S.; Moraca, F.; Ortuso, F.; Parrotta, L.;
Artese, A. Curr Pham Des, 2012, 0000, in press.
23
OR10
Lipid-Based Nanostructures for Drug Delivery:
Development of Hybrid Particle-Field Molecular Models
Antonio De Nicola,a Ying Zhao,b Toshihiro Kawakatsu,c Danilo Roccatano,d
Giuseppe Milanoa
a
Dipartimento di Chimica e Biologia, Università di Salerno, I-84084 via Ponte don
Melillo Fisciano (SA), Italy
b
Dalian Institute of Chemical Physics, Chinese Academy of Science, 457
Zhongshan Road, Dalian, China (116023)
c
Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai
980-8578, Japan
d
Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
E-mail: [email protected]
Phospholipids are an important class of compound having both important
biological functions (e.g. cell membranes) and technological applications
(e.g.liposomes and micelles). They can undergo different phase transition in
aqueous environments characterized by different morphologies. When
phospholipids are no longer under the constraints that are imposed by
intermolecular interactions that are present within the biomembrane, they can form
non-lamellar (non-bilayer) phases. Hexagonal phases are characterized by tubular
aggregates and they can be composed either by normal or reverse aggregates.
Cubic phases are composed of curved bilayers or micelles. Depending on the water
concentration, micelles change their aggregation form from normal ('oil in water')
to reverse ('water in oil') micelles. With the advent of nanotechnology self
assembled structures of lipids started to be exploited in different ways. Lipids can
be used as templates for assembly of nanoparticle and as dispersant for carbon
nanotubes in aqueous media. Liposomes can be used for drug delivery and reverse
micelles can be used as templates for the nanofabrication of tubes of conductive
polymers.[1] In this framework, the development and validation of recent hybrid
particle-field [2] coarse-grained models of biological phospholipids [3] suitable for
these nanostructures will be explained.
[1]
[2]
[3]
24
Bolinger, PY.; Stamou, D.; Vogel H.. J. Am. Chem. Soc. 2004, 126, 8594.
(a) Milano, G.; Kawakatsu T.; J. Chem. Phys. 2009, 130, 214106. (b)
Milano, G.; Kawakatsu, T.. J. Chem. Phys. 2010, 133, 21.
(a) De Nicola, A.; Zhao Y.; Kawakatsu, T.; Roccatano, D.; Milano, G. J.
Chem. Theory Comput., 2011, 7, 2947. (b) De Nicola, A.; Zhao Y.;
Kawakatsu, T.; Roccatano, D.; Milano, G. Theor. Chem. Acc. In press.
OR11
On the origin of infrared spectral changes upon
protein folding/unfolding
Laura Zanetti,a Andrea Amadei,b Massimiliano Aschia and Isabella Daidonea
a
Department of Chemistry, Chemical Engineering and Materials, University of L’Aquila,
Via Vetoio (Coppito 1), 67010 L’Aquila, Italy
b
Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”,
Via della Ricerca Scientifica 1, 00133 Rome, Italy
E-mail: [email protected]
While the amide I absorption pattern of folded structural elements is rather well
understood, the physical origin of the spectroscopic behaviours of unfolded states is
much less understood, despite differences in the amide I bands of folded and
unfolded states having become a crucial spectral feature to follow protein and
peptide folding kinetics in time-resolved and temperature dependent IR
spectroscopies. Here, we study by means of a theoretical-computational method,
the Perturbed Matrix Method (PMM)1,2, the IR spectra in the amide I region of two
β-hairpin peptides. The main feature of the method is that the IR behavior can be
accurately reproduced not only for folded states but also for the very heterogeneous
unfolded states, whose IR spectrum is commonly difficult to be computed due to
their high conformational flexibility. The computed spectra result to be in good
agreement with the experimental ones, thus providing an explanation of the
physical origin underlying the differences of the unfolded- and folded-state spectra.
[1]
A. Amadei, I. Daidone, A. Di Nola and M. Aschi. Curr. Opin. Struct. Biol.
2010, 20:155–161
[2]
I. Daidone, M. Aschi, L. Zanetti-Polzi, A. Di Nola and A. Amadei. Chem.
Phys. Lett. 2010, 488:213-218
25
OR12
DFT simulation of NEXAFS spectra of molecules
adsorbed on surfaces: C2H4 on Si(100) case study
G. Fronzoni, G. Balducci, M. Stener, R. De Francesco, M. Romeo
Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L.
Giorgieri 1, 34127 TRIESTE
[email protected]
Adsorption of organic molecules on semiconductor surfaces has been attracting a
growing attention for its importance in emerging technologies. Since the properties
of the resulting materials are largely dependent on the organic/semiconductor
interface, fundamental research on the covalent bonding of molecules with the
surface can provide useful information. Problems that have been addressed include
the structure of the resulting systems and spectroscopic measurements often in
concert with theoretical calculations can assess the orientation and geometry of the
molecular adsorbate. NEXAFS spectroscopy is widely used to characterize
adsorbate structures on surfaces since it allows to investigate the adsorption mode
as well as the extent of the adsorbate-substrate interaction, through the comparison
between the spectra of the free and adsorbed molecule. Here we present a DFT
simulation of the NEXAFS spectra of ethylene adsorbed on a regular Si (100)
surface, considering several adsorption models. Cluster models have been
employed to mimic the molecule-surface system for the spectra simulation.
Surface models with and without the adsorbed molecule have been optimized by
means of periodic slab DFT calculations. Both total and angle dependent spectra
have been calculated and compared with the available polarization dependent
NEXAFS experiments; the good agreement between theoretical and experimental
results proves the reliability of the present computational strategy.
26
OR13
Function
Revealing electron delocalization through the Source
Carlo Gattia,b, Emanuele Monza,c Leonardo Lo Presti,c Gabriele Saleh,b,c
a
CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari Milano (Italy)
CMC, Center for Materials Crystallography, Aarhus (Denmark)
c
Dept. of Physical Chemistry and Electrochemistry, Università degli Studi, Milano
(Italy)
E-mail: [email protected]
b
The Source Function (SF) [1,2] enables one to view chemical bonding and other
chemical paradigms under a new perspective and using only information from the
electron density observable, ρ, and its derivatives. Being completely independent
from the tools used to get ρ, the SF represents a very useful descriptor, able in
many cases to bridge the gap between the rich information one gains from an abinitio wavefunction of an ideal system and that, quite often more limited, but
referred to a real system, obtained from an experimental ρ derived from X-ray
diffraction data.
The potential uses of the SF are, however, yet not fully explored. In this lecture we
discuss our recent work where the question of whether the SF is or is not capable to
reveal electron delocalization has been carefully addressed [3,4]. Question arose
because of a recent claim [5] according to which “π-electron delocalization in the
benzene ring is not manifest in the SF when the reference point (rp) - the point at
which the atomic sources for its density are calculated - is taken at the C-C bond
critical point (bcp)”. Reasoning behind this statement was the null contribution
from π molecular orbitals (MOs) to ρ in their nodal plane.
In all inspected cases and regardless of the theoretical or experimental derivation
of ρ, the answer to the question referred to above seems instead to be convincingly
positive. Such a SF ability to reveal electron delocalization is independent from a σ
and π separation of ρ, since the SF tool was applied to the total ρ. This observation
is important in view of the possibility to recover electron delocalization effects
using both ρ’s derived experimentally (hence without σ and π separation being
allowed) and ρ’s where the departure from symmetry inhibits a proper separation
of σ and π contributions. Using a MO approach, the σ and π contributions to the SF
values can also be revealed and quantified.
[1]
[2]
[3]
[4]
[5]
Bader, R.F.W., Gatti, C. Chem. Phys. Lett. 1998, 287, 233-238.
Gatti, C., Cargnoni, F., Bertini, L. J Comput Chem 2003, 24, 422-436.
Gatti, C. Struct. Bond. 2011, 1 $DOI: 10.1007/430_2010_31 2.
Monza, E., Gatti, C., Lo Presti, L., Ortoleva, E. J. Phys. Chem. A 2011, 115,
12864-12878.
Farrugia, L.J., P. Macchi, J. Phys. Chem. 2009, A113, 10058-10067.
27
OR14
The Central Cell Model: a cellular automata-based
tool to model molecular adsorption-diffusion processes in
microporous materials
Federico G. Pazzona, Giuseppe B. Suffritti, Pierfranco Demontis
Dipartimento di Chimica, Università degli Studi di Sassari and Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM),
Unità di Ricerca di Sassari, via Vienna, 2, I-07100 Sassari, Italy
E-mail: [email protected]
In this work we lay down the basis of a simple computational framework, the
Central Cell Model (CCM) [1], aimed to coarse-grain the simulation of static and
diffusion properties of molecular species confined within a microporous system
like a zeolite [2], in conditions of thermodynamic equilibrium. Based on a cellular
automaton algorithm specifically conceived for host-guest system (see for example
[3,4]), our model is probabilistic, hierarchic, local, and discrete, and mimics the
molecular motion in a confining system of pores as a stochastic sequence of
particle jumps both from one location to the other within the same pore, and from
one pore to the other. In the CCM, the memory effects in self-motion process,
arising mainly from the backscattering effect [2] (a major source of time correlation
causing the self-diffusivity to be less than what expected), are embedded in the
displacement autocorrelation function (DACF), the discrete counterpart of the
velocity autocorrelation function (VACF). Essentially, the CCM follows the
motion of one tagged particle in a small lattice of cells (representing the pores of
the confining material) where all the other particles are indistinguishable; the cells
closest to the one containing the tagged particle are simulated explicitly in the
canonical ensemble, whereas the border cells are treated as mean-field cells in the
grand-canonical ensemble in order to make the tagged particle “feel” an
environment very close to the one it would have experienced in an infinitely large
system of cells. The way the model is constructed allows mean-field equations for
the self-diffusivity to be derived with very good accuracy (they are exact at the
limit of infinite dilution) in the Green-Kubo formulation [3]. We apply the CCM
model to the coarse-grained simulation of transport and adsorption properties of
xenon in zeolite NaA.
[1]
[2]
[3]
[4]
28
Pazzona, F. G.; Demontis, P.; Suffritti, G. B. J. Chem. Phys. 2011, 134,
184109.
Kärger, J.; Ruthven, D. M. Diffusion in Zeolites and Other Microporous
Materials, 1st ed., Wiley, New York, 1992.
Pazzona, F. G.; Demontis, P.; Suffritti, G. B. J. Chem. Phys. 2009, 131,
234703 and 234704.
Pazzona, F. G. A Cellular Automata Model for Diffusion and Adsorption
in Zeolites: Construction of a Mesoscopic Model, Lambert Academic
Publishing, Germany, 2010.
OR15
Modeling interactions between peptides and metal ions
Giovanni La Pennaa
a
CNR-Consiglio nazionale delle ricerche, Istituto di chimica dei composti
organometallici(ICCOM-CNR), via Madonna del Piano 10, I-50019 Firenze, Italy
E-mail: [email protected]
The role of cofactors, like transition metal ions, in folding, misfolding and
aggregating proteins and peptides within cells and tissues is now well recognized
[1]. Due to the low degree of structure in protein regions involved in such
important interactions, experimental methods need complementary information
provided by models, these latter ranging from coarse-grained electrostatics to
accurate quantum-mechanical descriptions of forces, passing through empirical
force-fields used in atomistic simulations. In this contribution, the role of different
types of modeling techniques and of high-performance computing infrastructures
will be described, with particular emphasis on the contributions provided to the
understanding of the interactions between Zn/Cu and peptides involved in
neurodegenerative disorders like Creutzfeldt-Jacob (prion protein) [2,3] and
Alzheimer's diseases (amyloid-beta peptides) [4,5,6].
[1]
Zatta, P.; Drago, D.; Bolognin, S.; Sensi, S.L. Trends Pharmacol. Sci. 2009,
30, 346.
[2]
Furlan, S.; La Penna, G.; Guerrieri, F.; Morante, S.; Rossi, G.C.; J. Biol.
Inorg. Chem. 2007, 12, 571.
Guerrieri, F.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Furlan, S.; La Penna,
G. J. Biol. Inorg. Chem. 2009, 14, 361.
Furlan, S.; La Penna, G. Phys. Chem. Chem. Phys. 2009, 11, 6468.
Furlan, S.; Hureau, C.; Faller, P.; La Penna, G. J. Phys. Chem. B 2010, 114,
15119.
Giannozzi, P.; Jansen, K.; La Penna, G.; Minicozzi, V.; Morante, S.; Rossi,
G.C.; Stellato F. Metallomics 2012, DOI: 10.1039/c2mt00148a.
[3]
[4]
[5]
[6]
29
OR16
Simulating azobenzenes Self Assembled Monolayers:
structural properties and a new classical force field
Silvio Pipolo,a,b Enrico Benassi,b Stefano Cornib
a
Dept. of Physics, Universita` di Modena e Reggio Emilia, via G. Campi 213/a,
41125 Modena
b
S3 center, CNR NANO, via G. Campi 213/a, 41125 Modena
E-mail: [email protected]
The photoisomerization process of azobenzene has been widely studied both in
solution and on metal surfaces[1,2], because of its efficiency and controllability.
These features make the azobenzene self assembled monolayers (azo-SAM) a
promising tool for controlling the movement of nano-objects with light. In recent
works, classical [3] and semiclassical [4] approaches have been used to simulate
the isomerization process of azobenzenes. Prompted by these results a dedicated set
of force field parameters has been optimized for thio-azobenzenes. The
optimization procedure and some preliminary results concerning structural
properties of the azo-SAM on gold (111) will be presented and discussed.
Regarding the methodology, a detailed sampling of the potential energy surface
(PES) has been done by means of Quantum Mechanical (QM) methods, then force
field parameters have been obtained by minimizing the difference between the
QM-PES sample and the same PES sample calculated at a Molecular Mechanics
level (MM-PES). The robustness of the parameter set has also been tested against
different set of atomic charges obtained by different flavours of the RESP
procedure. In addition a computational procedure capable to simulate an
experimental investigation on the mechanical stiffness of the monolayer has been
set up. Computational results and approximations inherent in the model will be
presented, finally a comparison with available experimental data will be
discussed[5].
[1]
[2]
[3]
[4]
[5]
30
G. Pace, V. Ferri, C. Grave, M. Elbing, C. von Hanisch, M. Zharnikov,
M. Mayor, M.A. Rampi, P. Samorì, Proc. Nat. Acc. Science 2005, 104,
9937.
V. Ferri, M. Elbing, G. Pace, M.D. Dickey, M. Zharnikov, P. Samorì, M.
Mayor, and M.A. Rampi, Angew. Chem. Int. Engl. Ed. 2008, 47, 3407.
G. Tiberio et al., Chem. Phys. Chem. 2010, 11, 1018.
T. Cusati, G. Granucci, M. Persico, J. Am. Chem. Soc. 2011, 133, 5109.
E. Tirosh, E. Benassi, S. Pipolo, M. Mayor, M. Valasek, V. Frydman, S.
Corni, S. Cohen, Beilstein J. Nanotechnol. 2011, 2, 834.
OR17
QUANTUM COMPUTATIONAL SIMULATIONS OF
MOLECULAR EVOLUTION IN EARLY UNIVERSE REACTIONS AND IN
PLANETARY ATMOSPHERES
F.A. Gianturco
Department of Chemistry, The University of Rome “ Sapienza”, Piazzale A. Moro
5, 00185 Rome, Italy
As the Universe expanded, atoms and molecules were formed from free nucleons
and electrons as photoionization and photodissociation processes became gradually
less effective because of the cooling of the radiation environment. As chemistry
began with the appearance of the first neutral molecules of H2, the corresponding
lithium-based chemistry was also initiated by radiative recombination of Li+ with
the environmental hydrogen , i.e. by association processes with atomic hydrogen
that could in turn activate alkaly-hydrogen reactive processes
or
LiH(X1Σ+)+H(2S) → Li(2S)+H2(X1Σ+)
(1)
LiH+ (X2Σ+)+H(2S) → Li+(1S)+He (X1Σ)
(2)
which become important processes within the lithium chemistry network in the
primordial Universe [1,2]. The corresponding quantum computational simulations
are therefore an essential ingredient for gathering meaningful information on how
the above reactions can evolve in either directions [3,4]. Our group has carried out
extensive ab initio evaluation of such reactive potential energy surface (PESs) that
have been employed in turn to generate quantum reaction probabilities for both
processes[3,4] and to analyse photon-induced processes.Another interesting set of
data deals with the interactions of both LiH(X1Σ+) and LiH+ (X2Σ+) with He atoms
to establish the possible presence of low-T complex formations and even the
occurrence exchange reactions like [5]
LiH+ (X2Σ+)+He(1S) → Li(2S)+HeH+(X1Σ+)
(3)
Additionally, the interactions with Li2(1Σg+), Li2(3Σu) and Li2+(2Σg+) with He atoms
have also been considered important elements in modelling interstellar abundances
,so that we have examined the corresponding dynamics in the low-T regimes
[6,7,8,9]. Another current question is also the possibility that Polycondensed
Aromatic Hydrocarbons (PAHs) be formed in the planetary atmospheres via
anionic reactions[9,10],a question that ,if time permits, we shall also address in this
talk.
[1]
[2]
S.Bovino,M.Tacconi, F.A.Gianturco, D.Galli, Astron. & Astrophys., 529,
A140 (2011).
S. Lepp, P.C. Stancil and A. Dalgarno, J. Phys. B, 35, R57 (2002).
31
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
32
N.J. Clarke et al., Chem. Phys. 233, 9 (1998).
E. Scifoni, E. Bodo, F.A. Gianturco, J. Chem. Phys. 122, 224312 (2005).
M. Wernli, E. Bodo, F.A. Gianturco, Eur. Phys. J. D 45, 267 (2007).
L. Gonzalez-Sanchez, E. Bodo, F.A. Gianturco, J. Chem. Phys. 127, 244315
(2007).
S.Bovino, M.Wernli, F.A.Gianturco,Ap.J.699, 383 (2009).
S. Bovino,T.Stoecklin,F.A.Gianturco, Ap.J.,708 , 560 (2010).
F.Carelli,I.Baccarelli,F.Sebastianelli, F.A.Gianturco,ApJ 708, 350 (2010)
F.Carelli and F.A. Gianturco, Ap.J., 743, 151 (2011).
OR18
Specific solvent effects in ionic liquids. From reactivity
to solvatochromism
Christian Silvio Pomellia, Cinzia Chiappeb
a
Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 33,
56126 Pisa, Italy
b
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via
Risorgimento 35, 56126 Pisa, Italy.
The interpretation and the rationalization of the effects of Ionic Liquids on organic
reactivity is a little explored field. In fact scholars have tried, and try, to classify
ionic liquids solvent effects using the parameters and tools developed for molecular
solvents with alternating results. Among these there are solvatochromic parameters
like α, β, π* and ET(30) parameters [1]. Furthermore the values of the dielectric
constant, one of the most used solvent parameters, for ionic liquids are still an open
question. We have successful used [2-4] a microsolvation approach to rationalize
the organic reactivity via the specific effect of solvent first neighbors solvent ions.
The supermolecolar system of the solute and the first neighbors is studied at the
DFT level. Recently we try to extend this method to study these effects on
Reichardt’s dye at a semiempirical level [5]. From the computational point of view
this approach presents some difficulties: this supermolecolar system can be
constituted by 3 ore more molecular fragments that are not easy to handle. The
starting geometrical structures must be accurately prepared. This require an
expertise in both the fields of computational and organic chemistry. The
interpretation of the results is complex for the same reasons. In our
interdisciplinary group several studies of this kind has been performed about
different kinds of organic reactions. The results of calculations has been compared
with experimental results obtaining a good agreement. Using the information
derived from these studies we try to sketch some preliminary general concepts
about effects of ionic liquids on reactivity and spectroscopical properties of
organic solutes.
[1]
[2]
[3]
[4]
[5]
C. Chiappe, C.S. Pomelli, S. Rajamani J. Phys. Chem. B 2011, 115, 9653.
R. Bini, C. Chiappe, V. Llopsis Mestre, C. S. Pomelli, T. Welton, Theor.
Chem. Acc. 2009, 123, 347.
R. Bini, C. Chiappe, C.S. Pomelli, B. Parisi, J. Org. Chem. 2009 74, 8522.
C. Chiappe, B. Mennucci, C.S. Pomelli, A. Sanzone, A. Marra PCCP 2010,
2, 1958.
C. Chiappe, C. S. Pomelli, Theor. Chem. Acc. in press.
33
OR19
Growth of pentacene on C60 from vapor deposition
simulations
Luca Muccioli,a Gabriele D’Avino,a Claudio Zannonia
a
Dipartimento di Chimica Fisica e Inorganica, Università di Bologna, viale
Risorgimento 4, IT-40136 Bologna, Italy E-mail: [email protected]
The growth of small molecule thin films on organic and inorganic substrates is
regulated by several parameters, and among these the chemical and physical
properties of the target surface play a very important role [1]. Here, with the help of
atomistic modeling techniques, we attempt to predict the mechanism of growth of
pentacene on Buckminster fullerene, with an approach inspired by the organic
vacuum beam deposition technique. To simulate the growth of pentacene on a C60
(001) surface we performed Molecular Dynamics simulations within the NVT
ensemble at T=500 K, inserting into the box a pentacene molecule every 250
picoseconds. Simulations predict [2] a quasi 2D layer-by-layer growth, assisted by
a coverage-dependent reorientation mechanism. The resulting pentacene thin film
shows a structure remarkably different from the bulk phase one, suggesting the
existence of a polymorph induced by the peculiar structure of the C60 surface [3].
The growth of monolayers of
pentacene on C60 (001)
proceeds in two coveragedependent steps: in the first,
pentacene molecules lay flat
and disordered on the surface,
with a steady growth of the
Figure 1 Change on the structure of the first
monolayer (ML) of pentacene on C60 (001) induced film height. In the second,
pentacene molecules reorient
by increasing the coverage.
perpendicular to the surface
and assume a crystalline packing, with incoming molecules positioning themselves
at island edges (see figure below). This mechanism is governed by the fact that a
pentacene molecule standing in a pentacene monolayer is two or three times more
stable than the isolated, flat one, condition necessary for a layer-by-layer growth
[4]. This study represents a significant progress towards demonstrating in full the
growth mechanism of organic crystals with atomistic simulations, and opens the
way to systematic investigations of organic semiconductor interfaces.
[1]
Ruiz, R. et al., Chem. Mater. 2004, 16, 4497; Beljonne, D.; Cornil, J.;
Muccioli, L.; Zannoni, C.; Brédas, J.-L.; Castet, F. Chem. Mater. 2011, 23,
591.
[2]
Muccioli, L.; D’Avino, G.; Zannoni, C. Adv. Mater. 2011, 23, 4532.
[3]
Dougherty, D. B.; Jin, W.; Cullen, W. G.; Reutt-Robey, J. E.; Robey, S. W.
Appl. Phys. Lett. 2009, 94, 023103.
[4]
Choudhary, D.; Clancy, P.; Shetty, R.; Escobedo F. Adv. Funct. Mater.
2006, 16, 1768.
34
OR20
Assessing the performance of global, range-separated
and double hybrid functionals for crystalline systems
Bartolomeo Civalleri,a Davide Presti,a Simona Fabre,a Matteo Ferrabone,a
Lorenzo Maschio,a Silvia Casassaa
a
Dipartimento di Chimica IFM e Centro di Eccellenza NIS, Università di Torino,
Via P. Giuria 7, 10125 Torino, Italy
E-mail: [email protected]
In the last decades, the inclusion of exact exchange in DFT methods have been
shown to be crucial for the accurate prediction of thermochemistry of molecules
[1]. Recently, it has shown that thermochemical results of hybrid HF/DFT methods
can be further improved by including a PT2 correction (i.e. MP2-like) to the
correlation functional [2]. Such methods have been denoted as double-hybrid
functionals [2]. In this work, the performance of global (GH), range-separated
(RSH) [3] and double hybrid (DH) [2] functionals have been assessed when applied
to periodic systems. To this purpose, RSH and DH functionals have been
implemented in the CRYSTAL09 code [4]. For DH, the PT2 correction has then
been calculated by using the CRYSCOR09 program [5]. Different flavors of rangeseparated hybrids [3] have been considered, namely; screened-coulomb, long-range
corrected and middle-range corrected functionals. B2-PLYP, B2GP-PLYP and
mPW2-PLYP [2] double hybrids have been compared to MP2 and SCS-MP2
methods. Simple model systems have been chosen for which very accurate
benchmark data (i.e. CCSD(T), QMC) and experimental data are available (e.g.
cohesion energy, structural data). In particular, we focused on solid LiH and alkali
halides, HF and HCl infinite chains and molecular crystals. GH and RSH
functionals have also been assessed in the prediction of band gap of a large set of
systems [6] ranging from very narrow to very wide band gap solids. Very large
Gaussian-type basis sets of the cc-pVXZ (X=D,T,Q,…) family have been
employed to extrapolate results to the complete basis set limit. Overall results show
that DH provide accurate cohesion energies although they still show some
drawbacks for weakly bound periodic systems. GH and screened-coulomb RSH
methods give similar accuracy in the prediction of the band gap of solids, while
long-range corrected tend to overestimate band gaps.
[1]
[2]
[3]
[4]
[5]
[6]
Goerigk, L.; Stefan Grimme, S. Phys. Chem. Chem. Phys., 2011, 13, 6670
Grimme, S. J. Chem. Phys. 2006, 124, 034108; Schwabe, T; Grimme, S.
Phys. Chem. Chem. Phys. 2006, 8, 4398. Karton, A.; et al. J. Phys. Chem. A
2008, 112, 12868
Janesko, B.G.; et al. Phys. Chem. Chem. Phys., 2009, 11, 443
Dovesi, R.; et al. CRYSTAL09 User’s Manual, Università di Torino, 2009.
Pisani, C.; et al. CRYSCOR09 User’s Manual, Università di Torino, 2009.
Presti, D.; Civalleri, B.; Ferrabone, M.; Savin, A.; Dovesi, R. in preparation
35
OR21
Physisorption, diffusion and chemisorbed pathways of
H2 molecule on Graphene and Single Walled Nanotube by first
principle calculations
Francesca Costanzo, Francesco Ancilotto, Pier Luigi Silvestrelli
Dipartimento di Fisica “G. Galilei”, Università di Padova, Via Marzolo 8, I-35131
Padova Italy.
We investigate the interaction of the H2 molecule with a graphene (G) layer and
with a single wall carbon nanotube (SCNT) by Density Functional Theory. H2 can
interact with a CNT [1,2] both through physisorption and chemisorption, although
chemisorption is typically assumed to be irreversible, and thus it is probably
technologically less relevant. The physisorption mechanism involves the
condensation of the hydrogen molecule inside or between the nanotubes as a result
of weak van der Waals forces, while the chemisorption mechanism involves the
preliminary dissociation of the hydrogen molecule and the subsequent reaction of
hydrogen atoms with the unsatured C-C bonds to form C-H bonds.
We take in to account vdW interactions in DFT using the new method (DFT/vdWWF) [3] recently developed in our group based on the concept of maximally
localized Wannier functions. This new technique aims at combining the simplicity
of the semiempirical formalism with the accuracy of the first principles approaches.
We explore several adsorption sites and orientation of hydrogen molecule relative
to the graphene plane: hollow, bridge and top site. The most stable physisorbed
state is the hollow site with a binding energy of 54 meV. This value, in agreement
with experimental results is also compared to that obtained by other vdW
correction methods.
The analysis of diffusion paths among physisorbed states show that molecular
hydrogen can diffuse at room temperature from one configuration to another with
typical energy barriers of ~10 meV.
The situation is different when the hydrogen molecules approach the carbon
surface and dissociate allowing the chemisorption on the carbon surface (G or
SCNT), provided that they are able to overcome the activation energy barriers. In
particular, we calculate the potential energy surfaces for the dissociative
adsorption of H2 on highly symmetric sites of graphene (orto, meta and para
position). The lowest activation barrier of 2.67 eV is that one that describes the
process going from the hollow physisorbed state to the para chemisorbed state.
Other energy paths are characterized by higher activation barriers (> 3.eV).
[1]
[2]
[3]
36
Scipioni Roberto; Ohno Takahisa, Chem. Phys. Lett., 492, 263 (2010)
Scipioni Roberto; Boero Mauro; Ohno Takahisa, Chem. Phys. Lett., 480,
215, (2009)
Pier Luigi Silvestrelli, Physical Review Letters, 100, 053002 (2008)
OR22
Ab Initio Modeling of PbSe Quantum Dots
Maurizio Cossi, Mario Argeri, Fabio Grassi, Leo Marchese
Dipartimento di Scienze e Tecnologie Avanzate (DISIT), Università del Piemonte
Orientale
The surface passivation and the shape of PbSe small nanoclusters are studied by
DFT calculations, to understand the different behaviour of the crystallographic
faces towards organic ligands, and their effects on the cluster growth.
DFT theory is used to compute the energy of different crystallographic faces of
PbSe and the addition energies of several organic ligands, commony used as
capping agents in nanocrystals synthesis. It is found that charged ligands can
reverse the stability order of the PbSe faces, influencing the prevalence of one face
and hence the final shape of the particle; this can also explain the excess of lead
experimentally observed in PbSe quantum dots in some conditions.
Complexes of PbSe QD and organic dyes (cyanines) have been proposed as
efficient solar energy harvesters in dye-sensitized solar cells (DSC). Such
complexes have been studied at the same level of theory. Besides examining the
preferred addition geometries and stability, the absorption/emission spectra of
cyanine/QD complexes are predicted the TD-DFT level. Large complex systems
formed by PbSe QD / squaraine / TiO2 substrate have also been modeled to get
some insight about the optimal matching of electronic levels and electron transfer
processes.
37
OR23
Post-Hartree-Fock treatment of crystalline periodic
systems: the CRYSCOR code
Lorenzo Maschio,a Silvia Casassa, a Martin Schütz, b Denis Usvyatb
a
Dipartimento di Chimica IFM, and Centre of Excellence NIS (Nanostructured
Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)
b
Institute for Physical and Theoretical Chemistry, Universitat Regensburg,
Universitaetsstrasse 31, D-93040 Regensburg (Germany)
E-mail: [email protected]
Local post Hartree-Fock methods for molecules have seen a considerable success
in recent years, allowing for high-level quantum chemical calculations on complex
molecular systems, at a reasonable computational cost. These powerful techniques
have been only recently made available also for the study of crystalline systems
and implemented in the CRYSCOR code [1].
Thanks to the features of the local approach, the implementation of fast integral
evaluation techniques such as density fitting [2] and an efficient parallel
implementation [3], MP2 calculations on systems with more than one hundred
atoms and a few thousands atomic orbitals in the unit cell
can be achieved in a few hours.
This approach has been demonstrated to be effective, and
superior to standard DFT methods, for the study of
cohesive energy of weakly bound molecular crystals [4],
surface adsorption of molecules [5], relative stabilities of
crystalline
polymorphs,
pressure-induced
phase
transitions [6], simulation of Compton profiles, formation
of nanostructures such as multi-walled nanotubes and nanoscrolls.
In this contribution the main features of the program will be outlined, with a focus
on the most recent advancements and applications.
[1]
[2]
[3]
[4]
[5]
[6]
38
C. Pisani, L. Maschio, S. Casassa, M. Halo, M. Schütz, D. Usvyat, J.
Comput. Chem. 2008, 29 (13), 2113-2124. www.cryscor.unito.it
(a) L. Maschio, D. Usvyat, F. R. Manby, S. Casassa, C. Pisani, M. Schütz,
Phys. Rev. B 2007, 76, 075101; (b) L. Maschio. D. Usvyat, Phys. Rev. B
2008, 78, 073102
L. Maschio, J. Chem. Theory Comput. 2011, 7, 2818
(a) L. Maschio, D. Usvyat, M. Schütz, B. Civalleri, J. Chem. Phys. 2010,
132, 134706 ; (b) L. Maschio, D. Usvyat, B. Civalleri, CrystEngComm
2010, 12, 2429
R. Martinez-Casado, G. Mallia, D. Usvyat, L. Maschio, S. Casassa, M.
Schütz, N. M. Harrison, J. Chem. Phys. 2011 134, 014706.
A. Erba, L. Maschio, S. Salustro, S. Casassa, J. Chem. Phys. 2011, 134,
074502.
OR24
Typicality of the response by quantum pure states
Barbara Fresch, Giorgio J. Moro
Dipartimento di Science Chimiche, Università di Padova, via Marzolo 1, 35131
Padova, Italy
Mainly because of the objective of realizing quantum computers, in recent years an
intense research activity has been developed about the statistical and dynamical
properties of quantum pure states, that is of quantum systems without entanglement
with the environment. In such a framework several fundamental issues have been
risen, concerning for instance the description of equilibrium properties [1-4].
Indeed, in opposition to standard microcanonical quantum description, one has to
take into account that different quantum pure states, with well defined sets of
populations for the Hamiltonian eigenstates [5], are compatible with a given
macrostate. We have proposed the Random Pure State Ensemble (RPSE) as the
self-consistent statistical ensemble of quantum pure states, which is able to
generate a macroscopic description in agreement with thermodynamics [6,7]. More
recently we have analyzed the predictions of RPSE statistics in presence of an
external time dependent field, in order to test its capability of supplying the correct
framework for the study of dynamical properties [8]. Several important features
emerge from the simulations of spin systems, like the relaxation after a quench. It is
shown that typicality of equilibrium states is generalized to the response, so that the
dynamical properties become independent of the particular realization of the
quantum pure state.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
J. Gemmer, M. Michel, G. Mahler, Quantum Thermodynamics (Springer,
New York, 2004).
S. Goldestein, J.L. Lebowitz, R. Tumulka, N. Zanghi, Phys. Rev. Lett. 96
(2006), 050403; S. Goldstein, J.L. Lebowitz, C. Mastrodonato, R. Tumulka,
N. Zanghi, Phys. Rev. E 81 (2010), 0111098.
S. Popescu, A.J. Short, A. Winter, Nature Phys. 2 (2006); N. Linden, S.
Popescu, A.J. Short, A. Winter, Phys. Rev. E 79 (2009), 055021.
P. Reiman, Phys. Rev. Lett. 99 (2007) 160404, Phys. Rev. Lett. 101 (2008)
190403.
B. Fresch and G. J. Moro, J. Phys. Chem. A 113 (2009), 14502.
B. Fresch and G. J. Moro J. Chem. Phys. 133 (2010), 034509, 034510.
B. Fresch and G. J. Moro, J. Chem. Phys. 134 (2011), 054510.
B. Fresch and G. J. Moro, (2011) arXiv:1104.4625.
39
OR25
On the fly modeling of the photodynamics of spin
changing processes in organic molecules
Giovanni Granuccia, Maurizio Persicoa, Lara Martínezb, Inés Corralb
a
Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, I-56126
Pisa, Italy. bDepartamento de Química, Universidad Autónoma de Madrid 28049,
Cantoblanco, Madrid, Spain.
E-mail: [email protected]
We propose a procedure accounting for nonradiative spin forbidden transitions in
molecular dynamics simulations, in the framework of the mixed quantum-classical
surface hopping (SH) scheme. It is connected to the direct dynamics scheme
developed in our group [1], where energies and couplings are evaluated
semiempirically, and includes an original algorithm for the evaluation of the
analytical gradient of the energy of a spin-mixed wavefunction [2]. Our method is
applied to the simulation of the excited state dynamics of 6-thioguanine, where
both nonadiabatic couplings and spin orbit interactions play an important role.
[1]
[2]
40
(a) Granucci, G.; Toniolo, A.; Persico, M. J. Chem. Phys. 2001, 114, 10608.
(b) Ciminelli, C.; Granucci, G.; Persico, M. J. Chem. Phys. 2005, 123,
174317.
Granucci, G.; Persico, M. J. Comput. Chem. 2011, 32, 2690.
OR26
Predicting the NMR spectra of paramagnetic
molecules by DFT Calculations
A. Bagnoa, F. Rastrellia
a
Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35151
Padova (Italy)
E-mail: [email protected]
All basic NMR textbooks warn the reader against attempting to run the spectrum of
a paramagnetic substance. Indeed, running the 1H NMR spectrum of a
paramagnetic substance using standard acquisition parameters leads to
unpredictable, but most often disappointing, results, from awfully broad lines
(often at very uncomfortable chemical shifts), to nothing at all. In this
communication, we show that DFT calculation of structural and spectroscopic
paramaters (orbital shieldings, g-factor and hyperfine couplings) leads to the
prediction of contact and pseudocontact shifts and line widths which can greatly aid
in the experimental setup and assignment of such spectra [1,2].
Figure 1. Calculated (top) and experimental (bottom) 1H NMR spectra of 4hydroxy-TEMPO butyrate (600 MHz, T = 290 K).
[1]
[2]
F. Rastrelli, A. Bagno, Chem. Eur. J. 2009, 15, 7990.
F. Rastrelli, A. Bagno, Magn. Reson. Chem. 2010, 48, S132.
41
OR27
Towards a fully polarizable QM/MM/PCM approach
Filippo Lipparini,a Vincenzo Baronea
a
Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
E-mail: [email protected]
Multiscale calculations are nowadays an important tool to model complex systems,
like a molecule in solution or a chromophore in a macromolecule. In this
contribution, we present the preliminary implementation of fluctuating charge1
(FQ) polarizable force field coupled both to the polarizable continuum model
(PCM) and to Self Consistent Field (SCF) based quantum mechanical calculations.
The coupling of the FQ force field and of the PCM2 can be exploited to perform
molecular dynamics simulations with non-periodic boundary conditions3, which
can be advantageous to simulate
intrinsically non-periodic systems, like a
molecule in solution. In a timeindependent perspective, we have
implemented analytical first derivatives
of the energy for the full QM/MM/PCM
Hamiltonian; we are working on the
implementation of analytical second
derivatives with the goal of a fully
polarizable model to accurately describe
the spectroscopical properties of
molecules in a complex, specifically
interacting environment.
[1]
[2]
[3]
42
Rick, S.W.; Stuart, S.J.; Berne, B.J. J. Chem. Phys. 1994, 101, 6141-6156.
Lipparini, F.; Barone, V. J. Chem. Theory Comput. 2011, 7, 3711-3724.
Brancato, G.; Rega, N.; Barone, V. J. Chem. Phys. 2008, 128, 144501.
OR28
Nonadiabatic quantum collisions on three coupled
1 +
1 +
PESs: The O
+N2 X Σ g
O
+N2 X Σ g quenching
(
)
(
)
Paolo Defazio,a Pablo Gamallo,b Carlo Petrongoloc
a
Dipartimento €
di Chimica, Università di
€ Siena, Via A. Moro 2, I-53100 Siena, Italy
Departament de Química Física i IQTC-UB, Universitat de Barcelona, C/ Martí i
Franquès 1, 08028, Barcelona, Spain
c
IPCF-CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
E-mail: [email protected]
b
We present the spin-orbit (SO) and Renner-Teller (RT) quantum dynamics of the
spin-forbidden quenching O
+N2 X 1Σ +g →O
+N2 X 1Σ +g on the N2O X˜ 1A' ,
(
)
(
)
a˜ A" , and b˜ 3A' coupled PESs. We use the permutation-inversion symmetry,
3
€
propagate coupled-channel (CC) real wavepackets, and compute initial-stateresolved probabilities and cross sections
for the ground vibrational
€ and the first
€
€
two
€ rotational states of N2, =0 and 1.
Labeling symmetry angular states by and , we report selection rules for and
for the minimum
value associated with any electronic state, showing that a˜ 3A"
is uncoupled in the centrifugal-sudden (CS) approximation at =0. The dynamics
is resonance-dominated, the probabilities are larger at low ,
decrease with
the collision energy and increase with , and the CS
is lower than
€ the CC one.
The nonadiabatic interactions play different roles on the quenching dynamics,
1
3
3
3
because the X˜ A'−b˜ A' SO effects are those most important while the a˜ A"−b˜ A'
RT ones are negligible.
€
€
43
OR29
Study of the dynamics of the N+O associative
ionization process through a time-dependent calculation
Dimitris Skouteris,a Antonio Lagana’,a Fernando Pirania
a
Dipartimento di Chimica, Universita’ degli Studi di Perugia, Via Elce di Sotto, 8,
06132 Perugia, Italy
E-mail: [email protected]
We have studied the associative ionization process N+O → NO+ + e- using a timedependent wavepacket method [1-3]. The wavepacket propagation takes place on a
single surface (for the N+O) system,
whereby the wavepacket itself is prepared
in the asymptotic region (where there is
practically no interaction between the two
atoms) and is subsequently propagated
through the time-dependent Schrodinger
equation.
No se puede mostrar la imagen. Puede que su equipo no tenga suficiente memoria para abrir la imagen o que ésta esté dañada. Reinicie
el equipo y, a continuación, abra el archivo de nuevo. Si sigue apareciendo la x roja, puede que tenga que borrar la imagen e insertarla de
nuevo.
Using a Chebyshev expansion scheme for
the time-dependent Green function, the
propagation is very fast. In order to compute
state-specific relative cross sections, a
Franck-Condon
type
(sudden)
approximation is used, whereby the
interaction matrix elements between the
N+O surface and the diatom (NO+) surface do not depend on the interatomic
distance. Within our approximation, we have been able to calculate relative cross
sections for all relevant rovibrational states of the NO+ diatom as a function of
collision energy. An interesting energy-dependent Franck-Condon effect is
observed.
[1]
[2]
44
{a} Balucani, N.; Skouteris, D.; Cartechini, L.; Capozza, G.; Segoloni, E.;
Casavecchia, P.; Alexander, M.H.; Capecchi, G.; Werner, H.-J. Phys.Rev.
Lett. 2003, 91, Art. N. 13201 (b) Balucani, N.; Skouteris, D.; Capozza, G.;
Segoloni, E.; Casavecchia, P.; Alexander, M.H.; Capecchi, G.; Werner, H.J. Phys. Chem. Chem. Phys. 2004, 6, 5007.
(a) Skouteris, D.; Lagana', A.; Capecchi, G.; Werner H.-J. Int. J. Quant.
Chem. 2004, 96, 562. (b) Skouteris, D.; Lagana', A.; Capecchi, G.; Werner
H.-J. Int. J. Quant. Chem. 2004, 99, 577.
[3] Skouteris, D.; Gervasi, O.; Lagana', A. Comp. Phys. Comm. 2009,
180, 459.
OR30
Collision dynamics for the interaction of oxygen atoms
and molecules on a silica surface
Maria Rutigliano,a Sergio Orlandini,a Nico Sannab and Mario Cacciatore,a
a
CNR-Consiglio Nazionale delle Ricerche, Istituto di Metodologie Inorganiche e
dei Plasmi (CNR-IMIP), UOS di Bari, via G. Amendola 122/D, I-70126 Bari, Italy
b
CASPUR , Via dei Tizii 6, I-00185 Roma, Italy
E-mail: [email protected]
Reactive and non-reactive processes due to the interaction of oxygen atoms and
molecules with silica and silica-based materials are of great importance both for the
chemistry at the gas-surface interlayer or in the bulk of the dissociated gas of
various laboratories and natural oxygen plasma systems. Of particular interest is the
dynamics and energetics of O atom recombination at surface. This reaction is, in
fact, exothermic so that part of the exothermic energy can be shared among the
internal degrees of freedom of the formed O2 molecules while the remaining part is
transferred to the silica surface as heat flux. The energy shearing mechanism
depends on the catalytic activity of the silica substrate that controls the dynamics of
various chemical-physics processes involving O and O2 at the surface.
In this contribution we focus on the dynamics of: 1) O atoms adsorption; 2) O atoms
recombination, via Eley-Rideal mechanism; 3) O2 molecule dissociation and
deactivation. We performed Molecular Dynamics calculations using the accurate
Potential Energy Surface for the interaction of O, O2 with the silica substrate
determined by electronic structure calculations in Ref.[1]. The semiclassical
collisional method [2] is applied to describe the dynamics of the nuclear motions of
the atoms/molecules over the calculated potential energy surface.
[1]
[2]
Rutigliano M., Zazza C., Sanna N., Pieretti A., Mancini G., Barone V. and
Cacciatore M. J. Phys. Chem. A 2009, 113, 15366.
Billing G. D., Dynamics of Molecule Surface Interactions, John
Wiley&Sons, NY, 2000; Cacciatore M. and Billing G.D. Surf.Sci.
1990,232,35
45
OR31
Ab-initio g-tensor of transition-metal complexes from the
orbital magnetization
Davide Ceresolia
a
Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Molecolari
(CNR-ISTM), via Golgi 19, 20133 Milan, Italy
We present first principles, density functional theory calculations of the Electronic
Paramagnetic Resonance (EPR) spectrum of mononuclear organic transition metal
complexes, that constitute building block of more complicated catalysts for the
water splitting reaction.
We apply here the “Modern Theory of Orbital Magnetization” [1] and we obtain
the EPR g-tensor by computing the derivative of the orbital magnetization with
respect to the electronic spin flip [2]. This method allows explore the performance
of advanced DFT methods such as DFT+U and hybrid functionals in correcting the
the self-interaction error (SIE) that plagues standard semi-local functionals.
We found that DFT+U method improves the agreement with respect to experiment,
of the EPR g-tensor and hyperfine couplings parameters for high spin complexes.
Finally, we will discuss the success and failures of DFT+U as an energy functional,
and the importance of benchmarking improved- or post-DFT methods (such as
hybrid functionals) against the EPR spectra of transition metals complexes.
[1]
[2]
46
T. Thonhauser, D. Ceresoli, D. Vanderbilt, and R. Resta, Phys. Rev. Lett.
95, 137205 (2005).
D. Ceresoli, U. Gerstmann, A. P. Seitsonen and F. Mauri, Phys. Rev. B 81,
060409 (2010).
Posters
P01 Mg/Zn Mixed-Metal Borohydride for hydrogen storage: abinitio periodic computational study of the phase stability and
decomposition
Elisa Albanese,a Bartolomeo Civalleria
a
Dipartimento di Chimica IFM e Centro di Eccellenza NIS, Università di Torino,
via Pietro Giuria 7, Torino, 10125, ITALIA
E-mail: [email protected]
Metal borohydrides are considered promising materials for their application in
efficient and reversible hydrogen storage. However, simple metal borohydrides are
either too thermodynamically stable or kinetically too slow. Therefore, current
research is seeking for mixed metal systems. Indeed, the manipulation of multication combination may provide a general route for tuning the thermodynamic
stability of borohydrides [1]. In this work, we investigate the Mg-Zn system for
which the estimate decomposition enthalpy (with respect to metal hydrides, boron
and hydrogen) is in the range of interest (≈ 40 kJ/mol H2).
Calculations have been carried out at PBE-D* level of theory (PBE with Grimme’s
DFT-D2 dispersion correction [2], as modified for solids by Civalleri et al. [3]) and
performed with the periodic ab-initio CRYSTAL09 [4] program.
For both Mg and Zn simple compounds, the phase stability of four different phases
has been calculated, as well as their decomposition enthalpy. Mg/Zn mixed metal
borohydrides, MgxZny(BH4)z, have then been studied by generating different solid
solutions from the most stable structure of Mg(BH4)2 (α-phase, space group P6122)
with several Mg/Zn atomic percentages. The formation enthalpies of the these
compounds were calculated considering the following reaction paths:
The computed results indicate that MgxZny(BH4)z compounds can be formed from
chlorides and their decomposition enthalpies are close to the range of interest.
Therefore, Mg-Zn mixed metal borohydrides appears to be promising candidate for
hydrogen storage and deserve to be also explored experimentally.
[1]
[2]
[3]
[4]
Fang, Z.-Z.; Kang, X.-D.; Luo, J.-H.; Wang, P.; Li, H.-W.; Orimo. S. J. Phys. Chem. C 2010, 114,
22736–22741.
Grimme, S. J. Comput. Chem. 2006, 27,1787–1799.
Civalleri, B.; Zicovich-Wilson, C. M.; Valenzano, L.; Ugliengo, P. CrystEngComm. 2008, 10, 405410.
Saunders, V. R.; Dovesi, R.; Roetti, C.; Orlando, R.; Zicovich-Wilson, C. M.; Pascale, F.; Harrison,
N. M.; Doll, K.; Civalleri, B.; Bush, I. J.; D’Arco, P.; Llunell, M. CRYSTAL09 User’s Manual,
Torino 2009.
49
P02 Computational modelling of the effect of metal nanoparticles
on the extent of Electronic Energy Transfer between organic
chromophores
Ambra Irene Angioni*, Stefano Corni§, Benedetta Mennucci*
* Dipartimento di Chimica, Università di Pisa – Via Risorgimento 35, 56126 Pisa, Italy.
§ Center S3, CNR Institute of Nanoscience – Via Campi 213/A, 41125 Modena, Italy.
Electronic Energy Transfer (EET) plays an important role in biological systems
such as the photosyntetic complexes of plants and bacteria, and it has already been
successfully applied to investigate a wide range of biological processes. In this
study we combined a linear response approach with the polarizable continuum
model (PCM) in order to describe solvation effects on EET [1], but our focus was
mainly directed on the effect of metal nanoparticles on the extent of EET. The
metal is described as a continuous body, characterized by its frequency dependent
local dielectric constant [2]. As model system for our analysis we chose N-N’dimethylperylene-3,4,9,10-dicarboximide (PDI) [3] and we investigated the role of
a set of parameters (nature and shape of the metal, distance between chromophore
and metal, relative orientation of the chromophore pair, solvent environment) on
the extent of Energy Transfer. We also compared the rate of EET between the
chromophore pair with respect to that of EET to the metal (nonradiative decay) and
we looked for proper conditions of EET enhancement in model systems of
possible design interest. Applications of the proposed model on biological systems
are also of great interest and they will soon be explored.
[1]
[2]
[3]
50
Iozzi, M. F.; Mennucci, B.; Tomasi, J.; Cammi, R. J. Chem. Phys. 2004,
120, 7029.
Andreussi, O.; Corni, S.; Mennucci B.; Tomasi J. J. Chem. Phys. 2004, 121,
10190.
Vukovic, S.; Corni, S.; Mennucci B. J.Phys. Chem. C 2009, 113, 121.
P03 MOF derivatives as molecular tools to trap metal azides
Nerina Armata, Remedios Cortese, Dario Duca, Roberto Triolo
Dipartimento di Chimica “S. Cannizzaro”, Università di Palermo, viale delle
Scienze, Ed. 17, 90128 Palermo, Italy
E-mail: [email protected]
The research on High Energy Density Material (HEDM) family has, in recent
years, attracted much interest while efforts in this field are mostly devoted to
identify new systems and procedures to HEDM stabilization [1]. Among HEDMs,
polynitrogen compounds have been studied both theoretically and experimentally
and several metal azides have been identified as their
precursors [2]. Tools useful in removing metal azides
from their solutions are especially important in order
to synthesize and stabilize polynitrogen compounds.
Metal-Organic-Framework (MOF) materials appear
suitable for this purpose and as a consequence we
decided to model, at DFT level, the interaction among
MOF porous solids and alkaline metal azides. MOF-5
is one of the most studied species. This porous solid is
the first member of the Iso-Reticular-Metal-OrganicFramework (IRMOF) family, composed by hybrid
compounds having the same reticular topology [3]. Figure 1: IRMOF-3 model used
to study metal azide interactions
Structures of the family above are based on Zn4O
clusters and polytopic linkers derived by functionalizing 1,4 Benzendicarboxylate
(BDC) moieties. The present study has been focused on the interactions of the
alkaline metal azides with IRMOF-1 and IRMOF-3 derivatives. These could
interact with the azide anions – relocating their negative charges on the IRMOF
vertices – and with the alkaline cations – forming π complexes with the IRMOF
BDC aromatic rings –. The electron effects of the carbonyl groups and the benzene
rings belonging to same BDC moiety were at first studied; then, we analyzed the
IRMOF systems, trying to rationalize also the effect of the inorganic vertices. The
computational approach allowed us to obtain preliminary results able to suggest
hints to individuate promising IRMOF species of use in azide capture processes.
[1]
[2]
[3]
K. O. Christie, W. W. Wilson, J. A. Sheehy and J. A. Boatz, Angew. Chem. Int.
Ed., 38, 1999, 2004.
M. D. Brown, J. M. Dyke, F. Ferrante, W. Levason, J. S. Ogden and M. Webster,
Chem. Eur. J., 12, 2006, 2620.
M. Eddaoudi, J Kim, N. Rosi, D Vodak, J. Watcher, M. O'Keeffe, and O. M.
Yaghi, Science, 295, 2002, 469
51
P04 Glycine adsorption on Anatase surface: a DFT periodic
study
Audagnotto Martina and Anna Maria Ferraria
a
Dipartimento di Chimica IFM, Università di Torino and NIS -Nanostructured
Interfaces and Surfaces - Centre of Excellence, Via P. Giuria 7, 10125, Torino,
Italy.
Starting from the results of a preliminary work where the simulation of adsorbed
glycine had been addressed only for the case of a very low coverage and only for
the 101 surface [1], and we have extended the study to a detailed analysis of the
coverage effects up to the limit beyond which repulsions between the molecules are
the dominant phenomena. Unlike results from the previous study, we have
identified a new order of stability adopted by the adsorbed species: the most stable
glycine conformer, labeled d10, adopts a glycinate structure for all the analyzed
coverages, and it is characterized by a strong adsorption energy (Eads (101) = -33.7
kcal/mol).
We have also investigated the adsorption of molecular and dissociated glycine
structures on the 001 Anatase surface. The most stable configurations, again the
dissociated form d10, shows an adsorption energy Eads (001) = -56.5 kcal/mol,
remarkably higher than on the 101 surface. In order to explain the high reactivity
of the (001) anatase surface we have probed the basicity and acidity of the (001)
and (101) surfaces with different small molecules like water, ammonia, formic acid
and carbon dioxide.
[1]
[2]
52
Denes Szieberth, Anna Maria Ferrari and Xing Dong, Phys. Rev. B 2010,
63, 11033-11040.
L.Mino , A.M.Ferrari , V.Lacivita , G.Spoto , S.Bordiga and A.Zecchina,
Phys. Chem. Chem. Phys 2011, 115, 7694-7700.
P05 Comparison of vertical and adiabatic harmonic approaches
for the calculation of the vibrational structure of electronic spectra
Francisco Avilaa and Fabrizio Santoroa
a
CNR--Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
E-mail: [email protected];
We focus on effective models for the simulation of the vibrational structure
associated to electronic spectra (VSaES) in large semi-rigid molecules with
negligible nonadiabatic couplings. Any description of such a VSaES requires the
determination of the potential energy surfaces (PES) of the electronic states
involved in the transition. For large systems (dozens of atoms) an exhaustive
exploration of the PESs on a grid of points is out of reach, and harmonic
expansions of the PES around topical structures often represent the only viable
route. In this context, two possible approaches can be adopted, namely the
expansion of the final state PES around its own equilibrium geometry (Adiabatic)
or around the initial state one (Vertical). Moreover, even within Harmonic
approximation each of the two approaches gives rise to a hierarchy of models of
different accuracy, depending on whether no constrain is imposed on the final state
PES, apart from being harmonic (AH, Adiabatic Hessian or VH, Vertical Hessian),
or the normal modes of the initial and final state are assumed to be the same but
with possibly different frequencies (ASF, Adiabatic Shift and Frequencies or VGF,
Vertical Gradient and Frequencies), or finally the two PES are assumed to be
identical apart from a displacement of the minimum (AS, Adiabatic Shift or VG,
Vertical Gradient). When it is necessary to go beyond the Franck-Condon (FC)
approximation, including the Herzberg-Teller (HT) linear variation of the transition
dipole as a function of the nuclear coordinates, other two different options are
possible: namely, performing the expansion around the equilibrium geometry of the
initial or final state. All these different models have been implemented in a version
of our code FCclasses [1] that computes VSaES on the ground of effective prescreening techniques to preselect only the relevant transitions in the dense manifold
of possible final states [2]. The relative performance of these models on a number
of prototypical dyes at low and room temperature will be discussed.
[1]
[2]
Santoro. F.; FCclasses a Fortran 77 code, 2008 http://village.pi.iccom.cnr.it
(a) Santoro, F.; Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys.
2007, 126, 084509, (b) Santoro, F.; Improta, R.; Lami, A.; Barone, V. J.
Chem. Phys. 2007, 126, 184102. (c) Santoro, F.; Improta, R.; Lami, A.;
Bloino, J.; Barone, V. J. Chem. Phys. 2008, 128, 224311. (d) Bloino, J.;
Biczysko, M.; Santoro, F.; Barone, V., J. Chem. Theory and Comp. 2010,
1256. .
53
P06 Photophysical properties of Ruthenium dyes for applications
in solar cells. A computational study on N3 dye
Francisco Avila,a Maria Grazia Lobello,b Filippo De Angelis,b Fabrizio
Santoroa
a
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
b
CNR-Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie
Moleculari del CNR (ISTM-CNR), Via Elce di Sotto 8, I-06123, Perugia, Italy
E-mail: [email protected]
Solar cells based on charge transfer dye sensitizers adsorbed on anastase TiO2
nanoparticles have a promising future for their low cost and high performance. Up
to date the most efficient dyes employed in these cells are polypyridil complexes of
ruthenium reaching a rate of solar light to electric power conversion of 11.3%.
With the aim of getting a better understanding of the photophysical processes
involved in the energy conversion of these devices, we report the results of a
theoretical analysis of the phosphorescence and emission spectra of the cysRu[((4,4’-COOH)2-2,2’-bipyridine)2(NCS)2] known as the N3 dye in different
environments, like gas phase, ethanol and water, and different states of protonation.
Our methodology is based on DTF and TD-DFT calculations, and employs recent
developments in Polarizable Continuum Model [2] and PCM/TD-DFT statespecific calculations (SS) [3], giving a non-empirical determination of the polar
contribution to inhomogeneous broadening [4]. The vibrationally resolved spectra
have been computed according to time-independent standard sum-over-state
expression, through effective a priori selection of the possible vibronic transitions
[5]. We discuss the properties of the electronic spectra, and the reasons for their
width. Moreover we document the possible occurrence of a dynamical interplay
between local and delocalized characters in the lowest energy singlet and triplet
excited states.
[1]
[2]
[3]
[4]
[5]
54
(a) B. O’Regan, M. Grätzel, Nature. 1991, 353, 737-740.; (b) M. Grätzel, Nature
2001, 414, 338-344.
Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999.
(a) Improta, R.; Barone, V.; Scalmani, G.; Frisch, M.J. J. Chem. Phys. 2006, 125,
54103. (b) Improta, R.; Scalmani, G.; Frisch, M.J.; Barone, V. J. Chem. Phys.
2007, 127, 074504.
Avila Ferrer,F.J.; Improta, R.; Santoro, F.; Barone, V. Phys. Chem. Chem. Phys.
2011, 13, 17007
(a) Santoro, F.; Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys. 2007,
126, 084509, ibidem 2007, 126, 169903. (b) Santoro, F.; Improta, R.; Lami, A.;
Barone, V. J. Chem. Phys. 2007, 126, 184102. (c) Santoro, F.; Improta, R.; Lami,
A.; Bloino, J.; Barone, V. J. Chem. Phys. 2008, 128, 224311. (d) Bloino, J.;
Biczysko, M.; Santoro, F.; Barone, V., J. Chem. Theory and Comp. 2010, 1256.
P07 QM/MM characterization of redox-active Trp radicals in
LiP and LiP-like systems
Caterina Bernini,a Rebecca Pogni,a Riccardo Basosi,a Adalgisa Sinicropia
a
Dipartimento di Chimica, Università di Siena, Via A. De Gasperi 2, 53100 Siena,
Italy
E-mail: [email protected]
A catalytically active tryptophan radical (Trp171) has been demonstrated to be
involved in the long-range electron transfer to the heme cofactor of the oxidative
enzyme Lignin Peroxidase (LiP) that plays a central role in the biodegradation of
the plant cell wall constituent lignin and is able to catalyze the oxidation of a
variety of high redox potential compounds [1]. However, no direct evidence via
EPR measurements for the formation of the Trp171 radical intermediate has been
reported to date. Site-directed mutagenesis has been used to manipulate the
microenvironment of Trp171 site in LiP (E250Q+E168Q), allowing the detection
by EPR spectroscopy of the Trp171 radical species [2]. The same engineeringbased approach has been also applied to introduce the catalytic Trp and its acidic
environment into Coprinus cinereus Peroxidase (CiP) that has similar protein fold
but lacks oxidation activity. A Trp radical in the resulting CiP triple variant
(D178W+R257E+R271D) has been identified and characterized by multifrequency
EPR spectroscopy (9 and 285 GHz) [2]. The availability of EPR experimental data
on these LiP-like systems has stimulated the computational characterization of Trp
radicals embedded in the protein matrices of these systems. In particular, the use of
a QM/MM (DFT/CHARMM) strategy, already applied successfully to the study of
Trp and Tyr radical intermediates in a Versatile Peroxidase and in its W164Y
mutant [3], allowed a direct comparison between experimental and computed data.
The nature of the Trp radicals is discussed together with the analysis of their
environment with the aim of understanding the different behaviour of pristine LiP
in comparison to that of LiP and CiP variants [4].
[1]
[2]
[3]
[4]
Blodig, W.; Smith, A.T.; Doyle, W.A.; Piontek, K. J. Mol. Biol., 2001, 305,
851.
Smith, A.T.; Doyle, W.A.; Dorlet, P.; Ivancich, A. PNAS, 2009, 106, 16084.
Bernini, C.; Pogni, R.; Ruiz-Duenãs, F.J.; Martínez, A.T.; Basosi R.;
Sinicropi, A. Phys. Chem. Chem. Phys., 2011, 13, 5078.
Bernini, C.; Pogni, R.; Basosi R.; Sinicropi, A. Proteins: Structure,
Function, and Bioinformatics, 2012, submitted.
55
P08 Modelling fluorescence of intercalating and minor groovebinding molecular probes for nucleic acids: a combined quantummechanical and spectroscopic study
Alessandro Biancardi, Tarita Biver, Benedetta Mennucci, Fernando Secco
Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, 56126 – Pisa
(IT)
E-mail: [email protected]
A Density Functional Theory (DFT) study of the absorbance and fluorescence
emission characteristics of Thiazole Orange (TO) [1] and 4',6-diamidino-2phenylindole (DAPI) [2] in solution and when bounded to DNA, was carried out in
combination with spectrophotometric and spectrofluorometric experiments under
different conditions (temperature, concentration, solvent viscosity). The overall
data collected provided information on the features of the “light-switch” by
fluorescent probes and the comparison between experimental and calculated photophysical properties allowed to explain and rationalize both shifts and
quenching/enhancing effects on fluorescence due to solvation, dimerisation,
intercalation and minor groove binding.
[1]
[2]
56
Biancardi, A.; Biver, T.; Marini, A.; Mennucci, B.; Secco, F. Phys. Chem.
Chem. Phys. 2011, 13, 12595.
Biancardi, A.; Biver, T.; Mennucci, B.; Secco, F. (in preparation)
P09 Theoretical description of ionic liquids: highlights from
recent calculations
E. Bodo
Dept. of Chemistry and CNISM, University of Rome “La Sapienza”, Italy
E-mail: [email protected]
Among the most exciting and successful materials developed and studied in the last
twenty years, ionic liquids [1] are among those that can certainly claim one of the
most rich field of applications in industry and in applied technological research.
Conventionally, ILs are chemicals that show a melting point lower than 100 C,
therefore often liquid under ambient conditions and that are composed entirely of
ionic species. Their very low (in many cases, negligible) vapor pressure, high
thermal stability, large tunability of several properties (including polarity,
hydrophobicity, density, solvating activity) has allowed the use of these materials
as solvents for a constantly increasing range of applications [2]. Therefore, it is
clear that the range of physico-chemical properties to be rationalized is extremely
wide and requires a joint use of complementary techniques. We have recently [3]
analyzed the behavior of such compounds by means of a combination of
experimental and theoretical techniques. We will report some of our results on
various systems including protic and non-protic ionic liquids. In particular we will
report on the structure of geminal di-imidazolium ionic liquids explored by
molecular dynamics simulations and we will present the study of a series of protic
molten salts, through a joint analysis made by Vibrational Raman spectroscopy, Xray diffraction and theoretical calculations.
[1]
[2]
[3]
Rogers, R. D., Seddon, K. R., Eds. Ionic Liquids IIIA: Fundamentals,
Progress, Challenges, and Opportunities: Properties and Structure; ACS
Symp. Ser.; American Chemical Society, Washington D.C., 2005; Vol. 901;
p 356;
(a) Gaune-Escard, M., Seddon, K. R., Eds. Molten Salts and Ionic Liquids:
Never the Twain?; Wiley, 2010; p 441; (b) Plechkova, N. V.; Seddon, K. R.
Chem. Soc. Rev. 2008, 37, 123–150;
(a) Bodo, E.; Caminiti, R. J. Chem. Phys. A 2010, 114, 12506; (b) Bodo, E.;
Gontrani, L.; Caminiti, R.; Plechkova, N. V.; Seddon, K. R.; Triolo, A. J.
Phys. Chem. B 2010, 114, 16398. (c) E. Bodo, P. Postorino, S.
Mangialardo, G. Piacente, F. Ramondo, F. Bosi, P. Ballirano, and R.
Caminiti, J. Phys. Chem. B, 115 (2011), 13149-13161. (d) E. Bodo, M.
Chiricotto and R. Caminiti, J. Phys. Chem. B 115, 14341-14347, (2011).
57
P10 Excited states of N- and O-donor ligands coordinated to YF3
compared to the resonance levels of visible and NIR-emitting
lanthanide ions
Marco Bortoluzzi,a Gino Paolucci,a Francesco Enrichi,b Mattia Gatto,a
Stefania Roppa a
a
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di
Venezia, Dorsoduro 2137, 30123 Venezia, Italy.
b
CIVEN, Coordinamento Interuniversitario Veneto per le Nanotecnologie, Via
delle Industrie 5, 30175 Marghera (Venezia), Italy.
E-mail: [email protected]
The synthesis of visible and NIR-emitting lanthanide complexes with antennaligands is a growing field of research [1]. We have recently observed [2] that
pyrazole-based [N,N,N]-donor ligands behave as antennae for visible-emitting Ln3+
ions such as Eu3+ and Tb3+ and for the NIR-emitting Yb3+ ion. Only
photoluminescent NIR-emitting ytterbium complexes have been instead obtained
by replacing the pyrazole rings with indazole. [N,N,O]-donor ligands containing
the same N-donor heterocycles have been also studied. The antenna-effect in the
visible range can occur if the O-donor fragment is a carboxylate group, while only
NIR emission from Yb(III) has been observed in the presence of a phenate dent.
The antenna-effect is related to the energy difference between the resonance levels
of the lanthanide ion and the excited states of the ligand. In this communication we
report a TD-SCF study on the model system YF3(L), where L is a neutral N-donor
heterocycle or an anionic O-donor species. All the singlet and triplet excited states
of the coordinated ligands have been optimized. Theoretical and experimental data
regarding light absorption and emission have been compared. The relative energy
values of the resonance levels of Eu3+, Tb3+ and Yb3+ with respect to selected
excited states of the coordinated ligands explain the observed experimental results.
[1]
[2]
58
(a) Bünzli, J-C. G. Chem. Rev. 2010, 110, 2729. (b) Bünzli, J-C. G.; Chauvin, AS.; Kim, H. K.; Deiters, E.; Eliseeva, S. Coord. Chem. Rev. 2010, 254, 2623. (c)
Eliseeva, S. V.; Bünzli, J-C. G. Chem. Soc. Rev. 2010, 39, 189. (d) Ma, Y.; Wang,
Y. Coord. Chem. Rev. 2010, 254, 972. (e) Armelao, L.; Quici, S.; Barigelletti, F.;
Accorsi, G.; Bottaro, G.; Cavazzini, M.; Tondello, E. Coord. Chem. Rev. 2010,
254, 487.
(a) Bortoluzzi, M.; Bellotto, L.; Paolucci, G.; Polizzi, S.; Buffo, M.; Enrichi, F. in
New Trends in Coordination, Bioinorganic and Applied Inorganic Chemistry,
Melník M., Segla P., Tatarko M. (Eds.), Press of Slovak University of Technology,
Bratislava, 2011, pagg. 6-24. (b) Bortoluzzi, M.; Paolucci, G.; Polizzi, S.; Bellotto,
L.; Enrichi, F.; Ciorba, S.; Richards, B. S. Inorg. Chem. Commun. 2011, 14, 1762.
P11 Towards an efficient parallel implementation of the GLOB
model Giuseppe Brancato, Costantino Zazza and Vincenzo Barone
Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
E-mail: [email protected]
Molecular simulations of complex systems in the soft-condensed matter, such as
solute-solvent systems, polymers and liquid crystals, are typically carried out using
periodic boundary conditions (PBC) despite the lack of any intrinsic periodicity.
However, one should be aware of possible artifacts introduced by the adoption of a
physically inconsistent model. Recently, we have developed an effective and
integrated discrete/continuum methodology, based on the General Liquid
Optimized Boundary (GLOB)1,2 model, which is particularly well suited for
simulating solute-solvent systems of variable size and at different levels of theory,
from purely classical force fields to more accurate mixed QM/MM and full QM
methods. Here, we present some new developments concerning the adoption of a
Fast Multipole Method (FMM), which allows the effective treatment of the
computationally expensive non-bonded interactions, and a parallel implementation
based on the OPENMP interface well suited for shared-memory HPC machines,
such as the recently introduced multi-core architectures. Preliminary results show
that an almost linear scaling with respect to system size and number of threads is
foreseeable, so allowing the simulation of large soft-matter systems with more
natural boundary conditions.
[1]
[2]
Brancato, G.; Rega, N.; Barone, V., A hybrid explicit/implicit
solvation method for first-principle molecular dynamics simulations,
J. Chem. Phys. 2008, 128, 144501.
Brancato, G.; Rega, N.; Barone, V., Molecular dynamics simulations
in a NpT ensemble using non-periodic boundary conditions, Chem.
Phys. Lett. 2009, 483, 177.
59
P12 Transferability of nonadiabatic transition rates: a key to fast
excited state dynamics?
Valentina Cantatorea, Giovanni Granuccia, Maurizio Persicoa
a
Università di Pisa, Dipartimento di Chimica e Chimica Industriale,
via Risorgimento 35, 56126 Pisa (Italy)
The new method that we propose, called PNAD (Parametrized Non-Adiabatic
Dynamics) starts from the observation that the essential information
in VACUO
about the excited state dynamics of a given chromophore is partially
transferable among different environments. To begin with, we want to show the
transferability of the nonadiabatic transition rates in different environments when
expressed as functions of the electronic energy difference ΔE and of the kinetic
energy of the most important atoms, Ek. As a test case, we choose the
photoisomerization of trans-azobenzene excited in the n→π* band, because of our
previous results with standard on the fly surface hopping dynamics [1], that provide
a good benchmark to check the new results. In our test we consider two
environments that differ in viscosity:
vacuo and ethylene glycol. We show
that even if the decay times in the two
in ETHYLENE GLYCOL
cases are quite different, the transition
rate function R(ΔE, Ek) is substantially
the same. The medium affects the
nuclear dynamics, i.e. the regions of
the phase space that are explored, and
this determines the differences in the
decay times. Based on these results,
we propose a three step procedure:
• First, we run a ”model dynamics”
with the usual nonadiabatic trajectory methods such as TSH (Trajectory
Surface Hopping), in conditions that allow to reduce the computational burden
by at least two orders of magnitude (one chromophore, normally in vacuo, and
few trajectories, stopped shortly after reaching the ground state).
• Second, we extract from the results of the model dynamics the nonadiabatic
transition rates and we fit them as functions of the electronic energy difference
and of the kinetic energy of the most important atoms.
• Third, we use a ground state force-field and the information obtained in the
second step to compute the transition rates in order to run the PNAD
simulations for more complex systems (many interacting chromophores, long
simulation times covering (hot) ground state processes, many trajectories if
needed to obtain statistically significant results, etc). In this way we expect a
computational cost close to standard ground state Molecular Dynamics.
[1] Cusati T.; Granucci G.; Persico M. J. Am. Chem. Soc. 2011, 128, 194
60
P13 Including environment effects on Electronic Energy Transfer
processes: a fully polarisable QM/discrete/continuum approach
Stefano Caprasecca, Ambra Irene Angioni, Benedetta Mennucci
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via
Risorgimento 35, 56126 Pisa, Italy
E-mail: [email protected]
The inclusion of environment effects in the study of photophysical properties of
molecules in solution, or in more complex environments, is of critical importance
in several fields of research. In quantum mechanical (QM) studies, the explicit
inclusion of solvent molecules at QM level is, in practice, unfeasible, and
alternative models need to be used, where the solvent is described at a lower level.
In particular, continuum models, like the Polarisable Continuum Model (PCM [1]),
describe the solvent as a structureless continuum characterised by its dielectric
properties. Such treatment accounts for average long-range solvent effects, but
disregards specific interactions. Alternatively, discrete models include the
environment atoms at a MM level; particularly, in the MMPol model [2], the
solvent is described by a classical force field, as a set of fixed charges and induced
dipoles, interacting with the solute.
A fully polarisable mixed QM/discrete/continuum method, MMPCM, has been
developed to allow calculations where the QM part interacts with some explicit
solvent molecules at MMPol level, while the solvent bulk is represented as a PCM.
It is thus possible to include both average long-range and specific effects; a TDDFT linear response scheme is employed for the calculation of electronic
excitations and couplings. Such method has been implemented in the Gaussian
suite and employed to perform calculations on Electronic Energy Transfer [3]
processes between chromophores.
Results on different test systems are presented, where the importance of such
mixed environment description is assessed on a case-to-case basis.
[1]
[2]
[3]
J. Tomasi, B. Mennucci and R. Cammi, Chem. Rev., 105, 2999 (2005)
C. Curutchet, A. Muñoz-Losa, S. Monti, J. Kongsted, G. D. Scholes and B.
Mennucci, J. Chem. Theory Comput., 5, 1838 (2009)
M. F. Iozzi, B. Mennucci, J. Tomasi and R. Cammi, J. Chem. Phys., 120,
7029 (2004)
61
P14 Charge transfer in model bio-inspired porphyrin-carotene
dyads
Silvia Carlotto,a Laura Orian,a Marilena Di Valentin,a Antonino Polimenoa
a
Dipartimento di Scienze Chimiche dell’Università degli Studi di Padova, Via
Marzolo 1, 35131, Padova, Italy
E-mail: [email protected]
We present a computational study based on accurate DFT and TD-DFT methods on
model bio-inspired donor-acceptor (DA) dyads formed by a carotenoid (C)
covalently linked to a tetraphenylporphyrin (TPP) at the ortho position of one of
the TPP phenyl rings [1]. The mutual orientation of the components and their
distance closely resembles the geometry of the dyad chlorophyll-peridinin in PCP
[2]. Dyadic systems are intensively studied for potential application in the
construction of organic solar cells and development of efficient photocatalytic
systems for the solar energy conversion for the unique advantages they offer with
regard to synthetic feasibility. The recent progress in computational methodologies,
especially the development of DFT rooted methods suitable to describe charge
transfer (CT) processes, allow to perform systematic investigations in silico of
those molecular features which might be important to design high performance bioinspired artificial devices.
Charge
Transfer
Focussed on CT process, this study aims (i) at better understanding the effect of
slight chemical modifications on the absorption spectra, in particular on the lowest
CT bands, as well as (ii) at gaining deeper insight on the role of H2O and hystidine
(Hys) in the biological system. The coordination of H2O or Hys might occur in two
62
different positions: it can be sandwiched between the carotene and the porphyrin
ring or can be coordinated to the metal under the porphyrin plane.
Effects of different metals of biological interest, i.e. Mg, Fe, Ni and Zn, and of H2O
and histidine molecules coordinated to the metals in different axial positions, are
investigated to rationalize the fine tuning of the CT process.
[1]
[2]
Gust, D.; Moore, T.A.; Moore, A.L.; Devadoss, C.; Liddell, P.A.; Hermant,
R.; Nieman, R.A.; Demanche, L.J.; DeGraziano, J.M., Gouni, I. J. Am.
Chem. Soc. 1992, 114, 3593.
Hofmann, E.; Wrench, P.M.; Sharples, F.P.; Hiller, R.G.; Welte, W.;
Diederichs, K. Science 1996, 272, 1788
63
P15 A first-principle periodic approach to the study of Ice
Clathrates
Alessandro Erba,a Luana Lambiase,a Andrea Molino,a Lorenzo Maschio,a
Silvia Casassaa
a
Gruppo di Chimica Teorica, Dipartimento di Chimica I.F.M. Università di
Torino, Via P. Giuria 5, 10125, Torino, Italy
E-mail: [email protected]
Ice Clathrates are crystalline, non-stoichiometric compounds formed by a
lattice of water molecules with cages where small molecules, as hydrogen and
methane, can be trapped. They form when the constituents come into contact at low
temperature and high pressure. The physical properties of these compounds gives
rise to numerous application in the broad areas of energy and climate effects.
In particular, Clathrate compounds of hydrogen have evolved to an active research
field when theirs storage capability
has been discovered [1]. Moreover,
methane Clathrates, which occur
naturally along the continental
shelves, offer a largely unexploited
means of energy recovery and
transportation and could play
significant role in the future
climate change. The early discover
of stable methane hydrate above 2
GPa1, named type III, has open a new debate about the range of stability of these
structures and their role in the formation model of some planetary bodies [2].
In order to investigate the behaviour of these compounds as a function of pressure,
temperature and chemical composition we have undertaken a theoretical study on two
cubic proton-ordered structure of Clathrates by means of the quantum-mechanical ab
initio codes CRYSTAL [3] and CRYSCOR [4].
A first part of the work has been devoted to the assessment of the proton-ordered
model of the lattice structure. Then, the calibration of the computational parameters
(basis set, Hamiltonian, etc.) and the geometry optimization have been performed.
Finally, energetic data and vibrational spectra of the empty and filled hydrated
structures (with both H2 and CH4 molecules) have been evaluated and will be
presented and discussed in the light of the most recent and controversial
experimental findings.
[1]
64
Mao, W. L.; Mao H. K.; Goncharov, A. F.; Struzhkin, V. V.; Guo, Q.; Hu,
J.; Hemley, R. J.; Somayazulu, M.; Zhao, Y. Science 2002, 297, 2247.
[2]
[3]
[4]
J.S. Loveday, J. S; Nelmes, R. J; Guthrie, M; Belmonte, S. A; Allan, D. R;
Klug, D. D; Tse, J. T; Handa, J. P., Nature 2001, 410, 661.
Dovesi, R.; Saunders, V. R.; Roetti, C.; Orlando, R.; Zicovich-Wilson, C.
M.; Pascale, F.; Doll, K.; Harrison, N., M.; Civalleri B.; Bush I.J. et al.,
CRYSTAL09 User’s Manual (Universita` di Torino, Torino, 2010),
[http://www.crystal.unito.it].
(a) Pisani, C.; Maschio, L.; Casassa, S.; Halo, M.; Schuetz, M.; Usvyat,D.
J. Comput. Chem. 2008, 29, 2113. (b) Erba, A.; Maschio, L.; Salustro, S.;
Casassa, S. J. Chem. Phys. 2001, 134, 074502.
(c) [http://www.cryscor.unito.it].
65
P16 Free energy estimates using molecular dynamics simulations
with dynamical freezing
Paolo Nicolini, Riccardo Chelli
Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
E-mail: [email protected]
An important limitation of nonequilibrium molecular dynamics simulations in
recovering free energy differences1,2 is the poor convergence of path-ensemble
averages. Therefore, a large number of fast-switching trajectories needs to achieve
free energy estimates with acceptable accuracy. We propose a method to improve
free energy estimates by drastically lowering the computational cost of steered
molecular dynamics simulations employed to realize such trajectories3. This is
accomplished by generating trajectories where the particles not directly involved in
the driven process are dynamically frozen. Such a freezing is dynamical rather than
thermal because it is reached by a synchronous scaling of atomic masses and
velocities keeping the kinetic energy of each particle unchanged. The forces
between dynamically frozen particles can then be calculated rarely. Thus, it is
possible to generate realizations of a process whose computational cost is not
correlated with the size of the whole system, but only with that of the reaction site.
The method is illustrated on a simple dynamical model (Lennard-Jones fluid).
[1]
[2]
[3]
66
Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690.
Crooks, G. E. J. Stat. Phys. 1998, 90, 1481.
Nicolini, P.; Chelli, R. Phys. Rev. E 2009, 80, 041124
P17 Linear and non-linear optical properties of molecular
crystals: An ab-initio periodic computational study
Bartolomeo Civalleri,a Roberto Orlando,a Michel Rerat,b Mauro Ferrero,a
Radovan Bast c
a
Dipartimento di Chimica IFM e Centro di Eccellenza NIS, Università di Torino,
Via P. Giuria 7, 10125 Torino, Italy
b
Equipe de Chimie Physique, IPREM UMR5254, Université de Pau, 64000 Pau,
France
c
Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3 (Paul
Sabatier) 118 route de Narbonne, 31062 Toulouse, France
E-mail: [email protected]
Linear and nonlinear optical properties of molecular crystals have attracted
considerable attention for both practical and theoretical reasons for the use of
organic materials in optoelectronic devices. Here, linear and non-linear optical
properties of a set of molecular crystals have been studied by means of an ab-initio
periodic approach [1]. Examined molecular crystals are: m-nitroaniline (m-NA), pnitroaniline (p-NA), 2-methyl-4-nitroaniline (MNA), 3-methyl-4-nitropyridine Noxide (POM), 2-carboxylic acid-4-nitropyridine-1-oxide (POA), and urea. Results
for static first- and second-order electric susceptibilities are compared with other
computational schemes (i.e. the oriented gas model, without and with local field
corrections, and the supermolecular approach) and experimental data. The fully
periodic approach, that permits to include all crystal packing effects, is shown to
provide very good results. For POM and urea, the dynamic first-order
susceptibilities have been computed, with results in nice agreement with available
experimental data. For urea, the effect of the crystal packing and hydrogen bonding
(HB) on the first- and second-order electric susceptibilities is also investigated.
During crystal assembling, the largest enhancement occurs when the molecules
interact at a medium/short-range and HB starts playing a relevant role. The role of
HB is also analyzed in terms of changes in the electronic structure and through a
topological analysis of the electron density. Calculations were carried out at the
B3LYP level of theory with a TZ2P quality basis set by using the CPKS scheme
for periodic systems [2] recently implemented in the CRYSTAL09 code [3].
[1]
[2]
[3]
(a) Ferrero, M.; Civalleri, B.; Rerat, M.; Orlando, R.; Dovesi, R. J. Chem. Phys.
2009, 131, 214704. (b) Civalleri, B.; Rerat, M.; Orlando, R.; Bast, R. in
preparation
Ferrero, M.; Rerat, M.; Orlando, R.; Dovesi, R. J. Comput. Chem. 2008, 29, 1450;
Ibidem. J. Chem. Phys. 2008, 128, 014110. Ferrero, M.; Rerat, M.; Kirtman, B.;
Dovesi, R. J. Chem. Phys. 2008, 129, 244110. Orlando, R.; Lacivita, V.; Bast, R.;
Ruud, K. J. Chem. Phys. 2010, 132, 244106.
Dovesi, R.; et al. CRYSTAL09 User’s Manual, Università di Torino, 2009.
67
P18 Dynamic Modeling of Heterogeneous Ziegler-Natta Catalytic
Systems
Andrea Correaa,b and Luigi Cavalloa,b
a
Dipartimento di Chimica e Biologia, Università di Salerno, Via Ponte don Melillo,
Fisciano I-84084, Italy
b
Dutch Polymer Institute (DPI), PO Box 902, 5600 AX Eindhoven, The
Netherlands.
E-mail: [email protected]
The characterization of heterogeneous Ziegler-Natta catalytic systems has been
attempt by means of several experimental and computational approaches,[1-7] but
definitive answers have not been obtained. Recently, Busico and co-workers
reported on the relative stabilities of MgCl2 faces.[7] In this study they confirm the
higher stability of (104) lateral cut, presenting 5-coordinated Mg atoms, with
respect to the (110) lateral cut, where Mg atoms are 4-coordinated. The (100)
lateral cut, with its complicated sequence of three-, five-, and six- coordinated Mg
atoms, has been predict to be highly unstable. Nevertheless, almost all these studies
have been performed with static calculations.[3-7] One of the few exceptions,
based on ab initio molecular dynamics (AIMD) simulations,[6] suggested that the
MgCl2 lateral cuts can undergo unpredictable reconstruction of the surfaces that,
however, could be not reproduced by recent static calculations.[7] The origin of
this discrepancy is unclear. With this on mind, we have investigated by AIMD
simulations the structure of heterogeneous Ziegler-Natta catalytic system starting
from the naked surfaces then moving to the behavior of Ti species and donors
attached on them.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
Corradini, P.; Busico, V.; Guerra, G. Monoalkene Polymerization:
Stereospecificity. In Comprehensive Polymer Science; Pergamon
Press:Oxford, U.K., 1998; Vol. 4. Chapter 3.
Giannini, U.; Giunchi, G.; Albizzati, E.; NATO ASI Ser. C 1987, 215, 473.
Toto, M.; Morini, G.; Guerra, G.; Corradini, P.; Cavallo, L.; Macromolecules
2000, 33, 1134
Correa, A.; Piemontesi, F.; Morini, G.; Cavallo, L.; Macromolecules, 2007,
40, 9181
Seth, M.; Margl, P.M.; Ziegler, T.; Macromolecules 2002, 35, 7815.
Boero, M.; Parrinello, M.; Weiss, H.; Hueffer, S.; J Phys. Chem. A.2001,
105, 5096.
Busico, V.; Causa, M.; Cipullo, R.; Credentino, R.; Cutillo, F.; Friederichs,
N.; La manna, R.; Segre, A.; Van Axel Castelli, V.; J. Phys. Chem. 2008,
112, 1081.
This work is part of the Research Programme of the Dutch Polymer Institute DPI,
Eindhoven, the Netherlands, project nr. #707"
68
P19 Computational approaches used in the POLYCAT EU
project
Francesco Ferrante, Nerina Armata, Remedios Cortese, Fabrizio Lo Celso,
Antonio Prestianni, Dario Duca
Dipartimento di Chimica “S. Cannizzaro” Università di Palermo,Viale delle
Scienze, Ed. 17 90128 Palermo, Italy
URL: http://cccp.unipa.it
Aim of the FP7 EU POLYCAT project [1] is the accomplishment of an integrated
approach to develop novel heterogeneous polymer based catalysts, active in
pharmaceutical and crop protection syntheses. Experimental sections of this project
are integrated by modelling approaches. These are oriented to both time-dependent
and -independent in-silico simulations and/or calculations of structural,
conformational, spectroscopic and kinetic properties. Catalytic Atomistic Level
Modelling, using commercial and home-made codes, is performed, starting from
experimental information related to
catalyst synthesis and optimization
as well as to structural and kinetic
characterization [2]. To get local
information, high-level quantum
mechanical (QM) approaches are
employed while molecular dynamics
(MD) methods are mostly used for
reaching coarser information. Many
different computational minor tools as, for instance, a Monte Carlo (MC) CrossLinker-Algorithm (CLA) and an in-silico porometer algorithm (ISPA) were
developed. These tools should simulate and characterize Hyper-Cross-LinkedPolystyrene (HPS) especially used as catalytic support in the title project. Pathways
for various catalytic processes, investigated in the experimental sections of this
project, were studied performing high-level QM calculations. Different metal/HPS
supported catalysts were modelled and their reactivity has been evaluated for
different reactions. Finally, multi level approaches involving QM, MD and MC
methods are employed to integrate the information concerning the metal (Ru, Au
and Pd) cluster formation and the metal/support interaction.
[1]
[2]
POLYCAT: Modern polymer-based catalysts and micro-flow conditions as
key elements of innovations in fine chemical synthesis; G.A. No. CP-IP
246095 –http://polycat-fp7.eu/
N. Armata, G. Baldissin, G. Barone, R. Cortese, V. D’Anna, F. Ferrante, S.
Giuffrida, G. Li Manni, A. Prestianni, T. Rubino, Zs. Varga, D. Duca, Top.
Catal., 52, 2009, 431; Top. Catal., 52, 2009, 444
69
P20 Computational investigation on the spectroscopic properties
of Thiophene based Europium β-diketonate complexes
Ugo Cosentinoa, Giorgio Morob
a
Dipartimento di Scienze dell’Ambiente e del Territorio, Università di MilanoBicocca; Piazza della Scienza 1, 20126 Milano, Italy
b
Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca;
Piazza della Scienza 2, 20126 Milano, Italy
e-mail: [email protected]
The photophysical properties of lanthanide (Ln) complexes, based on π-conjugated
ligands, acting as light antennae, have been fully assessed. [1] The emission of ions
spans from visible to IR according to the Ln(III) chosen, allowing for applications
in different fields.
One of the most studied class of ligands is constituted by β-diketonate derivatives
(β-DK) in view of their chemical stability, ease of preparation, and noticeable
emission properties due to the effectiveness of the energy transfer (ET) from this
ligand to the Ln(III) ion. Particularly, europium β-DK complexes have attracted
more interest in optoelectronic applications because of their strong and narrow red
emission.
Europium
tris(2-thienoyltrifluoroacetonate)-3-phenantroline
[Eu(TTA)3(Phen] (1) is one of the most efficient Europium complexes in the β-DK
series.
[Eu(L)3(Phen)]
Phen
(1) L: TTA
(2) L: Br-TTA
(3) L: DTDK
(4) L: MeT-TTA
Here we present the results of a preliminary theoretical investigation on the
spectroscopic properties of the Europium tris β-DK/ phenantroline complexes (1)(4), which photophysical characterization has been recently reported in literature,
both in solid state (thin film) and in CH2Cl2 solutions. [2]
Calculations, performed with the Gaussian 09 program, were done both in vacuo
and in CH2Cl2 solutions at the Density Functional Theory (DFT) level, using the
hybrid functional PBE1PBE. For the Europium ion, large-core quasi-relativistic
effective core potential (ECP) and the related [5s4p3d]-GTO valence basis sets was
used. For the ligand atoms, the 6-31G* basis set was used. Solvent effects were
evaluated by the Gaussian09 implementation of the PCM, using the C-PCM variant
70
and the UAHF solute cavity. Geometry optimizations of the ground state and the
lowest triplet state of compounds (1)-(4) were performed starting from the
available crystallographic structures. The energy of the lowest triplet state was
determined from TD-DFT and ΔSCF approaches and compared to the measured 00 transition of each complex. The photoluminescence quantum yield of these
complexes is then discussed comparing the triplet state energy with respect to the
5
D1 level of Eu(III) ion.
[1]
[2]
Bünzli, J-C. G.; Piguet, C. Chem. Soc. Rev. 2005, 34, 1048.
Freund, C.; Porzio, W.; Giovanella, U.; Vignali, F.; Pasini, M.; Destri, S.;
Mech, A.; Di Pietro S.; Di Bari, L.; Mineo, P., Inorg. Chem. 2011, 50, 5417.
71
P21 Use of symmetry in the configurational analysis for the
simulation of disordered solids
Ph. D’Arcoa, M. De La Pierreb, M. Ferraboneb, S. Mustaphac, Y. Noëla, R.
Dovesib
a
Institut des Sciences de la Terre de Paris (UMR 7193 UPMC-CNRS), UPMC,
Sorbonne Universités, Paris, France
b
Dipartimento di Chimica, Università di Torino and NIS - Nanostructured
Interfaces and Surfaces - Centre of Excellence, Via P. Giuria 7, 10125 Torino, Italy
c
Institut de Mathématiques de Jussieu (UMR 7586 UPMC-CNRS), UPMC,
Sorbonne Universités, Paris, France
E-mail: [email protected]
The starting point for a quantum mechanical investigation of disordered systems
usually implies calculations on a limited subset of configurations, generated by
defining either the composition of interest or a set of compositions from one end
member to another, within an appropriate supercell of the primitive cell of the pure
compound.
The way symmetry can be used in the identification of symmetry independent
configurations (SICs) is here discussed. First, Pólya's enumeration theory is
introduced to determine the number of SICs, for varying and fixed composition,
and for two or more colors. The case where colors are symmetry related (e.g. spin
up and down in magnetic systems) is analyzed through the De Bruijn's
generalization.
Then, an orderly generation approach is presented, based on a combination of
lexicographical ordering and surjective resolution principle, which permits to
efficiently obtain a representative for each SIC.
The whole scheme is documented by means of examples: the abstract case of a
square with C4v symmetry, and the real cases of garnet and olivine mineral families
72
P22 Calculating optical rotations of organic molecules insolution:
coupling solvent effects to the anharmonic vibrational
contributions
Franco Egidi,a Vincenzo Barone ,a Julien Bloino, b Chiara Cappellia,c
a
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
CNR, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G.
Moruzzi 1, 56124 Pisa, Italy
c
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via
Risorgimento 35, 56126 Pisa, Italy
E-mail: [email protected]
b
We present a newly implemented methodology [1] to evaluate vibrational
contributions (harmonic and anharmonic) to the optical rotation of solvated
systems where the solvent is described by means of the polarizable continuum
model (PCM) [2]. Proper account of an incomplete solvation regime in the
treatment of both the electronic property and the molecular vibrations (i.e. the nonequilibrium effect [3]) is considered, as well as the inclusion of cavity field effects
[4], in order to fully couple the evaluation of the vibrational corrections [5] with
solvation effects. In order to assess the quality of our approach, test calculations on
(R)-methyloxirane in various solvents and (S)-N-acetylproline amide in
cyclohexane and aqueous solution are presented.
[1]
[2]
[3]
[4]
[5]
Egidi F.; Barone V.; Bloino J.; Cappelli C. J. Chem. Theo. Comput. in
press.
Tomasi J.; Mennucci B.; Cammi R. Chem. Rev. 105 (2005) 2999-3093.
Cappelli C.; Lipparini F.; Bloino J.; Barone V.; J. Chem. Phys. 135 (2011)
104505-104518.
Cammi R.; Cappelli C.; Mennucci B.; Tomasi J. J. Phys. Chem. A 104
(2000) 9874-9879
Ruud K.; Zanasi R. Angew. Chem. Int. Ed. 44 (2001) 3594 –3596
73
P23 Ab initio molecular dynamic simulation of photoactive
proteins in action
Wagner Brandeburgo, Grisell Diaz Leines, Siri van Keulen, Evert Jan Meijer,
Jocelyne Vreede, Peter Bolhuis, and Bernd Ensing
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
E-mail: [email protected]
Modeling the signal transduction within
sensor proteins requires simulation techniques
that can handle a variety of processes,
including electronic excitation, chemical
rearrangements, and protein conformational
dynamics. Here, I will present two such
simulation techniques. We use transition path
sampling in combination with Born
Oppenheimer (DFT) molecular dynamics
simulations to sample reactive pathways of
the proton transfer reaction that takes place in
the initial steps of the photo cycle of the
photoactive yellow protein. The second advanced sampling technique is our
recently developed path-metadynamics method, which allows us to simultaneously
locate the most likely transition path in the space of a large number of collective
variables and compute the free energy profile of the reaction. The same strategy
applied at the classical (forcefield) molecular dynamics level of theory allows us to
understand the long timescale part of the photo cycle, which involves the partial
unfolding of the protein as it reaches the signaling state.
74
P24 Nuclear Motion (Temperature) Effects on the Density Matrix
of Crystals: An ab initio Monte Carlo Harmonic Approach
Cesare Pisani,a Alessandro Erba,a Matteo Ferrabonea and Roberto Dovesia
a
Dipartimento di Chimica IFM and Centre of Excellence NIS (Nanostructured
Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)
E-mail: [email protected]
Quite recently, the entrance into the fourth age of molecular quantum chemistry has
been declared: “In the fourth age we are able to incorporate into our quantum chemical
treatment the motion of nuclei [...] and compute accurate, temperature-dependent,
effective properties, thus closing the gap between measurements and electronic
structure computations” [1]. Nowadays, a variety of solid state ab initio quantum
chemical methods is available for the study of many properties of the ground state of
crystals at zero temperature. However, the experimental determination of many solid
state properties such as the equilibrium structure, the vibrational spectrum, the electron
charge and momentum density [2], the structure factors and the directional Compton
profiles [3-4] only rarely is obtained at very low temperature. It follows that, in order
to compare the outcomes of an experiment directly to those of a simulation without
extra data processing on the experimental side (that is the most convenient procedure),
the inclusion of temperature effects on computed quantities would be desirable.
In this contribution we present a harmonic Monte Carlo ab initio approach that goes
in that direction and allows for the description, even if approximate, of nuclear motion
(i.e. temperature) effects on the electronic density matrix of crystalline materials [5-7].
In the frame of the Born-Oppenheimer approximation, nuclear motions in crystals can
be simulated rather accurately using a harmonic model. In turn, the electronic firstorder density matrix can be expressed as the statistically weighted average over all its
determinations each resulting from an instantaneous nuclear configuration. This model
has been implemented in a computational scheme which adopts ab initio one-electron
Hamiltonians in the CRYSTAL program. This scheme has allowed us to develop
algorithms and parallelization strategies of the code that point toward the ab initio
Molecular Dynamics for crystals which represents our final goal.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
A. G. Császár, C. Fábri, T. Szidarovszky, E. Mátyus, T. Furtenbacher, and G. Czakó, Phys.
Chem. Chem. Phys. 14, 1085 (2012).
A. ERBA, M. Itou, Y. Sakurai, R. Yamaki, M. Ito, S. Casassa, L. Maschio, A. Terentjevs,
and C. Pisani, Phys. Rev. B, 83, 125208 (2011)
C. Pisani, A. ERBA, S. Casassa, M. Itou and Y. Sakurai, Phys. Rev. B, 84, 245102 (2011)
A. ERBA, C. Pisani, S. Casassa, L. Maschio, M. Schütz and D. Usvyat, Phys, Rev. B, 83,
125208 (2011)
C. Pisani, A. ERBA, M. Ferrabone and R. Dovesi, in preparation (2012)
A. ERBA, M. Ferrabone and R. Dovesi, in preparation (2012)
A. ERBA, M. Ferrabone, R. Dovesi, M. Itou and Y. Sakurai, in preparation (2012)
75
P25 Phonons with the CRYSTAL code Matteo Ferrabonea, Michel Rèratb,Fabien Pascalec, Jacopo Baimaa and
Roberto Dovesia
a
Università degli Studi di Torino, Via Pietro Giuria 5, I-10125 Torino, Italy
Université de Pau et des Pays de l’Adour, 64000 Pau, France
c
Université Henri Poincaré Nancy I, Nancy (France)
E-mail: [email protected]
b
Two recent developments of the CRYSTAL[1] code as regards the simulations of
vibrational spectra are presented.
a) Phonon dispersion can be computed adopting a direct approach which requires
the calculation of the Hessian matrix on supercells. This allows to obtain accurate
thermodynamic properties and phonon bands and density of states representations.
b) New methods have been implemented to deal with anharmonicity in Г. Third
and fourth order derivatives of the energy with respect to normal coordinates are
computed by means of finite difference formulas, following the proposal of Ref.
[2]. Two and three mode coupling derivatives can be constructed. The anharmonic
correction to the vibrational frequencies can be obtained by means of perturbative
methods (TOSH, Ref. [2]), or a Self Consistent Field procedure (VSCF, Ref [3]).
Preliminary results show that the proper sampling of the Potential Energy Surface
is not trivial. Work is currently underway in order to define some reliable scheme
for the description of the anharmonic potential.
[1]
[2]
[3]
76
R. Dovesi, V. R. Saunders, C. Roetti et al. CRYSTAL 2009 User’s Manual
C. Y. Lin, A. T. B. Gilbert, P. M. W. Gill Theor. Chem. Account. 120, 23–
35 (2008)
J. M. Bowman Acc. Chem. Res. 19, 202 (1986)
P26 On the use of symmetry in SCF calculations of finite and
infinite systems: the case of fullerenes and carbon nanotubes
Anna Maria Ferrari,a Yves Noel,b Marco Delapierre,a Ph. D'Arco,b Roberto
Dovesia
a
Dipartimento di Chimica IFM, Università di Torino and NIS, Nanostructured
Interfaces and Surfaces -Centre of Excellence, via P. Giuria 7, 10125, Torino, Italy.
b
Institut des Sciences de la Terre de Paris (UMR 7193 UPMC-CNRS), UPMC,
Sorbonne Universites, Paris, France
The full exploitation of point symmetry permits to drastically reduce the CPU time
and memory allocation in SCF calculations for molecules and solids. In the present
implementation of the CRYSTAL1 code, symmetry is used at various steps:
1. in the calculation of bielectronic integrals, whose number reduces by a
factor N where N s the number of point symmetry operators in the group
2. in the selection of the k points of the First Brillouin Zone at which the Fock
matrix is diagonalized (this applies to periodic systems only). The time
saving factor is also in this case close to N
3. in the diagonalization of the Fock matrix, by using a SACO (Symmetry
Adapted Crystalline Orbitals) or SAMO (Symmetry Adapted Molecular
Orbitals) basis set. The reduction in cost is here even larger, as it is roughly
proportional to the third power of the ratio between MAO (number of AOs
in the basis) and MAXIR dimension of the largest block in the Fock matrix
once represented in the SACO basis).
As regards memory, the crucial point is to avoid the representation of the Fock,
overlap, density matrices (and related quantities) as full square matrices in the
AOs basis. The direct transformation from Firr, the irreducible Fock matrix
represented in a compact form, to FSACO, the block diagonal form in the SACOs
basis, reduces the bottleneck of memory allocation by a factor proportional to the
square of the ratio MAO/MAXIR.
Examples refer to systems characterized by very high symmetry: carbon fullerenes
of the (n,n) family (120 symmetry operators and up to 1500 atoms) and carbon
nanotubes of the (n,0) family (up to 600 symmetry operators). The electron
properties of selected systems have been analyzed and compared to the graphene
sheet.
1
R. Dovesi and V. R. Saunders and C. Roetti and R. Orlando and C. M. Zicovich-Wilson and F.
Pascale and B. Civalleri and K. Doll and N. M. Harrison and I. J. Bush and Ph. D'Arco and M.
Llunell, CRYSTAL 2009 User’s Manual, 2009, University of Torino, Torino
77
P27 Semi-empirical dispersion correction at the metal/organic
interface: accurate description of molecular adsorption on Ag(111).
Daniel Forrer,a Michele Pavone,b Maurizio Casarin,a Vincenzo Baronec
a
Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131
Padova, Italy;
b
Dipartimento di Chimica “Paolo Corradini”, Università “Federico II” di Napoli,
Via Cintia, 80126 Napoli, Italy
c
Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
E-mail: [email protected]
It is well known that common local and semi-local density functionals
poorly describe molecular physisorption on metal surfaces due to the lack of
dispersion interactions. In the last decade, several correction schemes have been
proposed to solve this fundamental issue of Density Functional Theory (DFT).
Using as prototype case the adsorption of C6H6 on Ag(111), the accuracy of three
different dispersion-correction methods is discussed and a reparameterization of the
DFT-D2 approach is presented. This was obtained by means of a fitting procedure
against accurate MP2 data and then tested on the adsorption of metal-free
phyhalocyanine on the same substrate.
78
P28 Adsorption of gases in nanoporous dipeptide-based
materials. Computer simulation and experimental study
Alberto Fraccarollo,a Angiolina Comotti,b Maurizio Cossi,a Leonardo
Marchese a
a
Dipartimento di Scienze e Tecnologie Avanzate (DISTA), Università del
Piemonte Orientale, via T. Michel 11, 15121 Alessandria, Italy.
b
Department of Materials Science, University of Milano Bicocca, Via R. Cozzi 53,
Milano, Italy.
E-mail: [email protected]
The storage and separation of important
gases, such as H2, N2, CH4, and CO2, is
a challenging researchfield, due to the
impending energy crisis and related
global pollution that are dramatic issues
today [1]. A range of approaches have
been explored to utilize materials of
different property and construction:
metal–organic frameworks, mesoporous
metal oxides, porous organosilicas,
organic polymers and crystals [2]. Here
we present a study on eight crystalline dipeptides; these consist of
different combinations of two amino acids bonded by a single peptide bond, and
they are characterized by two different space groups: P61 and P65.
A combined computational study (DFT calculation on periodic crystal and Monte
Carlo simulation method) allowed to obtain adsorption simulated isotherms with
various gases at different pressures and temperatures. the results were compared
with experimental data.
[1]
[2]
Wenliang Li, Jingping Zhang, Haichao Guo, and Godefroid Gahungu, J.
Phys. Chem. C 2011, 115, 4935–4942.
Angiolina Comotti, Silvia Bracco, Gaetano Distefano, and Piero Sozzani,
Chem. Commun., 2009, 284–286.
79
P29 Modeling the chiral nematic phase of oligonucleotides: phase
chirality as a reporter of changes in DNA-DNA interactions?
Elisa Frezza, Alberta Ferrarini
Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
E-mail: [email protected]
Recently, it was found that solutions of oligomers of double-stranded nucleic acids
(dsNAs), with 6 to 20 base pairs, form a chiral nematic (N*) phase at high
concentration [1]. This was ascribed to end-to-end stacking interactions between
NA duplexes, which would promote the formation of long linear aggregates, with
length-to-width ratio sufficiently high to induce nematic ordering [2]. Despite the
right-handedness of duplexes, both left- and right-handed N* phases were found,
depending on the sequence, the length, and the nature of end-to-end interactions
[3].
We have investigated the relation between the sequence of
oligonucleotides and the properties of their N* phases using
a statistical mechanics approach [4]. A pair potential
comprising excluded volume and screened electrostatic
interactions between duplexes was assumed. The structural
differences deriving from the sequence were taken into
Figure 1.
account by a coarse-grained representation of linear
aggregates of dsNAs, based on crystallographic data (Figure 1) [5]. We have
analyzed the effect of sequence on the N*-I (isotropic) phase transition and on the
material properties, chiral strength and twist elastic constant, which determine the
handedness and pitch of the helical organization in the N* phase. We propose that
the change of N* handedness, observed experimentally, is the amplification of a
change in NA-NA interactions, occurring at very high concentration.
[1]
[2]
[3]
[4]
[5]
80
(a) Nakata, M.; Zanchetta, G.; Champman, B.D.; Jones, C.D.; Cross, J.O.;
Pindak, R.; Bellini, T.; Clark, N.A. Science 2007, 318, 1276. (b) Zanchetta,
G.; Nakata, M.; Bellini, T.; Clark, N.A. J. Am. Chem. Soc. 2008, 130,
12864.
Onsager, L. Ann. N.Y. Acad. Sci. 1949, 51, 627-659.
Zanchetta, G.; Giavazzi, F.; Nakata, M.; Buscaglia, M.; Cerbino, R.; Clark,
N.A.; Bellini, T. PNAS 2010, 107, 17497.
(a) Tombolato, F.; Ferrarini, A. J. Chem. Phys. 2005, 122, 054908. (b)
Frezza, E.; Tombolato, F.; Ferrarini, A. Soft Matter 2011, 7, 9291.
(a) Drew, H.R.; Wing, R.M.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.;
Dickerson, R.E. PNAS 1981, 78, 2179 . (b) Campos, L. et al Biophys. J.
2005, 91, 892. (c) Gan, J.; Tropea, J.E.; Austin, B.P.; Court, D.L.; Waugh,
D.S.; Ji, X. Structure 2005, 13, 1435.
P30 CMD and DFT calculations as a challenge for MAS-NMR
spectra interpretation: a route toward the elucidation of silicate
glass structures
Elisa Gambuzzi, Alfonso Pedone, Gianluca Malavasi, M. Cristina Menziani
Dipartimento di Chimica, Università degli Studi di Modena e Reggio Emilia, Via
G. Campi 183, 41125 Modena, Italia
e-mail: [email protected]
The structure of silicate and alumino-silicate glasses, systems whose geological and
technological importance is well known,[1] has been studied by classical Molecular
Dynamics simulations and DFT calculations. Moreover, these techniques have
been coupled to generate MAS and MQ-MAS Solid State Spectra[2] of important
active nuclei such as 23Na, 43Ca and 17O.
The results obtained by direct comparison with experimental data will be presented
in order to confirm or deny the presence of several structural features speculated by
experimentalist[3],[4].
[1]
[2]
[3]
[4]
Angeli F.; Gaillard M.; Jollivet P.; Charpentier T.; Chem. Phys. Letters,
2007, 440, 324-328.
Pedone A.; Charpentier T.; Menziani M. C.; Phys. Chem. Chem. Phys.,
2010, 12, 6054-6066.
Lee S. K.; Stebbins J. F.; Am. Miner, 1999, 84, 937-945.
Stebbins J.F.; Xu Z.; Nature, 1997, 390, 60-62.
81
P31 DFT-TDDFT Study of Squaraine Adsorption on PbSe
Surfaces
Fabio Grassia, Maurizio Cossia, Mario Argeria, Caterina Benzib, Alberto
Fraccarolloa, Leonardo Marchesea.
a
DiSTA, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121,
Alessandria
b
Dipartimento di Chimica Inorganica Fisica e dei Materiali, Università di Torino,
Via Pietro Giuria 7, 10125, Torino
E-mail: [email protected]
In the field of renewable energy, quantum dot-sensitized solar cells
(QDSSCs) have attracted attention due to the possibility to exploit multiple exciton
generation (MEG)[1] in PbSe quantum dots as a potential means to overcome the
Shockley-Queisser limit. The use of a modified VG0 squaraine dye [2] as the linker
molecule between TiO2 and PbSe has been investigated at DFT-TDDFT level using
the Gaussian03 and Turbomole 6 software packages: first the absorption spectrum
of the squaraine dye was calculated using different functionals, both in a vacuum
and in a simulated solvent environment using the Polarizable Continuum Model
(PCM). Counterpoise-corrected addition energies of several squaraine dye-PbSe
adducts, each differing by the dye’s anchoring moieties and PbSe surface type,
were calculated. For each adduct the absorption spectrum was also computed.
Results point to the evidence that the dye has no preferred anchoring group and that
attachment could take place with either –COOH or –NH2 groups at room
temperature. The computational
schemes
that
most
closely
reproduced
the
experimentally
observed absorption spectrum of the
dye featured pure (as opposed to
hybrid) density functionals and the
PCM. This combination proved to
be too costly for the calculation of
the absorption spectra of the dyePbSe adducts, which were computed
1: calculated
absorption
spectraeffect:
of modified
at Figure
B3LYP
level with
no solvent
comparison of the thus obtained spectra of
VG0 molecule (blue) and dye-PbSe adduct (red).
the dye molecule and the adducts showed that adsorption of the squaraine onto a
PbSe cluster results in a red shift of the absorption peaks.
[1]
[2]
82
Nano Letters, Vol. 6, No. 12, 2006, 2856-2863
Chemical Physics Letters, 475 (2009), 49-53
P32 An integrated computational methodology to bridge the
molecular and elastic properties of a bent-core liquid crystal
Cristina Greco,a Ronald Y. Dong,b Alberto Marini,c Elisa Frezzaa, Alberta
Ferrarinia
a Dipartimento di Scienze Chimiche,Università di Padova, via Marzolo 1, 35131
Padova, Italy. b Department of Physics and Astronomy, University of British
Columbia, Vancouver, BC, V6T 1Z1, Canada
c Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, Università
di Pisa, 56126 Pisa, Italy. E-mail:[email protected]
The ability to access and bridge different length scales is a fundamental challenge
in materials modeling. An important example is given by liquid crystals (LCs),
whose macroscopic properties show an intriguing - and often elusive - dependence
on the molecular structure of the constituents. In the last years a new class of LCs
has aroused strong interest because of their unconventional properties: the so-called
bent-core mesogens [1], one example
of which, A131, is shown below.
Despite the extensive experimental
work devoted to these systems, the
interpretation of their unusual features
is still the object of much controversy.
To shed light on these questions, a
clear understanding of the relation between the molecular and the phase properties
is needed. Recently we have developed a methodology which, through an
integrated stepwise procedure, enables to consistently analyze the molecular and
the material behavior. DFT calculations are used to obtain accurate molecular
geometries and torsional potential profiles; this information is then employed to
generate molecular conformations through a Monte Carlo sampling strategy.
Finally the connection between the atomic level and the macroscopic scale is
established, within a molecular field theory [2]. Here we wish to present our model
and the results obtained for A131; in particular we will show how we can
simultaneously predict the 13C-NMR chemical shifts [3] and the elastic constants
of the LC phase [4].
[1]
[2]
[3]
[4]
Keith, C.; Lehmann, A.; Baumeister, U.; Prehm, M.; Tschierske, C. Soft
Matter, 2010, 6, 1704-1721.
Cestari, M. PhD thesis, Università di Padova, 2009.
Dong, R. Y.; Marini, A. J. Phys. Chem. B, 2009, 113, 14062-14072.
Sathyanarayana, P.; Mathews, M.; Li, Q.; Sastry, V. S. S.; Kundu, B.; Le,
K. V.; Takezoe, H.; Dhara, S. Phys. Rev. E, 2010, 81, 010702R: 1-4.
83
P33 Vibrationally resolved absorption and emission spectra of
oligothiophenes in gas phase and solution by first principle
calculations
Emiliano Stendardo,a Francisco Avila,b Fabrizio Santoro,b Roberto Improta,a
a
CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini
(IBB-CNR), Via Mezzocannone 16, I-80136, Napoli, Italy
b
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
E-mail: [email protected]
Due to their use in several important applications in optoelectronic devices, the
absorption and emission properties of poly- and oligothiophenes have been
extensively studied.[1] With the aim of getting a deeper understanding of their
vibronic properties, we report the preliminary results of an extensive computational
analysis of the absorption and emission spectra of several oligothiophene
(containing from 2 to 7 units) in different environments, from the gas phase to
polar solvents. Our approach is based on TD-DFT calculations and exploits recent
developments in Polarizable Continuum Model [2] and PCM/TD-DFT calculations,
namely state-specific (SS) treatment [3], enabling also a non-empirical
determination of polar contribution to inhomogeneous broadening.[4] Optical lineshapes can be computed, including both Duschinsky and Herzberg Teller effects,
with a method developed in our group [5]. The computed spectra are in remarkable
agreement with experiments, allowing us to critically compare the performances of
different functionals and to highlight the main chemical physical effects
modulating the observed lineshapes.
[1]
[2]
[3]
[4]
[5]
84
Gierschner, J.; Cornil, J.; Egelhaaf, H-J. Adv. Mater. 2007, 19, 173.
Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999.
(a) Improta, R.; Barone, V.; Scalmani, G.; Frisch, M.J. J. Chem. Phys. 2006,
125, 54103. (b) Improta, R.; Scalmani, G.; Frisch, M.J.; Barone, V. J.
Chem. Phys. 2007, 127, 074504.
Avila Ferrer,F.J.; Improta, R.; Santoro, F.; Barone, V. Phys. Chem. Chem.
Phys. 2011, 13, 17007.
(a) Santoro, F.; Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys.
2007, 126, 084509, ibidem 2007, 126, 169903. (b) Santoro, F.; Improta, R.;
Lami, A.; Barone, V. J. Chem. Phys. 2007, 126, 184102. (c) Santoro, F.;
Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys. 2008, 128,
224311. (d) Bloino, J.; Biczysko, M.; Santoro, F.; Barone, V., J. Chem.
Theory and Comp. 2010, 1256.
P34 Computational study of the interactions between iron-gall
dyes and wool fibers
Sandro Jurinovich, Ilaria Degano, Benedetta Mennucci
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via
Risorgimento, 35, 56126 Pisa (Italy)
E-mail: [email protected]
The state of conservation of historic handicraft textiles may differ in dependence of
numerous factors and different kind of degradation effects can be observed.
Particularly, it is possible to notice that tannin dyed textiles usually show more
extended degradation phenomena than tissues dyed with other coloring materials,
even in the same condition of preservation. In order to understand these phenomena
a proper molecular modeling study has been conducted. This study is based on a
computational investigation at the DFT level of theory which consists of three
steps:
(1) the iron-gallic acid complex, which represents the simplest dye model of a
tannin based dye bath, has been theoretically investigated with respect to
bond lengths, atomic charges, MO analysis and the effect of water
solvation;
(2) the interactions of the iron-gallic acid complex with some free aminoacids,
which represent a zero-order approximation of a polypeptide chain forming
the wool fibers, have been investigated with respect to different
coordination modes, relative energies of different isomers and binding
energies involved in the ternary complex formation;
(3) starting from the results obtained in the previous steps, possible interactions
in the dye-iron-protein system have been modeled extracting a fragment
probe from a coiled coil protein of microfibrillar sheepskin.
85
P35 Calculation of longitudinal polarizability and second
hyperpolarizability of polyacetylene with the Coupled Perturbed
Hartree-Fock/Kohn-Sham scheme. Where it is shown how finite
oligomer chains tend to the infinite periodic polymer [1].
Valentina Lacivita,a Michel Rèrat,b Roberto Orlando,a Mauro Ferrero,a
Roberto Dovesia
a
Dipartimento di Chimica IFM, Università di Torino and NIS
- Nanostructured Interfaces and Surfaces - Centre of Excellence,
http://www.nis.unito.it, Via P. Giuria 7, 10125 Torino, Italy
b
Equipe de Chimie Physique, IPREM UMR5254,
Universitè de Pau, 64000 Pau, France
E-mail: [email protected]
The Coupled Perturbed Hartree-Fock/Kohn-Sham scheme, as implemented in the
periodic CRYSTAL code [2,3]
on a local Gaussian-type basis, has been used to calculate the longitudinal
polarizability, αxx,
and second hyperpolarizability, γxxxx, of polyacetylene.
For the first time, performances of pure local (LDA), gradient corrected (PBE) and
hybrid (B3LYP and PBE0) density functionals on a periodic polyene are compared
with those of
the Hartree-Fock hamiltonian.
It turns out that oligomers H-(C2H2)m-H with m up to 50 (202 atoms) provide an
extremely poor representation of the infinite chain
(hyper)polarizabilities when the gap is smaller than 0.2 eV (as for LDA and PBE),
that is in connection to the well known DFT catastrophe [4], reported in the
literature about short oligomers.
For the infinite model the ratio between LDA (or PBE) and HF becomes even more
dramatic: about 500 for αxx and 1010 for γxxxx. Previous systematic comparisons
with MP2 and Coupled Cluster results (obtained
for finite chains) lend higher reliability to HF periodic calculations.
The DFT criticalities in describing the electronic structure of small-band gap
systems impose very
tight computational conditions to reach convergence and maintain consistency
with the oligomers trend. γxxxx, in particular, is very sensitive to the number of k
points in reciprocal space
(LDA yields an energy gap as small as 0.01 eV and requires at least 1200 k points
to obtain well converged results), and to the extension of summations of the exact
exchange series (e.g. for PBE0 - band gap 1.4 eV – it goes to about 130 Å far from
the origin cell).
86
[1]
Lacivita, V.; Rèrat, M.; Orlando, R.; Ferrero, M., Dovesi, R. Submitted.
[2]
CRYSTAL09 User's Manual. Dovesi, R.; Saunders, V. R.; Roetti, C.;
Orlando, R.; Zicovich-Wilson, C.M.; Pascale, F.; Doll, K.; Harrison, N.M.;
Civalleri, B.; and Bush, I.J., D'Arco, Ph.; Llunell, M. Università di Torino,
Torino, 2009.
(a) Ferrero, M.; Rèrat, M.; Orlando, R.; Dovesi, R. J. Comput. Chem. 2008,
29, 1450. (b) Ferrero, M.; Rèrat, M.; Orlando, R.; Dovesi
, R.; Bush, I. J. Phys. Conf. Ser. 2008, 117, 12016. (c) Ferrero, M.; Rèrat,
M.; Kirtman, B.; Dovesi, R. J. Chem. Phys. 2008, 129, 244110.
(a) Champagne, B.; Perpéte, E.A.; van
Gisbergen, S.J.A.; Baerends, E.J.; Snijders, J.G.; Soubra-Ghaoui, C.;
Robins, K.A.; Kirtman, B. J. Chem. Phys. 1998, 109, 10489. (b)
Champagne, B.; Perpéte, E.A.; van
Gisbergen, S.J.A.; Baerends, E.J.; Snijders, J.G.; Soubra-Ghaoui, C.;
Robins, K.A.; Kirtman, B. J. Chem. Phys. 1999, 110, 11664.
[3]
[4]
87
P36 Electronic and dielectric properties of TiO2 nanotubes
Anna M. Ferraria, Martina Lessioa, Michel Rératb
a
Dipartimento di Chimica IFM, Università di Torino and NIS -Nanostructured Interfaces and
Surfaces - Centre of Excellence, http://www.nis.unito.it, Via P. Giuria 7, 10125 Torino, Italy
b
Equipe de Chimie Physique, IPREM UMR5254, Université de Pau, 64000 Pau,
France
Due to the spatial confinement , oxide nanosheets are characterized by peculiar
chemical and physical properties. They grow on appropriate metal substrate or self
assembly as nanotubes, nanorods or nanowires. In particular TiO2 nanotubes have
attracted a lot of attentions in the last decade because of their unique chemical and
physical properties[1]. One of the most interesting applications is connected to the
preparation of dye sensitized solar cells where the one dimensional structures of the
tubes are expected to significantly improve the electron transport properties,
whereas the high surface area optimize the number of sensitizers anchored to the
oxide[2]. The performances of the device however are related to the size, length,
thickness and structure of the titania tubes.
As a consequence, Lepidocrocite nanotubes stability and their electronic properties
dependence on their geometry have been widely studiedI II III IV V VI. Moreover some
studies on the interaction between them and water have been conducted showing a
stability increase compared with not hydratated structures. Anyway, despite the
great interest toward this kind of systems showed in the last period, their dielectric
properties still remain not investigated. The importance of studying also the
dielectric behavior of these systems is mainly due to their application in optical
devices such as lasers, lenses and fibers and to the fact that this kind of properties
are involved in spectroscopy techniques such as Raman spectroscopy.
In this work TiO2 nanotubes constructed from lepidocrocite TiO2 layers were
investigated with DFT methods and by employing the periodic CRYSTAL09
code[9].
Dependence of electronic and dielectric properties (dielectric
constant,polarizability and hyperpolarizability) on size and morphology of the
tubes has been investigated in the 20-60 Å range[6].
[1] D.V. Bavykin, J.M. Friedrich, F.C. Walsh; Adv. Mater. 18 2006, 2807
[2] P. Roy, D. Kim, K. Lee, E. Spiecker, P. Scmuki, Nanoscale 2 2010, 45
[3] Enyashin, A.N.; Seifert, G. Phys. Stat. Sol. (b) 2005, 242, 1361-1370.
[4] Wang J.; Wang L.; Ma L.; Zhao J.; Wang B.; Wang G. Physica E 2009 ,41,838–842.
[5] Ferrari A.M.; Lessio M.; Szieberth D.; Maschio L. J. Phys. Chem. C 2010, 114, 21219–21225.
[6] Szieberth, D.; Ferrari, A.M.; Noel, Y.; Ferrabone, M. Nanoscale 2010,2, 81-89.
[7] Szieberth, D.; Ferrari, A.M.; D’Arco, P. ; Orlando, R. ,Nanoscale, 2011,3,1113-9.
[8] A. M. Ferrari ; D. Szieberth ;Y. Noel, J. Mater. Chem., 2011, 21, 4568-4580.
[9] R. Dovesi, V. R. Saunders, R. Roetti, R. Orlando, C. M. Zicovich-Wilson, F. Pascale, B. Civalleri, K. Doll,
N. M. Harrison, I. J. Bush, P. D’Arco, and M. Llunell, CRYSTAL09 (CRYSTAL09 User's Manual. University
of Torino, Torino, 2009).
I
Enyashin, A.N.; Seifert, G. Phys. Stat. Sol. (b) 2005, 242, 1361-1370.
II
Wang J.; Wang L.; Ma L.; Zhao J.; Wang B.; Wang G. Physica E 2009 ,41,838–842.
III
Ferrari A.M.; Lessio M.; Szieberth D.; Maschio L. J. Phys. Chem. C 2010, 114, 21219–21225.
IV
Szieberth, D.; Ferrari, A.M.; Noel, Y.; Ferrabone, M. Nanoscale 2010,2, 81-89.
V
Szieberth, D.; Ferrari, A.M.; D’Arco, P. ; Orlando, R. ,Nanoscale, 2011,3,1113-9.
VI
A. M. Ferrari ; D. Szieberth ;Y. Noel, J. Mater. Chem., 2011, 21, 4568-4580
88
P37 Energy balance in CO2 + CO2 high temperature collisions
A. Lombardia, A. Laganàa, F. Pirania, M. Bartolomeib
a
Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8
06123, Perugia, ITALY
b
Instituto de Fisica Fundamental,
CSIC, Serrano 123,
28006, Madrid, SPAIN
The energy exchange occurring in collisions involving small molecules is largely
responsible for energy relaxation and state population of gas phase, and therefore
plays a key role in determining the energy balance of gaseous systems such
planetary atmospheres (see e.g. [1]).
Carbon dioxide is an important component of planetary atmospheres. Being a
triatomic molecule, the inter-exchange of internal, rotational and translational
energy upon collision can be relevant and is a key step in its contribution to the
energy balance of the atmospheres. The behaviour of CO2 in inelastic collisions
with itself or other species (e.g. N2 and CO) deserves considerable interest and also
finds interesting applications in plasma chemistry and hypersonic aerodynamics.
Extended ensembles of quasi-classical trajectories (QCT) have been run for the
CO2 + CO2 collisions in a wide range of energies, using a semiempirical potential
energy surface (PES) that makes use of a recently introduced bond-bond approach
[2], whose parameters have been refined by electronic structure calculations
performed at a CCSD(T) level (to integrate previous MP2 results [3]). State-tostate vibrational exchange cross sections, thermal rate coefficients and energy
distributions have been calculated, exporting the PES into the VENUS [4] program.
The calculated quantities are the necessary input of kinetic models of use in gas
dynamics, aircraft re-entry studies, and many other technological applications.
[1]
[2]
[3]
[4]
A. O. Semenov, G. M. Shved, Icarus 194, 290 (2008).
D. Cappelletti, F. Pirani, B. Bussery-Honvault, L. Gomez and M.
Bartolomei, Phys. Chem. Chem. Phys. 10, 4282 (2008).
M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 03, Revision
C.02, Gaussian, Inc., Wallingford CT, 2004.
VENUS96: http://monte.chem.ttu.edu/group/venus.html
89
P38 Hyperspherical separation of the internal degrees of freedom
in triatomic molecules: X-A-X linear symmetric case
A. Lombardia, A. Laganàa, F. Pirania, M. Bartolomeib, V. Aquilantia
a
Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8
06123, Perugia, ITALY
b
Instituto de Fisica Fundamental,
CSIC, Serrano 123,
28006, Madrid, SPAIN
The energy exchange occurring in collisions involving small molecules is largely
responsible for energy relaxation and state population of gas phase, and therefore
plays a key role in determining the energy balance of gaseous systems such
planetary atmospheres (see e.g. [1]). Triatomic molecules, such as carbon dioxide
(linear symmetric triatomic molecule) are important components of planetary
atmospheres, whose behaviour in inelastic collisions deserves considerable interest
and also finds interesting applications in plasma chemistry and hypersonic
aerodynamics. In critical conditions occurring at high temperatures and/or in
plasmas, the internal degrees of freedom of the molecules can be strongly excited,
undergoing large amplitude motions, and in these cases their behaviour can no
longer be safely modelled by the harmonic approximation.
Hyperspherical coordinates, widely used in quantum reactive scattering studies, can
indeed be generalized to adhere to classical mechanics [2] and have already been
shown to be indicated for a sufficiently decoupled description of the energy
partition among internal modes at high amplitudes in classical molecular dynamics
simulations (see e.g. [3]).
The case of linear symmetric triatomic molecules is discussed here, following the
hyperspherical approach, and examples of quasi-classical trajectories (QCT) run
for the CO2 + CO2 collisions at high energies (using a semiempirical potential
energy surface (PES) that makes use of a recently introduced bond-bond approach
[4]) are discussed.
[1]
[2]
[3]
[4]
90
A. O. Semenov, G. M. Shved, Icarus 194, 290 (2008).
M. B. Sevryuk, A. Lombardi, and V. Aquilanti, Phys. Rev. A 72, 033201
(2005).
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430, 424-428 (2006).
D. Cappelletti, F. Pirani, B. Bussery-Honvault, L. Gomez and M.
Bartolomei, Phys. Chem. Chem. Phys. 10, 4282 (2008).
P39 Ab initio analytical infrared and Raman intensities for
periodic systems through a CPHF method
Lorenzo Maschio,a Michel Rèrat, b Bernard Kirtman, c Roberto Orlando,a
Roberto Dovesia
a
Dipartimento di Chimica IFM, and Centre of Excellence NIS (Nanostructured
Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)
b
Equipe de Chimie Physique, Universitè de Pau, 64000 Pau, France
c
Department of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, USA
E-mail: [email protected]
The theoretical simulation of the infrared and Raman vibrational spectra of
crystalline materials has become in recent years an extremely powerful tool to
support and complement the analysis of experimental data. In this view it is important not only to determine the position of the absorption peaks, i.e. the frequency of
vibrational modes, but also the corresponding peak intensity, in order to simulate
the full spectrum of a given compound. While the analytical calculation of such
intensities was available for molecules already in the 80s[1], fundamental problems
arise when trying to formulate a computable analogue expression for periodic
crystalline systems, which historically delayed the development of such techniques
for the solid state [2]. Up to date available methods are mostly based, implicitly or
explicitly, on numerical derivatives or on the Berry phase approach.
A fully analytical formulation will be presented, for calculating the infrared
intensities of crystalline periodic systems, as recently implemented in the
CRYSTAL program, which uses a local Gaussian type basis set. The formalism is
based on the combination of energy gradients of the integrals [3] with a Coupled
Perturbed Hartree-Fock/Kohn Sham (CPHF/KS) scheme [4] for the response of the
density with respect to the electric field. An expression is derived which is
computationally optimal, and does not imply neither Berry phase techniques, nor
explicit derivatives of the density with respect to the position of the nuclei. The
method is demonstrated on benchmark systems, including crystals periodic in one
(polymers) two (slabs) and three (bulk) dimensions.
[1]
[2]
[3]
[4]
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(a) R. Resta, Rev. Mod. Phys. 1994, 66, 809. (b) R. King-Smith and D.
Vanderbilt, Phys. Rev. B 1993, 47, 1651.
K. Doll; N. M. Harrison; V. R. Saunders, Int. J. Quant. Chem. 2001, 82, 1.
(a) M. Ferrero; M. Rèrat; B. Kirtman; R. Dovesi, J. Chem. Phys. 2008, 129,
244110. (b) M. Ferrero; M. Rèrat; R. Orlando; R. Dovesi, J. Comp. Chem.
2008, 29, 1450.
91
P40 Homogeneous Gold Catalysis: Hydration of 1,2diphenylacetylene with methanol in aqueous media. A theoretical
viewpoint.
Gloria Mazzone, Nino Russo, Emilia Sicilia
Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per
Elaborazioni Parallele e Distribuite-Centro d’Eccellenza MIUR, Università della
Calabria, I-87036 Arcavacata di Rende, Italy
E-mail: [email protected]
The hydration of unsatured carbon compounds is one of the most environmentally
benign and economically attractive route to form carbon-oxygen bond. It has long
been known that water can be added quite easily to activated electron-rich alkynes
in the presence of an acid catalyst. The reaction of simple alkynes, instead, needs
co-catalysts, typically mercury(II) salts, to enhance the reactivity. Such catalysts
have been extensively used in high-scale industrial processes1 until the discovery of
the toxicity of mercury salts. Among the alternative systems, gold compounds have
gradually taken a prominent place, beneficially replacing mercury salts [1].
Hydration of alkynes to the corresponding ketones can be afforded in high yields at
room temperature by using gold(I)-phosphine complexes as catalyst, with no acidic
co-catalysts required [2]. A detailed DFT computational study of the nucleophilic
attack of methanol to 1,2-diphenylacetylene assisted by [(Ph3P)Au]+ catalyst has
been carried out to shed light on the mechanistic aspects of such process. The effect
of the presence of an additional molecule of water that assists the reaction has been
investigated. Calculations suggest that the rate-determining step of the whole
process is the addition of a second nucleophile molecule to the formed enol ether to
yield the final ketone product, along the pathway that describes the second part of
the reaction. Comparison with an analogous study for the nucleophilic attack of
water [3] shows that, according to experimental findings, addition to
diphenylacetylene of MeOH is faster than H2O.
[1]
[2]
[3]
92
(a) Teles, J. H.; Brode, S.; Chabanas, M. Angew. Chem., Int. Ed. 1998, 37,
1415. (b) R Casado, R.; Contel, M.; Laguna, M.; Romero, P.; Sanz, S. J.
Am. Chem. Soc. 2003, 125, 11925. (c) Mizushima, E.; Sato, K.; Hayashi, T.;
Tanaka, M. Angew. Chem., Int. Ed. 2002, 41, 4563.
Leyva, A.; Corma, A. J. Org. Chem. 2009, 74, 2067.
Mazzone, G.; Russo N.; Sicilia E. J. Chem. Theory Comput. 2010, 6, 2782.
P41 Electrostatic Effects Induced by the Light-Driven Retinal
Chromophore Isomerization in Bovine Rhodopsin
Federico Melaccio,a,b Igor Schapiro,c,# Massimo Olivucci b,c
a
CINECA-Consorzio Interuniversitario, via Magnanelli 6/3, I-40033 Casalecchio di Reno
(Bologna), Italy
b
Dipartimento di Chimica, Università degli Studi di Siena, via A. De Gasperi 2, I-53100, Siena,
Italy
c
Chemistry Department, Bowling Green State University, 43403, Bowling Green, Ohio, United
States
#
Current address: Max Planck Institute for Bioinorganic Chemistry, Muelheim an der Ruhr,
Germany
E-mail: [email protected]
Rhodopsin (Rh) is the vertebrate visual pigment, featuring an 11-cis retinal
chromophore bound to a lysine side-chain via a protonated Schiff base (pSb)
linkage. [1] Light absorption triggers ultrafast (< 200 fs), highly efficient cis-trans
isomerization, [2] mediated by a conical intersection. The time evolution after the
initial photochemical event was addressed both experimentally [3] and
computationally. [3, 4, 5] Starting from the available ab initio QM/MM CASSCF
molecular dynamics trajectory, [5] the evolution of the electrostatic potential
projected by the retinal onto each residue belonging to the Rh binding pocket
hydrogen bond network (HBN) was analyzed. Chromophore atoms were assigned
the QM/MM-derived Mulliken charges and the electrostatic potential was
computed by numerically solving the Poisson-Boltzmann equation (as
implemented in APBS [6]). Results show that a large transient variation of the
electrostatic potential occurs for those residues. Compared to initial ground state
values, an increased potential is obtained in the region away from the pSb, which
reduces when approaching the pSb. Glu181 marks the transition region where the
variation is zero and then negative. These changes are observed in a 30-fs range
centered on the conical intersection. The spatial distribution of such electrostatic
effects allows us to postulate a reorganization of the HBN upon
photoisomerization, which may have a function in Rh activation.
[1]
[2]
[3]
[4]
[5]
[6]
T. Okada, M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel, V. Buss, J. Mol. Biol. 2004,
342, 571.
P. Kukura, D. W. McCamant, S. Yoon, D. B. Wandschneider, R. A. Mathies, Science
2005, 310, 1006.
D. Polli, P. Altoe, O. Weingart, K. M. Spillane, C. Manzoni, D. Brida, G. Tomasello, G.
Orlandi, P. Kukura, R. A. Mathies, M. Garavelli, G. Cerullo, Nature 2010, 467, 440.
L. M. Frutos, T. Andruniow, F. Santoro, N. Ferré, M. Olivucci, Proc. Natl. Acad. Sci. USA
2007, 104, 7764.
I. Schapiro, M. N. Ryazantsev, L. M. Frutos, N. Ferré, R. Lindh, M. Olivucci, J. Am.
Chem. Soc. 2011, 133, 3354.
N. A. Baker, D. Sept, S. Joseph, M. J. Holst, J. A. McCammon, Proc. Natl. Acad. Sci. USA
2001, 98, 10037.
93
P42 Characterization of the extracellular subunit-subunit
interface of the 5-HT3 Receptors by means of Computational
Alanine Scanning Mutagenesis and Molecular Dynamics
Francesca De Rienzo,1,2 Marta del Cadia,1 Maria J. Ramos,3 Maria C.
Menziani1
1
Department of Chemistry, University of Modena and Reggio Emilia, Via G.
Campi 183, 41100 Modena, Italy
2
Center S3 Institute Nanoscience-CNR, Via Campi 213A, 41125 Modena, Italy
34
REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre, 687, 4169-007 Porto, Portugal
The functional serotonin type-3 receptor (5-HT3R) is the target of many
neuroactive drugs. Although its 3D structure is not available, the 5-HT3R is known
to be a pseudo-symmetric pentamer made either of five identical subunits A
(homomeric 5-HT3A-R) or of subunits A and B (heteromeric 5-HT3A/B-R) and to
have its serotonin binding site located at the extracellular interface between two
monomers. Interestingly, the homopentameric 5-HT3B-R is non functional,
implying that an interface made of two identical subunits B cannot activate the
receptor.
In this work, Molecular Dynamics simulations and computational alanine scanning
are applied to the a modelled structure of the extracellular homomeric 5-HT3A-R in
order to characterize its subunit-subunit interface, point out the main residues
involved in the complex stabilization, and analyze the coupling of
agonist/antagonist binding to channel activation/inactivation. Direct comparison of
the main features shown by the A-A interface with those of the B-B interface is
also performed to get clues about the possible reasons that cause the 5-HT3B-R to
be non-functional.
[1]
[2]
94
Moura Barbosa A.J., De Rienzo F., Ramos M.J., Menziani M.C.,
“Computational analysis of ligand recognition sites of homo- and
heteropentameric 5-HT 3 receptors” Eur. J. Med. Chem. 2010, 45: 4746
(and references therein).
Francesca De Rienzo, Arménio J. Moura Barbosa, Marta A.S. Perez, Pedro
A. Fernandes, Maria J. Ramos, Maria Cristina Menziani “The extracellular
subunit interface of the 5-HT3 Receptors: a Computational Alanine
Scanning Mutagenesis study”, in press.
P43 Protein-protein interactions in the complex ERK2-KIM
peptide and identification of putative high affinity mutant KIM
peptides: a computational investigation.
G. Moroa, A. Arrigonic, L. De Gioiaa, U. Cosentinob, R. Brambillac
a
Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca;
piazza della Scienza 2, 20126 Milano, Italy
b
Dipartimento di Scienze dell’Ambiente e del territorio, Università di MilanoBicocca; piazza della Scienza 1, 20126 Milano, Italy
c
Dipartimento di Biologia Molecolare e Genomica Funzionale, Fondazione S.
Raffaele del Monte Tabor, via Olgettina 60, 20132 Milano, Italy
E-mail: [email protected]
MAP kinases have a central role in determining the transduction of a great
number of stimuli, such as neurotrasmitters, hormones, cellular stress and
cytokines. Any deregulation capable of influencing the normal activity of this
pathway can potentially lead to a wide variety of diseases, including Alzheimer's
disease, Parkinson's disease, and various types of cancers. The catalytic activity of
MAP kinases is mainly regulated by phosphorylation: protein kinases and
phosphatases interact with the MAP kinases via a
conserved region (KIM), which constitutes a pivotal
determinant for the formation of a stable complex.
In the present work, we devised a computational
procedure based on MD simulations and free energy
perturbation in order to select mutant KIM peptides
which can putatively bind ERK2 with higher
affinity than the wild type. Our approach features an
initial set of MD simulations of the mutant peptides
ERK2- KIM peptide complex
in complex with ERK2, followed by an analysis of
the persistence of the electrostatic and hydrophobic interactions at the complex
interface during the simulations. This provided a qualitative insight which led us to
the identification of promising mutant peptides. These putative high affinity mutant
peptides could be used to prevent other interacting protein partners from binding
ERK2, therefore modulating its catalytic activity and function during the cell cycle.
[1]
[2]
[3]
[4]
J.P.Sun, B.Zhou, Z.Y.Zhang, Proc. Natl. Acad. Sci., 103, 2006, 5326.
T.Tanoue, M.Adachi, T.Moriguchi, E.Nishida, Nat. Cell. Biol., 2, 2000, 110.
B.Zhou, L.Wu, K.Shen, J.Zhang, D.S.Lawrence, Z.Y.Zhang, J. Biol. Chem., 276,
2001, 6506.
E.K.Kim, E.J.Choi, Biochim. Biophys. Acta, 1802, 2010, 396.
Grant from CARIPLO Foundation is gratefully acknowledged.
95
P44 Quantum reactive scattering calculations on Graphic
Processing Units
Leonardo Pacifici and Antonio Laganà
Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia
E-mail: [email protected]
A few years ago we tackled the problem of simulating in an ab initio fashion a
chemical experiment by developing a simulator for crossed beam experiments
named SIMBEX [1]. SIMBEX was designed to take from the literature a potential
energy surface (PES), usually of ab initio (of the highest level of theory possible)
origin and run on it dynamical calculations to the end of evaluating the main
reactive scattering quantities and help the experimentalist to compare their
measurements with theory. In these years SIMBEX has evolved into GEMS [2], a
Grid Empowered Molecular Simulator able to simulate on the Grid [3] molecular
processes starting from first principles and to calculate directly measurable
quantities like the intensity of the product beam scattered in a particular value of
the steric angle in a crossed beam experimental apparatus [4].
Because of the heavy computational requirements of some GEMS components, as
is the case of the codes calculating dynamical properties of reactive chemical
processes, the possibility of implementing quantum reactive scattering programs on
cheap platforms, often used for graphic purposes even in non experiment driven
installations, has been investigated using a NVIDIA GPU. After a conversion of
the code considered from Fortran to C and a deep restructuring for exploiting the
GPU key features, significant speedups have been obtained for RWAVEPR [5], a
time dependent quantum reactive scattering code propagating in time a complex
wavepacket. As benchmark systems the Cl + H2 and the N + N2 reactions have
been considered.
[1]
[2]
[3]
[4]
[5]
96
Gervasi, O.; Laganà, A. Fut. Gen. Comp. Syst., 1995, 20, 703-715.
Costantini, A.; Gervasi, O.; Manuali, C.; Faginas Lago, N.; Rampino, S.;
Laganà, A. Journal of Grid Computing, 2010, 8 (4), 571-586.
EGI-InSPIRE project RI-261323; website: http://www.egi.eu (Last access:
26/09/2011).
Laganà, A.; Balucani, N.; Crocchianti, S.; Casavecchia, P.; Garcia, E.;
Saracibar, A. Lecture Notes on Computer Science, 2011, 6784, 453-465.
Skouteris, D.; Pacifici, L.; Laganà, A. Molecular Physics, 2004, 102, 22372248.
P45 Adiabatic and Nonadiabatic Vibronic Approaches to the
Simulation of Electronic Circular Dichroism Spectra
Daniele Padula,a Lorenzo Di Bari,a Gennaro Pescitelli,a Alessandro Lami,b
Antonio Rizzo,b Fabrizio Santorob
a
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via
Risorgimento 35, 56126, Pisa, Italy
b
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
e-mail: [email protected]
Here we present applications of a hierarchy of models to simulate and analyze
vibronic features of Electronic Circular Dichroism (ECD) spectra of semi-rigid
dyes. Depending on the system, the vibrational structure associated to ECD is
computed within an adiabatic framework, i.e. neglecting the coupling between
electronic states or in a complete nonadiabatic framework. For adiabatic problems,
we have recently developed in our labs time-independent methods, based on
effective pre-screening techniques [1] that currently allow to describe the effect on
the spectral lineshapes of the whole set of vibrational modes, even for large
systems (hundreds of coordinates). Nonadiabatic systems, are better described
through time-dependent, quantum dynamical approaches. At the state of the art,
these latter still require the reduction of the system size to 10-20 normal modes, but
they allow to describe the effect of state mixings in a variational fashion.
Adiabatic models are applied to unravel the vibronic origin of a shoulder on a band
in the ECD spectrum of a piridinophane [2,3]. This analysis revealed a dual
vibronic origin of such spectroscopic feature: a broad spectral lineshape due to
strong vibronic progressions and a Herzberg-Teller effect.
As a typical case of a nonadiabatic system, we investigated a dimer of two coupled
anthracene chromophores [4]. We analyzed the coupling of the chromophores
through analysis of MOs and PES calculation along a normal mode. We then
calculated the vibronically resolved ECD spectrum via an adiabatic approach,
which does not take into account chromophores coupling, and via a nonadiabtic
approach, computing the required correlation functions via MCTDH [5] quantumdynamical propagations of suitable wavepackets.
[1]
a) J. Bloino, M. Biczysko, F. Santoro, V. Barone, J. Chem. Theory Comput.,
2010, 6, 1256;
b) F. Santoro, A. Lami, R. Improta, J. Bloino, V. Barone, J. Chem. Phys.,
2008, 128, 224311;
c) F. Santoro, A. Lami, R. Improta, V. Barone, J. Chem. Phys., 2007, 126,
084509.
97
[2]
[3]
[4]
[5]
98
a) M. Fedorovsky, H. Gerlach, W. Hug, Helv. Chim. Acta, 2009, 92, 1451;
b) H. Gerlach, E. Huber, Helv. Chim. Acta, 1968, 51, 2027.
D. Padula et al., submitted.
N. Harada, Y. Takuma, H. Uda, J. Am. Chem. Soc., 1978, 100, 4029.
M. H. Beck, A. Jäckle, G. A. Worth, H.-D. Meyer, Phys. Rep., 2000, 324, 1.
P46 Fluorine Environment in Bioactive Glasses: First-Principles
Calculations and 19F, 29Si and 23Na Solid State NMR Spectroscopy.
Alfonso Pedone,1* Thibault Charpentier,2 and Maria Cristina Menziani
1
Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi
183, 41125 Modena, ITALIA
2
CEA, IRAMIS, Service Interdisciplinaire sur les Systèmes Moléculaires et
Matériaux, LSDRM, UMR CEA/CNRS 3299, F-91191 Gif-sur-Yvette cedex,
FRANCE
E-mail: [email protected]
Fluoride-containing
bioactive
glasses are attracting particular
interest in many fields of dentistry
and orthopedic because they
combine the bone-bonding ability
of bioactive glasses with the
anticariogenic protection provided
by fluoride ions.[1] Because the
surface
reactivity
and
the
biomedical applications of these
materials critically depends on the
release of ionic species in the
surrounding physiological environment, it is very important to know the structure
of FBGs at the atomic level.[2]
In this communication, Carr-Parrinello Molecular Dynamics Simulations together
with GIPAW[3] calculation of the NMR parameters will be presented and
compared with experimental Solid-State NMR Spectra. The very accurate
characterization of the fluorine environment in a 45S5 Bioglass composition in
which 10% of CaO has been replaced with CaF2 has allowed us to resolve some
longstanding issues about the atomic structure of fluorinated bioglasses.[4]
[1] Hench, L. L. J. Mater. Sci. Mater. Med. 2006, 17, 967.
[2] Lusvardi, G.; Malavasi, G.; Tarsitano, F.; Menabue, L.; Menziani, M. C.;
Pedone, A. J. Phys. Chem. B 2009, 113, 10331.
[3] Pickard, C. J.; Mauri, F. Phys. Rev. B 2001, 63, 245101.
[4] Christie, J. K.; Pedone, A.; Menziani, M. C.; Tilocca, A. J. Phys. Chem. B
2011, 115, 2038
99
P47 Effective coordinates for Quantum Dynamics on conically
intersecting quadratic Potential Energy Surfaces. Investigating the
role of Duschinsky effects
David Picconi,a,b Alessandro Lami,b Fabrizio Santorob
a
Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
E-mail: [email protected]
b
Conical intersection (CI) topologies are ubiquitous in molecular systems and their
abundance grows with the dimensionality of the system. The ultrafast nuclear
dynamics induced by CIs in polyatomic molecules is essentially a quantum effect,
which involves electronically excited states. Due to its intrinsically quantum
nature, this dynamics is properly investigated by methods of quantum wavepacket
propagation. However, even powerful quantum dynamical algorithms such as the
multiconfigurational time-dependent Hartree (MCTDH) method are feasible for a
limited number of degrees of freedom, and the dynamics of a general multimode
system remains a challenging task.
For this reason there is a strong interest in developing reduced dimensionality
models which allow to substitute an Hamiltonian depending on a large number of
nuclear coordinates with another one depending on few effective modes, which
accurately accounts for the dynamics on a short time scale. This effective-mode
scheme has been formulated by Cederbaum et al. [1] for a linear vibronic coupling
(LVC) model for the Hamiltonian, where the excited states potential energy
surfaces (PES) are modelled as harmonic, with the same normal modes of the
ground state, just displaced to the corresponding minima. Anyway, the normal
coordinates of the excited states may be consistently different from those of the
ground state. Since the definition of the normal modes in a model Hamiltonian may
affect relevant quantities, such as the reorganization energy or the spacing of
spectral lines, the LVC model may lead to misleading predictions of the population
dynamics and the photoabsorption spectra. Thus, a better form for the excited state
PESs should be given by a quadratic vibronic coupling (QVC) model, where the
Duschinsky transformation which converts the normal modes of the ground state to
those of the excited states is taken into account. This leads to potential energy
surfaces (PES) for the excited states where the force constant matrices are non
longer diagonal, i.e. bilinear terms appear.
100
In this poster, we present an effective-mode formulation which holds for systems
where an arbitrary number of electronic states are involved, and a general QVC
description for the PESs is allowed. We show how the full Hamiltonian of the
system can be converted into a hierarchic sequence of reduced-dimensionality
Hamiltonians, in such a way that the short-time dynamics is recovered, within a
very good approximation, by the first members of this hierarchy. We adopt this
formulation to model the ππ*→nπ* transfer in UV-photoexcited thymine.[2]
The PESs are modelled both with a LVC and a QVC model. The effectiveness of
the reduced-dimensionality scheme is tested by quantum dynamical simulations
and the results obtained with the two approaches are compared, so to evaluate how
Duschinsky transformations affect the dynamics. [1]
Cederbaum, L. S.; Gindensperger, E.; Burghardt, I. Phys. Rev. Lett. 2005,
94, 113003.
[2]
Picconi, D.; Barone, V.; Lami, A.; Santoro, F.; Improta, R. ChemPhysChem
2011, 12, 1957.
101
P48 Accurate and reliable modeling of magnetic interactions in
organic diradicals
Vincenzo Baronea, Corentin Boilleaua, Ivo Cacellib, Alessandro Ferretti c,
Susanna Monti c, Giacomo Prampolinid
a
Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
Dipartimento di Chimica e Chimica industriale, Università di Pisa, Via
Risorgimento 35, I-56, Italy
c
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
d
CNR-Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici,
UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
b
A survey on the research that we have performed in the last few years in the field
of organic diradicals made by magnetic moieties bridged by unsaturated ligands
will be presented. We will show how the development of a multireference CI
computational route which exploit
molecular fragmentation, modified
virtual orbitals and a suitable partition
of the orbital space in two sets, one
treated variationally and one considered
by second order perturbation, allows an
accurate and reliable computation of the
singlet-triplet energy gap for diradicals
of medium size.
[1]
[2]
[3]
[4]
102
V. Barone, I. Cacelli, A. Ferretti and G. Prampolini J. Chem. Phys., 131
(2009) 224103
V. Barone, I. Cacelli, P. Cimino, A. Ferretti, S. Monti and G. Prampolini, ”,
J. Phys. Chem. A 113 (2009) 15150.
V. Barone, I. Cacelli, A. Ferretti, S. Monti and G. Prampolini, Phys. Chem.
Chem. Phys., 13 (2011) 4709.
V. Barone, I. Cacelli, A. Ferretti, S. Monti and G. Prampolini, J. Chem.
Theor. And Comput. 7 (2011) 699.
P49 Computational 17O-NMR spectroscopy of organic acids and
peracids: comparison of solvation models
Alberto Baggioli,a Orlando Crescenzi,b Martin J. Field,c Franca Castiglionea and
Guido Raosa
a
Dipartimento di Chimica, Materiali e Ing. Chimica “G. Natta”, Politecnico di Milano, via
Mancinelli 7, I-20131 Milano, Italy
b
Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via
Cintia, I-80126 Napoli, Italy
c
Institut de Biologie Structurale — Jean-Pierre Ebel, (CEA/CNRS/UJF s UMR 5075), 41
Rue Jules Horowitz, F-38027 Grenoble, Cedex 01, France
E-mail: [email protected]
We examine several computational strategies for the prediction of the 17O-NMR shielding
constants for a selection of organic acids and peracids in aqueous solution (see ref.[1] for
the experimental spectra and preliminary computational work). First of all, we
demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis
provides an excellent compromise between computational cost and accuracy in the
calculation of the shielding constants. Next, we move on to the problem of the solvent
representation. Our results confirm the difficulties encountered by Polarizable Continuum
Models (PCM) for strongly hydrogen-bonded system,[2] but at the same time they
demonstrate its strength within a molecular-continuum approach, with an explicit
representation of some solvent molecules. We examine different models of the solvation
shells, using both energy minimizations of finite clusters and molecular dynamics
simulations of bulk systems. Hybrid QM/MM simulations,[3] in which the solute is
described at the PM6 level and the solvent by the TIP3P model, provide a promising
sampling method for medium-to-large sized systems.
Left: the 17O-NMR spectrum of peracetic acid.[1] Right: a model including 30 waters.
[1]
Castiglione, F.; Baggioli, A.; Citterio, A.; Mele, A.; Raos, G., J. Phys. Chem. A, in
press (DOI: 10.1021/jp210679y).
[2]
Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999.
[3]
Field, M. J. J. Chem. Theory Comput. 2008, 4, 1151.
103
P50 A QM/MM Study on Human Melanopsin, a New and
Atypical Non-Visual Photoreceptor
Silvia Rinaldi,a Alice Carpini,a Federico Melaccio,a,b Massimo Olivucci a,c
a
Dipartimento di Chimica, Università degli Studi di Siena, via A. De Gasperi 2, I-53100, Siena,
Italy
b
CINECA-Consorzio Interuniversitario, via Magnanelli 6/3, I-40033 Casalecchio di Reno
(Bologna), Italy
c
Chemistry Department, Bowling Green State University, 43403, Bowling Green, Ohio, United
States
E-mail: [email protected]
Human melanopsin (Hm) is an atypical vertebrate, non-visual opsin, expressed in
the intrinsically photosensitive retinal ganglion cells (ipRGC). [1] Hm plays a key
role in the regulation of circadian rhythms, papillary lights reflex and other
responses to light. [2] Its 11-cis retinal chromophore, bound to a lysine side-chain
via a protonated Schiff base (pSb) linkage, isomerizes to trans upon light
absorption. Surprisingly, Hm aminoacid sequence and signaling transduction
mechanism are similar to those of invertebrate opsins, [3, 4] therefore showing
bistability and dual photosensory and photoisomerase functions. [5] Using squid
rhodopsin X-ray crystal structure as a template, the first computational model of
Hm was built by comparative modeling, in collaboration with Dr. Francesca Fanelli
(University of Modena). Subsequently QM/MM CASSCF/AMBER optimization
and excited state molecular dynamics were carried out, along with CASPT2 single
point for spectroscopy evaluation, according to a well established method for
rhodopsins. [6-8] Squid and bovine rhodopsins were also modeled for validation.
Photochemical properties were reproduced with good accuracy (error <3 kcal mol1
). The melanopsin excited state dynamics shows an ultrafast isomerization
occurring with a “bicycle pedal” mechanism, where the chromophore bond length
alternation changes and the pSb positive charge moves along the retinal skeleton,
as for bovine rhodopsin. [7] These results confirm the validity of the computational
model as a starting point for further studies.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
104
I. Provencio, G. Jiang, W. J. De Grip, W. P. r. Hayes, M. D. Rollag, Proc. Natl. Acad. Sci.
USA 1998, 95, 340.
C. Lok, Nature 2011, 469, 284.
D. Arendt, Int. J. Dev. Biol. 2003, 47, 563.
M. C. Isoldi, M. D. Rollag, A. M. de Lauro Castrucci, I. Provencio, Proc. Natl. Acad. Sci.
USA 2005, 102, 1217.
L. S. Mure, P.-L. Cornut, C. Rieux, E. Drouyer, P. Denis, C. Gronfier, H. M. Cooper, PLoS
ONE 2009, 4, e5991.
N. Ferré, M. Olivucci, J. Am. Chem. Soc. 2003, 125, 6868.
L. M. Frutos, T. Andruniow, F. Santoro, N. Ferré, M. Olivucci, Proc. Natl. Acad. Sci. USA
2007, 104, 7764.
I. Schapiro, M. N. Ryazantsev, L. M. Frutos, N. Ferré, R. Lindh, M. Olivucci, J. Am.
Chem. Soc. 2011, 133, 3354.
P51 Relativistic DFT calculations of the NMR properties and
reactivity of transition metal methane σ-complexes: insights on C–
H bond activation
Giacomo Saielli,a Alessandro Bagnob
a
CNR-Istituto per la Tecnologia delle Membrane, Unità di Padova, via Marzolo, 1
– 35131, Padova, Italy
b
Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo, 1 – 35131,
Padova, Italy
E-mail: [email protected]
Relativistic ZORA DFT methods have been
employed to predict the NMR properties of
methane and methyl hydride complexes of rhodium
and iridium. Two of these compounds, the rhodium
methane and the iridium methyl hydride
complexes, have been recently characterized by
NMR spectroscopy: [(PONOP)Rh(CH4)][B(ArF)4]
and [(PONOP)IrH(CH3)][B(ArF)4], where PONOP
= 2,6-(t-Bu2PO)2C5H3N and ArF = [3,5(CF3)2C6H3]- have been identified in solution of
CDCl2F at -110 °C [1]. Key signatures of the formation of the Rh-methane σcomplex, indeed the most interesting being the first one discovered since now, are
the NMR parameters: 1H and 13C chemical shifts, as well as coupling constants
with 103Rh.
Our calculations [2] reveal that relativistic effects are largely responsible of
the high shielding observed for the proton and carbon resonances of the methane
moiety. The key steps for the reaction mechanism of C–H cleavage catalyzed by
both compounds (in Figure the TS for the oxidative addition of hydrogen to the
metal centre of the Ir complex) have been investigated at the relativistic level.
Although the structure of the intermediates and TSs for the Rh and Ir complexes is
rather similar, subtle differences in the energetics are responsible of the different
catalytic activity of the two complexes.
[1]
[2]
Bernskoetter, W. H.; Schauer, C. K.; Goldberg, K. I.; Brookhart, M.
Science, 2009, 326, 553.
Saielli, G.; Bagno, A. Phys. Chem. Chem. Phys. 2011, 13, 4285.
105
P52 Coarse-Grained MD Simulations of Ionic Liquid Crystals
Giacomo Saielli,a
a
CNR-Consiglio Nazionale delle Ricerche, Istituto per la Tecnologia delle
Membrane (ITM-CNR), UOS di Padova, Via Marzolo, 1, I-35131 Padova, Italy
E-mail: [email protected]
Ionic Liquid Crystals (ILCs) are beginning to attract some attention since they are
expected to combine the technological properties of Ionic Liquids (ILs) and Liquid
Crystals (LCs). ILCs are usually made by an organic cation, such as imidazolium
or pyridinium N-quaternized with a relatively long alkyl chain, and an inorganic
anion such as BF4-, PF6-, bistriflimide (CF3SO2)2N-, to mention but the most
common ones [1,2]. However a clear understanding of the many structural factors
that stabilize a given ionic mesophase, very often a SmA, is sill lacking. Computer
simulations are a formidable tool to understand the microscopic structure and
dynamics of condensed phases. However the high viscosity of ILCs and the long
range of action of the electrostatic forces, playing a dominant role in such ionic
compounds, require a meaningful simulation to last for several hundreds of ns and
the simulation box to contain several hundreds of molecules. Thus Coarse-Grained
Force Fields, CGFF, are very useful to speed up the simulation even at the cost of
loosing some structural details. In this work we present a CG-MD simulation of 1hexadecyl-3-methylimidazolium nitrate, C16mimNO3, based on the CGFF
developed by Wang et al. [3]. The system has been experimentally characterized by
Guillet et al. [4]. First we have explored the phase behavior in the NVT ensemble
for a system made of 512 ion pairs in the temperature range from 385 K up to 600
K, to locate the relevant phase transitions. Simulations lasted, on average, up to
0.1-0.2 µs. Then, additional runs of 0.1 µs followed in the NPT ensemble. A
smectic A phase has been found in the temperature range 500-525 K. Thus a larger
system, obtained by replicating the original box by 3x3x3, has been simulated to
obtain the relevant structural and dynamical data of the ionic mesophase. All
simulations were run with the software package DL_POLY [5] using the CINECA
[6] and LICC [7] facilities.
[1]
[2]
[3]
[4]
[5]
[6]
[7]
106
Binnemans, K. Chem. Rev. 2005, 105, 4148.
Causin, V.; Saielli, G. “Ionic Liquid Crystals” in Green Solvents Properties
and Applications of Ionic Liquids, Mohamadd A, Inamuddin, Dr. Eds.,
Springer UK, 2012.
Wang, Y.; Feng, S.; Voth, G. J. Chem. Theory Comput. 2009, 5, 1091.
Guillet, E.; Imbert, D.; Scopelliti, R.; Bunzli, J.-C. G. Chem. Mater. 2004,
16, 4063.
Smith, W.; Forester, T.R.; Todorov, I.T. DL_POLY Classic, v. 1.0
www.cineca.it, project HP10BB7HYH.
www.chimica.unipd.it/licc
P53 EPR, UV-VIS and RR spectral parameter shifts of
tryptophan radicals embedded in contrasting hydrophobic and
hydrophilic environments computed from QM/MM Models of
Pseudomonas aeruginosa azurin
Caterina Bernini,a Tadeus Andruniów,b Massimo Olivucci,a,c Rebecca Pogni,a
Riccardo Basosi,a Adalgisa Sinicropia
a
Dipartimento di Chimica, Università di Siena, Via A. De Gasperi 2, 53100 Siena,
Italy
b
Institute of Physical and Theoretical Chemistry, Wroclaw University of
Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
c
Chemistry Department, Bowling Green State University, Bowling Green OH,
USA
E-mail: [email protected]
Redox active tryptophan radicals take place as key intermediates in many
enzymatic reactions stimulating a number of experimental and theoretical
investigations of these radical species [1]. In this framework, the electronic,
magnetic and vibrational spectra of a photogenerated long lived neutral Trp radical
(W48•) in the hydrophobic core of a Pseudomonas aeruginosa azurin mutant
(Az48W) have been reported [2]. The spectroscopic properties of this radical are
compared to those of a previously studied solvent-exposed neutral Trp radical
(W108•) generated in a rhenium-labeled Az108W mutant (ReAz108W) [3]. We
use state-of-the-art quantum-mechanics/molecular-mechanics (QM/MM) methods
to compute the absorption maxima, the RR spectra and EPR spectral parameters (gtensors and hyperfine coupling constants) of W48• and W108• in the protein matrix
of Az48W and ReAz108W. These data compare well with the experimental values
and demonstrate that our strategy is able to reproduce the observed spectral shifts
of Trp• embedded in contrasting hydrophobic and hydrophilic environments. We
believe that this achievement is a preliminary effort along the route to a
quantitative investigation of Trp radical reactivity in proteins. Furthermore, this is
the first QM/MM study devoted to the characterization of Trp radicals inside the
protein matrix of blue copper proteins.
[1]
[2]
[3]
(a) Dempsey, J.L.; Winkler, J.R; Gray, H.B. Chem. Rev. 2010, 110, 7024.
Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999. (b)
Bernini, C.; Pogni, R.; Ruiz-Duenãs, F.J.; Martínez, A.T.; Basosi R.;
Sinicropi A. Phys. Chem. Chem. Phys. 2011, 13, 5078.
Shafaat, H.S.; Leigh, B.S.; Tauber, M.J.; Kim, J.E. J. Am. Chem. Soc. 2010,
132, 9030.
Miller, J.E.; Gradinaru, C.; Crane, B.R.; Di Bilio, A.J.; Wehbi, W.A.; Un,
S.; Winkler, J.R.; Gray, H.B. J. Am. Chem. Soc. 2003, 125, 14220.
107
P54 Essential-state description of resonance energy transfer
Cristina Sissa,a Francesca Terenziani,a Anna Painelli,a Arun K. Manna,b
Swapan K. Pati b
a
Dipartimento di Chimica GIAF, Viale delle scienze 17/A, Università di Parma &
INSTM UdR Parma, 43124 Parma, Italy
b
Theoretical Science Unit, JNCASR, Jakkur P.O., Bangalore 560064, India
E-mail: [email protected]
Low-energy properties of charge-transfer (CT) chromophores, an interesting family
of π-conjugated dyes for functional applications, are governed by the resonance
among few valence bond structures. Essential state models (ESMs) select these
structures as the minimal basis to describe the electronic problem. Molecular
vibrations and polar solvation enter quite naturally into the scheme, leading to
robust phenomenological models, that have been successfully applied to rationalize
optical spectra of several families of chromophores in solution. Excitonic effects in
multichromophoric assemblies have also been described based on ESM, extended
to account for electrostatic interchromophores interactions. [1]
The same interactions responsible for excitonic effects in multichromophoric
assemblies dominate resonance energy transfer (RET) processes in energy donoracceptor pairs, suggesting an extension of the ESM machinery to RET. RET is a
widely investigated process, crucial for energy storage and conversion applications.
In the late forties Förster developed an efficient approach relating the rate of RET
to spectroscopically accessible quantities. [2] Based on the dipolar approximation
for the description of electrostatic interactions, the Förster model limits RET
processes only between pair of one-photon allowed states (i.e. bright states).
Here ESMs are applied to investigate the limits of the dipolar approximation for the
description of RET between CT dyes, and to address the possible active role in
RET processes of dark states, i.e. of states with vanishing transition dipole moment
from the ground state. Our results [3], supported by TDDFT calculations,
demonstrate a limited range of applicability of the dipolar approximation. Even
more important, we prove that at short intermolecular distances, dark states can
provide effective and sometimes dominant channels for RET. ESMs allow to relate
the intensity of intermolecular interactions responsible for RET to the geometrical
arrangement of the energy donor-acceptor partners, providing reliable design
strategies for optimized RET.
[1]
[2]
[3]
108
(a) Terenziani, F.; D'Avino, G; Painelli, A.; ChemPhysChem, 2007, 8 2433; (b)
Terenziani, F.; Sissa, C.; Painelli, A. J. Phys. Chem. B 2008, 112, 5079
Th. Förster, Ann. Phys., 2, 55 (1948)
Sissa, C.; Manna, A.K., Terenziani, F; Painelli, A.; Pati, S. K., Phys. Chem. Chem.
Phys. 2011, 13, 12734
P55 The absorption and emission spectra of oligo-thiophene
based biomarkers: a PCM/TD-DFT study.
Emiliano Stendardo,a Francisco Avila,b Fabrizio Santoro,b Roberto Improtaa
a
CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini
(IBB-CNR), Via Mezzocannone 16, I-80136, Napoli, Italy
b
CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti
OrganoMetallici(ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
E-mail: [email protected]
Besides their relevance for optoelectronics, suitably functionalized oligothiophene
have shown promising performances as biomarkers[1], explaining the interest in
their excited state properties. We report the computed absorption and emission
spectra of N-succinimidyl-ester and methyl-amide derivatives of bis and
terthiophene, in different environments, from the gas phase to polar solvents,
checking for the effects of methylsulphanyl substituents in different positions. Our
approach is based on TD-DFT calculations and exploits recent developments in
Polarizable Continuum Model [2] and PCM/TD-DFT calculations, namely statespecific (SS) treatment [3], enabling also a non-empirical determination of polar
contribution to inhomogeneous broadening.[4] Optical line-shapes can be
computed, including both Duschinsky and Herzberg Teller effects, with a method
developed in our group [5]. The computed spectra are in good agreement with
experiments, providing interesting indications on the performances of different
functionals and on the main chemical-physical effects (e.g. position and
conformation of the substituents) modulating the excited state properties of these
compounds.
[1]
Piacenza, M.; Zambianchi, M.; Barbarella, G.; Gigli, G.; Della Salal, F.
Phys. Chem. Chem. Phy, 2008, 10, 5363-5373.
[2]
Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999.
[3]
(a) Improta, R.; Barone, V.; Scalmani, G.; Frisch, M.J. J. Chem. Phys. 2006,
125, 54103. (b) Improta, R.; Scalmani, G.; Frisch, M.J.; Barone, V. J.
Chem. Phys. 2007, 127, 074504.
[4]
Avila Ferrer,F.J.; Improta, R.; Santoro, F.; Barone, V. Phys. Chem. Chem.
Phys. 2011, 13, 17007.
[5]
(a) Santoro, F.; Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys.
2007, 126, 084509, ibidem 2007, 126, 169903. (b) Santoro, F.; Improta, R.;
Lami, A.; Barone, V. J. Chem. Phys. 2007, 126, 184102. (c) Santoro, F.;
Improta, R.; Lami, A.; Bloino, J.; Barone, V. J. Chem. Phys. 2008, 128,
224311. (d) Bloino, J.; Biczysko, M.; Santoro, F.; Barone, V., J. Chem.
Theory and Comp. 2010, 1256.
109
P56 Resonant circular dichroism of chiral metal-organic complex
M. Stenera,b,c, D. Catone d, P. Declevaa,b,c, G. Contini d, N. Zema d, T. Prosperi d,
V. Feyere, K. C. Princee, f and S. Turchini d
a
Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L.
Giorgieri 1, I-34127 TRIESTE, ITALY
b
Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali,
INSTM, Unita’ di Trieste
c
DEMOCRITOS CNR-IOM National Simulation Center, Trieste, Italy
d
Istituto Struttura della Materia, C.N.R. Via Del Fosso del Cavaliere 100, 00133
Roma, Italy
e
Sincrotrone Trieste, I-34149 Basovizza (Trieste)- ITALY
f
IOM-CNR, I-34149, Basovizza (Trieste) – ITALY
A sizeable enhancement of the circular dichroism in photoelectron spectroscopy
has been measured and computed for the metal complex Δ-Cobalt(III) trisacetylacetonate HOMO state in the region of
the Co 3p → 3d Fano-resonance [1]. In the
resonance the dichroism reaches the
maximum value of 5% and even changes its
sign as compared to the direct
photoionization channel. We ascribe this
enhancement
to
electron
correlation
processes, namely with the coupling between
discrete excitations and the continuum,
which is correctly described in the Time
Dependent Density Functional Theory
framework. These findings open new
physical aspects of photoelectron circular
dichroism that now can be interpreted not
only via the simple direct ionization, but also
through more complex electron correlation
processes. The satisfactory agreement
between theory and experimental results in
the off-resonance region proves that the
TDDFT procedure can also account for the
structural and electronic sensitivity of the circular dichroism in direct as well as
resonant ionization regime.
[1] D. Catone, M. Stener, P. Decleva, G. Contini, N. Zema, T. Prosperi, V. Feyer,
K. C. Prince and S. Turchini, Phys. Rev. Lett. 2012, 000, 0000.
110
P57 A theoretical protocol for the determination of the metal-site
structure in metalloprotein superfamilies
Rosario G. Viglione, Orlando Crescenzi
Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso
Universitario Monte Sant’Angelo,Via Cintia, I-80126 Napoli, Italy
E-mail: [email protected]
NMR spectroscopy is a powerful experimental tool used for the determination of
protein structure. Recently, several papers have appeared which suggest that
reasonably accurate protein structures can be determined directly from chemical
shifts [1-3]. In the present work we introduced ab initio computation of chemical
shifts as a tool for the structural validation of metal binding site(s) of
metalloprotein structures. EF-hand calcium-binding proteins represent a suitable
test application, since accurate databases of structural and NMR properties are
available. We have explored the convergence of calculated calbindin D9k (CAB)
chemical shifts, as a function of the size of the QM partition within a hybrid
quantum mechanical (QM) / molecular mechanical (MM) approach, namely the
ONIOM method as implemented in the Gaussian package. Once a satisfactory
partition scheme has been devised, more realistic computations were sought by
including motional averaging effects. In the adopted procedure we performed a
classical MD simulation of the biomacromolecule (in explicit solvent), then we
extracted snapshots at regular time intervals and averaged the results of QM/MM
calculations performed on each frame [4]; the
influence of the solvent was modeled by
partial charges. The calculated chemical shifts
display sizeable oscillations, which are larger
for the apo form of CAB, and more moderate
for the calcium-loaded form, probably
reflecting the hardening of the local binding
site structure. In the latter case, comparisons
between experimental data [5] and theoretical
determinations are very encouraging.
[1]
[2]
[3]
[4]
[5]
Gong, H.; Shen, Y.; Rose, G.D. Protein Sci. 2007, 16, 1515.
Cavalli, A.; Salvatella, X.; Dobson, C.M.; Vendruscolo, M. Proc. Natl. Acad. Sci.
USA 2007, 104, 9615.
Shen, Y.; Lange, O.; Delaglio, F.; Rossi, P. et al. Proc. Natl. Acad. Sci. USA 2008,
105, 4685.
Cui, Q.; Karplus, M. J. Phys. Chem. B 2000, 104, 3721.
Oktaviani, N.A.; Otten, R.; Dijkstra, K.; Scheek, R.M. et al. Biomol NMR Assign.
2011, 5, 79.
111
P58 Computational studies on iron-based coordination polymers
of interest in cultural heritage
Sara Zaccaron,a Renzo Ganzerla,a Marco Bortoluzzi a
a
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di
Venezia, Dorsoduro 2137, 30123 Venezia, Italy
E-mail: [email protected]
Iron gall complexes are well known inks, which have been the most used writing
material since the 12th century. Recent studies have shown that these species are
polymers where several iron metal centres are bridged by the conjugate base (L) of
the gallic acid (H4L) [1]. The excess of negative charge is neutralized by the H3O+
cations. The deep blue colour of iron gall species is probably attributable to a
strong electronic delocalisation among the metal ions, but no detailed study is
currently present in the literature and the real oxidation state of iron centres is not
unambiguously ascertained. The understanding of the electronic configuration of
the ground and the excited states of these inks is of paramount interest for the
development of methodologies useful for heritage preservation. Moreover,
important archival holdings show noticeable degradation phenomena caused by the
destructive effects of iron gall inks interacting with cellulose and the scarce
information still present in the literature about the electronic features of these
molecules makes the degradation mechanisms unclear.
In the present communication we report a computational study on the electronic
structure of the ground states of models of iron gall inks, using the HF method and
pure and hybrid DFT functionals. Mononuclear complexes, oligomers having three
iron centres bridged by gallic acid molecules and coordination polymers with Fe:L
ratio 1:2 have been studied. Bond lengths, angles and periodic boundary conditions
come from experimental data obtained from X-Ray structure diffraction. The
ground-state multiplicity has been determined. No evidence of metal-metal
interaction is present in all the model compounds. The computational results agree
with a quite oxidant behaviour of the iron inks when all the metal centres have
formal 3+ charge. Complexes where one of the iron ions is formally 2+ result
stable and a wide delocalisation of the extra-electron occurs, in particular on the
phenyl rings bound to the metal centres through the phenate oxygen atoms. The
presented computational results agree, together with data coming from
experiments, with a picture where iron gall inks can be better described as mixedvalence coordination compounds.
We acknowledge the CINECA Award N. HP10CRPVUO, 2011 for the availability
of high performance computing resources and support.
[1]
112
a) Wunderlich, C.H. Z Anorg Allg Chem. 1991, 598-599, 371. b) Wunderlich, C.H.
Restauro 1994, 100, 414.
P59 Integrated approaches to NMR spin relaxation in flexible
biomelecules: application to polysaccharides
Mirco Zerbettoa, Dmytro Kotsyubynskyyb, Maria Soltesovab, Jozef
Kowalewskib, Eva Meirovitchc, Goran Widmalmb, Antonino Polimenoa
a
Dipartimento di Scienze Chimiche, Università degli Sutdi di Padova, Padova
35131, Italy
b
Department of Physical, Inorganic and Structural Chemistry, Stockholm
University, 10691 Stockholm, Sweden
c
The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University,
Ramat-Gan 52900, Israel
E-mail: [email protected]
We address the interpretation of molecular dynamics from nuclear magnetic
resonance measurements of flexible molecules via stochastic modeling. We focus
our attention on the family of flexible molecules which internal relevant dynamics,
with respect to nuclear magnetic resonance (NMR) observables, is expressed in
terms of torsional angles. Thus, we deal with molecules that from the point of view
of NMR spectroscopy can be associated to open chains of rigid fragments
connected by joints around which torsion is possible. The complete dynamics
comprises the, coupled, global tumbling and internal flexibility. This model has
just been applied with success to the interpretation of electron spin resonance
spectra and nuclear magnetic resonance relaxation data of simple molecules in
isotropic and ordered media [1,2]. Here we apply the same approach to the
interpretation of slow dynamics from NMR relaxation of oligosaccharide
molecules, which have a primary interest in the fields of biology, related to cellular
recognition, and of theoretical / computational chemistry, being good and tunable
test cases. We show that merging to quantum mechanical, molecular dynamics and
hydrodynamics methods many of the molecular properties entering the stochastic
model can be evaluated a priori leaving a very reduced set of free parameters to be
determined by fitting.
[1]
[2]
Zerbetto, M.; Polimeno, A.; Cimino, P.; Barone, V. J. Chem. Phys. 2008,
128, 024501.
Zerbetto, M.; Polimeno, A.; Kotsyubiynskyy, D.; Ghalebani, L.;
Kowalewski, J.; Meirovitch, E.; Olsson, U.; Widmalm, G. J. Chem. Phys.
2009, 131, 234501
113