here - Universität Leipzig

Transcription

Monday
09.02.2013
Tuesday
09.03.2013
Wednesday
09.04.2013
Material Science
Honored Guest Day
Life Science
08:00
08:15
08:30
08:45
09:00
Registration
09:15
09:30
Teodoro Laino
09:45
10:00 Opening Ceremony of CPMD 2013
10:15
Matthias Scheffler
10:30
10:45
Nicola Marzari
11:00
Evert Jan Meijer
11:15
11:30
coffee break
coffee break
11:45
12:00
Alfredo Pasquarello Jochen Blumberger
12:15
12:30
Mark Tuckerman
Marialore Sulpizi
12:45
13:00
13:15
13:30
lunch break
lunch break
13:45
14:00
14:15
14:30
Stefan Wippermann
14:45
Thomas Lippert
15:00
Marcella Iannuzzi
15:15
15:30
Mauro Boero
15:45
Michiel Sprik
16:00
Carlo Pignedoli
16:15
16:30
coffee break
16:45
17:00
Bernd Meyer
17:15
Poster Session
17:30
Rochus Schmid
17:45
18:00
Ding Pan
18:15
18:30
18:45
19:00
19:15
19:30
19:45
20:00
Thursday
Friday
09.05.2013
09.06.2013
AIMD‐based Methods AIMD‐based Methods I
II
Ralph Gebauer
Rodolphe Vuilleumier
Carme Rovira
Simone Raugei
Juerg Hutter
Frank Uhlig
Alessandro Curioni
coffee break
coffee break
coffee break
Angelos Michaelides
Davide Branduardi
Brandon Wood
Xifan Wu
Jun Cheng
Wanda Andreoni
Patricia Hunt
lunch break
lunch break
Carlo Camilloni
Giovanni Bussi
Ursula Roethlisberger
Walter Thiel
Jens Dreyer
coffee break
Vittorio Limongelli
Jorge Kohanoff
coffee break
Giulia Rossetti
Gareth Tribello
Francesco Luigi Gervasio
Jeremy Palmer
Fabio Pietrucci
Conference Dinner
(till midnight)
Closing remarks
Abstracts of Talks
All talks are given in the
Large Lecture Hall
(“Arthur-Hantzsch-Hörsaal”)
Fakultät für Chemie und Mineralogie
Johannisallee 29
04103 Leipzig
Keynote Lecture
T.1
Quantum simulations in electrochemical environments
Nicola Marzari1
1
École Polytechnique Fédérale de Lausanne (EPFL)
I’ll present some of our recent methodological developments aimed at performing firstprinciples simulations in realistic electrochemical environments - i.e. in the presence
of a complex environment that can include a liquid solvent, [1] a dissociated electrolyte
and an applied electrochemical potential, [2] and varying pH. [3]
Work done in collaboration with O. Andreussi (U. of Pisa), I. Dabo (Penn State), N.
Bonnet (AIST Tsukuba), and C. Dupont (CNRS).
References
[1] Andreussi, O.; Dabo, I.; Marzari, N. J. Chem. Phys. 2012, 136, 064102.
[2] Dabo, I.; Cancès, E.; Li, Y. L.; Marzari, N. ArXiv e-prints 2009, .
[3] Bonnet, N.; Marzari, N. Phys. Rev. Lett. 2013, 110, 086104.
2
Material Science
T.2
Determining Defect Energy Levels: Finite-Size Effects and
Electronic-Structure Method
Alfredo Pasquarello1
1
Chaire de Simulation à l’Echelle Atomique (CSEA), École Polytechnique Fédérale de
Lausanne (EPFL)
Defects generally play an important role in all functional materials: Either they are undesired and need to be controled or passivated, or they are introduced on purpose to
achieve specific functionalities. In any event, given the experimental difficulties in unveiling the nature of the observed defects, theoretical approaches are often called upon
to provide insight. It is thus important to achieve theoretical tools with predictive power.
With this in mind, we here focus on the determination of defect energy levels in the form
of charge transition levels. The talk will focus on two aspects. First, the issue of finite
size effects will be addressed. Proper treatment of finite size effects remains an important issue in order to achieve converged defect levels. We will review current supercell
techniques used for correcting defect levels calculated in bulk materials [1] and show
how these methods can be extended to cover surfaces and interfaces [2]. Next, we
address to what extent various electronic-structure methods, as different as semilocal
density functional, hybrid density functional [3–7], and many-body perturbation theory
in the GW approximation [8, 9] provide a consistent description of the position of defect
levels with respect to the band edges of the host. The comparison with experimental
data is illustrated and discussed [10, 11].
Work done in collaboration with A. Alkauskas, P. Broqvist, W. Chen, and H.-P. Komsa.
References
[1] Komsa, H.-P.; Rantala, T. T.; Pasquarello, A. Phys. Rev. B 2012, 86,.
[2] Komsa, H.-P.; Pasquarello, A. Phys. Rev. Lett. 2013, 110, 095505.
[3] Alkauskas, A.; Broqvist, P.; Pasquarello, A. Phys. Rev. Lett. 2008, 101, 046405.
[4] Alkauskas, A.; Broqvist, P.; Devynck, F.; Pasquarello, A. Phys. Rev. Lett. 2008, 101, 106802.
[5] Alkauskas, A.; Broqvist, P.; Pasquarello, A. Phys. Status Solidi B 2011, 248, 775-789.
[6] Komsa, H.-P.; Broqvist, P.; Pasquarello, A. Phys. Rev. B 2010, 81,.
[7] Alkauskas, A.; Pasquarello, A. Phys. Rev. B 2011, 84, 125206.
[8] Chen, W.; Pasquarello, A. PHYSICAL REVIEW B 2012, 86, 035134.
[9] Chen, W.; Pasquarello, A. Unpublished data.
[10] Broqvist, P.; Alkauskas, A.; Pasquarello, A. Phys. Rev. B 2008, 78, 075203.
[11] Komsa, H.-P.; Pasquarello, A. Phys. Rev. B 2011, 84, 075207.
3
Material Science
T.3
The mechanism of proton conduction in phosphate based
liquids and solids studied by ab initio molecular dynamics
Mark E. Tuckerman1
1
Department of Chemistry and Courant Institute of Mathematical Sciences, New York
University
Phosphoric acid based polymer electrolyte membrane materials are the only quasianhydrous separator electrolytes for intermediate temperature fuel cell applications
currently in use. Pure phosphoric acid has the highest known intrinsic proton conductivity of any known substance, [1] but this conductivity is highly sensitive to doping
with Brønsted-Lowry bases. In this talk, we will present results of ab initio molecular
dynamics calculations of a series of phosphate based materials including pure liquid
phosphoric acid, solid cesium dihydrogen phosphate (CDP), a 2:1 mixture of phosphoric acid and imidazole, and a 1:1 mixture of phosphoric acid and water. In liquid
phosphoric acid [2] and solid CDP, [3] the simulations reveal that proton conduction is
driven by strong, polarizable hydrogen bonds that produce concerted proton motion
and a pronounced protic dielectric response. These effects lead to the formation of
extended, polarized hydrogen- bonded chains. The interplay between these chains
and a frustrated hydrogen-bond network is posted to lead to the high proton conductivity. This mechanism is contrasted to the transport of excess protons in water. The
aforementioned sensitivity to doping is also confirmed by simulations of a 2:1 mixture
of phosphoric acid and imidazole, [4] and the reduction in proton conductivity [5] is connected to the high proton affinity of imidazole and the consequent formation of stable
imidazolium-dihydrogen phosphate complexes. In the 1:1 mixture of phosphoric acid
and water, [6] both species can act as charge carriers, and the similarity in strength of
the hydrogen bonds in Eigen- and Zundel-like complexes and those formed between
these and neighboring phosphate species allows for facile proton transfer between water and phosphate species, thereby leading to a high observed proton conductivity.
References
[1] Dippel, T.; Kreuer, K.; Lassègues, J.; Rodriguez, D. Solid State Ionics 1993, 61, 41 - 46.
[2] Vilčiauskas, L.; Tuckerman, M. E.; Bester, G.; Paddison, S. J.; Kreuer, K.-D. Nat. Chem.
2012, 4, 461–466.
[3] Lee, H.-S.; Tuckerman, M. E. J. Phys. Chem. C 2008, 112, 9917-9930.
[4] Vilčiauskas, L.; Tuckerman, M. E.; Melchior, J. P.; Bester, G.; Kreuer, K.-D. Solid State
Ionics 2013, in press, -.
[5] Schechter, A.; Savinell, R. F. Solid State Ionics 2002, 147, 181 - 187.
[6] Vilčiauskas, L.; Tuckerman, M. E.; Kreuer, K.-D. in preparation.
4
Material Science
T.4
Complementary transport channels in Si-ZnS
nanocomposites: first principles simulations
S. Wippermann1,2,3 , M. Vörös1 , A. Gali4 , G. Zimanyi3 , F. Gygi5 , G. Galli2,3
1
Interface Chemistry and Surface Engineering Department, Max-Planck-Institute for
Iron Research GmbH, Düsseldorf
2
Department of Chemistry, University of California, Davis, California
3
4
Department of Physics, University of California, Davis, California
Department of Atomic Physics, Budapest University of Technology and Economics,
Budapest
5
Department of Computer Science, University of California, Davis, California
We present density functional and many body perturbation theory calculations of the
electronic, optical and transport properties of Si nanoparticles (NPs) embedded in ZnS,
a system that was used as a charge transport layer in recent experiments. A realistic
model of the NP-matrix interface was created from ab-initio molecular dynamics simulations. In analogy to Si NPs embedded in SiO2 we found a strong gap reduction
and corresponding red-shifted optical absorption, caused by chemical shifts at the NPmatrix interface. We found that this nanocomposite exhibits complementary transport
channels, where electron transport occurs by hopping between NPs and hole transport
through the ZnS-matrix. For these reasons Si NPs embedded in II-VI sulfide charge
transport matrices may be promising candidate material systems for solar energy conversion.
5
Material Science
T.5
Adsorption processes on metallic surfaces
Marcella Iannuzzi1
1
Institute of Physical Chemistry, University of Zurich
We present an overview of our recent efforts to devise efficient computational strategies
based on DFT, [1] which allow the investigation of properties and processes at complex interfaces between metallic substrates and adsorbed molecular systems. Reliable
models of such interfaces require large simulation cells consisting of a sufficiently thick
slab structure for the substrate, in order to reproduce the correct electronic properties at
the metallic surface. Moreover the lateral dimensions should be large enough to allow
the description of possible reconstructions, as well as the simulation of processes like
functionalization, assembly, dynamics of adsorbed subsystemsetc. Working in close
collaboration with experimentalists, we are constantly challenged to reproduce and/or
interpret the experimental findings and the observed processes. The final goal is to
acquire in depth knowledge of the studied systems such to lead to the development of
new materials with tailored properties.
Trade-off between the size of the model and the accuracy of the computational set up
becomes critical in order to properly address the materials of interest. Typically, we
have to go beyond a basic Kohn-Sham DFT description, e.g., introducing corrections
for the dispersion forces, applying hybrid functionals, using the broken symmetry theory for the magnetic properties, or relying on multiscale approaches.
One class of systems discussed here are modern nanotemplates based on hexagonal
boron nitride or graphene grown on transition metals. [2–5] The mismatch between the
lattice constant of the sp2 overlayer and the substrate produces modulated structures,
which are robust and promising substrates for self-assembly, electron confinement or
intercalation. We have investigated the absorption of molecules and the formation and
dynamics of defects by applying advanced sampling techniques and tuned analysis
tools for the characterization.
Another class of systems are self assembled monolayers of single molecule magnet
(SMM) (as organic free radicals with specific magnetic properties or functionalized clusters of transition metal ions) to be used as high density memory storage systems or
spintronic devices. The challenge in this case is to shed some light on the magnetic
properties of the molecules once grafted on surfaces and to explore the complexity
of the structural rearrangement of the functionalized systems and how this affects the
magnetic properties. [6]
Recently the coordination of transition metals to tailored ligands over metallic substrates has awakened great interest, since it provides an alternative versatile approach
for the construction of highly organized molecular arrangements. In collaboration with
experimental partners, suitable prototypical models are investigated in order to rationalize atomic structures, electronic properties, and chemical bonding. Atomistic modeling is expected to be very useful in monitoring electronic and magnetic properties by
changing compounds and design, and for the investigation of reaction processes and
dynamics at finite temperature. [7]
6
Material Science
T.5
Finally, we propose a QM/MM approach to describe the interaction between physisorbed molecules and metallic substrates, where image charges within the substrate
are used to model the response of the metallic electronic structure to the electrostatic
potential generated by the adsorbed molecule. [8]
The method is employed, for instance, for the simulation of liquid/metal interfaces,
where the liquid (water) is treated QM and the metal is described by an empirical
force field, while the image charge scheme accounts for the polarization effects. Obviously, the computational costs are significantly with respect to a full electronic structure
calculation. [9]
Figure: a) Optimized structure of six Ar atoms implanted between hexagonal boron nitride and
the Rh(111) surface. The Ar atoms aggregate at wire cross section sites. b) Cluster of Mn ions
([Mn(III)6 O2 (R-sao)6 (O2 C-th)2 L], where HO2 C-th=3-thiophene carboxylic acid, saoH2 = salicylaldoxime, R = H and L = (EtOH)4 ) grafted on Au(111) surface. Notice the depression induced by
the cluster on the gold surface. c) Snapshot of the water/Pt(111) interface as extracted by a MD
simulation carried out with the image-charge-augmented QM/MM model.
References
[1] Hutter, J.; Iannuzzi, M.; Schiffmann, F.; VandeVondele, J. WIREs Comput. Mol. Sci. 2013,
n/a–n/a.
[2] Diaz, J. G.; Ding, Y.; Koitz, R.; Seitsonen, A. P.; Iannuzzi, M.; Hutter, J. Theor. Chem. Acc.
2013, 132,.
[3] Ma, H.; Ding, Y.; Iannuzzi, M.; Brugger, T.; Berner, S.; Hutter, J.; Osterwalder, J.; Greber, T.
Langmuir 2012, 28, 15246–15250.
[4] Joshi, S.; Ecija, D.; Koitz, R.; Iannuzzi, M.; Seitsonen, A. P.; Hutter, J.; Sachdev, H.;
Vijayaraghavan, S.; Bischoff, F.; Seufert, K.; Barth, J. V.; Auwaerter, W. Nano Lett. 2012,
12, 5821–5828.
[5] Cun, H.; Iannuzzi, M.; Hemmi, A.; Roth, S.; Osterwalder, J.; Greber, T. Nano Lett. 2013,
13, 2098–2103.
[6] Totti, F.; Rajaraman, G.; Iannuzzi, M.; Sessoli, R. J. Phys. Chem. C 2013, 117, 7186–7190.
[7] Schlickum, U.; Klappenberger, F.; Decker, R.; Zoppellaro, G.; Klyatskaya, S.; Ruben, M.;
Kern, K.; Brune, H.; Barth, J. V. J. Phys. Chem. C 2010, 114, 15602–15606.
[8] Siepmann, J. I.; Sprik, M. J. Chem. Phys. 1995, 102, 511–524.
[9] Golze, D.; Iannuzzi, M.; Passerone, D.; Hutter, J. WIREs Comput. Mol. Sci. 2013, n/a–n/a.
7
Material Science
T.6
Metal-Organic Molecule-Metal Nano-Junctions: A close
contact between first-principle simulations and experiments
Mauro Boero1
1
Institut de Physique et Chimie des Materiaux de Strasbourg (IPCMS), University of
Strasbourg and CNRS
The realization of functional metal-molecule junctions for future electronic devices relies on our ability in assembling these heterogeneous objects at a molecular level and
in understanding the nature and the behavior of the electronic states at the interface [1].
In particular, delocalized interface states near the metal Fermi level are considered a
key ingredient for tailoring charge injection [2]. Interfacial electron delocalization depends on a large number of chemical, structural, and morphological parameters, all
influencing the spatial extension of the electron wave functions. In this talk, we show
that a double-decker organometallic compound, namely the ferrocene molecule, can
be deposited on a Cu(111) surface without giving rise to dissociation, providing an
ideal system to investigate the adsorption, the interface states or even localized spin
states [3] at a metal-organometallic interface. Adsorbed ferrocene is shown to produce
a 2D-like interface state strongly resembling the Shockley surface-state of Cu. By a
subsequent deposition of single metal atoms on the molecular layer, we analyze the
sensitivity of the interface state to local modifications of the interface potential. Accurate large-scale dynamical simulations, combined with experiments [4], provide an
insight into adsorption and charge redistribution processes. and charge redistribution
processes. Our findings demonstrate the feasibility of exploiting the chemical reactivity
of molecules to modify the electron behavior at a metal-molecule interface.
References
[1] Cuniberti, G.; Fagas, G.; Richter, K., Eds.; Introducing Molecular Electronics; Springer:
Berlin, 2005.
[2] Zhu, X.-Y. Sur. Sci. Rep. 2004, 56, 1 - 83.
[3] Komeda, T.; Isshiki, H.; Liu, J.; Zhang, Y.-F.; Lorente, N.; Katoh, K.; Breedlove, B. K.;
Yamashita, M. Nat. Commun. 2011, 2, 217.
[4] Heinrich, B. W.; Limot, L.; Rastei, M. V.; Iacovita, C.; Bucher, J. P.; Djimbi, D. M.; Massobrio, C.; Boero, M. Phys. Rev. Lett. 2011, 107, 216801.
8
Material Science
T.7
Atomistic Simulations in the Synthesis and
Characterization of Graphene Based Heterostructures
C.A. Pignedoli1 , P. Ruffieux1 , J. Cai1 , R. Jaafar1 , L. Talirz1 , H. Soede1 , S.
Blankenburg1 , D. Passerone1 , N.C. Plumb2 , L. Patthey2 , D. Prezzi3 , A.
Ferretti3 , E. Molinari3 , X. Feng4 , K. Muellen4 , R. Fasel1
1
Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf
2
Swiss Light Source, Paul Scherrer Institut, Villigen
3
Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Modena
4
Max Planck Institut for Polymer Research, Mainz
The application of graphene in microelectronics is, in principle, hampered by the absence of a band gap in its electronic structure. However, one way to induce a band gap
into the electronic structure of graphene is to introduce nanopatterned defects such as
holes or to cut it into nanometre-wide ribbons, termed graphene nanoribbons (GNRs),
that are promising building blocks for the fabrication of novel graphenebased electronic
devices [1]. However, standard fabrication techniques, based on top-down approaches
for cutting graphene or carbon nanotubes into GNR like structures, are not suitable for
ribbons narrower than ∼5 nm and the resulting lack of control over the edge roughness
and edge A bottom-up approach based on surface-assisted cyclodehydrogenation reactions has recently emerged as a promising route to the synthesis of nanoribbons
and nanographenes [2, 3]. The key step of this bottom-up GNR fabrication method is
the thermally induced cyclodehydrogenation of linear polyphenylenes on noble-metal
templates (see Figure 1). I will discuss the role played by atomistic simulations in our
most recent results for the synthesis [4] and characterization [5,6] of atomically precise
graphene based heterostructures.
Figure: Bottom-up approach for the surfacesupported synthesis of a atomically precise N=7
armchair GNR. (a) Chemical sketch of the procedure (b) STM measurement of the polymer chain
(obtained annealing at temperature T1) superimposed to the corresponding simulated STM image.
(c) After annealing at T2 T1 7-AGNRs are formed.
References
[1] Dutta, S.; Pati, S. K. J. Mater. Chem. 2010, 20, 8207-8223.
[2] Cai, J. et al. Nature 2010, 466, 470–473.
[3] Treier, M. et al. Nat. Chem. 2011, 3, 61–67.
[4] Blankenburg, S. et al. ACS Nano 2012, 6, 2020-2025.
[5] Talirz, L. et al. J. Am. Chem. Soc. 2013, 135, 2060-2063.
[6] Ruffieux, P. et al. ACS Nano 2012, 6, 6930-6935.
9
Material Science
T.8
Metadynamics for Computational Heterogeneous Catalysis
Bernd Meyer1 , Johannes Frenzel2 , Dominik Marx2
1
Interdisciplinary Center for Molecular Materials (ICMM) and
Computer-Chemistry-Center (CCC), Friedrich-Alexander-Universität
Erlangen-Nürnberg
2
Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum
Although methanol synthesis from CO and H2 over ZnO catalysts seems to be a simple chemical reaction, the interplay of physical and chemical processes at the ZnO
surfaces give rise to a complex free energy landscape. The preferred charge state
of oxygen vacancies is dictated by the chemical composition and the thermodynamic
properties of the gas phase in contact with ZnO. [1] In turn, reaction intermediates and
pathways along the catalytic cycle taking place at or close to these defects depend in
a sensitive way on their oxidation state. [2]
Instead of constructing the potential energy landscape for this reaction ‘by hand’ using static DFT and NEB calculations as traditionally done, we show that the underlying complex reaction network from CO to methanol can be generated based ab-initio
metadynamics simulations. [3,4] In addition to be able to ‘synthesize’ all previously discussed reaction intermediates, novel species are found and mechanistic insights into
the reaction network of this surface chemical reaction are obtained by a global exploration of the free energy landscape. In a second step, the global picture is refined by
investigating individual reaction pathways, taking into account different charge states of
the oxygen vacancies. Finally, first insights into the structure and reactivity of the much
more complex Cu/ZnO catalyst, which is subject to so-called ‘strong metal–support
interactions’ (SMSI), will be presented. [5]
References
[1] Kiss, J.; Witt, A.; Meyer, B.; Marx, D. J. Chem. Phys. 2009, 130, 184706.
[2] Kiss, J.; Frenzel, J.; Meyer, B.; Marx, D. J. Chem. Phys. 2013, 139, 044705.
[3] Kiss, J.; Frenzel, J.; Nair, N. N.; Meyer, B.; Marx, D. J. Chem. Phys. 2011, 134, 064710.
[4] Frenzel, J.; Kiss, J.; Nair, N. N.; Meyer, B.; Marx, D. Phys. Status Solidi B 2013, 250,
1174–1190.
[5] Martı́nez-Suárez, L.; Frenzel, J.; Marx, D.; Meyer, B. Phys. Rev. Lett. 2013, 110, 086108.
10
Material Science
T.9
Structure, Dynamics and Host-Guest Interactions in Porous
Hybrid Materials: Exploring Configurational Space by First
Principles Derived Force-Fields
Rochus Schmid1
1
Computational Materials Chemistry Group, Chair of Inorganic Chemistry 2,
Ruhr-University Bochum, Germany
Porous coordination polymers, usually referred to as Metal-Organic Frameworks (MOFs),
are a new class of porous crystalline materials with great potential in various areas like
gas storage and separation, sensing or catalysis. A major feature is the conformational
flexibility due to the organic linker molecules and the softness of coordination bonds.
This flexibility generates the need for efficient sampling strategies in order to cope with
disorder of building blocks, mobility of flexible side chains or guest molecules.
Over the last years we have developed a new first principles derived force field MOF-FF,
which is systematically parametrized by a genetic algorithm optimization method with
respect to DFT reference data. In the presentation the force field and parametrization
strategy will briefly be discussed. It will be shown how structural prediction by a so
called Reversed Topological Approach (RTA) is possible. In addition, further applications of the force field to explore the configurational space will presented.
11
Material Science
T.10
Dielectric properties of water under extreme conditions
and transport of carbonates in the deep Earth
Ding Pan1 , Leonardo Spanu1 , Brandon Harrison2 , Dimitri Sverjensky2 , Giulia
Galli1,3
1
2
Department of Chemistry, University of California Davis, Davis, CA 95616, USA
Department of Earth & Planetary Sciences, Johns Hopkins University Baltimore, MD
21218, USA
3
Department of Physics, University of California Davis, Davis, CA 95616, USA
Knowledge of the dielectric constant of water as a function of pressure (P) and temperature (T) plays a critical role in understanding the chemistry of aqueous fluids in
the Earth mantle [1, 2]. By using ab initio molecular dynamics, we computed [2] the dielectric constant of water (0 ) under conditions of the Earth’s upper mantle, predicting
values beyond the reach of current experiments. We found that changes in the molecular dipole moment and hydrogen bond network upon compression greatly affect the
dielectric constant of the liquid. Such changes are not accounted for by classical potentials, which yield values of 0 substantially different from those of ab initio simulations.
Based on the predicted dielectric constants, the solubility products of carbonate minerals were computed. We found that at P ∼ 10 GPa and T = 1000 K, MgCO3 (magnesite)
is at least slightly soluble in water at the millimolal level. This result suggests that water
in the Earth’s mantle has the capacity to store and transport significant quantities of
oxidized carbon, leading to the hypothesis that the Earth’s deep carbon could possibly
be recycled through aqueous transport on a large scale through subduction zones. An
investigation of the electronic properties of water under pressure is underway and will
be discussed as well.
References
[1] Galli, G.; Pan, D. Proc. Natl. Acad. Sci. USA 2013, 110, 6250–6251.
[2] Pan, D.; Spanu, L.; Harrison, B.; Sverjensky, D. A.; Galli, G. Proc. Natl. Acad. Sci. USA
2013, .
12
Honored Guest Day
T.11
Making Li-Air Batteries the energy reservoir of the future:
Computational Material Challenges.
Teodoro Laino1 , Katharina Meyer1 , Alessandro Curioni1
1
IBM Zurich Research Laboratory, Rueschlikon, Zurich
Lithium-air batteries have captured worldwide attention because, theoretically, their
specific energy far exceeds the best achieved with modern battery solutions, allowing
an electric vehicle to run for mileage ranges similar to the ones of gasoline vehicles.
However, lithium/air batteries, still present significant challenges, mostly related to materials. In this talk, I will review the status and computational materials challenges for
non-aqueous lithium/air electrochemical cells with particular attention to (1) the chemical stability of different candidate solvents versus lithium peroxide and (2) to the understanding of novel lithium-ion conducting ceramics.
13
Keynote Lecture
T.12
Thermodynamics and Statistical Mechanics from First
Principles for Surfaces and Interfaces: Theoretical
Challenges, Concepts, and Insights
Matthias Scheffler1
1
Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin
Over the last 3 decades “ab initio (atomistic) thermodynamics” and “ab initio kinetic
Monte Carlo” have evolved into standard approaches in application areas such as materials growth, corrosion, sensing, and heterogeneous catalysis (see [1] and references
therein).
For many systems of present interest (e.g. metal oxides, organic materials, and hybrid organic/inorganic materials) the accuracy of the widely used exchange-correlation
functions is problematic. Furthermore, for interfaces and surfaces it turns out that doping (intentional or unintentional) is not just providing an electron or hole reservoir, but
it builds up an extended space-charge layer and band bending (typically 10-100 nm
thick). While this is well known in principle, we will show here, how it can be considered properly in ab initio studies.
In this talk I will discuss advances in exchange-correlations functionals beyond the
random-phase approximation, [2, 3] and I will show that Gibbs free energies, defect
concentrations and much of the physical and chemical properties of surfaces and interfaces of the above mentioned systems are significantly affected by the space-charge
layer [4]
References
[1] Reuter, K.; Stampfl, C.; Scheffler, M. Handbook of Materials Modeling, Part A. Methods. In ;
Yip, S., Ed.; Ab Initio Thermodynamics and Statistical Mechanics of Surface Properties and
Functions Springer: Berlin, 2005.
[2] Ren, X.; Rinke, P.; Scuseria, G.; Scheffler, M. “Renormalized Second-order Perturbation
Theory for The Electron Correlation Energy: Concept, Implementation, and Benchmarks”,
2013 submitted.
[3] Ren, X.; Rinke, P.; Joas, C.; Scheffler, M. Journal of Materials Science 2012, 47, 7447-7471.
[4] Richter, N.; Sicolo, S.; Levchenko, S.; Sauer, J.; Scheffler, M. “Concentration of Vacancies
at Metal Oxide Surfaces: Case Study of MgO (100)”, 2013 submitted.
14
Honored Guest Day
T.13
Modeling chemical reactions in hydrogen-bonding solvents
Evert Jan Meijer1 and Anna Pavlova1
1
Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park
904, NL-1098 XH Amsterdam, The Nethverlands
We have applied DFT-based molecular dynamics simulations to study proto-type reactions involving proton transport in solutions of water and methanol. In this contribution we address two specific reactions: 1) silica oligomerization which is a key step in
sol-gel chemistry and zeolite synthesis [1] and 2) homogeneously catalyzed transfer
hydrogenation of ketones [2]. Using free-energy methods and transition-path-sampling
techniques we demonstrate how to arrive at a quantitative picture of the thermodynamic and kinetic aspects of the reactions. For both reactions, the simulation clearly
demonstrate that the solvent molecules plays a crucial role in inducing reactive events.
References
[1] Pavlova, A.; Trinh, T. T.; van Santen, R. A.; Meijer, E. J. Phys. Chem. Chem. Phys. 2013, 15,
1123 - 1129.
[2] Pavlova, A.; Meijer, E. J. Chem. Phys. Chem. 2012, 13, 3492–3496.
15
Honored Guest Day
T.14
to be announced
Jochen Blumberger1
1
Department of Physics and Astronomy, University College London
16
Honored Guest Day
T.15
Water interfaces: structure and vibrational spectroscopy
from DFT-based MD simulations
Marialore Sulpizi1 , Mathieu Salanne2 , Michiel Sprik3 , Marie-Pierre Gaigeot4
1
Department of Physics, Johannes Gutenberg Universität, Mainz
2
3
4
UPMC Université Paris 06, CNRS, ESPCI, Paris
Department of Chemistry, University of Cambridge
Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université
d’Évry val d’Essonne, Évry
Water properties at the interface can be quite different from bulk properties and have
been central to several recent investigations. Here we present DFT-based molecular
dynamics simulations (DFT-MD) on solid/water and water/vapor interfaces providing a
microscopic interpretation of recent experimental results from surface sensitive Vibrational Sum Frequency Generation spectroscopy (VSFG). Organization of water at the
interface with silica and alumina oxides will be presented. The interfacial hydrogen
bond network has been investigated in details and has been related to the chemistry of
the oxide surfaces. Vibrational IR spectra at these interfaces have been extracted from
the DFT-MD trajectories and have been used in order to give assignments of VSFG experimental signals in terms of interfacial water H-bond donors (“liquid-like”) and water
H-bond acceptors (“ice-like”) to the surface silanols/aluminols. In the case of the liquid
water/vapor interface, the VSFG spectrum has been computed from DFT-MD trajectories, as well as interfacial IR and Raman spectra. The real and imaginary parts of
the VSFG spectrum are found in good agreement with the experimental data, and we
provide an assignment of the VSFG bands according to the dipole orientation of the interfacial water molecules. By calculating the Infrared and Raman spectra for interfaces
of varying thickness, we show that the bulk signatures appear after a thin layer of 2−3
Å only.
References
[1] Sulpizi, M.; Salanne, M.; Sprik, M.; Gaigeot, M.-P. The Journal of Physical Chemistry Letters
2013, 4, 83-87.
[2] Gaigeot, M.-P.; Sprik, M.; Sulpizi, M. Journal of Physics: Condensed Matter 2012, 24,
124106.
[3] Sulpizi, M.; Gaigeot, M.-P.; Sprik, M. Journal of Chemical Theory and Computation 2012, 8,
1037-1047.
17
Keynote Lecture
T.16
to be announced
Thomas Lippert1
1
Institute for Advanced Simulation (IAS) Jülich Supercomputing Centre (JSC)
18
Keynote Lecture
T.17
Car-Parrinello computational electrochemistry
Jun Cheng1 , John Kattirtzi1 , Xiandong Liu1,2 , Marialore Sulpizi3 , Joost
VandeVondele4 , Michiel Sprik1
1
2
School of Earth Sciences and Engineering, Nanjing University, Nanjing
3
Department of Physics, Johannes Gutenberg University, Mainz
4
Department of Materials, ETH, Zurich
The electrodes of electrochemistry are interfaces between electronic and ionic conductors. The electronic conductor can be a metal or semiconductor and the ionic conductor an aqueous electrolyte, ionic liquid or solid ion conductor. Such heterogeneous
systems should be ideal model systems for Car-Parrinello (CP) simulation combining
electronic structure and ionic motion at a fundamental level. Physical electrochemistry
can be roughly divided up in the study of electrode potentials and electrode dynamics.
The research of the group has focused on the computation of electrode potentials and
alignment of energy levels at electrochemical interfaces. This proved already to be
a major challenge. A key step in the method development was a CP hydrogen electrode using the free energy for insertion of a proton as energy reference, unifying the
computation of reduction potentials and acidity constants. This enabled us to compare
directly to standard hydrogen potentials of experiment without introducing an additional
interface to vacuum. It also made it possible to assess the effect of the delocalization
error in the common density functionals used in CP dynamics, which turns out to be the
major source of error. In this talk, after a short technical introduction, we will discuss
two applications involving first row transition metals. The computation of the oxidation
potentials of a number of model aqua-cations (Cu+ , Ag+ and Fe2+ ) and the alignment
of energy levels at the rutile MnO2 -water interface (for our work on TiO2 see the talk by
Jun Cheng).
References
[1] Adriaanse, C.; Cheng, J.; Chau, V.;
J. Phys. Chem. Lett. 2012, 3, 3411-3415.
Sulpizi, M.;
VandeVondele, J.;
Sprik, M.
[2] Cheng, J.; Sprik, M. Phys. Chem. Chem. Phys. 2012, 14, 11245-11267.
[3] Cheng, J.; Sulpizi, M.; VandeVondele, J.; Sprik, M. ChemCatChem 2012, 4, 636–640.
[4] Costanzo, F.; Sulpizi, M.; Valle, R. G. D.; Sprik, M. J. Chem. Phys. 2011, 134, 244508.
19
Keynote Lecture
T.18
Sweet mysteries of nature: reactive processes in
carbohydrate-active enzymes
Carme Rovira1,2
1
2
Department of Organic Chemistry, University of Barcelona
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona
One of the great scientific challenges of our time is to find new molecules as potential
new drugs to fight disease. Carbohydrate-active enzymes are the focus of enormous
interest due to the critically important roles that complex glycans play in health and
disease, as well as the rekindled interest in enzymatic biomass conversion. Nature
has created a multitude of ingenious methods to cleave and form glycosidic bonds in
carbohydrates. Here we will summarize our work of the last few years on the prediction
of sugar binding and catalytic mechanisms of these enzymes, using classical/ab initio
(QM/MM) molecular dynamics and metadynamics methods.
References
[1] Rovira, C. Wiley Interdisciplinary Reviews: Computational Molecular Science 2013, 3, 393–
407.
20
Life Science
T.19
Structure and Dynamics of the Hydrated Electron
Frank Uhlig1 , Ondrej Marsalek1 , Pavel Jungwirth1
1
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech
Republic
The structure of the hydrated electron, a key intermediate in radiation chemistry, at
the water/vapor interface has been discussed controversially in recent literature. Initial
measurements of the binding energy of the hydrated electron in a liquid water microjet
setup indicated two distinct isomers [1], one isomer with a high binding energy, attributed to a compact, bulk-solvated electron, and a lower-binding isomer, assigned to
a diffuse, surface-bound state. Later measurements with similar setups could not confirm the existence of the weakly bound electron at the water surface. [2–4] We perform
ab initio molecular dynamics simulations of both an electron solvated at the water surface and in bulk water. The electronic structure in both systems is described by density
functional theory for 64 water molecules and the excess electron, coupled electrostatically to 960 water molecules treated by an empirical force field. Both, the hydrated
electron at the water surface and in bulk water have a binding energy of about 3.0 - 3.3
eV, in good comparison to experimental data [1–4] (3.3 - 3.6 eV) for the bulk-hydrated
electron. This similarity is also reflected in the solvation structure of the hydrated electron. Only about 10 % of the hydrated electron at water surface protrude into the
vapor phase. It is thus not half dehydrated, but retains its complete first solvation shell
and only starting from the second solvation shell a distinct difference can be observed
due to the anisotropy of the water/vapor interface. [5, 6] The size of the bulk-hydrated
electron can be determined from the experimental absorption spectrum by moment
analysis and is in quantitative agreement with our data from the simulations. However,
experimentally the change in size during the localization of an excess electron to bulk
water is not directly accessible. We determine the size of the hydrated electron by
following the electron localization process and monitor the optical absorption with timedependent density functional theory along this non-equilibrium process. This allows us
to put a measure on the size of the electron over a wide spectral range.
Hydrated electron in bulk water . . . and at water/vapor interface
21
Life Science
T.19
References
[1] Siefermann, K. R.; Liu, Y.; Lugovoy, E.; Link, O.; Faubel, M.; Buck, U.; Winter, B.; Abel, B.
Nature Chem. 2010, 2, 274-279.
[2] Shreve, A. T.; Yen, T. A.; Neumark, D. M. Chem. Phys. Lett. 2010, 493, 216 - 219.
[3] Tang, Y.; Shen, H.; Sekiguchi, K.; Kurahashi, N.; Mizuno, T.; Suzuki, Y.-I.; Suzuki, T. Phys.
Chem. Chem. Phys. 2010, 12, 3653-3655.
[4] Buchner, F.; Schultz, T.; Lubcke, A. Phys. Chem. Chem. Phys. 2012, 14, 5837-5842.
[5] Uhlig, F.; Marsalek, O.; Jungwirth, P. J. Phys. Chem. Lett. 2012, 3, 3071-3075.
[6] Uhlig, F.; Marsalek, O.; Jungwirth, P. J. Phys. Chem. Lett. 2013, 4, 338-343.
22
Keynote Lecture
T.20
Ab initio studies of ionization potentials of hydrated
hydroxide and hydronium
Xifan Wu1
1
Temple University, Philadelphia
The ionization potential distributions of hydrated hydroxide and hydronium are computed with many-body approach for electron excitations with configurations generated
by ab initio molecular dynamics. The experimental features are well reproduced and
found to be closely related to the molecular excitations. In the stable configurations,
the ionization potential is mainly perturbed by solvent water molecules within the first
solvation shell. On the other hand, electron excitation is delocalized on both proton
receiving and donating complex during proton transfer, which shifts the excitation energies and broadens the spectra for both hydrated ions.
23
Life Science
T.21
Linking electronic and molecular structure: Insight into
aqueous chloride solvation
Patricia Hunt1 , Ling Ge1 , Leonardo Bernasconi2
1
2
Department of Chemistry, Imperial College London
STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire
Aqueous chloride solutions are ubiquitous and diverse; systems include sea water,
atmospheric droplets, geological processes and biological organisms. However, despite considerable effort, a complete microscopic model of the hydration shell, and
local electronic structure of the aqueous chloride ion and its dynamics has not been
established. [1, 2] In this work we employ ab-initio molecular dynamics to study an
aqueous chloride solution. In particular, local solvation events and the electronic structure around the chloride ion are interrogated. We employ the Effective Molecular Orbital (EMO) method which partitions the electronic structure into solute and solvent
components while maintaining a rigorous quantum mechanical description of both. [3]
Movement of the chloride highest occupied molecular orbital (HOMO) energy within
the valence band of water is revealed. The chloride ion has little impact on the average
water electronic structure, however, locally the electronic effect of the chloride ion is
significant. The chloride ion prefers to be symmetrically solvated by six H-bonding water molecules, however, the chloride HOMO energy and coordination number oscillate
in response to local fluctuations driven by the dynamics of the bulk water. We relate the
local electronic and nuclear structure to the position of the chloride ion near the centre
of the Hofmeister series.
Figure: Evolution of
the Cl ion and water HOMO band over
time
References
[1] Tobias, D. J.; Hemminger, J. C. Science 2008, 319, 1197–1198.
[2] Paschek, D.; Ludwig, R. Angew. Chem. Int. Edit. 2011, 50, 352–353.
[3] Hunt, P.; Sprik, M.; Vuilleumier, R. Chemical Physics Letters 2003, 376, 68–74.
24
Life Science
T.22
Multi Scale Characterisation of an Enzymatic Reaction:
from NMR to DFT and back
Carlo Camilloni1 , Aleksander Sahakyan1 , Michael Holliday2 , Elan Z.
Eisenmesser2 , Michele Vendruscolo1
1
2
Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora
Cyclophilin A is an enzyme that catalyses proline isomerisation [1, 2], which is a ubiquitous process that plays a key role in protein folding and regulation [3]. Here, by combining NMR measurements, molecular dynamics simulations and density functional
theory calculations, we found that cyclophilin A provides an electrostatic environment
that acts on the substrate through an electrostatic lever mechanism. In this mechanism,
the electrostatic field turns the electric dipole associated with the carboxylic group of
the glycine preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. These results illustrate how the complementary
use of NMR spectroscopy and molecular simulations can elucidate the mechanisms of
catalysis.
References
[1] Davis, T. L.; Walker, J. R.; Campagna-Slater, V.; Finerty, P. J.; Paramanathan, R.; Bernstein, G.; MacKenzie, F.; Tempel, W.; Ouyang, H.; Lee, W. H.; Eisenmesser, E. Z.; DhePaganon, S. PLoS Biol 2010, 8, e1000439.
[2] Leone, V.; Lattanzi, G.; Molteni, C.; Carloni, P. PLoS Comput. Biol. 2009, 5, e1000309.
[3] Göthel, S. F.; Marahiel, M. A. Cell. Mol. Life. Sci 1999, 55, 423–436.
25
Life Science
T.23
to be announced
Ursula Roethlisberger1
1
Institut des sciences et ingénierie chimiques, Ecole polytechnique fédérale de
Lausanne
26
Life Science
T.24
Proton transport in a biological ion channel embedded in a
DMPC bilayer - role of the membrane dipole potential
Jens Dreyer1,2 , Chao Zhang1,2 , Emiliano Ippoliti1,2 , Paolo Carloni1,2
1
Computational Biophysics, German Research School for Simulation Sciences, Joint
venture of RWTH Aachen University and Forschungszentrum Jülich
2
IAS-5, Computational Biomedicine, Institute for Advanced Simulations,
Forschungszentrum Jülich
The cation-selective membrane channel gramicidin A (gA) is a widely used antibiotic
against gram-positive bacteria. Particularly prominent is gA’s effi-ciency in conducting
protons [1]. In spite of the low relevance of tunneling effects [2, 3], gA permeates H+
ions at a faster rate than any other membrane channel.
The membrane potential at the water/phospholipid interfaces may play a key role for
proton conduction of gramicidin A (gA). Here we address this issue by Density Functional Theory-based molecular dynamics and metadynamics simulations. The calculations, performed on gA embedded in a solvated 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane environment (about 2,000 atoms), indicate that the membrane dipole potential rises at the channel mouth the calculated free energy barrier
is located at the channel entrance, consistent with experiments comparing gA proton
conduction in different bilayers. The electronic structures of the proton ligands (water
molecules and peptide units) are similar to those in the bulk solvent. Based on these
results, we suggest an important role of the membrane dipole potential for the free
energy barrier of proton permeation of gA. This may provide a rationale for the large increase in the rate of proton conduction under application of a transmembrane voltage,
as observed experimentally. Our calculations point also to a role for proton desolvation
for the permeation process.
References
[1] Cukierman, S. Biophys. J. 2000, 78, 1825-1834.
[2] Chernyshev, A.; Pomès, R.; Cukierman, S. Biophysical Chemistry 2003, 103, 179 - 190.
[3] Pomès, R.; Roux, B. Biophys. J. 2002, 82, 2304.
27
Life Science
T.25
DNA damage by low-energy electrons from ab initio MD
simulations
Jorge Kohanoff1 , Lila Bouëssel du Bourg 1,2 , Bin Gu1,3 , Maeve McAllister 1 ,
Gareth Tribello 1 , Maeve Smyth 1
1
Atomistic Simulation Centre, Queen’s University Belfast, Northern Ireland, UK
2
3
Department of Chemistry, ENS Paris, France
Department of Physics, NUIST, Nanjing, China
DNA damage caused by irradiation has been studied for many decades. Motivations
include assessing the dangers posed by radiation, and understanding how to improve
its efficiency in combating cancer. Surprisingly, low energy electrons play an important
role in this damage. In this presentation we describe a programme of work that aims
at understanding the behaviour of DNA components in a realistic, physiological-like
environment, due to the presence of such electrons.
To this end we conducted a series of first-principles molecular dynamics studies of excess electrons in condensed phase models of increasingly complex DNA fragments
solvated in water and also nucleobases in aminoacids. Dynamical simulations after
vertical attachment show the excess electron initially delocalized between the DNA
fragment and the water, in a pre-solvated state. This, however, rapidly localizes around
the bases within a 15-25 fs timescale [1]. Simulations of excess electrons in polynucleotides exhibit a rich pattern of localization and fluctuation between the various bases,
which depends on the sequence. The timescale of fluctuations is significantly longer,
of the order of 100-200 fs. The role of histones was studied by simulating nucleobases
solvated in glycine. In this case the excess electron can localize in the zwitterionic form
of glycine, or stabilized in the base by proton transfer, thus highlighting the protective
role of proteins in chromatin [2]
Free energy barriers for phosphodiester bond cleavage were calculated by means of
constrained first-principles molecular dynamics simulations, and compared to minimum
energy paths obtained by constrained geometry optimizations. We found barriers of
the order of 5-10 kcal/mol, suggesting that bond cleavage is a regular feature at 300K.
These barriers are obtained only when thermal and solvent fluctuations are included
explicitly [3]. For single-stranded samples, protonation is a competing mechanism that
can delay bond cleavage, or even inhibit it. We studied this competition by means of a
double constraint on protonation of the base and bond cleavage.
Finally, we studied the effects of sequencing in trinucleotides and tetranucleotides,
both at the level of localization and bond breaks, using metadynamics on a collective
variable made of the product of switching functions for the 4 and 6 bond lengths, respectively. We found that the two phenomena of localization and bond breaks are not
necessarily related, in the sense that the break does not need to occur close to where
the excess electron resides.
28
Life Science
T.25
References
[1] Smyth, M.; Kohanoff, J. Phys. Rev. Lett. 2011, 106, 238108.
[2] Gu, B.; Smyth, M.; Kohanoff, J. submitted to Phys. Chem. Chem. Phys.
[3] Smyth, M.; Kohanoff, J. J. Am. Chem. Soc. 2012, 134, 9122-9125.
29
Life Science
T.26
Towards a Description of Copper(II) ions Binding to
Intrinsically Disordered Proteins: a Molecular Simulation
Approach
G. Rossetti1
1
John von Neumann Institut für Computing, Computational Biophysics, German
Research School for Simulation Sciences and Institute for Advanced Simulation
IAS-5, Computational Biomedicine, Forschungszentrum Jülich
Institute for Research in Biomedicine and Barcelona Supercomputing Center Joint
Research Program on Computational Biology, Barcelona Science Park
The interaction between copper(II) ions (Cu(II)) and their target intrinsically disordered
proteins(IDPs) play a key role for a variety of neurodegenerative diseases. In particular, this interaction is likely to be harmful in Parkinson’s and neuroprotective in prion
diseases. [1, 2] Unfortunately, understanding its role at the molecular level poses challenges because of the current difficulties in describing IDPs and by the subtle sterechemistry of Cu(II) sites in proteins.
Here we have predicted the structural ensemble of two different systems — the totally
unstructured protein α-synuclein (AS) acetylated at the N-term in Parkinson (∼140
amino acids) and the N-term unstructured domain of the Prion protein (PrP) (∼100
amino acids), using completely different computational approaches. In case that structural information is available, such in the case of AS, we have first tested a computational protocol based on enhanced sampling techniques against biophysical data.
Then, we have predicted the structural determinants of the physiologically relevant
form — the N-acetylated form. As for the prion protein N-term, for which structural
information is not available, we have used advanced bioinformatics tools and Replica[U+2010]exchange Monte Carlo (REMC) simulations with PROFASI (PROtein Folding
and Aggregation Simulator). [9] We are now investigate their Cu(II) binding to these
proteins by QM/MM [12]-force matching procedure. [13] This research is supported financially by a DFG grant and it is in collaborations with the molecular biology labs of
Prof. Legname (SISSA, Trieste, Italy) and C. Fernandez (U. Rosario, Argentina)
References
[1] Gaggelli, E.; Kozlowski, H.; Valensin, D.; Valensin, G. Chem. Rev. 2006, 106, 1995-2044.
[2] Bush, A. I. Curr. Opin. Chem. Biol. 2000, 4, 184 - 191.
[3] Brown, D. R. Metallomics 2010, 2, 186-194.
[4] Wong, B.-S.; Chen, S. G.; Colucci, M.; Xie, Z.; Pan, T.; Liu, T.; Li, R.; Gambetti, P.;
Sy, M.-S.; Brown, D. R. J. Neurochem. 2001, 78, 1400–1408.
[5] Frisch, M. J. et al. “Gaussian 09 Revision A.1”, Gaussian Inc. Wallingford CT 2009.
30
Life Science
T.26
[6] Kim, K.; Jordan, K. D. J. Phys. Chem. 1994, 98, 10089-10094.
[7] Strati, G. L.; Willett, J. L.; Momany, F. A. Carbohydrate Research 2002, 337, 1851 - 1859.
[8] Klewpatinond, M.; Viles, J. H. FEBS letters 2007, 581, 1430–1434.
[9] Irbäck, A.; Mohanty, S. J. Comput. Chem. 2006, 27, 1548–1555.
[10] FEARNLEY, J. M.; LEES, A. J. Brain 1991, 114, 2283-2301.
[11] Spillantini, M. G.; Schmidt, M. L.; Lee, V. M.-Y.; Trojanowski, J. Q.; Jakes, R.; Goedert, M.
Nature 1997, 388, 839–840.
[12] Binolfi, A.; Rodriguez, E. E.; Valensin, D.; D’Amelio, N.; Ippoliti, E.; Obal, G.; Duran, R.;
Magistrato, A.; Pritsch, O.; Zweckstetter, M.; Valensin, G.; Carloni, P.; Quintanar, L.;
Griesinger, C.; Fernández, C. O. Inorg. Chem. 2010, 49, 10668-10679.
[13] Maurer, P.; Laio, A.; Hugosson, H. W.; Colombo, M. C.; Rothlisberger, U. J. Chem. Theory Comput. 2007, 3, 628-639.
31
Life Science
T.27
Conformational changes and allosteric regulation in
kinases
Francesco Luigi Gervasio1
1
Chemistry Department, University College London, London
Protein kinases (PK) show a remarkable conformational dynamics that is tightly regulated in physiological conditions, often by allosteric signals. A shift of the conformational ensemble towards the active state, with the consequent hyper-activation of the
PK, leads to a number of human diseases, including cancer. Thus, understanding
how allosteric signals regulate the inactive to active equilibrium in PK could lead to the
rational design of a new class of allosteric drugs.
Historically, drug discovery programs have been dominated by efforts to develop antagonists that compete for binding with endogenous ligands at orthosteric sites. However,
allosteric drugs might offer several therapeutic advantages over traditional orthosteric
ligands, including greater safety and/or selectivity. Here, by combining state-of-the-art
computer simulations with spectroscopy, chemical and molecular biology approaches
we study in great details the role of conformational changes and oncogenic mutations
in the allosteric control of pharmaceutically relevant kinases such as: cAbl [1], EGFR [2]
and FGFr [3, 4].
References
[1] Lovera, S.; Sutto, L.; Boubeva, R.; Scapozza, L.;
J. Am. Chem. Soc. 2012, 134, 2496-2499.
Dölker, N.;
[2] Sutto, L.; Gervasio, F. L. Proc. Natl. Acad. Sci. USA 2013, in press,.
[3] Bono, F. et al., Cancer Cell 2013, 23, 477–488.
[4] Herbert, C. et al., Cancer Cell 2013, 23, 489–501.
32
Gervasio, F. L.
AIMD based Methods I
T.28
Rational design of molecular electrocatalysts for oxidation
and production of H2
Ming-Hsun Ho1 , Shentan Chen1 , Roger Rousseau1 , Michel Dupuis1 , Morris
Bullock1 and Simone Raugei1
1
Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division,
Pacific Northwest National Laboratory, Richland, Washington
Recent advances in bio-inspired catalysts obtained in the Center for Molecular Electrocatalysis at the Pacific Northwest National Laboratory demonstrated the electrocatalytic oxidation and production of H2 using catalysts containing inexpensive, abundant
metals such as Ni, Mn and Fe. A key feature in our studies is the incorporation of a
pendant amine as a proton relay into the ligand, generally at a distance that will preclude formation of a M-N bond. In these catalysts the transformation between H2 and
protons proceeds via an interplay between proton, hydride and electron transfer steps
and involves the interaction of a H2 molecule with both a metal center and pendant
amine bases. By using large-scale ab initio molecular dynamics, advanced statistical mechanics tools for free energy calculations and microkinetic modeling, we carried
out an exhaustive characterization of these molecular catalysts. Our studies revealed
that the metal center and the pendant amine act as a frustrated Lewis acid/base pairs,
making the H2 bond cleavage or formation facile processes. It will be shown that to
maximize catalytic rates it is of critical importance to precisely control delivery of protons to the pendant amines and match the energetics of various species involved in the
catalysis. Toward the rational design of catalysts with optimal rates and overpotentials,
we will discuss the development of linear free energy relationships, based on extensive ab initio thermodynamic and kinetic data, to be employed in a theoretically driven
refinement of catalysts.
Acknowledgments. This research was supported as part of the Center for Molecular
Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department
of Energy, Office of Science, Office of Basic Energy Sciences.
References
[1] Stewart, M. P.; Ho, M.-H.; Wiese, S.; Lindstrom, M. L.; Thogerson, C. E.; Raugei, S.;
Bullock, R. M.; Helm, M. L. J. Am. Chem. Soc. 2013, 135, 6033-6046.
[2] O’Hagan, M.; Ho, M.-H.; Yang, J. Y.; Appel, A. M.; DuBois, M. R.; Raugei, S.; Shaw, W. J.;
DuBois, D. L.; Bullock, R. M. J. Am. Chem. Soc. 2012, 134, 19409-19424.
[3] Raugei, S.; Chen, S.; Ho, M.-H.; Ginovska-Pangovska, B.; Rousseau, R. J.; Dupuis, M.;
DuBois, D. L.; Bullock, R. M. Chem. Eur. J. 2012, 18, 6493–6506.
[4] Chen, S.; Rousseau, R.; Raugei, S.; Dupuis, M.; DuBois, D. L.; Bullock, R. M.
Organometallics 2011, 30, 6108-6118.
[5] O’Hagan, M.; Shaw, W. J.; Raugei, S.; Chen, S.; Yang, J. Y.; Kilgore, U. J.; DuBois, D. L.;
Bullock, R. M. J. Am. Chem. Soc. 2011, 133, 14301-14312.
33
T.29
CPMD: what’s next ?
Alessandro Curioni1
1
IBM Research Zurich
In this presentation I will give an overview of our recent work to extend the impact and
applicability of ab-initio Molecular Dynamics simulations by algorithms re-engineering
and their proper mapping to massively parallel machines, with particular emphasis to a
novel implementation scheme for a highly efficient evaluation of the Hartree–Fock exact exchange (HFX), specifically tailored for condensed phase simulations. To demonstrate the importance and impact of this work, a recent successful application to the
investigation of the complex chemistry of Li-Air battery will be also discussed.
34
T.30
String method meets metadynamics: ATP-Mg2+
conformational transitions and microsolvation effects.
Davide Branduardi1 , Fabrizio Marinelli1 , José D. Faraldo-Gómez1
1
Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics,
Frankfurt am Main
The string method [1] is a technique aimed at calculating a free energy in high dimensionality on a limited portion of phase space. This provides a very detailed understanding of a certain chemical reaction, conformational transition or activated event
that is meaningful only when there are no other competitive pathways. In this respect
metadynamics [2] is complementary, since it is generally used on a much lower dimensionality and with an exploratory intent so to sample many possible pathways that
connect distinct metastable states.
Here, by using a combination of bias-exchange metadynamics [3], a novel flavour of
roto-translational invariant string method in Cartesian space [4] and metadynamics with
path collective variables [5] we show that it is possible to achieve a broad, yet accurate
description of a process.
In particular we concentrate on the conformational transitions of adenosine-5’-triphosphate (ATP) complexed with Mg2+ ion in water. In this system the cation is able to
stabilize different conformers of ATP that allow binding to a wide range of biomolecules.
We investigate the main conformational barriers and interestingly we observe how microsolvation plays a key role that cannot be captured with traditional coordination parameters.
References
[1] Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. J. Chem. Phys. 2006, 125,
024106.
[2] Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2002, 99, 12562–12566.
[3] Piana, S.; Laio, A. J. Phys. Chem. B 2007, 111, 4553–4559.
[4] Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103.
[5] Branduardi, D.; Faraldo-Gómez, J. D. submitted.
35
Keynote Lecture
T.31
Disclosing new reaction pathways with CPMD simulations:
from CO2 capture to nanocarbon transformations
Wanda Andreoni1
1
Institute of Theoretical Physics, C3PN Ecole Polytechnique Fédérale de Lausanne
36
T.32
RNAs in silico: learning from molecular dynamics and
enhanced sampling techniques
Giovanni Bussi1
1
Scuola Internazionale Superiore di Studi Avanzati, SISSA, Trieste
Ribonucleic acid (RNA) is acquiring a large importance in cell biology, as more functions that it accomplishes are discovered. However, experimental characterization of
RNAs dynamical behavior at atomistic level is difficult. Molecular simulations at atomistic detail, in combination with state-of-the-art free-energy techniques, can bridge the
gap providing an unparalleled perspective on the mechanism and dynamics of RNA
folding and conformational transitions and of RNA/protein interactions. Two recent applications of these techniques will be discussed. The first is focused on a characterization of the zipping and unzipping mechanisms for a RNA double strand [1]. Here
conventional steered molecular dynamics is analyzed with a novel reweighting technique. Results are compared with experimental findings, including analysis of X-ray
data, [2] ultrafast spectroscopy, [3] and thermodynamic data [4]. Implications on the
directionality of RNA and DNA processing enzymes are also discussed.The second
application is a study of the interaction between TAR RNA from HIV and a cyclic binding peptide of pharmaceutical relevance [5]. This is done by introducing a suitable
acceleration technique based on using the electrostatic interaction free energy as a biased collective variable and allows for a blind prediction of the bound structure. Results
are in nice agreement with previous NMR experiments [6].
References
[1] Colizzi, F.; Bussi, G. J. Am. Chem. Soc. 2012, 134, 5173–5179.
[2] Mohan, S.; Hsiao, C.; VanDeusen, H.; Gallagher, R.; Krohn, E.; Kalahar, B.; Wartell, R. M.;
Williams, L. D. J. Phys. Chem. B 2009, 113, 2614–2623.
[3] Liu, J. D.; Zhao, L.; Xia, T. Biochemistry 2008, 47, 5962–5975 PMID: 18457418.
[4] Turner, D. H.; Sugimoto, N.; Freier, S. M. Ann. Rev. Biophys. Biophys. Chem. 1988, 17,
167–192 PMID: 2456074.
[5] Do, T. N.; Carloni, P.; Varani, G.; Bussi, G. J. Chem. Theory Comput. 2013, 9, 1720–1730.
[6] Davidson, A.; Leeper, T. C.; Athanassiou, Z.; Patora-Komisarska, K.; Karn, J.; Robinson, J. A.; Varani, G. Proc. Natl. Acad. Sci. USA 2009, 106, 11931–11936.
37
Keynote Lecture
T.33
Surface-hopping excited-state dynamics
Walter Thiel1
1
Max-Planck-Institut für Kohlenforschung, Mülheim
Semiempirical quantum-chemical methods are well-established tools for computational
studies of large molecules. [1] Methods with explicit orthogonalization corrections (OM1,
OM2, OM3) offer better overall accuracy in standard statistical evaluations of groundstate properties as well as qualitative improvements for hydrogen bonding and conformational properties. [2] OMx-based studies of electronically excited states employ
a general implementation of the GUGACI approach in a semiempirical framework [3]
which provides analytic gradients and nonadiabatic couplings. [4] Comparisons with
experimental and high-level ab initio benchmark data show that OMx-MRCI methods
describe electronically excited states reasonably well. [5] They can thus be used in
mixed quantum-classical dynamics [6] to investigate fast nonradiative relaxation processes after photoexcitation that often occur through conical intersections. [7] Numerous such surface-hopping dynamics studies have been carried out at the OM2-MRCI
level in recent years. [8–18] These simulations have provided insight into the photostability of DNA bases in different environments (gas phase, aqueous solution, singlestranded and double-stranded DNA oligomers), [8–12] the mechanism of photoinduced
molecular rotors, [13] the complete photochemical cycle of a GFP chromophore with ultrafast excited-state proton transfer, [14] the chiral pathways and mode-specific tuning
of photoisomerization in azobenzenes, [15,16] the competition between concerted and
stepwise mechanisms in the ultrafast photoinduced Wolff rearrangement of 2-diaza-1naphthoquinone, [17] and the photodynamics of a prototypical Schiff base. [18] The lecture will address the theoretical background of surface-hopping dynamics and present
selected OM2/MRCI applications.
References
[1] Thiel, W. WIREs Comput. Mol. Sci. 2013, accepted.
[2] Otte, N.; Scholten, M.; Thiel, W. J. Phys. Chem. A 2007, 111, 5751-5755.
[3] Koslowski, A.; Beck, M. E.; Thiel, W. J. Comput. Chem. 2003, 24, 714–726.
[4] Patchkovskii, S.; Koslowski, A.; Thiel, W. Theor. Chem. Acc. 2005, 114, 84-89.
[5] Silva-Junior, M. R.; Thiel, W. J. Chem. Theory Comput. 2010, 6, 1546-1564.
[6] Fabiano, E.; Keal, T.; Thiel, W. Chem. Phys. 2008, 349, 334 - 347.
[7] Keal, T. W.; Koslowski, A.; Thiel, W. Theor. Chem. Acc. 2007, 118, 837-844.
[8] Fabiano*, E.; Thiel, W. J. Phys. Chem. A 2008, 112, 6859-6863.
[9] Lan, Z.; Fabiano, E.; Thiel, W. J. Phys. Chem. B 2009, 113, 3548-3555.
[10] Lan, Z.; Lu, Y.; Fabiano, E.; Thiel, W. Chem. Phys. Chem. 2011, 12, 1989–1998.
38
Keynote Lecture
T.33
[11] Lu, Y.; Lan, Z.; Thiel, W. Angew. Chem. Int. Ed. Engl. 2011, 50, 6864–6867.
[12] Heggen, B.; Lan, Z.; Thiel, W. Phys. Chem. Chem. Phys. 2012, 14, 8137-8146.
[13] Kazaryan, A.; Lan, Z.; Schäfer, L. V.; Thiel, W.; Filatov, M. J. Chem. Theory Comput. 2011,
7, 2189-2199.
[14] Cui, G.; Lan, Z.; Thiel, W. J. Am. Chem. Soc. 2012, 134, 1662-1672.
[15] Weingart, O.; Lan, Z.; Koslowski, A.; Thiel, W. J. Phys. Chem. Lett. 2011, 2, 1506-1509.
[16] Gámez, J. A.; Weingart, O.; Koslowski, A.; Thiel, W. J. Chem. Theory Comput. 2012, 8,
2352-2358.
[17] Cui, G.; Thiel, W. Angew. Chem. Int. Ed. Engl. 2013, 52, 433–436.
[18] Spörkel, L.; Cui, G.; Thiel, W. J. Phys. Chem. A 2013, 117, 4574-4583.
39
T.34
Free Energy Landscapes in Biological Systems
Vittorio Limongelli1
1
Department of Pharmacy, University of Naples ”Federico II”, Naples
A detailed description of the molecular events ruling biologically relevant phenomena,
such as protein/DNA folding or ligand/target interaction, with an accurate estimation
of the free energy is of great help in speeding drug discovery strategies. In an ideal
situation, this information comes from structural studies (X-ray and NMR), however
these standard procedures often fail when either large conformational changes or solvent effects occur. Here, I will report on our recent advances in studying such motion
and ligand/protein interaction using enhanced sampling simulations. Particularly, I will
show the case of Cylooxygenases, Adenosine Deaminase and Thrombin Binding Aptamer [1–3], that demonstrate the important role played by target motion and waters
in ligand binding and the biological relevance of sampling even transient states during
these complex mechanisms. I will also illustrate recent advances in computing ligand
binding free energy in difficult docking cases [4] and the potentiality of combining enhanced sampling and coarse-grain methods to sample very long time-scale events in
large systems at a reasonable computational cost.
References
[1] Limongelli, V.; Bonomi, M.; Marinelli, L.; Gervasio, F. L.; Cavalli, A.; Novellino, E.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5411-5416.
[2] Limongelli, V.; Marinelli, L.; Cosconati, S.; La Motta, C.; Sartini, S.; Mugnaini, L.; Da Settimo, F.; Novellino, E.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1467-1472.
[3] Limongelli, V.; De Tito, S.; Cerofolini, L.; Fragai, M.; Pagano, B.; Trotta, R.; Cosconati, S.;
Marinelli, L.; Novellino, E.; Bertini, I.; Randazzo, A.; Luchinat, C.; Parrinello, M.
Angew. Chem. 2013, 125, 2325–2329.
[4] Limongelli, V.; Bonomi, M.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 63586363.
40
T.35
Dimensionality reduction as a tool for understanding
complex free energy landscapes
Gareth A. Tribello1
1
Atomistic Simulation Centre, Queen’s University Belfast
Atomistic simulation methodologies are now frequently used to shed light on the atomic
scale mechanisms that underlie experimentally-observed phenomena. However, as
the systems examined using simulations become progressively more and more complicated the sheer resolution of the data that is obtainable from a simulation begins to
present a problem. Atomistic simulations, by their very nature, provide high-dimensionality data, which oftentimes can only be interpreted by using physical/chemical intuition
obtained from experiments. This is obviously problematic if we want to predict new
chemical structures or novel reaction mechanisms based on simulations alone. Hence,
there is a growing interest in using machine learning algorithms and smart visualization
software to generate simplified representations of the data obtainable from atomistic
simulations so that it can be more easily understood and interpreted by a human user.
In my talk I will describe a new, dimensionality-reduction-based approach [1, 2] called
sketch-map that we have developed for visualizing the results from molecular dynamics (MD) simulations. In this approach we first select a set of landmark frames from
the trajectory and try to map out the spatial relationships between them in a lowerdimensionality space. This procedure gives us a set of bespoke collective variables
(CVs) that we can then use to project the free energy landscape. I will show two case
studies that demonstrate how this analysis can be used in practice. In the first I will
show how the coordinates extracted with this sketch-map analysis can be used to understand changes in the free energy surface of a Lennard-Jones cluster that occur as
a function of temperature [3]. In the second I will show how we can use sketch-map to
understand how point mutations affect the free energy surface for a short protein. I will
also show how bias potentials can be constructed as a function of the sketch-map coordinates and how these potentials can increase the rate at which configuration space
is sampled [2].
References
[1] Ceriotti, M.; Tribello, G. A.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2011, .
[2] Tribello, G. A.; Ceriotti, M.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2012, 109, 5196-5201.
[3] Ceriotti, M.; Tribello, G. A.; Parrinello, M. J. Chem. Theory Comput. 2013, 9, 1521-1532.
41
T.36
Computational techniques for investigating liquid
polyamorphism in water models
Jeremy C. Palmer1 , Fausto Martelli2 , Roberto Car2 and Pablo G.
Debenedetti1
1
Department of Chemical and Biological Engineering, Princeton University, NJ
2
Department of Chemistry, Princeton University, NJ
Many of the well-known thermodynamic anomalies of water, such as its negative thermal expansion and increased compressibility upon cooling, become more pronounced
when it is cooled below its freezing point into a metastable liquid. One thermodynamically consistent interpretation of water’s anomalies posits that water becomes highly
compressible when cooled below its freezing point due to the presence of a second critical point associated with a first-order phase transition between two metastable liquid
phases [1]. Because the region of the phase diagram where this hypothetical critical
point would occur is below the homogenous nucleation temperature of bulk water, obtaining direct experimental evidence to falsify the second critical point hypothesis has
so far proved to be a significant challenge.
We examine the phase behavior of the ST2 water model [2] under deeply supercooled conditions, using umbrella sampling (US) and well-tempered metadynamics
(WT-MetaD) to compute the reversible free energy surface parameterized by density
and bond-orientational order. We find that free energy surfaces computed with both
techniques clearly show two liquid phases in coexistence, in agreement with our earlier
US and grand canonical Monte Carlo calculations [3, 4]. The nature of the liquid-liquid
phase transition is also investigated by examining the finite-size scaling behavior of
the free energy barrier separating the two liquids. Our calculations show that the barrier height obeys the N 2/3 scaling law expected for a first-order transition, suggesting
the existence of an associated second critical point in ST2 water. Finally, we analyze the computational performance of the US and WT-MetaD methods. While we find
that US and WT-MetaD produce consistent free energy surfaces, the latter technique
is estimated to be more computationally efficient by an order of magnitude. Despite
its superior efficiency, however, several challenges have been identified in applying
WT-MetaD to study liquid-liquid phase transitions. Such challenges are discussed in
detail along with recent methodological advances that may improve the performance
of metadynamics.
References
[1] Poole, P. H.; Sciortino, F.; Essmann, U.; Stanley, H. E. Nature 6402, 360, 324–328.
[2] Stillinger, F. H.; Rahman, A. J. Chem. Phys. 1974, 60, 1545-1557.
42
T.36
[3] Liu, Y.; Palmer, J. C.; Panagiotopoulos, A. Z.; Debenedetti, P. G. J. Chem. Phys. 2012, 137,
214505.
[4] Liu, Y.; Panagiotopoulos, A. Z.; Debenedetti, P. G. J. Chem. Phys. 2009, 131, 104508.
43
T.37
Combining graph theory with molecular dynamics:
efficient exploration of complex reaction pathways from
nanostructures to proteins
Fabio Pietrucci1 , Grégoire A. Gallet1 , Wanda Andreoni1
1
Institute of Theoretical Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL)
Viewing a molecule or a condensed matter system as a network of chemical bonds
allows to employ in computational chemistry a number of powerful tools borrowed from
graph theory. Traditionally, this has been exploited in an attempt to build catalogues in
which static molecular geometries are correlated with useful physico-chemical properties. I will present a different point of view, where graph theory is exploited in combination with (ab initio or classical) molecular dynamics and enhanced sampling techniques
to greatly extend the accessible timescale, allowing to discover complex multi-step reaction pathways and leading to an efficient characterization of high-dimensional free
energy landscapes. At the core of the methodology lies the development of new topological coordinates derived from the adjacency matrix of chemical bonds and invariant
upon permutation of identical atoms [1, 2]. I will illustrate three problems which can be
tackled in a fresh new way by means of our approaches: complex transformations of
nanostructures [1,3], chemical reactions in water solution [2], and large conformational
changes of proteins [4, 5].
References
[1] Pietrucci, F.; Andreoni, W. Phys. Rev. Lett. 2011, 107, 085504.
[2] Gallet, G. A.; Pietrucci, F. (submitted) 2013.
[3] Pietrucci, F.; Andreoni, W. (submitted) 2013.
[4] Pietrucci, F.; Laio, A. J. Chem. Theory Comput. 2009, 5, 2197.
[5] Pietrucci, F.; Mollica, L.; Blackledge, M. J. Phys. Chem. Lett. 2013, 4, 1943-1948.
44
AIMD based Methods II
T.38
A new functional approach for correlated many electron
systems
Ralph Gebauer1 , Morrel H. Cohen2,3 , Roberto Car3
1
ICTP – The Abdus Salam International Centre for Theoretical Physics, Trieste
2
Department of Physics and Astronomy, Rutgers University, Piscataway
3
Department of Chemistry, Princeton University, Princeton
Computing the ground state energy of N interacting electrons is a central problem
in quantum chemistry and condensed matter physics. Finding ways to solve it with
reduced complexity compared to that of the many-body wavefunction has been a major
goal of research since the early days of quantum mechanics. Maximal reduction is
achieved in density-functional theory (DFT), which uses the electron density as the
basic variable. This approach has had a transformative impact on many sciences,
but difficulties have remained in finding accurate, parameter-free approximations to its
exchange-correlation energy functional which avoid self-interaction and capture strong
electron correlations.
In this talk, I will present a new approach to this problem where the basic variables
are the eigenfunctions of the single-particle reduced density matrix (i.e. the natural orbitals), its eigenvalues and two-particle joint occupation probabilities. In its simplest
formulation, the scheme retains the scaling with size of Hartree Fock (HF) theory, albeit with a considerably higher prefactor. Yet, it describes the dissociation of simple diatomic molecules and multi-atom chains with comparable accuracy of doubly occupied
configuration interaction, an approach that uses a compact basis of Slater determinants
but retains exponential scaling with size. Our approach is particularly powerful in the
high correlation limit, i.e. at intermediate and large interatomic separations where the
HF approximation fails badly due to the multi-reference character of the ground state
wavefunction. In this regime, the new approach outperforms not only HF and/or DFT
but also popular quantum chemistry methods like coupled cluster with single, double
and perturbative triple electron-hole excitations (CCSD(T)), which is often taken as a
standard of accuracy near equilibrium separations.
45
T.39
Building Classical Force-Fields from Maximally Localized
Wannier Orbitals
Rodolphe Vuilleumier1 , Sami Tazi2 , Christian Simon2 , Benjamin Rotenberg2 ,
Mathieu Salanne2
1
Ecole Normale Supérieure, UPMC Paris 06, Paris
2
UPMC Paris 06, CNRS, ESPCI, Paris
Using ab initio simulations for determining force-fields has the main advantage that the
electronic structure is then adapted to the environment of the system to be modeled.
However, such determination of force-fields is often based on fitting a number of parameters describing the force-field. Here, we show that maximally localized Wannier
orbitals (WO) can offer an alternative route for building force-fields from ab initio simulations. These orbitals allow for a description of the electronic structure in terms of
chemical bonds and lone pairs. Not only are they useful for describing the electrostatic
interaction between fragments and, for example, obtain in situ polarizabilities, but we
derive all terms of the interaction consistently, including repulsion and long-range dispersion, from the geometrical properties of these orbitals [1]. We first demonstrate the
validity of this approach on two very different materials: molten salts and liquid water,
for predicting both structural and thermodynamical quantities. The localized WOs provide the missing link between electronic structure in condensed-phase and material
properties.
Similarly, we used WO to derive polarizable force-fields for aqueous ions (Li+ , Na+ ,
K+ , Rb+ , Cs+ , Mg2+ , Ca2+ , Sr2+ and Cl− ). These force-fields are found to reproduce
structural, thermodynamical and transport properties of these ions. More importantly,
it is also shown that these force-fields can reproduce both the infinite dilution solutions
and the crystals, and are transferable to high concentration solutions [2].
References
[1] Rotenberg, B.; Salanne, M.; Simon, C.; Vuilleumier, R. Phys. Rev. Lett. 2010, 104, 138301.
[2] Tazi, S.; Molina, J. J.; Rotenberg, B.; Turq, P.; Vuilleumier, R.; Salanne, M. The Journal of
Chemical Physics 2012, 136, 114507.
46
T.40
The GPW-RI Method for Periodic Hartree-Fock, MP2, and
RPA Calculations.
Jürg Hutter1
1
Physikalisch-Chemisches Institut, Universität Zürich
Second-order Moller-Plesset perturbation energy (MP2) and the Random Phase Approximation (RPA) correlation energy, are popular post-Kohn-Sham correlation methods. A novel algorithm, based on a hybrid Gaussian and Plane Waves (GPW) approach with the resolution-of-identity (RI) approximation, is developed for MP2, scaled
opposite-spin MP2 (SOS-MP2) and direct-RPA (dRPA) correlation energies of finite
and extended system. Three center electron repulsion integrals necessary in the RI
approximation are computed by direct integration between the products of Gaussian
basis functions and the electrostatic potential arising from the RI fitting densities. The
electrostatic potential is obtained in a plane waves basis set after solving the Poisson
equation in Fourier space. This scheme is highly efficient for condensed phase systems and offers a particularly easy way for parallel implementation. The RI approximation allows to speed up the MP2 energy calculations by a factor 10 to 15 compared to
the canonical implementation, but still requires O(N5 ) operations. On the other hand the
combination of RI with a Laplace approach in SOS-MP2 and an imaginary frequency
integration in dRPA, reduces the computational effort to O(N4 ) in both cases. Our implementations have low memory requirements and display excellent parallel scalability
up to tens of thousands of processes and can make efficient use of graphics processing units (GPU). In this way, RI-MP2, RI-SOS-MP2 and RI-dRPA calculations for
condensed phase systems containing hundreds of atoms and thousands of basis functions can be performed within minutes employing few thousands of processes. In order
to validate the presented methods, various molecular crystals have been calculated as
benchmark systems to assess the performance, while solid LiH has been used to study
the convergence with respect to basis set and system size in the case of RI-MP2 and
RI-dRPA. First results on the properties of liquid water using these methods have been
have been calculated using an isothermal-isobaric Monte Carlo procedure.
47
T.41
Water and ice at surfaces
Angelos Michaelides1
1
Thomas Young Centre, Department of Chemistry & London Centre for
Nanotechnology, University College London
Water/solid interfaces are relevant to a broad range of physicochemical phenomena
and technological processes such as corrosion, lubrication, heterogeneous catalysis
and electrochemistry [1]. In this talk some of our recent work in this area will be discussed. This includes a discussion on the importance of quantum nuclear effects in
hydrogen-bonded clusters, crystals, and overlayers [2,3] along with a discussion of the
importance of van der Waals forces in water adsorption [4] and high pressure ice [5].
Time permitting, our suggestion that the surface of crystalline ice exhibits properties
redolent of an amorphous material will also be discussed [6].
References
[1] Carrasco, J.; Hodgson, A.; Michaelides, A. Nat. Mater. 2012, 11, 667–674.
[2] Li, X.-Z.; Probert, M. I. J.; Alavi, A.; Michaelides, A. Phys. Rev. Lett. 2010, 104, 066102.
[3] Li, X.-Z.; Walker, B.; Michaelides, A. Proceedings of the National Academy of Sciences 2011,
108, 6369-6373.
[4] Carrasco, J.; Santra, B.; Klimeš, J. c. v.; Michaelides, A. Phys. Rev. Lett. 2011, 106, 026101.
[5] Santra, B.; Klimeš, J. c. v.; Alfè, D.; Tkatchenko, A.; Slater, B.; Michaelides, A.; Car, R.;
Scheffler, M. Phys. Rev. Lett. 2011, 107, 185701.
[6] Watkins, M.; Pan, D.; Wang, E. G.; Michaelides, A.; VandeVondele, J.; Slater, B. Nat. Mater.
2011, 10, 794–798.
48
T.42
Structure and chemistry of III-V semiconductor-water
interfaces for solar hydrogen production
Brandon C. Wood1 , Eric Schwegler1 , Woon Ih Choi1 , Tadashi Ogitsu1
1
Lawrence Livermore National Laboratory, USA
Photoelectrochemical cells promise sustainable production of hydrogen from water using sunlight. The most efficient photocathodes are based on III-V phosphides; however,
photocorrosion in the electrolyte solution remains a significant challenge. Much of the
difficulty arises from a fundamental lack of understanding of the complex chemistry active at the solid-liquid interface. Accordingly, we have performed Car-Parrinello molecular dynamics simulations of model GaP(001) and InP(001) surfaces at the interface
with water. In addition to explicitly accounting for the presence of liquid water, we have
also studied the effect of experimentally reported, oxygen-derived surface adsorbates.
Our results show that surface oxygen dramatically alters the chemical properties of the
electrode-electrolyte interface, providing a kinetically feasible pathway for water dissociation [1]. This nucleates formation of an interfacial hydrogen-bond network, consisting primarily of surface-adsorbed hydroxyl and molecular water [2]. Interestingly, GaP
and InP demonstrate qualitatively different interfacial dynamics and hydrogen-bond
network structures, despite having identical crystal structures and very similar electronic properties. For instance, the InP-water interface exhibits much greater network
fluidity, exploring a larger topological space of hydrogen bonding. Similarly, surfaceadsorbed water and hydroxyl exchange dynamically with the solvent environment on
InP, but these same processes are kinetically inaccessible on GaP. We suggest that this
translates to the capability of InP for long-range hydrogen transport in a way kinetically
inaccessible to GaP [3].
In light of available experimental evidence, we will discuss potential implications of
the comparative interfacial dynamics of InP and GaP, including the relationship to the
mechanisms that underlie hydrogen evolution, electrochemical surface stability, and
native corrosion resistance. Our results point to the importance of key dynamical processes in determining the electrochemical properties of the semiconductor-water interface.
This work was performed under the auspices of the U.S. Department of Energy by
Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
References
[1] Wood, B. C.; Ogitsu, T.; Schwegler, E. J. Chem. Phys. 2012, 136, 064705.
[2] Wood, B. C.; Ogitsu, T.; Schwegler, E. J. Photon. Energy 2011, 1, 016002.
[3] Wood, B. C.; Schwegler, E.; Choi, W. I.; Ogitsu, T. submitted 2013, .
49
T.43
Proton coupled electron transfer in water photo-oxidation at
TiO2 water interface
Jun Cheng1 , Marialore Sulpizi2 , Joost VandeVondele3 , Michiel Sprik1
1
2
Department of Physics, Johannes Gutenberg University, Mainz
3
Department of Materials, ETH, Zurich
Four-electron transfer reactions in water photo-oxidation on TiO2 have been studied
using a newly developed method. This method combines ab intio molecular dynamics
simulations and free energy perturbation theory to compute thermochemistry of proton
coupled electron transfer (PCET) [1]. Decomposition of dehydrogenation into deprotonation and oxidation allows us to scrutinize the PCET steps at the interface and
better understand the activity/inactivity of catalysts. On the other hand, such a separation is crucial to understand the error in the calculations using standard GGA density
functionals [2]. The inaccuracy in GGAs, namely delocalization error, has profound
consequence in calculation of defects in semiconductors, and has been widely studied
and relatively well understood in solid state community [3]. In this respect, there is
a close parallel between semiconductor photoelectrocatalysis and defect physics [4].
Inclusion of a fraction of exact exchange in density functionals can alleviate this error,
giving rise to correct localization of electronic holes on reaction intermediates at the
interface. On the basis of understanding of delocalization error, we will present the
energetics of reaction intermediates calculated by using a screened hybrid functional
(HSE06 [5]). We find that the main catalytic activity of TiO2 lies on aligning the pKa’s
of reaction intermediates along the reaction pathway, while redox potentials are still
far from ideal alignment. A simple model is proposed to understand how the band
structures of materials modulate the electronic energy levels (redox potentials) of intermediates, which may have important implications on designing catalytic materials with
optimal band structures in order to facilitate electron transfer at interfaces.
References
[2] Cheng, J.; Sulpizi, M.; VandeVondele, J.; Sprik, M. ChemCatChem 2012, 4, 636–640.
[3] Van de Walle, C. G.; Janotti, A. Phys. Status Solidi B 2011, 248, 19–27.
[4] Adriaanse, C.; Cheng, J.; Chau, V.;
J. Phys. Chem. Lett. 2012, 3, 3411-3415.
Sulpizi, M.;
VandeVondele, J.;
Sprik, M.
[5] Krukau, A. V.; Vydrov, O. A.; Izmaylov, A. F.; Scuseria, G. E. J. Chem. Phys. 2006, 125,
224106.
50
Abstracts of Posters
Poster discussion with refreshments and snacks
Tuesday, September 03
4.30 pm - 6.30 pm
Foyer of the
Fakultät für Chemie und Mineralogie
Johannisallee 29
04103 Leipzig
Please have your Posters pinned before Tuesday’s afternoon Session (2.30 pm) and
make sure to remove your Posters till Wednesday evening.
Postersession
P.1
Structure, Dynamics and Spectroscopy of ionic cluster by
DFT-MD simulations: Modeling IR-PD experiments
Sacha Abadie1 , Riccardo Spezia1 , Marie-Pierre Gaigeot1
1
Laboratoire Analyse et Modelisation pour la Biologie et Environnement (LAMBE)
Our purpose is to model the absorption and redistribution of energy in clusters and matrices in order to 1) directly model IR-PD experiments (InfraRed PreDissociation) from
our partner Prof Lisy at Urbana-Champaign USA where one photon is absorbed and
leads to the departure of argon from the ionic cluster, and 2) isomerization of solutes
in argon matrices following one photon absorption in collaboration with R.B. Gerber in
Finland. We develop methods in order to absorb one photon in selected modes, taking
quantum effects into account, and follow in time the redistribution of energy within the
system and the consequences in terms of structural dynamics of the system. We will
illustrate these points using DFT-based molecular dynamics simulations achieved with
the CP2K package on two model systems: (Cl-NMA)Ar in the gas phase (IRPD) and
trans-cis Formic Acid isomerization in argon matrix.
52
Postersession
P.2
An Ab Initio Microscope: Molecular Contributions to the
Femtosecond Time-Dependent Fluorescence Shift of a
Reichardt-Type Dye
Christoph Allolio1 , Mohsen Sajadi2 , Nikolaus Ernsting2 , Daniel Sebastiani1
1
Department of Chemistry, Martin-Luther Universität Halle-Wittenberg
2
Department of Chemistry, Humboldt-Universität zu Berlin
The molecular probe N -methyl-6-quinolone (MQ) gives spectroscopic access to its
local environment. [1] Using ab-initio molecular dynamics, we have simulated the excited state solvation of MQ [2] and the time evolution of its Stokes shift in aqueous
solution. [3] Results are in good agreement with experimental data obtained using femtosecond spectroscopy. The effect of electronic excitation is decomposed into contributions from spatial domains around the chromophore. An important contribution to the
time-dependent Stokes shift originates from a group of water molecules that strongly
interact with the molecular dipole of MQ.
References
[1] Pérez Lustres, J. L.; Kovalenko, S. A.; Mosquera, M.; Senyushkina, T.; Flasche, W.; Ernsting, N. P. Angew. Chem. Int. Ed. Engl. 2005, 44, 5635–5639.
[2] Allolio, C.; Sebastiani, D. Phys. Chem. Chem. Phys. 2011, 13, 16395–16403.
[3] Allolio, C.; Sajadi, M.; Ernsting, N. P.; Sebastiani, D. Angew. Chem. Int. Ed. Engl. 2013, 52,
1813–1816.
[4] Sajadi, M.; Ajaj, Y.; Ioffe, I.; Weingärtner, H.; Ernsting, N. Angew. Chem. Int. Ed. Engl. 2010,
49, 454–457.
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Car-Parrinello molecular dynamics with a time-dependent
potential field
Tobias Alznauer1 , Jörg August Becker1
1
Institut für Physikalische Chemie und Elektrochemie, Universität Hannover
We have implemented into the Car-Parrinello molecular dynamics code a sinusoidal
potential field which may change temporally and spatially. Electric fields may have an
effect on the formation of clusters in the gas phase. Applications to the first-principles
molecular dynamics simulation of MgO clusters are discussed.
The figure shows a (MgO)9 cluster and the potential field.
54
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QM/MM CPMD study on the reaction mechanism of Nylon
oligomer Hydrolase
T. Baba1 , K. Kamiya2 , M. Boero3 , M. Nakano1 , S. Negoro4 , Y. Shigeta1
1
Graduate School of Engineering Science, Osaka University, 1-1 Machikaneyama,
Toyonaka, Osaka
2
Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1
Tennodai,Tsukuba, Ibaraki
3
4
Institut de Physique et Chimie des Materiauxde Strasbourg (IPCMS)
CNRS-University of Strasbourg 23 rue du Loess 67034 Strasbourg
Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo
Nylon-6 is a long polymer generally consisting of more than one hundred units of 6aminohexanoate (Ahx). The byproducts (Ahx-linear and Ahx-cyclic oligomers), generated during the production stage, represent wastes to be disposed and possibly recovered as raw material. Recently, the enzymatic hydrolysis of the Ahx-linear dimer (Ald)
into the Ahx has become a target of increasing research efforts in order to develop a
highly active nylon-6 byproducts-degrading enzyme (nylon oligomer hydrolase, NylB),
which may lead to advanced environmental cleanup systems. On the basis of the enzymatic activity of several mutants, the catalytic sites could be unraveled: They are
composed of Ser112, Lys115, Tyr170 and Tyr 215. [1] Although the reaction mechanism of NylB resembles that of a protease, details are still unknown. A major difference
between the NylB and the protease is existence of Tyr170, which belongs to a loop region and binds to the substrate.
In order to clarify the role of Tyr170, we inspected mutational effects (Tyr170 to Phe170)
on substrate-enzyme binding structures [2] and the reaction mechanism of the hydrolysis undergoing in this enzyme by using classical Molecular Dynamics and QM/MM CarParrinello Molecular Dynamics with a metadynamics approach, respectively. We found
that the substrate bound to the Y170F mutant looses several hydrogen bonds resulting in worse stability with respect to the WT. The reaction mechanism for the wild-type
(WT) is determined and two possible reasons for mutation are identified both from the
binding structures and the obtained reaction mechanism.
References
[1] Negoro, S.; Ohki, T.; Shibata, N.; Sasa, K.; Hayashi, H.; Nakano, H.; Yasuhira, K.; ichiro
Kato, D.; Takeo, M.; Higuchi, Y. J. Mol.Biol. 2007, 370, 142 - 156.
[2] Baba, T.; Kamiya, K.; Matsui, T.; Shibata, N.; Higuchi, Y.; Kobayashi, T.; Negoro, S.;
Shigeta, Y. Chem. Phys. Lett. 2011, 507, 157 - 161.
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Electronic structure of liquid water
Imre Bakó1 , Kersti Hermannson2
1
Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest
2
Department of Materials Chemistry, Uppsala University, Ångström Lab, Uppsala
Water plays a crucial role in many biological, chemical and environmental processes.
Despite the tremenditous effort put in this field the microscopic structure of ambient
liquid water is still a matter of current debate. It is clear, that the H-bonding interaction
is one of the major force in determining the spatial arrangement of water molecule
in liquid water. We present ab initio molecular dynamic simulation studies on liquid
water using density functional theory (BLYP) with empirical van der Waals (Grimme
D3) correction at 300 K and 350 K. Our results show an excellent agreement between
the calculated and “measured” O· · · O radial distribution function at both temperatures.
We investigated also the correlation between the dipole moment, density of states of
molecular orbital and the H-bonded neighbouring number
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Vibrational spectroscopy with DFTB-MD in the gas phase:
is it accurate enough in comparison to DFT-MD?
Marie-Laure Bonnet1 , James M. Lisy2 , Marie-Pierre Gaigeot1
1
UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement,
Université d’Évry-Val-d’Essonne
2
University of Illinois at Urbana Champaign, Chemistry department, Urbana, Illinois
We benchmark here the performances of DFTB-MD (DFT Tight-Binding electronic representation) [1–4] on vibrational spectroscopy of neutral NMA (N-Methyl-Acetamide)
and protonated peptides (Ala2 H+ , Ala3 H+ , Ala7 H+ ): the benchmark is performed with
respect to spectra obtained by DFT-MD in previous works of the group. [5–7] A particular emphasis is given on DFTB-MD on charged peptides, as DFTB-MD is known to
have some problems to describe correctly charged organic molecules.
References
[1] Foulkes, W. M. C.; Haydock, R. Phys. Rev. B 1989, 39, 12520–12536.
[2] Porezag, D.; Frauenheim, T.; Köhler, T.; Seifert, G.; Kaschner, R. Phys. Rev. B 1995, 51,
12947–12957.
[3] Seifert, G.; Porezag, D.; Frauenheim, T. Int. J. Quant. Chem. 1996, 58, 185–192.
[4] Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.;
Seifert, G. Phys. Rev. B 1998, 58, 7260–7268.
[5] Gaigeot, M. P.; Vuilleumier, R.; Sprik, M.; Borgis, D. J. Chem. Theory Comput. 2005, 1,
772-789.
[6] Marinica, D. C.; Grégoire, G.; Desfrançois, C.; Schermann, J. P.; Borgis, D.; Gaigeot, M. P.
J. Phys. Chem. A 2006, 110, 8802-8810 PMID: 16836443.
[7] Cimas, A.; Vaden, T. D.; de Boer, T. S. J. A.; Snoek, L. C.; Gaigeot, M.-P. J. Chem. Theory Comput. 2009, 5, 1068-1078.
57
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Magnetic interactions in the Mn4 CaO5 core of Photosystem
II by Quantum Mechanics / Molecular Mechanics
simulations at room temperature
Daniele Bovi1 , Daniele Narzi1 , Leonardo Guidoni1,2
1
2
Dept. of Physics, Sapienza - University of Rome
Dept. of Phisical and Chemical Sciences, University of L’Aquila
The molecular mechanisms of water splitting in the oxygen evolving complex (OEC) of
Photosystem II are still unclear and partially unknown. The understanding of the catalytic strategies used by the OEC core, the Mn4 CaO5 active site, is important to unravel
the mechanisms of water oxidation in photosynthesis and can also serves to inspire
the modelling and design of biomimetic catalysts based on Mn, which is a largely nontoxic, earth abundant element. In the computational modelling of such complex system, several ingredients may play an important role: the appropriate description of the
electron correlation effects in the metal cluster, [1] the inclusion of the middle and longrange effect of the surrounding proteins, and the effect of temperature on the stability of
different states. To take all these issues into account, we used a Quantum Mechanics
/ Molecular Mechanics Approach based on DFT+U broken symmetry ab initio molecular dynamics simulations, considering as quantum system the Mn4 CaO5 cluster and
its surrounding residues and water molecules (206 atoms totally). [2] The two different
structural models (model A and model B) proposed for the S2 state, [3] with high-spin
and low-spin ground states respectively, were stable during the simulated time of 15 ps.
Along both simulations we analyse the dynamics fluctuations of the magnetic coupling
constants and the geometry of the Mn4 CaO5 cluster. By Fourier transforming the time
autocorrelation function of the atomic velocities, vibrational frequencies and modes are
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extracted from the QM/MM molecular dynamics following the effective normal mode
procedure described in, [4] thus taking into account the temperature and anharmonicity effects. A comparison between the cluster modes and the changes of the coupling
constants Jij allow us to understand the role of the environment and temperature fluctuations on the magnetic interactions of the OEC core, as already done in the case of
Anabaena ferredoxin. [5] Differences and similarities between the calculated spectra
for the two models (A and B) will be also described in the 300-700 cm−1 region.
References
[1] Bovi, D.; Guidoni, L. J. Chem. Phys. 2012, 137, 114107.
[2] Bovi, D.; Narzi, D.; Guidoni, L. “Magnetic interactions in the catalyst used by nature to split
water: a DFT+U multiscale study on the Mn4CaO5 core in Photosystem II and Spin Surfaces
in the S2 State of the Oxygen-Evolving Complex of Photosystem II”, 2013 submitted.
[3] Pantazis, D. A.; Ames, W.; Cox, N.; Lubitz, W.; Neese, F. Angew. Chem. Int. Ed. Engl. 2012,
51, 9935–9940.
[4] Gaigeot, M.-P.; Martinez, M.; Vuilleumier, R. Mol. Phys. 2007, 105, 2857-2878.
[5] Schreiner, E.; Nair, N. N.; Pollet, R.; Staemmler, V.; Marx, D. Proc. Natl. Acad. Sci. U.S.A.
2007, 104, 20725-20730.
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P.9
String method with optimal molecular alignment for freely
tumbling systems
Davide Branduardi1 , José D. Faraldo-Gómez1,2
1
Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics,
Frankfurt am Main
2
Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute,
National Institutes of Health, Bethesda
The string method [1] is a molecular-simulation technique that aims to calculate the
minimum free-energy path of a chemical reaction or conformational transition, in the
space of a predefined set of reaction coordinates that is typically highly dimensional.
Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates [2] of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a nontrivial problem, in that they are not invariant to
rigid-body molecular rotations and translations, which ideally ought to be unrestricted in
the simulations. To overcome this difficulty, we reformulate the framework of the string
method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use
of Cartesian reaction coordinates in freely tumbling molecular systems. [3] In addition,
this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism
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of the simulated process. This detailed analysis also provides a physically meaningful
criterion to coarse-grain the representation of the path. To demonstrate the accuracy
of the method, we analyze the isomerization of the alanine dipeptide in a vacuum and
the chair-to-inverted-chair transition of ?-D mannose in explicit water. Notwithstanding
the simplicity of these systems, the SOMA approach reveals novel insights into the
atomic mechanism of these isomerizations. In both cases, we find that the dynamics
and the energetics of the isomerization process are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show
that a coarse-grained SOMA calculation defined in terms of these subsets of atoms
yields near-identical minimum free-energy paths and committor distributions to those
obtained via a highly dimensional string.
References
[1] Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. J. Chem. Phys. 2006, 125,
024106.
[2] Khavrutskii, I. V.; J. Andrew McCammon, J. A. J. Chem. Phys. 2007, 124901.
[3] Branduardi, D.; Faraldo-Gómez, J. D. Unpublished data.
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P.10
Structural predictions of platinated proteins involved in the
resistance mechanisms of the anticancer drug cisplatin
Vania Calandrini1 , Trung Hai Nguyen1 , Fabio Arnesano5 , Emiliano Ippoliti1 ,
Giulia Rossetti3,4 , Giovanni Natile5 , Paolo Carloni1,2
1
Computational Biophysics, German Research School for Simulation Sciences, Jülich
2
3
4
Institute for Advanced Simulation IAS-5, Computational Biomedicine,
Forschungszentrum Jülich
John von Neumann Institut for Computing (JSC), Forschungszentrum Jülich
IRB-BSC Computational Biology Programme, Institute of Research in Biomedicine,
Parc Cientıfic de Barcelona
5
Department of Chemistry, University of Bari “A. Moro”, Bari
The clinical efficiency of the widely used drug cisplatin is severely limited by the emergence of resistance. At the molecular level, this is related, among other factors, to drug
binding to proteins involved in maintenance of copper homeostasis. Structural information on the platinated proteins, required to understand drug resistance mechanisms
and eventual counteract them, is unfortunately mostly lacking. Here we use QM/MM
simulations approaches to predict the structure of the platinated adducts involving two
of these proteins, ATP7A and Atox1, recently characterized by some of us by molecular spectroscopy. Comparison between calculated and experimental NMR and CD
data allow us to establish the predictive power of our calculations. These are among
the very first studies, at the theoretical level, of cisplatin-resistance mechanisms.
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β2–α2 loop landscape in prion protein
Enrico Caldarulo1 , Alessandro Barducci1,2 and Michele Parrinello1
1
Computational Science, Department of Chemistry and Applied Biosciences, ETH
Zurich, and Facoltà di Informatica, Istituto di Scienze Computazionali, USI Campus,
Lugano
2
Laboratory of Statistical Biophysics, Institute of Theoretical Physics, École
Polytechnique Fédérale de Lausanne
Transmissible spongiform encephalopathies (TSEs) are lethal neurodegenerative diseases that affect humans and a large variety of animals. According to the “protein only
hypothesis”, the infectious agent responsible for TSEs is an abnormally folded and aggregated protein that propagates itself by imposing its conformation onto the cellular
prion protein of the host. The conversion is the result of a posttranslational process
whereby most α-helical motifs are replaced by the β-sheet secondary structures, albeit
no atomistic-resolution structural information is available.
In the prion protein (PrP) conserved scaffold, a surface area including the loop that
connects the strand β2 with the helix α2 has attracted special interest due to its high
sequence and three-dimensional structure variability among mammalian PrPs. Several
studies have indicated that a surface epitope that includes the β2–α2 loop plays an
important role in prion pathology.
NMR experiments performed by the group of Prof. K. Wütrich on the mouse PrP, suggested that this loop is likely to be dynamic equilibrium and to populate multiple conformations. Mutations in the loop can significantly affect this equilibrium, indeed for
the WT the major state is the 310 -helical whereas the I β-turn state is the most populated in the Y169A mutant. We characterize with atomistic details the conformational
landscape of the mouse PrP β2-α2 loop for the WT and the mutant Y169A using an
advanced computational scheme combining the Well-Tempered Ensemble with Parallel
Tempering (WTE+PT) simulations. WTE uses a bias on the total potential energy of the
solvated protein and enhances the conformational fluctuations of the system. These
enhanced fluctuations facilitate higher exchange probabilities with fewer replicas in the
PT simulation. In this way, we extend the NMR results providing a free energy landscape and an ensemble of conformers, including the low populated states that are not
characterizable by the NMR experiment.
To represent our data we use a dimensional reduction method (sketch map) developed
in our group which is able to represent the configurations of the β2-α2 loop in a two
dimensional plane.
In (Fig. 1 and 2) panel a we show the free energy landscape projected on our coordinate system at 300K. In the WT (Fig. 1 panel a) four clearly defined states can be
identified three, of the 310-helical turn type (HT1 HT2 HT3) one of the I β-turn type
(BT). These states are dynamically well defined as can be seen in panel b where we
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show the conformations visited in standard MD simulation, initiated from configurations
of the four types. It is clearly seen during the four runs which lasted 100ns no interconversion between the different conformers are observed.
The data for the mutant Y169A are shown in Fig. 2 panel a here three different states
can be seen HT, BT1, BT2. This time are two of the I β-turn type (BT1, BT2) and one
of the 310 -helical turn type (HT). All these are dynamically stable (see Fig. 2 panel b).
Figure 1: Panel a - Free energy landscape
Panel b - Conformations visited in standard MD simulations
Figure 2: Panel a - Free energy landscape
Panel b - Conformations visited in standard MD simulations
64
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P.13
Car-Parrinello molecular dynamics study of some aromatic
molecules in water
Ashu Choudhary1 , Amalendu Chandra2
1
Department of Chemistry, Indian Institute of Technology, Kanpur
We present an ab initio molecular dynamics study of benzene dissolved in ambient and
supercritical water by using the Car–Parrinello method [1] and CPMD code. [2] The
changes in the hydration structure with temperature are reflected in the pair correlation
functions of solute-water in axial and equatorial regions around the aromatic solutes. [3,
4] The orientational relaxation times and diffusion coefficients of solvent molecules,
calculated in different angular conical regions around aromatic solutes, shows that the
water molecules present axial to the rings can reorient and translate faster than water
molecules present equatorial to the rings. The changes of coordinated water molecules
in the hydration shell of solutes with increase of temperature and decrease of density
have also been studied. Most probable region for πH-bonding found is axial region
around benzene C6 axis with conical angle of 45 ◦ .
References
[1] Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471–2474.
[2] Hutter, J. t. CPMD Program Package.
[3] Raschke, T. M.; Levitt, M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6777-6782.
[4] Raschke, T. M.; Levitt, M. The Journal of Physical Chemistry B 2004, 108, 13492-13500.
[5] Suzuki, S.; Green, P. G.; Bumgarner, R. E.; Dasgupta, S.; Goddard, W. A.; Blake, G. A.
Science 1992, 257, 942-945.
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P.14
Evidence and characterisation of nuclear quantum effects
in condensed matter
Jérôme Cuny1 , Ali A. Hassanali2 , Michele Ceriotti3 , Mickaël Deschamps4 ,
Michele Parrinello2
1
Laboratoire de Chimie et Physique Quantiques, Université Paul Sabatier, Toulouse
Department of Chemistry and Applied Biosciences, ETH Zurich and Università della
Svizzera Italiana, Lugano
3
Physical & Theoretical Chemistry Laboratory, Oxford
4
CEMHTI-CNRS UPR3079, Conditions Extrêmes et Matériaux: Haute Température et
Irradiation, Orléans
Nuclear quantum effects (NQE) are generally neglected when modelling condensed
phase systems. Although generally correct, the studies by M. Parrinello and M. Tuckerman on the structure and the mechanisms of proton transfer have shown the limit
of this approximation. [1] We have recently revisited this problematic, not only in the
case of liquid systems, but in the case of solid-state compounds. In particular, I will
present studies on hydrogen chloride hydrates for which we have evidenced a major
influence of NQE on their nuclear magnetic resonance (NMR) properties (see Figure)
and on their proton momentum distributions. [2] Then, I will present an extension of
these studies concerning phosphate materials. In these compounds, our combined
experimental/theoretical work have clearly evidenced the fundamental role of NQE on
the proton NMR properties with respect to the temperature. These studies have, from
our point of view, important implications to understand the role of NQE in hydrogen
bonded materials.
2
Figure: Distribution of 1 H shielding of protons compressed in O-H-O motifs in the hydrogen chloride di-hydrate obtained from a quantum molecular dynamics simulation. [2]
References
[1] Tuckerman, M. E.; Marx, D.; Parrinello, M. Nature 2002, 417, 925–929.
[2] Hassanali, A. A.; Cuny, J.; Ceriotti, M.; Pickard, C. J.; Parrinello, M. J. Am. Chem. Soc.
2012, 134, 8557-8569.
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P.16
Rate constants from equilibrium simulations: a new method
Janos Daru1,2 , Andras Stirling2
1
2
Physical Chemistry Department, Eötvös Loránd University
Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungary
On the timescale of molecular simulations, reactions are rare-events. In most cases
direct calculation of rate constants requires unaffordable computational costs. We have
developed a theory and an algorithm to calculate rate constant from equilibrium simulations in a consistent and relatively cheap manner. The method requires the free
energy profile of the reaction, implying that a suitable reaction coordinate is already
identified. The ideas behind the method are to define the Reactive Segment (RS)
within the reactant state and to recognize that the corresponding rate constant, kRS
can be calculated very efficiently. The phenomenological rate constant can be easily
recovered by reweighing kRS with the statistical weight of the selected RS within the
full reactant state. If necessary the calculated rate constants can be used to derive activation free energies and related quantities. This can be useful to test the applicability
of a kinetic model or to make contact with previous results.
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Molecular Dynamics Perspective On the Intramolecular
Hydrogen Bond in Solution
Przemyslaw Dopieralski1 , Charles L. Perrin2 , Zdzislaw Latajka1
1
Faculty of Chemistry, University of Wroclaw
Department of Chemistry & Biochemistry, La Jolla, California
The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures
(sodium and potassium salts), then to aqueous solution, and finally in the presence of
counterions. By Car–Parrinello [1–3] and Path Integral Molecular Dynamics [4–6] simulations it is demonstrated that the position of the proton in the intramolecular hydrogen
bond of aqueous hydrogen maleate anion is entirely related to the solvation pattern
around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion
has an asymmetric hydrogen bond, with the proton always located on the oxygen atom
that is less well solvated, owing to the instantaneous solvation environment. Simulations on water solutions of hydrogen maleate ion with two different counterions, K+ and
Na+ , surprisingly show that the intramolecular hydrogen-bond potential in the case of
the Na+ salt is always asymmetric, regardless of the hydrogen bonds to water, whereas
for the K+ salt the potential for H motion depends on the location of the K+ . It is proposed that repulsion by the larger and more hydrated K+ is weaker than for Na+ and
competitive with solvation by water.
2
It is the water decision
References
[1] Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
[2] Hutter, J. t. CPMD Program Package.
[3] Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods;
Cambridge University Press: Cambridge, 2009.
[4] Marx, D.; Parrinello, M. Z. Phys. B 1994, 95, 143-144.
[5] Marx, D.; Parrinello, M. J. Chem. Phys. 1996, 104, 4077-4082.
[6] Tuckerman, M.; Marx, D.; Klein, M.; Parrinello, M. J. Chem. Phys. 1996, 104, 5579-5588.
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The Effects of Fast Molecular Motions and Solvation on
NMR Parameters
Martin Dračı́nský1,2 , Petr Bouř2 , Thomas Exner3 , and Paul Hodgkinson1
1
2
3
Department of Chemistry, Durham University, Durham
Institute of Organic Chemistry and Biochemistry, Prague
Institute of Pharmacy, Eberhard Karls University, Tübingen
It is well established that fast molecular motions, such as vibrations, conformational averaging, molecular aggregation, will average NMR parameters. Isotope shifts and the
temperature dependence of NMR parameters are experimental manifestations of such
dynamic averaging effects. Quantum chemical calculations are typically performed
using static structures, i.e. at 0 K, and neglecting zero-point motion and dynamics
can lead to significant discrepancies between computed and experimental data. In
solutions, where the configurations of neighbours change dynamically, the intermolecular contributions to shielding also change with changing configurations. Therefore,
dynamic averaging needs to be taken into account, even when there are no significant strong intermolecular interactions, such as hydrogen bonding. In the solid state,
local dynamics will average the NMR tensor parameters, such as the chemical shift
anisotropy (CSA), dipolar interactions and quadrupolar interactions, leading to discrepancies between calculated data and experimental measurements (which are usually
performed at ambient temperature).
Solvent modeling has become a standard part of first principles computations of molecular properties. However, a universal solvent approach is particularly difficult for the
NMR shielding and spin-spin coupling constants that in part result from collective delocalized properties of the solute and the environment. In this work, bulk and specific
solvent effects are discussed on experimental and theoretical model systems comprising hydrated neutral (zwitterionic), cationic, and anionic forms of alanine, hydrated Nmethyl acetamide, and chloroform molecules in a series of solvents. Classical molecular dynamics (MD) simulations are compared to Car-Parrinello MD (CPMD) simulations. The quantum mechanical CPMD approach revealed a more structured solvent
and significant differences in the radial and angular distributions of the water molecules
around the solute. [1] NMR chemical shifts were calculated based on the generated
ensembles by density functional theory (DFT) and averaged. Obtained values were
significantly closer to experimental parameters than those calculated by the conventional implicit dielectric solvent model. [2] The NMR results also quantitatively reflect
the superiority of the CPMD over the MD explicit solvent treatment. [1, 3] Differently
positioned water molecules in the clusters cause an unexpectedly large variation of
the NMR parameters. The NMR chemical shift was found to be much more sensitive
to the molecular solvation than the coupling. The results thus indicate a large potential of the NMR spectroscopy and quantum simulations to probe not only the structure
of molecules but also their interactions with the environment. The results also show
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that computationally efficient solvent modeling is possible and can reveal fine details of
molecular structure, solvation, and dynamics.
The influence of fast molecular motions on NMR parameters in molecular organic solids
is explored on a set of amino acids and nucleic acid bases. A combination of DFT
molecular dynamics and calculations of shielding and electric field gradient (EFG) tensors reveals the impact of vibrational motions on isotropic chemical shifts, chemical
shift anisotropies and quadrupolar interactions. We demonstrate that molecular motion has a significant effect on average molecular structures, and that neglecting the
effects of motion on crystal structures derived by diffraction methods may lead to significant errors of calculated isotropic chemical shifts. Re-orientation of the NMR tensors
by molecular motion reduces the magnitudes of the NMR anisotropies, and inclusion
of molecular dynamics can significantly improve the agreement between calculated
quadrupolar couplings and experimental values. [4]
References
[1] Dračı́nský, M.; Kaminský, J.; Bouř, P. J. Phys. Chem. B 2009, 113, 14698-14707 PMID:
19863140.
[2] Dračı́nský, M.; Bouř, P. J. Chem. Theory Comput. 2010, 6, 288-299.
[3] Dračı́nský, M.; Möller, H. M.; Exner, T. E. J. Chem. Theory Comput. 2013, 9, 3806-3815.
[4] Dračı́nský, M.; Hodgkinson, P. CrystEngComm 2013.
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Collective proton tunnelling in ordinary ice
Christof Drechsel-Grau1 , Dominik Marx1
1
Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum
Nuclear quantum effects are well known to affect proton motion along individual hydrogen bonds. In ordinary ice Ih , an ubiquitous and prototypical hydrogen-bonded system, they lead to zero-point motional broadening of each individual proton. Although
nuclear quantum effects are generally rationalised at the single-particle level, recent
experimental work on hydrogen- bonded molecular crystals hints at the existence of
concerted tunnelling of many protons, which remains poorly understood. Here, using
ab initio path integral simulations of proton-disordered ice Ih , we show that correlated
quantum motion at low temperature corresponds to collective proton tunnelling. In this
regime, the six protons in proton-ordered hexagonal rings move concertedly without
violating the ice rules due to collective tunnelling, thus forming a quasi-particle described by a global order parameter. This collective motion is in stark contrast to both
the high-temperature hopping and the usual single-proton tunnelling along individual
hydrogen bonds via creation of topological charge defects. These fundamental findings shed new light on correlated many-body tunnelling in hydrogen-bonded networks
in the condensed phase whose implications extend far beyond this important example.
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Methanol synthesis from molecular dynamics
Johannes Frenzel1 , Luis Martı́nez-Suárez 1 , Bernd Meyer1 ,2 , Dominik Marx 1
1
2
Lehrstuhl für Theoretische Chemie, Ruhr–Universität Bochum
present address: Interdisziplinäres Zentrum für Molekulare Materialen (ICMM) and
Computer-Chemie-Centrum (CCC), Universität Erlangen-Nürnberg
Understanding structure–reactivity relationships and ultimately predicting reactivity is
a key objective in fundamental research in heterogeneous catalysis. Unfortunately,
the relevant catalytically active surface structures often only evolve under the temperature and pressure conditions of the running chemical reaction. By calculation of
a thermodynamic phase diagram (see figure) we provide an atomistic understanding
of the morphological changes in ZnO supported Cu nanocatalysts, which are subject
to strong metal–support interactions (SMSI), in response to the redox properties of
the surrounding gas phase. [1] It is shown that at the conditions of industrial methanol
synthesis complex electronic charge transfer processes across the metal/support interface, driven by morphological and electronic changes, explain the enhanced catalytic
reactivity. [1] An unexpectedly rich picture is unveiled by advanced molecular dynamics techniques [2, 3] when applied to methanol synthesis from CO and H2 on defective
ZnO surfaces, which itself are catalytically active. [4, 5] Using this approach for computational heterogeneous catalysis we find the underlying complex reaction network
from CO to methanol to be generated in the first place from ab inito molecular dynamics. [4, 5] The chemical reaction occurring on a seemingly well-defined appears to be
astonishingly complex. The intermediates along the catalytic cycle are found to depend in a sensitive way on the oxidation state of the surface. [5] In addition, it is seen
that the gas phase close to the surface might be transiently involved in some non-trivial
manner. [5]
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References
[1] Martı́nez-Suárez, L.; Frenzel, J.; Marx, D.; Meyer, B. Phys. Rev. Lett. 2013, 110, 086108.
[2] Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12562-12566.
[3] Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302.
[4] Kiss, J.; Frenzel, J.; Nair, N. N.; Meyer, B.; Marx, D. J. Chem. Phys. 2011, 134, 064710.
[5] Frenzel, J.; Kiss, J.; Nair, N. N.; Meyer, B.; Marx, D. Phys. Status Solidi B 2013, 250,
1174–1190 accepted.
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Proton transfer throught the water gossamer
Ali A. Hassanali1 , Federico Giberti1 , Jérôme Cuny2 , Thomas Kühne3 ,
Michele Parrinello1
1
2
Laboratoire de Chimie et Physique Quantiques - UMR 5626, Toulouse
3
Institute for Physical Chemistry, University of Mainz
The diffusion of protons through water is understood within the framework of the Grotthuss mechanism which requires that they undergo structural diffusion in a stepwise
manner throughout the water network. Despite long study, this picture oversimplifies
and neglects the complexity of the supramolecular structure of water. We use first principles calculations and look at the structure of water as a 3D network which allows us
to reveal medium range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated
with proton wires. These wires are the conduits for long proton jumps over several
hydrogen bonds. Proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that
emerges is that proton transfer is a multiscale and multidynamical process involving a
broader distribution of pathways and timescales than currently assumed.
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Implementation of image charges in QM/MM
Dorothea Golze1 , Marcella Iannuzzi1 , Jürg Hutter1
1
University of Zurich
A method for including polarization effects within hybrid quantum mechanics/molecular
mechanics (QM/MM) simulations of adsorbate-metal systems is presented. In a standard QM/MM description, the adsorbed molecules are treated by QM and the metal by
MM. The interactions between adsorbate and metal are usually described by an empirical potential where electrostatic interactions are neglected. However, polar adsorbates
can induce charges in the metal and interact with these charges. This classical phenomenon is referred to as image effect. It was shown that image charges are important
for determining the assembling behavior of organic molecules on metal surfaces. [1]
Image charges are also needed for a comprehensive description of processes at electrode interfaces. [2] In this work, the image charge method was implemented in the
QM/MM module [3, 4] of the CP2K [5] program package. The implementation is based
on the Siepmann-Sprik scheme, [6] where the image charge distribution in the metal
is modeled by a set of Gaussian charges centered at the metal atoms. The image
charges are determined self-consistently by imposing the constant-potential condition
within the metal. The structural and electronic effects due to the introduced polarization
were studied for benzene, nitrobenzene and DNA bases adsorbed at Au(111) as well
as for water on Pt(111). Large-scale molecular dynamics simulations of a water film
in contact with a Pt(111) surface show that our method is suitable for simulations of
liquid/metal interfaces at reduced computational cost.
References
[1] Tomba, G.; Stengel, M.; Schneider, W.-D.; Baldereschi, A.; De Vita, A. ACS Nano 2010, 4,
7545-7551.
[2] Reed, S. K.; Lanning, O. J.; Madden, P. A. J. Chem. Phys. 2007, 126, 084704.
[3] Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2005, 1, 11761184.
[4] Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2006, 2, 13701378.
[5] “The CP2K developers group”, 2013 CP2K is freely available from: http://www.cp2k.org/.
[6] Siepmann, J. I.; Sprik, M. J. Chem. Phys. 1995, 102, 511-524.
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The conformational free energy landscape of
2-deoxy-β-D-glucopyranose by ab initio metadynamics.
Implications for catalysis of β-glycosidases.
Javier Iglesias-Fernández1 , Albert Ardèvol2 , Xevi Biarnés3 , Antoni Planas3 ,
Carme Rovira1,4
1
Universitat de Barcelona and Institut de Quı́mica Teòrica i Computacional
2
Department of Chemistry and Applied Biosciences, ETH Zurich
3
4
Institut Quı́mic de Sarrià, Universitat Ramon Llull, Barcelona
During the past decade, structural studies have demonstrated that glycoside hydrolases (GH) usually bind the substrate in a distorted conformation. [1] Specifically, for
pyranoses, the saccharide unit located at the -I enzyme subsite distorts away from
the 4 C1 chair conformation into a boat or skew-boat conformation. Previous investigations in our group showed that these ring distorted conformations are “on the
path” towards the transition state (TS) of the enzymatic reaction, favoring the cleavage
of the glycosidic bond. [3] Therefore, knowledge of the precise substrate conformation in the Michaelis complex (E·S complex) is key to understand the conformational
route that the substrate follows during catalysis (the so-called “catalytic conformational
itinerary”). [1, 4]
2-deoxy glycosides normally act as GHs inhibitors due to the absence of the stabilizing
H-bond interaction at the 2 position of the sugar molecule. Surprisingly, kinetic assays on 1,3-1,4-β-glucanase show that the 2-deoxy substrate behaves in an opposite
way: it accelerates the enzymatic reaction. We applied Car-Parrinello molecular dynamics combined with the metadynamics approach [5, 6] to obtain the conformational
free-energy landscape [7, 8] for a 2-deoxy-β-D-glucopyranose molecule. Analysis of
changes in free energy, internal structure and the electronic changes with ring conformation provides insight into the question why this substrate exhibits an anomalous
behavior.
References
[1] Vocadlo, D. J.; Davies, G. J. Curr. Opin. Chem. Biol. 2008, 12, 539 - 555.
[2] Planas, A.; Nieto, J.; Abel, M.; Segade, A. Biocatalysis and Biotransformation 2003, 21,
223-231.
[3] Biarnés, X.; Nieto, J.; Planas, A.; Rovira, C. J. Biol. Chem. 2006, 281, 1432-1441.
[4] Davies, G. J.; Planas, A.; Rovira, C. Acc. Chem. Res. 2012, 45, 308-316.
[5] Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471–2474.
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[6] Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566.
[7] Biarnés, X.; Ardèvol, A.; Planas, A.; Rovira, C.; Laio, A.; Parrinello, M. J. Am. Chem. Soc.
2007, 129, 10686-10693.
[8] Ardèvol, A.; Biarnés, X.; Planas, A.; Rovira, C. J. Am. Chem. Soc. 2010, 132, 16058-16065.
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Mechanistic Investigation of the Wacker Process: A
Metadynamics Ab Initio Molecular Dynamics Study
Venkataramana Imandi1 , Sooraj Kunnikuruvan1 , Nisanth N. Nair1
1
Department of Chemistry, Indian Institute of Technology Kanpur
The Wacker process is a Pd/Cu catalyzed conversion of olefins to carbonyl compounds
through certain redox coupled reactions in the presence of water and molecular oxygen. The detailed reaction mechanism of the Wacker process has been studied by
both experiments and theory for the last few decades. Yet, the rate determining step
and the mode of water attack on the Pd complex are still a matter of debate. We have
studied the mechanism and kinetics [1] of this process at industrial conditions by using
the metadynamics technique in the framework of Ab Initio Molecular Dynamics. The
proposed mechanism has the ligand isomerization as the rate determining step. This
step occurs after the equillibrium hydroxypalladation step. This mechanism is an excellent agreement with experimental kinetics and kinetic isotopic effects. We have also
confirmed formation of Pd(0) is through reductive elimination and not via β-hydride
elimination.
References
[1] Imandi, V.; Kunnikuruvan, S.; Nair, N. N. Chem. Eur. J. 2013, 19, 4724–4731.
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Time evolution of the aromaticity index HOMA — a CPMD
approach
Aneta Jezierska-Mazzarello1 , Jarosław J. Panek1
1
Faculty of Chemistry, University of Wrocław
Aromaticity is a frequently invoked phenomenon, well understood qualitatively, but in
extreme cases difficult to be measured quantitatively; numerous indexes of aromaticity
have been introduced for this purpose. [1–3] Introduction of substituents makes it possible to modulate electronic structure of the aromatic moiety; an interesting phenomenon
is competition between substituents and elucidation of their conjugation pathways. Recent computational studies shed light on this subject in case of substituted benzene, [4]
benzoquinones [5] and naphthoquinones. [6] These studies are based on static DFT
calculations and investigations of correlations between structural parameters. High correlation coefficients were obtained for some pathways only, indicating the conjugation
routes.
The current study is based on the case of 2,3-naphthoquinone. [6] This compound
serves as a reference; two substitutions – 5-amino and 6-amino – were introduced and
tested independently. The Car-Parrinello and Born-Oppenheimer MD simulations were
carried out on isolated molecules of these compounds. Apart from the analysis of the
time evolution of the interatomic distances (bond lengths), Harmonic Oscillator Model
of Aromaticity (HOMA) index [1] was calculated along the MD trajectory to provide
additional information on modulation of the structure by the substituents.
We gratefully acknowledge the Wrocław Centre for Networking and Supercomputing
(WCSS Wrocław) and Interdisciplinary Centre for Mathematical and Computational
Modelling (ICM Warsaw) for the generous grants of computer time and facilities. This
work was supported by the National Science Centre (Poland) under the grant no. UMO2011/03/B/ST4/00699.
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References
[1] Krygowski, T. M.; Cyrański, M. K. Chem. Rev. 2001, 101, 1385-1420.
[2] Schleyer, P. v. R.; Maerker, C.; Dransfeld, A.;
J. Am. Chem. Soc. 1996, 118, 6317-6318.
Jiao, H.;
Hommes, N. J. R. v. E.
[3] Matta, C. F.; Hernández-Trujillo, J. J. Phys. Chem. A 2005, 109, 10798-10798.
[4] Krygowski, T. M.; Dobrowolski, M. A.; Cyrański, M. K.; Oziminski, W. P.; Bultinck, P. Comput.
Theor. Chem. 2012, 984, 36 - 42.
[5] Szatyłowicz, H.; Krygowski, T. M.; Palusiak, M.; Poater, J.; Solà, M. J. Org. Chem. 2011,
76, 550-556.
[6] Shahamirian, M.; Cyrański, M. K.; Krygowski, T. M. J. Phys. Chem. A 2011, 115, 1268812694.
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Uncoupling Proton Coupled Electron Transfer Reactions on
a MnO2 Surface
J. A. Kattirtzi1 , J. Cheng1 and M. Sprik1
1
A molecular level understanding of the interactions between a solid and an aqueous
solution is fundamental in many areas, including colloidal science, electrochemistry
and catalysis. Proton Coupled Electron Transfer reactions play a prominent role on
metal oxide surfaces in these areas of research. Uncoupling the reaction involves
studying the acidities, oxidation and dehydrogenation reactions.
MnO2 is a cheap naturally occurring electrochemical material with a widespread interest. In the fields of geological and interface sciences, the reactions on the surface in
aqueous solutions are important. Applications of the material include batteries, fuel
cells, super capacitors and electro-catalysts. Understanding the reactions on the surface of MnO2 has proven to be difficult and a computational understanding may aid
this.
The surface acidity is important in order to understand the reactions on the surface and
this is not directly accessible from experiment. The absolute positions of the energy
levels are required in order to develop MnO2 as a more efficient energy material. The
dehydrogenation of an absorbed water molecule allows investigation of MnO2 as a
catalyst for the PCET reaction of splitting a water molecule.
A method by Sulpizi and Sprik [1] using Density Functional Theory Molecular Dynamics (DFTMD) has been developed to calculate acidities. Cheng and Sprik [2] have
outlined methods available to calculate the positions of the electronic energy levels at
electrochemical interfaces.
In this work, we briefly present the H-insertion method that uses DFTMD to calculate
acidities, electronic energy levels and dehydrogenation levels. The method is applied
to the 110 Beta-MnO2 surface and the catalytic effect of splitting a water molecule on
the surface is investigated.
References
[1] Sulpizi, M.; Sprik, M. Phys. Chem. Chem. Phys. 2008, 10, 5238-5249.
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Clindamycin-bacterial ribosome interactions: a molecular
dynamics study
Katarzyna Kulczycka-Mierzejewska1 , Joanna Trylska2 , Joanna Sadlej3
1
College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences,
University of Warsaw
2
Centre of New Technologies, University of Warsaw
3
Faculty of Chemistry, University of Warsaw
Antibiotics are drugs that treat the diseases of bacterial and fungal origin. Secondary
uses include strengthening the immune system in cases of lowered immunity. Clindamycin is one of the antibiotics from the lincosamide class which are used to treat
diseases caused mostly by Gram-positive bacteria and against some protozoal diseases. Lincosamides interact with the bacterial large (50S) ribosomal subunit and
inhibit the process of protein synthesis leading to bacterial cell death. The increase
of resistance of many bacterial strains against known antibiotics is caused by the expanded use of antibiotics in medical practice and veterinary. This is a very important
reason for continuous work to find new, better and more effective antibacterial drugs.
Mutations of the antibiotic target are one of the common modifications that lead to
bacterial resistance because such alterations typically prevent proper binding of the
antibiotic in the targeted site. Currently, there are three structures of clindamycin in the
complex with the 50S ribosomal subunit available in the Protein Data Bank coming from
different organisms. Interestingly, two of the structures show significantly different conformations of the drug. The aim of this study was to compare the dynamic properties
of the clindamycin binding site in the 50S subunit with and without the A2058G mutation to understand why this nucleotide substitution blocks the binding of lincosamides.
To achieve this goal we applied full-atom molecular dynamics. Using the CP2K package we performed four types of simulations: (1) the complex of clindamycin with the
fragment of the 50S subunit of the ribosome as well as (2) the unbound ribosome fragment, (3) the complex of clindamycin with the mutated ribosome fragment and (4) the
unbound mutated ribosome fragment. To prepare the starting systems for the simulations we chose the 3OFZ 50S subunit structure from Escherichia coli, which consists
of ribosomal RNA, ribosomal proteins, one clindamycin molecule, magnesium and zinc
ions and crystal waters. For our simulations, we cut a sphere with the radius of about
20Åaround clindamycin to account for the long-range interactions of the antibiotics in
the 50S subunit. We added 228 K+ ions to neutralize the charge and approximately
27000 TIP3P water molecules to solvate the system shaped in a truncated octahedron around the complex. The effect of the mutation on clindamycin positioning in the
binding cleft resulting from these molecular dynamics simulations will be discussed.
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Exploring the reaction mechanism for OGT
glycosyltransferase using QM/MM molecular dynamics
Manju Kumari1 , Stanislav Kozmon1,2 , Igor Tvaroška3 , Jaroslav Koča1,2
1
CEITEC – Central-European Institute of Technology, Masaryk University (MU), Brno
2
National Centre for Biomolecular Research, Fac of Science, MU, Brno
3
Slovak Academy of Sciences, Institute of chemistry, Bratislava
Carbohydrates play a pivotal role in a plethora of the biological processes as they
are ubiquitously present in all cells in the variety of forms such as glycoproteins, proteoglycans and glycolipids collectively called as glyco-conjugates. Glyco-conjugates
carry the necessary information for cell-cell recognition [1–3] and their function is quite
diverse and vital for the cell. These glyco-conjugates are formed by the sequential
action of glycosyltransferases (GTase) which add saccharides onto proteins, lipids
etc. [4, 5] Our present study is focused on the exploring the reaction mechanisms of
O-GlcNAcylation process, where GlcNAc is transferred to –OH group of Ser/Thr of the
proteins. The aim of the study is to find the most probable reaction pathways and
corresponding transition states. Several mechanisms for the OGT glycosyltransferase
are already proposed on similar systems (Figure 1) [6–8]. The O-glycosylation reaction can utilize 1) HIS aminoacid residue as catalytic base [6], 2) α-phosphate as
base [7], and 3) water molecule for shunting proton out of the active site [8]. The hybrid
QM/MM method was used to model the proposed GTase mechanisms using the CPMD
software package. The reaction events are being enhanced by the metadynamics approach. The obtained results will be presented.
Figure:
Different
mechanisms
proposed for the OGT
glycosyltransferase.
1st mechanism
2nd mechanism
3rd mechanism
References
[1] QUIOCHO, F. Pure Appl. Chem. 1989, 61, 1293-1306.
[2] Vyas, N. K. Curr. Opin. Struct. Biol. 1991, 1, 732 - 740.
[3] Lee, Y. C.; Lee, R. T. Acc. Chem. Res. 1995, 28, 321-327.
[4] Breton, C.; Fournel-Gigleux, S.; Palcic, M. M. Curr. Opin. Struct. Biol. 2012, 22, 540 - 549.
[5] Lairson, L.; Henrissat, B.; Davies, G.; Withers, S. Annu. Rev. Biochem. 2008, 77, 521-555.
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[6] Tvaroska, I.; Kozmon, S.; Wimmerova, M.; Koca, J. J. Am. Chem. Soc. 2012, 134, 1556315571.
[7] Schimpl, M.; Zheng, X.; Borodkin, V. S.; Blair, D. E.; Ferenbach, A. T.; Schüttelkopf, A. W.;
Navratilova, I.; Aristotelous, T.; Albarbarawi, O.; Robinson, D. A.; Macnaughtan, M. A.; van
Aalten, D. M. F. Nat. Chem. Biol. 2012, 8, 969–974.
[8] Lazarus, M. B.; Jiang, J.; Gloster, T. M.; Zandberg, W. F.; Whitworth, G. E.; Vocadlo, D. J.;
Walker, S. Nat. Chem. Biol. 2012, 8, 966–968.
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Redox potential of Ag+ /Ag2+ and Cu+ /Cu2+ calculated with
FPMD
Xiandong Liu1,2 , Jun Cheng2 , Michiel Sprik2
1
State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and
Engineering, Nanjing University
2
Pourbaix diagram (or pH-Eh diagram) is a type of activity diagram, in which the area of
the predominance of one species is represented as a function of the activities of two or
more species (the usually used is activity of proton (i.e. pH) and activity of electron (i.e.
Eh)). For an aqueous electrochemical system, the most important thermodynamics
data for constructing pH-Eh diagram are acidity (pKa ) and redox potential (E0 ). pKa s
and E0 data have been well established for many species at ambient conditions, but
they are still lacking for most elements at elevated T-P conditions relevant to the Earth’s
interior.
Study of aqueous speciation has heavily relied on solubility experiments and related
thermodynamics calculations. Due to the experimental difficulty in high T-P conditions,
first principles molecular dynamics (FPMD) simulations have been attracting more and
more attentions. In this presentation, we will introduce FPMD based vertical energy
gap method developed by our group, which combines FPMD and free energy perturbation theory. With this technique, we have investigated several transition metal
aqua-cations: redox potential calculation examples include Ag+ /Ag2+ , Cu+ /Cu2+ and
Fe2+ /Fe3+ couples and pKa case studies include Fe3+ , Fe2+ aqua-cations and molybdic acid. The comparisons with experiment validate the methodology over a wide T-P
range.
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Inverse Simulation Annealing for the determination of
amorphous structures
Jan H. Los1 and Thomas D. Kühne1
1
Institute of Physical Chemistry and Center for Computational Science, Johannes
Gutenberg University Mainz
A novel method, called Inverse Simulated Annealing (ISA), for the efficient and accurate determination of amorphous structures in best agreement with available experimental data is presented. In conjunction with a new minimization procedure, reminiscent to hybrid Monte Carlo simulation, ISA is applicable at a DFT level of theory. This
opens the possibility to include, besides geometrical properties, also properties involving the electronic structure in the objective function to be minimized, such as the band
gap and/or absorption spectra.
Here we illustrate the method by presenting results for amorphous carbon and InSb.
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Li-ion migration in garnet-like oxides: Insights from
first-principles calculations
Katharina Meier1 , Teodoro Laino1 , Alessandro Curioni1
1
IBM Zurich Research Laboratory, Computational Sciences, Rüschlikon
Garnet-like LLZO (Li7 La3 Zr2 O12 ) materials are attracting lots of attention as solid electrolytes for lithium/air batteries due to their high Li-ion conductivity and electrochemical
stability. LLZO exhibits a tetragonal phase with low Li-ion conductivity as well as a cubic
phase with an up to two orders higher Li-ion conductivity. We investigated the characteristics of Li-ion migration in the bulk phase of tetragonal and cubic LLZO by means of
density functional theory calculations and ab-initio molecular dynamics simulations.
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Funnel Metadynamics calculation of the Berberine binding
free energy with human telomeric DNA G-quadruplex
Federica Moraca1,3 , Vittorio Limongelli2 , Stefano Alcaro1 , Francesco
Ortuso1 , Ettore Novellino2 , Michele Parrinello3
1
Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro
2
3
Department of Pharmacy, University of Naples “Federico II” via D. Montesano,
Naples
Zurich, USI Campus, Lugano
The isoquinoline alkaloid Berberine has been shown to exhibit an anti-tumoral activity by inhibiting the telomerase enzyme. [1] Its mechanism of action depends on the
binding to theG-quadruplex DNA by mean of its aromatic moiety that forms suitable
stacking interactions at the external 5’ and 3’-end G-quartets (see pdbcode 3r6r and
figure). However, the binding behaviour of this promising molecule with G-quadruplex
DNA is not entirely understood. This information can be obtained using enhanced
sampling techniques such as metadynamics. [2] This technique has also been successfully applied to study G-quadruplex folding. It works by accelerating rare events
through the addition of a bias potential that acts on a few selected collective variables.
In this work, the new formalism funnel-metadynamics [3] has been applied on the Gquadruplex/Berberine complex to elucidate the binding mechanism of such ligand. Using this technique, we have been able to reconstruct the ligang binding free-energy
surface with an accurate estimation of the ligand/protein absolute binding free energy
(∆G0b ). Our results have revealed also an alternative binding mode of Berberine to Gquadruplex. The GBPM method [4] will used to generate an unbiased pharmacophore
model for such ligand. Our study represents the first application on DNA of this newly
method providing crucial information for designing new G-quadruplex ligands with antitumor properties.
Figure 1: The DNA G-quadruplex (yellow cartoon) complexed in ratio 4:1 with Berberine ligands (sticks). The funnel-metadynamics simulations were performed only on the
BER 23, represented in green sticks.
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This research work is supported by the Italian Ministry of Education FIRB IDEAS (code
RBID082ATK 002), PRIN 2009 (code 2009MFRKZ8 002) and by “Commissione Europea, FondoSociale Europeo - Regione Calabria”.
References
[1] Naasani, I.; Seimiya, H.; Yamori, T.; Tsuruo, T. Cancer Res 1999, 59, 4004-4011.
[3] Limongelli, V.; Bonomi, M.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 6358-6363.
[4] Ortuso, F.; Langer, T.; Alcaro, S. Bioinformatics 2006, 22, 1449-1455.
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Development of CPMD-GULP Interface: An Efficient Tool for
Hybrid QM/MM Molecular Dynamics Simulation of Solids
Sudhir K. Sahoo1 and Nisanth N. Nair1
1
Department of Chemistry, Indian Institute of Technology Kanpur, E-Mail:sudhirs
iitk.ac.in
Development of a hybrid QM/MM interface which combines ab initio molecular dynamics (MD) with force field based MD for periodic solids, is presented here. CPMD, code
is used for the quantum part whereas GULP, a widely used code for simulating periodic
solids is taken as the classical counterpart. This interface has the advantage of parallelization of both codes under the same MPI framework, still independently parallelized,
to address large systems with a million number of atoms. This QM/MM scheme uses
electronic embedding method to compute electrostatic interaction between QM and
MM regions, where the electronic density on QM atoms interact with point charges of
MM atoms and long range interactions are computed through multipole expansion to
minimize the computational cost. Special care has been taken to deal with covalent
bonds between MM and QM atoms, and a modified potential used for electron spill
out effect. The CPMD code is chosen as main MD driver so that user can take the
advantages of existing features of CPMD like TDDFT, Metadynamics etc. This interface allows us to look at various chemically complex systems like low concentration
vacancies, steps and other defects on solids, adsorptions and reactions in metal organic frameworks, zeolites, solid-solid interface, supported metal catalysis etc. Some
of the benchmark calculations and initial results of its applications will be presented.
90
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P.36
Evaluating functions of positive-definite matrices using
colored noise thermostats
M. Nava1 , C. Dryzun, M. Ceriotti and M. Parrinello
1
Department of Chemistry and Applied Biosciences, ETH Zurich
The evaluation of the elements of a function of a large matrix is generally a non-trivial
operation that is frequently encountered in many fields of computational science. A
commonly used approach involves the computation of the eigenvalue decomposition,
a task that in general, has a computing time that scales with the cube of the size of the
matrix.
We have developed a method that can be used to evaluate the elements of a function
of a matrix to an arbitrary precision, with a scaling that is linear for sparse matrices
and square in the general case. This methodology is based on the properties the
dynamics of a multidimensional harmonic oscillator coupled with colored noise generalized Langevin equation thermostats [1]. With a particular choice of the stochastic
dynamics, in fact, the matrix elements of the function are retrieved from the momentum fluctuations of the system and the eigenvalue decomposition of the matrix is thus
avoided in favor of a better scaling molecular dynamics algorithm.
We show the scaling behavior of the method for both dense and sparse problems and
compare the results with other existing exact methodologies.
References
[1] Ceriotti, M.; Bussi, G.; Parrinello, M. Phys. Rev. Lett. 2009, 102, 020601.
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Accuracy vs price: comparison of classical and ab initio
models for water
Nikita Orekhov1 , Grigory Smirnov1 , Vladimir Stegailov1
1
Joint Institute for High Temperatures RAS, Moscow Institute of Physics and
Technology
The models of interatomic interaction are crucial for the success of atomistic modelling
and simulation. The main direction of the developments in this field can be separated into 1) the creation of more and more sophisticated empirical models and 2) the
creation of fast ab initio based algorithms with controllable level of accuracy. For the
proper choice of the a particular model for the given problem one should be able to find
the best ratio between the accuracy of the model and the computational price that it
demands.
We present a set of new benchmarks for water obtained for the classical models and
for the DFT level of theory. We also analyze the benchmark results available in the
literature. We combine the timings obtained at different high performance computing
facilities in the common metrics in order to make a comparison.
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Free energy profiles in hydroxy-naphthoic acids
Jarosław J. Panek1 , Aneta Jezierska-Mazzarello1
1
Faculty of Chemistry, University of Wrocław
Substituted naphthoic acids are compounds in which interplay between several phenomena can be studied. First, hydrogen bonding between the monomers influences their
spectroscopic properties. Second, substitution in the aromatic ring alters electronic
structure of the rings, modifying also the hydrogen bonds. Third, dispersion forces
between the electron-rich ring planes is a factor influencing the solid state structure of
this class of organic compounds.
Our study is devoted to a class of naphthoic acids in which an additional factor appears:
hydroxy-naphthoic acids with an intramolecular hydrogen bond (an exemplary compound, 1-hydroxy-2-naphthoic acid, depicted below). Car-Parrinello MD simulations
were carried out to study the spectroscopic signatures of representatives of this class
of carboxylic acids. Further, proton dynamics in the intra- and inter-molecular bridges
was examined by generating free energy profiles for the proton motion in the bridge.
Both constrained MD [1] and metadynamics [2, 3] were used for this purpose. Apart
from generation of the free energy profiles, the obtained distorted structures allowed us
to describe the impact of proton position on the aromaticity index HOMA [4] and electronic structure parameters defined within the framework of the Atoms in Molecules
theory [5] (the use of AIM parameters as descriptors of the strength of hydrogen bonding is well-established [6, 7] although its accuracy has been recently questioned [8]).
We gratefully acknowledge the Wrocław Centre for Networking and Supercomputing
(WCSS Wrocław), CI TASK (Gdańsk), and Interdisciplinary Centre for Mathematical
and Computational Modelling (ICM Warsaw) for the generous grants of computer time
and facilities. This work was supported by the National Science Centre (Poland) under
the grant no. UMO-2011/03/B/ST4/00699.
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References
[1] Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737-7744.
[3] Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302.
[4] Krygowski, T. M.; Cyrański, M. K. Chem. Rev. 2001, 101, 1385-1420.
[5] Bader, R. Atoms in Molecules: A Quantum Theory; International Ser. of Monogr. on Chem
Oxford University Press, Incorporated: Oxford, 1994.
[6] Koch, U.; Popelier, P. L. A. J. Phys. Chem. 1995, 99, 9747-9754.
[7] Pacios, L. Struct. Chem. 2005, 16, 223-241.
[8] Mo, Y. The Journal of Physical Chemistry A 2012, 116, 5240-5246.
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Mechanism of the metabolite induced self-cleavage reaction
in the glmS riboswitch as revealed by QM/MM simulations
Jung Mee Park1
1
School of Computational Sciences, Korea Insititute for Advanced Study, Seoul
Riboswitches are recently discovered noncoding segments of mRNAs which function
as metabolite-responsive genetic switches. Riboswitches regulate the expression of
proteins encoded in the mRNAs upon sensing their small metabolite molecules, which
are often products of the encoded proteins. In the glmS riboswitch, the RNA cleavage
triggered by binding of its specific metabolite ligand, glucosamine-6-phosphate, regulates gene expression. Despite extensive experimental studies, the reaction mechanism of the metabolite-induced self-cleavage of the glmS riboswitch is still elusive. In
this presentation, I present the reaction mechanism revealed by the hybrid QM/MM
simulations combined with free energy methods such as blue moon sampling and
metadynamics. My results show that the reaction takes place in two-steps. In the
first step, the stable reactant state changes into the less stable reactant state, which
turned to be active to the RNA cleavage, through a proton relay mechanism mediated
by the metabolite ligand, the active site guanine, and two water molecules. In the second step, the RNA cleavage reaction proceeds from the produced active reactant state
in which the deprotonated guanine acts as a general base to activate a nucleophile and
the protonated amine group of the metabolite ligand acts as a general acid in breaking
the P-O bond. The first step is found to be slow with the higher free energy barrier than
that of the RNA cleavage reaction.
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Syntheses of Coumarins in Environmentally Friendly Ionics
Liquids
Sanita Pavlovica1 , Andris Zicmanis1
1
Univeristy of Latvia, E-mail: sanita.pavlovica gmail.com
Nowadays ionic liquids (ILs) are widely used as solvents for various organic transformations in place of common organic solvents. It is possible to form purposely
the very best structure of the IL for the selected reaction. The main disadvantages
of ILs that are in use at present are their high toxicity and low biodegradability. A
systematic investigation of highly biodegradable and only slightly toxic ionic liquids
– (2-hydroxyethyl)ammonium carboxylates has demonstrated the usefulness of these
materials for condensation reactions in our laboratory. ILs 1 – 3 can be easily prepared in high yields by a simple reaction of carboxylic acids with corresponding (2hydroxyethyl)amines [1, 2].
The mentioned ILs have turned out to be not only very harmless solvents for organic
syntheses but have also successfully served both as reaction media and as catalysts
simultaneously for condensation reactions of aromatic aldehydes with activated methylene compounds, including also the syntheses of coumarins [1–3].
Figure:
The yield of 2-imino-2H-1benzopyran-3-carboxylic acid ethyl ester
in ILs – formates (1a – 2a); acetates (1b
– 3b) and lactates (1c – 3c) (after 30 minutes at temperature 25 ◦ C and molar ratio: salicylaldehyde : ethylcyano acetate :
ionic liquid = 1 : 2 : 2)
Figure:
The yield of coumarin-3carboxylic acid in ILs – formates (1a
– 2a); acetates (1b – 3b) and lactates
(1c – 3c) (after 1 h at temperature 90 ◦ C
and molar ratio: salicylaldehyde : malonic
acid : ionic liquid = 1 : 1,2 : 2).
References
[1] Zicmanis, A. et al. Latvian J. Chem. 2010, 49, 269–276.
[2] Pavlovica, S. et al. Green and Sustainable Chemistry 2011, 1, 103–110.
[3] Su, C.; Chen, Z.-C.; Zheng, Q.-G. Synthesis 2003, 2003, 555–559.
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Ab initio simulations of Sr-substituted Photosystem II
Fabio Pitari1 , Daniele Narzi2 , Daniele Bovi2 and Leonardo Guidoni1
1
Dept. of Phisical and Chemical Sciences, University of L’Aquila
2
Dept. of Physics, Sapienza - University of Rome
Photosynthesis is a chemical process which allows green plants and some bacteria to
store sun energy producing organic substances from carbon dioxide and water. Photosynthesis happens in thylakoids membranes and in particular in some groups of pigments called “photosystems”. Sun energy excite electrons of the pigments that, with a
chain mechanism, are transferred to the so called Oxygen Evolving Complex (OEC),
which catalyze the water splitting reaction:
2H2 O → 4H + + 4e− + O2
(1)
Water-splitting is the most relevant process in the photosynthesis from the energetic
point of view and one of the most interesting from the industrial one, since the Oxygen Evolving Complex might inspire similar mechanisms for an “artificial leaf” that can
produce clean fuels (e.g. hydrogen) starting from water. [1] OEC is a cuban-shaped
complex composed by four manganese atoms, five oxygen atoms and a Calcium one.
The chemical mechanisms that rules the water splitting reaction through OEC is still
pretty unclear, as the role of OEC structure and OEC calcium. It is widely accepted that
OEC complex moves trough different oxidation states during its catalytic action. [2] PSII
structure was not well-known since 2011, when an intermediate S1-S2 crystal structure with resolution 1.9 Å has been obtained from “Thermosynechococcus elongatus”
bacterium. [3] Moreover it has been found that the S2 state exhibits two different EPR
signals starting from two different preparation conditions, pointing out that both spin
1/2 and 5/2 are possible in particular conditions, and that they can be interconverted
by near-infrared illumination at cryogenic temperatures; Pantazis et al. proved that this
can be explained with two different structures. [4]
Although crystal structure is now pretty well known, the reaction mechanism of the water splitting is still matter of debate, and the role of structure and Calcium ion is not clear
too; in order to elucidate these latter points Sr-PSII have been obtained biosynthetically; in the present work we perform DFT+U simulations on a subsystem of PSII containing the OEC, in order to compensate the experimental approach already present in
literature.
References
[1] Nocera, D. G. Acc. Chem. Res. 2012, 45, 767-776.
[2] Ames, W.; Pantazis, D. A.; Krewald, V.; Cox, N.; Messinger, J.; Lubitz, W.; Neese, F.
J. Am. Chem. Soc. 2011, 133, 19743-19757.
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[3] Umena, Y.; Kawakami, K.; Shen, J.-R.; Kamiya, N. Nature 2011, 473, 55–60.
[4] Pantazis, D. A.; Ames, W.; Cox, N.; Lubitz, W.; Neese, F. Angew. Chem. Int. Ed. Engl. 2012,
51, 9935–9940.
[5] Cox, N.; Rapatskiy, L.; Su, J.-H.; Pantazis, D. A.; Sugiura, M.; Kulik, L.; Dorlet, P.; Rutherford, A. W.; Neese, F.; Boussac, A.; Lubitz, W.; Messinger, J. J. Am. Chem. Soc. 2011, 133,
3635-3648.
[6] Koua, F. H. M.; Umena, Y.; Kawakami, K.; Shen, J.-R. Proceedings of the National Academy
of Sciences 2013, 110, 3889-3894.
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Ab Initio Molecular Dynamics Approach to Ion Pairing in
Water: The pathological case of lithium fluoride
Eva Pluharova1 , Pavel Jungwirth1
1
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech
Republic, Prague
Structure of salt solutions has been intensely studied both experimentally by neutron
scattering and theoretically employing classical molecular dynamics simulations. Theoretical predictions were shown to be sensitive to the details of the empirical force fields,
therefore, the next logical step is to use ab initio based approaches which are less dependent on empirical parameters. Standard force fields are expected to be inaccurate
especially for small ions with high charge density, like lithium, fluoride, or multivalent
ions, where hydration is strong and charge transfer to solvent comes into play. Here,
we discuss the results obtained for the lithium fluoride ion pair in bulk water.
Our aim is to employ DFT based Born-Oppenheimer MD using CP2K program package
and to obtain free energy as a potential of mean force, i. e., constraining the ion-ion
distance, evaluating the mean force along that distance, and integrating the obtained
curve. In order to obtain meaningful results, we carefully checked two major sources
of uncertainties, the level of the electronic structure theory and the duration of the
simulations. In addition to that we analyzed hydration of the ion pair and took the
advantage of having electron density to assign ionic charges and the amount of charge
transfered to solvent based on the Bader population scheme.
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Formation of a covalent glycosyl-enzyme intermediate in a
retaining glycosyltransferase
V. Rojas-Cervellera1 , A. Ardèvol1 , M. Boero2 , A. Planas3 , C. Rovira1,4
1
Departament de Quı́mica Orgànica. Universitat de Barcelona
2
3
Institut de Physique et Chimie des Matériaux de Strasbourg
Laboratory of Biochemistry, Institut Quı́mic de Sarrià, Universitat Ramon Llull,
Barcelona
4
The catalytic mechanism of retaining glycosyltransferases (GTs) remains a controversial issue in glycobiology. Two different scenarios were provided, depending on the
absence or presence of a putative nucleophile in the active site. Many GTs do not
have a putative nucleophile residue, suggesting that these GTs operate via a front side
single displacement (SNi-like mechanism). On the other hand, other GTs do have a
putative nucleophilic residue properly oriented in the active site to participate in the
catalytic reaction. In this case, a double-displacement mechanism is feasible.
By means of hybrid QM/MM metadynamics simulations, we demonstrate that α3-galactosyltransferase (α3GalT), a protein with a putative nucleophilic residue in the active
site, operates via a double-displacement mechanism, with the formation of a glycosylenzyme covalent intermediate.
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Density functional/molecular dynamics study of amorphous
chalcogenide glasses: AgAsS2 and Ag20 (Ge42 S58 )80
M. Ropo1,2 , J. Akola1,2,3 , R. O. Jones3
1
Department of Physics, Tampere University of Technology, Tampere
2
COMP, Department of Applied Physics, Aalto University
3
PGI-1, Forschungszentrum Jülich GmbH, Jülich
Phase change materials (PCM) have been subject of intensive research due to their
great potential for applications in nonvolatile memory technology [1]. These materials
are already used widely in rewritable optical digital storage, such as DVD and Blu-ray
Disc, where GeSbTe alloys have been the materials of choice for many years. The
applicability of PCMs is due to the existence of different phases of the material with
remarkably different optical and/ or electronic properties, and that these materials can
cycle repeatedly and very rapidly between these phases [2].
We focus here on two chalcogenide glasses containing silver: AgAsS2 and
Ag20 (Ge42 S58 )80 . Silver and copper are often mixed with chalcogenides in PCMs, because they are highly mobile and form a solid state electrolyte [3]. This means that
stable silver (or copper) filaments (nanowires) can form between the cathode and the
anode and allow switching between states with high and low resistance. This is the
basis of the conductive-bridging random-access-memory (CBRAM) or electrochemical
metallization cell (EMC) technology.
We have performed several 30-ps sequences of density functional/molecular dynamics simulations for amorphous AgAsS2 and Ag20 (Ge42 S58 )80 at various temperatures,
using the CPMD program with the PBEsol functional. The simulation cell contains 560
and 500 atoms, respectively, in order to minimize the effect of periodic boundary conditions and improve statistics. Diffusion coefficients, details of Ag mobility, and structural
properties (including radial distribution functions) are extracted from the simulation trajectories, and we compare the two compounds. Ag exhibits diffusive motion well below
the glass transition temperature of the parent chalcogenide material (< 600 K).
References
[1] Burr, G. W.; Breitwisch, M. J.; Franceschini, M.; Garetto, D.; Gopalakrishnan, K.; Jackson, B.; Kurdi, B.; Lam, C.; Lastras, L. A.; Padilla, A.; Rajendran, B.; Raoux, S.;
Shenoy, R. S. J. Vac. Sci. Technol. B 2010, 28, 223-262.
[2] Kalikka, J.; Akola, J.; Larrucea, J.; Jones, R. O. Phys. Rev. B 2012, 86, 144113.
[3] Mitkova, M.; Sakaguchi, Y.; Tenne, D.; Bhagat, S. K.; Alford, T. L. Phys. Status Solidi A
2010, 207, 621-626.
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The interaction of nucleic acid bases with the Au(111)
surface
M. Rosa1,2 , S. Corni1 , R. Di Felce1
1
Center S3, CNR Institute of Nanoscience, Modena
2
Università di Modena e Reggio Emilia, Modena
The fate of an individual DNA molecule when it is deposited on a hard inorganic surface
in a “dry” environment is unknown, while it is a crucial determinant for nanotechnology
applications of nucleic acids. In the absence of experimental approaches that are able
to unravel the three- dimensional atomic structure of the target system, here we tackle
the first step towards a computational solution of the problem. By using first-principles
quantum mechanical calculations of the four nucleobases on the Au(111) surface, we
propose a simple force field that will enable classical simulations of DNA on Au(111)
to investigate the structural modifications of the duplex in these non-native conditions.
Furthermore, we fully characterize each system at the individual level. We find that
van der Waals interactions are crucial for a correct description of the geometry and
energetics. However, the mechanism of adsorption is well beyond pure dispersion
interactions. Indeed, we find charge transfer between the substrate and the adsorbate,
the formation of hybrid orbitals and even bonding orbitals.
Thanks to quantum mechanical results, we were able to parametrize a force field suitable for molecular dynamics calculations of more complex DNA structures adsorbed on
gold. To verify our method and the results obtained, we make a comparison between
DFT, MD and experimental results on DNA bases monolayers adsorbed on Au(111)
and we were able to find a remarkable agreement.
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Calcium Oxalate/water interfaces using ab initio Molecular
Dynamics
Leila Salimi Parvaneh1,2 , Davide Donadio1 and Marialore Sulpizi2
1
2
Max Planck Institute for Polymer Research, Mainz
Condensed Matter Theory, Physics Department, Johannes Gutenberg University,
Mainz
Calcium oxalate is the most significant component of kidney stones [1]. The presence
of bio-polymers such as polyacrylate, poly-aspartate and poly-glutamate has a great
impact on the crystalline phase, morphology and growth rate of calcium oxalate [2–
4]. Ab initio molecular dynamics study of the interactions of the water/mineral and
water/polymer/mineral interfaces shed light on the biomineralization process and on
the mechanisms responsible for its inhibition.
We performed Density Functional Theory (DFT) based Molecular dynamics simulations [5] to study the structure of the interfaces between calcium oxalate di-hydrate
(COD) (100) and (101) and water. Our study reveals differences in the coordination of
calcium ions at the surface with water, which is also responsible for different interactions with biopolymers. We also characterize the interaction between different surfaces
of COD and biomolecules. As a first step we consider acetate as a model system containing a carboxylic group, and we estimate its binding structure and free energies on
different COD surfaces at different coverage. Such free energies are then compared to
the binding free energy of Ca and acetate in solution.
Preferential binding of carboxylate to the 100 surface is found, therefore explaining
recent experimental results on anisotropic growth of COD crystals in the presence of
biopolymers [2].
References
[1] Prein, E. L.; Frondel, C. J. Urol. 1947, 57, 949.
[2] Fischer, V.; Landfester, K.; Muñoz Espı́, R. Cryst. Growth Des. 2011, 11, 1880–1890.
[3] Thomas, A.; Rosseeva, E.; Hochrein, O.; Carrillo-Cabrera, W.; Simon, P.; Duchstein, P.;
Zahn, D.; Kniep, R. Chem. Eur. J. 2012, 18, 4000–4009.
[4] Jung, T.; Kim, W.-S.; Choi, C. K. Journal of Crystal Growth 2005, 279, 154 – 162.
[5] CP2K/QUICKSTEP http://cp2k.berlios.de/.
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QM/MM Metadynamics Simulations for Mechanistic Study
on Endocyclic Cleavage-Induced Anomerization Reaction of
Glycosides
Hiroko Satoh1 , Teodoro Laino2 , Jürg Hutter3
1
National Institute of Informatics (NII), Tokyo
2
IBM Research Zurich
3
University of Zurich
Pyranosides carrying 2,3-trans-carbamate easily undergo endocyclic cleavage-induced
anomerization from the β-form to the α-form in the presence of a weak Lewis acid, despite of the fact that the endocyclic cleavage is assumed to be a minor cleavage mode
of glycosides. Manabe reported experimental evidence that confirms the existance of
endocleavage in the class of compounds. [1] With DFT calculations as well as further
experiments, we and coworkers concluded that, for glycosides with 2,3-trans cyclic protecting group, inner strain caused by the fused rings is the primary factor enhancing
the endocleavage reaction. [2] We performed ab initio QM/MM metadynamics simulations of the anomerization reaction to gain a better understanding of the reaction
mechanism in solution as well as conformational details along the reaction pathway.
The simulations demonstrate unequivocally that the reaction path is characterized by
peculiar conformational changes promoting the endocyclic way. In contrast, the simulations reveal that a typical pyranoside undergoes different conformational changes
that hinder the C1- C2 bond rotations, which is an essential step of the endocyclic
cleavage-induced anomerization reactions. We will report here the first results of the
simulation study.
References
[1] Manabe, S.; Ishii, K.; Hashizume, D.; Koshino, H.; Ito, Y. Chem. Eur. J. 2009, 15, 6894–6901.
[2] Satoh, H.; Manabe, S.; Ito, Y.; Lüthi, H. P.; Laino, T.; Hutter, J. J. Am. Chem. Soc. 2011,
133, 5610-5619.
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Eigensystem Representation of the Electronic
Susceptibility Tensor
A. Scherrer1 , A. C. Ihrig1 , V. Verschinin1 and D. Sebastiani1
1
Martin-Luther-Universität Halle-Wittenberg
We present an implementation for the explicit representation of the electronic susceptibility tensor within density functional theory. The susceptibility is represented by means
of its eigensystem, which is computed using an iterative Lanczos diagonalization technique for the susceptibility tensor within density functional perturbation theory. We
show that a representation in a finite basis of eigenstates is sufficiently accurate to
compute the linear response of the electronic density to external potentials.
We further analyze the response of the molecular electronic charge distribution to a
geometric distortion in terms of the electronic susceptibility. We first show that the
electronic susceptibility is almost invariant to small changes in the molecular geometry.
We then compute the dipole moments from the response density induced by the geometrical changes. We verify the accuracy by comparing the results to the corresponding values obtained from the self-consistent calculations of the ground-state densities
in both geometries. The results illustrate the potential of the approach for the firstprinciples calculation of supramolecular interactions in complex disordered systems in
the condensed phase.
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Liquid Methanol from DFT and DFT/MM Molecular
Dynamics Simulations
Nicolas Sieffert1 , Michael Bühl1 , Marie-Pierre Gaigeot3,4 , Carole A. Morrison5
1
CNRS UMR-5250 Département de Chimie Moléculaire, Université Joseph Fourier
Grenoble I
2
3
EaStCHEM School of Chemistry, University of St. Andrews
LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et
l’Environnement, Université d’Evry val d’Essonne
4
5
Institut Universitaire de France (IUF), Paris
School of Chemistry and EaSTCHEM Research School, The University of Edinburgh
We present a comparative study of computational protocols for the description of liquid
methanol from ab initio molecular dynamics simulations, in view of further applications
directed at modeling of chemical reactivity of organic and organometallic molecules
in (explicit) methanol solution. We tested density functional theory molecular dynamics (DFT-MD) in its Car-Parrinello Molecular Dynamics (CPMD) and Quickstep/BornOppenheimer MD (CP2K) implementations, employing six popular density functionals
with and without corrections for dispersion interactions (namely BLYP, BLYP-D2, BLYPD3, BP86, BP86-D2 and B97-D2). Selected functionals were also tested within the two
QM/MM frameworks implemented in CPMD and CP2K, considering one DFT molecule
in a MM environment (described by the OPLS model of methanol).
The accuracy of each of these methods at describing the
bulk liquid phase under ambient conditions was evaluated by analyzing their ability to reproduce: i. the average structure of the liquid, ii. the mean squared displacement of methanol molecules, iii. the average molecular
dipole moments, and iv. the gas-to-liquid red-shift observed in their infrared spectra. We show that it is difficult
to find a DFT functional that describe these four properties equally well within full DFT-MD simulations, despite
a good overall performance of B97-D2. On the other
hand, DFT/MM-MD provides a satisfactory description of the solvent-solute polarization effects with all functionals, and thus represents a good alternative for the modeling
of methanol solutions in the context of chemical reactivity in explicit environment.
References
[1] Sieffert, N.; Bühl, M.; Gaigeot, M.-P.; Morrison, C. A. Journal of Chemical Theory and
Computation 2013, 9, 106-118.
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Homogeneus nucleation and growth of the phase change
material GeTe via LARGE SCALE Molecular Dynamics
simulations
G.C. Sosso1 , G. Miceli2 , S. Caravati3 , J. Behler4 , M. Bernasconi3 and M.
Parrinello1
1
Zurich, Lugano
2
Chaire de Simulation l’Echelle Atomique (CSEA), Ecole Polytechnique Fdrale de
Lausanne (EPFL), Lausanne
3
Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Milano
4
Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum
State of the art optical (DVDs, Blue-Ray discs) and electronic (phase change memories, PCMs) data storage devices are based upon a class of systems known as phase
change materials [1,2]. The materials of choice in this context are tipically chalcogenide
alloys like Ge2 Sb2 Te5 , GeTe and related compounds, which upon heating — induced
by laser irradiation or Joule effect in optical and electronic devices respectively — display a fast (about 10 ns) and reversible transformation between the crystalline and
amorphous phases. The two states of the memory can be distinguished thanks to
the large difference in optical reflectivity and electronic conductivity of the two different phases. Atomistic simulations, in particular molecular dynamics (MD) simulations
based on density functional theory (DFT) have provided in the last decade useful insights (Refs. [3–5] are some of our contributions) on a number of properties of phase
change materials. However, several key issues including the crystallization dynamics
from the amorphous and the supercooled liquid phases are still matter of debate. In
fact, an atomistic investigation of such issues require huge models (103 atoms) and
long simulation times (103 ps), which are both far beyond the reach of DFT simulations because of their high computational cost. The development of reliable classical
interatomic potentials is a possible route to overcome the limitations in system size and
time scale of DFT molecular dynamics. However, traditional approaches based on the
fitting of simple functional forms for the interatomic potentials are very challenging due
to the complexity of the chemical bonding in the crystal and amorphous phases. Thus,
we employed an approach proposed recently by Behler and Parrinello [6], by which
one can develop an empirical interatomic potential with close to DFT accuracy via the
fitting of a large DFT database thanks to a Neural Network (NN) algorithm. By means
of this technique, we have recently built and validated an interatomic potential for GeTe
(Refs. [7, 8] are some of our NN results), which is one of the compounds of interest
for PCM devices. In here, we investigate the dynamical properties of the supercooled
liquid GeTe close to the glass transition temperature and the crystallization dynamics in
the temperature range of interest for PCM applications. Our NN potential allows large
scale (about 4000 atoms for about 5 ns) MD simulations of GeTe that indeed provide
an atomistic description of crystal nucleation and growth.
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References
[1] Lencer, D.; Salinga, M.; Wuttig, M. Adv. Mater. 2011, 23, 2030–2058.
[2] Mazzarello, R.; Caravati, S.; Angioletti-Uberti, S.;
Phys. Rev. Lett. 2010, 104, 085503.
Bernasconi, M.;
Parrinello, M.
[3] Sosso, G. C.; Caravati, S.; Mazzarello, R.; Bernasconi, M. Phys. Rev. B 2011, 83, 134201.
[4] Behler, J.; Parrinello, M. Phys. Rev. Lett. 2007, 98, 146401.
[5] Sosso, G. C.; Miceli, G.; Caravati, S.; Behler, J.; Bernasconi, M. Phys. Rev. B 2012, 85,
174103.
[6] Wuttig, M.; Yamada, N. Nat. Mater. 2007, 6, 824–832.
[7] Caravati, S.; Bernasconi, M.; Kuhne, T. D.; Krack, M.; Parrinello, M. Appl. Phys. Lett. 2007,
91, 171906.
[8] Sosso, G. C.; Donadio, D.; Caravati, S.; Behler, J.; Bernasconi, M. Phys. Rev. B 2012, 86,
104301.
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Coupling DFT-based molecular dynamics with single sweep
method for free energy surfaces of systems containing
lanthanoids and actinoids in liquid water
Riccardo Spezia1 , Rodolphe Vuilleumier2
1
Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, CNRS UMR
8587, Université d0 Evry Val d’Essonne
2
Ecole Normale Supérieure, Départment de Chimie and UPMC Univ Paris 06
We are interested in characterizing free energy surfaces of systems composed by ions
in water that can have different coordination number and eventually induce deprotonation of bound molecules, as can be the case for lanthanoid(III) and actinoid(III) ions in
water. [1] Here, we have studied two prototypical cases: (a) coordination free energy
profile of Cm(III) and Th(IV) in liquid water; (b) the effect of La(III) bound to silic acid in
lowering its pKa . At this aim we coupled Car-Parrinello molecular dynamics with single
sweep method. [2, 3] The free energy profiles have been obtained from single sweep
method in three steps: (1) Defining the reaction coordinate; (2) Running a molecular dynamics setting the temperature of the reaction coordinate at a high value (here
15000 K) by means of an extended Lagrangian coupled to a Langevin thermostat; (3)
Selecting points along the reaction coordinate spanned in step 2 and run simulations
with constrained reaction coordinate. Thus, the free energy was reconstructed by using
an interpolation scheme. For ion water coordination, we used the usual Fermi function
as collective coordinate, while for O-H acidity we used the O-H distance. In the case of
ion coordination, we show that for Cm(III) the system can easily change coordination
number from eight to nine, while for Th(IV) the CN=9 structure is much more stable,
thus confirming experimental and theoretical results obtained from free classical simulations. [4–6] For the La(H4 SiO4 )3+ complex, we obtained that the O-H groups bound
to La(III) are about three pKa units more acid than those pointing to bulk water (which
pKa is the same of H4 SiO4 alone in bulk water).
References
[1] D’Angelo, P.; Spezia, R. Chem. Eur. J. 2012, 18, 11162–11178.
[2] Maragliano, L.; Vanden-Eijnden, E. J. Chem. Phys. 2008, 128, 184110.
[3] Monteferrante, M.; Bonella, S.; Meloni, S.; vanden Eijnden, E.; Ciccotti, G. Sci. Model. Simul.
2008, 15, 187–206.
[4] Duvail, M.; Martelli, F.; Vitorge, P.; Spezia, R. J. Chem. Phys. 2011, 135, 044503.
[5] Spezia, R.; Beuchat, C.; Vuilleumier, R.; D’Angelo, P.; Gagliardi, L. J. Phys. Chem. B 2012,
116, 6465-6475.
[6] D0 Angelo, P.; Martelli, F.; Spezia, R.; Filipponi, A.; Denecke, M. A. Inorg. Chem. 2013, in
press, DOI: 10.1021/ic400678u.
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Interatomic potentials accuracy: how do they bridge the
scales? U-Mo fuel case
Alexey Kuksin1 , Daria Smirnova1 , Sergey Starikov1 , Vladmir Stegailov1
1
Joint Institute for High Temperatures RAS, Moscow Institute of Physics and
Technology
Perspective reliable multiscale models of radiation damage in nuclear fuels should
bridge a gap between atomistic level dynamics and kinetic rate theory (or phase field
theory) at mesoscopic level. Radiation defects evolution models comprised of millions
of atoms are required to resolve essential physical effects (point defects clustering, interaction with dislocation loops, grain boundaries etc). Empirical potential models are
the main tool for transferring to the meso-level the peculiarities of atomic interactions
that can be captured only using sophisticated quantum methods. That is why the accuracy of the interatomic potentials is of utmost importance for predictive modelling and
simulation of nuclear fuels.
We have built a set of interatomic potential models targeted at the description of U-Mo
fuels. The developed central symmetric EAM many-body potential models have been
shown to provide decent accuracy for pure Mo [1], pure U [2] and U-Mo alloys [3].
Recently an angular dependent ADP model for the U-Mo alloy has been built as well.
All potentials are constructed using force-matching method and fitted to the values of
ab initio interatomic forces, energies and stresses. As a question of verification we
discuss the loss of information at the corresponding “data transfer” between quantum
and classical levels. The validation and application of the resulting models include the
following issues:
1. Structure of α-U, γ–U, bcc Mo, U2 Mo compound and U-Mo alloys.
2. Elastic constants, melting temperatures, thermal expansion and room-temperature isotherms of U-Mo system and the Grüneisen parameter for liquid and solid
U.
3. Point defect formation energies, diffusion mechanisms and diffusivities.
We also discuss a consistent way to include Xe in the U-Mo model and present the
simulation results on Xe diffusion and bubble formation.
References
[1] Starikov, S. V.; Insepov, Z.; Rest, J.; Kuksin, A. Y.; Norman, G. E.; Stegailov, V. V.;
Yanilkin, A. V. Phys. Rev. B 2011, 84, 104109.
[2] Smirnova, D. E.; Starikov, S. V.; Stegailov, V. V. J. Phys.: Cond. Mat. 2012, 24, 015702.
[3] Smirnova, D. E.; Kuksin, A. Y.; Starikov, S. V.; Stegailov, V. V.; Insepov, Z.; Rest, J.;
Yacout, A. M. Modelling Simul. Mater. Sci. Eng. 2013, 21, 035011.
110
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Car-Parrinello MD and blue-moon ensemble study on
reductive decomposition of carbonate-based solvent in
lithium ion battery
Yoshitaka Tateyama1,2,3 , Keisuke Ushirogata1,4 , Keitaro Sodeyama1,3 ,
Yukihiro Okuno1,4
1
International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute
for Materials Science (NIMS), Tsukuba, Ibaraki
2
3
PRESTO and CREST, Japan Science and Technology Agency (JST), Kawaguchi,
Saitama
Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, Kyoto
4
Research and Development Management Headquarters, FUJIFILM Corporation,
Minamiashigara, Kanagawa
Solid electrolyte interphase (SEI) on the electrode - electrolyte interfaces formed
through the reductive decomposition of organic solvent molecules plays a crucial role in
the stability and capability of lithium ion battery (LIB). Additives to the electrolyte often
exhibit a large impact on the SEI quality. A typical example is vinylene carbonate (VC)
additive to the ethylene carbonate (EC) solvent (See Figure). Here we investigated the
effects of VC additive to the EC solvent on the reductive decomposition and the initial
stage of SEI formation. [1]
We focused on the thermodynamics as well as the kinetics of the possible processes.
We used DFT-based Car-Parrinello MD (CPMD) with explicit solvent molecules for the
equilibrium properties, and carried out the free energy profile calculations along the
reaction pathways using the blue-moon ensemble technique with constraint CPMD.
We considered Li+ in only EC solvent (EC system) and in EC solvent with a VC additive (EC/VC system) to elucidate the additive effect. The supercells involving 32 EC
molecules or 31 EC with one VC molecules, with one Li atom, were adopted. It is cubic
box with a length of 15.24 Å to reproduce the experimental EC density, and periodic
boundary condition is applied for keeping the liquid density constant. We used the
Nosé thermostat with a temperature of 353 K, PBE exchange correlation functional,
cutoff energy of 90 Ry with norm-conserving pseudopotentials. Further tuning of the
CPMD code was made for the use of the ten-petaflops supercomputer (K computer) in
Japan.
The results in this study reproduce the gaseous products observed in the experiments,
and are also consistent with the two electron reduction mechanism recently proposed
by Leung for the EC decomposition. [2] Such consistency verifies the accuracy of our
calculations. In addition to standard CPMD simulations of the equilibrium states, we
calculated free energy profiles as exemplified in Figure, where the EC decomposition
case is shown. The path (1) corresponds to the CE -O2 breaking, while the CC -O2
breaking is denoted in the path (2). The free energy profiles in Figure show that the
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path (1) is more probable with the reaction and activation free energies of -25 and +5
kcal/mol for the EC decomposition. We have also calculated the same reactions in
the EC/VC system as well, and found that the VC decomposition has similar activation
barrier through the CC -O2 bond breaking. With calculations of the excess electron
stability before the decomposition, we conclude that the reductive decomposition of
EC is comparable to that of VC, which is different from the conventional scenario that
VC additive is preferentially reduced and decomposed compared to the EC solvent.
In this presentation, we will discuss the several possible mechanisms of the reductive
decomposition of the EC solvent with the VC additive near the negative electrode.
Figure: (Left) Structures of EC and VC. (Middle) Reaction schemes of one electron reductive decomposition of EC. (Right) Free energy profiles, ∆A, of one electron reductive decomposition of EC solvent, corresponding to the paths (1) and (2), respectively.
References
[1] K, U.; Sodeyama, K.; Okuno, Y.; Tateyama, Y. in press.
[2] Leung, K. Chem. Phys. Lett. 2013, 568–569, 1 - 8.
112
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Molecular dynamics simulations of the β3-adrenergic
receptor bound with putative ligands
P. Tewatia1 , Nikhil Aggarwal2 , Mahender Gaur2 , B.K. Malik1 , Shakti Sahi2
1
Centre for Bioinformatics, Amity Institiute of Biotechnology, Amity University, Noida
2
School of Biotechnology, Gautam Buddha University, Greater Noida
β3-adrenergic receptors (β3-ARs) belong to the G-protein coupled receptor (GPCR)
super family’s Class A’s beta adrenergic receptors. They are found to mediate lipolysis and thermogenesis in the plasma membrane of both white and brown adipocytes.
Recent studies have reported that the activation of β3-AR by selective agonists produces anti-diabetic and anti-obesity effects. Although the crystal structures of Bovine
Rhodopsin, β1-AR and β2-AR have been resolved, to date there is no three dimensional (3D) structural information on β3AR. This poses problem to develop new leads
against this receptor subtype. The β3-AR models based on X-Ray structures of β2-AR
have provided insights into the ligand-receptor interactions for β3-AR. The establishment of topographical location of active sites could drive the rational structure-based
design of novel compounds and elucidate the structural basis of their function. The dynamic perturbations observed in of unbound and bound form of β3-AR in phospholipid
bilayer has been probed by means of MD simulations totaling ∼0.75 µs. The simulations were started from receptor structures bound to the shortlisted potential agonists
derived from virtual screening techniques. The bound and unbound form of β3-AR
were embedded in 2-dipalmitoyl-sn-phosphocholine (DPPC) bilayer, which was then
explicitly solvated using SPC water model and the system was neutralized by adding
chlorine ions. Conformations were saved every 50 ps and analysis was calculated on
MD simulation trajectories. MD simulation studies revealed compound 3, 4 and 6 to
act as potential agonists for β3-AR based their structural consistency in terms of free
binding energies, RMSD and molecular interactions. Their binding free energies and
van der waal interaction energies were found to be better than the known agonists of
the β3-AR. The interaction energies of compound 3, 4 and 6 display better free energy
of binding of -91.24 Kcal/mol, -85.623 Kcal/mol, -88.5941 Kcal/mol which was better
than the binding energy of known agonist solabegron -80.453 Kcal/mol. This shows
that Compound 3, 4 and 6 could be better agonists of β3-AR compared to other known
agonists. In the lieu of the non availability of crystal structure molecular dynamics study
provided a reliable model to understand the binding mode of the potential agonists inside the binding pocket of β3-AR as well as the conformational changes brought about
in the receptor by the presence of different shortlisted ligands.
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Exploring cluster melting in the well tempered ensemble
Omar Valsson1 , Michele Parrinello2
1
Universita della Svizzera italiana
2
ETH Zurich
Small atomic and molecular cluster can have a melting behavior which is very different
from their bulk counterparts [1]. These cluster melt by undergoing a quasi first-order
like phase-transition, where there is a range of temperatures where both solid-like and
liquid-like forms of the cluster are thermodynamically stable.
Here, we consider the prototypical case of a Lennard-Jones cluster and demonstrate
how the recently introduced well tempered ensemble (WTE) [2] can be employed to
achieve a detailed understanding of the phase-transition underlying the melting. To
accomplish this, we introduce a theoretical scheme that allows us to obtain from the
WTE an accurate description of the density of states, from which we can deduce the
thermodynamic properties of the system. We also discuss ideas on how our scheme
can be extended in order to investigate more complicated systems.
References
[1] Wales, D. J. Energy Landscapes; Cambridge University Press: Cambridge, 2003.
[2] Bonomi, M.; Parrinello, M. Phys. Rev. Lett. 2010, 104, 190601.
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Combined Computational and Experimental NMR Study of
Calix[4]arene Derivatives
Vincenzo Verdolino,1 Laura Baldini,2 Ferruccio Palazzesi,1 Federico Giberti,1
and Michele Parrinello1
1
2
Dipartimento di Chimica Organica e Industriale, Università di Parma
A combined computational and experimental study of a complex supramolecular system constituted by calix[4]arene derivatives that dimerize upon CO2 binding is presented. The theoretical investigation includes ab initio density functional theory, molecular dynamics, and metadynamics analysis of both monomers and dimers. The ab initio calculation of the dimerization energy demonstrates the exergonic character of the
process, due to the formation of a strong hydrogen bond network between ammonium
and carbamate groups. The dimerization is driven by −31.1 kcal/mol in the case of
the fully outward orientation of the carbamic hydrogens, while it results in a weaker
process when different carbamic orientations are considered. The molecular dynamics
simulations show the critical conformational degrees of freedom driving monomers and
dimers toward common structures. These conformations show tilted orientations of the
carbamic groups highlighting the fundamental role of dynamics in evaluating the most
stable configurations. Metadynamics simulations describe, in agreement with the other
computational tools, the conformational free energy surface of these calix[4]arenes
defining three stable conformational families. ROESY and variable temperature 1 H
NMR experiments are in agreement with our simulations. The presented approach
aims to be the reference for investigating complex supramolecular systems.
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Car-Parrinello molecular dynamics with a time-dependent
potential field
Tobias Alznauer1 , Jörg August Becker1 , Vanessa Werth1
1
Institut für Physikalische Chemie und Elektrochemie, Universität Hannover
External fields can have many different effects on matter. Electrical fields may induce
charge transport. This plays an important role in the field of molecular electronics. We
have implemented a sinusoidal potential field into the Car-Parrinello molecular dynamics code, which may change temporally and spatially. Applications to the first-principles
molecular dynamics simulation of charge migration are discussed. Objects of study are
delocalized π-electron systems like anthracene linked between two gold clusters.
In addition the effect of electron-withdrawing and donating groups on the efficiency of
the charge transport are investigated.
116

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