XVIth International Workshop on Quantum Systems in Chemistry and Physics 

Abstracts (Posters) 
FirstPrinciples Calculations of Hydrogen Impurities in Graphenes and Carbon Nanotubes 
Mohammad Shafiul Alam,^{1} Nyayu Siti Nurainun,^{1,2} Fahdzi Muttaqien,^{1,2} Agung Setiadi^{1,2} and Mineo Saito^{1,3}
^{1}Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology,Kanazawa University, Kakuma Kanazawa 9201192, Japan
^{2}Department of Computational Science, Bandung Institute of Technology, Indonesia
^{3}Collaborative Research Center for Frontier Simulation Software for Industrial Science, Institute of Industrial Science, University of Tokyo, 461 Komaba, Meguroku Tokyo 1538505, Japan

Carbon Nanomaterials have attracted much attention since they are candidates for postsilicon materials. Since hydrogen is a common impurity in graphene [13] and carbon nanotubes (CNT), it is important to clarify how the hydrogen impurity affects the electronic structure of graphene and carbon nanotubes.
Now we are going to study monohydrogen in graphene, CNT (5,5) and CNT (10,0). We perform spinpolarized generalized gradient approximation by using firstprinciples calculations. In the most stable structure of monohydrogen, the hydrogen atom is bonded to one of the carbon atom in the graphene sheet [Fig. 1(a)] and also hydrogen atom is located on the outer side of CNT (5,5) [Fig. 1(b)] and CNT (10,0) [Fig. 1(c)]. The bond lengths between the hydrogen atom and the nearest neighbor carbon atom are 1.14 Å, 1.12 Å and 1.12 Å for graphene, CNT (5,5) and CNT (10,0), respectively. These bond lengths are close to that in a CH_{4} molecule (1.09 Å), which is typical for sp^{3} CH bond lengths. In these three cases [Fig. 1] the spin polarized states are found to be most stable and the magnetic moments are 1 μ_{B}.
References:
[1] M. Khazaei et al. CARBON 47, 3306 (2009).
[2] A. Ranjbar et al. Phys. Rev. B. 82, 165446 (2010).
[3] E. J. Duplock et al. Phys. Rev. Lett. 92, 2255021 (2004).

Figure 1. Spin densities of the monohydrogen in the graphene, CNT (5,5) and CNT (10,0).



First principle theory for the material constants 
Marco Anelli, Dan Jonsson, Kenneth Ruud
Centre for Theoretical and Computational Chemistry, Department of
Chemistry, University of Tromsoe , 9037 Tromsoe , Norway 
The interactions between matter and electromagnetic fields are commonly analyzed using the constitutive relations,
which relate the applied electric and magnetic fields (E,B) to the response fields (D,H) through the material constants.
Therefore, material constants (also known as constitutive tensors) describe the response of the matter to the external fields.
In the case of a static perturbation, material constants are observable/measurable quantities, and they can been defined using multipole theory.
In contrast, when a dynamic field is considered, multipole theory leads to origindependent expressions for the material constants, and thus do not correspond to
physically acceptable observable quantities. There is therefore a need for originindependent definitions of the material constants.
Originindependent expressions of the material constants have been derived by Raab and de Lange applying a transformed multipole theory. They have also derived expressions for the material constants based on a covariant formulation of the constitutive relations. Both these theories provide expressions of the material constants
which are covariant, originindependent and preserve the spatial invariance of the wave equations. In the dynamic case, a unique definitions of the material constants still do not exist, and the possibility of deriving unique definitions for these quantities is still unresolved.
We will discuss our recent analysis of the problem, focusing on the pure electric and magnetic material constants, namely the electric permittivity and the inverse permeability. In particular, we will provide arguments in order to distinguish between the two possible definitions of the material constants proposed so far.
An important part of our analysis will be how to relate the material constants to wellknown measurable quantities. We propose that the absorption coefficient and the scattering amplitude, as defined in QED, can be expressed in terms of the electric permittivity, consistently with the definition provided by transformed multipole theory.


The potential energy surface of Li_{2}^{+}(X^{2}Σ_{g}^{+}) alkali dimer colliding with the Xe atom 
S. Saidi^{1}, C. Ghanmi^{1}, F. Hassen^{2} and H. Berriche^{*1,3}
^{1}Laboratoire de Physique et Chimie des Interfaces, Département de Physique, Faculté des Sciences de Monastir, Avenue de l’Environnement, 5019 Monastir, Tunisia.
^{2}Laboratoire de Physique des Semiconducteurs et des Composants Electroniques, Faculté des Sciences, Avenue de l’environnement, 5019 Monastir, Tunisie
^{3}Physics Department, College of Science, King Khalid University, P. O. Box 9004, Abha, Saudi Arabia
^{*}Corresponding author: hamid.berriche@fsm.rnu.tn, hamidberriche@yahoo.fr

The potential energy surface describing the collision between Li_{2}^{+}(X^{2}Σ_{g}^{+}) alkali dimer and the Xenon atom have been calculated for the equilibrium distance of the Li_{2}^{+}(X^{2}Σ_{g}^{+}) and for an extensive range of the two Jacobi coordinates, R and γ. We have used an ab initio approach based on nonempirical pseudopotential and a parametrized ldependent polarization potential [1]. The corecore interactions for Li^{+}Xe is included using the (CCSD(T)) accurate potential of Lozeille et al [2]. This numerical potential is interpolated using the analytical form of Tang and Toennies [3] for a better description of the interactions at intermediate and large distances between Li+ and Xe. This technique has reduced the number of active electrons of Li_{2}^{+}(X^{2}Σ_{g}^{+})Xe system to only one active electron. The ThreeBody interactions are also considered in this calculation and an analytical fitting of the potential energy surface has been realized. To our knowledge, there are neither experimental nor theoretical studies on the collision between the Li_{2}^{+}(X^{2}Σ_{g}^{+}) alkali ionic molecule and the Xenon atom. Therefore, our results are presented here for the first time. In addition the analytical potential energy surface will be used to investigate solvation of Li_{2}^{+} ionic alkali molecule in Xenon small clusters.
References
[1] Ph. Durand and J. C. Barthelat, theorit. Chim. Acta. 38 (1979) 283.
[2] Lozeille et al, Phys. Chem. Chem. Phys. 4 (2002) 3601)
[3] K. T. Tang and J. P. Toennies, J. Chem. Phys. 80 (1984) 3726.


Solvation of Li_{2}^{+}(X^{2}Σ_{g}^{+}) in small Xe_{n} clusters: structure and stability 
S. Saidi^{a}, C. Ghanmi^{a}, F. Hassen^{b} and H. Berriche^{*a,c}
^{a}Laboratoire de Physique et Chimie des Interfaces, Faculté des sciences, Université de de Monastir, Avenue de l’Environnement, 5019 Monastir, Tunisie
^{b}Laboratoire de Physique des Semiconducteurs et des Composants Electroniques, Faculté des Sciences, Avenue de l’environnement, 5019 Monastir, Tunisie
^{c}Physics Department, College of Science, King Khalid University, P. O. B. 9004, Abha, Saudi Arabia
^{*}Email address: hamidberriche@yahoo.fr 
The structure and geometries of the small Li_{2}^{+}(X^{2}Σ_{g}^{+})Xe_{n} clusters taken in different geometries with special symmetry groups, are examined. A oneelectron pseudopotential approach is used to generate the potential energy surface of the Li_{2}^{+}Xe triatomic system for a fixed distance between the two Li alkali atoms (the Li_{2}^{+} equilibrium distance) and for different angles and distances between the Xenon and the Li_{2}^{+} center of mass. In this approach, the effect of the Li+ core and the electronXe interactions are replaced by effective potentials. This has permitted to reduce the number of active electrons of the triatomic system to only one valence electron. In addition, the Li_{2}^{+}Xe interactions are introduced using an analytical form to describe the collision between the alkali ionic dimer and the Xe atom. However, a LennardJones form is used for the XeXe interactions and then included in the total potential energy surface describing the Li_{2}^{+}Xe_{n} cluster. The optimized and stable geometries are performed using the MonteCarlo Bassin Hoping method. This study has shown that the optimal structures correspond to those where Xenon atoms are aggregated on one or both ends of Li_{2}^{+} dimer.
Key words: Pseudopotential, Microsolvation of clusters, MonteCarlo, Structure, 

Examining the Limits of Physical Theory:
Analytical Principles and Logical Implications

Erkki J. Brändas
Department of Physical and Analytical Chemistry
Quantum Chemistr
Uppsala University
SE751 20 Uppsala, Sweden

Our aim is to examine the characteristics and the rationale for developing an analytic foundation for rigorous extensions of quantum mechanics beyond its longestablished domain in physics, chemistry and biology. Paradoxical and inconsistent issues related to the various attempts to apply microscopic organization to derive scientific laws in the macroworld are considered. The theoretical framework is augmented with quantum logical principles via a reformulation of Gödel’s theorems. We arrange the assemblage of the mathematical ideas as follows. First we give a detailed examination of the second order differential equation with respect to specific boundary conditions and associated spectral expansions, followed by a description in terms of general complex symmetric representations exemplified and derived from dilation analytic transformations. Associated dynamical time scales are represented and investigated via the corresponding Dunford formula. Relevant applications are reviewed and compared with conventional scattering theory analysing the directive performance and stability of the method. The manifestation and generation of triangular Jordan block entities are derived and further investigated in thermally excited scattering environments of open dissipative systems. Illustrative applications to condensed and soft condensed matter are provided, and a surprising treatment is given to the Einstein laws of relativity. As a conclusion we emphasize the computational and model building advantages of a conceptual extension of quantum mechanics to rigorously incorporate universal complex resonance structures, their life times and associated localization properties. We also prove the appearance of nonconventional time evolution including the emergence of Jordan blocks in the propagator, which leads to the origin of socalled coherent dissipative structures derived via uniquely defined spatiotemporal neumatic units. This organization yields specific information bearing transformations, cf. the Gödel encoding system, which might connect developmental and building matters with functional issues within a biological framework at the same time providing background dependent features of both special and general relativity theory. 

Ab initio calculations of methane dimer interaction energies and
molecular dynamics simulation of fluid methane

Arvin HuangTe Li and Sheng D. Chao
Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan ROC.

Intermolecular interaction potentials of the methane dimers have been calculated for 12 symmetric conformations using the secondorder MøllerPlesset (MP2) perturbation theory and the coupledcluster with single and double and perturbative triple excitations (CCSD(T)) theory. With increasing basis size, a large basis set (augccpVTZ) is required to converge the binding energy at a chemical accuracy (~0.01 kcal/mol). Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The binding energy calculated and the equilibrium bond length using the CCSD(T) method are close to the results at the basis set limit. For molecular dynamics (MD) simulation, a 4site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. MD simulations using the ab initio PES show good agreement on both the atomwise radial distribution functions and the selfdiffusion coefficients over a wide range of experimental conditions. 

Ultrafast electronic motion in hydrogen molecular ion induced by a high power intense laser 
H. Mineo^{1} , Y. Teranishi^{2} , S.D. Chao^{1}, and S.H. Lin^{3,4}
^{1} Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan ROC
^{2} Department of Physics, National Chiao Tung University, Hsinchu 300, Taiwan
^{3} Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23166, Taipei 106, Taiwan ROC
^{4} Institute of Applied Chemistry, Institute of Molecular Science, ChiaoTung University, HsinChu, Taiwan ROC

In this report we show how to control the electronic localization in a molecular ion on attosecond time scale by high intense laser based on two different excitation mechanisms, i.e., one takes place during ionization, and the other one sequentially takes place after the ionization [1]. The electronic excited states of hydrogen molecular ion are created during the ionization by taking the configuration interaction (CI) mixing of neutral molecule into account. Photoionization process is calculated by the generalized KeldyshFaisalReiss (KFR) theory [2]. We detect ultrafast oscillatory electronic motion between two atoms in a hydrogen molecular ion due to the creation of excited states during the ionization.
[1] H. Mineo, Y. Teranishi, S.D. Chao, and S.H. Lin, CPL 499, 45 (2010).
[2] L. V. Keldysh, Sov. Phys. JETP 20, 1307 (1965); F. H. M. Faisal, J. Phys. B6, L89 (1973); H. R. Reiss, Phys. Rev. A22, 1786 (1980).


Valence XPS and Raman Spectral analysis of chitosan film modified by Kr^{+} ion beam bombardments by quantum chemical calculations 
K. Endo^{1}, H. Shinomiya^{1}, T. Ida^{2}, S. Shimada^{2},K. Takahashi^{1}, Y. Suzuki^{3}, H. Yajima^{1}
^{1}Center for Colloid and Interface Science, Tokyo University of Science, 13 Kagurazaka, Shinjukuku, Tokyo 1628601 Japan,
^{2}Laboratory of Theoretical Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 9201192, Japan,
^{3}Advanced Development and Supporting Center, RIKEN, 21 Hirosawa, Wako, Saitama, 3510198, Japan 
Valence Xray photoelectron and Raman spectra of chitosan film modified by Kr^{+} ion beam bombardments were analyzed from quantum chemical calculations. Experimental Raman spectra of the Kr^{+} ion bombarded film were foundout to be due to four component contributions of chitosan (Chito), diamondlike carbon (DLC), graphite carbon (GC) and amorphous carbon (AC). By considering the four components contribution, we performed depth profile assignments of nm and μm orders for the chitosan film in valence XPS and Raman experiments, respectively from MODFT hybrid calculations in GAUSSIAN 09 using the model molecules of the four components. Carbonizations of the film by Kr^{+} irradiation were obtained as Chito: DLC: AC : GC = 2:1:0.5:0.375 in the μm order from Raman shift spectral analysis, while they were determined as Chito: DLC: AC : GC = 2:1:1:2 in the nm order from valence XPS analysis.
References
[1] K. Takahashi, R. Shizume, K. Uchida, H. Yajima, J. Biorheol, 21,64(2009).
[2] S. Danielache, M. Mizuno, S. Shimada, K. Endo, T. Ida, K. Takaoka, E.Z. Kurmaev, Polym. J. 37,2129(2005).
[3] K. Tamura, K. Endo, Y. Takagi, K. Kato, D. Matsumoto, T. Ida, M. Mizuno, Y. Suzuki, K. Takahashi, K. Uchida, H. Yajima, J. Surf. Anal. 14, 344347(2008).
[4] Gaussian 09, Revision B.01, http://www.gaussian.com.


Valence XPS, IR,and C13 NMR Spectral analysisof 6 polymers by quantum chemical calculations 
Kazunaka Endo^{1}, Tomonori Ida^{2}, Shingo Shimada^{2}
^{1}Research Center for Colloid and Interface Science, Tokyo University of Science 13, Kagurazaka, Shinjukuku 1628601, Japan,
^{2}Laboratory of Theoretical Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 9201192, Japan 
Valence XPS, IR, and C13 NMR spectra of 6 polymers (PE, PS, PMMA, PET, Nylon6, PVC) have been analyzed by quantum chemical calculations using the polymer model oligomers from B3LYP/631G** basis calculations in GAUSSIAN 09. Simulated valence XPS, IR, and C13 NMR spectra of PS as an example are in good accordance with the experimental results.
References
[1] Gaussian 09, Revision B.01, http://www.gaussian.com.
[2] K. Endo, Y. Kaneda, H. Okada, D. P. Chong, P. Duffy, J. Phys. Chem.,100, 19455 (1996).
[3] Scott A.P., Radom L., J. Phys. Chem., 100, 16502 (1996). 

Second Hyperpolarizabilities of OpenShell Singlet Extended Metal Atom Chains (EMACs) 
Hitoshi Fukui,^{1} Yudai Inoue,^{1} Yasuteru Shigeta,^{1} Benoît Champagne^{2} and Masayoshi Nakano^{1}
^{1}Graduate School of Engineering Science, Osaka University, Japan
^{2}Laboratoire de Chimie Théorique, Facultés Universitaires NotreDame de la Paix (FUNDP), Belgium 
We have theoretically investigated openshell singlet molecules as a novel class of nonlinear optical (NLO) systems, and have revealed their structure−property relationship: singlet diradical systems with intermediate diradical characters (y) tend to exhibit larger second hyperpolarizabilities (γ) than pure diradical and closedshell systems [1,2]. In addition to organic compounds, polynuclear transition metal complexes are expected to show singlet multiradical nature due to the unpaired electrons in the metal dorbitals [3]. In particular, openshell singlet extended metal atom chains (SEMACs), which have metal−metal direct bonds between transition metal atoms are promising NLO candidates because of the extended d−d conjugation and the singlet multiradical characters originating from the interactions between the dorbitals, which can create dσ, dπ and dδ electron conjugation. In the present study, we theoretically investigate the multiradical characters of the dσ, dπ and dδ orbitals as well as the γ values of SEMACs of chromium(II) without ligands. We also analyze the contributions of these orbital electrons to γ [γ(dX), where X = σ, π or δ] in order to reveal relationships between the orbital symmetry, the multiradical character and the γ value.
[1] M. Nakano et al., J. Phys. Chem. A 109, 885 (2005).
[2] M. Nakano et al., J. Chem. Phys., 125, 074113 (2006); Phys. Rev. Lett., 99, 033011 (2007).
[3] H. Fukui et al., J. Phys. Chem. Lett. 10.1021/jz2007897 (2011). 

Laser ElectronGammaNuclear Spectroscopy of Atoms and Multicharged Ions and NEET Effects in Heavy Nuclei: Relativistic Energy Approach 
Alexander V. Glushkov,^{1,2} Olga Yu. Khetselius^{1} Svetlana Malinovskaya^{1} and Andrey A. Svinarenko^{1}
^{1}Odessa University, Odessa9, SE, Ukraine
^{2}ISAN, Russian Academy of Sciences, Troitsk, Moscow reg., Russia 
In the resonant process of nuclear excitation by electron transition (NEET) or electron capture (NEEC) an electron is captured into a bound atomic shell with the simultaneous excitation of the nucleus. The excited nucleus can then decay radiatively or by internal conversion. In the latter case, a resonant inelastic electron scattering on the nucleus occurs. Here we present consistent, relativistic approach to calculation of the probabilities of the different cooperative laser electrongammanuclear processes in atoms, ions, nuclei and resonant NEET (NEEC) processes in heavy nuclei, based on the relativistic density functional (DF) formalism and energy approach (Smatrix formalism of GellMann and Low) [2]. Decay and excitation probability is linked with the imaginary part of energy of the excited state for the “electron shell nucleusphotons” system. For radiate decays it is manifested as effect of retarding in interaction and selfaction and calculated within QED DFT theory [2]. We firstly present data about intensities of the electron satellites in gammaspectra of nuclei in the neutral (low lying transitions) and multicharged Oand Flike ions for isotopes 57Fe, 133Cs, 171Yb and discover a new effect of the giant increasing electron satellites intensities under transition from the neutral atoms to multicharged ions. We present new, more accurate data about NEET probabilities in the nuclei of 189Os, 197Au (with comparison with theoretical data by Tkalya and experimantal data of Argonne Nat.Lab. and Japan Synchrotron Centre [3]) and firstly for nuclei of 193Ir, 235U, 268Mt.
References:
[1]. L.N.Ivanov, V.S.Letokhov, JETP. 93, 396 (1987); A.V.Glushkov, L.Ivanov, Phys.Lett.A 170, 33 (1992); A.V.Glushkov, L.N.Ivanov, V.S.Letokhov, Preprint of ISAN N AS4, Troitsk, (1992); E.V.Tkalya, Phys.Rev.A.75, 022509 (2007); T.J. Burvenichm J.Evers, C.H.Keitel, Phys. Rev. C. 74, 044601 (2007) ; A.Shahbaz, C.Muller, A.Staudt, T.J.Burvenich, C.H.Keitel, Phys.Rev.Lett.98, 263901 (2007).
[2]. A.Glushkov et al, J.Phys.CS. 11, 188 (2005); 35, 425 (2005); Int.J.Quant.Chem. 104, 512, 562 (2005); 99, 889, 936 (2004); Europ.Phys.Journ. 160, 195 (2009); Phys.Scr.T135, 014022 (2009).
[3]. S.Kishimoto, Y.Yoda, Y.Kobayashi etal, Phys.Rev.C74, 031301 (2006); I. Ahmad, R.Dunfird, H.Esbensen etal, Phys.Rev.C61, 051304 (2000). 

Theoretical Study on the Redox Reaction of Azurin in Water Solvent 
Masashi Iwayama, Hiroaki Saito, Kazutomo Kawaguchi and Hidemi Nagao
Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Japan 
Metalloproteins including a transitionmetal ion in the active site have important characteristics such as the metabolism and the intracellular signaling in vivo. In metalloproteins, Azurin is a kind of blue copper protein containing a copper atom in the active site, and has been known to show the oxidationreduction reaction by charge transfer between the active sites of proteins in the solution. In this study, we carry out molecular dynamics simulations and the quantum mechanics calculations of the oxidized Azurin (Az(Ⅱ)) and reduced Azurin (Az(Ⅰ)) in water solvent to reveal the redox character of Azurin in water solvent. According to the BornHaber Cycle model, the free energy change of the solute molecule in solvent can be expressed as a summation of the free energy change of solute in gas phase and the difference of solvation free energies of the solute. From these results, we estimate of the redox potential of Azurin and compare with the experimental value. 

Calculation of Magnetic Properties and Spectroscopic Parameters of Manganese Clusters with Density Functional Theory Methods 
Keita Kanda, Toru Saito, Yasutaka Kitagawa, Takashi Kawakamai, Shushuke Yamanaka, Kizashi Yamaguchi and Mitsutaka Okumura
Graduate School of Science, Osaka University, Japan 
Many manganese complexes bridged by μoxo ligands are synthesized as model of the oxygenevolving complex (OEC) in Photosystem II. Catalytic cycle and oxidation states of Mn cluster in OEC is still unrevealed. Spectroscopic parameters for those model complex, especially hyperfine coupling constants (HFCs) measured by EPR suggest deep insight for electronic structure.
Many calculation of HFCs have been carried out with ab initio DFT methods, however, there is very few investigation of functional dependence. Today’s Density Functional Theory approximates exchangecorrelation terms, which may cause inaccurate spin density nearby nuclei. We have done benchmark calculations to check the accuracy of various functionals for HFC of several manganeseμoxo systems. In addition, the most reliable functional for estimations of sd exchange interactions was identified. 

Ab initio and density functional calculation of calcium binding sphingomyelin lipid molecules: A pin holder model approach 
Hiroyuki Kawabe^{1} and Kimikazu Sugimori^{2}
^{1}Department of Social Work, Faculty of Social Work, Kinjo University, Japan
^{2}Department of Physical Therapy, Faculty of Health Sciences, Kinjo University, Japan 
One of the phospholipids, sphingomyelin (SM, Nacylsphingosine1phosphorylcholine) is the most abundant component of mammalian membranes in brain and nervous tissues. It plays an important role for apoptosis, aging, signal transduction with cations. Recently, Yappert and coworkers have shown that human lens sphingomyelin and its hydrogenated derivative, dihydrosphingomyelin (DHSM) are interacted with Ca^{2+} ions to develop human cataracts [1,2]. Previously we have investigated conformational differences between an isolated SM / DHSM molecule and Ca^{2+} coordinated form by using density functional theory (DFT) which B3LYP functional and 631G(d,p) doublezeta splitvalence basis set is applied for geometry optimization and normal mode analysis. As a result, one of conformers of SMs has hydrogen bonding between hydroxyl group and phosphate group, whereas another conformer has hydrogen bonding between hydroxyl and phosphate amide group [3]. Moreover, ^{31}PNuclear Magnetic Resonance (NMR) shielding constants of the obtained conformers are investigated by using ab initio and DFT with gauge invariant atomic orbitals (NMRGIAO) calculations [4].
In this study, we apply previous results to dimer and trimer model of lipid molecules with Ca^{2+} and water molecules by quantum chemical calculations. We assume that tails of the lipids arbitrary fixed specific length in plasma membrane, like pin holder. Except for fixed tail groups, all of molecular structure of head group and solvated Ca^{2+} are fully optimized. We analyze potential energy surface (PES) with the fixed parameters that are length between tails of lipid and coordinate of Ca^{2+} approaching from outer region to phosphate.
References
[1] M. Rujoi, D. Borchman, D. B. Dupré, and M. C. Yappert, Biophys. J. 82 (2002) 30963104.
[2] M. C. Yappert and D. Borchman, Chem. Phys. Lipids 129 (2004) 120.
[3] K. Sugimori, H. Kawabe, H. Nagao and K. Nishikawa, Int. J. Quantum Chem. 108, 29352942 (2008). doi:10.1002/qua.21858
[4] K. Sugimori, H. Kawabe, H. Nagao, and K. Nishikawa, Int. J. Quantum Chem., 109 (2009) 36853693. doi:10.1002/qua.22404


Structural analysis of ligand binding mechanism of Hsp90 
Kazutomo Kawaguchi, Acep Purqon, Hiroaki Saito, Hidemi Nagao
Institute of Science and Engineering, Kanazawa University, Kanazawa 9201192 Japan 
Hsp90 is one of the molecular chaperones which protect their client proteins in the folding processes. Hsp90 usually forms a dimer and undergoes large conformational changes during its functional cycle. Binding and hydrolysis of ATP to ADP are required for these conformational changes. We performed molecular dynamics simulation of Hsp90 with ADP to elucidate molecular mechanisms of ligand binding process. The results of structural analysis of ligand binding process of Hsp90 will be presented and discussed through recent calculations. 

Blackbody, synchrotron radiation, bremsstrahlung and plasmon analyzed by Tsallis nonextensive entropy 
Jun Kawai, Abbas Alshehabi, Hiroyuki Iwasaki, Koretaka Yuge, Ágnes Nagy*
Kyoto University, Department of Materials Science and Engineering,
Sakyoku, Kyoto 6068501, Japan
*Debrecen University, H4010 Debrecen, Hungary

Manne Siegbahn once wrote that “the curve (bremsstrahlung from Xray tube) rises abruptly on the short wavelength side. In this respect the curve differs fundamentally from the curve for the radiation of a ‘black’ body, though otherwise the curves have an external resemblance”[1]. Blackbody and bremsstrahlung or synchrotron radiation are similar in their overall spectral shape but a minor difference exists [24]. The Planck’s blackbody equation is expressed through the Tsallis nonextensive entropy [5]: N(E)=1/[(1+(q1)x)^{1/(q1)}1], where N is the number of photons, x=E/kT, and q the Tsallis parameter [6,7]. When q>1 , the above equation becomes Plank’s blackbody equation. We have fitted Eqn.(1) to a synchrotron radiation (relativistic bremsstrahlung) and when q=1.05 the agreement is best and satisfactory as shown in Fig. 1. The parameter q >1 means the longrange correlation due to nonextensitivity. The blackbody is ideal gas of photons without interaction, but the photons are weakly interacting each other for the synchrotron radiation.
Similarly the plasmon energy loss peaks when Si is irradiated by e.g., 1500 eV electron beam, decays exponentially from the 1st loss to the higher orders. The deviation from the exponential decay is also expressed by the Tsallis q parameter, which indicate the intrinsic and extrinsic paths of the plasmon energy loss processes.
exp(E/kT)appears in physical chemistry, and the deviation from exponential could be interpreted by the long range interaction through the Tsallis parameter q.
References
[1] M. Siegbahn, “The Spectroscopy of XRays”, transl. G. A. Lindsay, Oxford Univ. Press, London, 1925, p. 206.
[2] J. Kawai, H. Ishii, Spectrochim. Acta, Part B, 60, 1586 (2005).
[3] J. Kawai, H. Ishii, Radiation Phys. Chem., 75, 1716 (2006).
[4] T. Tanigaki, J. Kawai, XRay Spectrom., 36, 321 (2007).
[5] C. Tsallis, Introduction to Nonextensive Statistical Mechanics, Springer (2009).
[6] Q. A. Wang, A. Le Mehaute, Phys. Lett. A, 242, 301 (1998).
[7] S. Martnez, F. Pennini, A. Plastino, C. J. Tessone, Physica A, 309, 85 (2002).


Figure 1. Comparison of synchrotron radiation (dotted)and blackbody radiation (solid line) with q=1.05.

Figure 2. Plasmon energy loss spectra.



Calculation of magnetic constants D in ZeroField Splitting by ab initio methods 
Takashi Kawakami, Keiji Kinoshita, Akira Ito, Yasutaka Kitagawa, Shusuke Yamanaka, Kizashi Yamaguchi, Mitsutaka Okumura
Graduate School of Science, Osaka University, Japan 
For theoretical treatments of ZFS parameters, previously Pederson and coworkers have developed a method calculating the ZFS parameters with the DFT methods. In the series of our studies, we developed new ab initio MO program package ("Q" by Ryo Takeda in our group). The Pederson's treatments are also included in this program. Thus, several ab initio MO methods can be applied to calculating zerofield splitting parameters caused by mainly spinorbit coupling. We examine the behavior and tendency of the method by applying it to some basic molecules such as small molecules (ex. carbene), pure organic molecular magnets, singlemolecular magnets (SMM), etc. It shows the method has good accuracy. We suggest applicable region of the method.
In addition, Neese has also developed another calculation scheme with coupledperturbed equation. This method is involved in their program package "ORCA". Thus, we also evaluated ZFS parameters by Neese's methods.


Free energy of cellpenetrating peptide in lipid bilayer membrane: coarsegrained simulation 
Shuhei Kawamoto^{1}, Takeshi Miyakawa^{2}, Masako Takasu^{2}, Ryota Morikawa^{2}, Tatsuki Oda^{1}, Hiroaki Saito^{1}, Shiroh Futaki^{3} and Hidemi Nagao^{1}
^{1}Graduate School of Natural Science and Technology, Kanazawa University
^{2}School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
^{3}Institute for Chemical Research, Kyoto University

Cellpenetrating peptides (CPPs) can permeate plasma membrane [1], and are useful for delivery of drugs and transfection of DNA. Free energy ΔG to insert a molecule into lipid bilayer membrane is important to investigate the permeability of the molecule through the membrane. ΔG of small molecules, such as water and oxygen, are obtained by allatom simulations [2] with cavity insertion method. However, large molecules, such as CPP, are difficult to insert into the cavity in lipid bilayer membrane.
We estimate ΔG of CPP by steered MD method with our coarsegrained model [3]. When there is large attractive potential between CPP and lipid heads, the CPP makes inverted micelle in the lipid bilayer membrane, and the difference of ΔG between water region and lipid bilayer region is more than 66 kBT. It suggests that the spontaneous permeation of CPPs needs large driving force to overcome the barrier.
[1] I. Nakase, T. Takeuchi, G. Tanaka, S. Futaki, Adv. Drug Deliv., 60, 598 (2008)
[2] K. Shinoda, W. Shinoda, T. Baba, M. Mikami, J. Chem. Phys., 121, 9648 (2004)
[3] S. Kawamoto, et al., J. Chem. Phys., 134 095103 (2011)


NuclearRelativistic ManyBody Perturbation Theory to Parity Nonconservation Effect in Heavy Atoms and Nuclei 
Olga Yu. Khetselius
Department of Mathematics, Odessa OSENU University, Odessa9, Ukraine 
During the past two decades, the nuclear and atomicoptical experiments to detect parity nonconservation (PNC) have progressed to the point where PNC amplitudes can be measured with accuracy on the level of a few percents in certain heavy atoms and significantly worse in some nuclei (Mossbauer spectroscopy). Nowadays the PNC in atoms has a potential to probe a new physics beyond the standard model. Promising idea (Forston) is to apply the techniques of laser cooling and ion trapping to measurement of the PNC in 6s^{2}S_{1/2}5d^{2}D_{3/2} transition of the Ba^{+}. In our paper we systematically apply the nuclearrelativistic manybody perturbation theory formalism [1] to precise studying PNC effect in heavy atoms with account for nuclear, correlation and QED corrections. There are determined the PNC radiative amplitudes for a set of nuclei (atoms): 133Cs, 137Ba^{+}, 173Yb with account of the exchangecorrelation, Breit, weak ee interactions, QED and nuclear (magnetic moment distribution, finite size, neutron skin) corrections, nuclearspin dependent corrections due to anapole moment, Zboson [(A_{n}V_{e}) current] exchange, hyperfineZ exchange [(V_{n}A_{e}) current]. The weak charge is found for 133Cs, 205Tl and 173Yb and comparison with Standard Model is done. Using the experimental value (E_{PNC}/b)= 39mV/cm (Tsigutkin et al, 2009) and our calculated amplitude value 9.707*10^{10} iea_{B}one could find for 173Yb (Z=70, N=103) the weak charge value Q_{W}=92.31 (the SM gives Q_{W}=95.44). The received data are compared with known earlier and recent results [1,2]. The role of the nuclear effects contribution (corepolarization contributions, which are induced by valent protons of a nucleus), spatial distribution of magnetization in a nucleus (the BohrWeisskopf effect), neutron skin correction and the nonaccounted high order QED corrections are analyzed.
References
[1] O.Khetselius, Phys.Scripta T34, 014023 (2009); Int.J.Quant.Chem. 109, 3330 (2009); A.V.Glushkov, O.Khetselius etal, Frontiers in Quantum Systems in Chem. and Phys. (Springer) 18, 505 (2008).
[2] W. Johnson, M.S.Safronova, U.I.Safronova, Phys.Rev. A69, 062106 (2003); V.V.Flambaum, J.S.Ginges, Phys.Rev. A72, 052115 (2005).


Computational study of conformational preferences in intermediates and transition states of the hydrolysis of dimethyl phosphate 
Makoto Kita,^{1} Haruki Nakamura^{1} and Yu Takano^{1}
^{1}Institute for Protein Research, Osaka University, Japan

Phosphate diester is a basic structure in DNA and RNA. Hydrolysis mechanism of phosphate diester is important for understanding decomposition reaction of nucleic acid.
In this study, we have explored the hydrolysis reaction pathway of dimethyl phosphate, which is the simplest phosphate diester, with two nucleophiles (hydroxide and water), using the density functional theory (B3LYP/6311++G(2d,2p)) with PCM (polarizablecontinuum model). Since it was reported that the conformations of intermediates and transition states influence the reaction mechanism of transacylation of methyl acetate with methoxide [1], we focused on the conformational preferences in the hydrolysis reaction. The computed reaction pathway was confirmed by IRC (intrinsic reaction coordinate) calculation.
In hydrolysis of dimethyl phosphate with hydroxide, a concerted reaction pathway was obtained in the gas phase, whereas a stepwise reaction pathway was obtained in the aqueous phase. In the gas phase, the conformation of the transition state was different from that of the earlier study [2], but the reaction mechanism was similar to each other. The conformations hardly influence the energetics of the gasphase hydrolysis of dimethyl phosphate. On the other hand, in the aqueous phase, the reaction pathway and the activation and reaction energies were very different from those of the earlier study [2], due to the differences in the computational procedure.
We have also explored the reaction mechanism of the hydrolysis of dimethyl phosphate with water. In the gas phase, the most stable conformation of the reactant (conf1) changed to the other conformation (conf2). The reaction proceeded with conf2, and the stepwise reaction pathway was obtained. This is because the activation energy of the hydrolysis of conf2 is lower than that of conf1, and because the activation energy of conformational change from conf1 to conf2 is as low as 2.2 kcal/mol. In the aqueous phase, the proton transfer, the first step of hydrolysis, did not occur, implying that the hydrolysis occurs by a proton shuttle mechanism.
References
[1] Takano, Y.; Houk, N. K. J. Phys. Chem. A 2004, 108(52), 1174011751.
[2] Ribeiro, J. M. A.; Ramos, J. M.; Fernandes, A. P. J. Chem. Theory Comput. 2010, 6(8), 22812292.


The band 12 issue of norbornane: a comparison between symmetry adapted cluster expansion configuration interaction (SACCI) and the third order algebraic diagrammatic construction scheme [ADC(3)] 
S. Knippenberg^{1} and B. Hajgató
^{1} Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, B7000 Mons, Belgium
^{2} Eenheid Algemene Chemie, Vrije Universiteit Brussel (VUB), Faculteit Wetenschappen, Pleinlaan 2, 1050 Brussels, Belgium 
In line with a recent study of the electronic structure of the cage compound norbornane [1, 2], symmetry adapted cluster expansion configuration interaction (SACCI) general R calculations have been performed and compared with results obtained by the third order algebraic diagrammatic construction scheme [ADC(3)]. Comparison has been made with previously performed electron momentum spectroscopy (EMS) and ultra violet photoelectron measurements. The region around 25 eV (band 12), characterized by an elaborated band in the EMS spectrum which is missing in previous Green's function and ADC calculations, is investigated. This study is completed with outervalence Green's function (OVGF) and SACCI/SDR calculations. Since ADC(3) only includes 2h1p shakeup states, while SACCI generalR also includes higher order ones, the agreement between both methods assures that the higher order shakeup states do not play an important role in the ionization spectra of norbornane. The band12 issue of norbornane is therefore still open, while a tentative description in terms of ultrafast nuclear dynamical effects and autoionization processes has become more plausible.
[1] S. Knippenberg, K. L. Nixon, M. J. Brunger, T. Maddern, L. Campbell, N. Trout, F. Wang, W. R. Newell, M. S. Deleuze, J.P. François, D. A. Winkler, J. Chem. Phys. 121 (2004), 10525.
[2] S. Knippenberg, M. S. Deleuze, T. J. Cleij, J.P. François, L. S. Cederbaum, J. H. D. Eland, J. Phys. Chem. A 109 (2005), 4267.


Analysis for constructing protein nanofiber including metal ions

Yu Komatsu,^{1} Shuhei Kawamoto,^{2} Takeshi Miyakawa,^{1} Ryota Morikawa,^{1} Masako Takasu,^{1} Satoshi Akanuma^{1} and Akihiko Yamagishi^{1}
^{1}School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Japan
^{2}Graduate School of Natural Science & Technology, Kanazawa University, Japan 
As materials used in nanotechnology, proteins can be applied to many fields. Our aim is to fabricate a nanofiber using arbitrary proteins as maintaining their native structures. By inducing mutations in the adaptor proteins, hydrophobic and electrostatic interaction can be modified. By means of mixing the two proteins, the fiber may be organized spontaneously. As the materials of nanofiber formation, we are testing three proteins: LARFH, Sulerythrin and IPMDH.
In this research, we analyzed the three proteins which are candidates for constructing a nanofiber and investigated conditions that show high stability using molecular dynamics (MD). Sulerythrin contains two pairs of Zn^{2}+ and Fe^{2+}. We perform quantum calculation to investigate how these ions affect the stability as a fiber by quantum computing. Moreover, we perform umbrella sampling simulations to obtain PMF (Potential of Mean Force), from which binding energy Δ G_{bind} is calculated.
References
［1］S. Akanuma et al., J. Biochem, 147, 371 (2010)
［2］J. A. Lemkul et al., J. Phys. Chem. B, 114, 1652 (2010)


General Coalescence Conditions for the Exact Wave Functions 
Yusaku I. Kurokawa, Hiroyuki Nakashima, and Hiroshi Nakatsuji
Quantum Chemistry Research Institute, JST, CREST, Kyodai Katsura Venture Plaza 106, Goryo Oohara 136, Nishikyoku, Kyoto 6158245, Japan 
We derived necessary conditions for exact wave functions of the timeindependent Schrödinger equation that must be satisfied at a coalescence (or cusp) region. Some of such conditions are already known as the Kato's cusp conditions (CC) [1] and Rassolov and Chipman's CC [2]. In this study, we have generalized them to be relations among higher order derivatives of wave functions. Furthermore, we have extended them to be applicable not only to the Coulombic system but also to any systems where the interaction between two particles is represented in power series of interparticle distance. We named these conditions to be General Coalescence Conditions (GCCs). Any wave functions must satisfy GCCs; otherwise they never become exact. The Kato's CC and Rassolov and Chipman's CC are included in GCCs as special cases.
We applied the Free Complement (FC) wave functions [3] (which is nearly exact) of the hydrogen atom in the ground and excited states, the harmonic oscillator, a system with interacting potential of V = r, and the helium atom to GCCs and confirmed that the FC wave functions satisfy GCCs.
[1] T. Kato, Commun. Pure Appl. Math. 10, 151 (1957).
[2] V. A. Rassolov and D. M. Chipman, J. Chem. Phys. 104 (24), 9908 (1996).
[3] H. Nakatsuji, Phys. Rev. Lett. 93 (3), 030403 (2004); H. Nakatsuji, Phys. Rev. A 72 (6), 062110 (2005).


Laser ElectronGammaNuclear Spectroscopy of Diatomic and Multiatomic Molecules 
Svetlana V. Malinovskaya,^{1} and Andrey A. Svinarenko^{2}
^{1}Department of Chemistry, Odessa University, Odessa9, Ukraine
^{2}Department of Mathematics, Odessa University, Odessa9, Ukraine 
An important class of problems connected with modelling the cooperative laserelectrongammanuclear phenomena in diatomic and multiatomic molecules [1,2] is now of a great interest. It includes a calculation of the probabilities and energies of the mixed gammanuclear and optical quantum transitions in molecules, intensities of the complicated gammatransitions due to the changing of the molecular excited states because of the gamma nuclear transition. We present a consistent, quantum approach to calculation of the probabilities of the different cooperative laser electrongammanuclear processes in different molecules [2] (including the set of electron or vibrationrotational satellites of the gammanuclear spectrum). The calculation results for the electrongammanuclear transition probabilities in the diatomic (the nucleus 127I with E=203keV in molecule of H^{127}I) and vibrationnuclear transition probabilities for some threeatomic XY_{2}, fiveatomic XY_{4} molecules are given. In particular, we present the results of calculation for the vibrationnuclear transition probabilities in a case of the emission and absorption spectrum of nucleus 188Os (E=155 keV) in the molecule of OsO_{4} and nucleus 191Ir (E=82 keV) in the molecule IrO_{4}.
References:
[1]. V.S.Letokhov, V.Minogin, JETP. 69, 1369 (1975); A.Glushkov, L.Ivanov, Phys.Lett.A 170, 33 (1992); A.Glushkov, L.N.Ivanov, V.S.Letokhov, Preprint of ISAN N AS4, MoscowTroitsk, (1991);
[2]. A.Glushkov, S.Malinovskaya, O.Khetselius, Europ.Phys.Journ. T160, 195 (2009); Molec.Phys.(UK) 108, 1257 (2008); Int.J. Quant. Chem. 104, 496 (2005); Frontiers in Quantum Systems in Chem. and Phys. (Springer) 18, 523 (2008).


From Koopmans to accurate estimates of molecular core ionization energies
through parameterized allometric scaling 
Jean Maruani and Christiane Bonnelle
Laboratoire de Chimie Physique  Matière et Rayonnement
11, rue Pierre et Marie Curie  75005 Paris, France 


Spin Catalysis of Dioxygen Activation by Enzymes 
Boris Minaev,^{1,2} Valentina Minaeva^{1} and Hans Agren^{2}
^{1}Department of Chemistry, Bogdan Khmelnitskij National University, Cherkasy, Ukraine
^{2}Department of Theoretical Chemistry, Institute of Biotechnology, Royal Institute of Technology, Stockholm, Sweden 
In stable organic substances all electron spins are paired and molecules have the singlet ground state. In order to activate chemical transformations and cleave the chemical bond one has to produce spin uncoupling. Interaction with collision partner in bimolecular reactions of diamagnetic species usually leads to activation barrier produced by avoided crossing of the closed shell reactant state and the doublytriplet excited singlet state. In order to lower the barrier one can add new nonpaired electrons to the reacting system or induce spin flip for enhancement of the intersystem crossing to the singlyexcited triplet state. This can be done by exchange interaction with paramagnetic transition metal, or by internal (spinorbit coupling) and external magnetic fields. This is the key idea behind spincatalysis [17].
Activation barriers in chemical reactions are determined by the exchange repulsion between molecules in the singlet ground states. The barriers are often getting much lower when, at least, two spins are unpaired, thus when the singlettriplet transition occurs. Chemical reactivity is often coded by the triplet excited state of the molecule, in which two spins are unpaired (because exchange interaction destabilizes chemical bond in this case). Enzymatic reactions in live matter are so efficient because they often involve strong spin uncoupling induced by transition metals. This is especially important for O_{2} (dioxygen) production by photosynthesis of green plants and for dioxygen consumption by respiration of mammals.
Molecular oxygen is a vital elixir beneath the sun. Lavoisier had established that dioxygen is essential for aerobic life and is the oxidant for combustion of organic fuels. But the main puzzle of molecular oxygen is still unclear in modern biochemistry: the O_{2} molecule has a triplet ground state and how it can react with stable organic substances at 36.7 C to produce water and CO_{2} if the processes are spinforbidden? These transformations are equivalent to combustion in the net energetic and material balance. Combustion is a radical chain process. In order to burn a fuel one needs to produce a spark (to create first radical). The radical can interact with triplet O_{2} and create new radical (the brunch chain reaction). In mammals the organic food is not burned by radical chain process, since the temperature is lower than in the fire. Though the oxidation of food produces enough energy for life, the reactions are spinforbidden and can be activated and controlled by oxidase enzymes. This should involve particular spin catalysis: the strictly controlled TS transition in the enzyme active site with low activation energy, which does not produce any radicals, but only shortlived biradical intermediate. The TS transition means the subsequent spin flip in the biradical.
We present DFT calculations of the electronic structure, zerofield splitting (ZFS) and the phosphorescence spectra of biopolymers that contain chromophores being excited to the triplet state (porphyrin systems, chlorophylls and bacteriochlorophylls, aromatic amino acids, polypeptides and proteins, riboflavin, FAD, FADH_{2}, nicotinamide, NAD^{+}, NADH and active centers of glucose oxidase, copper amine oxidase, hemoglobin, horsereddish peroxidase and cytochrome P450). This is used for better understanding of the role of spectra in structural analysis of biopolymers and also for predictions of spin catalysis models in electron transfer and oxygen activation processes in these biosystems. The spin transitions are important for enzymatic reactions with and without paramagnetic transition metal involvement. Both types of spin catalysis are studied by DFT calculations of reaction models.
Our experience in fine structure calculations and spinselective photoprocesses in ZFS triplet states helps us to consider the influence of external magnetic field on the TS transitions in dark enzymatic reactions. Analysis of possible magnetic field effects on bioprocesses, including birds navigation in the Earth field, is also presented.
1. B.F. Minaev. Electronic mechanisms of molecular oxygen activation. Rus. Chem. Rev., 76 (2007) 9981023.
2. B.F. Minaev, V.A. Minaeva. Spindependent binding of dioxygen to heme. Ukrainica Bioorganica Acta,2 (2008) 5664.
3. B.F. Minaev. Solvent induced emission of singlet oxygen. J. Mol. Struct. (Theochem), 183 (1989) 207214.
4. B.F. Minaev. Intensities of spinforbidden transitions in molecular oxygen and selective heavyatom effects. Int. J. Quant. Chem., 17 (1980) 367374.
5. R. Prabhakar, P. Siegbahn, B.F. Minaev, H. Agren. Activation of dioxygen by glucose oxidase. J. Phys. Chem., B, 106 (2002) 37423750.
6. B.F. Minaev. Spin effects in reductive activation of O_{2} by oxidases. RIKEN Rev., 44 (2002) 147149.
7. B.F. Minaev, H. Agren. Spin catalysis phenomena. Int. J. Quant. Chem., 57 (1996) 510525. 

Intermonomer Interaction Effect on the Electromagnetically Induced Transparency on Molecular Aggregate Model 
Takuya Minami and Masayoshi Nakano
Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 5608531, Japan 
The intermonomer interaction effect on the electromagnetically induced transparency (EIT) for a dipolecoupled dimer model is investigated. The absorption properties are evaluated based on the imaginary part of the dynamic polarizability α using the quantum master equation approach [1]. In order to investigate the intermonomer interaction effect on the EIT, several orientations and intermonomer distances are examined. We have found that the EIT can be observed even in the presence of neardegenerete excitation states induced by the intermonomer interaction through an adjustment of the incident field frequency.
[1] M. Nakano et al., J. Phys. Chem. A 105, 22, 5473 (2001); T. Minami et al., J. Phys. Chem. C 114, 13, 60676076 (2010).


The potentials of the atoms around Mg^{2+} in the Hras GTP complex and in the Hras GDP complex 
Takeshi Miyakawa,^{1} Ryota Morikawa^{1}, Masako Takasu^{1}, Kimikazu Sugimori^{2}, Kazutomo Kawaguchi^{3}, Hiroaki Saito^{3} and Hidemi Nagao^{3}
^{1}School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Japan
^{2}Department of Physical Therapy, Kinjo University, Japan
^{3}Institute of Science and Engineering, Kanazawa University, Japan

In the Hras GTP complex and the Hras GDP complex, the coordination bonds between Mg^{2+} and oxygen atoms are very important. We derived the potentials of atoms around Mg^{2+} in Hras GTP complex and in the Hras GDP complex by quantum chemical calculations in order to modify the AMBER fields ff03.
Because it is not clear if SER17 and THR35 have OH group around Mg^{2+}, we consider two candidate subsystems. In one system, SER17 and THR35 have OH group, although in the other system, SER17 and THR35 have O instead of OH group. The details will be shown at the presentation.


Validation of quantum chemical methods for geometrical optimizations of sulfonamide derivatives 
Akifumi Oda,^{1,2} Yu Takano^{2} and Ohgi Takahashi^{1}
^{1}Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, Japan
^{2}Institute for Protein Research, Osaka University, Japan 
Sulfonamide is one of the most important chemical groups in drug design because sulfonamide derivatives are stable in living cells and watersoluble. In this study, we assessed the validity of quantum chemical methods and basis sets for the geometrical parameters of various sulfonamides compared to crystallographic data. Introducing ftype polarization functions into basis sets improved the geometry optimizations using HartreeFock, MP2, and B3LYP, indicating that ftype polarization functions play an important role in the description of chemical bonds in sulfonamide derivatives. 

Theoretical investigation of the heterojunction effect in polymer stabilized precious metal clsuters 
Mitsutaka Okumura,^{1,2} Yasutaka Kitagawa,^{1} Takashi Kawakamai,^{1}and Shushuke Yamanaka^{1}
^{1}Department of Chemistry, Graduate School of Science, Osaka University, Japan
^{2}Core Research for Evaluational Science and Technology, Japan 
In recent years, gold is attracting industrial and scientific interests for its catalytic activity in such reactions as propylene partial oxidation, odor decomposition H2O2 direct production and CO oxidation at low temperatures, especially when Au is deposited as nanoparticles on selected metal oxides. Highly dispersed gold catalysts exhibit unique catalytic features in lowtemperature CO oxidation. In this reaction, the use of oxides of several 3d transition metals and the hydroxides of alkaline earth metals as supports leads to high activities even at a temperature as low as 203 K.
Lately, Tsukuda has found that the Au nanoclusters stabilized by poly(NVinyl2pyrrolidone) [PVP; (C_{6}H_{9}ON)_{n}] , abbreviated as Au:PVP, can oxidize phydroxybenzyl alcohol selectively into the corresponding aldehyde in water without degradation.
This observation indicates that Au cluster can exhibit high catalytic activity without any metal oxide supports. Therefore, the interaction (heterojunction) between Au cluster and PVP seems to be an important factor to oxidize benzylic alcohols to the corresponding aldehyde over the Au:PVP catalyst.
These results suggest that the heterojunctions, such as metal clustersupport junctions in heterogeneous catalysts, metalligands junctions in metal complex, active sites in enzymes, metal clusterstabilizer junction in the polymer stabilized clusters and etc., are the key factors to promote and/or modify the catalytic reaction over several types of catalysts. Therefore, we have carried out hybrid density functional theory (DFT) calculations on the heterojunction effect between Au clusters and PVP. The present theoretical study has been undertaken to explain the heterojunction effect between PVP molecules and Au clusters as a first step for understanding the heterojunction effect of the catalytic reactions over the polymer stabilized Au nanoclusters.


Origin of the variety of the Cu_{2}S_{2} core structure of the Cu_{A} sites: a density functional theory study 
Orio Okuyama^{1}, Yasuteru Shigeta^{1,2}, Haruki Nakamura^{1}, and Yu Takano^{1}
^{1}Institute for Protein Research, Osaka University, Japan
^{2}Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Japan 
The Cu_{A} site, a proximate electrontransfer intermediate from an electron source, is contained both in cytochrome c oxidase (C cO), the terminal electron acceptor in aerobic respiration, and in nitrous oxide reductase (N_{2}OR), the terminal acceptor in anaerobic respiration. The Cu_{A} site is a binuclear copper site with two bridging cystenyl thiolate groups. Each copper ion is coordinated by a histidine side chain and a methionine side chain or a carbonyl oxygen of the backbone.
Spectroscopic studies have suggested the σ_{u}* ground state of the oxidized Cu_{A} site is due to the direct Cu–Cu interaction, facilitating a rapid electron transfer over long distances with low driving forces. We have shown that the ground state of the Cu_{2}S_{2} core is the πu state even with a shorter Cu–Cu distance in the oxidized state, and that a combination of electrostatic and orbital interactions is required to stabilized the σ_{u}* state of the Cu_{2}S_{2} core rather than the π_{u} state [1].
High resolution Xray crystal structures of the Cu_{A} sites in several proteins have so far been reported. The threedimensional structures of the Cu_{2}S_{2} core of the Cu_{A} sites show various Cu–Cu or S–S distances, 2.35–2.59 Å for the Cu–Cu distance and 3.76–4.24 Å for the S–S distance. In order to elucidate the origin of the variety of the Cu_{2}S_{2} core structure of several Cu_{A} sites, we have examined electronic structures of the Cu_{2}S_{2} core of the Cu_{A} sites, using the density functional theory (DFT) with Gaussian09 program.
We built models from 10 types of C cO (PDB ID: 1V54, 1V55, 2CUA, 2GSM, 2DYR, 2EIJ, 3ABK, 3ABM, 3AG2, 3AG3), 3 types of N_{2}OR (PDB ID: 1FWX, 2IWF, 2IWK), and an engineered CuA azurin (PDB ID: 1CC3). DFT calculations were performed using the exchangecorrelation functional, M06, because the M06 functional reproduces the energy difference of the Cu_{2}S_{2} core between the σ_{u}* and πu states at the CCSD(T) level of theory. Wachters+f basis set was used for copper ions and the other atoms were treated with 6311G++(df,pd) basis set.
[1] Y. Takano, Y. Shigeta, K. Koizumi, H. Nakamura, Int. J. Quantum Chem. in press. 

Structure and dynamics of glutathione and glutathionetransferaseT22: a molecular dynamics study 
Yuriko Omae, Hiroaki Saito, Kazutomo Kawaguchi and Hidemi Nagao
Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University 
Glutathione is an antioxidant concerned with the detoxification metabolism in vivo and has a function to defecate toxic compounds from cells. Glutathione transferase has been known to reduce the reactivity of toxic compounds by catalyzing their conjugation with glutathione. The function of glutathione and glutathione transferase has been through to implicate in detoxification. Thus, the understanding of the binding character between the glutathione and glutathione transferase should be important in the realization of catalytic reaction mechanism and contribute the development of antibiotic drug. In this study, we carry out the molecular dynamics simulation of glutathione transferase T22 in the presence and absence of glutathione in water solvent to analyze the dynamical structure of binding site of the ligandprotein complexes. We calculate the binding energy of the glutathione by these simulations. The specific interactions, which contribute to the binding stability of the ligand molecule, between the glutathione and glutathione transferase T22 are shown in detail by these analyses. 

Determination of Atomic Charges in Molecules and Ions 
Valentin Oshchapovsky
Lviv State University of Vital Activity Safety
35 Kleparivska Str., Lviv, 79007, Ukraine

A new method of calculation of the lattice energy of binary ionic crystals of MX type was developed [1]. It enabled to deduce a new universal formula for the lattice energy calculation taking into account only ion radii values without introducing any additional arbitrary factors. It is pointed out that the exactness of Ulat calculation depends upon the ionnity bond degree [1].
The abovementioned allowed deducting an equation for a priori calculation of the length of interatomic distances in crystals and gaseous molecules assuming that all the bonds are of pure ionic type [2].
Furthermore, the equation for the calculation of ion radii with an arbitrary effective charge was deduced [3]. The ion radii in the binary nonpolar molecules of halogens, chalcogens etc. were calculated: e.g., R^{IV}(F^{+}) = 0.255 Å, R^{IV}(Br^{+}) = 0.918 Å, R^{IV}(At^{+}) = 1.147 Å .
On the basis of these values, during the use of the previously received equation for a priori determination of interatomic distances [2] there were calculated R_{12} values for the large group of molecules of different type: halogens, interhalogenides, chalcogens, nitrogens and their combinations. It allowed to solve a reverse side of the problem i.e., to estimate the atomic charges of the large group of binary gaseous molecules according to the value of internuclear distance: Î_{2} (O^{1.92+}O^{1.92–}), ÑÎ (C^{1.76+}C^{1.76–}), CO_{2} (C^{3.68+}O^{1.84–}), N_{2} (N^{2.69+}N^{2.69–}), NO (N^{1.87+}O^{1.87–}), NO_{2} (N^{3.83+}O^{1.915–}).
Considering the experimental R12 values there were also calculated the values of atomic charges in the ionized molecules, e.g. Î_{2}^{+} (O^{2.87+}O^{1.87–}) and Î_{2}^{–} (O^{0.97+}O^{1.97–}). The radius of He^{+} ion was calculated. The possibility of estimation of ion coordination, bond multiplicity as well as some correction of ion radii R sizes is shown.
1. Oshchapovskii V.V. Russian J. of General Chemistry, 2008, V.78, No. 4, p.532542.
2. Oshchapovskii V.V. Russian J. of Inorganic Chemistry, 2010, V.55, No. 3, p. 401409.
3. Oshchapovskii V.V. Russian J. of Inorganic Chemistry (in press).


Electronic structure calculations on vacancymanganese center in nanodiamond systems 
Takao Otsuka,^{1} Yoshitaka Tateyama,^{2,3} Masahito Morita,^{4} Makoto Taiji^{1}
^{1}RIKEN Quantitative Biology Center (QBiC), Kobe, Hyogo, Japan
^{2}International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, Japan
^{3}CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
^{4}WPI Immunology Frontier Research Center (iFReC), Osaka University, Suita, Osaka, Japan

We present our theoretical study on vacancymanganese center in nanodiamond systems by electronic structure calculations. We investigate the stability of spin states in some vacancymanganese complexes in nanodiamond by using cluster models calculations. From the analysis of electronic structures by density functional theory (DFT) and HartreeFock with the perturbative correction calculation (with unrestricted/restricted openshell), we found that the high spin state of [VMnV] complex is most probable among different spin states and defect types. The results on the surface oxidation systems will be also reported. 

Calculation of Energy Deposition by Swift Ions in Biomolecules: Glycine to DNA 
John R. Sabin,^{1,2} Stephan P. A. Sauer,{3 and Jens Oddershede^{1,2}
^{1}Department of Physics and Chemistry, University of Southern Denmark, Odense Denmark
^{2}Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida, USA
^{3}Department of Chemistry, University of Copenhagen, Copenhagen, Denmark 
The effects of energy transfer from swift ion radiation to biomolecules are best described by the stopping cross section of the target molecule for the projectile ion. In turn, the mean excitation energy of the target is the determining factor in the stopping cross section. Using polarization propagator methodology, the mean excitation energies of components of several biomolecular systems, ranging from amino acids to nucleotides have been calculated, and are reported here. The calculated mean excitation energies could then be used to determine the stopping cross sections of the various biomolecular systems.


Free energy profile of water across cholesterol containing lipid bilayer 
Hiroaki Saito^{1,3} and Wataru Shinoda^{2,3}
^{1} Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa 9201192 Japan
^{2} Nanosystem Research Institute (NRI), Research Institute of Advanced Industrial Science and Technology (AIST), Central 2, 111 Umezono, Tsukuba 3058568, Japan
^{3} CREST, Japan Science and Technology Agency (JST), 418 Honcho, Kawaguchi, Saitama 3320012, Japan

The free energy profiles of a water molecule across two different lipid bilayers of dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl sphingomyelin (PSM) in the absence and presence of cholesterol (050 mol%) have been studied by molecular dynamics simulations to elucidate the molecular mechanism of the reduction in water leakage across the membranes by the addition of cholesterol. An enhanced free energy barrier was observed in these membranes with increased cholesterol concentration, and this was explained by the reduced cavity density around the cholesterol in the hydrophobic membrane core. There was an increase of trans conformers in the hydrophobic lipid chains adjacent to the cholesterol, which determined the cavity density. At low cholesterol concentrations the PSM bilayer exhibited a higher free energy barrier than the DPPC bilayer for water permeation, while at greater than 30 mol% of cholesterol the difference became minor. This tendency for the PSM and DPPC bilayers to resemble each other at higher cholesterol concentrations is similar to commonly observed trends in several structural properties, such as order parameters, crosssectional area per molecule, and cavity density profiles in the hydrophobic regions of bilayer membranes. These results demonstrate that DPPC and PSM bilayers with high cholesterol contents possess similar physical properties, which suggests that the solubility of cholesterol in these lipid bilayers has importance for an understanding of multicomponent lipid membranes with cholesterol. 

Modifications for the electron and the polarization propagator formalisms 
Masaaki Saitow^{1}, Tomonori Ida^{2}, and Yuji Mochizuki^{1}
^{1} Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, 3341 Nishiikebukuro, Toshimaku, Tokyo 1718501, Japan
^{2} Department of Chemistry, Kanazawa University, Kakumamachi, Kanazawa 9201192, Japan 
We have derived some improvements for the ab initio Green's function formalisms including the electron and the polarization propagators. For the former case, which describes oneelectron detachment process, a spin adapted formalism was derived by considering spincoupling of the configuration space explicitly. And this approach gives improved description for the openshell species over the conventional method, although the working equation become rather cumbersome because of the structure of the spin functions. And for the polarization propagator theory, two distinct modifications for the second order framework are shown. The first approach is specifically effective for the Rydberg excitation, in which drastic rearrangement of the charges occur, and recognizable as a branch of denominator shift approach. The second approach improves the differential correlation in terms of the ground and excited states and gives good results for the strongly degenerated states. Both methods retain the polynomial scaling to O(N^5) .


Evaluation of multicenter integrals of Slater type orbitals and CoulombYukawa like electric field gradient potentials using their onerange addition theorems 
Nursen SECKIN GORGUN
Faculty of Science, Department of physics, Trakya university, Edirne, Turkey 
Using onerange addition theorems established in Ref.[1] for Slater type orbitals and CoulombYukawa like interaction potentials with the help of complete orthonormal sets of ψ^αexponential type orbitals (α=1,0,1,2,…) [2], the calculations are performed for multicenter electric field gradient integrals. The results of computations show good rate of convergence and numerical stability. The convergences of the series is tested by calculating multicenter electric field gradient integrals for the arbitrary values of parameters of potentials and location of orbitals.
[1] I. I. Guseinov, Bull. Chem. Soc. Jpn., 78 (2005) 611
[2] I. I. Guseinov, Int. J. Quantum Chem. ,90 (2002) 114


Cluster Embedding Method with NonOrthogonal Wave Functions: DFT KohnSham Embedding Equations and Vacant States 
Emma K. Shidlovskaya^{1,2}
^{1}Information Systems Management Institute, Riga, Latvia
^{2}Institute of Chemical Physics, University of Latvia, Riga, Latvia 
When we theoretically study processes in large or infinite electron systems we have to treat the whole quantum system as two subsystems: small fragment of the system (cluster) and the remaining part of it. Problem "cluster in the field of the rest of system" is successfully solved in the frameworks of embedded molecular cluster (EMC) model [1] with orthogonal wave functions. Unfortunately, standard realization of EMC model leads to wellpronounced boundary effects [2].
To overcome limitations of the standard EMC model, we have treated cluster embedding problem in the frameworks of oneelectron approximation with nonorthogonal wave functions. Equations for the cluster are obtained varying total energy of the system expressed in terms of nonorthogonal oneelectron wave functions. Using these cluster embedding equations we have developed modified cluster embedding scheme. We have demonstrated that application of this scheme may radically reduce boundary effects in EMC model [2].
Possibility to generalize our embedding approach on the case of DFT KohnSham oneelectron equations is studied. We demonstrate that our variation procedure is compatible with KohnSham method. Cluster embedding equations remain the same [3] if instead of Fock operator we use oneelectron KohnSham Hamiltonian.
For further applications of our cluster embedding method we should overcome limitations of oneelectron approximation. It may be done by configurations interaction (CI) or perturbation theory (PT) methods. For this purpose we need occupied and vacant cluster states of the same localization. We have established that our initial embedding equations [2] give localized in the cluster region occupied states and delocalized vacant ones [4]. To get the same localization degree for the both occupied and vacant states, modified equations are proposed [4].
Modified cluster embedding equations [4] lead to correct description of electron transitions from occupied states to vacant ones. Treatment of electron correlation effects by CI or PT and proper description of excited states both by CI or DFT become possible. As the result, our embedding scheme now may be applied for quantumchemical simulation of various phenomena.
[1] L.N.Kantorovich, J. Phys. C: Solid State Phys. 21, 5041 (1988).
[2] E.K. Shidlovskaya, Int. J. Quantum Chem. 89, 349 (2002).
[3] E.K. Shidlovskaya, in Topics in Chemistry and Material Science, Volume 2. Theoretical Aspects of Catalysis, eds. G. Vayssilov, T. Mineva, Heron Press, Sofia, 2009, pp. 1118.
[4] E.K. Shidlovskaya, Computer Modelling and New Technologies 10, No 4, 17 (2006).


RealTime TDDFT Simulation for Coherent Phonon Generation 
Yasushi Shinohara^{1}, Kazuhiro Yabana^{1,2}, JunIchi Iwata^{2}, Tomohito Otobe^{3} and George F. Bertsch^{4}
^{1}Graduate School for Pure and Applied Sciences, University of Tsukuba, Japan
^{2}Center for Computational Sciences, University of Tsukuba, Japan
^{3}Advanced Photon Research Center, Japan Atomic Energy Agency, Japan
^{4}Department of Physics, University of Washington, USA 
We have been developing a firstprinciples description for quantum dynamics of electrons and ions induced by an intense and ultrashort laser pulse. In our method, electron dynamics is described by the timedependent densityfunctional theory (TDDFT) solving the timedependent KohnSham equation in realtime, while the ion motion is described by classical mechanics with the force evaluated by the Ehrenfest theorem. We consider a dynamics under a spatiallyuniform electric field which includes the polarization field as well as the applied electric field. Our scheme is capable of describing dielectric function in the linear response regime [1]. It has also been applied to optical breakdown in nonlinear regime [2].
In my presentation, we report an application of our framework for coherent phonon generation in bulk Si [3]. Coherent phonon is a macroscopic lattice vibration induced by the ultrashort laser pulse whose duration is shorter than the vibration period.
The figure below shows the calculated force acting on optical phonon coordinate at photon frequencies of 2.25, 2.5 and 2.75 eV. In our calculation, direct band gap of bulk Si is 2.4 eV. When the laser frequency is below the direct band gap (2.25 eV, red solid line), the impulsive force is only seen during the irradiation of the laser pulse (016 fs). When the laser frequency is above the direct band gap (2.75 eV, blue dotted line), the force persists even after the laser pulse ends. These features are consistent with two mechanisms of coherent phonon generation which have been proposed in phenomenological studies, the impulsive stimulated Raman scattering (ISRS) and the diplacive excitation of coherent phonon (DECP). In the ISRS, the force is generated from virtual electronhole excitations. In the DECP, the force is generated from real electronhole excitations which persist even after the laser pulse ends. We thus conclude that, in our framework based on TDDFT, both mechanisms of ISRS and DECP are included in a unified way.
We also apply the method to semimetal, Sb. Preliminary results will be presented as well.
[1] G.F. Bertsch, J.I. Iwata, A. Rubio and K. Yabana, Phys. Rev. B 62, 7998 (2000)
[2] T. Otobe, M. Yamagiwa, J.I. Iwata, K. Yabana, T. Nakatsukasa and G.F. Bertsch, Phys. Rev. B 77,165104 (2008)
[3] Y. Shinohara, K. Yabana, Y. Kawashita, J.I. Iwata, T. Otobe and G.F. Bertsch, Phys. Rev. B 82, 155110 (2010)

Figure. The force on the optical phonon coordinate for three laser frequencies: 2.25 eV (red solid); 2.5 eV (green dashed); and 2.75 eV (blue dotted).



Theoretical study of isotopeinduced additivity of chemical shift in benzene 
Kimikazu Sugimori,^{1} Hiroyuki Kawabe^{2}, and Hideto Shimahara^{3}
^{1}Department of Physical Therapy, Faculty of Health Sciences, Kinjo University, Japan
^{2}Department of Social Work, Faculty of Social Work, Kinjo University, Japan
^{3}Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Japan 
The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state of the molecules through nuclearelectron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital (MO), density functional (DF) theory, and other empirical strategies. The BornOppenheimer (BO) approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion [1]. We have been reported for diatomic molecules [2].
In this study, we apply Morse anharmonic oscillator model to calculate average internuclear distance of isotopologues and isotopomers of methanlike molecules and benzene derivatives. NMR shielding constants are calculated again on the average distance by using GaugeIndependent Atomic Orbital (GIAO) method with B3LYP/ccpVTZ and CCSD/ccpVTZ. The calculated isotope shifts will be discussed with relation to additivity, charge distribution, and experimental values.
References
[1] A. C. de Dios and C. J. Jameson. Annu. Rep. NMR Spectrosc. 29 (1994) 169.
[2] K. Sugimori and H. Kawabe, Int. J. Quantum Chem. 110 (2010) 29892995. doi: 10.1002/qua.22917


Development of FirstPrinciples Maxwell+TDDFT MultiScale Simulator for
Propagation of HighIntensity Laser Pulse 
Takeru Sugiyama^{1},Yasushi Shinohara^{1},Tomohito Otobe^{2},Kazuhiro Yabana^{1,3} and George F. Bertsch^{4}
^{1}Graduate School for Pure and Applied Sciences, University of Tsukuba, Japan
^{2}Center for Computational Sciences, University of Tsukuba, Japan
^{3}Advanced Photon Research Center, Japan Atomic Energy Agency, Japan
^{4}Department of Physics, University of Washington, USA 
Interaction between light and matter is described by the Schroedinger and Maxwell equations. The Schroedinger equation describes electron dynamics while the Maxwell equation describes propagation of electromagnetic fields. For ordinary weak lightwave, one can apply the perturbation theory for the Schroedinger equation which decouples two equations with the dielectric function. However, for intensive laser pulses, one cannot separate them because of the nonlinear electron responses to the strong electric field of the laser pulse. Previously, we developed a framework in TDDFT to describe electron dynamics under spatiallyuniform timevarying electric field solving the timedependent KohnSham equation in realtime [1,2]. We now extend it to a firstprinciples simulator calculating simultaneously the coupled nonlinear dynamics of electrons and electromagnetic field. Since the lengthscale is much different between the laser wavelength (μm) and the electron dynamics (nm), we employ two different spatial grids and express the vector potential in the macroscopic grids and the KohnSham orbitals in the microscopic grids. As a preliminary demonstration, we will show our calculation for the one dimensional propagation of electromagnetic field incident on bulk Si.
[1]T. Otobe et al. Phys.Rev.B77,165104(2008)
[2]Y. Shinohara et al. Phys.Rev.B82,155110(2010)

Figure. Laser pulse irradiated on bulk Si surface. The intensity and the frequency of the laser pulse is set to I=5×10^{12}W/cm^{2} and ℏw=1.55eV (below calculated bandgap, 2.4eV), respectively. The upper panels show propagation of electromagnetic field. The lower panels show the groundstate electron density (left) and the density change of electrons from that in the ground state at the surface (middle and right).



FRANCKCONDON FACTORS FOR DIATOMIC MOLECULES FOR AN ARBITRARY ANHARMONIC POTENTIAL 
L. Sandoval*, I. Urdaneta and A. Palma
*Facultad de Ciencias de la Computacion, Benemerita Universidad Autonoma
de Puebla. Puebla, Pue. 72570, Mexico
Instituto de Fisica, Benemerita Universidad Autonoma de Puebla. Puebla, Pue. 72570, Mexico 
In this work we develop a harmonic approximation of the FranckCondon Factors (FCF) for any anharmonic potential of diatomic molecules.
The method is based on the Taylor series expansion of the potential and the second quantization formalism. Well known recurrence relations are used to calculate the FCF, which are incorporated in the hamiltonian. Keeping then only the quadratic terms, by the BogoliubovTyablikov transformation the hamiltonian is found to be equivalent to an harmonic oscillator. The derivation is an alternative route to the Iterative Bogoliubov transformation (IBT), widely used to treat anharmonic potentials in a nonperturbative way. The FCF obtained by our method for the Morse potential are compared with numerical techniques like the RKR method and the Morse itself. Our results are in agreement with these numerical methods, being our technique entirely analytical and much simpler to use. 

Quantum Chemistry on Quantum Computers 
L. Veis and J. Pittner
J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic 
Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts, e.g. efficiently factore integers. Quantum chemistry could in principle benefit from them as well, for example by an efficient solution of manybody Hamiltonian eigenvalue problem [1]. As was shown in the seminal work by AspuruGuzik et. al. [2], quantum computers, if available, would be able to perform the full configuration interaction (FCI) energy calculations with only a polynomial scaling, in contrast to conventional computers where FCI scales exponentially.
We have developed a code for simulation of quantum computers and implemented our version of the quantum full configuration interaction (QFCI) method which uses the iterative phase estimation algorithm. This approach reduces demands on the total number of quantum bits (qubits) as only one is needed in the readout part of the quantum register and the whole algorithm proceeds in an iterative manner.
We have tested its performance and applicability for nonrelativistic as well as relativistic CI energy calculations. Nonrelativistic QFCI calculations of the four lowest lying electronic states of methylene molecule (CH_{2}), which exhibit a multireference character were performed [3]. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation even for nearly dissociated molecule. Relativistic Kramersrestricted CI calculations employing the QFCI algorithm have been applied to the spinorbit coupling in the SbH molecule [4]. We have also designed the quantum circuits for the simplest proofofprinciple physical realizations of relativistic quantum chemical computations on quantum computers.
[1] Abrams, D. S.; Lloyd, S. Phys.Rev.Lett. 1999, 83, 5162–5165.
[2] AspuruGuzik, A.; Dutoi, A. D.; Love, P. J.; HeadGordon, M. Science 2005, 309, 1704–1707.
[3] Veis, L.; Pittner, J. J. Chem. Phys. 2010, 133, 194106.
[4] Veis, L; Višnák, J.; Fleig, T.; Knecht, S.; Saue, T.; Visscher, L.; Pittner, J. in preparation


Antidot Structure Dependences of Openshell Characters and Aromaticities for Hexagonal Graphene Nanoflakes 
Kyohei Yoneda,^{1} Yudai Inoue,^{1} Tomoya Inui,^{1} Yasuteru Shigeta,^{1} Takashi Kubo,^{2} Benoît Champagne^{3} and Masayoshi Nakano^{1}
^{1}Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Japan
^{2}Department of Chemistry, Graduate School of Science, Osaka University, Japan
^{3}Laboratoire de Chimie Théorique (LCT), Facultés Universitaires NotreDame de la Paix (FUNDP), BELGIUM 
The openshell singlet state of graphene nanoflakes is at the origin of their unique physicochemical properties. In this study, we theoretically investigate the openshell characters and aromaticities of hexagonal graphene nanoflakes with different sizes of antidot structures, using the longrange corrected spinunrestricted density functional theory, LCUBLYP, method. It is found that the openshell character exhibits an oscillatory behavior with increasing the size of the antidot structure, and the nucleusindependent chemical shift (NICS) – an index of aromaticity – also depends on the openshell character. These antidot structure dependences are rationalized in terms of the variations in the HOMO–LUMO energy gaps, which is explained by the molecular orbital correlation diagram. 

Representation of structureproperty relationships in polymorphic systems 
Koretaka Yuge
Department of Materials Science and Engineering, Kyoto University, Kyoto 6068501, Japan 
While structureproperty relationships in crystals are fundamental prerequisite to design and optimize desirable materials, quantitative assessment for the relationships has been just beginning. Cluster expansion (CE) is one of the most successful approach based on abinitio calculation to predict configurational scalar as well as tensor properties such as internal energy, bandgap, density of states, and elasticity. However, application of the current CE is essentially limited to the single lattice, which makes it really difficult to applying to the polymorphic systems.
Here we introduce variable lattice CE (VLCE)[1] enabling to treat multiple structures in a single Hamiltonian, which overcomes the limitation in CE. We demonstrate derivation, concept, and interpretation of the proposed VLCE, and show application to 2dimensional system to search groundstate structure in polymorphs.
References
[1] K. Yuge, J. Phys.: Condens. Matter 22, 125402 (2010).


Use of onerange addition theorems in evaluation of multicenter electric field integrals of Slater type orbitals and Yukawalike interaction potential 
Nimet ZAIM
Department of Physics, Faculty of Sciences, Trakya University, Edirne, Turkey 
The calculation is performed for multicenter electric field integrals containing Slater type orbitals and Yukawalike interaction potential using their onerange addition theorems established in Ref.[1] with the help of complete orthonormal sets of ψ^{α} exponantial type orbitals (α=1,0,1,2,…) [2]. The results of computer calculations are presented. The convergences of the series is tested by calculating concrete cases for the arbitrary values of quantum numbers, orbital parameters and internuclear distances.
[1] I. I. Guseinov, Bull. Chem. Soc. Jpn., 78 (2005) 611
[2] I. I. Guseinov, Int. J. Quantum Chem. ,90 (2002) 114


Mndoped Thiolated Au_{25} Nanoclusters: Atomic Confguration, Magnetic Properties, and A Possible Highperformance Spin Filter 
M. Zhou,^{1} Y. Q. Cai,^{1} M. G. Zeng,^{1} C. Zhang,^{1,2} and Y. P. Feng^{1}
^{1}Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117542
^{2}Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 
We report an ab inito investigation on the groundstate atomic configuration, electronic structures, magnetic and spindependent transport properties of Mndoped Au_{25} nanoclusters protected by thiolate. It is found that the most stable dopant sites are near surfaces, rather than the center position of the nanoparticles. Transport calculations show that highperformance spin filters can be achieved by sandwiching these doped clusters between two nonmagnetic Au electrodes. The nearly perfect spin filtering ori g! inates from localized magnetic moments of these clusters that are well protected by ligands from the presence of electrodes 

