6nd European Symposium

on

Computing π-Conjugated Compounds

Olomouc

5th – 7th February 2015

Book of Abstracts

i

European Symposiums on Computing π-Conjugated Compounds (CπC) is a series of small symposia

on the computations of various properties of π-conjugated systems. This symposium covers from small

π-conjugated molecules up to very large systems as well as computational approaches ranging from

empirical force fields up to high-level quantum chemistry.

Previous CπC symposia were organized in Valencia (2010), Limoges (2011), Mons (2012), Marseille

(2013) and Linköping (2014). These meetings were very successful and stimulated several successful

collaborative activities among participants. We hope that you enjoy CπC meeting in Olomouc and

benefit from the newly established contacts and provoked ideas.

See you in Olomouc!

Michal Otyepka and Karel Berka

Local organizing committee

Michal Otyepka (+420 733 690 624)

Karel Berka (+420 723 953 791)

CπC scientific board

Johannes Gierschner IMDEA Nanoscience, Madrid Spain

Begoña Milián-Medina IMDEA Nanoscience, Madrid Spain

Patrick Trouillas University of Limoges France

Yoann Olivier University of Mons Belgium

Luca Muccioli University of Bologna Italy

Philippe Marsal University of Marseille France

Juan-Carlos Sancho-García University of Alicante Spain

Mathieu Linares University of Linköping Sweden

Michal Otyepka Palacký University Olomouc Czech Rep.

Mari Carmen Ruiz Delgado University of Malaga Spain

Roberto Improta IBB/CNR Naples Italy

ii

Venue

Faculty of Science, Palacký University Olomouc, Czech Republic

tř. 17. listopadu 12, Olomouc

GPS: 49.5924922,17.2632337

3rd

floor, lecture room 3.003 and PC room/refreshment 3.002

Faculty building from Google StreetView

Meeting sponsorship

iii

List of Participants

Karel Berka karel.berka@upol.cz Palacky Uni, Olomouc, CZE

Michal Biler michal.biler@seznam.cz Palacky Uni, Olomouc, CZE

Santanu Bhattacharyya b.santanu@imdea.org IMDEA Nanoscience, Madrid, ESP

María del

Carmen Ruiz Delgado

carmenrd@uma.es Uni Málaga, ESP

Petra Čechová cechovpe@seznam.cz Palacky Uni, Olomouc, CZE

Gabriele D'Avino gabriele.davino@gmail.com Uni Mons, BEL

Florent Di Meo flodi20@ifm.liu.se IFM, Linköping University, SWE

Matúš Dúbecký matus.dubecky@upol.cz Palacky Uni, Olomouc, CZE

Fabre Gabin gabin.fabre@unilim.fr Uni Limoges, FRA

Manoj Gali galismanoj@gmail.com Uni Bordeaux, FRA

Hugo Gattuso hugo.gattuso@univ-lorraine.fr Uni Lorraine, Nancy, FRA

Johannes Gierschner johannes.gierschner@imdea.org IMDEA Nanoscience, Madrid, ESP

Angelo Giussani angelo.giussani2@unibo.it Uni Bologna, ITA

Benjamin Grenier grenier@cinam.univ-mrs.fr CINAM, Marseille, FRA

Roberto Improta robimp@unina.it CNR, Uni degli Studi di Napoli, ITA

Pavel Jelínek jelinekp@fzu.cz Inst Physics, AS CR, Prague, CZE

Petr Jurečka petr.jurecka@upol.cz Palacky Uni, Olomouc, CZE

Stefan Knippenberg sknippen@kth.se KTH, Stockholm, SWE

Martin Kubala martin.kubala@upol.cz Palacky Uni, Olomouc, CZE

Petra Kührová petra.kuhrova@upol.cz Palacky Uni, Olomouc, CZE

Petr Lazar petr.lazar@upol.cz Palacky Uni, Olomouc, CZE

Mathieu Linares mathieu@ifm.liu.se Linköping Uni, SWE

Philippe Marsal philippe.marsal@univ-amu.fr CINaM/Uni d'Aix, Marseille, FRA

Micaela Matta pebbles.mika@gmail.com Uni Bordeaux, FRA

Begoña Milián-Medina milian@uv.es Uni Valencia, SPA

Antonio Monari antonio.monari@univ-lorraine.fr Uni Lorraine, Nancy, FRA

Monica Moral monicamoralm@gmail.com Uni Alicante, ESP

Luca Muccioli luca.muccioli@gmail.com Uni Bordeaux, FRA

Dana Nachtigallová dana.nachtigallova@uochb.cas.cz IOCB, AS CR, Prague, CZE

Veronika Navrátilová veronika.navratilova@upol.cz Palacky Uni, Olomouc, CZE

Yoann Olivier yoann.olivier@umons.ac.be Uni Mons, BEL

Michal Otyepka michal.otyepka@upol.cz Palacky Uni, Olomouc, CZE

Martin Pykal martin.pykal@upol.cz Palacky Uni, Olomouc, CZE

Olivier Rezazgui olivier.rezazgui@orange.fr LCSN, Limoges, FRA

Juan-Carlos

Sancho-García

jc.sancho@ua.es Uni Alicante, ESP

Sunandan Sarkar sunandan.sarkar@upol.cz Palacky Uni, Olomouc, CZE

Junqing Shi shi.junqing@imdea.org IMDEA Nanoscience, Madrid, ESP

Mária Sudolská maria.sudolska@upol.cz Palacky Uni, Olomouc, CZE

Jiří Šponer sponer@ncbr.muni.cz Inst Biophysics, AS CR, Brno, CZE

Martin Šrejber martin.srejber@gmail.com Palacky Uni, Olomouc, CZE

Patrick Trouillas patrick.trouillas@unilim.fr INSERM, Uni Limoges, FRA

Shinto Varghese sv26@st-andrews.ac.uk Uni St Andrews, UK

Riccardo Volpi ricvo@ifm.liu.se Linköping Uni, SWE

Michael Wykes michael.wykes@imdea.org IMDEA Nanoscience, Madrid, ESP

Marie Zgarbová marie.zgarbova@upol.cz Palacky Uni, Olomouc, CZE

http://fch.upol.cz/en/cpic

ABSTRACTS

Invited Lectures

2

Electronically Excited States of Nucleic Acid Bases:

Computational Study

Dana Nachtigallová

Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Czech Republic

Ab initio surface hopping dynamics calculations were performed to study the photophysical

behavior of nucleic acid bases embedded in DNA using a quantum mechanical/molecular

mechanics approach.

The photodynamics of 4-aminopyrimidine used as a model for adenine were performed by

embedding it between two stacking methyl-guanine molecules to determine the effect of spatial

restrictions on the ultrafast photodeactivation mechanism of this nucleobase. During the

dynamics the formation of a significant fraction of intra-strand hydrogen bonding from

4-aminopyrimidine to methyl-guanine above and below is observed. This type of hydrogen bond

may play an important role for the photodynamics within one DNA strand.

The effect of inter-strand hydrogen bonding was investigated for cytosine and guanine and found

to be affected in a completely different way by the hydrogen bonding to the DNA environment.

In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence

the relaxation time of cytosine significantly due to the generally small cytosine ring puckering

required to access the crossing region between excited and ground state. On the contrary, the

presence of hydrogen bonds significantly altered the photodynamics of guanine.

3

Nature and Magnitude of Aromatic Base Stacking in Nucleic Acids

Jiří Šponer

Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech

Republic, sponer@ncbr.muni.cz

Vertical (stacking) interactions of nucleic acid bases belong to the most fundamental energy

contributions that are shaping up structure and dynamics of nucleic acids (DNA and RNA). At

the same time, one can hardly find any energy contribution in nucleic acids that is associated

with so many myths, oversimplifications and misunderstandings in the literature.

In my talk, I will briefly explain the physical-chemistry origin of basis stacking as revealed by

modern electronic structure theory. Then I will explain how is it (im)possible to transfer this

knowledge to real structural biology and biochemical problems.

References

[1] J. Sponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base stacking. Nonempirical ab initio and

empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs.

Journal of Physical Chemistry 100, 1996, 5590-5596.

[2] J. Florian, J. Sponer, A. Warshel: Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid

bases in aqueous solution: ab initio/Langevine dipole study. Journal of Physical Chemistry B 103, 1999, 884-892.

[3] P. Hobza, J. Sponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio

calculations. Chemical Reviews 99, 1999, 3247-3276.

[4] J. Sponer, C.A. Morgado, D. Svozil: Comment on "Computational Model for Predicting Experimental RNA and

DNA Nearest-Neighbor Free Energy Rankings. Journal of Physical Chemistry B, 116, 2012, 8331-8332.

[5] J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, M. Otyepka: Nature and magnitude of aromatic base

stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 2013, 99,

978-988.

4

What We Can Learn from High-Resolution AFM/STM Images:

Experiment and Theory

Pavel Jelínek

Institute of Physics ASCR, Cukrovarnická 10, Prague 6, Czech Republic

The recent progress in Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy

(STM) using functionalized tips provided unprecedented atomic resolution of single organic

molecules [1,2]. However, the origin of the high-resolution AFM/STM imaging contrast is still

not well understood. Here we will present 3D maps of the force, tunneling current and

dissipation over a monolayer of PTCDA molecules deposited on Ag(111) acquired at 1.2 Kelvin

with Xe-functionalized tip (see Fig. 1.). We will compare detailed contrast features of the force

maps at various tip-sample separations to a numerical model [3,4]. The numerical model

describes relaxation of the functionalized tip due to Pauli repulsion and the electrostatic

interaction with surface. Combing the experimental and theoretical evidence, we will explain the

high-resolution imaging mechanism [3], artifacts [3,5] and a possibility to map out

intra-molecular charge distribution in real-space [4]. We will also discuss a possibility to use

experimental measurements to benchmark existing classical interatomic potentials (force fields)

and devise new forms of the potentials.

Fig.1. High resolution AFM/STM images of PTCDA molecules deposited on Ag(111) surface

acquired with Xe-functionalized tip at different tip sample distances.

References

[1] L. Gross et al., Science 325,1110 (2009).

[2] C. Weiss et al., Phys.Rev.Lett. 105, 086103 (2010).

[3] P. Hapala et al., Phys. Rev. B 90, 085421 (2014).

[4] P. Hapala et al., Phys. Rev. Lett. 113, 226101 (2014).

[5] J. Zhang et al., Science 342, 611 (2013).

5

ABSTRACTS

Oral Communications

6

Excited State Features and Dynamics in Conjugated Organic Materials

Johannes Gierschner, Begoña Milian-Medina, Michael Wykes,

Santanu Bhattacharyya, Shinto Varghese, Junqing Shi,

Rameesha Parambil, Benedikt Dähnekamp, Jorge Moreno

Madrid Institute for Advanced Studies, IMDEA Nanoscience, Madrid, Spain

Having now steady-state and time-resolved absorption and emission spectroscopy fully operative,

our team in Madrid has intensified the studies on excited state dynamics in conjugated organic

materials in solution and in the solid state by an integrative spectroscopic and computational

approach.

Isolated chains: With our expertise in polymer bandgap predictions, we are now investigating

low bandgap homopolymers, as well as co-polymers with strongly localized MOs, and the

impact on charge and exciton transport (Begoña). Following the series of previous fluorination

studies, we discover new symmetry breaking effects in latter-type oligophenylenes leading to

unprecedented optical properties (Benedikt & Begoña). Studying the excited state potential

surfaces of substituted distyrylbenzenes, we are elucidating the selectivity of specific substituent

position on the photophysics (Junqing & Begoña). New branches opened on metal-free organic

phosphors, on reactivity studies for novel fluorine sensors, and on acidochromic

(multi-responsive) materials.

Solid State: Quantum chemical studies finally helped to understand why some organic single

crystals are lasing and others not (Shinto). Careful quantum-chemical studies on molecular

aggregates allow for a detailed understanding of the emission process in aggregates of

-conjugated systems with respect to their AIEE properties (Junqing) and their vibronic structure

(Rameesha & Mike). Surprisingly strong emission properties of donor-acceptor co-crystals were

traced back to the specific nature of the excited singlet & triplet state manifolds (Santanu).

7

MO and Excited State Design of Low Bandgap Copolymers

Begoña Milián-Medina1,2, Johannes Gierschner2

1Department of Physical Chemistry, University of Valencia

c/ Dr. Moliner 50, 46100 Burjassot (Valencia) - (SPAIN) 2Madrid Institute for Advanced Studies, IMDEA Nanoscience

c/ Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid - (SPAIN)

e-mail: b.milian.medina@uv.es

Donor-acceptor low bandgap copolymers are frequently used in organic photovoltaics to

efficiently harvest the sunlight. However, manipulation of the bandgap via the donor-acceptor

approach also produces significant changes in the electronic properties and of the excited state

manifold through frontier MO localization. This might significantly influence optical properties,

intra-chain photophysics, and solid state exciton dynamics, charge transport and (re)combination.

Conceptual quantum-chemistry is used to elucidate the pre-requisites for specifically localized

MOs, and their impact on the copolymers' electronic, optical and photophysical properties.

8

Low-temperature Fine Structure via Atomistic Quantum Chemical

Franck-Condon Herzberg-Teller calculations.

Michael Wykes, Rameesha Mangattu Parambil, Johannes Gierschner

IMDEA Nanoscience, Madrid, Spain

Para-distyrylbenzene (DSB), a model compound for the first polymer (PPV) intensely

investigated for its electroluminescent properties, has been the focus of numerous experimental

and theoretical investigations into the fundamental photophysics of organic semiconductors. The

drastic change in optical properties of DSB upon transfer from the dilute solution phase to the

bulk crystalline phase has been linked to the herring-bone crystal structure of DSB, which leads

to the formation of H-aggregates in which the transition dipole moment of the lowest electronic

transition is greatly reduced. While the vibronic-fine structure of DSB seen in low-temperature

solution spectra has been fully interpreted on the basis of atomistic simulations combining

quantum chemical (QC) calculations and Franck-Condon models of vibronic coupling,1 the

optical spectra of crystal spectra have thus far been simulated using an alternative coarse-grained

phenomenological Holstein-type model in which molecules are treated as sites coupled to a

single effective intramolecular vibrational mode.2 Here we treat single molecules and model

DSB-aggregates on an equal footing, with atomistic models combining QC calculations and

Franck-Condon and Herzberg Teller models of vibronic coupling. We compare our simulated

spectra with coarse-grained Holstein-based simulations and experiments and discuss the

theoretical foundations of the two models as well as their advantages and disadvantages when

applied to molecular crystals.

References

[1] Gierschner, J.; Mack, H.-G.; Lüer, L.; Oelkrug, D. J. Chem. Phys. 2002, 116, 8596.

[2] Spano, F. C. J. Chem. Phys. 2003, 118, 981

9

Simulations of Excited Electronic States and Photochemistry

S. Knippenberg1, R. L. Gieseking2, D. R. Rehn3, M. Wormit3,

S. Mukhopadhyay2, J.-L. Brédas2, M. V. Bohnwagner3, P. H. P. Harbach3,

and A. Dreuw3

1Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, S-106

91 Stockholm, Sweden 2Center for Organic Materials for All-Optical Switching (COMAS), Georgia Institute of Technology, Atlanta,

Georgia 30332-0400 3Interdisciplinary Center for Scientific Computing, Ruprecht-Karls-University, Im Neuenheimer Feld 368, D-69120

Heidelberg, Germany

e-mail: sknippen@kth.se

The Algebraic Diagrammatic Construction (ADC) scheme, which is a powerful approach to

investigate excited states and their properties [1], is used for the first time to calculate second

hyperpolarizabilities [2]. A convenient sum-over-states (SOS) expression is applied and the

focus is put upon short and middle-sized streptocyanines. The real part of , denoting the

refraction index, is investigated for all compounds in the band 0.8-0.95 eV (1200-1550 nm),

which is of utmost importance for telecommunication purposes. Comparison has been made with

results obtained using packages which have been often applied in literature, like the powerful

symmetry adapted cluster configuration interaction (SAC-CI) method and the pragmatic

semi-empirical Zindo one. The two-photon absorption cross section has been profoundly focused

on, too. In the case of second order ADC [ADC(2)], it is calculated using a three-state expression

as well as by applying an analytically closed form. The data are found to be very comparable,

enforcing the two-photon SAC-CI, Zindo and higher order ADC results, which are only obtained

by means of the SOS formalism.

Focusing on photochemistry, the BisBODIPY compound and the influences of excitonic

coupling on its absorption spectra are investigated [3]. With the help of model systems, the

electronic coupling is quantized and its influence on energetics and oscillator strengths is

highlighted. For the explanation of the experimental spectrum, orbital interaction effects are

found to be important.

References

[1] J. Schirmer, Phys. Rev. A 26 (1982), 2395; J. Schirmer and A.B. Trofimov, J. Chem. Phys. 120 (2004) 11449;

Wormit, M.; Rehn, D.; Harbach, P. et al., Mol. Phys. 112 (2014), 774.

[2] S. Knippenberg, D. Rehn, M. Wormit et al., J. Chem. Phys. 136 (2012), 064107; S. Knippenberg, R. L.

Gieseking, D. Rehn, et al., to be submitted.

[3] M. Bröring, R. Krüger, S. Link et al., J. Phys. Chem. A 116 (2012), 12321; S. Knippenberg, M. V. Bohnwagner,

P. Harbach, A. Dreuw, submitted.

10

On the Computation of Two-dimensional Electronic Pump-Probe

Spectra

Angelo Giussani, Artur Nenov, Javier Segarra-Martí, Irene Conti,

Ivan Rivalta, Elise Dumont, Vishal K. Jaiswal, Salvatore Altavilla,

Shaul Mukamel, and Marco Garavelli

Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy

Angelo.Giussani2@unibo.it

Two-dimensional electronic spectroscopy is a promising technique expected to become a key

tool for the description of excited state decays. [1] The methodology is based on the detection

into a so-called two-dimensional electronic spectrum of all the intensive electronic transitions

caused by a UV or vis radiation (the pump signal) at time t1 and the subsequent interaction with a

second UV or vis radiation (the probe signal) at time t2 (t2 ≥ t1). Two-dimensional electronic

spectroscopy will then provide both high spectral and temporal resolution allowing the analysis

of ultrafast complex (multi-pathway) reactions.

The theoretical construction of two-dimensional electronic spectra requires at least the

knowledge of all the accessible electronic transitions by a defined pump signal from a particular

geometry and electronic states of the system, and all the accessible electronic transitions by a

defined probe signal from a particular geometry and electronic states. Such information is

obtained through the calculation of a considerable number of excited states energies and the

corresponding transition dipole moments at the pump and probe geometries. In order to obtain

quantitative outcomes for medium size molecules, as the canonical nucleobases, nowadays the

most suitable computational strategies are probably the CASSCF and CASPT2 (or RASSCF and

RASPT2) methods. Having the required data, using the qSpec2DUV program a two-dimensional

spectrum can then be produced.[1]

With the present contribution, the main features and potentialities of two-dimensional electronic

spectroscopy are presented, together with the machinery developed in the Garavelli's group in

order to compute two-dimensional electronic spectra, and the results of its application on the

study of the photophysics and photochemistry of adenine and of the adenine dimer.[2]

References

[1] a) Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M, Int. J. Quantum Chem., 2014, 114, 85–93. b) Nenov

A, Rivalta I, Cerullo G, Mukamel S, Garavelli M, J. Phys. Chem. Lett., 2014, 5, 767-771.

[2] Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal E, Altavilla S, Mukamel S,

Garavelli M, Accepted for the Faraday discussions: Temporally and spatially resolved molecular sciences, 2014,

Bangalore, India

11

The Role of Charge Transfer Excited Electronic States in

Photophysics and Photochemistry of DNA

Roberto Improta

Istituto Biostrutture e BioImmagini-CNR, Via Mezzocannone16, 80134, Napoli, Italy

The possible involvement of Charge Transfer (CT) excited states in the photoactivated dynamics

of DNA is one of the most controversial issues in the photochemistry of nucleic acids. Exploiting

Time Dependent DFT calculations using last generation functions (enabling an accurate

determination of the CT states stability) and taking solvent effect into account by the Polarizable

Continuum Model, we have studied realistic oligonucleotides, including also the

phospho-deoxyribose backbone and counter-ions, by combing stati and quantum dynamical

calculations. We provide clear indications that states with a noticeable, yet different, degree of

CT character are involved in the photophysics and photochemistry of several systems:

oligoAdenine,[1,2] d(TpT)[3,4] and d(TpC)[5] and d(Tp5methylC)[5] dinucleotides, Guanine

Quadruplex helices[6] Guanine nano-ribbons,[7] and Oxoguanine-Ade dinucleotides.[8] Our

predictions are fully consistent with the available experimental results, i.e. Steady State Circular

Dichrois m,[3,6] Time resolved fluorescence [1-7] and InfraRed spectra, which, fo r the first

time, show a clear spectral signature of CT states.[8] For quadruple helices, our studies also

provide a complete assignment of the optical spectra and indications on the fact ors influencing

the excited state dynamics (cation, conformation of the quadruplex...).[6] Finally, it has been

possible to explain the role of 5-methylation in the phot ochemistry of dinucleotides containing

Cytosine.[5].

References

[1] R. Improta, V. Barone, Angew. Chemie. 2011, 50 , 12016.

[2] A. Banyasz, et al. Chem. Eur. J. 2013, 19 , 3762.

[3] A.Banyasz, et al. J. Am. Chem. Soc. 2012, 134, 14834.

[4] R. Improta, J. Phys. Chem. B 2012, 116, 1426.1

[5] L. Esposito et al. J. Am. Chem. Soc. 2014, 136, 10838.

[6] R. Improta, Chem. Eur. J. 2014, 20, 8106.

[7] K. Hunger, et al. Chem. Eur. J. 2013, 19, 5425.

[8] Zhang, Y. et al. Proc. Nat. Acad. Sci. U.S.A. 2014, 111, 11612.

12

Electronic Circular Dichroism Spectra in Stacked Systems

Mathieu Linares

Division of Theoretical Chemistry, Department of Physics, Biology and Chemistry (IFM) Linköping University –

Sweden – mathieu@ifm.liu.se

During the last two decades Circular Dichroism (CD) has been widely used to understand the

chirality phenomenon. It has been possible to understand the physical, chemical and

conformational properties of chiral molecules, chiral assemblies, peptides and proteins.

The simulation of the ECD response of a single molecule, is a task well suited for standard

time-dependent density functional theory (TD-DFT)1 (or any other standard first-principles

response theory approach) in combination with the use of gauge-origin independent basis sets.2

It is clear that with the development of reduced scaling techniques, DFT can be applied to large

systems such as a cluster model of polymer aggregates. However, even if TD-DFT is suitable to

model small stacks,3 its use is prohibited in large supramolecular assemblies involving a high

density of excited states. A more suitable approach to bypass this problem is the use of a

resonant convergent formulation of response theory known as the complex polarization

propagator (CPP) approach. We recently applied this approach to the case of achiral and chiral

ethylene forming P and M stacks (Figure).4

Other approaches have been successfully applied to small sections of DNA such as SAC-CI,

5 but

the size of the system and the computational time appears to be a bottleneck for calculating the

ECD-spectra of long DNA sequences. In a recent paper, Padula et al. showed6 that it was

possible to reproduce the ECD spectra of crystal of Aryl Benzyl Sulfoxides by adding up the

ECD spectra of all the dimers composed of nearest neighbors in the lattice. In the present

contribution we follow this approach for the case of DNA, and shows that we can obtain spectra

in excellent agreement with experiment.

References

[1] Autschbach, J. et al. Top. Curr. Chem. 2011, 298, 1

[2] Helgaker, T. J. et al. Faraday Discuss. 1994, 99, 165

[3] Santoro, F. J. et al. Comput. Chem. 2007, 29, 957

[4] Norman, P. et al. Chirality, 2014, 26, 123.

[5] Miyahara, T. et al. J. Phys. Chem. A 2013, 117, 42

[6] Padula, D. et al. Chirality 2013, 26, 462

-120

-80

-40

0

40

80

120

170 180 190 200 210 220

Exnconcoefficient(L.m

ol-1.cm

-1)

Wavelength(nm)

P

M

13

Merging Non-local (van der Waals) Corrections

with Double-Hybrid Density Functionals

J.C. Sancho-García1, J. Calbo2, Y. Olivier3, E. Ortí2, J. Aragó2

1Department of Physical Chemistry, University of Alicante, E-03080, Alicante, Spain

2Institute of Molecular Science, University of Valencia, E-64980 Valencia, Spain

3Laboratory for Chemistry of Novel Materials, University of Mons, B-700 Mons, Belgium

Non-covalent interactions are known to drive the self-assembly and reactivity of molecules at

any length scale, which needs to be successfully and cost-efficiently incorporated into any

intended theoretical treatment of weakly interacting systems [1]. We have coupled a seamless

and truly non-local (NL) correlation functional with the most modern existing expressions for

exchange-correlation effects [2], such as the double-hybrid density functionals (DHDFs) named

as B2-PLYP or revPBE0-DH, providing a family of methods able to deal with any kind of

interactions (covalent and non-covalent) in an accurate way. This is demonstrated through their

excellent performance for a set of recently developed databases (S22, S66, NCCE31, S12L, and

L7) for benchmarking purposes [3,4], as well as for estimating the cohesive or lattice energies of

(bulk) organic molecular semiconductors [5,6].

References

[1] K.E. Riley, M. Pitonak, P. Jurecka, and P. Hobza, Chem. Rev. 110 (2010) 5023.

[2] J.C. Sancho-García, and C. Adamo, Phys. Chem. Chem. Phys. 15 (2013) 14581.

[3] J. Aragó, E. Ortí, and J.C. Sancho-García, J. Chem. Theory Comput. 9 (2013) 3437.

[4] J. Calbo, J.C. Sancho-García, E. Ortí, and J. Aragó, J. Chem. Theory Comput. (submitted).

[5] J.C. Sancho-García, J. Aragó, E. Ortí, and Y. Olivier, J. Chem. Phys. 138 (2013) 204304.

[6] J.C. Sancho-García, A.J. Pérez-Jiménez, and Y. Olivier, J. Chem. Phys. (submitted).

14

Induced Chirality in Porphyrins: Self-Assembly and Systems of

Biological Interest

Florent Di Meo, Mathieu Linares, Patrick Norman

Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University,

SE-58183 Linköping, Sweden

Email: flodi20@ifm.liu.se

Porphyrins are an important armamentarium of -conjugated compounds with a broad range of

physico-chemical and biological activities. Even though the porphyrin core is based on a simple

achiral tetrapyrrol core, the possibility to substitute meso positions and/or to include a metal

center leads to a huge variety of original compounds with different conformational features.

Furthermore, the environment (e.g., other porphyrins or biological systems such as DNA) may

deform tetrapyrrol core leading to a specific chiroactive structure. Such induced chirality can be

followed by electronic circular dichroism response in the typical Soret region.

Figure. Examples of (a) chiroactive porphyrin self-assembly and (b) supramolecular

metalloporphyrin G-quadruplex complex.

In the present work, the self-assembly of a chiral porphyrin (Fig. 1a) is first investigated.

Experiments suggest the self-assembly of four porphyrins into a cubic-like shape. Then, each

cube may also undergo a secondary self-assembly process leading to an important increase of the

ECD signal. MD simulations and ZINDO calculations allowed to elucidate (i) the

supramolecular assembly and (ii) the specific ECD response.

Then, the induction of chirality thought adsorption of achiral porphyrins with DNA

G-quadruplexes (e.g., Fig. 1b) is rationalized thanks to MD simulations. Interestingly,

experiments have exhibited an ECD response in the Soret region suggesting an induction of

chirality in the porphyrin core. MD simulations and first-principle calculations rationalized (i)

binding modes and (ii) porphryin deformations leading to an ECD response.

(a) (b)

15

Design and Study of Bio-Inspired Photoherbicide:

From Theory to Experiment

O. Rezazgui, P. Trouillas, S. Leroy-Lhez

1. Laboratoire de Chimie des Substances Naturelles, EA 1069, Université de Limoges,

123 avenue Albert Thomas, 87060 Limoges, France.

2. INSERM UMR-S850, Faculté de Pharmacie, Université de Limoges,

2 rue du Dr.Marcland, 87025 Limoges, France.

It is of utmost importance to prevent contamination of the environment of Earth's surface and of

groundwater. For this purpose, bio-inspired herbicides (e.g., porphyrins) are promising

alternative to the currently used toxic compounds.

To evaluate their biological effects in plants, the new herbicides must be tracked along plant

organs. To do so, the porphyrin herbicide can be associated with a fluorescent tag. This

molecular association needs to be achieved by a linker, which must be carefully chosen.

The linker is critical in the 3D arrangement of the corresponding molecular assembly

porphyrin-linker-fluorophore. DFT (density functional theory) calculations were performed to

evaluate conformational folding. Non-covalent interactions, in particular π-stacking, play a

crucial role in this case, therefore the use of DFT functionals including dispersion (DFT-D)

appeared mandatory. Solvent effects were taken into account implicitly, using PCM (polarizable

continuum model). This preliminary work has led to the selection of some linkers; as well to the

molecular assembly associated synthesis.

From the conformational analysis, the excited states (ES) were characterized by TD (time

dependent)-DFT calculations. UV absorption properties were thus rationalized based on the

molecular orbital scheme, showing the electronic transitions involved in the relevant ES. The

theoretical predictions seem to correlate experimental photo-physical evaluations. The

fluorescence emission analysis has highlighted energy transfer, which is in favor of the folded

conformer.

16

Capless HDAC Inhibitors: Molecular Modelling Reveals

the Structural Determinants of Their Selectivity Toward HDAC6

Benjamin Greniera,b, Nathalie Deschampsb, Carolina Dos Santos Passosb,

Alessandra Nurissob, Pierre-Alain Carruptb,

aCentre Interdisciplinaire de Nanoscience de Marseille (CINaM), UPR 3118 CNRS, Aix-Marseille Université,

Campus de Luminy, Case 913, F-13288 Marseille cedex 09, France bSchool of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, Quai Ernest-Ansermet,

CH-1211, Geneva, Switzerland

The development of selective histone deacetylase 6 (HDAC6) inhibitors is considered a

challenge not only for the conception of new biological probes but also for the development of

new drug candidates against aging-related and cancer diseases1, 2

. Recently, hydroxamic acid

derivatives without the surface-binding motif, a typical pharmacophoric element present in all

HDAC inhibitors, demonstrated the ability to preferentially inhibit HDAC6 rather than other

isoforms in vitro3. Here, a structural rationalization of such selectivity was carried out.

Comparison between the structural architecture of HDAC2 and HDAC6 catalytic domains

highlighted important areas of diversity. Indeed different pocket shapes are presented by these

two isoforms (Fig.1).Molecular docking and molecular dynamics simulations of three “cap” and

two “capless” compounds showed that HDAC6 selective compounds (an example is represented

in Fig.2) were in interaction by hydrogen bonds and hydrophobic interactions with His 500, Pro

608 and Val 650 HDAC6 residues. These interactions were not observed in HDAC2. So the

pocket size together with the presence of these three residues may be the responsible of the

observed HDAC6 selectivity.

Fig.1 Pocket comparison between

HDAC2 and HDAC6 active site in

gray and green respectively.

a, b, c and d highlight the four

active site areas.

Fig.2 An example of HDAC6

selective ligand, represented in

ball and stick with carbon in gray,

nitrogen in blue and oxygen in

red.

References

[1] Simões-Pires C, Zwick V, Nurisso A, Schenker E, Carrupt PA, Cuendet M (2013) HDAC6 as a target for

neurodegenerative diseases: what makes it different from the other HDACs? Mol Neurodegen 8: 1-16

[2] Yang P, Zhang L, Zhang Y, Zhang J, Xu W (2013) HDAC6: Physiological function and its selective inhibitors for

cancer treatment. JDDT 7: 233-24

[3] Wagner FF, Olson DE, Gale JP, Kaya T, Weïwer M, Aidoud N, Thomas M, Davoine EL, Lemercier BC, Zhang

YL, Holson EB (2013) Potent and selective inhibition of histone deacetylase 6 (HDAC6) does not require a

surface-binding motif. J Med Chem 56: 1772-1776

17

Oxidative Stress in Biological Lipid Membranes: The Influence of Electric Field

Antonio Monari

Theory-Modeling-Simulation, Université de Lorraine- Nancy and CNRS, France

The presence of reactive oxygen species (ROS) is the most common source of oxidative stress

that can be directed toward many biological macromolecules such as protein, nucleic acids or

lipid membranes. The presence of reactive radicals and ROS and the related oxidative processes

are connected with many relevant diseases such as inflammatory processes but also

carginogenesys, neurodegenerative disorder or aging. Experimental evidences exist that

biological membranes or artificial liposomes experience an enhanced oxidation when exposed to

an electric field. This exposition can result as an effect of novel therapeutic protocols

(electroporation) as well as by the effect of low energy oscillating electro-magnetic fields. In this

contribution we will analyze by using molecular dynamic and ab-initio molecular QM/MM

techniques the reactivity of insaturated lipids inn membrane bilayers. The most relevant

oxidation path will be analyzed as well as the influence of electric field in assuring the catalytic

effects. Our findings allow not only to clarify a fundamental biological process, but also to infer

on the role of electromagnetic pollution and to devise a rational molecular design of enhanced

antioxidants.

References

[1] N. A. Porter J. Org. Chem. 2013 78, 3511

[2] M. Macarone, N. Rosato, A. Finazzi Agro Biochem. Biophys. Res. Comm. 1995, 1, 238

[3] J. Garrec, A. Monari, X. Assfeld, L. M. mir, M. Tarek J. Phys. Chem. Lett. 2014 5, 1653

18

Environment Effects on the Spectra of Polycyclic Organic Molecules

Martin Kubala

Dept. of Biophysics, Faculty of Science, Palacký University in Olomouc, Czech Republic

The π -conjugated molecules can be examined in UV/VIS spectroscopy experiments. Although

spectroscopic data usually do not allow direct visualization of the molecular structure, numerous

parameters can be compared to molecular models. The recorded spectrum reflects both the

structure of the examined molecule itself as well as its interaction with other surrounding

molecules, in particular solvent molecules, ligands or macromolecules.

Measurement of absorption and emission spectra in various solvents can yield important

information about the examined molecule. They can concern the molecule itself, such as isomer

identification, characterization of the type of electronic transition (π→π* or n→π*) or

protonation state, or sensitivity to the environmental factors such as polarity or hydrogen

bonding. These observations can be used in further studies examining interaction of small π-conjugated molecules with large biopolymers such as nucleic acids or DNA. Correlation of the

spectroscopic data to some parameters obtained from molecular models can help to

understanding the structural details

19

Investigation of Antiradical and UV/Vis Absorption Properties of

Flavonolignans

Michal Bilera, b, Patrick Trouillasb,c, Martin Kubalaa, Vladimir Krend,

Jan Vaceke

a Department of Biophysics, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacký

University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic b INSERM UMR-S850, Univ. Limoges, School of Pharmacy, University de Limoges, 2 rue du Docteur Marcland,

87 025 Limoges, France c Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic d Institute of Microbiology, Laboratory of Biotransformation, Academy of Sciences of the Czech Republic,

Vídeňská 1083, 142 20 Prague, Czech Republic e Department of Medical Chemistry and Biochemistry, Faculty of Medecine and Dentistry, Palacký University,

Hněvotínská 3, 775 15 Olomouc, Czech Republic

Polyphenols are π-conjugated systems containing phenolic OH groups and many of them exhibit

free radical scavenging properties and other protective effects against oxidative stress. Density

functional theory (DFT) has been widely used to elucidate the role of the different OH groups of

polyphenols as radical scavengers. Here we have studied the O-H bond dissociation enthalpies

(BDEs) of a series of flavonolignans (silybin, silychristin, silydianin and their

dehydro-derivatives), which correlate to their capacity to scavenge the DPPH free radical and

cyclic voltammetry results. The spatial spin density distribution is a secondary quantum

descriptor, which accounts for extension of the π-conjugated path and allows rationalization of

the antiradical action.

The theoretical investigation of UV/Vis absorption properties enables a full physical-chemical

characterization of this series of compounds. The experimental measurements were performed in

the Britton-Robinson buffer (pH 2–12). The non-dehydroforms of the flavonolignans exhibit two

main peaks (i) ca. 288 nm with a hypochromic effect vs. pH increase, and (ii) ca. 326 nm with a

hyperchromic and hypsochromic shift vs. pH increase. On the other hand, the absorption spectra

of the dehydro-flavonolignans are bathochromic shifted vs. pH increase. The neutral and

deprotonated forms of the molecules were predicted by TD-DFT, using the B3P86 and

CAM-B3LYP functionals. Overestimation and underestimation of the spectral shifts between the

neutral and deprotonated form are observed with B3P86 and CAM-B3LYP, respectively. Finally,

electronic transitions between molecular orbitals were assigned to each peak of interest.

Acknowledgment

This work was supported by grant no. L01204 National program of Sustainability I, by grant IGA_PrF_2014_029

from Palacky University in Olomouc, and by the French embassy, which financially supports my cotutelle Ph.D.

program.

20

Excited State Dynamics

in Mixed Stack Donor-Acceptor Charge Transfer Co-Crystals

Santanu Bhattacharyyaa, Sang Kyu Parkb, SooYoung Parkb, Larry Luera,

Johannes Gierschnera

a) Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Ciudad Universitaria de

Cantoblanco, 28049 Madrid, Spain

b) Center for Suprameolcular Optoelectronic Materials and WCU Hybrid Materials Program, Department of

Materials Science and Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744, Korea

Solid state organic semiconductors have gained much attention in modern material research due

to applications in optoelectronics, such as organic light emitting diode (OLED), field effect

transistors (OFET’s), photovoltaics (OPV) etc. For many applications, ambipolar transport is

desired [1]

for which charge transfer (CT) complexes consisting of donor (D) and acceptor (A)

molecules were identified as potential materials. [2]

The field was recently pushed by a novel

approach using mixed stack DA CT co-crystals consisting of isosteric D = distrylbenzene and A

= dicyanodistrylbenzene molecules, providing balanced charge transport and surprisingly

efficient deep red CT luminescence,[3]

which further caught our attention. Keeping in mind that

CT states strongly impact the state ordering of the singlet & triplet manifolds, [4]

we here further

investigate the excited state dynamics in both single- and poly-crystalline samples by ultrafast

time resolved spectroscopy and quantum chemical calculations.

The strong frontier MO offset and close -stacking of the alternatively packed D, A molecules

affect significantly fundamental optical and electronic properties. Strongly red-shifted absorption

and emission are assigned to a strong, low lying CT band, while the main absorption originates

from the D-localized S0S3 transition Pumping in S3, the relaxation to the CT states (S1, S2) is

relatively slow due to the large S3-S2 energy difference. Emission from S1 is non-exponential,

exhibiting a long component of 200 ns. The latter is ascribed to thermally activated delayed

fluorescence (TADF), originating from T1 due the small S-T gap as generated by the large CT

character of the lowest excited state. At high laser flux, emission at em is effectively quenched

by singlet-singlet annihilation due to the high excited state density at em as generated by the

strong DA -overlap, preventing lasing. Our studies suggest this DA system as the first

example of highly efficient, intermolecular TADF emitter, which might be an interesting new

route for triplet harvesting in OLEDs.

References

[1] V. Coropceanu, J. Cornil, D. A. da Silva Filho, Y. Olivier, R. Silbey, J.-L. Brédas, Chem. Rev. 2007, 107,

926-952

[2] Zhu, L.; Yi, Y.; Li, Y.; Kim, E.-G.; Coropceanu, V.; Brédas, J.-L. J. Am. Chem. Soc. 2012, 134, 2340

[3] S. K. Park, S. Varghese, J. H. Kim, S.-J. Yoon, O. K. Kwon, B.-K. An, J. Gierschner, S. Y. Park, J. Am. Chem.

Soc. 2013, 135, 4757.

[4] B. Milián-Medina, J. Gierschner, Org. El. 13 (2012) 895

[5] S. Bhattacharyya, S. Kyu Park, S. Varghese, S. Y. Park, Larry Luer, J. Gierschner, in preparation

21

Electronic Ferroelectricity and Magnetoelectric Phenomena

in Mixed-stack Charge Transfer Crystals

Gabriele D’Avino1,2, Matthieu J. Verstraete1

1Physics Department, University of Liège and ETSF, Belgium

2Laboratory for Chemistry of Novel Materials, University of Mons, Belgium

Mixed-stack charge transfer (CT) crystals (e.g. TTF-CA, TTF-BA) are a spectacular example of

multifunctionality among organics materials. In these quasi-1D systems, featuring alternating

π-stacked electron donor (D) and acceptor (A) molecules (…DADA…), the entanglement of

charge, spin and lattice degrees of freedom leads to ferroelectric phases with an exceptionally

strong electronic polarization, magnetoelectric effects, and photoinduced phase transitions

triggered by multiexcitonic phenomena.

We present a theoretical investigation of the ferroelectricity of mixed-stack CT crystals, based on

the Peierls-Hubbard model [1] and first-principles calculations for its parame- trization. This

approach is first validated by reproducing the temperature-induced transition of TTF-CA and

TTF-BA, and then applied to a novel series of hydrogen- bonded CT crystals, for which room

temperature ferroelectricity has recently been claimed [2]. Our analysis shows that the

hydrogen-bonded systems present a very low degree of CT and hence support a negligible

polarization [3]. A critical reexamination of experimental data supports our findings, shedding

doubts on the ferroelectricity of these systems. The qualitative differences between the transition

of TTF-CA and TTF-BA, the coexistence of electrical polarization and antiferromagnetic order,

and the magnetic-field control over ferroelectricity will be also discussed.

References

[1] G. D’Avino et al., Phys. Rev. Lett. 99, 156407 (2007); G. D’Avino et al., Phys. Rev. B 83, 161105R (2011)

[2] A. Tayi et al., Nature 488, 485 (2012)

[3] G. D’Avino and M. Verstrate, Phys. Rev. Lett., accepted (2014)

22

Charge Transport in π-conjugated Polymers:

A Combined Classical-Quantum Approach

to Establish Structure-Property Relationships

Y. Olivier, V. Lemaur, R. Lazzaroni, D. Beljonne, J. Cornil

University of Mons, Belgium

Organic conjugated polymers have attracted an increasing interest over the years for use in

organic opto-electronic devices such as light-emitting diodes, solar cells, or field-effect

transistors as a result of their low cost, light weight and ease of processing from solution. One of

the main challenges to improve the efficiencies of opto-electronic devices is to get a deep

understanding, at the molecular scale, of the charge transport properties of the organic layer.

Indeed, charge transport is known to be very sensitive to the relative position of the molecules in

the organic layer [1]. Based on quantum-chemically parameterized force fields, the

supramolecular organization of p- and n-type conjugated polymers has been investigated [2-5].

The efficiency of charge transfer has then been estimated through the use of the Marcus theory

by evaluating, at the quantum-chemical level, the main parameters governing charge transport,

i.e., the reorganization energies and intermolecular hopping transfer integrals. This strategy

provides a deep insight into structure-property relationships of organic conjugated compounds in

the solid state and paves the way towards the design of a new generation of materials with

enhanced charge transport properties.

References

[1] J.L. Brédas, J.P. Calbert, D.A. da Silva Filho, J. Cornil, PNAS 2002, 99, 5804.

[2] P. Brocorens, A. Van Vooren, M.L. Chabinyc, M.F. Toney, M. Shkunov, M. Heeney, I. McCulloch, J. Cornil, R.

Lazzaroni, Adv. Mat. 2009, 21, 1193.

[3] D. Niedzialek, V. Lemaur, D. Dudenko, J. Shu, M.R. Hansen, J.W. Andreasen, W. Pisula, K. Müllen, J. Cornil, D.

Beljonne, Adv. Mat. 2013, 25, 1939.

[4] G.A.H. Wetzelaer, M. Kuik, Y. Olivier, V. Lemaur, J. Cornil, S. Fabiano, M.A. Loi, P.W.M. Blom, Phys. Rev. B

2012, 86, 165203.

[5] V. Lemaur, L. Muccioli, C. Zannoni, D. Beljonne, R. Lazzaroni, J. Cornil, Y. Olivier, Macromolecules 2013, 46,

8171.

23

Study of Blue Emitters Compounds for OLEDs

Using a New (TADF) Mechanism

M. Moral1, L. Muccioli2, Y. Olivier3, J. C. Sancho-García1

1Dpto. Química Física, Universidad de Alicante, 03080 Alicante, Spain

2Laboratoire de Chimie des Polymères Organiques, University of Bordeaux, 33607 Pessac, France

3Laboratory for Chemistry of Novel Materials, University of Mons, 7000 Mons, Belgium

Since the discovery of OLEDs (Organic Light Emitting Diode) almost two decades ago,

1 their

use have been extensively reported for the display fabrication of smartphones, screens and in

other solid-light emitting applications. In the last years, their efficiency have largely been

improved using metal (phosphorescence) emitters, with an external quantum efficiency reaching

up to 20%.2

Recently, a new mechanism called Thermally Activated Delayed Fluorescence (TADF) has been

promisingly investigated (see Figure 1) to increase the efficiency of OLEDs without resorting to

rare-earth metals. For the most efficient triplet-to-singlet conversion, and always dealing with

conjugated molecules, a small energy gap (ΔEST) between singlet (S1 state) and triplet

(T1 state) excitons is required, which is strongly connected with a large spatial separation

between the highest occupied (HO) and lowest unoccupied (LU) molecular orbital (MO).3,4

N

N N

NO

NO

O

N N

NO

NO

O

N N

NO

N

N N

NO

A

B

2-A

2-B

Figure 1: Energy diagram showing the main light

emitting process for OLEDs aplications.

Figure 2: Chemical structure of the molecule

studied.

In this work, aimed at rationalizing the underlying physical principle behind the TADF

mechanism and motivated by their experimental use as suitable candidates [5], we have

theoretically studied the use of a set of molecules containing electron-withdrawing (oxadiazole

and triazole) together with electron-donating (phenyl-phenoxazine) moieties (see Figure 2). Our

results help to understand the different behaviour of these candidate molecules in real device.5

References

[1] C.W. Tang and S.A. Vanslyke, Appl. Phys. Lett., 1987, 51, 913.

[2] C. Adachi, M.A. Baldo, M.E. Thompsono, S.R. Forrest, J. Appl. Phys., 2001, 90, 5048.

[3] M.Moral, L. Muccioli, W-J. Son, Y. Olivier, J.C. Sancho-García, JCTC, 2014, in press.

[4] J. Gierschner and B. Milian-Medina, Org. Electr. 13 (2012) 985.

[5] J. Lee, K. Shizu. H. Tanaka, H. Nomura, T. Yasuda, C. Adachi, J. Phys. Chem. C., 2013, 1, 4599.

∆EST

Singlet Excited

State (S1)

Triplet excited

state (T1)

Singlet Ground

State (S0)

FL

UO

RE

SC

EN

CE

PH

OS

PH

OR

ES

CE

NC

E

e- : h+

25 %

75 %

TA

DF

24

Charge Transport

in an Amorphous Triphenylamine-fluorene Copolymer

S. M. Gali1, G. D'Avino2,3, L. Muccioli1,3, C. Zannoni3,

T. Papadopoulos 4,5, Y. Yi4, V. Coropceanu4, J.-L. Brédas4,6

1 Laboratoire de Chimie des Polymères Organiques, Université de Bordeaux, France

2 Department of Physics, University of Liège, Belgium

3 Dipartimento di Chimica Industriale “Toso Montanari”, University of Bologna, Italy

4 School of Chemistry & Biochemistry, Georgia Institute of Technology, United States

5 Department of Engineering, University of Bolton, United Kingdom

6 Solar & Photovoltaic Engineering Research Center, KAUST, Saudi Arabia

The alternate copolymer poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4′-(N-(4-sec- butylphenyl))

diphenylamine, also known as TFB, is widely used as hole transporting and electron blocking

polymer layer in OLEDs, and also constitutes a model system for more fundamental studies [2],

because of its rather good semiconducting properties and its ease of processing. Actually,

discovering the microscopic origin of its hole mobility [3], surprisingly high for an amorphous

system, and possibly learning some lessons applicable to other amorphous system, is the main

objective of this computational study. We first customized a united-atom force field adapt to

model TFB, and then used it to produce the morphology of bulk TFB pentamers at room

temperature with molecular dynamics simulations. Then we evaluated the charge transport

parameters (electronic coupling and reorganization energies) with semiempirical calculations

along the simulation trajectory, and injected them in a kinetic Monte Carlo scheme to evaluate

the charge carrier mobility [4]. In this talk, we will compare the results produced by

Miller-Abrahams and Marcus kinetic models, and discuss the physical and chemical origins of

TFB hole mobility.

References

[1] A. W. Hains, T. J. Marks, Appl. Phys. Lett. 92, 023504 (2008); L.-P. Lu, D. Kabra, K. Johnson, R. H. Friend, Adv.

Funct. Mater 22, 144. (2012)

[2] A. Bruno, L. X. Reynolds, C. Dyer-Smith, J. Nelson, S. A. Haque, J. Phys. Chem. C 117, 19832 (2013)

[3] H. H. Fong, A. Papadimitratos, G. G. Malliaras, Appl. Phys. Lett. 89, 172116 (2006); R. U. A. Khan, D.

Poplavskyy, T. Kreouzis, D. D. C. Bradley, Phys. Rev. B 75, 035215 (2007)

[4] Y. Olivier, L. Muccioli, V. Lemaur, Y. H. Geerts, C. Zannoni, J. Cornil, J. Phys. Chem. B, 113, 14102 (2009)

25

The Origin of Photoluminescence from

Oxygen Containing Graphene Nanoflakes:

A TDDFT Approach

Sunandan Sarkar, Michal Otyepka

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry,Faculty of Science,

Palacky University, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic

Over the recent years, the intensive research of graphene,1 chemically derived graphene

nanoflakes (GNFs) have attracted great interest due to the candidate status instead of graphene in

the aspects of facile synthesis and potential applications.2,3

The large optical absorptivity and

widely tunable band gap of GNFs makes them promising nanomaterials for optoelectronic

devices.4 To improve the performance in optical devices, functionalization of GNFs is an

important way which controls the interaction between the GNFs and the other active components

in the devices. One of the functionalized form is graphene oxide nanoflakes (GONFs), which

consists of various types of oxygen-containing functional groups on the basal plane and at the

edge sites allow to serve as building blocks of the complex carbon based nanomaterials such as

graphene oxides (GOs) and carbon dots (CDs).5,6

Due to the irregular and inhomogeneous

structure, the origin of the photoluminescence (PL) properties of both GOs and CDs materials is

now an important topic of discussion.5-8

Despite the plenty endeavour on the PL properties of the

oxygen containing complex carbon nanomaterials, theoretical studies addressing the optical

properties are scarce. Here we present a systematic investigation on the optical properties from

oxygen containing GNFs using time dependent density functional theory (TDDFT) which could

be a possible description of the origin of PL behaviour from the complex carbon nanomaterials.

References

[1] Novoselov, K. S.; Geim, A. K.; Morozov, S. V.; Jiang, D.; Katsnelson, M. I.; Grigorieva, I. V.; Dubonos, S. V.;

Firsov, A. A. Nature 2005, 438, 197-200.

[2] Pan, D. Y.; Zhang, J. C.; Li, Z.; Wu, M. H. Adv. Mater. 2010, 22, 734-738.

[3] Yan, X.; Cui, X.; Li, L. S. J. Am. Chem. Soc. 2010, 132, 5944-5945.

[4] Zhu, S. J.; Tang, S. J.; Zhang, J. H.; Yang, B. Chem. Commun. 2012, 48, 4527-4539.

[5] Eda, G.; Chhowalla, M. Adv. Mater. 2010, 22, 2392-2415.

[6] Baker, S. N.; Baker, G. A. Angew. Chem., Int. Ed. 2010, 49, 6726-6744.

[7] Loh, K. P.; Bao, Q.; Eda, G.; Chhowalla, M. Nature Chemistry 2010, 2, 1015-1024.

[8] Bourlinos, A. B.; Stassinopoulos, A.; Anglos, D.; Zboril, R.; Georgakilas, V.; Giannelis, E. P. Chem. Mater. 2008,

20, 4539-4541.

26

Exciton Simulations:

From Liquid Crystals to Porphyrin-CNT Aggregates

Micaela Matta1,2, Francesco Zerbetto1

1 Dipartimento di Chimica ”G. Ciamician”, Università di Bologna, Italy

2 Laboratoire de Chimie des Polymères Organiques, UMR 5629, Université de Bordeaux, France

The photophysical behaviour of π-interacting molecular aggregates depends on several factors,

such as: i) the aggregate size, ii) the degree of order, iii) the environment. In order to fully

characterize these systems it is often necessary to employ a joint theoretical and experimental

approach.

In this regard, an algorithm[1]

for the simulation of exciton dynamics has been implemented and

used to reproduce the spectroscopical features of different self-organized systems with

applications in organic photovoltaics. It has been employed successfully to reproduce the

emission spectrum of substituted oligo-phenyleneethynylene (OPE) liquid crystals[2]

, which

presents a strong red shift due to both excimer formation and aggregation in the solid state. The

model has been also adapted to describe the absorption spectrum of protonated porphyrins

(H4P2+

) and carbon nanotubes (CNTs) aggregates[3]

, that is characterized by the simultaneous

presence of H- and J-aggregate bands.

References

[1] L. K. Gallos, A. V. Pimenov, I. G. Scheblykin, M. Van der Auweraer, G. Hungerford, O. P. Varnavsky,

A. G. Vitukhnovsky and P. Argyrakis, J. Phys. Chem. B, 104 (2000), 3918-3923.

[2] K. Toth, J. K. Molloy, M. Matta, B. Heinrich, D. Guillon, G. Bergamini, F. Zerbetto, B. Donnio, P. Ceroni and

D. Felder-Flesch, Angew. Chem. Int. Ed. 52 (2013), 12303-12307.

[4] T. Hasobe, S. Fukuzumi and P. V. Kamat, J. Am. Chem. Soc. 127 (2005), 11884-11885.

[5] T. Hasobe, S. Fukuzumi and P. V. Kamat, J. Phys. Chem. B, 110 (2006), 25477-25484.

27

Tuning the Electronic Properties in Benzochalcogenodiazole-Based

D−A Type Copolymers by Heteroatom Substitution

M. Carmen Ruiz Delgado,1 D. Herrero-Carvajal,1 G.L. Gibson,2

D.S. Seferos,2 J.T. López Navarrete1

1Department of Physical Chemistry, University of Málaga, Spain

2Lash Miller Chemical Lab, Department of Chemistry, University of Toronto, Canada

Donor−acceptor (D−A) approach to conjugated polymer design has become a widely used

method for preparing conjugated polymers with narrow band gaps.1 One outstanding D−A

polymer is poly(cyclopentadithiophene)benzothiadiazole, PCPDTBT (P1 in Figure 1), for which

power conversion efficiencies in solar cells of 4.5-5.5% are reported.2 In this work, we use

resonance Raman (RR) and density functional theory (DFT) calculations to investigate the tuning

of the electronic and structural properties of cyclopentadithiophene-benzochalcogenodiazole

D−A polymers, wherein a single atom in the benzochalcogenodiazole unit is varied from sulfur

to selenium to tellurium (Fig. 1).3 By analyzing the enhancement pattern in the RR spectra using

Raman excitation wavelengths coincident with the various transitions in the copolymers, it was

possible to describe excited state geometric distortion, which in turn is used to define the nature

of the electronic excitation. These experimental findings are corroborated by DFT calculations

using long-range corrected functionals, considering both tuned and default range-separation

parameters.

Figure 1. D-A copolymers under study. Their synthesis are reported In Ref. 4

References

[1] (a) P. M. Beaujuge, C. M. Amb, J. R. Reynolds, Acc. Chem. Res. 2010, 43, 1396−1407; (b) X. Guo, M.D. Watson,

Macromolecules 2011, 44, 6711−6716.

[2] (a) S. Albrecht, S. Janietz, W. Schindler, J. Frisch, J. Kurpiers, J. Kniepert, S. Inal, P. Pingel, K. Fostiropoulos, N.

Koch, D.J. Neher, J. Am. Chem. Soc. 2012, 134, 14932−14944; (b) F. S. U. Fischer, K. Tremel, A. K. Saur, S. Link,

N. Kayunkid, M. Brinkmann, D. Herrero-Carvajal, J.T. López Navarrete, M.C. Ruiz Delgado, S. Ludwigs,

Macromolecules 2013, 46, 4924-4931.

[3] D. Herrero-Carvajal, G. L. Gibson, D. S. Seferos, S. Salman, V. Hernández, J.T. López Navarrete, M. Carmen

Ruiz Delgado, in preparation

[4] G. L. Gibson, T. M. McCormick, D. S. Seferos, J. Am. Chem.Soc. 2012, 134, 539−547.

28

ABSTRACTS

Posters

29

Optical Properties of

π-conjugated Azo Derivatives and Related Conformational Features

Petra Čechováa, Patrick Trouillasb,c, Martin Kubala,a Bruno Therriend

a Department of Biophysics, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacký

University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic b INSERM UMR-S850, Univ. Limoges, School of Pharmacy, University de Limoges, 2 rue du Docteur Marcland,

87 025 Limoges, France c Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic d Institute of Chemistry, University of Neuchatel, Ave de Bellevaux 51, CH-2000 Neuchatel, Switzerland

Bipyridines may be used to synthetize Ru-cationic metallarectangles. The specific molecular

structure of these rectangles provides various biological activities including antiproliferative

effects (on A2780 ovarian cancer cells).1 Bipyridines derivatives can exist in their E- or Z-

forms. The E→Z transformation is induced by UV light. Various other linkers can be envisaged

(azo derivatives) to synthetized metallarectangles, for which this transformation must be

perfectly rationalized. Time-dependent density functional theory (TD-DFT) has been widely

used to study the opto-electronic properties of π-conjugated compounds. A series of symmetrical

pyridyl and benzyl derivatives was studied for their conformational features in the E- and Z-

forms, with respect to UV-light absorption. The comprehensive evaluation of potential energy

surfaces in ground state (GS) and excited states (ES) has been initiated for two relevant

prototypes, namely azobenzene and 4,4'-azopyridine. The E→Z transformation is likely and

unlikely for the former and the latter compound, respectively. Significant differences in UV/Vis

absorption spectra were observed, which is discussed in terms of electronic transitions between

the molecular orbitals involved in the GS→ES transition.

Figure: Chemical structures of 4,4'-azopyridine (right) and azobenzene (left)

References

[1] J. Mattsson, P. Govindaswamy, A. K. Renfrew, P. J. Dyson, P. Štĕpnička, G. Süss-Fink, B. Therrien,

Organometallics 28 (2009), 4350

Acknowledgments:

This work was supported by grant no. L01204 National program of Sustainability I, and by grant

IGA_PrF_2014_029 from Palacky University in Olomouc

30

Modeling the Electronic Circular Dichroism of DNA and

Photosensitized DNA

Hugo Gattuso, Xavier Assfeld, Antonio Monari

Université de Lorraine, Théorie-Modélisation-Simulation, SRSMC UMR 7565, Vandoeuvre-Lès-Nancy, France

CNRS, Théorie-Modélisation-Simulation, SRSMC UMR 7565, Vandoeuvre-Lès-Nancy, France

The modeling of DNA photochemistry and its interactions with photosensitizers have recently

gained interest because it allows the understanding of DNA photodegradation processes.

Moreover photosensitization can be exploited for cancer treatment or simply DNA probing. One

of the key aspects that need to be better characterized are the specific modes with whom

sensitizers interact with DNA as well as the structural modifications induced in its global

structure.

To do so, we studied the electronic circular dichroism (ECD) of two types of B-DNA, the

poly(d[AT]) and poly(d[CG]) double strands, with and without photosensitizers and we

compared the evolution occurring in the spectra. ECDs were simulated using the Frenkel exciton

theory and the conformational space was explored using classical molecular dynamics. Excited

states were obtained using QM/MM methods at the TD-DFT level of theory.

31

Are Waters Around RNA More Than Just a Solvent? – An Insight from

Molecular Dynamics Simulations

Petra Kührová,1 Michal Otyepka,1,2 Jiří Šponer,2,3 and Pavel Banáš*1,2

1 Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacky University, tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic

2 Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech

Republic

3 CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech

Republic

Hydrating water molecules are believed to be an inherent part of the RNA structure and have a

considerable impact on RNA conformation. However, the magnitude and mechanism of the

interplay between water molecules and the RNA structure are still poorly understood. In

principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our

recent MD studies,(1, 2) we observed that the choice of water model has a visible impact on

the predicted structure and structural dynamics of RNA, and in particular, has a larger effect than

type, parameterization and concentration of the ions. Furthermore, the water model effect is

sequence dependent and modulates the sequence dependence of A-RNA helical parameters.

Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a

rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless

suggest that the sequence dependence of the A-RNA structure, usually attributed to base stacking,

might be driven by the structural dynamics of specific hydration. Here, we present a systematic

MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity, and

(ii) discover whether and to what extent specific hydration modulates the A-RNA structural

variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes

with TIP3P,(3) TIP4P/2005,(4) TIP5P(5)and SPC/E(6) explicit water models and found that

different water models provided a different extent of water bridging between 2’-OH groups

across the minor groove, which in turn influences their distance and consequently also

inclination, roll and slide parameters. Minor groove hydration is also responsible for the

sequence dependence of these helical parameters.

References

[1] I. Besseova et al., Phys Chem Chem Phys 11, 10701 (2009).

[2] I. Besseova et al., J. Phys.Chem. B 116, 9899 (Aug 23, 2012).

[3] W. L. Jorgensen et al., Journal of Chemical Physics 79, 926 (1983).

[4] J. L. F. Abascal et al., J Chem Phys 123, (Dec 15, 2005).

[5] M. W. Mahoney et al., J Chem Phys 112, 8910 (May 22, 2000).

[6] H. J. C. Berendsen et al., J Phys Chem 91, 6269 (Nov 19, 1987).

32

The Strength of Noble Metal-Graphene Interaction

Petr Lazar

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacky University, tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic

We present a combined theoretical and experimental study of the noble metal-graphene

interactions. We studied the adsorption of Au, Ag, Cu, and Pd atoms and small clusters on

graphene using the density functional theory including the exact exchange (EE) and

non-empirical van der Waals (vdW-DF) corrections. We measured the strength of

metal-graphene interaction using dynamic atomic force microscopy with probes coated by

various metals. The combination of advanced AFM technique measuring forces at ambient

conditions with the density functional theory calculations enabled us to i) quantify the interaction

force between metalized AFM tips and graphene, and ii) test to the possibility of AFM-based

identification of derivatives of graphene (fluorographene, graphene oxide).

33

Lipid Enhanced Exfoliation for Production of Graphene Nanosheets

M. Pykal,† K. Šafářová,† K. Machalová Šišková,† P. Jurecka,†

A. B. Bourlinos,‡ R. Zbořil,† M. Otyepka†

†Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacký University Olomouc, 17. Listopadu 12, 771 46 Olomouc, Czech Republic ‡Physics Department, University of Ioannina, 45110 Ioannina, Greece

Liquid-phase exfoliation of graphite is a widely used method to obtain graphene nanosheets, and

therefore the development of a simple and efficient exfoliation procedure remains challenging.

Here, we present a one-step method of graphene exfoliation in lecithin/chloroform solution. The

graphene nanosheets produced by the lecithin assisted exfoliation method were analyzed by

microscopy techniques, including statistical analysis of atomic force microscopy images and

Raman spectroscopy, which both indicate the presence of few-layer graphene nanosheets,

including substantial content of three-layer sheets. Molecular dynamics simulations on the time

scale of 0.5+ μs suggested that stability of the obtained colloid might originate from formation

of lecithin reverse hemimicelles and micelles, which prevent the aggregation of exfoliated

graphene flakes by entropic repulsion of the lipid hydrophobic chains.

34

Solid State Luminescence Enhancement in Dicyano-Distyrylbenzenes:

Intra- and Intermolecular Contributions

Junqing Shi,1 Seong-Jun Yoon,2 Sang Kyu Park,2 Soo Young Park,2

Shinto Varghese,1 Begoña Milián-Medina,1 Johannes Gierschner1

1 Madrid Institute for Advanced Studies - IMDEA Nanoscience, Madrid, Spain

Tel: +34 912998765 E-mail: shi.junqing@imdea.org 2 Center for Supramolecular Optoelectronic Materials, Department of Materials Science and Engineering, Seoul

National University, Seoul, South Korea

Within the last few decades, aggregation-induced enhanced emission (AIEE) of conjugated

organic compounds has drawn much attention, in particular due to applications in

optoelectronics.[1]

However, the mechanism is not yet fully elucidated, being a complex

synergetic process determined by both intra- and intermolecular factors.[2,3]

Hence, gaining

deeper insights into the AIEE mechanism is highly beneficial towards targeted design strategies

for optoelectronic applications.

We investigate here structure–property relationships of functionalized dicyano-distyrylbenzenes

(DCS, Fig. 1), being a AIEE prototype material. Intra- and intermolecular factors are

elucidated independently both in solution and in the solid state through an integrative approach

combining steady-state and time-resolved fluorescence and pump-probe techniques with

computational methods.[4]

Our library of molecules with systematic variation of the

cyano-substituent position (α/β), the presence of additional alkoxy substituents in the central

and/or terminal phenyl rings, allows for systematic tuning of solution and solid state

luminescence properties, providing an in-depth understanding of the AIEE mechanism and

suggesting design strategies for highly effective functionalized DSB-based materials.[4]

Fig. 1: Functionalization of DSB

References

[1] (a) S.-J. Yoon et al, J. Am. Chem. Soc. 132 (2010) 13675. (b) X. Luo et al, J. Phys. Chem. C 116 (2012) 21967. [2] J. Gierschner et al, J. Phys. Chem. Lett. 4 (2013) 2686. [3] J. Gierschner, S. Y. Park, J. Mater. Chem. C 1 (2013) 5818. [4] J. Shi et al, in preparation.

35

Cytochrome P450 Oxidoreductase Simulations:

Cofactors Movement and Structural Changes

Martin Šrejber, Veronika Navrátilová, Karel Berka

Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, Czech Republic

The NADPH-dependent Cytochrome P450 oxidoreductase (CYPOR) is large 677 amino-acid

long microsomal multidomain enzyme responsible for electron donation to its redox partner

cytochrome P450 (CYP). Electron transfer chain is mediated by two riboflavin - based cofactors

flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) within their respective

domains and nicotinamide adenine dinucleotide phosphate (NADPH). During this electron

transfer CYPOR undergoes several structural changes in open and closed state of both domains

in different degree of contact. In spite of the fact that CYP-CYPOR complexes play a key role in

drug metabolism, no complete atomistic mechanism of structural rearrangements during

complex electron transfers has been described yet. Here we present the results of our preliminary

study on structural changes during CYPOR multidomain complex movement between individual

electron transfers using molecular dynamics (MD) simulations with cofactors of NADPH, FAD

and FMN in resting state.

Homology model of human CYPOR was embedded into pure dioleoylphosphatidylcholine

(DOPC) membrane composed of 250 lipids in each layer in several orientations. After system

equilibration, structural changes of protein, anchor and cofactor movement were studied. Anchor

did not move upper or deeper into the membrane, but we were able to suggest possible

CYPOR-membrane orientation which would allow interaction with cytochrome P450. As for the

internal motions - FMN and FAD cofactor remained in close van der Waals contact during the

100-ns long simulation stabilized by π stack interaction of FAD with Trp676, whereas continual

movement of NADPH weakens its π stack interaction with FAD. The results so far pointed on

the necessity of reparametrization of cofactors in various oxidation states in order to fully

comprehend the domain movements during whole electron transfer cycle.

36

Exciton Diffusion Measurements in DTS Derivatives

Shinto Varghese and Ifor D. W. Samuel

Organic Semiconductor Optoelectronics, School of Physics and Astronomy

University of St-Andrews, UK.

E-mail : sv26@st-andrews.ac.uk

Exciton diffusion is one of the basic process in the operation of organic optoelectronic devices

which needs to be understood and tuned to utilise the full potential of the device. In a bulk hetero

junction solar cell, the exciton formed in one component (donor) of the blend must diffuse to an

interface with the acceptor, at which the offset of the energy levels lead to charge separation.

Understanding organic solar cells therefore requires the understanding of exciton diffusion.1

Materials with long exciton diffusion lengths are appreciable as solar cell materials, as this will

ensure the excitons generated in the active layer reaches the interface and generate charges.

However the scenario is just the opposite in light emitting devices such as organic light emitting

diodes and laser. Long Exciton diffusion length is detrimental for the high efficiency as the

exciton can met another exciton in its lifetime and decay to ground state non-radiatively. This

process is called Exciton annihilation. This will reduce the efficiency of the device and is quiet

critical in the optoelectronic devices that works at very high exciton densities such as LASERs.

Exciton diffusion can be investigated by different methods however all the methods have its own

advantages and weakness. The methods we utilised for the determination of the exciton diffusion

lengths are volume quenching, surface quenching and exciton-exciton Annihilation.1,2

The

quenching efficiency will be monitored by the time resolved fluorescence measurements and

modelled to appropriate quenching model. Our investigation to a class of small molecule donor

which exhibits high efficiency bulk hetero junction solar cell will be presented in the poster.

References

[1] Ruseckas A., Shaw P. E., Samuel I. D.,W. Dalton Trans, 2009, 10040-10043.

[2] Ward A. J., Ruseckas, A., Samuel I. D. W.J. Phys. Chem C. 2012,116, 23931-23937.

37

Transition Fields in Organic Materials:

From Percolation to Inverted Marcus Regime.

A Consistent Monte-Carlo Method

Riccardo Volpi, Sven Stafström, Mathieu Linares

Department of Physics, Chemistry and Biology (IFM), Linköping University

ricvo@ifm.liu.se

In the last decades organic semiconductors, and in particular polymeric materials, have attracted

a huge interest among scientists. They are low cost to produce and exhibit peculiar

characteristics that can lead to new promising applications such as: organic light-emitting diodes

(OLED) and organic solar cells (OPV). Theoretical studies are very useful for the improvement

of such devices in terms of the understanding of their supramolecular organization and to help

the polymers design process. The intrinsic probabilistic nature of the conduction, together with

the structural disorder exhibited by these materials, render difficult an analytical expression of

the conductivity; however these aspects are instead suitable to be modeled in a Monte Carlo

simulation [1]. In this study we focus on the mobility dependence in organic materials for a

broad range of electric field strenghts. It is well known in literature that to analyze correctly this

field dependence, the spatial correlation effects in the energetic landscape has to be taken into

account [2-3]. We propose here a model suitable for an extended electric field range, [0,1.6e7]

V/cm. The mobility field dependence is not reducible to a single functional expression, such as

Poole-Frenkel [4], instead we have to take into account the existence of different operating

regions. In particular we identify the transition fields between these regions and explain their

physical origin. In principle, this allows us to characterize the mobility field dependence for any

organic material, changing the parameters in the transition fields equation. Monte-Carlo

simulations of holes hopping in disordered PPV are presented and analyzed to support our thesis.

References

[1] M. Jakobsson, M. Linares, S. Stafström. Monte Carlo simulations of charge transport in organic systems with

true off-diagonal disorder. J. Chem. Phys. 137, 114901 (2012)

[2] D. Dunlap, V. Kenkre, P. Parris. What is behind the √E J. Imag. Sci. and Tech. 43, 437 (1999)

[3] S. Novikov, A. Vannikov. Cluster Structure in the Distribution of the Electrostatic Potential in a Lattice of

Randomly Oriented Dipoles. J. Phys. Chem. 99, 14573 (1995)

[4] J. Frenkel. On Pre-Breakdown Phenomena in Insulators and Electronic Semi-Conductors. Phys. Rev. 54, 647

(1938).

38

Toward Improved Description of DNA Backbone

Marie Zgarbová,1 Michal Otyepka,1 Pavel Banáš,1 F. Javier Luque,2

Thomas E. Cheatham, III,3 Jiří Šponer,4 Petr Jurecka1

1Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science,

Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic 2Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona,

Avgda Diagonal 643, Barcelona 08028, Spain

3Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, United States

4Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech

Republic

e-mail: marie.zgarbova@upol.cz, petr.jurecka@upol.cz

Torsion parameters are known to strongly influence description of nucleic acids backbone in

molecular dynamics (MD) simulations. Recently, we have introduced a reparameterization of the

epsilon and zeta torsion parameters of the Cornell et al. force field, which relies on high-level

quantum-mechanical calculations and accounts for the conformation-dependent solvation effects

that are not covered by the standard explicit solvent models in MD simulations. Here we present

an exhaustive analysis of the performance of the refined parameters based on extended

molecular dynamics simulations for several representative systems. The results showed that the

epsilon/zeta refinement improves the backbone description of B-DNA double helices. The

resulting twist and sequence dependence is in better agreement with solution NMR data.

Furthermore, the parameters improved the description of groove widths and substantially

reduced the RMSD of the sugar-phosphate backbone as compared to the ff99bsc0 MD

simulations. The balance between populations of BI and BII backbone sub-states was shifted

towards the BII state, in better agreement with ensemble-refined solution experimental results.

Tests were also performed on other DNA structures, including DNA A-tracts, G-DNA and

Z-DNA. The refinement is suggested as a possible alternative to the current epsilon/zeta torsion

potential, which may enable more accurate modeling of nucleic acids.

39

Map for

Dinners and Lunches

Map of Olomouc with directions

Program

Thursday 5th

February 2015

19:00 Meeting at Holy Trinity Column (UNESCO), Horní náměstí, Olomouc

19:30 Dinner at Michalský Výpad restaurant, Blažejské náměstí 10, Olomouc

Friday 6th

February 2015 17. listopadu 12, Olomouc, room 3.003

Excited States of Conjugated Systems chair: Patrick Trouillas

8:00-8:15 Welcome

8:15-8:30 Gierschner Excited State Features and Dynamics in Conjugated Organic Materials

8:30-8:55 Milián-Medina MO and Excited State Design of Low Bandgap Copolymers

8:55-9:20 Wykes

Fluorescence in Distyrylbenzene Single-crystals: Interpreting the

Low-temperature Fine Structure via Atomistic Quantum Chemical

Franck-Condon Herzberg-Teller calculations

9:20-9:45 Knippenberg Simulations of Excited Electronic States and Photochemistry

9:45-10:00 Giussani On the Computation of Two-dimensional Electronic Pump-Probe Spectra

10:00-10:30 Coffee Break (3.002) + Posters (atrium 3rd

floor)

10:30-11:15 Nachtigallová Electronically Excited States of Nucleic Acid Bases: Computational

Study

11:15-11:40 Improta The Role of Charge Transfer Excited Electronic States in The

Photophysics and Photochemistry of DNA

11:40-12:05 Linares Electronic Circular Dichroism Spectra in Stacked Systems

12:05-12:30 Sancho-García Merging Non-local (van der Waals) Corrections with Double-Hybrid

Density Functionals

12:30-14:00 Lunch (3.002)

13:15-14:00 Committee Meeting (3.031)

Conjugated Systems in Biology chair: Michal Otyepka

14:00-14:45 Šponer Nature and Magnitude of Aromatic Base Stacking in Nucleic Acids

14:45-15:10 Di Meo Induced Chirality in Porphyrins: Self-Assembly and Systems of Biological

Interest

15:10-15:35 Rezazgui Design and Study of Bio-Inspired Photoherbicide: From Theory to

Experiment

15:35-16:00 Grenier Capless HDAC Inhibitors: Molecular Modelling Reveals the Structural

Determinants of Their Selectivity Toward HDAC6

16:00-17:00 Coffee Break (3.002) + Posters (atrium 3rd

floor)

17:00-17:25 Monari Oxidative Stress in Biological Lipid Membranes: The Influence of Electric

Field

17:25-17:50 Kubala Environment Effects on the Spectra of Polycyclic Organic Molecules

17:50-18:15 Biler Investigation of Antiradical and UV/Vis Absorption Properties of

Flavonolignans

18:15-18:30 Concluding Remarks of the Day

19:00 Dinner at Moravská restaurant, Horní náměstí 23, Olomouc

Saturday 7th

February 2015 17. listopadu 12, Olomouc, room 3.003

Conjugation in Material Science chair: Mathieu Linares

8:00-8:45 Jelínek What We Can Learn from High-Resolution AFM/STM Images:

Experiment and Theory

8:45-9:10 Bjattacharrya Excited State Dynamics in Mixed Stack Donor-Acceptor Charge Transfer

Co-Crystals

9:10-9:35 D'Avino Electronic Ferroelectricity and Magnetoelectric Phenomena in Mixed-stack

Charge Transfer Crystals

9:35-10:00 Olivier Charge Transport in π-conjugated Polymers: A Combined

Classical-quantum Approach to Establish Structure-Property Relationships

10:00-10:25 Moral Study of Blue Emitters Compounds for OLEDs Using a New (TADF)

Mechanism

10:30-11:00 Coffee Break (3.002) + Posters (atrium 3rd

floor)

11:00-11:25 Gali Charge Transport in an Amorphous Triphenylamine-fluorene Copolymer

11:25-11:50 Sarkar The Origin of Photoluminescence from Oxygen Containing Graphene

Nanoflakes : A TDDFT Approach

11:50-12:15 Matta Exciton Simulations: From Liquid Crystals to Porphyrin-CNT Aggregates

12:15-12:40 Carmen Ruiz

Delgado

Tuning the Electronic Properties in Benzochalcogenodiazole-Based D−A

Type Copolymers by Heteroatom Substitution

12:40-12:50 Concluding Remarks

13:30-16:00 Lunch at M3 restaurant, Masarykova třída 889/3, Olomouc (200 CZK)

List of Posters

Čechová Optical Properties of π-conjugated Azo Derivatives and Related Conformational

Features

Gattuso Modeling the Electronic Circular Dichroism of DNA and Photosensitized DNA

Kührová Are Waters Around RNA More Than Just a Solvent? – An Insight from Molecular

Dynamics Simulations

Lazar The Strength of Noble Metal-Graphene Interaction

Pykal Lipid Enhanced Exfoliation for Production of Graphene Nanosheets

Shi Solid State Luminescence Enhancement in Dicyano-Distyrylbenzenes: Intra- and

Intermolecular Contributions

Šrejber Cytochrome P450 Oxidoreductase Simulations: Cofactors Movement and Structural

Changes

Varghese Exciton Diffusion Measurements in DTS Derivatives

Volpi Transition Fields in Organic Materials: From Percolation to Inverted Marcus Regime.

A Consistent Monte-Carlo Method.

Zgarbová Toward Improved Description of DNA Backbone