Abstracts of Poster Presentations,Sep. 4329

4PP-01

Development and Implementation of a Manifestly Spin-Free StateSpecific Multi-Reference Coupled Cluster (SS-MRCC) Theory Usinga Multi-Exponential Type of Cluster Expansion
Rahul Maitra, Debalina Sinha and Debashis Mukherjee
Raman Center for Atomic, Molecular and Optical Sciences,
Indian Association for the Cultivation of Science,
Jadavpur, Kolkata,India

In this poster, we present the formulation and the implementation of a spin-free StateSpecific Multi-Reference Coupled Cluster (SS-MRCC) theory using a multi-exponential
type of cluster expansion of the wave-operator . Our Ansatz for  is a natural spin-freeextension of the spin-orbital based Jeziorski-Monkhorst (JM) recipe. Although Datta andMukherjee recently suggested an alternative spin-free generalization of the JM Ansatz, its
structure is more involved. In contrast, our Ansatz is relatively simpler; it uses aterminating series, and it uses ordinary Wick algebra to generate the working equations.
Just as in the case of the spin-orbital based SS-MRCC theory, there are redundancies in
the cluster operators, which is exploited to ensure size-extensivity and avoidance of
intruders via suitable sufficiency conditions. We demonstrate that our formulation is anappropriate compromise between the accuracy achieved by the more involved DattaMukherjee Ansatz leading to a finite expansion of the working equations and theunphysical and non-terminating Ansatz involving the pure exponential cluster operatorswith spin-free unitary generators.

330

4PP-02

Formulation and Implementation of a State-Specific Multi-reference Coupledcluster (SS-MRCC) Theory Using an Internally Contracted Reference
Function.
Debalina Sinha, Rahul Maitra and Debashis Mukherjee
Raman Center for Atomic, Molecular and Optical Sciences,
Indian Association for the Cultivation of Science,
Jadavpur, Kolkata,India

In this poster we discuss the development and implementation of a State -SpecificMulti-Reference Coupled Cluster theory which uses the common doubly occupied ‘core’ of themodel functions as the vacuum for bringing in the effect of virtual excitations in the exact functionof a many electron system. The Ansatz for the wave-operator  in our formulation is, unlike that ina Jeziorski-Monkhorst prescription, that of a single exponential type. Potential linear dependence ofthe cluster operators involving active orbitals are eliminated by choosing appropriately the linearly
independent subspace of excitations. In this development, we make use of an Automatic Program
Generation (APG) strategy using a Generalized Tensor Contraction Engine (TCE) developed by us.
APG involves generation of the expressions for the working equations followed by the generationof the program.

331

4PP-03

Active CI space for ionized systems as defined byKoopmans’ theorem
A.V. Novikov,1 T.E. Prokhorov,2 N.E. Polygalova,2 A.V. Moskvin,2 B.N. Plakhutin 1
1

Laboratory of Quantum Chemistry, Boreskov Institute of Catalysis RAS, Russia
2
Novosibirsk State University, Russia.

According to the CI-based formulation of Koopmans’ theorem (KT) in the ROHF method [1,2], the energy of an ion in a one-electron process X o X ±j defined by Koopmans in the “frozen” orbital approximation, E ( X ±j ) E frozen ( X ±j ) ,is equal to theenergy derived within the limited CI approach, i.e., E frozen ( X ±j )ECI ( X ±j ) , with a

special choice of the active CI space.
The active CI space defined by KT is specific for an ion under study and varies from asingle excitation CI in the respective occupied subspace [1] for ions described in the
ROHF method by a one-determinantal wave function to a combination of CI subspaces
with different levels of excitation [3] for ions with arbitrary (non-integer) orbital occupancies. The main difficulty in constructing the desired CI space is a correct separationof configuration state functions (CSFs) corresponding to intruder states.
The paper presents a general and simple technique for constructing the active CI spacesatisfying the conditions of KT for arbitrary open-shell systems. A starting point is theCI matrix in the basis of Slater determinants derived with the ORMAS–CI method [4]implemented in the GAMESS suite of programs [5]. The key point of the algorithm isa two-step procedure for separating CSFs which contribute to intruder states. To illustrate the efficiency of the algorithm we compare KT estimates of the ionization potentials for a series of ions derived by the present CI method with the corresponding KT
estimates derived by the canonical ROHF method [3,6] and with the respective experimental data.
1. B.N. Plakhutin and E.R. Davidson, J. Phys. Chem. A. 113, 12386 (2009).
2. E.R. Davidson and B.N. Plakhutin, J. Chem. Phys. 132, 184110 (2010).
3. B.N. Plakhutin, submitted (see also the Abstract in this book).
4. J. Ivanic, J. Chem. Phys. 119, 9364 (2003).
5. http://www.msg.ameslab.gov/GAMESS/GAMESS.html
6. B.N. Plakhutin, E.V. Gorelik, and N.N. Breslavskaya, J. Chem. Phys. 125, 204110(2006).


332

4PP-04

Open-Shell Coupled-Cluster Theory with Spin-Orbit Coupling
Fan Wang,1 Zheyan Tu,1 Jürgen Gauss2
1
College of Chemistry, Sichuan University, P. R. China
2
Institut für Physikalische Chemie, Universität Mainz, Mainz, Germany
Recently we proposed a two-component coupled-cluster (CC) approach forclosed-shell molecules using relativistic effective core potential to treat relativistic
effects and with spin-orbit coupling (SOC) included in the CC part. The total energy1,
analytic first2 and second order derivatives3 of this two-component CC approach were
implemented at the CCSD and CCSD(T)) levels. Both time-reversal symmetry andpoint group symmetry are exploited in total energy and analytical energy gradients
calculations. This approach is efficient and accurate in treating closed-shell moleculeswith SOC. However, SOC is generally more significant for open-shell systems. This
two-component CC method can be extended readily to open-shell systems that are
spatially non-degenerate. Otherwise convergence problem in solving CC equations willarise.
In present work, we developed the equation-of-motion method based on thistwo-component CCSD approach to circumvent this problem. We implemented
EOM-CCSD to calculate excitation energies (EOMEE) and ionization energies (EOMIP)of closed-shell molecules. We can thus calculate open-shell excited states of a moleculewith closed-shell ground state or both ground and excited states of open-shell moleculesthat can be reached by removing one electron from a closed-shell reference state. In thismethod, SOC can be included either at the CC part or only in the EOM equation. The
latter approach, although not size-consistent, provide an economic way to treat SOC
effects especially in EOMIP-CCSD and results show that it can lead to rather accurate
results even for 5p element compounds. We further demonstrate implementation ofanalytic energy gradient for the two-component EOMEE-CCSD, which facilitates
location of stationary points on excited state potential energy surfaces and harmonicfrequencies of these stationary points.
Reference
1 F. Wang, J. Gauss and C. van Wüllen, J. Chem. Phys. 129, 064113 (2008).
2 F. Wang and J. Gauss, J. Chem. Phys. J. Chem. Phys. 129, 174110 (2008).
3 F. Wang and J. Gauss, J. Chem. Phys. 131, 164113 (2009).

333

4PP-05

Multilevel extension of the cluster-in-molecule method
for the chemical reactions of large molecules
Wei Li,1,2 Piotr Piecuch2
1
School of Chemistry and Chemical Engineering, Nanjing University, China
2
Department of Chemistry, Michigan State University, USA
The linear scaling local correlation approach, termed “cluster-in-molecule(CIM)”,1-4 is extended to multilevel calculation,5 which enables one to combine different
quantum chemistry methods to treat the different regions in a large molecule. In themultilevel calculations, the reactive part of a large molecular system is treated byhigher-level methods, such as coupled cluster (CC) with singes and doubes (CCSD) or
the completely renormalized CC approach with singles, doubles, and noniterative triples,
termed CR-CC(2,3). And the chemically inactive regions are treated by lower-level
methods, such as the second-order Møller-Plesset perturbation theory (MP2). The key
features of all CIM methods, such as the use oforthonormal localized orbitals and quasi-canonicalmolecular orbitals (QCMO), the and coarse-grain

S2

parallelism, can be preserved. Our illustrative
calculations show that the multilevel CIM-CC/MP2
reduces the alreadly relatively low costs of the

P

S1

MP2

singe-level CIM-CC while keeps similar accuracy.5[1] Li, S.; Ma, J.; Jiang,Y. J. Comput. Chem. 2002, 23, 237.
[2] Li, S.; Shen, J.; Li, W.; Jiang, Y. J. Chem. Phys. 2006, 125, 074109.
[3] Li, W.; Piecuch, P.; Gour, J. R.; Li, S. J. Chem. Phys. 2009, 131, 114109.
[4] Li, W.; Piecuch, P. J. Phys. Chem. A 2010, 114, 8644.
[5] Li, W.; Piecuch, P. J. Phys. Chem. A 2010, 114, 6721.

334

CC

4PP-06

Multireference Perturbation Theory
Can Predict a False Ground StateHenryk A. Witek,1 Cristopher Camacho,1 Renzo Cimiraglia2
1
Department of Applied Chemistry and Institute of Molecular Science,National Chiao
Tung University, 30010 Hsinchu, Taiwan
2
Dipartimento di Chimica, Universita di Ferrara,Via Borsari 46, I-44100 Ferrara, Italy

We have recently discovered [1, 2] that popular variants of multireference
perturbation theory (CASPT2 and MRMP) can predict a false ground state for aremarkably simple chemical system: the scandium dimer. The MRMP and CASPT2
calculations on Sc2 using a reduced valence (12o, 6e) active space were found to suffer
severely from intruder states (i.e., the quasi-degeneracies in the spectrum of thezeroth-order Hamiltonian); employing intruder state removal techniques helped us toobtain smooth and continuous potential energy curves. Unfortunately, the shape of thecurves and their energy order depended strongly on the magnitude of the shift parameter
ı; for small values of ı, MRMP and CASPT2 predicted that the ground state of Sc2
is 3 6 u , while for large values of ı, they predicted 5 6 u . Analogous calculations
performed with NEVPT2—a recent variant of multireference perturbation theory freefrom the intruder state problem owing to a partially bielectronic definition of thezeroth-order Hamiltonian—showed clearly [3] that the ground state is 5 6 u . Our
calculations clearly show that CASPT2 and MRMP used in conjunction with the
intruder-state removal techniques are capable of predicting a false ground state even forvery simple molecular systems. This finding casts serious doubts on the validity of theshift techniques in the framework of multireference perturbation theory and shows that
this direction of development can be a dead-end street.

References:[1] C. Camacho, R. Cimiraglia, and H. A. Witek, “Multireference perturbation theory
can predict a false ground state”, Phys. Chem. Chem. Phys. 12, 5058–5060 (2010)[2] C. Camacho, R. Cimiraglia, and H. A. Witek, “Reply to the ‘Comment on»Multireference perturbation theory can predict a false ground state«’ by J, Soto, F. Avila,
J. C. Otero, and J. F. Arenas”, Phys. Chem. Chem. Phys. 13, 7232–7233 (2011)[3] C. Camacho, H. A. Witek, and R. Cimiraglia, “The low-lying states of the scandium
dimer”, J. Chem. Phys. 132, 244306 (2010)335

4PP-07

Antisymmetric product of strongly orthogonal geminals (APSG):
Its acceleration and extension to open-shell systems
Moto Tarumi,1 Masato Kobayashi,1,2 Hiromi Nakai1,3,4
1School of Advanced Science and Engineering, Waseda University, Japan
2
Institute for Molecular Science, Japan
3
Reserch Institute for Science and Engineering, Waseda University, Japan
4
CREST, Japan Science and Technology Agency, Japan
I. Introduction
Antisymmetric product of strongly orthogonal geminals (APSG) method [1,2] is awave-function theory that can effectively treat the static electron correlation. In the
APSG method, the all-electron wave function is constructed as the antisymmetricproduct of two-electron wave functions, called geminals. However, there are several
problems in this method that should be overcome for its practical applications. First, the
APSG procedure occasionally faces on the convergence problem. In this study, we
introduced the direct inversion in the iterative subspace (DIIS) method into the APSG
optimization process. In addition, we extended the APSG method to open-shell system
calculations by using one-electron orbitals for the open-shell part, as Rassolov [3]introduced into his geminal theory.
II. Acceleration with DIIS method
In the APSG method, a geminal \ is composed of mutually exclusive naturalorbitals M,\ I x1 , x2 ¦ CmI M m r1 M m r2 1- 1,2 ,(1)mI

where - 1,2 is the antisymmetric spin function, and natural orbitals M are represented
as a unitary transformation of orthonormal orbitals I with T, which is optimized with
the Newton-Raphson method until the orbital gradient g becomes zero. C is thecoefficient matrix determined by the local Schrödinger equation for each geminal. In
this study, DIIS method is introduced into the optimization process of T. This method
reduces the computational time for the APSG calculation to 30%-50% of the original.
III. Extension to open-shell systems
In open-shell systems, we define the APSG wave function with two-electron
geminals and one-electron natural orbitals as follows:) APSG Aˆ \ 1 x1 , x2 \ 2 x3 , x4 \ N C 2 x N C 1 , x N C M1 x N C 1 M N O x N C  N O , (2)1>@where Â is antisymmetrization operator, and NC and NO mean numbers of electrons inclosed and open shells, respectively. We implemented this method into GAMESS
program, and have succeeded in describing the radical dissociation of the OH molecule.
[1] W. Kutzelnigg, J. Chem. Phys. 40, 3640 (1964).
[2] P. R. Surján, Correlation and Localization, Springer, Berlin, pp. 63-88 (1999).
[3] V. A. Rassolov, J. Chem. Phys. 117, 5978 (2002).

336

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337

4PP-09

Numerical analysis for eigenvalue problems in quantum mechanics
and atomic structure calculations
Hideaki Ishikawa
Home, Hadano-shi, Kanagawa-ken, Japan
I. Introduction
In order to get fruitful insights into structures and electronic states of atoms,
molecules and solids based on first-principles, we have to carry out highly accurate andfast numerical calculations. Numerical methods widely used thus far have provided
8-digits and 5-digits accuracy at most, for atomic structure and molecular orbital
calculations, respectively. We have to realize high accuracy with more than or equal to
13-digits and 10-digits accuracy for atomic structure and molecular orbital calculations,
respectively. We report here a new set of highly accurate and fast methods of numericalsolutions for eigenvalue problems in quantum mechanics and atomic structures.
II. Numerical methods of calculation
In the one-body problems we solve the eigenvalue problem of the Schr·dinger
equation for a given potential [1-4]. For one-dimensional problems, we establishedhighly accurate methods of numerical calculation for interpolation, derivatives,
integration, and initial-value problems of the second-order ordinary differential
equations (ODEs). We realized highly accurate methods of numerical solution for the
eigenvalue problems by using the discretized matrix eigenvalue method and theshooting method. For central-force-field problems we developed a method of solution
for ODEs around singularities (power and asymptotic series expansions) and solved
radial eigenvalue problems by using the shooting method.
In the many-body problems, we solve the eigenvalue problems for the Schr·dinger
equation in the mean field approximation. For the atomic structure calculations, wedeveloped a new set of highly accurate numerical methods of indefinite integrations andof solutions for the initial-value problems of the first-order ODEs for calculating
potentials. In addition, we solved self-consistently the radial eigenvalue problem andpotential calculation [5].
III. Results
We obtained from 13- to 15-digits accuracy for the eigenvalues. The maximum
absolute error of the eigenfunctions was of order less than 5x10-13.
[1] H. Ishikawa, J. Phys. A35 (2002) 4435.
[2] H. Ishikawa, J. Comput. Appl. Math. 208 (2007) 404.
[3] H. Ishikawa, J. Comput. Chem. Jpn. 10 (2010) 89.
[4] H. Ishikawa, in Quantum Mechanics, edited by J. P. Groffe, NOVA Science, New
York, 2010, in press.
[5] H. Ishikawa, unpublished.

338

4PP-10

An Overlap Fitted RIJCOSX TheoryRóbert Izsák,1 Frank Neese1
1
Lehrstuhl für Theoretische Chemie, Institut für Physikalische und Theoretische
Chemie, Universität Bonn, Germany
The acceleration and extension of present standard theoretical methodologies forlarge molecular systems is in the forefront of modern Quantum Chemical research.
The RIJCOSX algorithm1 addresses the problem of integral evaluation in particular.
This algorithm combines the advantages of the Split-RI-J approximation2 for theevaluation of Coulomb integrals, and follows closely the pseudo-spectral approachof Friesner3 for the exchange integrals. The “chain of spheres” (COSX) algorithm
approximates two electron integrals by performing analytic integration with respect
to the coordinates of only one of the two electrons, whereas for the remaining coordinates integration is carried out numerically through the evaluation of basis functions
over grid points to reduce the cost of the calculation. In the present work, we attempt to minimize the eﬀect of numerical errors in the COSX procedure, whichmakes it necessary to use rather large grids to achieve chemical accuracy. The idea
based on the work of Friesner, and futher explored by Ten-no, is that we look for asolution of the equation:
S = QXT
where S is the analytic overlap matrix of basisfunctions, X contains basisfunction
values evaluated over the grid, and Q is therefore a matrix which makes the numerical evaluation of overlap integrals exact. Subsequently, Q can be used to evaluate
the exchange integrals in the COSX algorithm. This results in a reduction of grid
sizes necessary for chemical accuracy, and a corresponding 30% speed up over theoriginal RIJCOSX procedure for single point energy and gradient calculations. The
new method is referred to as the overlap ﬁtted RIJCOSX theory.
[1] F. Neese, F. Wennmohs, A. Hansen, U. Becker, Chem. Phys., 356, 98 (2009).
[2] F. Neese, J. Comput. Chem., 24, 1740 (2003).
[3] R. A. Friesner, Chem. Phys. Lett., 116, 39 (1985).

339

4PP-11Development and Applications of Theoretical Methods
for Solvated Molecular System
Hirofumi Sato
Department of Molecular Engineering, Kyoto University, Japan
I. Introduction
Recent development of experimental technique makes it increasingly clear thatthe electronic structure of a molecule is signiﬁcantly changed when it is dissolved
into polar solvent. This means electronic structure, which is treated by quantum
chemistry, and solvation structure, which is governed by statistical mechanics, arecoupled each other. In this regards, development of new theory that can bridge
between these two methodologies is indispensable to properly understand ordinary
chemical processes. In the last few decades, various types of hybrid method, suchas polarizable continuum model (PCM) and QM/MM, have been developed andapplied to a variety of chemical phenomena [1].
II. RISM-SCF-SEDD method and its applications
We have been developing RISM-SCF, which combines two ab initio methods intheoretical chemistry: one is the reference interaction site model (RISM), and theother is ab initio molecular orbital (MO) theory. The method determines electronic
structure of a solute molecule and statistical solvent distribution around it in aself-consistent manner. It is a remarkable advantage of RISM-SCF method thatprovides microscopic solvation structure based on the statistical mechanics. RISMSCF-SEDD [2] is regarded as a new generation method and signiﬁcantly expands
the versatility of the RISM-SCF family. The method has been successfully applied
to numerous molecular phenomena such as chemical reactions and equilibria.
In this contribution, we will review our theoretical methods together with recent
applications for several chemical phenomena in solution phase including chemical
reactions in ionic liquids, electronic excitation of solvated molecules and so on [3].
[1] “Continuum Solvation Models in Chemical Physics: From Theory to Applications” Eds. by B. Mennucci, R. Cammi, John Wiley & Sons, (2008).
[2] D. Yokogawa, H. Sato and S. Sakaki, J. Chem. Phys., 123, 211102 (2005);
D. Yokogawa, H. Sato and S. Sakaki, J. Chem. Phys., 125, 114102 (2006).
[3] K. Iida, D. Yokogawa, H. Sato and S. Sakaki, Chem. Phys. Lett., 443, 264(2007); S. Hayaki, D. Yokogawa, H. Sato and S. Sakaki, Chem. Phys. Lett., 458,
329 (2008); S. Hayaki, K. Kido, D. Yokogawa, H. Sato and S. Sakaki, J. Phys.
Chem. B, 113, 8227 (2009); S. Hayaki, K. Kido, H. Sato and S. Sakaki, Phys.
Chem. Chem. Phys., 12, 1822 (2010); D. Yokogawa, H. Sato, S. Sakaki and Y.
Kimura, J. Phys. Chem. B, 114, 910 (2010); H. Sato, C. Kikumori and S. Sakaki,
Phys. Chem. Chem. Phys., 13, 309 (2011); N. Umeda, K. Hirano, T. Satoh, N.
Shibata, H. Sato and M. Miura, J. Org. Chem., 76, 13 (2011).

340

4PP-12

A new procedure for the calculation of electron transfer
coupling matrix element
Mitsuo Shoji,1 Kyohei Hanaoka,2 Moonyoung Yang,2 Daiki Kondo,2Katsumasa Kamiya,2 Kenji Shiraishi2
1
Center for Computational Science, University of Tsukuba, Japan
2
Graduate School of Pure and Applied Sciences, University of Tsukuba, Japan

Electron transfer (ET) steps are critical for many biological processes such as
photosynthesis, respiration and many enzyme reactions. Characterization of ET
reactions is of great importance in a variety of chemical and biological systems. One of
the key factors in determining the ET rate is electron transfer coupling matrix, T value.
For symmetric systems, the T value can be easily evaluated from the orbital energy gap,
however, this procedure is limited to symmetric systems.
In this study, a new procedure for the T value evaluation for asymmetric systems is
proposed through the utilization of the orbital localization method. This new procedure
is applied to three typical ET cases, phenoxyl radical-phenol, DNA sequences, andcopper containing nitrite reductase (CuNiR).
It is demonstrated that T values are properly evaluated. Other related parameters, stateenergy gap (E) and localization index (L), and localized molecular orbitals are very
useful to characterize the electron transfer reactions and redox-active orbitals (Fig.1).
This new approach can be utilized for other general ET reactions.

Fig. 1 internal electron transfer in a phenoxyl radical-phenol system.

341

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4PP-14

Cracking Reaction of C2-C4 Alkanes Sorbed in ZSM-5
Kanjarat Sukrat,1 Daniel Tunega,2,3 Adelia J.A. Aquino,2 Hans Lischka,2 Vudhichai
Parasuk1
1
Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd.,
Patumwan, Bangkok, 10330 Thailand
2
Institute of Theoretical Chemistry, University of Vienna, Währingerstraȕe 17, A-1090,
Vienna, Austria
3Institute of Soil Research, University of Natural Resources and Applied Life Sciences,
Peter-Jordan-Straȕe 82, A-1190, Vienna, Austria
Quantum chemical methods were performed by various cluster models todetermine adsorption energies and reaction barriers (activation energy) for cracking
reactions of small alkanes (C2-C4) in zeolite ZSM-5. The characteristics and behaviors of
the alkane molecules inside ZSM-5 were revealed from the optimized geometries ofadsorption and transition state (TS). Two protonated positions on the C-C bond of alkanesof the zeolitic proton (pathway 1 and 2) were studied. Bond distances between breaking
carbon atoms and proton can be used to predict the outcome of products. Effects such as
cluster size, zero point energy, basis set, and electron correlation have also beenmonitored. An extrapolation technique incorporating such effects has been proposed. The
cluster size showed largest impact on both adsorption energy and reaction barrier, whileother effects were small. The reaction barrier of the cracking reaction suggests pathway 2
is more favorable than pathway 1. Computed energies agree well with experiments.

343

4PP-15

Giant SAC-CI method: Application to proteins1

Tomoo Miyahara and Hiroshi Nakatsuji
Quantum Chemistry Research Institute (QCRI), Kyodai Katsura Venture Plaza, Northbuilding 106, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245, Japan
2
Japan Science and Technology Agency, CREST

The SAC/SAC-CI method is a useful established method for studying ground,
excited, ionized and electron attached states of molecules [1-3]. It is widely distributed
through Gaussian09 [4]. However, it is difficult to calculate large molecules such asproteins and crystals etc. Therefore, we are developing a new method by extending the
SAC/SAC-CI methodology to giant molecular systems like molecular crystals etc [5].
We call it Giant SAC/SAC-CI method. Recently, this method is designed to be much
faster than the original method with the same chemical accuracy.

Figure 1䠊The structure of glycine polypeptide
We developed the Giant SAC-CI program for non-periodic systems and applied toglycine polypeptide (Fig. 1) as a test molecule. Glycine has no D,L isomer and is
optically inactive, because glycine is the simplest amino acid and does not have any
asymmetric carbon atom. However, glycine polypeptide is optically active because thesymmetry is broken when glycine is linked with peptide bond. Therefore, we calculated
the excitation energies and rotatory strengths of polypeptide.
We compared the results obtained from the Giant SAC-CI method with the Gaussian
09 (standard) SAC-CI method. The differences of the excitation energies were verysmall and the Giant SAC-CI could provide the same accuracy as the standard SAC-CI.
Nevertheless, the computational cost was much reduced to one-seventh. We cancalculate more efficiently, when the system is larger. We will present the result of otherproteins
References[1] Nakatsuji, H. Chem. Phys. Lett.1978, 59, 362.; 1979, 67,329,334; Bull. Chem. Soc.
Jap. 2005, 78, 1705.
[2] SAC-CI homepage. http://www.qcri.or.jp/sacci/ (6/6/2005)[3] Ehara, M.; Hasegawa, J.; Nakatsuji, H. Theory and applications of Computational
Chemistry, The First 40 Years, Elsevior Oxford, 2005; p1099.
[4] Frisch, M. J.; et at. GAUSSIAN 09, Gaussian, Inc. Wallingford CT, 2009.
[5] H. Nakatsuji, T. Miyahara, R. Fukuda, J. Chem. Phys. 2007, 126, 084104

344

4PP-16

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.RUHDI.

Introduction

The emission of the greenhouse gas mostly from the fossil fuel induces severe damages
on the climate and ecology of the planet. Worldwide efforts to reduce carbon in theatmosphere are going on in the industrial and academic fields. Metal-Organic Framework(MOF) is promising material to capture carbon in several aspects that it can contain carbon
voluminous scale and the restoration energy is quite small compared to Monoethanolamine(MEA) used widely in the plant.
II.

Abstracts

The capability of metals to adsorb CO2 with reference to the MOF-74 was studied.
MOF-74 structure has the open metal site and the metal directly binds to CO2. All the metals
in the first transition metal series together with Mg and Ca was investigated using firstprinciple method equipped in VASP. Though the Mg-MOF-74 has been known to have highadsorption enthalpy, Ca, Ti, and V are shown to have better capabilities for CO2 adsorption.
Among them, Ti is most powerful adsorbent with 5kJ/mol higher than Mg. The tendency ofadsorptivity is consistent with metals in the order of Mg, Ni, Zn, Co, and Cu as reported
earlier. Though the absolute magnitude of adsorption enthalpy is smaller than experimental
value, DFT shows a reliable data to measure the adsorption qualitatively. The effect of cellrelaxation (MOF+CO2) and the dispersion energy between the CO2 molecules (RIMP2/BSSE,
QChem) contribute less than 2kJ/mol to the adsorption enthalpy, respectively. All thebindings of CO2 on the open metal sites belong to physisorption regime.
III.

Table and Figure/1(/I'ZRGTKOGPV 

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345

4PP-17

Combination of spin-restricted and spin-projected calculations
for a geometry optimization of large biradical systems
Yasutaka Kitagawa, Toru Saito, Yusuke Kataoka, Natsumi Yasuda, Hiroshi Hatake,
Toru Matsui, Takashi Kawakami, Shusuke Yamanaka, Mitsutaka Okumura andKizashi Yamaguch
Graduate School of Science, Osaka University, Japan
With the recent progress in quantum chemistry, we can calculate electronic
structures, energies and energy derivatives of large molecules by the first principle
methods. A broken-symmetry (BS) (or an unrestricted: U) method approximately but
easily corrects the static correlation at the lower computational costs. However the BS
method involves a serious problem called a spin contamination error (SCE). For the
problem, our group has proposed a spin-projection method to eliminate the SCE fromthe energy derivatives based on Yamaguchi’s approximate spin projection (AP)procedure [1-4]. By the AP method, one can optimize the geometry of the biradical
systems without SCE at the costs of the BS level calculations. However one mustcarry out 6N (N = optimizing atoms) times single-point calculations previous to thegeometry optimization because it uses a numerical derivative for d<S2>/dR values. In
addition, it also requires both the low-spin and the high-spin state calculations during
the geometry optimization. Therefore the reduction of thecomputational costs is a problem of the AP method for the
optimization of the larger biradical systems such as a binuclear
metal complex (e.g. Figure 1). In this study, we attempt tocombine the AP method and the spin-restricted (R) methods, i.e.
two-layer QM/QM’ approach based on ONIOM method. In themethod, the effect of the outer-ligands is included by the
restricted method whilst an energy gradient of the core is
calculated by the AP method using a reduced (small) model.
The detail about the method and results are illustrated in the Fig. 1
Cr2(O2C(CHMe2)3)4
presentation.
References[1] Y. Kitagawa, T. Saito, M. Ito, M. Shoji, K. Koizumi, S. Yamanaka, T. Kawakami,
M. Okumura, K. Yamaguchi, Chem. Phys. Lett. 2007, 442, 445.
[2] T. Saito, Y. Kitagawa, M. Shoji, Y. Nakanishi, M. Ito, T. Kawakami, M. Okumura,
K. Yamaguchi, Chem. Phys. Lett. 2008, 456, 76.
[3] T. Saito, S. Nishihara, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T.
Kawakami, M. Okumura, K. Yamaguchi, Chem. Phys. Lett., 2009, 483, 168.
[4] Y. Kitagawa, T. Saito, Y. Nakanishi, Y. Kataoka, T. Matsui, T. Kawakami, M.
Okumura, K. Yamaguchi, J. Phys. Chem. A., 2009, 113, 15041.

346

4PP-18

Norm-conserving stochastic Hartree-Fock calculation on electronic
states in molecules
Tatsuji Sano
Department of Engineering Sciences, The University of Electro-Communications, Japan
It is a difficult computational problem to solve the Schrödinger equation for a manyelectron system. Therefore, development of accurate and computationally efficientmethods for calculating the ground and excited electronic states of molecules is one of
the biggest challenges in the theoretical chemical physics. Generally, exact strategies formany-body problems need computational costs scaling up exponentially with thenumber of electrons. Recently Juillet and Chomaz proposed a stochastic time-dependent
Hartree-Fock approach in which the quantum N-body dynamics with two-bodyinteractions is exactly decomposed into the average of N one-body stochastic evolutions
and thereby the usual exponential scaling of computational costs can be eliminated [1].
However, the norms of the one-body stochastic wavefunctions grow exponentially. Thisis related to the sign or phase problem which occurs in the auxiliary field Monte-Carloapproach. In order to overcome the above drawback, an exact one-body decompositionof time-dependent Schrödinger equation for a many-electron system in which one-body
wavefunctions obey Ito-type stochastic time-dependent norm-coserving equations has
been derived and applied to calculation of the low energy spectrum in Helium atom [2].
In this study we apply the norm-conserving stochastic time-dependent Hartree-Fockmethod to calculation of the electronic ground and excited states in molecules. The Nelectron wavefunction is expressed in terms of an ensemble average over stochastic
Slater determinants. The Coulomb (two-body) interaction part of the Hamiltonian isrepresented as a sum of products of one-body operators and treated as a source of noise.
The stochastic differentials of complex general spin-orbitals are determined by Ito-type
stochastic wave equations which conserve norm but do not orthogonality. Numericalintegration was performed with the stochastic generalization of the fourth order RungeKutta scheme. The energy spectrum can be expressed as the Fourier transform of thetime auto-correlation function. From another point of view we try to extend the normconserving stochastic Hartree-Fock interpretation of the evolution process to imaginary
time in order to obtain the correlated N-body ground state in the limit of large imaginary
time. Numerical results of our test calculations will be reported.
[1] O. Juillet, Ph. Chomaz, Phys. Rev. Lett. 88 (2002) 142503.
[2] L. Tessieri, J. Wilkie, M. Cetinbas, J. Phys. A 38 (2005) 943.

347

4PP-19

Dispersion Energy of van der Waals Complex; Approximate
Evaluation with Pair-wise Correlation EffectMilind M. Deshmukh,1 Shigeyoshi Sakaki1
1
Fukui Institute for Fundamental Chemistry, Kyoto University, Japan
I. Introduction: Accurate estimation of dispersion energy is essential for study of vander Waals (vdW) complex; however such estimation is computationally demanding
especially when many monomers are involved. To reduced computational cost, basis set
extension methodologies [1] and many-body decomposition schemes were proposed [2].
Although these methods are effective to certain extend, the MP2, MP3 and CCSD(T)levels are computationally demanding even with basis set of medium size.
II. Computational Details: We propose new approximate equation for accurate
estimation of dispersion energy based on the idea that molecular orbitals of dimer
system AB are little different from those of AB moiety in total vdW complex. We
analytically showed that the total dispersion energy of vdW complex can be accurately
evaluated as sum of the dispersion contribution of all possible dimers in vdW complex.
Based on this, the binding energy (BE) of vdW complex is calculated as;
BE = BE(HF) +{BE A -B (correlate d level) - BE A -B (HF)},(1)
A>B
where A and B are interacting monomers. The first term is usual Hartree-Fock (HF)
binding energy. The second term is sum of the difference in two-body binding energy
between correlated and HF level. The MP2 and MP2.5 methods [3] were employed. The
aug-cc-pVTZ and aug-cc-pVQZ basis sets were used.
III. Results and Discussion: Binding energies of various vdW complexes generatedusing dimers reported in S22 data set, are evaluated. Highly accurate binding energies
are obtained with proposed equations; See Figure 1. Also, precise minimum on PES is
obtained with these equations (Table 1). Application to transition metal complexes
suggests that these equations are useful to study aurophilic interactions.

¦

Table 1: Comparison of minimum position (Å)
on MP2.5 PES between reference (Rref.) and by
the approximate equations (Raaprox.).
Complexes
Minimum position
Rapprox.
Rref.
CO2-trimer
3.541
3.533
Figure 1: Comparison of BE calculated
CS2-trimer
4.318
4.326
between the reference value (BEref.)a
Acetylene-trimer
1.742
1.741
and approximate eq. (1).
Water-trimer
2.420
2.420
a)
BE ref . = E t ( M i : M j : ...) − ¦ E ( M i )Mi[1] Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 6624 and references therein.
[2] Pedulla, J. M.; Vila, F; Jordan, K. D. J. Chem. Phys. 1996, 105, 11091.
[3] PitoĖák, M.; Neogrády, P.; CČrny´, J.; Grimme, S.; Hobza, P. Chem. Phys. Chem. 2009,10, 282.

348

4PP-20

OpenMP/MPI hybrid parallelization of GAMESS
Hiroaki Umeda,1,2 Mitsuhisa Sato,21Institute for Molecular Science, National Institute of Natural Sciences, Japan
2
Center for Computational Sciences, University of Tsukuba, Japan
I. Introduction
Hybrid parallelization with OpenMP and MPI becomes unavoidable programing
model for the recent HPC computer system, which has massive processor cores. We
have modified GAMESS program [1] with OpenMP/MPI hybrid parallelization modelto acquire large fragment molecular orbital (FMO) calculation [2] on the massively
parallel HPC system.
II. GAMESS and Parallelization
The GAMESS program is parallelized with distributed data interface (DDI) as amessage-passing API to realize remote memory access (RMA) operations. Using
RMA functions of DDI library, we can easily parallelize program with dynamic
load-balancing scheme, where small tasks are evenly distributed through a single global
counter. For a massively parallel computer, this global counter could become abottleneck of parallelization efficiencies, thus we have evaluated the performance ofvarious DDI implementations.
Parallelization with OpenMP has performed only for FMO calculation with RI-MP2.
Because the FMO calculation treats relatively small fragments or fragment-pairs, wehave implemented both direct and in-core scheme for HF calculation. The most of
RI-MP2 calculation spend CPU time for matrix-matrix multiplies with DGEMM routine
in BLAS library; therefore the OpenMP parallelization is easily obtained using
OpenMP-supported BLAS library.
III. Benchmark Results
Benchmark calculations were performed on the T2K Tsukuba system [3] inUniversity of Tsukuba. Comparison with various DDI implementations shows the
DDI implementation with ARMCI library is the best performance for HF calculation,
where main communication bottleneck is the access to the global counter. In addition
to the implementation of DDI, we found the importance of the processor affinity.
Large benchmark calculations of FMO/RI-MP2 method were also performed with
10,240 processor cores with/without OpenMP parallelization. The OpenMP/MPI
hybrid parallel execution shows better performance than the flat MPI parallel execution.
[1] M.W.Schmidt, et al., “General Atomic and Molecular Electronic Structure System”,
J. Comput. Chem. 14, 1347-1363, 1993.
[2] K. Kitaura, et al., “Fragment molecular orbital method: an approximate computational
method for large molecules”, Chem. Phys. Lett. 313, 701-706, (1999).
[3] http://www.ccs.tsukuba.ac.jp/CCS/eng/research-activities/supercomputers#T2K.

349

4PP-21

Theoretical Study on the Working Mechanism of Stilbene
Light-Driven Molecular Rotary Motor
Fengyi Liu, Keiji Morokuma
Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
Artificial synthesized light-driven molecular motors, which convert external energy
to mechanical force, have been widespread in the past decade. We carried out the
CASSCF/CASPT2 calculations to explore the rotary potential energy surface of ageometrically
overcrowded,
chiralstiff-stilbene
molecular
motor((2R,2R)-2,2ʹ,7,7ʹ-tetramethyl-1,1ʹ-bis(indanylidene), see Figure 1), as well tocharacterize the interaction between the PESs of the involved electronic states. The
reaction paths of the two photo-initiated cis-trans (or E/Z) isomerization steps, namely,[P,P]-cis ė [M,M]-unstable-trans and [P,P]-trans ė [M,M]-unstable-cis have been
explored. The minimal energy reaction paths (MEPs) of these two processes are parallelon the PESs and show remarkably steep slope, which drives C=C bond rotate
unidirectionaly. The bias on the excited-state MEPs are caused by the asymmetricsubstituents on the "fjord" region as well as that between the phenyl moieties. The
reactions are supported to flow a three-state, multi-modes mechanism: The excitedmolecules on 1B state first crossthesloped
1B/2A
conicalintersections (1B/2A CIs), thenpreferentially approach one of thetwo 2A/1A CIs flowing two
cooperative torsional reaction
modes. The findings of the present
study are expected to shed light onunderstanding
theworkingmechanismofthestilbenemolecular motor and to rationalize
the unidirectionality of thephoto-initiated
C=C
rotationprocesses.

[1] Pollard, M. M.; Meetsma, A.;
Feringa, B. L. Org. Biomol. Chem.
2008, 6, 507–512.
Figure 1. Four-step rotation scheme instiff-stilbene light-driven molecular rotary
motor 3 (Ref 1).

350

4PP-22

Massively parallel second-order Møller–Plesset perturbation
calculations based on divide-and-conquer method
Michio Katouda,1 Masato Kobayashi,1,2 Hiromi Nakai,2,3,4 Shigeru Nagase1
1
Institute for Molecular Science, Japan
2
School of Advanced Science and Engineering, Waseda University, Japan
3
Research Institute for Science and Engineering, Waseda University, Japan
4
CREST, Japan Science and Technology Agency, Japan
I. Introduction
The divide-and-conquer (DC) method is the promising tool for the density
functional theory (DFT) and Hartree-Fock (HF) calculation of large molecules. In the
DC method, a target system is spatially divided into small fragments and then theenergy and the properties are evaluated by accumulating contributions of fragmented
systems. The DC method has been extended to the second-order Møller–Plesset
perturbation (MP2) method (DC-MP2) [1,2]. DC-MP2 and DC-HF have been
implemented into the GAMESS-US program. In this study, we present recent
developments of the computational techniques for the rapid DC-MP2 calculations using
massively parallel computers.
II. Two-level hierarchical parallelization scheme for DC-MP2 calculations [3]
We developed a two-level hierarchical parallelization scheme for the DC-MP2
calculations that is suitable for massively parallel computing. The parallelization
scheme is a combination of the coarse-grain parallelization assigning each subsystem toa group of processors and the fine-grain parallelization where the computational tasks
for evaluating the MP2 correlation energy of the assigned subsystem are distributed
among processors in the group. Test calculations demonstrate the high parallel efficiencyof the present two-level hierarchical parallel implementation, making the DC-MP2
calculations feasible for extended systems using massively parallel computers.
III. Semi-direct DC-MP2 method [3] and DC-RI-MP2 method
We developed a parallel semi-direct DC-MP2 code for the rapid calculations using
the commodity PC clusters. This code is based on the semi-direct algorithm, in which
third-quarter transformed integrals are stored on disks to avoid redundant multiple
evaluation of electron repulsion integrals (ERIs). Furthermore, we developed a
DC-RI-MP2 method by utilizing the resolution of identity (RI) approximation of ERIs
to reduce the computational prefactor for the integral transformations and the disk andmemory requirements. Test calculations demonstrate that these new implementations
considerably speed up the DC-MP2 calculations of large molecules.
[1] M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys. 127, 074103 (2007).
[2] M. Kobayashi and H. Nakai, Int. J. Quant. Chem. 109, 2227 (2009).
[3] M. Katouda, M. Kobayashi, H. Nakai, and S. Nagase, J. Comput. Chem. in press.

351

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352

4PP-24

Divide-and-conquer symmetry-adapted cluster method
Takeshi Yoshikawa,1 Masato Kobayashi,1,2 Hiromi Nakai1,3,4
School of Advanced Science and Engineering, Waseda University, Japan
2
Institute for Molecular Science, Japan
3
Research Institute for Science and Engineering, Waseda University, Japan
4
CREST, Japan Science and Technology Agency, Japan
1

Correlation Energy Ecorr [hartree]

I. Introduction
We have implemented and assessed the divide-and-conquer (DC) self-consistent
field (SCF) method and extended the DC method to the post-HF correlation theories [1].
In this presentation, we will report the extension of the DC method to thesymmetry-adapted cluster (SAC) theory [2] and show some illustrative applications.
II. Theory
In the DC-SAC method, the total correlation energy is estimated by summing up
correlation energies corresponding to individual subsystems. The correlation energy of asubsystem is estimated using subsystem MOs, composed of the AOs of the
non-overlapping central region and the environmental buffer region.
The SAC method introduces the perturbative configuration selection for reducing
computational time. Namely, the double excitation operators (ǅD) whose second-ordercontribution to the energy ED, given in Eq. (1), is greater than a given threshold (λg =10-5 for level 1, 10-6 for level 3) are only included in the cluster expansion.
2
H 0D
ED =
, H ab = Φ a H Φ b(1)
H DD − H 00
III. Results
The present DC-SAC method was assessed
DC-SAC(level 1)
DC-SAC(level 3)
in calculations of a hydrogen fluoride oligomer
DC-SAC(Noselection)
DC-CCSD-0.55
SAC(level 1)(FH)6. In the DC calculations, one FH unit was-0.60
adopted as a central region and several adjacent
SAC(level 3)-0.65
FH units were treated as the corresponding buffer-0.70
region. Figure 1 shows buffer size (nb)
SAC(Noselection)
dependence of the correlation energies obtained-0.75
by the DC-SAC and DC-CCSD calculations.
-0.80
CCSD
While the CCSD energy difference between DC
-0.85
1
2
3
4
5
and conventional calculation for nb = 1 is less thanbuffer size nb
1.5 mhartree, the SAC energy difference (nb = 1)
Fig. 1. Buffer-size dependence ofis 78.2 mhartree at level 3. On the other hand, theDC-SAC and CCSD correlation
DC-SAC data (nb = 1) at level 3 is close to that ofenergies of (FH)6.
the conventional without selection (green line) as
well as the DC-SAC data (nb = 1) without selection. This means that the perturbation
selection with the small buffer efficiently describes the correlation effect, which is thesimilar effect as reported for SAC calculations with the localized orbitals [3].
[1] M. Kobayashi and H. Nakai, in Linear-scaling techniques in computational chemistry andphysics (Springer, 2011), pp. 97–127.
[2] H. Nakatsuji and K. Hirao, J. Chem. Phys. 68, 2053 (1978).
[3] K. Toyota, M Ehara, and H.Nakatsuji, Chem. Phys. Lett. 356, 1 (2002).

353

4PP-25

Fast Diffusion of Water Confined Between
Plane Surfaces Coated with Water Monolayer
Lukman Hakim,1 Masakazu Matsumoto,1 Hideki Tanaka1
1
Graduate school of Natural Science and Technology, Okayama University, Japan
I. Introduction
The structure of water at interfaces can influence the physical and chemical process
in biological and human-made systems. Water molecules can be chemically bound on
the surface of certain material such as Pt to give a thin film of immobilized water [1].
Considering the variety of surface materials that can be prepared, it is plausible toobtain a particular arrangement of water molecules that exhibit property of interest. For
example, water monolayer on the surface of Pt and Pd was reported to be hydrophobic
on which water diffusion is facile [2]. Here we show that a simple model of watermonolayer can give hydrophilic or hydrophobic-like property by varying its
intermolecular distance, and further can accelerate the lateral diffusion of water
confined between two plane surfaces coated with water monolayer.
II. Simulations
The water monolayer is modeled with the (111) surface of cubic ice having
diamond-like structure. The system consists of two planes of wall, which are separated
by 5 nm distance. The water monolayer is then immobilized on the wall surface andmassive water molecules are confined between those walls. The structure and dynamics
of water in liquid phase and in monolayer is investigated using molecular dynamics
simulation at constant overall density of 1 g cm-3 and temperature of 298 K.
III. Results
The water monolayer of interest is exhibiting strong hydrophilic properties when
the intermolecular distance is equal to those of cubic ice, followed by the low diffusion
rate of water in adjacent layer. Whenthe immobilized water molecule isbrought to closer distance, themonolayer shows a hydrophobic-like
properties where the hydrogen bondwith the adjacent layer is not wellformed, and consequently having
higher diffusion rate which extends to
the remaining water molecules.
[1] M. Morgenstern, T. Michely, G.
Comsa, Phys. Rev. Lett. 77, 4 (1996)[2] G. A. Kimmel, N. G. Petrik, Z.
Dohnalek, B. D. Kay, J. Chem. Phys.
126, 114702 (2007)

Fig 1. Lateral diffusion constant of the confined water.
The water monolayer is located at Lz = 2.5 nm from thecenter of cell.

354

4PP-26

On the Thermodynamic Stability of Hydrogen Hydratesof ice Ic and ice II structures: a theoretical and simulation study
Lukman Hakim,1 Kenichiro Koga,1 Hideki Tanaka1
1
Graduate school of Natural Science and Technology, Okayama University, Japan
I. Introduction
Demand for a clean and renewable energy source leads to a wide investigation on
alternative fuel materials. The simplest element for this purpose is perhaps hydrogen,which exhausts only water vapor when burnt. But the question on how to storage thisgas for practical purpose is a challenge that drives engineers and scientists to consider
hydrate compounds as an alternative. For that purpose, detail knowledge on thethermodynamic properties of hydrogen hydrate is required. Here we describe atheoretical-calculation and a Monte Carlo (MC) simulation that are both useful to accessthe thermodynamic properties of hydrogen hydrate of ice Ic and ice II structures [1].
II. Simulations and theoretical calculations
A hybrid type of MC simulations in grand-canonical ensemble is carried out toinvestigate the occupancy of hydrogen gas inside ice Ic and ice II, and the stability ofboth hydrates. The MC step consists of a trial of insertion-or-deletion of hydrogen gas
inside the hydrate, a trial of displacement of hydrogen or water molecules, and a trial tochange the system volume at constant pressure. The stability is quantified in term ofchemical potentials through a theoretical calculation based on modified van der Waals
Platteeuw theory [2]. An analysis for a relevant thermodynamic potential is done toderive the isothermal compressibility of both hydrates.
III. Results
The MC simulations provide a detail on hydrate structures and hydrogen gas
occupancy at various thermodynamic states. The simulations also show the instability of ice
Ic under partial occupancy of hydrogen gas, which lead to the formation of amorphous ice athigh pressure. The gradual increase of hydrogen gas occupancy inside ice II during
compression gives an anomalous compressibility curve. The phase boundaries can beestablished from the equilibrium stateof one, two, and three-phases between
pure ices, filled ices, and hydrogen
fluid, from which a global phase
diagram in pressure, temperature, andchemical composition spaces isconstructed.
[1] L. Hakim, K. Koga, H. Tanaka,
Phys. Rev. Lett. 104, 11 (2010)[2] H. Tanaka, T. Kiyohara, J. Chem.
Phys. 98, 4098 (1993)

Fig 1. The structure of hydrogen hydrate of ice II (left)
and ice Ic (right) structure from simulation.

355

4PP-28

Description of time evolution and dielectric response
based on Rigged QED
Masato Senami,1 Akitomo Tachibana,11Department of Micro Engineering, Kyoto University, Japan
It is presented that a calculation code of time evolution of a system based on
the Rigged QED theory [1,2]. QED has been proven as a very successful theory
due to e.g. the prediction of the magnetic dipole moment of muon and scattering
processes of free particles. However, its success is restricted if the assumption offree particle as an asymptotic ﬁeld is good. Theories describing bound states, suchas Bethe-Salpeter equation and NRQED [3], are still insuﬃcient ones for us. Hence,
we consider a method based on quantum theory of ﬁelds in this work, i.e. electrons,
nucleus, and photons in bound states are described with creation/annihilation operators.
Matter ﬁelds are given as Schroedinger ﬁelds in our code. These are expandedas Ψ̂(t, x) = p êp (t)ψp (Ep , x), where êp (t) is an annihilation operator. We use thesolution of the Schroedinger equation as the basis function, ψ. The time evolutionof a ﬁeld is given by,1dZe ˆ 2 Zei Ψ̂ = Ĥ Ψ̂, Ĥ =−i∇ − A + Â0 .
dt
2
c
c
ˆ
ˆ
 contains both real photon particles A
The photon ﬁeld A
rad and interaction ﬁelds AA ,i.e. virtual photons. These eﬀects in ﬁeld theory are much diﬀerent from quantum
mechanics. Particularly, the eﬀect that long wavelength photons take energy awayfrom a system can correctly be described in our method.
The time evolution of the operator is given by,


2

d
1
Ze
ˆ
 − Ze Ai êp (t) =d3xψp† (Ep , x)−i∇+ Â0 ψq (Eq , x)êq (t).
dt
2
c
c
q

Actually, pursuing the evolution is very hard task. One reason is that after somesteps the operator is very high order polynomial of some operators, and hence algebraic computation using commutation relation are very hard. Moreover, the problemof the divergence from loop diagrams is not so simple for the dynamics of boundstates, since ordinary renormalization is formulated for an asymptotic free ﬁeld.
Hence, we should take special care of a prescription of renormalization. In thiswork, we present the polarization response of a system by injection photon by using
our calculation code.
[1] A. Tachibana, J. Mol. Modelling 11, 301 (2005).
[2] A. Tachibana, J. Mol. Struct. (THEOCHEM), 943, 138 (2010).
[3] W. E. Caswell and G. P. Lepage, Phys. Lett. 167B, 437 (1986).

356

4PP-29

A comparative ab initio multireference Møller-Plesset perturbation
study for N2O binding and activation by atomic excited states of Au,
Pd, Pt and Rh
Oscar Olvera-Neria,1 Virineya Bertin,2 Víctor Hugo Uc-Rosas,1 Alberto Rubio-Ponce,1and Enrique Poulain11Área de Física Atómica Molecular Aplicada (FAMA), CBI, Universidad Autónoma
Metropolitana-Azcapotzalco, México
2
Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa,México
I. Introduction
Nitrous oxide (N2O) is an intermediate compound formed during catalysis
occurring in automobile exhaust pipes. Therefore, it is important to propose somemechanisms to reduce N2O to N2 employing platinum group metals (PGMs) as
catalysts.
Calculations were performed using the multireference plus second-order
perturbation theory (MRPT2) level of theory, the ab initio method of choice for thiskind of work. The study consider the interaction of N2O with a single Pd, Pt, Rh and Au
atoms, respectively, in ground and excited states, as well as their corresponding cations,with the aim of achieving a satisfactory interpretation of the catalytic reaction
mechanism for the formation of the corresponding adducts and the dissociation of N2O.
II. Results
We found that ground state of Rh and Au atoms are not able to capture nitrous
oxide. Reactions 1-6 show that the excited states of Rh, Pt and Au atoms are active inthe capture and dissociation of N2O, according to the reactions for the active atomic
lowest energy state:
RhN2O (6Aƍ) o RhO (6Aƍ) + N2 (16g+)
Au (4Aƍ) + N2O (16+) o AuO (4Aƍ) + N2 (16g+)
Au+ (5Aƍ) + N2O (16+) o NAuNO+ (5Aƍ)
Pt (5Aƍ) + N2O (16+) o PtO (5Aƍ) + N2 (16g+)
Pt+ (6Aƍ) + N2O (16+) o Pt+ (4Aƍ) + N2 (16g+) + O (3P2)

(1)
(2)
(3)
(4)
(5)

Pd atom does not activate the nitrous oxide, even in excited state. Although Pt and Au
atoms reduce N2O to N2, the Rh atom requires less energy to carry out thetransformation, because their ground and active lowest excited state are overlapped. On
the three-way catalytic converters, Rh is used for reduction reactions and Pt and Pd in
the oxidation reactions, as is also shown in these calculations. Rh, Pt and Au excitedstates role on the N2O activation is to promote the charge transfer from transition metal
to N2O, this process does not occur with Pd as catalyst.
[1] William B. Tolman, Angew. Chem. Int. Ed. 49 (6), 1018-1024 (2010).

357

4PP-30First principle calculation for hydriding reaction of metal boride
Y. Kawamura1, T. Matsunaga1, Y. Takeda1, K. Miwa2
1
Toyota Motor Corporation, Japan2
Toyota central R&D laboratory, Japan

Amount of H2 absorption(experimental) [wt%]I. Introduction
Boron hydride complexes, such as LiBH4, Mg(BH4)2, are expected as the hydrogenstorage materials because of its high gravimetric hydrogen density. The hydriding
reaction from boron, 2B + 2LiH + 3H2 Æ 2LiBH4, requires very high temperature andhigh pressure of hydrogen (873K, 35MPa H2) [1]. In contrast, the reaction from metal
boride, such as MgB2, proceeds under comparatively low temperature and pressure [2].
MgB2 + 2LiH + 4H2Æ 2LiBH4+MgH2@ 588K, 0.5MPa H2(1)
In order to clarify the mechanism of these reactions, density functional calculation was
performed and the difference of the reactivity was examined.
II. Method
In this work, the intermediates of the initial steps of hydriding reactions were examined.
Energy differences ('E) between the reactant (B,
MgB2) and the intermediate were evaluated as a Table 1. Energy difference ǻE between
descriptor of reactivity. All calculations were reactant and intermediate [kJ/mol H2]
B
MgB2
AlB2
performed within the GGA framework by using intermediate
H solvation
459
109
203
PBE functional. The planewave basis and
326
162
215
ultrasoft pseudopotential were used as B defectB defect + H2
246
104
202
implemented in CASTEP program package.
Metal defect-172
59
III. Results and discussion
M defect + H2
-73
144
The calculated 'E values of MgB2 were small
compared to boron (Table 1). In particular,
1.8hydrogen addition to boron in MgB2 produces
relatively stable intermediates, which implies
Li-dope MgB2
1.5
small reaction barriers of the hydriding steps for
MgB2
reaction (1). Ion doping effect was also
1.2
investigated and the result shows that Li doping
decreases 'E value (Fig. 1). The Li(or0.9
Al-dope MgB2Al)-doped MgB2 were synthesized by the heat
treatment to the mixture of Mg, B, and LiH(or
0.6
Al). Absorbed H2 amount of Li-doped MgB2
0
60
120
180
Calculated 'E value of H solvation.
was successfully improved, as expected by the[kJ/mol H2]
calculated intermediate stability (Fig. 1).
Fig. 1. Correlation between calculated'E values and experimentallymeasured H2 amount of absorption.

[1] S. Orimo, et al, J. Alloys and Comp., 404 (2005) 427.
[2] J. Barkhordarian, et al, J. Alloys and Comp., 440 (2007) L18.

358

4PP-31“Paired interacting orbitals(PIO)” analysis of phenoxyimine-based
olefin polymerization catalysts
Akinobu Shiga,1,2 Zygmunt Flisak,3
1
Frontier Research Center, Tokyo Institute of Technology, Japan
2
LUMMOX Research Lab., Japan
3
Faculty of Chemistry, University of Opole, Poland
I. Introduction
Polyolefin is one of the most useful plastics for modern human life. Saving energy
and resources, which is the most important issue of polyolefin production, is attained byusing high mileage polymerization catalysts, e.g. phenoxyimine-based (FI) systems thatbelong to the post metallocene gloup. Here we clarify the role of phenoxyimine ligand
by using PIO analysis, proposed by Fujimoto et al [1a].
II. Models and calculation methods
We employed the TS of ethylene insertion of four isomeric FI-methyl-Ti/ethylene
systems: (a) N,Ncis-O,Otrans ethylene(E) trans to N, (b) N,Ntrans-O,Ocis E to O, (c)N,Ncis-O,Ocis_E to N, (d) N,Ncis-O,Ocis_E to O [2].
We divided the TS structures into two parts: fragment [A]:catalyst with the counter
anion, and fragment [B]:ethylene, as shown in Figure 1. PIO calculation was carried out
on the LUMMOXTM system[1b]III. Results and discussion
Overlap populations (OP) of PIO-1 and PIO-2
Fragment[B]and ΣOP of each TS are summarized in Table 1.
The larger the OP, the larger the reactivity toward
the insertion. We can estimate that the reactivity
decreases in the following order: (c) > (a) > (d) >(b). This order coincides with the order of insertion
barriers obtained by DFT calculations with the
exception of (c). The reason why is presented in
Fragment[A]the poster.
Figure 1 The fragmentation of TS
Table 1 Overlap Populations(OP) of PIO-1 and PIO-2 and ȈOP of each TS.
Model

ethylene

Insertion barriers(kcal/mol)[2]

PIO-1

PIO-2

ȈOP

(a) N,Ncis-O,Otrans trans to N

0.17430.20500.37936.9(b) N,Ntrans-O,Ocis trans to O

0.16730.17080.338119.4(c) N,Ncis-O,Ocis

trans to N

0.21170.23240.4441

17.1(d) N,Ncis-O,Ocis

trans to O

0.18330.1796

0.362911.0[1] a) H.Fujimoto, Acc. Chem. Res., 20 448 (1987). b) T. Motoki, A. Shiga, J. Computational Chem., 25
106 (2004). [2] Z. Flisak, P. Suchorska, Organometallics, 29 6196 (2010)359

4PP-32

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360

4PP-33

Acceleration of CASSCF–MD Simulation and its Application to
Intramolecular Charge Transfer System
Masaki Okoshi1 and Hiromi Nakai1,2,3
1School of Advanced Science and Engineering, Waseda University, Japan
2
Research Institute for Science and Engineering, Waseda University, Japan
3
JST-CREST, Japan Science and Technology Agency, Japan
Excited-states dynamics such as photo-induced chemical reactions andphoto-induced charge transfers plays an important role in photo-functional materials.
4-(N,N-Dimethylamino)benzonitrile (DMABN; Figure 1) is one of the mostinvestigated compounds, which causes an intramolecular charge transfer (ICT) alongwith geometric relaxations in the S1 excited state.
Although the electronic dynamics and thegeometric changes have been extensively
investigated experimentally and theoretically [1, 2],
Figure 1. Structure of DMABN
the mechanism of ICT remains under debate.
The ab initio molecular dynamics (AIMD) simulation is one of the most suitableand promising methods, which enables microscopic modelings and direct observationsof dynamical processes regarding chemical reactions. However, the system sizes and/or
the simulation time are limited due to the extremely high computational cost of ab initio
calculations. Thus, our group has proposed acceleration techniques named the Lagrange
interpolation of molecular orbital (LIMO) method [3] and the least square of molecularorbital (LSMO) method [4], which enhance the convergence of self-consistent-fieldcalculation at each AIMD step.
In the present study, the LIMO method is extended to CASSCF in order to perform
efficient AIMD simulations for excited states. Using the accelerated AIMD simulations,the mechanism of ICT of DMABN accompanying the geometric relaxations istheoretically investigated.
The analyses confirm that ICT occurs with the elongation of the bond between the
NMe2 group and the benzene ring. The elongation of the bond hinders the coupling
between the p orbital of the NMe2 group and the S conjugated system of the benzonitrilegroup, and as a result, leads to the electron transfer from the NMe2 to benzonitrilegroups.
[1] J. Dreyer and A. Kummrow, J. Am. Chem. Soc. 122, 2577 (2000).
[2]J.M. Rhinehart et al., J. Phys. Chem. B 114, 14646 (2010).
[3] T. Atsumi and H. Nakai, J. Chem. Phys. 128, 094101 (2008).
[4] T. Atsumi and H. Nakai, Chem. Phys. Lett. 490, 102 (2010).

361

4PP-34

Theoretical study on the reaction mechanism of formation of
3,5-diacetyl-1,4-dihydrolutidine
Hiroyuki Teramae1, Yasuko Y. Maruo2, Jiro Nakamura 2
1
Department of Chemistry, Josai University, Japan
2
NTT Energy & Environmental Labs., Japan
I. Introduction
The measurement of the formaldehyde is based on the acetyl acetone method (NashReagent) in the aqueous solution as shown in scheme Fig 1. The method utilizes thereaction of two acetyl acetone molecule, ammonium ion, and formaldehyde moleculeyielding the lutidine derivative. Very recently, Maruo and co-workers [1] found that E
diketones (pentane-2,4-dione (R1,R2 = CH3) 1-phenyl-1,3-butanedione (R1=CH3, R2=Ph)
or 1,3-diphenyl-1-3-propanedione (R1=Ph, R2 =Ph)), and ammonium salts in porous glasscan be used for a measurement of formaldehyde in the gas phase. As a first step offiguring out the behavior of the lutidine derivative in porous glass, we perform ab initio
molecular orbital calculations to obtain the reaction path from pentane-2,4-dione to thelutidine derivative.
II. Method of Calculations
The HF/3-21G and MP2/6-31G** level molecular orbital calculations are
performed on the lutidine derivative (3,5-diacetyl-1,4-dihydrolutidine, IUPAC name
3,5-diacetyl-1,4-dihydro-2,6- dimethylpyridine
O H
H
H
H O
O
R
R2
C
C
C
C
NH4+ +
2 1 C
+
C
R
C
C
R1
C
1
H
H
O
O
C
C
R2
N
R2
R1=CH 3 R2=CH 3
R1=Ph R 2=CH 3
R1=Ph R2=Ph

H

Figure 1. The reaction formula of the formation of the lutidine derivatives,
III. Results and discussion
The first step of the reaction, for example, would be a formation of
4-amino-3-penten-2-one (FLUORAL-P) from 2,4-pentanedione and ammonia. The
largest barrier height was found to be about 57 kcal/mol at HF/3-21G level, which is theH2O elimination yielding FLUORAL-P. The barrier height is reduced to about 52
kcal/mol at the MP2/6-31G**. The energy is still high, however, will be further reducedby the solvation.
[1] Maruo, Y. Y.; Nakamura, J.; Uchiyama, M., Talanta, 74 (2008) 1141–1147.

362

4PP-35

DFT Study of Methyl/Halogen Exchange Reaction on Pt Complexes
with Phosphine Ligand
Noriko Tsuchida,1 Mari Takashima,2 Yuka Shigesato,3 Masumi Itazaki, 3 Hiroshi
Nakazawa, 3 and Keiko Takano2
1
Ochadai Academic Production, Ochanomizu University, Japan
2
Gradute School of Humanities and Sciences,Ochanomizu University, Japan3
Department of Chemistry, Graduate School of Science, Osaka City University, Japanԥ G (kcal/mol)

Phosphine ligands, PR3, are inactive perse, but provide the central metal with specificelectronic, steric, or chiral environment. In
this context, structural change of thephosphine ligand in complexes would not be
preferable. However, several reactions
associated with structural change of theligand are observed in phosphine complexes.
The studies of these reactions have attracted
considerable attention from the viewpoint of catalytic functions [1]. We recently foundunprecedented Me/X (X = Cl, Br) exchange reaction for PtMe2{PX(NCH3CH2)2}2 (1)..
Understanding the mechanistic feature of this reaction is crucial for development ofphosphine complex catalysts. The exchange reaction pathway was examined using
quantum chemical calculations.
Two reaction pathways, Routes A and B, are conceivable for the Me/X exchange
reaction (Scheme 1) [1-3]. To examine which reaction pathway is more feasible, we
conducted DFT calculations for 1. All calculations were carried out using the50
B3PW91/SDD with PCM.
In Route A for the Me/X exchange
30
involving metallaphosphoranes (3 and 5) as
10.27
7.58
10
3.91
0
intermediates, stationary points were not
7
6
-9.82
1
-12.68 -11.93-10found for metallaphosphoranes as stable
8
4
-27.1
intermediates. In contrast, complex 1 can be-30
9 -34.09
converted into 4 with small activation energy
2-50
in Route B. The activation free energies of
Me migration (from 6 to 7 and from 8 to 9)-70
for the Me/Br exchange reaction is 6.36 and Figure 1. Energy diagram of Me/Br exchange reaction in
2.11 kcal/mol, respectively (Figure 1). Route Route B calculated by B3PW91/SDD with PCM.
B for Me/X (X = Cl, Br) is more preferable to Route A for the conversion of 1 into 2.
[1] R. N. Perutz, et al., Chem. Commun., 2749 (2002) [2] R. N. Perutz, et al., J. Am. Chem. Soc.,
130, 15499 (2008) [3] S. A. Macgregor, et al., J. Am. Chem. Soc., 130, 15490 (2008)363

4PP-36

FMO-MD simulations for hydrated trivalent lanthanide ions using
4f-in-core model core potentials
Takayuki Fujiwara1, Yuji Mochizuki1,2, Hirotoshi Mori3, Yuto Komeiji4,Tatsuya Nakano2,5, Yoshio Okiyama2, Eisaku Miyoshi6
1
Rikkyo University, Tokyo, Japan,
2
Institute of Industrial Science, Tokyo University, Tokyo, Japan.
3
Division of Advanced Sciences, Ochanomizu University, Tokyo, Japan.
4
National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
5
Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan.
6
Graduate School of Engineering Sciences, Kyushu University, Fukuoka, Japan.
I. Introduction
The hydration phenomena of metal ions have attracted considerable interests. In
the field of inorganic chemistry, the lanthanide contraction as well as the gadolinium
break have been well known. However, the number of theoretical studies on these israther limited. In the present study, we perform the method of fragment molecularorbital-based molecular dynamics (FMO-MD [1]) simulations for the droplet models
containing Ln3+ (Ln=La, Eu, Gd, Tb, Lu). The hydration structures are evaluated, andthe charge distributions in hydration shells are analyzed in detail.
II. Computational procedure
We first prepared the large-core MCP basis sets in which the chemically inert 4f
electrons in Ln3+ are treated through effective potentials (termed as 4f-in-core MCPs)[2]. The use of this MCP technique enabled the closed-shell calculations throughout,leading to the computational benefits. The MD simulations were done for Ln(H2O)643+
droplet model at the FMO3-HF level under the Nosé–Hoover chains method, and thestatistical quantities were evaluated with a series of configurations during 1-3 ps at 300 K.
III. Results and discussion
As the representative indices of hydration structure, we here address the first peak
positions of radial distribution functions (RDFs) of Ln3+-O for the Ln3+ = La3+ and Lu3+
cases. The respective values were predicted to be 2.59 Å and 2.31 Å, and the lanthanide
contraction in our simulation was 0.28 Å. The theoretically predicted Ln3+-O lengths
were in good agreement with the EXAFS observations as 2.54 Å and 2.31 Å. The
coordination numbers of Ln3+ were 9 for La3+ and 8 for Lu3+. The difference in thehydration environments was clearly reflected in the different characteristics of theangular distribution functions (ADFs) of O-Ln-O as well as the natural populations, too.
Detailed discussion including correlation effect will be presented at the poster session.
[1] Y. Komeiji et al., Chem. Phys. Lett., 484, 380 (2010).
[2] T. Fujiwara et al., Chem. Phys. Lett., 510, 261 (2011).

364

4PP-37

Quantum dynamics study of the MuFF reaction system
Tomokazu Tanaka,1 Toshiyuki Takayanagi1
1Department of Chemistry, Saitama University, Japan
I. Introduction
Muonium (Mu) which is an ultralight isotope of hydrogen composed of a positive
muon (μ+) and an electron (e), since the mass of μ+ is about 1/9 of the proton mass.
Although the lifetime of Mu is quite short (~ 2.2 μs), this timescale is long enough forinvestigating chemical reactions from the experimental side. In particular, Mu has long
been used to probe important quantum effects including tunneling and quantizedvibrations in reaction dynamics fields and there have been many studies reporting
anomalous isotope effects.
Quantum dynamics calculations for the Mu + F2 ψ MuF + F and F + MuF ψ FMu+ F reactions have been performed on a global potential energy surface developed at an
ab initio multi-reference configuration interaction electronic structure level. Although
thermal rate constants for the Mu + F2 reaction were calculated to be slightly smaller
than experimental measurements, the strongly curved behavior observed in the
Arrhenius plot of the measured data has been reproduced by the present quantum
dynamics calculations.
In the case of F + MuF ψ FMu + F exchange reaction, we have observed very large
resonance peaks around the asymptotic F + MuF(v,j) energy level(Figure 1). Detailed
analyses show that the observed resonances are associated with the quasi-bound states
localized around the F···MuF potential well having a strong hydrogen bonded character.
We found that those states can significantly contribute to the reaction probabilities
above the reaction threshold energy.

Figure 1
Cumulative reaction probabilities
for the F + MuF ψ FMu + F
exchange reactions as a function of
the total energy, which is measured
from the F + MuF asymptotic
potential bottom. The asymptotic
energy levels for F + MuF(v,j) arealso shown, where v and j arevibrational and rotational quantum
numbers, respectively.

365

4PP-38

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4PP-39

Noble Features in Oxidative Addition of B−Br σ−Bond of
Bromoborane to M(PMe3)2 (M= Pt or Pd): Theoretical Study
Guixiang Zeng1, Shigeyoshi Sakaki*1
1
Fukui Institute for Fundamental Chemistry, Kyoto University
I. Introduction
Formation processes of cis−boryl complex via oxidative additions of B−H, B−B,
and B−E (E═Si, Ge, or Sn) bonds to low−valent transition−metal complexes havebeen clarified theoretically.1 However, the mechanism for trans-boryl complex
produced by the oxidative addition of B−X (X═Cl, Br, or I) bond to Pd(0) and Pt(0)complexes remains unclear yet, in which the cis−trans isomerization is proposed to be
involved. However, the cis-trans isomerization occurs via spin conversion process ingeneral, 2 but the cis-trans isomerization taking place on single potential surface has
not been investigated well. Here, we theoretically investigated the oxidative additionof the B−Br bond of bromoborane Br2B(OSiMe3) to M(PMe3)2 (M ═ Pt or Pd) to
explore possible reaction pathways and to clarify the process of the thermal cis−transisomerization in this reaction.3
II. Computational Details
Geometry and frequency calculations were carried out by DFT method withtriple-zeta quality basis sets. The singlet−triplet energy difference was evaluated with
DFT and MP2 to MP4(SDQ) methods.
III. Results and Discussion
The first step is the coordination of Br2B(OSiMe3) with M(PMe3)2 (M ═ Pt or Pd)
to form a precursor
complex. The next is the
B−Br bond cleavage. In
the Pt system, tworeactioncoursesarepossible (Scheme 1); oneis the nucleophilic attack
pathway which directlyaffords the trans-product.
The other one is the
stepwisereaction
Scheme 1
pathway which includes
Ea (kcal/mol) is Gibbs energy barrier in solventthe cis−oxidative addition(toluene),followed by the cis−transisomerization. The former reaction course is more favorable. In the Pd system, only
the stepwise pathway was found. Interestingly, the thermal cis−trans isomerization
was found to occur on the singlet potential energy surface due to the strong donation
ability of the boryl group.
[1] Burgess, K.; Ohlmeyer, M. J. Chem. Rev. 1991, 91, 1179. [2] Gaspar, A. B.;
Ksenofontov, V.; Seredyuk, M.; Gütlich, P. Coord. Chem. Rev. 2005, 249, 2661.
[3] Zeng, G.; Sakaki, S. Inorg. Chem. 2011, 50, 5290.
367

4PP-40

Theoretical study on aquation reaction of cis-platin complex using
RISM-SCF-SEDD.
Daisuke Yokogawa,1 Kohei Ono,2 Hirofumi Sato2, and Shigeyoshi Sakaki3
1Institute for Protein Research, Osaka University, Japan
2Department of Molecular Engineering, Graduate School of Engineering, Kyoto

University, Japan
3Institute for Integrated Cell-Material Sciences, Kyoto University, JapanThe cis-diamminedichloro-platinum (II) (cis-platin) is a well-known anti-cancer
drug established in 1970’s and still being used. In the human body, injected cis-platin(1) is hydrolyzed to lose a chloride anion.
Pt(NH3)2Cl2 + H2O ĺ [Pt(NH3)2Cl(H2O)]+ + Cl-䎃The monoaqua complex (2) reacts with another water to afford diaqua complex (3),[Pt(NH3)2Cl(H2O)]+ + H2O ĺ [Pt(NH3)2(H2O)2]2+ + Cl- .

We investigated the reactions using RISM-SCF-SEDD, which is a hybrid approach ofquantum chemical method and statistical mechanics. The geometries were computed
using DFT/B3LYP in gas phase. The energies in gas phase and aqueous phase were
evaluated with CCSD(T).
In Fig. 1, free energy changes of the reaction in the gas phase and in aqueous phaseare shown. The first dissociation step of chloride anion in gas phase requires large
amounts of energy (108.2kcal/mol) to overcome the strong electrostatic interaction
between Pt complex and chloride anion. The dissociation of another chloride anion incomplex 2 requires 195.7 kcal/mol. In
aqueous phase, on the other hand, thedissociation steps are greatly
stabilized by solvent waters. This isbecause the strong attractive
interaction between two charged
species is screened by solvent waters.
The free energy in aqueous phaseindicates that the aquation reaction
occurs under a mild condition inwater.

Figure 1. Free energy changes of the reaction in
the gas phase, and in aqueous phase.

368

4PP-41

Theoretical Study of the Mechanism of the Excited-state Double
Proton Transfer in 7-azaindole Dimer
Xue-fang Yu, Shohei Yamazaki, and Tetsuya Taketsugu
Department of Chemistry, Graduate School of Science, Hokkaido University, JapanThe excited-state double proton transfer (ESDPT) in 7-azaindole dimer istheoretically investigated by means of high-level electronic-structure calculations. The
long-range corrected (LC) TDDFT [1] method and CASPT2 method are employed forgeometry optimizations as well as single-point energy calculations of the excited-state
potential energy profiles along the reaction paths. The resulting potential energy curves
suggest that the ESDPT in the gas phase can proceed in the lowest locally-excited statethrough single transition state and without any intermediate for single proton transferredcomponent [2]. It is therefore likely that the ESDPT in locally-excited state follows theconcerted mechanism [3-4]. The concerted ESDPT is found to occur asynchronously inCs symmetry rather than synchronously in C2h symmetry. The step-wise mechanism [5]of ESDPT via the charge transfer state is also examined using LC-TDDFT method.

Figure 1. Concerted mechanism and step-wise mechanism of ESDPT in 7AI-dimer.

[1] M. Chiba, T. Tsuneda and K. Hirao, J. Chem. Phys., 124, 144106 (2006).
[2] X.-f. Yu, S. Yamazaki and T. Taketsugu, J. Chem. Theo. Comp., 7, 1006 (2011).
[3] S. Takeuchi and T. Tahara, PNAS, 104, 5285 (2007).
[4] H. Sekiya, J. Photochem. Photobiol. C, 9, 81 (2008).
[5] A. H. Zewail, PNAS, 104, 8703 (2007).

369

4PP-42

Solvation Effect on Hydrolysis of cis- and trans-Platins
Shinji Aono,1 Shigeyoshi Sakaki1*
1
Fukui Institute for Fundamental Chemistry, Kyoto University, Japan
I. Introduction: Cis-platin (cis-PtCl2(NH3)2) is well-known as an anti-tumor drug andits derivatives have been extensively investigated in both experimental and theoreticalfields. Before cis-platin interacts with the cellular DNA, hydrolysis of cis-platin occurs
as one of key steps (Scheme 1). The substitution of Cl- for H2O changes the net chargeof the Pt complex,
indicating that theequilibrium solvation
Scheme 1 : Hydrolysis of cis-platinstructure significantly changes. To understand the hydrolysis correctly, we need theclear insight into solvation. Here we investigated the hydrolysis of cis- and trans-platinswith the 3D-RISM-SCF method.
II. Computational Detail: The geometry optimization was carried out by the DFT
method with M06-2X functional. To evaluate the free energy, the MP2 calculation was
performed by using the 3D-RISM-RHF wavefunction as the zeroth order state. The
LANL2TZ(f) basis sets were used for Pt atom by replacing its 60 core electrons with the
Hay-Wadt ECP. The cc-pVTZ basis sets were used for all ligands and augmented
functions were added to O and Cl. To make the thermo-dynamical correction of solute
motion, the zero point energy, thermal energy, and entropy contribution were added [1].
III. Result: We consider the reactant dissociated state (RS) and associated state (RAS)
and product dissociative and associative states (PS and PAS); see Fig.1. In solution, theRS and RAS conceptually represent the same initial state, except for the different
position of one water treated quantum-mechanically. The small free energy difference
between the RS and RAS (Fig.1) indicates that the 3D-RISM-SCF method gives thereasonable description of hydrogen bonds near the Pt complex in a statistical classicalmanner. Taking RAS as the initial state, the activation and reaction free energies arecalculated to be 22.4 and 3.3 kcal/mol, which agree well with the experimental values,
24.1 and 3.6 kcal/mol. After the first hydrolysis, the substituted Cl- is found in the firstsolvation shell. We also discuss the effect of Cl- on the second hydrolysis.

Fig.1 : Geometry and free energy change in the first hydrolysis of cis-platin
Red and green lines are calculated with and without thermo-dynamical correction, respectively.
[1] Mammen, M.; Shakhnovich, E. I.; Deutch, J. M. and Whitesides, G. M., J. Org. Chem. 1998, 63, 3821

370

4PP-43

Ruthenium-catalyzed [3+2] cycloaddition via ruthenium-allenylidene
intermediate: A DFT study
Ken Sakata,1 Yoshihiro Miyake,2 Yoshiaki Nishibayashi2
1
Faculty of Pharmaceutical Sciences, Hoshi University, Japan
2
Institute of Engineering Innovation, School of Engineering, The University of Tokyo,
Japan
I. Introduction
We have recently found that the ruthenium-catalyzed [3+2] cycloaddition of
ethynylcyclopropanes with aldehydes and aldimines gives the corresponding 2-ethynyl-
tetrahydrofuranes or pyrrolidines in high to excellent yields with a high to excellent
diastereoselectivity [1]. Experimental results have indicated that the formation ofrutheniumallenylidene complexes via carbon-carbon bond cleavage is one of the mostimportant steps for the catalytic cycloaddition. Thus, we carried out the DFT
calculations using B3LYP hybrid functional for the model reaction system (Scheme 1).
Scheme 1.
+
Cp S Cp
Ru Ru
SCl MeMe• 



BF3
H

O

+
H



MeO2C CO2MeH+
Cp S Cp
Ru Ru
S
 F3B
Cl MeMe•
O
•
H
H

O H

+

Cp S Cp
Ru Ru
SCl MeMeCp S Cp
Ru Ru
SCl MeMe•

F3B
O

+H
O

H
H

C OMe
CO2Me

C OMe

CO2Me

H

BF3
O
H
H

MeO2C CO2Me

Ruthenium-allenylidene complex

II. Results and Discussion
The [3+2] cycloaddition has been clarified to proceed smoothly via therutheniumallenylidene complex. In the pathway, the transfer of the hydrogen atom atthe -carbon to the oxygen atom in the ester group and the bond cleavage between the
-carbon and the -carbon give the rutheniumallenylidene complex. Then, thenucleophilic attack of the -carbon to the carbonyl carbon atom of formaldehyde occurs
with low activation energy. The following some elementary processes give theproduct complex. The reaction pathway via the rutheniumallenylidene complex ispreferred to the concerted pathway in which the BF3-coordinated formaldehyde directly
attacks the cyclopropane ring in the reactive vinylidene complex. We also discuss thedifference between the reaction pathway examined in the present study and the pathway
which have been reported for the Lewis acid catalyzed cycloaddition of aldehydes withthe donor-acceptor cyclopropanes [2].
[1] Miyake, Y.; Endo, S.; Moriyama, T.; Sakata, K.; Nishibayashi, Y. submitted.
[2] Pohlhaus, P. D.; Sanders, S. D.; Parsons, A. T.; Li, W.; Johnson, J. S. J. Am. Chem.
Soc. 2008, 130, 8642.

371

4PP-44

Theoretical Study on Catalytic Activity ofMetal Surfaces on P-H Bond Cleavage of Hypophosphite Ion
Masahiro Kunimoto,1 Hiromi Nakai,2 Takayuki Homma11
Department of Applied Chemistry, 2Department of Chemistry and Biochemistry,
Waseda University, Japan
Electroless deposition process is technique to form metal thin films using reducing
agents as electron supply sources. We have analyzed reaction mechanism of the process
theoretically to achieve further precise control[1]. We particularly focus on catalytic
activity of metal surfaces on reducing agent reaction, which is one of the most important
aspects to control the overall reaction process. It is well known that Pd and Cu eachshow totally different behaviors in the catalytic activity. In order to elucidate thedifferent behavior, this paper reports interaction structure between metal surfaces, Pd
and Cu, and a widely used reducing agent, hypophosphite ion, H2PO2-.
It was found that a P-H elongating H2PO2-, which is called as “activated H2PO2-”,
showed characteristic interaction with each metal surface. On Pd, both HOMO andLUMO of activated H2PO2- interact with d-band of Pd to form bonding interactions(Fig.1(a)). On the other hand on Cu, neither HOMO nor LUMO form bonding
interaction with orbitals of Cu (Fig.1(b)). HOMO interacts with d-band to form
anti-bonding orbital. LUMO interacts with no orbitals of Cu surface. These results
indicate that Pd surface activates P-H dissociation of H2PO2-, whereas Cu surface doesnot. The difference is expected to be one of the most important factors to explain the
catalytic activity difference between Pd and Cu.
d-band of Pd

d-band of Cu

s-band of Pd
H2PO2HOMO of H2PO2-s-band of Cu
H2PO2HOMO of H2PO2-

-0.3

-0.2

-0.1
0
E-EF/hartree

0.1

DOS/-

DOS/-

H2PO2LUMO of H2PO2-

0.2

H2PO2LUMO of H2PO2-

-0.3

-0.2

-0.1
0
E-EF/hartree

0.1

0.2

(a)
(b)
Fig. 1. Density of states of each molecular orbital (EF = fermi level) (a) activated H2PO2and Pd surface, (b) activated H2PO2- and Cu surface[1] M. Kunimoto, T. Shimada, S. Odagiri, H. Nakai, T. Homma, J. Electrochem. Soc., inpress
Acknowledgements: This work was performed at the Global Center of Excellence(G-COE) program “Practical Chemical Wisdom” from The Ministry of Education,
Culture, Sports, Science and Technology, Japan and was financially supported in part by
the Grant-in-Aid for Scientific Research(B).

372

4PP-45

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373

4PP-46

Molecular dynamics study of the photodesorption process of
the CO molecule from the surface of interstellar ice
Marc C. van Hemert,1 Junko Takahashi,2 Ewine F. van Dishoeck3
1
Institute of Chemistry, University of Leiden, The Netherlands
2
Meiji Gakuin University, Japan
3
Leiden Observatory, University of Leiden, The Netherlands
I. Introduction
At the densities and temperatures in star-forming regions, all molecules other thanH2 should be kept frozen on dust grains within the timescales shorter than theinterstellar cloud lifetimes. But, gaseous CO is detected there. Thermal desorption is
negligible and thus photodesorption has been suggested as a possible mechanism. In thelaboratory, this process has been simulated by depositing CO on a 10 K surface andfollowing CO desorption upon irradiation of a D2 discharge lamp [1]. In order to study
this process theoretically, we performed classical molecular dynamics simulations of the
CO molecule excited with a photon on the surface of amorphous CO crystals.
II. Method
For the ground state interaction potential of the CO-CO dimer, we performed abinitio CCSD calculations on a large grid of orientations and inter- and intra- moleculardistances. We fit about 15000 data points to the interaction energy formula including therepulsive potential with the nonlinear alpha parameters, the dispersion potential, and theelectrostatic potential. For the excited state, we used the contracted CI method where
the two CO molecules lie in the same plane, the first CO has the ground state
equilibrium bond length, and the second CO has a bond length close to the A13 excitedstate one. We fit these data to the formula similar to the one used for the ground state,although we excluded all OCCO geometries.
We created amorphous CO crystals consisting of 200-1200 CO molecules. The
initial geometries were determined by adding CO molecules one by one to theenergetically most favored positions with a simplex method. These crystals weremodified by the molecular dynamics procedure of temperature cycling with the steps
from 0 to 50 K and back to 10 K for 10000 cycles with 20 au (~0.5 fs) time step. Then,
we brought a selected flake of the CO crystal into the excited state adiabatically with aphoton of 9.1-9.9 eV. After the dynamics for 5000-10000 cycles with 4 au (~0.1 fs) time
step, we brought back the flake into the ground state adiabatically and monitored thepositions of CO molecules for another 50000 au.
III. Results and discussion
We found that only 5-10% of the excited CO molecules were photodesorbed fromthe CO crystal. Of the total number of desorbed molecules, 20-25% were neighboring
molecules (3.5-4.0 Bohr), and a few percent next-neighboring ones (6.5-7.0 Bohr).
There was little effect of photon energy. The effect of the flake size was that the larger the
flake, the stronger molecules were bound in the surface layer of the CO crystal. We foundthat almost all of the molecules directly desorbed came from the surface layer, and thatthe surface layer molecules were also kicked out by the excited neighboring moleculesin the subsurface layer.
[1] Öberg et al., Astrophys. J., 2007, 662, L23; Astron & Astrophys. 2009. 496, 281.

374

4PP-47

Theoretical study of bifurcating reactions accompanying thetotally-symmetric valley-ridge inflection point
Yu Harabuchi1 and Tetsuya Taketsugu2
1
Graduate School of Chemical Sciences and Engineering, Hokkaido University, Japan
2
Graduate School of Science, Hokkaido University, Japan
Introduction
In theoretical study of chemical reactions, an intrinsic reaction coordinate (IRC) has
played a significant role for understanding the reaction mechanism. Since the IRC
belongs to the totally-symmetric irreducible representation of the molecular point group,
the reaction coordinate has no curvature coupling with the transverse normal
coordinates of non-total-symmetry, and thus the intrinsic reaction path (IRP) startingfrom TS sometimes reaches the second TS through the non-totally-symmetric VRI point.
If a non-totally-symmetric VRI appears on the IRP and the second TS is detected at theterminal, this TS connects two symmetrically equivalent product minima with the lower
symmetry. As to non-totally-symmetric VRI, there have been a lot of theoretical studies.
On the other hand, when there appears the totally-symmetric VRI point, the reaction
pathway can bifurcate, leading to two completely different product minima. In the target
reaction (Fig.1), it was shown that IRC calculations from the transition state (ET-TS) leadto different product minima, SUB(C) and (CET) [1], by using non-mass-weighted internal
coordinates and mass-weighted Cartesian coordinates, respectively. Ab initio molecular
dynamics simulations were also performed to discuss the branching ratio of the products[2]. From the viewpoint of bifurcating reactions, it is very interesting that two different setsof products could be generated.
To clarify the mechanism of bifurcation, we
performed geometry optimizations of stationary
points and IRC calculations for the reactions
XCHO- + CH3Cl (X = H, CH3) at theMP2/6-31+G(d) level. We also applied aprojection technique to obtain vibrationalfrequencies, the Mulliken net charge and spin
population of each atom, as well as the energy ofthe first-excited state, along the IRP. All
calculations were performed using the GAMESS Figure 1. The reaction scheme of
H(X)CO- + CH3Cl (X = H, Me)program package.
Results and Discussion
The IRC calculation from ET-TS leads to SUB(C) at the MP2/6-31+G(d) level. It isshown that the VRI point at the HF level [1] disappear in a system of X = H at the MP2 level.
On the other hand, in the second reaction (X = CH3), it is verified that the IRP has thetotally-symmetric VRI point leading to two different product minima on the PES. In thesame region of the totally-symmetric VRI point, the reaction-path tangent vector
changes its direction drastically in a localregion. We concluded that the change of the
IRP curvature is strongly related to the bifurcation [3].
References[1] S. Shaik et al., J. Am. Chem. Soc., 119, 9237 (1997).
[2] H. Yamataka et al., J. Phys. Org. Chem., 16, 475 (2003).
[3] Y. Harabuchi and T. Taketsugu, Theo. Chem. Acc., in press (2011).

375

4PP-48

Photodissociation, geminate recombination, and vibrational relaxation ofiodine in carbon tetrachloride: A molecular dynamics simulation
Jakob Petersen, Niels E. Henriksen, Klaus B. Møller
CMM – Centre for Molecular Movies, Department of Chemistry,
Technical University of Denmark
The photodissociation, subsequent geminate recombination, and vibrational relaxation of iodine in carbon tetrachloride are studied using classical nonequilibrium
molecular dynamics simulations. The time-dependence of the vibrational relaxation
associated with the cooling of iodine in the electronic ground state is found to be ingood agreement with previous experimental results. We show that the relaxation exhibits some degree of coherence even at 10 ps after laser excitation, and that a good
approximation to the time-dependent I-I distribution function can be extracted fromthe time-dependent vibration energy distribution. Hence, experimental results fromtime-resolved x-ray diﬀraction and optical spectroscopy studies can be compared.

376

4PP-49

Theoretical study on dehydrogenation reaction of methanol onanionic Au cluster
Karan Bobuatong,1 Sangita Karanjit,2 Masahiro Ehara1, Hidehiro Sakurai2
1
Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
2
Institute for Molecular Science 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, JapanThe aerobic oxidation of methanol to formic acid catalyzed by Au20- has beensystematically investigated quantum chemically using the M06 density functional. The
proposed reaction mechanism consists of three elementary steps: (1) formation offormaldehyde from methoxy species activated by superoxo-like anion on gold cluster;(2) nucleophilic addition by hydroxyl group of hydroperoxyl-like complex toformaldehyde leading to a hemiacetal intermediate and (3) formation of formic acid byhydrogen transfer from hemiacetal intermediate to atomic oxygen attached to goldcluster. A comparison of the computed energetics of various elementary steps indicatesthat the C-H bond dissociation of methoxy species leading to formation offormaldehyde is the rate-determining step. A possible reaction pathway involving
single-step hydrogen abstraction, concerted mechanism, is also discussed. The stabilityof reactants, intermediates and transition structures are governed by coordination
number of gold atoms, charge distribution, cooperative effect and structural distortion
which are the key parameters for understanding the relationship between structure ofgold cluster and catalytic activity of the aerobic oxidation of alcohol.

Figure 1. Reaction
pathways of the aerobic oxidation of methanol to formaldehyde
on Au20-.

377

4PP-50

Molecular dynamics simulations of azanaphthoquinone annelated
pyrrole derivatives as anti-cancer agent in DNA duplex
Pornpan Pungpo1, Auradee Punkvang1, Amonrat Kumkong1, Parit Khamsri1,
Patchreenart Saparpakorn2, Nipawan Pongprom1,
Peter Wolschann3 and Supa Hannongbua2
1
Department of Chemistry, Faculty of Science, Ubonratchathani University,
Ubonratchathani, Thailand
2
Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak,Bangkok, Thailand
3
Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
Abstract
To discover the new anti-cancer agent with high activity and low side effect,azanaphthoquinone annelated pyrrole derivatives, a class of the synthetic DNA
intercalating agent have been synthesized. These compounds exhibit high cytotoxic
activity against tumor cell lines. However, the binding modes of these anti-cancer
agents have not been investigated. In order to predict the potential binding modes ofthese compounds in DNA duplex, molecular dynamics (MD) simulations with AMBER
program were performed. Moreover, to calculate the binding free energy ofazanaphthoquinone annelated pyrrole derivatives in DNA binding site MM-PBSA
method was employed. Based on MD simulations, azanaphthoquinone annelated pyrrole
scaffolds of azanaphthoquinone annelated pyrrole derivatives are inserted into two basepair steps of cytosine (C) and guanine (G). The ʌ-ʌ interaction azanaphthoquinone
annelated pyrrole scaffold with base pairs of C and G is the crucial interaction forbinding of these anti-cancer agents. Moreover, the hydrogen bond interaction of R
substituents reinforces the binding of these compounds. Based on the calculated binding
free energy, the hydrogen bond interaction of R substituent could enhance the binding
affinity of azanaphthoquinone annelated pyrrole derivatives in DNA duplex. Therefore,
the obtained results should be helpful for understanding the binding modes and the
crucial interactions of azanaphthoquinone annelated pyrrole derivatives in DNA bindingsite. This information benefits for designing the novel anti-cancer agent with highactivity and low side effect.

378

4PP-51

Molecular modeling on anti-tuberculosis agent to investigate thestructural basis for improving potency against M. tuberculosis strain
Auradee Punkvang1, Patchareenart Saparpakorn2, Peter Wolschann3,
Supa Hannongbua2 and Pornpan Pungpo1
1Department of Chemistry, Faculty of Science, Ubonratchathani University,
Ubonratchathani, Thailand
2
Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak,Bangkok, Thailand
3
Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
Abstract
The tuberculosis treatment still remains the worldwide medical problem because of
the drug resistance. The enoyl-ACP reductase (InhA) from M. tuberculosis is an
attractive target for developing new antibiotic agents and has been identified as thetarget of isoniazid (INH), a first-line antibiotic for tuberculosis treatment. The highpotency of INH is diminished by the drug-resistance. To overcome the drug-resistantproblem of INH, arylamides as the direct InhA inhibitor have been identified. In thisstudy, molecular modeling approaches were employed to elucidate inhibitor-enzyme
interactions and structural basis for improving the affinity and potency ofanti-tuberculosis agents in class of isoniazid derivatives and arylamide derivatives.
Molecular docking calculations and QSAR methods were applied on series of isoniazid
and arylamide derivatives to gain an insight into the structural basis for improving
anti-tuberculosis activity. Moreover, to investigate the dynamics behaviors in the termof flexibility, structural features and ligand-enzyme interactions of anti-tuberculosis
agent in InhA binding site, molecular dynamics (MD) simulations were employed. The
integrated results from this study provide coincident information about the
inhibitor-enzyme interaction and structural requirement thus offering guidelines for thesynthesis of novel anti-tuberculosis agent with highly antibiotic activity.

379

4PP-52

STUDY ON THE MECHANISM FOR THE REACTION OF PBP2a
WITH BETA-TACLAM INHIBITORS BY ONIOM METHOD
Nguyen Hoa My(1), Hirao Hajime(2), Dang Ung Van(1), Keiji Morokuma(2)(1)Center for Computational Chemistry, Faculty of Chemistry, Ha Noi University of Science,
Vietnam(2)Fuikui Intitute of Fudamental Chemistry, Kyoto University, Japan
Abstract
Mechanisms of drug resistance constitute a very complicated research subject attracting scientists in
Vietnam and many other countries all around the world. We have calculated the mechanism of theMichaelis complex formation reactions between small E-lactam molecules (i.e. Methicilin and Nitrocefin)
and PBP2a using the ONIOM(B3LYP/6-31G*:AMBER) hybrid quantum mechanical/molecularmechanical (QM/MM) method. Active-site model calculations at the B3LYP/6-31G* level have also been
performed. All calculations have been performed on High Performance Computation System. This is thefirst time the ONIOM was applied to the reaction of PBP2a with E-lactam inhibitors. In the ONIOM
models, two systems (or layers) were defined for the entire system: the model system (the first layer)
which was calculated by the B3LYP method with the 6-31G* basis set and the real system was calculatedwith the AMBER force field. The calculations shows that the reaction mechanism involves at least twotransition states One of them is associated with C-O bond formation. The protein environment
significantly increased the activation energy of the acylation reaction. The details are discussed in thepresentation.

380

4PP-53

Molecular Dynamics Study on Complex between Prostacyclin
Synthetase and Prostaglandin H2
Ryo Watanabe, Yoshimura Takayoshi, Seiji Mori
Faculty of Science and Engineering, Ibaraki University, Japan
I. Introduction
Cytochrome P450 is a group of heme proteins widely distributed from microorganism
to plants and animals in the living world and is one of the important group of enzymes
involved in drug metabolisms and syntheses of steroids in vivo. Typical reactions
catalyzed by P450 are monooxygenation reactions. One is prostacyclin synthase (PGIS),
which catalyzes an isomerization reaction from prostaglandin H2 (PGH2) to prostacyclin(PGI2). PGIS doesn’t need any O2 nor NAD(P)H.
COOH
3
O

COOH

PGIS

O

O
OH
HO

Prostaglandin H2 (PGH2)

OH

Prostacyclin (PGI2)

The isomerization reaction mechanism was proposed based on density functional
studies by our group. 1) However, these studies haven’t considered the effect of protein
and solvent.
II. Method and Result
The crystal structure of human Prostacyclin Synthase (PGIS) binding an inhibitor
minoxidil (PDB:3B6H  Resolution: 1.62 Å
is used. After we have deleted aminoxidil from PGIS, We manually placed
PGH2. This initial conformation of the
PGH2 structure was taken from aliternature based on NMR structural
analyse.2) After we performedmolecular
dynamics simulation method (Program:Amber ver.10, ff03 force field, NPT
ensemble, 300K). Results were obtainedwith the substrate-heme coordination
structure. Around the catalytic pocket wefound only a number of water molecules.
1) Yanai, T. K.; Mori, S; Chem. Eur. J. 2009, 15, 4464-4473.
2) Ruan, K.H.; Wu, J; Cervantes, V. Biochemistry 2008, 47, 680-688.
381

4PP-54

Computational analysis for DNA religating reaction
by E.coli topoisomerase IA
Kyohei Hanaoka,1 Daiki Kondo,1 Moonyoung Yang, 1 Katsumasa Kamiya, 1
Mitsuo Shoji2, Kenji Shiraishi1
1
Graduate School of Pure and Applied Sciences, University of Tsukuba, Japan
2
Center for Computational Science, University of Tsukuba, Japan
I. Introduction
DNA topoisomerase IA cleavages and religates a single strand DNA to relax the
DNA super coil and promotes DNA metabolism. Inhibition of this function is known tolead to bacterial cell death. Thus, this enzyme is expected as a potent antibiotic target.
This enzyme forms a covalent intermediate in which catalytic tyrosine residue iscovalently bonded to the DNA backbone phosphate, after and before cleavage andreligation reaction. Thus the covalent intermediate is a key state in the catalytic
mechanism of religating for DNA topoisomerase IA. Recently, the crystal structure of
the covalent intermediate of E. coli topoisomerase IA in complexed with single strand
DNA was solved at 2.3A resolution (Figure.1) [1]. However, this structure does notreveal overall detail of the catalytic site of the religation reaction. This is because, tocapture intermediate, Asp111 in the catalytic site was mutated to Asn and divalentmagnesium ion, which is needed to the religation reaction, was neutralized by chelator.
Therefore, computational approaches are needed to complement the structure around thecatalytic site of religation reaction and reveal hydrogen bonding and salt bridge
networks which may contribute to the catalysis.
II. Computational study
In this study, we started from the crystal structure of covalent intermediate of DNA
topoisomerase IA in complexed with DNA substrate (PDB ID; 3PX7). We first modeled
Asp111 which has been mutated to Asn and added divalent magnesium ions to small
cavity around its catalytic site. Next we performed
molecular dynamics simulation to determine theposition of divalent magnesium ions and structure ofhydrogen bonding networks around the catalytic site.
And then, we performed DFT (density functional
theory) calculations to reveal the catalytic mechanismof the religation reaction. In the session, we will
discuss about roles of the individual components
contained in the catalytic site.
Fig.1 Crystal structure of
the covalent intermediate of
E. coli DNA topoisomerase IA

382

4PP-55

Density functional study of electronic structures of a characteristic[4Fe-4S] cluster, [Fe4S4(SCH3)3(CH3COO)], in dark-operative
protochlorophyllide oxidoreductase
Yu Takano,1 Yasushige Yonezawa,1 Yuichi Fujita,2 Genji Kurisu,1 Haruki Nakamura1
1
Institute for Protein Research, Osaka University, Japan
2
Graduate School of Bioagricultural Sciences, Nagoya University, Japan
The [4Fe-4S] clusters are ubiquitous in nature and play important roles in electrontransfer and catalysis such as in ferredoxins and nitrogenases. Recently, a X-ray
structure of the dark-operative protochlorophyllide oxidoreductase (DPOR) has been
determined at 2.3 Å resolution [1]. The [4Fe–4S] cluster in DPOR (NB cluster) has sucha characteristic structural feature that one of the iron ions is chelated by the carboxylategroup of Asp36, unlike conventional [4Fe-4S] clusters coordinated with four Cys
residues. To examine the effect of the Asp ligation on the enzymatic activities, three
NB-protein mutants, D36C, D36S, and D36A, were prepared. Although the D36C and
D36S substitutions almost nullified the activity, the D36A mutant exhibited 13 % of thewild-type level. The crystal structures of the D36C mutant was found to have theconventional [4Fe–4S] cluster coordinated with four Cys residues, while that of the
D36A mutant had a [4Fe–4S] cluster chelated by three Cys residues and an unknown
fourth non-protein ligand, which was likely to be the hydroxide or chloride ion. Thesefindings indicate that Asp ligation is important for the enzymatic activity.
In this study, we have explored the electronic structure of the NB cluster toelucidate the role of the Asp ligation to the [4Fe–4S] cluster in the catalysis of DPOR
using the density functional theory (B3LYP) [2]. The electronic structure of the NB
cluster is compared with those of the conventional [4Fe–4S] clusters in the D36C
variant and the putative [4Fe–4S] clusters in the D36A mutant. Although the electronic
structures are similar to each other, our computation shows that the redox potential of
the NB cluster is lower than that of the D36C model in the 2–/3– reduction reaction, in
an environment with the dielectric constant higher than 10, showing that the NB cluster
can transfer an electron more easily than the conventional [4Fe–4S] cluster. This redox
character demonstrates the important role of Asp36 in DPOR. It is also found that theelectron-donating character of the [4Fe–4S] clusters in the 2–/3– reduction in anenvironment with high dielectric constant is in the same order as the experimental
enzymatic activities of the wild type DPOR and its mutant, indicating that the fourth
ligand of the [4Fe–4S] cluster in the D36A mutant is likely to be a chloride ion.
[1] N. Muraki, J. Nomata, K. Ebata, T. Mizoguchi, T. Shiba, H. Tamiaki, G. Kurisu, Y.
Fujita, Nature 465 (2010) 110–114.
[2] Y. Takano, Y. Yonezawa, Y. Fujita, G. Kurisu, H. Nakamura, Chem. Phys. Lett. 503(2011) 296–300.

383

4PP-56

Ab inito study on triplet excitation energy transfer inphotosynthetic light harvesting complexes
Zhi-Qiang You,1,2,3 Chao-Ping Hsu,21
Taiwan International Graduate Program and 2 Institute of Chemistry, Academia
Sinica, 128 Section 2 Academia Road, Nankang, Taipei 11529, Taiwan
3
Department of Chemistry, National Tsing Hua University, 101 Section 2
Kuang-Fu Road, Hsinchu 30031, Taiwan
We have studied the triplet energy transfer (TET) for photosynthetic lightharvesting complexes, the bacterial light-harvesting complex II (LH2) of Rhodospirillum molischianum and Rhodopseudomonas acidophila, and the peridinin-chlorophyll
a protein (PCP) from Amphidinium carterae. The electronic coupling factor was calculated with the recently developed fragment spin diﬀerence scheme (You and Hsu,
J. Chem. Phys. 2010, 133, 074105), which is a general computational schemethat yields the overall coupling under the Hamiltonian employed. The TET rates
were estimated based on the couplings obtained. For all light-harvesting complexes
studied, there exist nanosecond triplet energy transfer from the chlorophylls to the
carotenoids. This result supports a direct triplet quenching mechanism for the photoprotection function of carotenoids. The TET rates are similar for a broad range of
carotenoid triplet state energy, which implies a general and robust TET quenchingrole for carotenoids in photosynthesis. This result is also consistent with the weak
dependence of TET kinetics on the type or the number of π conjugation lengths in
the carotenoids and their analogs reported in the literature. We have also exploredthe possibility of forming triplet excitons in these complexes. In B850 of LH2 or
the peridinin cluster in PCP, it is unlikely to have triplet exciton since the energy
diﬀerences of any two neighboring molecules are likely to be much larger than their
TET couplings. Our results provide theoretical limits to the possible photophysics
in the light-harvesting complexes. This work has been published in J. Phys. Chem.
A 2011, 115, 4092.

384

4PP-57

Quantum Chemical Study on Molecular-Level Affinity of DJ-1 Binding
Compounds
Yasuhiro Shigemitsu1
1Industrial Technology Center of Nagasaki, Japan
I. Introduction
DJ-1 is a 20-kDa protein comprising 189 amino acid residues ubiquitously expressedin various human tissues. The multifunctional protein plays essential roles in tissues
with higher order biological functions. Of the versatile functions, a mutation of DJ-1
was found to be responsible for familial Parkinson’s Disease (PD). Superfluous
oxidation of cysteine at amino acid 106 (Cys106) renders DJ-1 inactive, and suchoxidized DJ-1 has been observed in patients with the sporadic form of PD [1]. This
presentation aims to elucidate the structure-function relationship of DJ-1 through aseries of computational chemistry analysis.
II. Results and Discussion
The active (reduced) and inactive (oxidized) PDB structures were extracted from
1UCF and 1SOA, respectively. The starting structures were adequately modified andfurther refined through energy minimization and equilibrium steps by means of
AMBER molecular dynamics program. The obtained structures were analyzed for theactive site around Cys106 in HF-FMO/6-31G(d) level of theory by using Fragment
Molecular Orbital method implemented in GAMESS-US software.
The FMO analysis indicates the subtle change of the active site’s environment. The
closely contacted residues ( Arg156,Glu18,Gly75,His126 ) alter its relative positions in
response to the oxidation to Cys106. The interaction mechanism between DJ-1 andbinding compounds is discussed based on FMO and MM-PBSA analysis.

Figure 1. 1SOA structure (CPK-highlighted)

Figure 2. PIEDA for 1SOA

[1] S.Miyazaki, H.Ariga et al, J.Nurochemistry, Vol.105, pp.2418-2435 (2008)385

4PP-58

Theoretical study on hydrated DNA systems
by linear-scaling DFT code CONQUEST
Takao Otsuka,1 Tsuyoshi Miyazaki,2 David R. Bowler,3 Michael J. Gillan,31
Quantitative Biology Center(QBiC), RIKEN, Japan
2
National Institute for Materials Science, Japan
3
University College London, London, United Kingdom
We present our theoretical study on hydrated DNA system by using the linear
scaling (or order-N (O(N)) density functional theory (DFT) code CONQUEST. The
system we calculated consists of 3439 atoms (634 atoms for a DNA ofd(CCATTAATGG)2 (PDB code 1WQZ), 9 Mg counter ions and 932 water molecules).
We have found that our O(N) DFT
methodology is robust and accurate. The
dependence of the total energy on the cutoff
radius of the (auxiliary) density matrix isshown in figure 1 and we can see that theenergy converges very rapidly. We have also
compared the atomic forces and the totalenergies calculated by CONQUEST with Figure 1. Dependence of total energy on cutoff
those by AMBER. Figure 2 shows the force length RL of the auxiliary density matrix in O(N)components for the atoms of Ade3 part,which includes the atom having the largest
force components. We find that these two
methods show semi quantitative agreements
for these atoms. Figure 3 shows thecomparison of the total energy differences
between CONQUEST and AMMBER. The
van der Waals interaction seems to improve
the total energy differences. The results on
Figure 2. Atomic force components calculated
another DNA system will be also reported.
by CONQUEST and AMBER for the atoms ofAde3 part.

Figure 3. Comparison of total energy differences
between CONQUEST and AMBER[1] T. Otsuka, T. Miyazaki, T. Ohno, D. R. Bowler, M. J. Gillan, J. Phys. Condens. Matter 20,
29401 (2008).
[2] T. Otsuka, T. Miyazaki, D. R. Bowler, M. J. Gillan, to be appeared.

386

4PP-59

Electronic excited state of a series of porphyrin molecules;
Development of an eﬀective renormalization scheme
Masaaki Saitow, Yuji Mochizuki
Department of Chemistry and Research Center for Smart Molecules, Rikkyo
University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
I. Introduction
The porphyrin derivatives including chlorophyll and bacteriochlorophyll play thecentral role on the light reaction in the photosynthesis, by catching the energy ofphoton. Such the molecules possess the highly conjugated MOs, and vary its spectral
behavior depending on the substituent groups, structures and the environmental effects by the surrounding residues. By favor of this property, this kinds of molecules
are able to absorb almost whole range of a solar radiation. Moreover, it is pronounced these species show sharp peak at about 3 eV, known as B- or Soret-band
and the corresponding quantum yield reaches ∼100%. The other characteristic peakis located at nearly 2 eV, on the other hand, which is termed as Q-band with the far
smaller oscillator strength. From such attractive bio-chemical and -physical aspects,
there have been countless theoretical eﬀorts for the accurate description of porphyrinderivatives such based on as DFT/MRCI[1], SAC-CI[2], and EOM-CCSD[3]. Thesemethodologies have been considered more preferable to the lower order variants
like CIS(D) because of the closely degenerated character, doubly- and triply-excited
conﬁgurations predominantly account for up to ∼30%.
Then, our objective is to accomplish a theoretical approach that can be applicablefor even such the species, by utilizing eﬀective renormalization techniques composedof a so-called partial-renormalization[4] for the diﬀerential correlation term, and aself-energy shifting for the orbital relaxation term. The order of the formulas isseized at merely the second order.
II. Brief explanation of the results
The excitation energies for zinc-porphyrin (ZnP) are showed in the table below,
where CIS, CIS(D) and ADC(2) values were obtained with 6-31G*[6d/10f] basis
set using our local version of PSI3 quantum chemistry program suite. It is readily
recognizable the single reference values were aﬀected by the multireference characterof ZnP, which resulted in insuﬃcient agreement with the observed values.
The excitation energies, and corresponding oscillator strengths shown in parentheses for ZnP
calculated by various methodologies and the observed values.
1

1 Eu
21 E uCIS
2.54(0.0442)
4.75(2.61)

CIS(D)
2.79
3.47

ADC(2)a2.53(0.0000391)
3.59 (2.47)

DFT/MRCI∗
2.21(0.0050)
3.28(1.27)

SAC-CI∗∗
1.84(0.0129)
3.50(3.38)

Obs.
2.28∗
3.04, 3.22, 3.05∗∗ , ∗∗ These are from Ref.[1] and [2], respectively, and references therein.
a Oscillator strengths were calculated using ordinary dipole integral, instead of the generalized matrix element.

[1] A. B. J. Parusel, and S. Grimme, J. Porph. Phthal. 5, 225 (2001).
[2] T. Miyahara, H. Nakatsuji, J. Hasegawa, et. al., J. Chem. Phys. 117, 11196 (2002).
[3] P-.D. Fan, M. Valiev, and K. Kowalski, Chem. Phys. Lett. 458, 205 (2008).
[4] C. E. Dykstra, and E. R. Davidson, Int. J. Quantum Chem. 78, 226 (2000).

387

4PP-60

Interaction analysis of HIV-1 antibody 2G12 and glycans
using FMO calculations
Yuka Koyama1, Kaori Ueno-Noto2 and Keiko Takano1
1
Graduate School of Humanities and Sciences, Ochanomizu University, Japan
2
College of Liberal Arts and Sciences, Kitasato University, Japan
Ϩ. Introduction
Human antibody 2G12 is capable of recognizing the high-mannose glycans on the
HIV-1 surface glycoprotein, gp120 [1]. Doores et al. found that Fab-2G12 boundD-fructose and C-6 methyl mannose stronger than D-mannose [2]. Details of theantibody-neutral carbohydrate ligand interaction are still unclear. To investigate theaffinity of Fab 2G12 for glycans, we carried out the interaction energy analysis by abinitio fragment molecular orbital (FMO) calculations [3].
ϩ. Method
The FMO calculations at the MP2/6-31G(d) level were performed for various
glycan-Fab 2G12 complexes to analyze the difference in binding energy due to theglycan structures, D-mannose, D-fructose, C-5 or C-6 alkyl-substituted mannose, andC-6 methyl tetra mannose. The crystal structures of 2G12 and those glycan ligands were
utilized as calculation models (PDB ID: 1OP5, 1OP3, 3OAY, 3OAZ, 3OB0). To
evaluate the nature of the interaction energy, pair interaction energy decomposition
analysis (PIEDA) was applied, results of which were compared with experimental
results [2].
Ϫ. Results and discussion
Pair interaction energies are shown in
Figure 1. Results of glycan c, d and e accord
with the experimental data [2]. It was foundthat electrostatic interaction plays adominant role in stability and exchangeinteraction is a major destabilization factor.
In contrast, glycan a and b underestimatedthe affinity compared with the experimental
results, which suggests the significance ofwater molecules which exist at the bindingsite in the crystal structures. We further
investigated how the water molecules affectFigure 1. Total pair interaction energy
the antibody-glycan interaction by analyzing between Fab 2G12 and glycans
the models containing water molecules.
relative to mannose (kcal/mol)[1] D. A. Calarese et al. Science 2003 300, 2065. [2] K. J. Doores et al. PNAS 2010, 107,
17107. [3] D. G. Fedorov, K. Kitaura, J. Phys. Chem. A, 2007, 111, 6904.

388

4PP-61

Fragment-DFT calculation on the interaction energy between
HIV-1 protease and its inhibitor
Tomoyuki Iwase, Kenji Morihashi
Department of Chemistry, Graduate School of Pure and Applied Sciences,
University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
I. Introduction
The human immunodeficiency virus type 1 protease (HIV-1 PR) is a main target todevelop the anti-AIDS drugs. The main action of HIV-1 PR is to divide a large protein
which is the precursor of HIV. Two residues, Asp25 and Asp125, are known for theactive site of this action[1]. In this paper, the interaction energy between HIV-1
protease and its inhibitor was calculated by fragment density functional
theory (F-DFT)[2], where five inhibitors, TMC114, TMC126, DMP323,
indinavir, and lopinavir, were investigated, and were divided into several
fragments as fig. 1. Thus, we could estimate the interaction energy on eachpart of inhibitors. Especially, TMC126 highly resembles TMC114, but has
the greater inhibitive capacity than TMC114. Using these methods, we aim
to reveal which substituent of HIV-1 protease inhibitor is important to
obstruct the HIV-1 protease.
II. Results
The inhibitor-protease binding energies were predicted at the B3LYP
level of theory with the 6-31G basis set. The interaction energy calculationshows that the end part of inhibitor generally attracts the P2 binding
pocket[3] (Asp28, Asp29, Asp30, Ile50 and corresponding B chain residues),
and the hydroxyl group placed on center of inhibitor is attractive with active
site Asp25 of HIV-1 protease. TMC126 is more attractive with ASP130 than
TMC114 at the fragment D, as shown in fig.2. This is due to the difference ofa substituent, which could cause the good inhibitive capacity of TMC 126.
‵
O
O
O

″

O

O
N

‴ H

N

O
S

OH

X

‶
TMC114, X=NH 2
TMC126, X=OMe

fig.1 Fragmentation of TMC114 and TMC126

fig.2 Interaction energy between
fragment D and ASP130[1] J. Trylska et al., Protein Sci., 13, 513(2004) .
[2] Y. Shimodo et al., J. Mol. Struct.(Theochem), 770, 163(2006).
[3] K. Nivesanond et al., Int. J. Quantum Chem., 105, 292(2005) .

389

4PP-62

Theoretical study on the Photo-decarboxylation mechanismof Green Fluorescent Protein
Lina Ding, Lung Wa Chung, Keiji Morokuma*
Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto Japan
Wild-type green fluorescent protein (GFP), discovered from Aequorea victoria
jellyfish, and its variants have revolutionized GFP technology to visualize molecular
events that occur within living cells.[1-3] The absorption spectrum of WT-GFP at pH
8.0 shows two major peaks at 397 nm (A band) and 475 nm (B band) corresponding
to neutral and anion forms of the chromophore, respectively. After durative
UV/Visible light, photocoversion can occur which was discovered shortly after thecloning of the gfp gene. [4, 5] Mechanistic study on this photoconversion based on
different techniques separately supported that reversible and irreversible changes cantake place, presumably occurring together but expected to have different kinetics andquantum yields. [6]In this work, systematic high-level ab initio QM and ONIOM (QM:MM)calculations were performed to delineate the possible decarboxylation mechanism
involving intra- and inter-molecular charge-transfer(CT) excited states. The
calculations support that the decarboxylation process is initiated with theintramolecular CT excited state within the GFP chromophore and then accesses to aconical intersection (CI) channeling to the inter-molecular CT excited state. Theintermolecular CT excited state plays a key important role in the photo-induced
irreversible process, and finally decays to the ground state via the second CI.
Refs:
1.
2.
3.
4.
5.
6.

Tsien, R.Y., Ann. Rev. Biochem, 1998, 67, 509.
Zimmer, M., Chem. Rev, 2002, 102, 759.
Shaner, N. C., Patterson, G. H., Davidson, M. W. J. Cell. Sci, 2007, 120, 4247.
Chalfie, M., et al., Science, 1994, 263, 802.
Cubitt, A.B., et al., Trends. Biochem. sci, 1995, 20, 448.
van Thor, J.J., et al., J. Bio. Chem 2005, 280, 33652.

390

4PP-63

Effects of phospholipid bilayers on the hydrated
excess proton behavior: A computational study
Takefumi Yamashita1 and Gregory A. Voth2
1

Laboratory for Systems Biology and Medicine, Research Center for Advanced Scienceand Technology, University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo 153-8904, Japan2
Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics
and Computational Institute, University of Chicago, 5735 S Ellis Ave., Chicago, Illinois
60637, United States
I. Introduction
Proton transport near the phospholipid bilayers is an important and challenging
issue in both biophysics and physical chemistry. In this work, we performed atomistic
molecular dynamics (MD) simulations in order to study the effects of lipid bilayers on
the hydrated excess proton behavior.
II. Methods
In order to describe the proton behavior realistically, the third generation of themultistate empirical valence bond (MS-EVB3) model [1] was adopted. Thus, thecharacteristic Grotthuss shuttling of the hydrated excess proton is reasonably
reproduced in the MD simulations. We studied not only the DOPC bilayer but also the
DOPE bilayer and DOPG bilayer in order to investigate the effects of the head groupspecies.
III. Results
Whereas the excess proton forms a hydronium-like structure in the shallow
interface region, it forms the distorted Zundel ion in the deep interface region. In the
deep interface region, not only the phosphate oxygen atoms but also the carbonyl
oxygen atoms play an important role. More detailed results will be discussed in theposter presentation. (See Fig. 1.)

Figure 1: Hydrated excess protons (left) in the shallow DOPC
membrane/water interface region and (right) in the deep interface region.
[1] Y. J. Wu et al., J. Phys. Chem. B 112 467 (2008)[2] T. Yamashita and G. A. Voth, J. Phys. Chem. B 114 592 (2010)391

4PP-64

Effect of Crystal Packing on Protein Conformation and Dynamics
Osamu Miyashita, Ivan Vorontsov, Zak Campbell, Logan Ahlstrom
Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
Decades of investigation have confirmed the importance of protein dynamics forbiological functions. X-ray crystallography has played the major role in structural
biology, providing information on protein conformations. However, interpretation ofthis data is not always trivial. While proteins are flexible and adopt different
conformations, X-ray structures represent only a single snapshot of the conformational
ensemble. In addition, this static image may be subject to artificial forces such as
crystal packing. Some structures may represent conformations that are indeed moststable in solution environment, while some may be unrepresentative of thephysiologically relevant forms. It is especially important when several conformations ofa protein are available – some conformations reflect their biological context (such as anallosteric effector), whereas others may be under the effect of crystal packing. At
present, there is no general guideline for interpreting X-ray structures.
We have been studying several biological systems and examining how experimentally
determined structures correlate with the conformational ensembles to provide additional
insight to the structural mechanism of their functions. In particular, we established 1) a
protocol to perform molecular dynamics simulations of proteins in solution as well as
crystalline environment and 2) tools to analyze conformational ensembles using
clustering and network analysis. We applied our methods to study the effect of thecrystal environment on protein structures at multiple levels: side-chain conformations of
cyanovirin-N, mobile loop motions of luciferase, and large-scale domain motions of
λ-cro. We showed that, while the conformations of X-ray structures are energeticallyaccessible, they are not always the most energetically favorable conformation. The
crystallization processes also may influence the conformational state represented in
X-ray data. Thus, the X-ray structure itself is not sufficient to reveal the mechanism ofprotein function, and could even lead to inaccurate speculations. Our quantitative datafrom computation should provide useful information on the effect of crystal packing onprotein conformation.

[1] Vorontsov, I. I. & Miyashita, O. Solution and crystal molecular dynamics simulation
study of m4-cyanovirin-N mutants complexed with di-mannose. Biophys J 97,
2532-2540 (2009).
[2] Campbell, Z. T., Baldwin, T. O. & Miyashita, O. Analysis of the bacterial luciferase
mobile loop by replica-exchange molecular dynamics. Biophys J 99, 4012-4019 (2010).
[3] Ahlstrom, L.S. and Miyashita, O. submitted.

392

4PP-65

A theoretical analysis on the interaction between Siglec-7 andits ligand by molecular dynamics and ab initio FMO method
Kaori Ueno-Noto,1 Keiko Takano2
1
College of Liberal Arts and Sciences, Kitasato University, Japan
2
Graduate School of Humanities and Sciences, Ochanomizu University, Japan
Siglecs are a group of receptors in the immunoglobulin superfamily, which
specifically recognize glycans that contain sialic acids (Neu5Ac). Siglec-7 belonging toCD33-related Siglecs is mainly expressed on natural killer cell, and draws attentions for
its role in the immune system. Attrill et al. reported that the ligand binding of Siglec-7
changed by mutations [1]. The mechanism of the ligand recognition, however, has notbeen elucidated. In order to investigate the specificity of glycan binding of Siglec-7, weanalyzed the modulation of the interactions by site-specific mutagenesis.
MP2 level of ab initio fragment molecular orbital (FMO) electronic structure
calculations (FMO-MP2/6-31G**) [2] were performed with wild-type Siglec-7 as well
as seven mutants using the X-ray crystal structure (PDB ID: 2HRL) [1]. The detailed
ligand-Siglec interactions were analyzed by Pair Interaction Energy Decomposition
Analysis (PIEDA) [2]. We also carried out MD simulations for 9 ns on wild-type andmutants to see dynamical effects caused by mutations.
Figure 1 shows the difference in the ligand-Siglec-7 interaction energy between
seven mutants and that of wild type. The experimental results of ligand-binding assay
were also depicted [1]. We found a large decrease in the interaction energies in
R124A, K131A, N131A, and K135A mutants. These large decreases werepredominantly the reduction in electrostatic energy. The decline in W74F due to the
reduction in dispersion interaction was also found. These results agree well with theexperimental results. On the other hand, we found discrepancies in W85A anddW74F/W85A mutants. Figure 2 shows structural RMSD change of wild-type as wellas W85A, dW74F/W85A and R124A mutants obtained by MD simulations. We foundthe mutagenesis at W85 position significantly destabilized the protein structure.

Figure 1. Interaction energies between
the ligand and the mutants of Siglec-7
calculated with FMO-MP2/6-31G**[1] H. Attrill et al. J. Biol. Chem., 281, 32774 (2006)[2] D. G. Fedorov et al. J. Phys. Chem. A 111, 6904 (2007)

393

Figure 2. The RMSD of Siglec-7
atoms with respect to the crystal
structure (PDB ID;2HRL)4PP-66

Electron transfer from cytochrome f to plastocyanin
Tatsuya Joutsuka,1 Hirotaka Nishioka,1 Koji Ando1
1
Department of Chemistry, Graduate School of Science, Kyoto University, Japan
In photosynthesis, plastocyanin (Pc) shuttles an electron from cytochromef (Cf) to P700+. Pc is a small, soluble cupredoxin whose ligand structure around thecopper ion is distorted trigonal and consists of a cystein (Cys), two histidine (His), and amethionine (Met) residues as shown in Figure 1. Cf is an N-terminal soluble subunit ofcytochrome b6f that is anchored to the membrane complex by C-terminal helix. Itssoluble domain is an atypical c-type cytochrome because both its β-sheet secondary
structure and the unusual heme axial coordination with the N-terminal amino acid Tyr
acting as an axial ligand (Figure 1).
The structures of Pc observed by X-ray crystallography were very similar
between the reduced and the oxidized states, in contrast to those in typical inorganic
compounds where Cu(I) and Cu(II) tend toward tetrahedral and tetragonal geometries,
respectively. The small change indicates that theactive site reduces the reorganization energy andthereby accelerates the electron transfer (ET).
Hence, the position dependence of the residues
around the active site on the reorganization energy
can clarify their roles in ET.[1]For example, when an electron flows fromCf to Pc, they form a transient complex (Pc/Cf)
which is the transition state (TS) of ET. The His
residue is very close to the Tyr residue in thetransient complex. This indicates that the His
residue, in particular the solvent exposed one,may be crucial to elucidate the ET mechanism.
Accordingly, the purpose of thispresentation is to analyze the ET mechanism of
the complex Pc/Cf by ab initio quantum chemistry
methods.[2] Our focus is on the roles of theresidues in the active site of Pc to relate to ourprevious study.[1][1] Koji Ando, The Journal of Chemical Physics, Vol. 133,
No. 17, p. 175101, 2010.

[2] Hirotaka Nishioka and Koji Ando, Phys. Chem. Chem.
Figure 1. Active site structure of
the complex between Pc and Cf.

Phys., Vol. 13, pp. 7043–7059, 2011.

394

4PP-67

Structural properties and imino proton acidity of silver containing
5-substituted uracils
Toru Matsui1, 2, Hideaki Miyachi3, Yasuteru Shigeta1
1

Department of Material Engineering Science, Graduate School of Engineering Science,
Osaka University, 1-3 Machikaneyama, Toyonaka 560-8531, Japan.
2
Department of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka 560-0043, Japan.
3
School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670,
Japan.

Deoxyribonucleic acid (DNA) contains genetic instructions used in the development
and functioning of living organisms. Chemists’ interest in DNA has recently been
focused on its flexible functioning in living organisms. One of the promising
approaches to modify its properties is to coordinate metal ions to nucleobases,
nucleosides or nucleotides to form metal-complexed DNA. If metal ions, which havevarious electronic states, are captured in DNA duplex and controlled to systematicallyarray, one can obtain a hybrid material with multi-functions in mesoscopic scale. Thesedays, many researchers have developed such metal-DNA systems. An example ofmetal-DNA systems is the formation of [N-Ag2-N] (N: 5-substituted uracil) bridge by
substituting the C5 ligand (X) of deoxyuracil nucleo-oligomer. [N-Ag2-N] can beformed even in low pH in the case of CN (X=CN), while T (X=CH3) does not seem tocapture any silver ion.
We focused on [N-Ag2-N] bridges and showedfollowing
three
pointsbyusing
B3LYP/aug-cc-pVDZ + pseudo potential (PP) and6-31++G(d, p) level of theory: (1) The
replacement of an imino-proton with Ag(I)
increases the stability of the whole duplex innucleo-oligomer. (2) Four conformations of[N-Ag2-N] bridge and two of them (depicted in Figure: Possible conformers for the
Figure) are almost degenerate from the view of structure of [N-Ag -N] bridge.
2
potential energy. (3) The energy barriers among
three structures are no more than 6 kcal/mol. Thus, these structures may fluctuate atroom temperature. These results indicated that the replacement of imino-proton with
Ag(I) plays a key role in forming [N-Ag2-N] bridges. In the poster presentation, we will
also introduce a new computational method to provide a pKa value of an imino-proton
in silver mediated N and propose a scheme for the formation reaction of silver-mediatedbase pair [N-Ag2-N] from two N with two silver ions.

395

4PP-68

Electronic coupling calculation and pathway analysis of electrontransfer reaction by using ab initio fragment-based method
Hirotaka Nishioka,1 Koji Ando1
1
Graduate School of Science, Kyoto University, Japan
I. Introduction
Electron transfer (ET) reactions, playing important roles in the biological energy
conversion such as photosynthesis and respiration, take place via the electron tunnelingbetween redox centers separated by more than several Å where the tunneling electronuses the electronic states of the protein media as its virtual intermediate states.
Therefore, the electronic coupling factor TDA, regulating the biological ET rate, strongly
depends on the electronic states of intervening protein. Accurate estimation of TDA
requires ab initio quantum chemical methods[1] whose applications, however, havebeen limited owing to their huge computational cost. To overcome the difficulty, we
propose a novel approach to calculate TDA and analyze the tunneling pathway by using
the ab initio fragment-based electronic structure methods.
II. FMO-LCMO approach
The FMO-LCMO method, developed by Tsuneyuki et al.[2], produces one-electron
Hamiltonian of whole system using the output of the fragment molecular orbital (FMO)
calculation with computational cost much lower than conventional all-electron
calculations. Diagonalizing the FMO–LCMO Hamiltonian matrix, the molecularorbitals (MOs) of the whole system can be described by the linear combination of MOsof the fragments. In our approach[3], TDA is calculated from the energy splitting of thefrontier MOs of whole system or perturbation method in terms of the FMO-LCMO
Hamiltonian matrix. The tunneling pathway at fragment-based resolution is obtained
from the tunneling current method. Moreover, taking into account only the valence MOsof the fragments, we can considerably reduce computational cost to evaluate TDA. We
have succeeded in applying our approach to several ET systems.[3]III. Divide-and-Conquer approach with Natural Bond Orbital Analysis
The Divide-and-Conquer (DC)[4,5] and FMO-MO[6] methods produce theapproximated total density matrix of the system. For model protein ET systems, wehave analyzed the tunneling pathways in terms of localized MOs such as natural bondorbitals (NBOs) obtained from the DC or FMO-MO density matrix.
[1] H. Nishioka and K. Ando, Phys. Chem. Chem. Phys. 13, 7043 (2011)[2] S. Tsuneyuki et al. Chem. Phys. Lett., 476, 104 (2009)[3] H. Nishioka and K. Ando, J. Chem. Phys., 134, 204109 (2011)[4] W. Yang and T.-S. Lee, J. Chem. Phys., 103, 5674 (1995)[5] T. Akama et al. J. Comput. Chem., 28, 2003(2007)[6] Y. Inadomi et al. Chem. Phys. Lett. 364, 139 (2002)

396

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Application of DC-MP2 method to investigate the interaction energyof MK4965 in HIV-1 RT binding pockets
Patchreenart Saparpakorn,1,2 Masato Kobayashi,1,3 Hiromi Nakai1,4,5
1School of Advanced Science and Engineering, Waseda University, Japan2
Department of Chemistry, Faculty of Science, Kasetsart University, Thailand
3
Department of Theoretical and Computational Molecular Science, Institute for
Molecular Science, Japan
4
Research Institute for Science and Engineering, Waseda University, Japan
5
CREST, Japan Science and Technology Agency, Japan
I. Introduction
The reverse transcriptase (RT) of HIV-1 is an essential enzyme converting thesingle-stranded viral RNA genome into double-stranded proviral DNA prior to its
integration into the host genomic DNA. MK4965, a novel NNRTI, reveals high levels ofpotency against wild-type and some important HIV-1 RT mutants.
II. Methodology
DC-MP2 method [1,2] with 6-31G** basis set using GAMESS program is applied
to study the total interaction energies of MK4965 in WT and Y181C HIV-1 RTs.
Efficiency of the DC-MP2 method with the effects of SCF buffer radius and correlationbuffer radius is validated by comparing the energies and CPU times with those obtainedby the conventional MP2 method. The energy distribution of each subsystem of
MK4965 and amino acid is also examined.
III. Results and Discussion
Based on the accuracy and CPU times, 6.0 Å of SCF
buffer radius and 5.0 Å of correlation buffer radius areappropriate parameters for this study. The deviation of theinteraction energies are less than 0.5 kcal/mol for MP2 and
SCS-MP2 energies. The main energy distribution is causedby the interaction with Lys102 and chlrobenzonitrile ringsubsystems. In addition, the other important energy
distributions are from subsystems of Leu100, Lys103, Val106,
Tyr188, Phe227, and Leu234. Study of each subsystem of Figure 1. Binding pockets of
MK4965
MK4965 reveals that pyrazolopyridine ring causes the mainenergy distribution to Lys102. In this study, DC-method reveals the efficiency toinvestigate in the biological system with the less computing time and high accuracy of thecalculations. In addition, the results obtained by the DC-method are able to explain theenergy distribution in the binding of MK4965 and guide for the drug design.
[1] T. Akama, M. Kobayashi, and H. Nakai, J. Comput. Chem., 28, 2003-2012 (2007)[2] M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys., 127, 074103 (2007)

397

4PP-70

Binding free energy of oxidized Azurin – reduced Cytochrome c551
Complex
Hiroaki Saito,1 Masashi Iwayama,1 Taku Mizukami,2 Hidemi Nagao1
1
Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa
University, Kanazawa 920-1192 Japan2
Department of Materials Sciences, Japan Advanced Institute of Science andTechnology

Protein complexes have much interest in the mechanism of catalysis,
photosynthesis and physiology in vivo. For instance, the formation of metalloporoteinscomplex occurs the electron transfer between active site of the proteins, yielding theredox reaction in the protein complex. The synthesis and hydrolytic cleavage of
adenosine triphosphate (ATP) are important catalytic reactions concerning metabolism
of material and energy in vivo, and those are cased by binding to the protein complex.
Also, in the protein-ligand complex, the bound ligand functions as inactivator andchanges the dynamical structure correlating the protein functions. Thus, understandingof the binding characters of protein complexes should be a key subject to reveal thebiological function of protein system.
Azurin and Cytchrome c551 from Pseudomonas aeruginosa are metalloporoteins,
and the bound Az-Cyt protein complex shows the electron transfer between the active
sites in vivo. However, since this complex is not accessible to crystallographic
investigation, its docking structure in solution is not still known. We have carried out
the docking and MD simulations of the protein complex consist of the reduced Azurin(Azred) and oxidized Cytchrome c551 (Cytox) to reveal the structure and dynamics ofthe system. In these studies, we have shown the stability of the Azred-Cytox complex
and the dynamical correlations between residues.
In this study, to evaluate the binding energy of the AZ/C551 complex, at first, we
present a possible AZ/C551 complex structure in water solvent by docking AZ and
C551 proteins and carry out the MD simulation of AZ/C551 complex in water solvent.
From the coordinates in equilibrated state, we calculate the free energy of AZ/C551
complex by estimating the internal energies and the excess chemical potential. The
binding free energies are evaluated by the difference of free energy of protein complex
and those of monomer proteins. The variation of protein structures and binding freeenergy are also discussed in this study.

398

4PP-71

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399

4PP-72

Effect of Multivalent Ion on Attractive Interaction between
Like-Charged Macromolecules Immersed in an Electrolyte Solution
Ryo Akiyama,1 Ryo Sakata,1 Yoji Kubota1,
1
Department of Chemistry, Kyushu University, Japan
I. Introduction
In dilute electrolyte solution two like-charged macroions are repel each other. The
effective interaction is screened Coulomb interaction. However, the effective interaction
often becomes attractive in a bio-fluid. For example, G-actins make a strong polymer
and bundle structures in biological condition, although they are negatively charged
proteins. Another example is DNA, which is negatively charged long polymer. In diluteelectrolyte, it is stretched. When the electrolyte concentration becomes higher, thepolymer collapses. It means that the like-charged parts of polymer are effectively
attracted each other. However, the attraction disappears as the concentration increases.
The coil-globule transition is important in reading genetic information of DNA.
Therefore, this reentrant behavior is not only interest in chemical context, but also
important in biological context.
II. Theory and Model
The OZ-HNC theory was adopted in this study, because it was useful method inthis problem [1]. The equations were solved numerically. The details of the calculations
have been described in earlier publications [2]. Neutral hard spheres (the diameter is
2.8A) were adopted as the solvent molecules. This size is the effective size of watermolecule. The ions were modeled as charged hard spheres whose diameter was also
2.8A. Each anion and each cation had charge −e and e, respectively. The macroions
were also modeled as charged hard spheres. The diameter of macroion was set at 16.8A
and. The Coulomb potential was divided by 78.5, the dielectric constant of water.
II. Results
The effective interaction between two like-charged macromolecules were obtained.
The results showed the reentrant behavior. The attraction was explained by using theidea of classical “covalent bond”. The “bond” was analyzed by the Kirkwood superposition approximation. There was a good agreement between the stability of macroion
dimer and the local density between the macroions. It means that there is an analogy
between it and the linear combination of atomic orbital (LCAO) approximation forchemical bonds.
[1] G.N. Patey, J. Chem. Phys. 72, 5763 (1980)[2] M. Kinoshita and M. Harada, Mol. Phys. 74, 443 (1991).

400

4PP-73

Fragment molecular orbital study for interaction between influenza
virus neuraminidase and antiviral drug
Kaori Fukuzawa,1,2 Yuji Mochizuki,2,3 Hiroki Mibe,3 Chiduru Watanabe2, Shigenori
Tanaka4, Tatsuya Nakano2,5
1
Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku,
Tokyo 101-8443, Japan
2
Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku,
Tokyo 153-8505, Japan3
Department of Chemistry and Research Center for Smart Molecules, Faculty of
Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
4
Graduate School of System Informatics, Department of Computational Science, Kobe
University, 1-1, Rokkodai, Nada, Kobe 657-8501, Japan
5
Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1
Kamiyoga, Setagaya-ku, Tokyo 158-8501, JapanAb initio electronic structure calculations for interaction between influenza viralsurface proteins, neuraminidase (NA), and antiviral drug, oseltamivir (Tamiflu) andzanamivir (Relenza), have been performed on the basis of the fragment molecularorbital (FMO) method. The NA monomer (386 amino acid residues, 5749 atoms)
complexed with inhibitor agents were calculated at the FMO-MP2/6-31G level. Theinter-fragment interaction energy (IFIE) analysis
was performed to reveal the interactions between
inhibitor and its binding pocket. Hydrogen bond
network structures of interactions among theinhibitor and surrounding amino acid residues
were characterized, and difference of binding
mechanism between two inhibitors was
examined. Such theoretical analyses could be
helpful to develop the effective inhibitor agent
against the drug resistant mutant.
Acknowledgement
This work was supported by the RISS project at
the institute of Industrial Science (IIS) of the
University of Tokyo and the SFR project at
Rikkyo University.

Fig. IFIE between oseltamivir (yellow)
and each amino acid residue. Attractive
and repulsive interactions are coloredby red and blue, respectively.

Reference[1] Y. Mochizuki, K. Yamashita, K. Fukuzawa, et. al., Chem. Phys. Lett. 493, 346(2010).

401

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4PP-75

Orbital Views of Molecular Conductance Perturbed by Anchor
Units
Yuta Tsuji,1 Aleksandar Staykov,1 Kazunari Yoshizawa1
1
Institute for Materials Chemistry and Engineering and International Research Center
for Molecular Systems, Kyushu University, Japan
During the last two decades studies ofsingle-molecular electronic devices havegained great attention of the nanoscalescience and technology. The variety of
HOMO
LUMO
potential applications of moleculardevices such as switches, rectifiers, andmemories requires detailed understandingof the electron transport properties
through a single molecule. Site-specific
SOMO
SOMO
electron transport phenomena throughbenzene and benzenedithiol (BDT) Figure1. Frontier orbitals of p-BDT andsymmetry-allowed(solidderivatives are discussed on the basis of a m-BDT,
qualitative Hückel molecular orbital arrow), and symmetry-forbidden (dashedanalysis for better understanding of the arrow) routes for electron transport.
effect of anchoring sulfur atoms. A recent
work [1,2] for the orbital control of electron transport through aromatic hydrocarbons
provided an important concept for the design of high-conductance connections ofmolecule with anchoring atoms. In this work the origin of the frontier orbitals of BDT
derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport
properties, and the applicability of the theoretical concept on aromatic hydrocarbons
with the anchoring units are studied. The results demonstrate that the orbital view
predictions are applicable to molecules perturbed by the anchoring units. The electrontransport properties of benzene are found to be qualitatively consistent with those of
BDT with respect to the site dependence. To verify the result of the Hückel molecularorbital calculations, fragment molecular orbital analyses with the extended Hückel
molecular orbital theory and electron transport calculations with density functional
theory are performed. Calculated results are in good agreement with the orbital
interaction analysis. The phase, amplitude, and spatial distribution of the frontier
orbitals play an essential role in the design of the electron transport properties througharomatic hydrocarbons [3].
[1] Tada, T.; Yoshizawa, K. ChemPhysChem 2002, 3, 1035.
[2] Yoshizawa, K.; Tada, T.; Staykov, A. J. Am. Chem. Soc. 2008, 130, 9406.
[3] Tsuji, Y.; Staykov, A.; Yoshizawa, K. J. Am. Chem. Soc. 2011, 133, 5955.

403

4PP-76

Quantum dynamics for organic solar cells
Hiroyuki Tamura,1 Irene Burghardt,2 Masaru Tsukada 1
1
WPI-Advanced Institute for Material Research, Tohoku University, 2-1-1 Katahira,Aoba-ku, Sendai, 980-8577, Japan
2
Institute of Physical and Theoretical Chemistry,Goethe University
Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
Organic solar cells typically consisting of conjugated polymers and fullerenes are oneof promising next-generation photovoltaics owing to their potential for cost-effectiveenergy sources, so that great efforts have been devoted to the development ofhigh-efficiency organic solar cells. The energy conversion efficiency of organic solar
cells would be determined by several processes, including photoabsorption (exciton
generation), exciton diffusion in the donor material, exciton dissociation (charge transfer)at the donor-acceptor heterojunction, and transports of free electron and hole to theelectrodes. Understanding these mechanisms at microscopic level is important to provide
design rules for high-efficiency photovoltaics.
Here, we investigate the exciton dissociations at oligothiophene/C60 donor-acceptor
heterojunctions [1]. The non-perturbative charge transfer is analyzed based on quantum
dynamics calculations in a diabatic representation considering the vibronic coupling.
Our quasi-diabatization scheme [1] is convenient for analyzing photovoltaic processes,
and can be applied for any ab initio and DFT methods. The electronic structure and thevibronic coupling are calculated by using the long-range corrected TDDFT [2]. We takeadvantage of the hierarchical electron phonon (HEP) model [1,3] for systematic
renormalizations of the vibronic coupling of large systems. We have proven that thetruncated HEP Hamiltonian can exactly reproduce short-time dynamics of large systems.
The quantum dynamics calculations are performed by using the multi-configuration
time-dependent Hartree (MCTDH) method [4].
Our quantum dynamics calculations exhibit
ultrafast exciton dissociations owing to the strong
coupling between the exciton and charge transfer
states, as observed in the time-resolved
spectroscopies. The intra-molecular high-frequency
vibrational modes are found to dominate theultrafast dynamics. The coupling strength andrelative energy between the exciton and chargetransfer states depend sensitively on the stacking
structure of thiophene and C60, which in turn affects Time-evolution of the exciton
the absorption spectra and the dynamics of exciton population at the oligothiophene/C60
heterojunction
dissociations [1].
[1]H. Tamura, I. Burghardt, and M. Tsukada, J. Phys. Chem. C 115, 10205 (2011).
[2] Y. Towada, T. Tsuneda, S. Yanagisawa, Y. Yanai, K. Hirao, J. Chem. Phys. 120,
8425 (2004).
[3]H. Tamura, J.G.S. Ramon, E. R. Bittner, I. Burghardt, Phys. Rev. Lett. 100,107402(2008); H. Tamura, E. R. Bittner, I. Burghardt, J. Chem. Phys. 127, 034706 (2007).
[4]H. D. Meyer, U. Manthe, L. S. Cederbaum, Chem. Phys. Lett. 165, 73 (1990).

404

4PP-77

Determination of Local Chirality of Irregular Single-Walled Carbon
Nanotube Based on Individual Hexagons
Joonghan Kim and Keiji Morokuma
Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, JapanThe chirality of single-walled carbon nanotubes (SWCNTs) has a great importancesince their physical and electronic properties strongly depend on the chirality.
However, the chirality of irregular structures of SWCNT, for instance those formed
during growth of SWCNT, was difficult to define. Therefore, we have developed apowerful theoretical method for the determination of the local chirality based on
individual hexagons that compose SWCNT. The new method and code have been
applied to various SWCNT-like irregular structures that are formed during molecular
dynamics simulation of the growth process. The local chiral angles and theirdistributions are well defined and easily calculated for irregular structures as well as
ideal structures of SWCNT. This tool could aid the further investigation of thechirality-controlled SWCNT growth.

405

4PP-78

Fullerene formation from hydrocarbon combustions:
Quantum chemical molecular dynamics study
Hai-Bei Li,1 Stephan Irle,2 Keiji Morokuma1,3
1
Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, Japan
2
Institute for Advanced Research and Department of Chemistry, Nagoya University,
Nagoya, Japan
3
Cherry L. Emerson Center for Scientific Computation and Department of Chemistry,
Emory University, Atlanta, GA, USA
Combustion of hydrocarbon fuels in lean oxygen flame offers advantages for large-scale
fullerene production [1]. Saha et al. [2] performed high temperature simulations ofbenzene combustion by gradually reducing hydrogen atoms randomly using
density-functional tight-binding (DFTB)-based quantum chemical molecular dynamics(QM/MD).
In this work, we simulate fullerene formation from naphthalene
combustion at 1500 K and 2500 K. All QM/MD simulations were performed by
employing a Nose Hoover chain thermostat, and carbon densities of 0.119 and 0.026
g/cm3, respectively. A Monte Carlo-based hydrogen removal strategy was devised
where we calculate the probability factor for each candidate structure after removing
two hydrogen atoms in randomly selected positions, and select the candidate hydrogenpair randomly under consideration of Boltzmann weights for the environmental
temperature. One hydrogen pair is removed every 0.235 ps and 0.470 ps at 1500 K and2500 K, respectively, until all hydrogen is removed from the system. One selectedtrajectory is shown in the figure below. Although the mechanism of fullerene
formation is similar to previous results [2], in our simulation, lower carbon density andlower temperature favor the formation of smaller size fullerenes. Our new hydrogen
removal scheme tends to produce more cage structures than the random removal schemeof [2].

4.97ps

8.57ps

10.97ps

15.77ps

20.09ps25.30ps

40.20ps65.04ps[1] Homann, K. H. Angew. Chem. Int. Ed. 1998, 37, 2434.
[2] Saha, B.; Shindo, S.; Irle, S.; Morokuma, K. ACS Nano 2009, 3, 2241.

406

4PP-79

First-principles Study of STM-induced Melamine/Cu(001) Switch;
Energy Barrier Change with Bias and Various tip positions
Tatsuhiko Ohto,1,2 Ivan Rungger2, Koichi Yamashita,1 Stefano Sanvito2
and Hisao Nakamura3
1
Department of Chemical System Engineering, The University of Tokyo, Japan
2
School of Physics, Trinity College Dublin and CRANN, Ireland
3
Nanosystem Research Institute(NRI), RICS, AIST, Japan
I. Introduction
The manipulation or stimulation of molecules using
Scanning Tunneling Microscopy (STM) is highly promising.
Pan et al [1] found a STM-induced melamine/Cu(001) switch(C1 to C2, Figure1) and analyzed its mechanism by a typicalmodel. Such a model uses ad hoc parameters and the
Figure 1. Structures ofswitching mechanism is not fully understood. The validation melamine/Cu(001)system.[1]of them using first-principles calculations is required.
II. Method
Current-induced forces are calculated by SMEAGOL program code [2], which isbased on the nonequilibrium Green’s function method with density functional theory.
The explicit evaluation of the current-induced forces enables us to obtain stablestructures under arbital STM-tip configurations with a finite bias. The nudged elastic
band (NEB) method was implemented into SMEAGOL to obtain minimum energy path
(MEP) between C1 and C2 structures. Because the total energy of open systems is not
well-defined, we calculated the potential energy by integrating forces along MEP.
III. Results
The energy landscape calculated at zero bias was almost the same with that of Ref.
1. The energy barrier change was 0.06 eV within r1.0 V, which is attributed to thedipole-filed interaction (no electron-wind force). Therefore, this barrier change can be
reproduced by the calculation of a freemolecule in electric field. (Figure 2) When the
distance between the tip and the molecule isclose, the barrier change becomes large butthese configurations destroy the basic energy
landscape. However, the barrier change of 0.06
eV is 1/4 smaller than the assumption in Ref. 1.
The analysis of the switching mechanism by amaster equation using first principles results
Figure 2. Comparison of the energy
will be presented.
barrier with finite bias
[1] Pan S et al. PNAS106(2009)15159[2] Rocha A et al. PRB73(2006)085414, Zhang R et al. submitted

407

4PP-80

Functional Features of Voids of Nanosized Golden Fullerenes
Eugene S. Kryachko
Bogolyubov Institute for Theoretical Physics, Kiev, 03680 Ukraine
E-mail: eugene.kryachko@ulg.ac.be
Generally speaking, an arbitrary 3D molecular structure is either space-filled,
compact, without any void, or possesses some void(s) or emptiness that result in a hollow
cage shape. Fullerenes, such as the buckyball C60, belong to the latter category. Similar
fullerene-like structures or hollow cages have been recently discovered for otherchemical elements, among which gold is a particular one – definitely, ‘noblesse oblige’
works out – due to its rather unique properties mostly dictated by strong relativistic
effects.
When one molecule interacts with another, their outer space between them ispatterned by chemical bonds. In this sense, hollow molecular cages are distinguishably
different. If a void of an arbitrary fullerene is of a sufficient size, it enables to formchemical bond(s) in the interior, void space with guest atoms, ions or molecules which aretrapped inside, encapsulated or confined within void. This results in the formation of socalled ‘endohedral’ or @-fullerenes which are manifest in a variety of remarkablefeatures. Therefore, by the definition, molecular hollow cages possess atoms that arecapable, on the one hand, to form chemical bonds with molecules from the outer spaceand on the other, from the inner, void one. This implies a bifunctionality of the chemical
reactivity of such molecular systems - the outer or exo-reactivity, on the one hand, and theinner, void, or endo-reactivity on the other.
The present work further pursues the theme of the void molecular reactivity [1,2] andinvestigates the functional features of void reactivity of nanosized golden fullerenes Au32
and higher by invoking, instead of the global characteristics, such as the ionization energy
and electron affinity, which traditionally characterize chemical reactivity, the local ones:
the molecular electrostatic potential, HOMO-LUMO patterns, and atomic and ionicprobing species. The formation of the chemical bonding patters are studied for someencaged atoms and diatoms, and compared with the analogous endohedral C60-fullerenes.
A surprising confinement propensity of the 3D space-filled cluster Au20(Td) is underconsideration as well.
[1] E. S. Kryachko and F. Remacle. J. Phys.: Conf. Series 248, 012026 (2010).
[2] E. S. Kryachko and F. Remacle. In Advances in the Theory of Quantum Systems in
Chemistry and Physics. Ed. by P. Hoggan, J. Maruani, P. Piecuch, G. Delgado-Barrio, andE. J. Brändas. Springer, Berlin, 2011. Vol. B22.

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Theoretical investigation of charge-transport properties in organic
single crystals from constrained density functional theory
Shotaro Watanabe, Kenji Morihashi
Graduate School of Pure and Applied Sciences, University of Tsukuba, Japan
I. Introduction
The charge-transfer rate in electron and hole transfer is one of important factors thatshow transport properties of electronic materials. Therefore, a reliable method to computecharge-transfer rate in electronic materials would contribute much to the development ofelectronic devices. The computational methods of charge-transfer rate have beendeveloped on the basis of Marcus theory, and ab initio method and density functional
theory (DFT) have been used to calculate Marcus parameters. In this work, we used
constrained density functional theory (CDFT) [1] to calculate these parameters andestimated intermolecular charge-transfer rates in organic single crystals, naphthalene
and anthracene.
II. Calculations and Results
The intermolecular charge-transfer rate, k CT , can be written as [2]k CT§  'G 0  O 2 ·
2
2S
1
CT
¸
Vif
exp ¨
¨
¸
k
T
!
4
O
4SO k BTB©
¹

where Vif is the electronic coupling matrix
element between the initial and final states,0
O is the reorganization energy, and 'GCT
is the change in Gibbs free energy from initial
to final state. Using these parameters obtained
from CDFT calculations, we calculated
intermolecular charge-transfer rates shown in
Figure1. The hole transport properties ofnaphthalene crystal are compiled in Table 1.
Table 1. Marcus parameters.
Vif [eV]
T1
0.05799T2
0.03278P
0.06058

O [eV]
0.18260.18650.1845Figure 1. Crystal structure of organic
single crystal.
0
'GHT
[eV]
-0.17320.17320[1] Q. Wu and T. Van Voorhis Phys. Rev. 72, 024502 (2005).
[2] R. A. Marcus J. Chem. Phys. 24, 966-978 (1956).

409

k HT [s-1]1.312×1014
5.068×1010
2.401×1013

4PP-82

Catalytic activity of gold clusters on the “inert” h-BN surface
Min Gao, Andrey Lyalin, Tetsuya Taketsugu
Graduate School of Science, Hokkaido University, JapanThe unique catalytic activity of gold nanoparticles in oxidation reactions bymolecular oxygen was discovered experimentally more than 20 years ago [1]. It was
shown that the so-called "active" supports, such as metal oxides, considerably influencing
the catalytic activity of the supported gold clusters [2, 3]. Recently, it has been
demonstrated experimentally, that small gold clusters deposited on “insert” h-BN support
are efficient and robust catalysts [4]. However origin of the catalytic activity of goldclusters supported on h-BN has yet to be fully understood. The present work aimed toclarify whether the catalytic activity of Aun/h-BN is the intrinsic property of gold clusters
or not.
In the present work the structural and electronic properties of Au and Au 2 adsorbedon the regular h-BN surface, as well as on the impurity and vacancy defects on the h-BN
surface have been studied theoretically using DFT at the GGA level with the Wu-Chenfunctional. The most stable geometry structures, surface relaxations, adsorption energies
and charge transfers from the h-BN surface to Au and Au2 are investigated with the aim tounderstand the specific role played by the support in formation of the catalytic propertiesof gold. In order to model the catalytic activity of gold clusters supported on h-BN surface
we studied adsorption and activation of oxygen molecule on Au/h-BN and Au2/h-BN. We
demonstrate that catalytic activity ofgold clusters can be sensitive not only tothe interaction with the active support
materials, such as metal oxides, but also
to the interaction with the inert supports,such as h-BN. It is shown that vacancy
and impurity defects on h-BN surface
can promote the catalytic activity of the
supported Au clusters and enhance theactivation of the adsorbed O2. The chargetransfer from the support to the goldclusters plays an important role in Figure 1. PDOS projected on the O2 supported
formation of their catalytic properties [4, on h-BN/Au (solid line) and Au atom (dashed
5].
line)
[1] M. Haruta, T. Kobayashi, H. Sano, N. Yamada. Chem. Lett. 1987, 16, 405.
[2] M. Okumura, S. Tsubota, M. Haruta. J. Mol. Cat. A. 2003, 199, 73.
[3] A. Lyalin, T. Taketsugu. Faraday Discussions 2011, 152 (doi:10.1039/c1fd00013f).
[4] A. Lyalin, T. Taketsugu. J. Phys. Chem. C. 2010, 114, 2484.
[5] A. Lyalin, T. Taketsugu. J. Phys. Chem. Lett. 2010, 1, 1752.

410

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QM/MD Simulations of Graphene Hydrogenation
Ying Wang, Hu-Jun Qian, Stephan Irle
Institute for Advanced Research and Department of Chemistry, Nagoya University,
464-8601 Nagoya, Japan
Chemical adsorption of hydrogen atoms on graphite surfaces has attracted
considerable interest due to its relevance for a broad range of areas including
plasma/fusion physics, gap tuning in graphene, and hydrogen storage. We computed
counterpoise-corrected DFT, ROMP2, ROCCSD, and ROCCSD(T) potential energy
curves (PECs) based on relaxed-scan UB3LYP/cc-pVDZ geometries for the approach of
atomic hydrogen head-on to a carbon atom of an inner hexagon of pyrene C16H10 andcoronene C24H12. Such attack leads to the only global potential energy minimum
corresponding to chemisorbed H (relative energy for CCSD(T) around -0.4 eV), and abarrier (CCSD(T): 0.5 eV) for the H approach. Interestingly, ROCCSD(T)//UB3LYP
PECs are close to that of pure UB3LYP.
We then modified the C-H parameter set for the
spin-polarized self-consistent-charge density-functionaltight-binding (sSCC-DFTB) method to reproduce the
CCSD(T)-based PEC at a tiny fraction of the computational
cost.
Using this quantum chemical potential, we
performed direct Born-Oppenheimer MD simulations while“shooting” H atoms in 0.5 ps intervals with incident
Figure1.
All-para
hydrogenated graphene velocity of 0.4 eV aimed at a periodic graphite target withcorresponding to 25% randomly selected spin. The simulations were carried out
coverage as observed inexperiment[1]
and at a constant temperature of 300 K. Chemisorption may
during our QM/MD occur in principle in random positions on the graphite withsimulations.
little preference for the adsorption site, causing H-frustrated
adsorption patterns over time [1] as reported by Flores et al. [2]. However, during
prolong exposure to H bombardment, a para-adsorption pattern (see Figure 1), proposed
previously by Boukhvalov et al. [3], emerges as a consequence of repeated surface
reorganization due to associative H2 elimination [1].
[1] Haberer, D.; Guisca, C. E.; Wang, Y. et al. submitted (2011).
[2] Flores, M. Z. S.; Autreto, P. A. S.; Legoas, S. B.; Galvao, D. S. Nanotechnol. 20,
465704 (2009).
[3] Boukhvalov, D. W.; Katsnelson, M. I. Phy. Rev. B 78, 085413 (2008).

411

4PP-84

Finite length Armchair Carbon Nanotubes: HOMO-LUMO gap
oscillation and conjugated circuit
Noriyuki Mizoguchi
Meiji Pharmaceutical University, Kiyose, Tokyo 2-522-1, JapanAn interesting aspect of finite-length carbon nanotubes (CNTs) is the quantum
finite-size effects of the energy gap between the highest occupied molecular orbital(HOMO) and the lowest unoccupied molecular orbital (LUMO). It has been shown thatthe HOMO-LUMO gaps in armchair CNTs show the oscillation depending on thenumber of carbon layers along the tubular length axis. In this paper this oscillation of
HOMO-LUMO gaps are discussed in terms of Sachs graphs, conjugated circuits, andClar structures.
Sachs formula enables us to obtain the coefficients of the characteristic
polynomial for a conjugated molecule G. If the constant term aN(G) is zero, then themolecule's pi-system has non-bonding molecular orbitals.

A Sachs graph SN with all

the vertices in G is obtained by the superposition of two Kekule structures for G.
Circuits found in Sachs graphs SN are conjugated circuits for G.
Sachs graphs SN were studied for (n,n)m armchair CNT. Here m stands for thenumber of layers in CNT.

Figure 1 shows three Kekule structures and two Sachs

graphs for (2,2)2 armchair CNT. Superposition of K1 and K2 produces Sachs graphs SN1,
which contains two 6-membered conjugated circuits and one 8-membered conjugatedcircuit. Superposition of K1 and K3 produces Sachs graphs SN2, which is Clar formula for(2,2)2 armchair CNT. We found that Sachs graphs SN for (n,n)m armchair CNT containnot only 4k+2-membered but also 4k-membered conjugated circuit. Note that benzenoidhydrocarbons can have only 4k + 2 conjugated circuits. By using Sachs formula wefound that the constant term aN for (n,n)m armchair CNT is zero if m=3j, and non-zerootherwise. Thus it was shown that the oscillation of HOMO-LUMO gaps arises fromthe existence of 4k-membered conjugated circuits in (n,n)m armchair CNT.

Clar

formulae were found in Sachs graphs for (n,n)m armchair CNT with m=3j+2.

Fig.1 Three Kekule structures and two Sachs graphs for (2,2)2 armchair CNT

412

4PP-85

Relativistic quantum chemistry of heavy elements, hadronic atoms
and heavy ions collisions
Alexander Glushkov,1,2
1
Odessa OSENU University, P.O.Box 24a, Odessa-9, 65009, Ukraine
2
ISAN, Russian Academy of Scinces, Troitsk, Moscow reg., 142090, Russia
The gauge-invariant relativistic many-body perturbation theory approach [1] toconsistent calculation of the spectra for heavy and superheavy elements (isotopes) andhadronic atomic systems ions with an account of relativistic, correlation, nuclear,radiative effects is presented. Zeroth approximation is generated by the effective ab initio
model functional, constructed on the basis of the comprehensive gauge invariance QEDprocedure. The wave functions zeroth basis is found from the Klein-Gordon (pion atom)
or Dirac (kaon, hyperon) equation. The potential includes the core ab initio potential, theelectric and polarization potentials of a nucleus (the Gauss and Fermi models andrelativistic Dirac-Kohn-Sham approach for charge distribution in a nucleus are
considered). For superheavy ions the correlation corrections of high orders are accounted
for within the Green function method. The magnetic inter-electron interaction is
accounted for in the lowest order, the Lamb shift polarization part- in the Uhling-Serberapproximation and the self-energy part – within the Green functions method. We carriedout calculations :1).energy levels, hfs parameters for superheavy Li-like ions for different
models of the charge distribution in a nucleus and super heavy atoms Z=114-118; 3).
Shifts and widths of transitions (2p-1s,3d-2p, 4f-3d) in the pionic and kaonic atoms (He,U etc.). Further a new consistent unified quantum mechanics and QED approach isdeveloped and applied for description of the heavy ions collisions and heavy
quasimolecules. To calculate the collision cross-section and quasi-molecule energy
characteristics we use modified versions of the relativistic energy approach, based on the
S-matrix Gell-Mann and Low formalism, and operator perturbation theory approach [2].
The nuclear subsystem and electron subsystem has been considered as two parts of thecomplicated system, interacting with each other through the model potential. The nuclear
system dynamics has been treated within the Dirac equation with effective potential. The
calculation is carried out for the 238U+238U, 232Th+250Cf and 238U+248Cm systems anddiatomics with X112 , X114 atoms.
1. A.V.Glushkov, JETP Lett. 55 108 (1992), A.V.Glushkov, L.N.Ivanov, Phys.Lett.A. 170,
36 (1992); Preprint ISAN, Russian Acd.Sci., N-AS1-3, Troitsk-Moscow,1992;
A.V.Glushkov, In: Low Energy Antiproton Phys., AIP Serie.796, 206 (2005); Recent
Advances in Theory of Phys. and Chem. Systems (Springer), 15, 285-300 (2006);
2. A.V.Glushkov and L.N.Ivanov, J.Phys.B. 26, L379 (1993); Int. Journ. Quant.Chem. 99,
879 (2004); 105, 512 (2005); J.Phys.CS. 178, 188 (2005); 178, 199 (2005).

413