Abstracts of Invitedand Contributed Talks, Sep. 499

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Computational modeling of methyl transfer reactions catalyzed bycobalamin-dependent methionine synthase enzyme
Pawel M. Kozlowski,1 Manoj Kumar,1 and Neeraj Kumar1
1
Department of Chemistry, University of Louisville, 2320 South Brook Street,Louisville, Kentucky 40292, United States
The cobalamin-dependent methionine synthase enzyme (MetH) catalyzes thetransfer of the methyl group from methyltetrahydrofolate (CH3-H4folate) tohomocysteine (Hcy) thus forming methionine (Met). The key step in the catalytic cycle
involves displacement of the methyl group from the methylcobalamin cofactor (MeCbl)
to Hcy in which the cobalamin cofactor serves as an intermediate cycling between
hexa-coordinated methyl-cob(III)alamin and tetra-coordinated cob(I)alamin complexes.
It is generally believed that the enzyme operates via an SN2-type nucleophilic
displacement. However, a related mechanism, referred to as reductive cleavage has been
also suggested [1]. According to this mechanism, the cofactor is initially reduced bytransfer of an electron from the deprotonated Hcy, forming a S–corrin based radical,
followed by Co-C bond cleavage.
The transfer of the methyl group from the MeCbl cofactor to the Hcy substrate
results in the formation of the cob(I)alamin intermediate which exhibits a complex
electronic structure, between Co(I) and Co(II)-radical corrin states. It was found that thecorrelated ground state wave function consists of a closed-shell Co(I) (d8) configuration
and a diradical contribution, which can be described as a Co(II) (d7)-radical corrin (S )1
configuration. Moreover, the contribution of the two configurations depends on the
Co-N(His759) distance [2].
Once every ~2000 turnovers, the MetH-bound cobalamin cofactor (Co1+Cbx) isconverted to the inactive cob(II)alamin (Co2+Cbx) form, from which Co1+Cbx has to be
recovered in order to ensure efficient catalysis. The Co+2/Co+1 is a thermodynamicallychallenging reaction because the midpoint reduction potentials of the physiologicalreducing agents are considerably more positive than that of the Co2+Cbx cofactor. Basedon spectroscopic and X-ray structure studies the generation of tetra-coordinated
Co1+Cbx has been invoked to be the key molecular determinant of the enzyme-mediatedredox tuning of Co+2/Co+1 process. However an alternative catalytic strategy for driving
Co+2/Co+1 reduction can be envisioned if one takes into account the formation of abiologically relevant Co+1--H bond [3].
[1] M. Alfonso-Prieto, X. Biarnes, M. Kumar, C. Rovira, P. M. Kozlowski, J. Phys.
Chem. B, 2010, 114 (40), pp 12965–12971[2] N. Kumar, M. Alfonso-Prieto, C. Rovira, P. Lodowski, M. Jaworska, P. M. Kozlowski,
J. Chem. Theory Comput., 2011, 7(5), pp 1541-1551.
[3] M. Kumar, P. M. Kozlowski, Angew. Chemie. Int. Ed. 2011, accepted.

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Good Vibrations in Enzymatic H-Tunnelling: the Effect of Pressure on
Barrier Compression and Isotope Effects
Linus O. Johannissen,1 Sam Hay,2 Nigel S. Scrutton,2 Michael J. Sutcliffe1
1School of Chemical Engineering and Analytical Science and 2Faculty of Life Sciences,
Manchester Interdisciplinary Biocentre
The University of Manchester, UK
The shape of the reaction barrier is crucial for enzymatic hydrogen tunnelling
reactions, and therefore the concept of barrier compression is of fundamental
importance. Promoting vibrations are rapid, sub-picosecond donor-acceptor
compressive modes that transiently compress the barrier, enhancing the rate of
H-transfer. For reactions dominated by H-tunneling, such vibrations can be inferredfrom the kinetic isotope effect (KIE) and its temperature-dependence (ΔΔH‡). However,promoting vibrations cannot be directly observed experimentally, and their role inH-tunnelling reactions remains contentious. For the rate-limiting H-transfer in the
reductive half-reaction of morphinone reductase (MR), significant barrier compression
has been inferred from both the strong temperature-dependence of the KIE and its
counter-intuitive pressure-dependence, which has been explained by invoking an ad-hoc increase in the force constant for a low-frequency promoting vibration [1].
We present MM and QM/MM studies on the effect of pressure on donor-acceptor
compression, barrier shape and the KIE in MR. Using spectral density analysis anddigital filtering we identify the promoting vibration for this H-transfer (Figure 1) andconfirm the hypothesis that the force constant increases with pressure. Using a vibronic(wavefunction overlap) formalism we show how pressure affects the KIE, ΔΔH‡ and therate constant, demonstrating that changes in experimental observations are directly
coupled to the promoting vibration. Finally, QM/MM calculations reveal how theincrease in force constant affects the relationship between barrier width and height andhow this relates to the tunnelling parameters. [2]
NADH

C4
C4
FMN
N5

N5

Figure 1. Promoting vibration for the
H-transfer in MR at 1 bar.
[1] Hay, S.; Sutcliffe, M. J.; Scrutton, N. S. Proc. Natl. Acad. Sci. USA 2007, 104, 507.
[2] Johannissen, L. O.; Scrutton, N. S.; Sutcliffe, M. J. Angew. Chem. Int. Ed. Engl. 2011,
50, 2129.

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MD Simulations of Micelles Formation in C12Ex Solutions
Alia Tadjer, Maria Velinova, Yana Tsoneva, Anela Ivanova
Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
Since the dawn of polymeric micelles application as drug delivery systems in thelate 1980s [1], numerous polymer self-assemblies have been extensively investigated,designated to deliver various substances including: low-molecular-weight anticancer drugs,
contrast/imaging agents, proteins, etc. Promising building blocks of drug delivery
containers are deemed nonionic surfactants of the poly(ethylene glycol) alkyl ethers CnEm.
One of the purposes of the present study is to derive from first principles
calculations and test molecular mechanics parameters for such ethers to be used insubsequent all-atom simulations. Monomers and dimers with two different types of
periphery, which are short-chain prototypes of the amphiphilic surfactant ɋ12ȿx, were used
as model systems. The geometry of low-energy conformers is optimised (PBE and MP2) invacuum and in implicit solvent. Validation of the derived parameters provided thecomparison between the thermodynamic parameters obtained from MD simulations(Amber99/NPT/300 K) of diethyl ether and the existing experimental data.
On the other hand, the stability of the pre-aggregates is determined, which aresupposed to exist in aqueous solution before the actual micelles assembly, and to assess theaptitude to their formation. All-atom and coarse-grained molecular dynamic simulations(NPT/293 K) of two molecules of each species in explicit water (TIP4P) with PBC applied
were carried out to estimate the mutual orientation and the interaction between thesurfactants in the dimers. The derived force field parameters for the ether groups were used
for this aim. The structural aspects of the amphiphilic organization in aqueous medium
from the simulation data with the MARTINI CG force field for surfactant concentrations
are discussed.
[1] K. Kataoka, G.S. Kwon, M. Yokoyama, T. Okano, Y. Sakurai, J. Control. Release 24 (1993)
119

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4D-QSAR Analysis for the Cytotoxicity of Lamellarins Against Human
Hormone-Dependent T47D Breast Cancer Cells
Poonsiri Thipnate,1,2 Jianzhong Liu,3 Supa Hannongbua, 4,5 A. J. Hopfinger3,61
Department of Chemistry, Faculty of Science and Technology, Phetchaburi Rajabhat
University, Phetchaburi, 76000, Thailand
2

Natural Products Chemistry Research Unit, Faculty of Science and Technology,
Phetchaburi Rajabhat University, Phetchaburi, 76000, Thailand

3

College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New
Mexico 87131-000, USA
4

Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak,Bangkok 10900, Thailand

5

Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900,
Thailand6

The Chem21 Group, Incorporated, 1780 Wilson Drive, Lake Forest, IL 60045

4D-QSAR models were built and investigated for the cytotoxicity of a set of 26
lamellarins against human hormone dependent T47D breast cancer cells. 4D-QSAR
models were first constructed from the exploration of eight possible receptor bindingalignments for the entire training set. Since the training set is small (25 compounds), thegenerality of the 4D-QSAR paradigm was then exploited to devise a strategy to maximize
the extraction of binding information from the training set, and to also permit virtual
screening of diverse lamellarin chemistry. 4D-QSAR models were sought for only six ofthe most potent lamellarins of the training set as well as another subset composed oflamellarins with constrained ranges in molecular weight and lipophilicty. This overallmodeling strategy has permitted maximizing 3D-pharmacophore information from thissmall set of structurally complex lamellarins that can be used to drive future analog
synthesis and the selection of alternate scaffolds. Overall, it was found that formation of
an intermolecular hydrogen bond and hydrophobic interactions for substituents on the E
ring most modulate the cytotoxicity against T47D breast cancer cells. Hydrophobic
substitutions on the F-ring can also enhance cytotoxic potency. The optimized 4D-QSAR
model has a LOO cross-correlation value of xv-r2 = 0.947. This work reveals that it ispossible to develop significant QSAR, 3D-pharmacophore models for a small set oflamellarins showing cytotoxic behavior in breast cancer screens that can guide future
drug development based upon lamellarins.
[1] Thipnate P, Liu J, Hannongbua S, Hopfinger A J. Journal of Chemical Information andModeling 2009, 49, 2312-2322

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Open-boundary cluster model for electronic excited states ofadsorbate-surface systems
Tomokazu Yasuike and Katsuyuki Nobusada
Institute for Molecular Science, Japan
I. Introduction The importance of photo-excited interface has recently been growing [1]. It is relevant to a broad range of practical applications including dyesensitized solar cells and photo-catalysts. To investigate photo-excited interfacialsystems, it is crucial to calculate both of the potential energy curves and lifetimesof the excited states. We have recently developed the open-boudary cluster model(OCM) [2], a generalized cluster model by introducing the outgoing-wave boundary
condition at the edge of a model cluster mimicking an adsorbate-surface system. In
the present contribution, we report the formulation of the ﬁrst-principles approachbased on OCM and its application to a Cs/Cu(111) system.
II. Application to a Cs/Cu(111) system The OCM Kohn-Sham (KS) equationis constructed by adding the absorbing potential to the KS equation for a modelcluster. The ground-state energies of CsCun (n = 1 − 31) were calculated and it has
been found that the cluster-size convergence of the interaction energy of Cs-Cun isremarkably improved by the OCM procedure. This is because the artiﬁcial edges inherent in a conventional cluster model are removed by introducing the outgoing-wave
boundary condition. In the framework of OCM, the excited states are determinedby the linear-response of the ground state. Figures 1 and 2 show the potential energy curves and the electronic lifetimes, respectively, for low-lying states for CuCs,
the minimal model for Cs/Cu(111). The lowest excitation is Cu 4s→ Cs 6sσ. The
excitation energy (2.4 eV) and lifetime (50 fs) are in reasonable agreement with experimental observations, and thus the ﬁrst-principles OCM approach is considered
to be promising for investigating photo-excited interfacial systems.
8500

Cs RydCs 5d

9

10Lifetime ( fs )Total Energy ( eV )400

Cs 5d

11

Cu 4p

12

Cs 6s

300

200

Cs 5d, 5d

13

100

14

Cs 6s

Cu (4s)2
3

4

5

6

0

7

Cu–Cs distance Z (a0)

4.5

5.0

5.5

6.0

6.5

Cu–Cs distance Z (a0)

Fig.1 Potential energy curves for low-lying
states of Cs/Cu(111)Fig.2 Electronic lifetime of Cs 6sσ, 5dσ
excited states[1] C. D. Lindstrom and X.-Y. Zhu, Chem. Rev. 106, 4281 (2006).
[2] T. Yasuike and K. Nobusada, Phys. Rev. B 76, 235401 (2007); ibid 80, 035430(2009).

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Excited-State Nuclear Forces on the Adiabatic Potential Energy
Surfaces by Time-Dependent Density Functional Theory
Jun Haruyama, Takahiro Suzuki, Chunping Hu, Kazuyuki Watanabe
Department of Physics, Tokyo University of Science, Japan
Photoinduced processes are fundamental to physical, chemical, and biologicalphenomena. Owing to the recent developments in laser technology, the dynamical
reactions including structural deformation, dissociation, isomerization, etc., have been
investigated experimentally. To understand these excited-state dynamics theoretically,
the accurate and efficient quantum simulation is required.
The simulation of photoinduced excited-state dynamics needs two ingredients. One is
the nonadiabatic coupling terms (NACs) between the adiabatic states, and the other isthe nuclear forces acting on atoms or ions on the adiabatic potential energy surfaces(APES) [1]. Recently, Hu et al. developed the efficient methods for calculating NACs
using time-dependent density functional response theory [2]. However, the force
calculation is still computationally expensive. In order to find a computationallyreasonable force calculation method, we develop the excited-state force calculation
method using the Casida ansatz [3]. This formulation is very simple, and thecomputational cost for the excited-state forces is almost the same as that of the NAC
calculation.
First, we calculate the two APES for excited states of 1Ǜu- and 1Ȥg using adiabatic
local density approximation for N2 molecule. Comparing with the experimental value,
the bond lengths of each state are well described within 0.03Å. Next, we calculate theexcited-state forces using the Casida-ansatz formulation and compare it with thefinite-difference numerical derivative of each energy curves. The Casida-ansatz force
well reproduces the equilibrium bond length for 1Ȥg state, but overestimates that of1
Ǜu- by 0.1 Å. Thus, we consider that the forces on the APES with lower excitedenergies are well approximated by the Casida-ansatz force.
In the presentation, we discuss the difference in the force calculation method between
the Casida-ansatz formulation and previous studies[4,5]. We further discuss theCasida-ansatz forces for various kinds of molecules and show the simulation results ofthe excited-state dynamics.
[1] N. L. Doltsinis and D. Marx, J. Theor. Comput. Chem. 1, 319 (2002).
[2] C. Hu, H. Hirai, and O. Sugino, J. Chem. Phys. 127, 064103 (2007).
[3] M. E. Casida, in Recent Advances in Density-Functional Methods, Part 1, edited by
D. P. Chong (World Scientific, Singapore, 1995).
[4] N. L. Doltsinis and D. S. Kosov, J. Chem. Phys. 122, 144101 (2005).
[5] A. Sitt, L. Kronik, S. Ismail-Beigi, and J. R. Chelikowski, Phys. Rev. A 76, 054501(2007).

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Role of the interface in the chemical reactivity of ultrathin oxide film
Jaehoon Jung,1,2 Hyung-Joon Shin,3 Yousoo Kim,2 and Maki Kawai1
1
Department of Advanced Materials Science, The University of Tokyo, Japan
2
Advanced Science Institute, RIKEN, Japan3
School of Mechanical and Advanced Materials Engineering, UNIST, Republic of Korea
Ultrathin oxide films grown on metal substrate are of great interest not only as
supporting materials for chemically active nanoparticles but also as catalysts in the fieldof heterogeneous catalysis [1]. Using scanning tunneling microscopy (STM) and density
functional theory (DFT) calculations, we have demonstrated that the chemical reactivity
for water dissociation on an ultrathin MgO film grown on Ag(100) substrate depends
greatly on film thickness and is enhanced as compared to that achieved with their bulk
counterpart [2]. The change of chemical reactivity of ultrathin MgO film depending on
the film thickness can be explained by the strengthening of the interaction between theoxide and metal interface layers. This result implies that the artificial manipulation of
the local structure at the oxide-metal interface is expected to play a pivotal role incontrolling the catalytic activity of oxide film. Therefore, water dissociation on threemodel systems with defects at the oxide-metal interface of the 2-ML MgO/Ag(100) – anO vacancy (Fig. 1a), an Mg impurity, or an O impurity – has been examined andcompared with the case of a MgO film without defects using periodic DFT calculations[3]. Our results clearly show that such structural imperfections at the interface can
improve the chemical reactivity of ultrathin MgO film supported by Ag(100) substrate.
This is closely correlated with the accompanying change of charge distribution of theoxide surface due to the accumulation of transferred charge density at the interface (Fig.
1b). In addition, the chemical reactions on the(b)ultrathin oxide film surface can be tuned by (a)interface defects regardless of the charging ofadsorbates. Our study about water dissociationon MgO/Ag(100) not only reveals the potentialof an ultrathin oxide film as a catalyst but also
opens new vistas for the development oftechniques to control and measure the interface Figure 1. (a) Water dissociation on
structure of oxide film deposited on a metal MgO/Ag(100) with interface O vacancy
and (b) charge density difference map.
substrate.
[1]. H.-J. Freund, Chem. Eur. J. 16, 9384 (2010).
[2]. H.-J. Shin, J. Jung, K. Motobayashi, S. Yanagisawa, Y. Morikawa, Y. Kim, and M.
Kawai, Nat. Mater. 9, 442 (2010); J. Jung, H.-J. Shin, Y. Kim, and M. Kawai, Phys.
Rev. B 82, 085413 (2010).
[3]. J. Jung, H.-J. Shin, Y. Kim, and M. Kawai, J. Am. Chem. Soc. 133, 6142 (2011).

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Comparison of QM cluster calculations and QM/MM calculations forreactions in proteins

Ulf Ryde
Department of Theoretical Chemistry, Lund University, Sweden
During the latest decades, quantum mechanical (QM) calculations have become an
important complement to experiments for the study of the structure and function ofproteins. However, there is still no consensus on how such calculations should be
performed. Instead, two schools have emerged: In the first, a small model (50–200
atoms) of the active site is cut out from the protein and is studied in isolation by QM
methods. In the second approach, the entire protein, including some surrounding watermolecules are explicitly studied by the combined QM and molecular mechanics(QM/MM) approach, in which the active site (again 50–200 atoms) is studied by QM
methods, whereas the rest is modelled at the MM level.
We have studied the convergence of the QM cluster approach with respect to the sizeof the QM system and compared various methods to select atoms to include in thecalculations [1]. For our test system, a simple proton-transfer reaction in [Ni,Fe]hydrogenase, various approaches to add groups to the QM system converge after ~15
groups have been added and the effect of the continuum solvent becomes unimportant at
the same size. Unfortunately, different approaches to add groups converge to different
results that differ by up to ~60 kJ/mol.
Likewise, we have studied the accuracy of QM/MM calculations, compared to pure
QM calculations on a 446-atom model of [Ni,Fe] hydrogenase, again systematicallyincreasing the size of the QM system [2]. We have tested several variants of bothmechanical and electrostatic embedding. The results show that the junctions introduce
inaccuracies that are hard to correct if they are too close to the reactive centre. However,
QM/MM methods converge faster than QM-only methods. We will discuss how the two
approaches may be combined to obtain the most reliable results.
[1] L. Hu, J. Eliasson, J. Heimdal, U. Ryde (2009) J. Phys. Chem. A, 113, 11793.
[2] L. Hu, P. Söderhjelm, U. Ryde (2011) J. Chem. Theory Comput., DOI:
10.1021/ct100530r.

107

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Reaction Mechanisms of Novel Fluorescent Proteins
Xin Li,1 Lung Wa Chung,1 Hideaki Mizuno,2 Atsushi Miyawaki,2 Keiji Morokuma1,*
1
Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan,
2
Laboratory for Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1
Hirosawa, Wako-city, Saitama, 351-0198, Japan.
Wild-type green fluorescent proteins (GFP) and its variants play an important rolein biological imaging and analysis. Recently, a new class of fluorescent proteins, (suchas reversible photoswitching fluorescent proteins [1], irreversible photoconversion
fluorescent proteins [2] and photoactivatable fluorescent proteins [3]) has become
available and advanced our fluorescent protein technology. However, the reaction
mechanisms of new photophysical and photochemical processes in these novel
fluorescent proteins remain unclear.
We investigated possible reaction mechanisms for these novel fluorescent proteins
by high-level QM and ONIOM(QM:MM) methods. New mechanistic pathways (e.g.
photoisomerization coupled with excited-state proton transfer for Dronpa andcompetitive E1 and E1cb pathways for Kaede) were found [4-6]. In addition, we
employed our developed non-adiabatic ONIOM(QM/MM) MD simulations [5] toelucidate primary events of photodynamics of the GFP chromophore in different
environments. Significant effects of the environment on photodynamics were found andwill be discussed. We also plan to add some additional results of our recent progress.
Scheme 1. Proposed mechanisms for reversible photoswitching in Fluorescent Proteins[1] R. Ando, H. Mizuno, A. Miyawaki, Science 306, 1370 (2004).
[2] R. Ando, H. Hama, M. Yamamoto-Hino, H. Mizuno, A. Miyawaki, Proc. Natl. Acad.
Sci. U.S.A. 99, 12651 (2002).
[3] G. H. Patterson, J. Lippincott-Schwartz, Science 297, 1873 (2002).
[4] X. Li, L. W. Chung, H. Mizuno, A. Miyawaki, K. Morokuma, J. Phys. Chem. B 114,
1114 (2010).
[5] X. Li, L. W. Chung, H. Mizuno, A. Miyawaki, K. Morokuma, J. Phys. Chem. Lett. 1,
3328 (2010).
[6] X. Li, L. W. Chung, H. Mizuno, A. Miyawaki, K. Morokuma, J. Phys. Chem. B 114,
16666 (2010).

108

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Structural and Energetic Analysis of Mutant K103N HIV-1 Reverse
Transcriptase/Efavirenz Complex using ONIOM Calculations
Pornthip Boonsri,1,2 Mayuso Kuno,3 Supa Hannongbua 1,2
1
Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900,
Thailand2
Center of Nanotechnology KU, Kasetsart University and NANOTEC
Center of Excellence at Kasetsart University
3
Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok
10110, Thailand
The most frequently observed mutation on the NNRTIs resistant is the K103N
residue. Interestingly, there are still not clearly explained why this mutation encodes
resistance to a wide range of NNRTIs, especially Efavirenz (EFV) inhibitor.
Consequently, it is rather difficult to test and investigate experimentally. Therefore, a
two-layered ONIOM calculation was performed in order to compared the binding
interactions of EFV inhibitor and the HIV-1 RT binding pocket of both wild type (WT)and K103N mutant type, using a combination of different methods of calculation[B3LYP/6-31G(d,p), HF/6-31G(d,p), and PM3]. Additionally, the K103N mutation
reduces the binding affinity and stability of the inhibitor by approximately 5.81
kcal/mol as obtained from ONIOM2B (B3LYP/6-31G(d,p):PM3) method. These
indicate that the small loss of binding energy to K103N mutant can be attributed to aslightly weakened attractive interaction between the drug and residues surrounding thebinding pocket due to the adaptation of HIV-1 RT against drug-resistance, whichobserved from the deformation energy. This energy comes from the binding pocket of
K103N RT that requires more energy for the structural rearrangements than the WT byapproximately 4.0 kcal/mol based on the ONIOM2B calculations. Moreover, it isconfirmed that the non-bonded interaction of EFV to both wild type and K103N
mutation HIV-1 RT are also slightly changes. The substitution of the linear side chain of
K by the branched of N at 103 position appears to greatly affect the chemical
environmental in the K103N mutation, bring to the differences in interatomic distances,hydrogen bonding, electrostatic and hydrophobic interactions. Therefore, the knowledge
based of the main contribution, non-bonded interactions and also the binding energy of
EFV to WT and K103N RT complexes provide insight into the better understanding for
improving a new drug resistance mutation.
Key words: Efavirenz, HIV-1 RT, K103N mutation, ONIOM, non-bonded, hydrogenbonding, hydrophobic, electrostatic and binding pocket

109

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A coarse grained QM/MM approach for the description of holetransfer in DNA
Marcus Elstner, Karlsruhe Institute of Technology (Germany)
Charge transfer in DNA has received much attention in the last years due to
its role in oxidative damage and repair in DNA, but also due to possible
applications of DNA in nano-electronics. Despite intense experimental andtheoretical efforts, the mechanism underlying long range hole transport is stillunresolved. This is in particular due to the fact, that charge transfer sensitively
depends on the complex structure and dynamics of DNA and the interaction
with the solvent environment, which could not be addressed adequately in themodeling approaches up to now. We present a new computational strategy toevaluate the charge-transfer (CT) parameters for hole transfer in DNA. Basedon a fragment orbital approach, site energies and coupling integrals for acoarse grained tight binding description of the electronic structure of DNA canbe rapidly calculated using the approximate Density Functional method SCCDFTB (1,2). Environmental effects are captured using a combined quantum
mechanics/molecular mechanics (QM/MM) coupling scheme and dynamical
effects are included by evaluating these CT parameters along extensiveclassical molecular dynamics (MD) simulations. This methodology allows toanalyze in detail several factors responsible for CT in DNA. The fluctuations of
the counterions, strongly counterbalanced by the surrounding water, leads tolarge fluctuations of the site energies, which govern the hole propagation
along the DNA strand, while the electronic couplings depend strongly on DNA
conformation and are not affected by the solvent (2) . Using this methodology,
the time course of the hole can be followed by propagating the hole wave
function using the time dependent Schrödinger equation for the coarse
grained Hamiltonian (5,6).
1. T. Kubar, P. Woiczikowski, G. Cuniberti, M. Elstner, Efficient Calculationof Charge-Transfer Matrix Elements for Hole Transfer in DNA, J. Phys. Chem.
B, 112, (2008) 7937.
2. T. Kubar, M. Elstner, What governs the charge transfer in DNA? The roleof DNA conformation and environment. J. Phys. Chem. B, 112, (2008) 8788
3. T. Kubar, M. Elstner, Solvent reorganization energy of hole transfer in DNA,J. Phys. Chem. B, 113, 5653-5656.
4. P. Woiczikowski, T. Kubar , R. Gutierrez, R. Caetano, G. Cuniberti, M.
Elstner, Combined DFT and Landauer approach for hole transfer alongclassical MD simulations of DNA, J. Chem. Phys. 130 (2009) 215104.
5. T. Kubar, U. Kleinekathoefer, M. Elstner, Water Drives the Hole Transfer in
DNA: a Combined TD-DFT and Classical MD Study, J. Phys. Chem B, 113(2009) 13107.
6. T. Kubar, M. Elstner, Coarse-grained time-dependent density functional
simulation of charge transfer in complex systems: application to hole transfer
in DNA, J. Phys. Chem. B 114 (2010) 11221.

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Biomimetic design of Charged Brush-like Nanopores: Simulation studies
Prapasiri Pongprayoon1,2, Oliver Beckstein2, Mark SP Sansom2
Deaprtment of Chemistry, Kasetsart University, Chatuchak, Bangkok, Thailand 10900
2Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
1e-mail: fsciprpo@ku.ac.th
Ion channels and porins are nanopores that in many cases, display high levels ofsolute specificity. Their selectivity has been exploited in new technologies: for instane
synthetic functional nanopores have been fabricated based on the permeation
properties of biological channels. One of anion-selective channels, phosphate (Pi)selective outer membrane protein P (OprP) shows great ability for Pi selectivity overchloride ion. The previous simulation study indicates a crucial role of basic pore-lining
residues which provide a 'charged brush' in determining Pi selectivity. In this study,
OprP is used as a template for designing a series of computational models of synthetic
nanopores that exhibit both OprP's anion-vs-cation selectivity and a preference for Pi
over common chloride ion. The potential of mean force (PMF) has been used toinvestigate the energetic properties of modelled pores in comparison with that of OprP.
The PMF of modelled nanopores shows similar profile to that of OprP. The Kd valuesof the modelled pore computed from the PMFs are 0.45 nM for Pi and 0.17 µM for
Chloride corresponding to ~400-fold stronger binding of Pi than Chloride ion.
Importantly, the results show that the high selective properties of biological channels
can be transferred when their functional architecture and pore geometry are
duplicated.

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Solvent and Salt Effects on Structural Stability of Human Telomere
Yutaka Maruyama,1 Taku Matsushita,2 Masahiro Ohgidani,2Osamu Tanoue, 2 Ryuichi Ueoka,2 Fumio Hirata1
1Institute for Molecular Science, Japan
2Faculty of Biotechnology and Life science, Sojo University, Japan
I. Introduction
Human telomere DNA is of intense interest because of its role in the biology ofboth cancer and aging. The single-stranded telomere terminus can adopt the structure ofa G-quadruplex, which is of particular importance for anticancer drug discovery, andvarious G-quadruplex structure have been reported. However the structure of humantelomeric DNA has been controversial: the solution structure in the presence of Na+ has
been reported to be antiparallel basket-type G-quadruplex by NMR, while the crystal
structure in the presence of K+ has been reported to be parallel propeller-type. The
solution structure in the presence of K+ has drawn intense interest, as the intracellular
K+ concentration is higher than that of Na+, but the structure is still open to address.
II. Method
The 3D-RISM theory is a statistical mechanics theory of molecular liquids. This
theory can provide the solvation free energy and the force from solvent withoutsampling. We combined a structure optimization method (the Quasi-Newton method)with the 3D-RISM theory, and performed the optimization of the telomere structure inaqueous solution of electrolytes to investigate the stability of various structures.
III. Results and Discussion
In pure water, the chair-type conformation was found to be the most stablestructure, which is followed by basket-, hybrid-, and propeller-type structures in theorder. It is clarified that the order of the stability is determined essentially by thesolvation free energy, not by the conformational energy.
The order of the stability changes in 0.1 M NaCl solutions from that in pure water.
The basket-type structure becomes the most stable one in the electrolyte solution. The
theoretical finding is consistent with the experimental observation due to NMR. The
reversed order of the conformational stability was attributed to the salt effect, especially,to that from the Na+ ions bound at inter-strand spaces of DNA.
Concerning the conformational stability in KCl solutions, our results predict thatthe order is not changed from that in pure water, that is, the chair-type is the most stableone. The finding suggests that the effect of the potassium ion upon the structure is not
so strong as the sodium ion to change the order of the stability determined in pure water.
The result is consistent with our finding for RDFs of the ions bound at the inter-strand
spaces in DNA, which indicates clearly that the affinity of K+ to the binding site is
weaker than that of Na+.

112

4A4-5CComp
plexity in Molecular Recognition
Jörg Grunenberg 1
1
Department of Life Science,
S
Hagenring 30, 38106 Braunschweigg, Germany
Abstract
The anomer selectivity of artificial carbohydrate receptors was studiedd using in silico
methods in order to shed light on the thermodynamic driving forces at work duringmolecular recognition in geeneral. The contributions of relevant intermollecular hydrogenbonds were investigated byb means of generalized compliance constaants in order todissect important from less important non-covalent interactions. Even att this moderately
low rung on the ladder of complexitycessential aspects of molecular reccognition are notexplainable in terms of additive intermolecular interactions. Thoough molecular
recognition seems to bee complex an emergent property, a raational for the
diastereoselectivity of carrbohydrate receptors was obtained by a combination ofexperimental data, free enerrgy simulations and ab initio calculations.[1-33]

Superimposed structures of thhe 500 low energy conformers of the ȕ-octyl-glucooside (left) and theĮ-anomer (right). Due to a prronounced anomeric effect the Į-anomer is stabiliized by 15 kJ/mol΀ϭ΁ŽŵƉůĞǆŝƚǇŝŶDŽůĞĐƵůĂƌZĞĐŽŐŶŝƚŝŽŶ͘'ƌƵŶĞŶďĞƌŐ͕:ŽĞƌŐ͘WŚǇƐŝĐĂůŚĞŵŝƐƚƌǇŚĞŵŝĐĂWŚǇƐŝĐƐ͘;ϮϬϭϭͿ͕ĂĐĐĞƉƚĞĚ͖ ΀Ϯ΁ ĨĨŝĐŝĞŶƚ ĐŽŵƉƵƚĂƚŝŽŶ ŽĨ ĐŽŵƉůŝĂŶĐĞĞ ŵĂƚƌŝĐĞƐ ŝŶ ƌĞĚƵŶĚĂŶƚ ŝŶƚĞƌŶĂů ĐŽŽƌĚŝŶĂƚĞƐ ĨƌŽŵ ĂƌƚĞƐŝĂŶ ,ĞƐƐŝĂŶƐ ĨŽƌ ŶŽŶƐƚĂƚŝŽŶĂƌǇƉŽŝŶƚƐ͘ƌĂŶĚŚŽƌƐƚ͕<Ăŝ͖'ƌƵŶĞŶďĞƌŐ͕:ŽĞĞƌŐ͘:ŽƵƌŶĂůŽĨŚĞŵŝĐĂůWŚǇƐŝĐƐ;ϮϬϭϬͿ͕ϭϯϮ;ϭϴͿ͕ϭϴϰϭϬϭ΀ϯ΁ ,Žǁ ƐƚƌŽŶŐ ŝƐ ŝƚ͍ dŚĞ ŝŶƚĞƌƉƌĞƚĂƚŝŽŶ ŽĨ ĨŽƌĐĞ ĂŶĚ ĐŽŵƉůŝĂŶĐĞ ĐŽŶƐƚĂŶƚƐ ĂƐ ďŽŶĚ ƐƚƌĞŶŐƚŚ ĚĞƐĐƌƌŝƉƚŽƌƐ͘ ƌĂŶĚŚŽƌƐƚ͕ <Ăŝ͖'ƌƵŶĞŶďĞƌŐ͕:ŽĞƌŐ͘&ƌŽŵŚĞŵŝĐĂů^ŽĐŝĞĞƚǇZĞǀŝĞǁƐ;ϮϬϬϴͿ͕ϯϳ;ϴͿ͕ϭϱϱϴ113

4B1-1I

A general view on hydrophobicity
Kenichiro Koga, Mario Ishizaki
Department of Chemistry, Okayama University, Japan
Solubility of hydrophobes in water is very low. There are, however, many othercombinations of solutes and solvents that give low solubility. For example, argondissolves very little in hydrazine. What grants a special interest to hydrophobes inwater is the following observation: transfer of a hydrophobic solute in water is infact energetically favorable, that is, the transfer is entropically so unfavorable thatthe net solvation free energy is large and positive [1]. This is thermodynamicallyequivalent to that the solubility of hydrophobes in water becomes even lower as thetemperature is raised. This temperature dependence of solubility is well known for
noble gases and many hydrocarbons in water.
Above arguments implicitly assume the process of solvation or the process oftemperature change is carried out at ﬁxed pressures. The constant-pressure condition is a natural choice for most experiments; the constant-volume condition isanother possible choice, often employed in theoretical calculations. If the original
phase from which a solute is transferred is an ideal gas and the ﬁnal phase is somecondensed phase β, diﬀerence between solvation entropy ΔSp∗ for a constant-pressure
condition and ΔSV∗ for a constant-volume condition, or equivalently diﬀerence between solvation enthalpy ΔHp for a constant-pressure process and solvation energy
ΔUV for a constant-volume process, is given by
ΔSp∗ ΔSV∗ΔHp ΔUVβ VAβ
−1
−
=
−
=
k
k
kT
kT
kχβ
where β is the coeﬃcient of thermal expansion, χβ the isothermal compressibility,
and VAβ the molar volume of solute, all deﬁned in the β phase. For inﬁnitely dilute
Lennard-Jones (LJ) solutions [2], these solvation thermodynamic quantities are calculated as functions of ε and σ, the solute-solvent LJ energy and size parameters. It
was found that the solvation analogous to the hydrophobic hydration is realized fora wide range of the LJ parameters if the constant-volume process is assumed. If theconstant-pressure is assumed the range of the parameters in which the “hydrophobic
hydration” is realized still exists but is very small. We will compare what we found
for the LJ solution with those in a realistic model solvent of water.
[1] B. Widom, P. Bhimalapuram, and K. Koga, Phys. Chem. Chem. Phys., 5,3085-3093 (2003).
[2] M. Ishizaki, H. Tanaka, K. Koga, Phys. Chem. Chem. Phys. 13, 2328-2334(2011).

114

4B1-3I

Computational Investigations of Complex Aqueous Solutions andHeterogeneous Ice Nucleation
Gren Patey, Rini Gupta, Jingyi Yan
Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
This talk is divided into two parts. In the ﬁrst part, we will discuss recent
results for complex aqueous solutions such as mixtures of water and 2-butoxyethanol.
These solutions are complex because the solutes tend to associate even at very low
concentrations, giving structures on mesoscopic length scales. We will discuss thenature and origin of such structures in light of molecular dynamics simulations onvery large systems (up to 32,000 molecules), that are necessary to explore mesoscopic
behavior. Results for diﬀerent systems and models will be described, and where
possible comparisons will be made with experimental data.
The second part of the talk will describe surface induced ice nucleation. Heterogeneous ice nucleation is very important in many physical situations, being particularly important for cloud formation in the upper atmosphere. We will show thatsome particular surface-ﬁelds that extend only a short distance (∼ 10Å) from thesurface can eﬀectively cause ice to nucleate and grow in undercooled water.

115

4B1-5C

Hund’s rule and conjugate Fermi hole in two-electron atomic systems
Tokuei Sako
Laboratory of Physics, College of Science and Technology, Nihon University, Japan
Hund's rules initially derived empirically in atomic spectroscopy of pre-quantum-mechanics
era consist of three rules that predict the ordering of the energy levels possessing different spinand orbital angular momentum quantum numbers. These three rules, particularly the first one
concerning the spin multiplicity, proved to be almost universally valid not only for atomic
systems, but for molecules and artificial atoms [1]. Concerning the origin of this first rule, a
traditional interpretation given by Slater has been often quoted, which says that a higher spin state
has a smaller electron repulsion energy[2]. However, actual quantum chemical computations for
singly-excited states of the helium atom, performed initially by Davidson [3], have showed thatthe triplet state with the higher spin multiplicity has a larger electron repulsion energy than does
the corresponding singlet state possessing the lower spin. This indicates that the reason for alower energy of the triplet state relative to the corresponding singlet cannot be due to a decrease in
the electron repulsion potential, but must be ascribed to a more compact electron density
distribution of the triplet state, which then results in a much larger energy decrease due to the
nuclear attraction potential.Nonetheless, there still exists an ambiguity concerning the reason
why the triplet state has a more compact electron-density distribution than the corresponding
singlet state. In our previous study [1], the origin of the Hund's multiplicity rule in two-electron
artificial atoms was studied and the mechanism for a more compact electron density distribution
in the triplet state than that of the corresponding singlet state was clarified by examining thenodal pattern of the wave functions in the internal space. Motivated by this earlier analysis thepresent study examines the internal wave functions of the helium and He-like two-electron
atomic ions in order to provide a deeper understanding into the workings of the first Hund's rule.
The internal part of the full configuration interaction wave functions for low-lying
singlet-triplet pairs of states has been extracted and visualized in the three-dimensional internal
space ( r1 , r2 , I  ) . The electron-electron repulsion potential has been also visualized in theinternal space. It manifests itself by three striking poles, penetrating exactly into the spatial region
defined by the Fermi hole. Because of the existence of these strong potential poles in the vicinityof the Fermi hole, a major part of the singlet probability has to escape from this region. In contrast,
the corresponding triplet wave function is less affected by these poles thanks to the presence of
the Fermi hole. The evading singlet probability was shown to migrate far away from the original
region close to the origin to the region where either r1 or r2 are large. This results in a more diffuse
electron density distribution of the singlet state than the corresponding triplet state. The
mechanism of the evolution of the singlet probability towards the large ri (i = 1, 2) region in thepresence of the electron repulsion potential has been rationalized on the basis of a new concept of
the so-called conjugate Fermi hole [4].
[1] T. Sako, J. Paldus, G.H.F. Diercksen, Phys. Rev. A 81 (2010) 022501.
[2] J. C. Slater, Phys. Rev. 34 (1929) 1293.
[3] E.R. Davidson, J. Chem. Phys. 41 (1964) 656; ibid. 42 (1965) 4199.
[4] T. Sako, J. Paldus, A. Ichimura, G.H.F. Diercksen, Phys. Rev. A 83 (2011) 032511.

116

4B2-1CFirst-principles modelling of dynamic, dielectric and catalytic
properties of various materials for the production and storageof energy
Philippe Baranek
EDF R&D, Department MMC, Avenue des Renardières,F-77818 Moret-sur-Loing Cedex, France
Many of materials based on alkaline-earth or transition metals have a wide range ofapplications (fuel cell, storage of energy, catalysts, photovoltaic, thermoelectricity…) due
totheir
peculiar
properties(high-dielectric
constants,
ferroelectricity,
thermoelectricity…). The knowledge of their bulk and surface properties is essential indesigning targeted devices with high performance. For instance, ABO3 perovskites are
peculiarly interesting for their atomic structural flexibility(for instance, allowing highnumber of atoms substitutions) which gives them specific chemical and electricalproperties compared to the pure compounds. In this context, first-principles calculations
can be useful to understand the structural and electronic properties of these materials.
This contribution will focus on the use of the first-principles methods in various fields ofmaterials sciences and applications, such as phase transitions, catalysis, storage of energy,
thermoelectricity ….
Further examples of applications of quantum mechanical approaches of the oxides andinter-metals properties will be described: among them: the study of the pressure driven
phase transitions and their influences on the ABO3 high-dielectric response, the study of
CO2 tolerance and/or the protons diffusion in perovskites. The studies of the properties ofnovel thermoelectric materials based on inter-metallic compounds will be also presented.
All the studied phenomena are analysed in terms of evolutions of the atomic andelectronic structures, of the spontaneous polarization, electronic structure, phonon anddefects effects. It will be shown that a good agreement between calculated, and, othertheoretical and experimental various properties can be obtained. This contribution will
also illustrate the complementarity between the theoretical approaches and theexperimental methods used to characterize the various properties of materials (IR, Raman,
EXAFS, …), and, the link between the calculated observables and the physical data ofinterest (phonons, thermoelectric properties, …).

117

4B2-2C

Density functional theory study on charge-transfer and local
excitation states of Pentacene/C60 model complex
Takuya Minami,1 Masayoshi, Nakano,1 Fréderic Castet2
1
Department of Materials Engineering Science, Graduate School of Engineering Science,
Osaka University, Toyonaka, Osaka 560-8531, Japan
2
Université de Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, 351
Cours de la Libération, 33405 Talence, France
I. Introduction
The reliability of the calculation methods is investigated for the excited states on the
pentacene/C60 model complex as the minimal structural unit of the donor-acceptor
heterojunction in pentacene/C60 organic cells. We have focused on the lowest excitationenergies for the local excited state of pentacene (LXP) and the charge-transfer excitedstates (CTX), as well as their difference (CTX-LXP), which are the key factors for the
charge separation process in the pentacene/C60 organic cells. In this study, we clarify
the applicability of the long-range corrected density functional theory (LC-BLYP)
method together with a tuning scheme of its range separating parameter to thereproduction of the excitation energies of the pentacene/C60 model.
II. Results
The geometries are optimized at the B3LYP/6-31G** level of approximation for theisolated monomers. The range separating parameter (μ) of the LC-BLYP method is
optimized so as to meet the many-electron self-interaction free (ME-SIF) condition [1]both for the pentacene and C60, and thus we found the optimized parameter μ = 0.20.
Table 1 lists the excitation energies of the pentacene/C60 model (see Fig. 1). The
reference values are estimated from experimental data. All of the calculations [CIS,
B3LYP, LC-BLYP (μ = 0.00, 0.10, 0.20, 0.33, and 0.47)] are performed with the
6-31G* basis sets under the frozen core approximations. We found that the LC-BLYP(μ = 0.20) method under the ME-SIF condition semi-quantitatively reproduces thereference values all for LXP, CTX, and CTX-LXP, though the excitation energies are
sensitive to the calculation methods.
III. Reference
Table 1. Excitation energies in the pentacene/C60 model[1] Y. Zhang, W. Yang. J. Chem. [eV] (calculated by the 6-31G* basis sets)μMethodLXP CTX CTX-LXP
Phys. 109, 2604 (1998).

Figure 1. Pentacene/C60 model

Estimate--CIS--TD-B3LYP--TD-LC-BLYP 0.47
0.33
0.20
0.10
0.00

118

2.312
2.899
1.947
2.605
2.501
2.259
1.904
1.663

2.746
4.190
1.085
3.995
3.666
2.948
1.722
0.387

0.438
1.291
-0.862
1.390
1.165
0.689
-0.182-1.276

4B2-3C

Second hyperpolarizabilities of open-shell singlet metalmetal
multiple bonded systems
Hitoshi Fukui,1 Yudai Inoue,1 Yasuteru Shigeta,1 Masayoshi Nakano,1 Benoît
Champagne2
1
Graduate School of Engineering Science, Osaka University, Japan
2
Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix
(FUNDP), Belgium
I. Introduction
We have theoretically investigated open-shell singlet molecules as a novel class ofnonlinear optical (NLO) systems, and have revealed their structureproperty
relationship: singlet diradical systems with intermediate diradical characters (y) tend to
exhibit larger second hyperpolarizabilities () than pure diradical and closed-shell
systems [1,2]. Many polynuclear metal complexes are expected to show singlet
multi-radical nature due to the unpaired electrons in the d-orbitals of metal atoms. In
particular, metalmetal multiple bonded complexes are good NLO candidates because
they could present singlet multi-radical characters originating from interactions between
the d-orbitals, which can create d, d and d bonds as shown in Figure 1. In thepresent study, we theoretically investigate the diradical characters of d, d and d
orbitals [y(dX), where X = ,  or ] and  values of several dimetal systems withmultiple bond. We also analyze the contributions of these orbitals to  [(dX), where X= ,  or ] in order to reveal a relationship among the orbital symmetry, diradical
character and  value.
II. Results
Figure 2 shows the bond length (R) dependences of  and (dX) as well as those ofy(dX) for the dichromium system [Cr(II)Cr(II)] calculated by the UCCSD and UHF
methods. It is found that the d orbital dominantly contributes to , while thecontributions of the d and d orbitals are negligible. The (d) value is found to beenhanced in the intermediate y(d) region. The same results are observed for otherdimetal systems. We also discuss the effects of the charge on the  values and on thediradical characters.
1.0

1500

0.8

1000

0.6

500

0.4

0

0.2

d
d

-500
1.5

d

Figure 1. Molecular orbital diagramof dd interaction.

2.0

2.5

3.0

(d)
(d)
(d)
(total)

y [-]

d

d*

2000

 [a.u.]

d*
d*

y(d)
y(d)
y(d)

0.0
3.5

R [Å]

Figure 2. Variation of  and y withbond length (R) for Cr(II)Cr(II).

[1] M. Nakano et al., J. Chem. Phys., 125, 074113 (2006).
[2] M. Nakano et al., Phys. Rev. Lett., 99, 033011 (2007).

119

4B3-1I

Universal product angular-momentum distributions inphotodissociation and reaction collisions
G. G. Balint-Kurti1, P. S. Shternin2, O. S. Vasyutinskii2
1
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
2
Ioffe Institute, Russian Academy of Sciences, 194021 St.Petersburg, Russia
osv@pms.ioffe.ru
The talk reviews recent results on the full quantum mechanical treatment of the spin andorbital angular momentum recoil angle distributions of the products of chemical andphotochemical reactions in diatomic and polyatomic molecules. The distributions
obtained are presented in the body frame and in the molecular frame using the sphericaltensor formalism. The main result is that the recoil angle distribution can be written
irrespective of the reaction mechanism in a universal form in terms of the anisotropytransforming coefficients c KK i qi which contain all information regarding the reaction
dynamics and can be either directly determined from experiment, or calculated fromtheory.
The coefficients are scalar values which depend on the photofragment state
multipole rank (K), on the initial reagent spherical tensor rank (Ki ), and on component
qi of the ranks K and Ki projected onto the recoil direction k. An important newconservation rule is revealed through the analysis, namely that the component qi ispreserved in any scattering, or photolysis reaction. The coefficients c KK i qi act astransformation coefficients between the angular momentum anisotropy of the reactants
and that of the product. The results obtained are generalized to the case where thereaction reagents possess spin, or orbital electronic angular momentum polarization.
General expressions for the anisotropy-transforming coefficients beyond theaxial recoil limit contain scattering S-matrix elements and take into account all possible
types of nonadiabatic interactions in the reaction complex, as well as the full range ofpossible coherence effects. Several important particular cases of these expressions are
discussed. These are: (a) the role of the Coriolis interactions in the photolysis of linear
molecules which result is the molecular helicity non-conservation; (b) quasiclassicalapproximation of the molecular scattering function in the high-J limit.
The talk also reviews recent experimental results on photodissociation of anumber of polyatomic molecules and shows how the investigation of the determinedvalues of the speed-dependent parameter ȕ and higher rank anisotropy parameterssupported the interpretation of the photodissociation dynamics.
.
References[1] A. G. Smolin, O. S. Vasyutinskii, A..J. Orr-Ewing, Mol. Phys. 105, 885 (2007)[2] P. S. Shternin and O.S. Vasyutinskii, J. Chem. Phys. 128, 194314 (2008).
[3] A. G. Suits and O. S. Vasyutinskii, Chem. Rev. 106, 3706 (2008).
[4] V. V. Kuznetsov, P. S. Shternin, O. S. Vasyutinskii, J. Chem. Phys., 130, 134312(2009).
[5] G. G. Balint-Kurti and O. S. Vasyutinskii, J. Phys. Chem. A, 113, 14281 (2009)[6] M. B. Krasilnikov, V. V. Kuznetsov, A. G. Suits, O. S. Vasyutinskii, PCCP, 13,
8163 (2011)120

4B3-3I

StudiesofsolventmediatedlongͲrangeelectrontransferIBrͲ*...CO2and
excitedstatedynamicsofICNͲ*AnneB.McCoy
DepartmentofChemistryTheOhioStateUniversity
Columbus,OH43210USAIn this talk, I will discuss two recent studies in which understanding the spectroscopy and
dynamics of relatively small systems: IBrͲ CO2 and ICNͲ has led to insights into much broaderquestions.Specifically,whenIBrͲispromotedtoelectronicallyexcitedstatesthatcorrelatetoaʋ Å ʍ or a ʍ* Å ʍ transition it will dissociate to form IͲ+Br or I+BrͲ, respectively.  The
introduction of a single CO2 molecule is sufficient to open the charge transfer channel.
Interestinglyinthefirstcase(theʋÅʍexcitation)thistransferoccursata7ÅIͲBrseparation.
Investigating the origins of this observation provides insights into the mechanism for such alongͲrangechargetransfer.Inthesecondpartofthetalk,Iwillturnmyattentiontohowtheofvibrational and rotational structure to one of the photofragments affects the resultingdynamicsuponelectronicexcitationandelectrondetachment,andfocusonrecentstudiesonthe photoexcitation dynamics of ICNͲ.  In spite of the extensive literature on the electronic
structureanddissociationdynamicsofICN,muchlessisknownaboutICNͲ,andthisworkseeksto shed light on some surprising aspects of the excited state dynamics and photoelectron
spectrumofthisanion.


121

4B4-1I

The performance of Density Functional Theory for Hydrogen Bonded
Systems: Shortcomings and Solutions
S. Xantheas1, S. Yoo1, E. Aprà2, T. Ebata3
1

Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, 902
2

Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, WA 99352, USA
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak
Ridge, TN 37831, USA
3
Department of Chemistry, Graduate School of Science, Hiroshima University,
Higashi-Hiroshima, 739-8526, Japan

We will present an assessment of the accuracy of various density functionals indescribing non-covalent interactions between guest molecules (H2 H2O, NH3, CH4,
C2H2) and host functional molecules (calixarenes) (1) and thecoordination of hydroxide ions in water clusters (2). The
results of high-level electronic structure calculations at the
CCSD(T) level areused as benchmarks toassess the importanceof
dispersion
inrecentlydeveloped
density functionals.
We subsequently
evaluate the performance of functionals withand without dispersion corrections indescribing the melting temperature of liquidwater (3, 4). Based on these results we rely
on a relative-to-the-melting (Tm) rather than an
absolute temperature scale for comparing
results obtained with various models withexperiment.
Preliminary results on that
relative scale include the 2-D infrared (IR)
spectra (5) and the anisotropy of liquid water(6).
(1) N. Hontama, Y. Inokuchi, T. Ebata, C. Dedonder-Lardeux, C. Jouvet, and S. S. Xantheas, J. Phys.
Chem. A 114, 2967 (2010)(2) X. Sun, S. Yoo, S. S. Xantheas, L. X. Dang, Chem. Phys. Lett. 481, 9 (2009)(3) S. Yoo, X. C. Zeng and S. S. Xantheas, J. Chem. Phys. 130, 221102 (2009)(4) S. Yoo and S. S. Xantheas, J. Chem. Phys. 134, 121105 (2011)(5) F. Paesani, S. S. Xantheas and G. A. Voth, J. Phys. Chem. B, 113, 13118 (2009)(6) F. Paesani, S. Yoo, H. J. Bakker and S. S. Xantheas, J. Phys. Chem. Lett. 1, 2316 (2010).

122

4B4-3C

Ab initio fragment molecular orbital-molecular dynamics (FMO-MD)
study of solvation differences between cis- and trans-platins in water
Hirotoshi Mori,1 Natsumi Hirayama,2 Yuto Komeiji,3 Yuji Mochizuki4

1
Division of Advanced Sciences, Ocha-dai Academic Production,
Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan2
Department of Chemistry and Biochemistry, Ochanomizu University,
Graduate School of Humanities and Sciences,2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
3
National Institute of Advanced Industrial Science and Technology, Central 2, Tsukuba 305-8568, Japan
4
Department of Chemistry, Faculty of Science, Rikkyo University,
3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan

Since cis-platin ([PtIICl2(NH3)2]) is recognized as an anticancer substance, a lot of
studies have been devoted to the bio-chemical functions of its derivatives [1]. The
anticancer functions of cis- and trans-platins are completely different, namely cis-platin
is highly effective in treating various cancers while trans-platin has less anti-tumor
activity, on the basis of their distinct spatial arrangement of ligands to DNA. Despite
the extensive research on cis- and trans-platins and their derivatives, understanding of
the biochemical activities of these compounds still needs to be developed. It is wellknown that the final step of the antitumor treatment is the combination between
cis-platin and DNA, further leading to the physical and chemical modifications to the
DNA structure. On the other hand, it is believed that some preliminary steps, such assolvation process before reaching the final target, are also important to the efficacy ofdrugs. To reveal the different nature on the medical application between cis- andtrans-platins, their solvation in water, as the first step of biophysical chemistry
processes in living system, deserves to be investigated.
In this study, water solvation structures of cis/trans-platin were studied using
relativistic FMO-MD (fragment molecular orbital method based molecular dynamics)
simulations [2]. Time evolutions of natural charges
in hydrated cis/trans-platin are shown in Figure 1.
The widths of charge fluctuations are larger for Cl
and Pt than for NH3.
Further, the charge
fluctuations of Cl and Pt show good correlation witheach other, suggesting that there are charge transfer
interactions between them. The frequency of thecharge fluctuation is predicted to be 334 cm-1. The Figure 1: Time evolution of net chargefrequency is well assigned to the H2O-platin obtained by FMO(3)-MP2/MCPdzp.
intermolecular vibrational modes (311-321 cm-1) [3,4]shown in Figure 2. This means that the Cl-Pt bondstretching motion couples with those of hydrationwaters. Comparing the two isomers, we could
observe much more intense Cl/Pt charge fluctuation
for cis-platin. The difference of hydration between
cis/trans-platins and further quantum insights of the Figure 2: Intermolecular vibrationalmode between cis-platin and H2O.
solvation dynamics will be discussed.
Acknowledgement HM is supported by the Ocha-dai Academic Production project operated by Japan Science and Technology
agency (JST), Sumitomo Foundation, and Kyushu Univ. Advanced Scientific Computing project. Three (HM, YK, and YM) of theauthors also would acknowledge a Special Fund for Research by Rykkyo University.
References [1] A. V. Klein, T. W. Hambley, Chem. Rev. 2009, 109, 4911. [2] Y. Komeiji et al., Chem. Phys. Lett., 2003, 372, 342.
[3] Y. Mochizuki et al., Chem. Phys. Lett. 2011, 504, 95. [4] H. Mori et al., Chem. Phys. Lett. 2009, 476, 317.

123

4B4-4C

Multi component molecular theory
for hydrogen bonded systems and positronic compounds
Masanori Tachikawa1
1
Graduate School of Nano-Science, Yokohama-City University, Seto 22-2,
Kanazawa-ku, Yokohama 236-0027, Japantachi@yokohama-cu.ac.jp
Recently, we have developed some first-principles approaches for multi-component
systems including both electrons and nuclei (or positron) quantum-mechanically: (I)
Multi-component molecular orbital (MC_MO) [1,2], DFT (MC_DFT) [3], quantum
Monte Carlo (MC_QMC) [4], and (II) ab initio path integral molecular dynamics(PIMD) [5,6,7] methods.
First, we would like to show some application to positronic compounds of some
nitrile (-CN functional group) species. Recently, we have demonstrated that HCN, as thesimplest nitrile molecule, can bind a positron by the QMC approach [4]. We have also
found that the positron affinity (PA) value of acetonitrile with electronic
6-31++G(2df,2pd) and positronic [15s15p3d2f1g] basis set with the CI scheme of
MC_MO method is calculated as 4.96 mhartree [2], which agrees to within 25% withthe recent experimental value of 6.6 mhartree by Danielson et al. [8]. Our PA values ofacrylonitrile and propionitrile (5.70 and 6.04 mhartree) are largest among these species,
which is consistent with the relatively large dipole moments.
Next, we will show some results for nuclear quantum effect on some hydrogenbonded systems by using path integral simulation with 2nd and 4th order Trotter
expansion. We have elucidated the H/D isotope effect on deprotonated water dimer
anion H3O2- [5, 6] and fluoride ion-water cluster [7], particularly focusing on thegeometrical isotope effect.

References[1] T. Ishimoto, M. Tachikawa, and U. Nagashima, J. Chem. Phys., 124, 014112 (2006).
[2] M. Tachikawa, Y. Kita, and R. J. Buenker, Phys. Chem. Chem. Phys., 13, 2701
(2011).
[3] T. Udagawa and M. Tachikawa, J. Chem. Phys., 125, 244105 (2006).
[4] Y. Kita, R. Maezono, M. Tachikawa, M. Towler, and R. J. Needs, J. Chem. Phys.,131, 134310 (2009).
[5] M. Tachikawa and M. Shiga, J. Am. Chem. Soc., 127, 11908 (2005).
[6] K. Suzuki, M. Shiga, and M. Tachikawa, J. Chem. Phys., 129, 144310 (2008).
[7] K. Suzuki, M. Tachikawa, and M. Shiga, J. Chem. Phys., 132, 144108 (2010).
[8] J. R. Danielson, J. J. Gosselin, and C. M. Surko, Phys. Rev. Lett., 104, 233201(2010).

124

4B4-5C

 Anions Dramatically Enhance Proton Transfer across Water
Interfaces

Himanshu Mishra1,2,3, Shinichi Enami3,4,5, Robert J. Nielsen2, Michael R. Hoffmann1,3,William A. Goddard III1,2,6 and Agustín J. Colussi1,31Division of Engineering and Applied Sciences, California Institute of Technology,
California 91125, USA
2
Materials and Process Simulation Center, California Institute of Technology,
California 91125, USA
3
W. M. Keck Laboratories, California Institute of Technology, California 91125, USA
4
Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
5
Japan Research Institute for Sustainable Humanosphere, Kyoto University, Uji
611-0011, Japan
6
Division of Chemistry and Chemical Engineering, California Institute of Technology,
California 91125, USA

Many fundamental processes in chemistry and biology are driven by proton transfer(PT) across water interfaces with hydrophobic media. However, what distinguishes PT‘on water’ at the interface from conventional PT ‘in water’ in the bulk remains unclear.
Here we show that PT from gaseous nitric acid to liquid water is dramaticallyaccelerated by non-specific anions. We found experimentally that HNO3(g) fails todissociate on pure water surfaces but is fully deprotonated at the surface for 1 mM NaCland other electrolytes. Quantum mechanical (QM) calculations confirm that HNO3(g)dissociation on the surface of pure water is unfavorable despite its strong acidity in thebulk liquid. QM also shows that chloride polarizes and pre-organizes interfacial water,
thereby enhancing HNO3(g) adsorption and setting the stage for adiabatic PT. Ourfindings in this prototype system provide direct evidence of the critical role electrostatic
pre-organization plays in catalyzing proton transfers across water-hydrophobe interfaces,such as those involved in cloud acidification and enzymatic events.

1254C1-1I

Strong correlation of electrons in molecules and solids
Garnet Kin-Lic Chan,1
1
Department of Chemistry and Chemical Biology, Cornell University, USAI will discuss our work to treat electronic structure far away from mean-ﬁeld
in both molecules and solids, using one or more of the following approaches: (i)generalized correlator-Pfaﬃan wavefunctions, (ii) density matrix renormalizationgroup and related techniques, and (iii) density matrix embedding theory.

126

4C1-3I

The existence of thermodynamic limit and size-consistent design
So Hirata
Department of Chemistry, University of Illinois at Urbana-Champaign,
600 South Mathews Avenue, Urbana, Illinois 61801, U.S.A.
Why is energy extensive and is an application of statistical thermodynamics tochemistry valid? It has taken 40 years for mathematicians to complete the proof of theextensivity of energy or, equivalently, the existence of thermodynamic (infinite-volume)
limit of energy density. I will offer an alternative, more accessible proof of the extensivity of energy for electrically neutral, metallic and nonmetallic crystals by establishing
the same for its individual energy components, namely, the kinetic, Coulomb, exchange,
and correlation energies. On this basis, I will address size-consistent design of electronic and vibrational many-body methods. Our findings are summarized as follows: The
significance of the distinct use of the intermediate and standard normalization for extensive and intensive operator amplitudes, respectively; The extensive and intensive diagram theorems, which serve as the foolproof criteria for determining size consistency ofa method for extensive and intensive quantities; The extensive-intensive operator consistency theorem, which stipulates the precise balance between the determinant spaces
reached by extensive and intensive operators in a size-consistent excited-state method.
This work is financially supported by University of Illinois, U.S. National Science
Foundation (CHE-1118616 CAREER and OCI-1102418), and U.S. Department of Energy (DE-FG02-11ER16211). S.H. is a Camille Dreyfus Teacher-Scholar and an Alumni Research Scholar.

127

4C1-5C

Generalization of Constrained Unrestricted Mean-Field Methods forControlling Spin-Contamination: Application to Singlet-Triplet Splittings
Takashi Tsuchimochi,1 Gustavo E. Scuseria1,2
1
Department of Chemistry, Rice University, Houston, TX 77005-1892
2
Department of Physics and Astronomy, Rice University, Houston, TX 77005-1892
We have recently shown that unrestricted Hartree-Fock (UHF) variationally reduces to high-spin restricted open-shell Hartree-Fock when constraints are imposedon the eigenvalues of the spin density matrix[1]. This scheme, called constrained
UHF (CUHF), however, always reduces to restricted Hartree-Fock (RHF) for singlet systems even though they may exhibit an open-shell singlet electronic structure,
where a single reference wave function of RHF is well known to be inadequate. In thistalk, we extend the ideas behind CUHF and propose to control spin-contaminationin UHF by releasing the constraints in an active space while imposing elsewhere. If
the active space is properly chosen, our generalized CUHF method greatly beneﬁts
from a controlled broken-symmetry eﬀect while avoiding the massive spin contamination arising in the traditional UHF[2]. We show a simple generalization of MøllerPlesset perturbation theory in CUHF to include weak correlation, and also applyLöwdin’s projection operator to CUHF and obtain multireference wave functions
with moderate computational cost. We report results on singlet-triplet energy gaps
to show that our constrained scheme outperforms fully unrestricted methods. This
constrained approach can be readily used in Kohn-Sham (KS) density functional
theory with similar favorable eﬀects, provided that spin-contamination is given by
the KS orbitals as in UHF.
[1] T. Tsuchimochi and G. E. Scuseria, J. Chem. Phys. 133, 141102 (2010).
[2] T. Tsuchimochi and G. E. Scuseria, J. Chem. Phys. 134, 064101 (2011).

128

4C1-6C

Novel Basis-Set Free Approaches to Solving the Electronic
Schrödinger Equation
James S. M. Anderson,1 Paul W. Ayers2
1
2

Department of Physics, The University of Tokyo, Japan

Department of Chemistry and Chemical Biology, Canada

Few electronic structure methods are able to obtain the accuracy required to predictexperiments (less than a milliHartree error). The most obvious method for reliably
achieving this accuracy is the full-configuration interaction (Full-CI) method. However,Full-CI is very computationally expensive (exponential scaling) and as such is rarely usefulother than for benchmarking calculations. Full-CI is a method that would work forarbitrary Hamiltonians. Thus, Full-CI does not take advantage of the inherent smoothness
associated with the solutions to the electronic Hamiltonian. In the molecular electronic
structure problem simplicity arises from every electron being identical, and that theelectronic-Hamiltonian only contains one- and two-body symmetric operators. Thismodern grid-based approach takes into account these advantages neglected in the Full-CI
approach. Grid-based methods, often termed “basis-set free” methods, have been seen as
anathemas resulting from their reputation of exponential scaling. However, recent resultsfrom Griebel and others in the mathematics literature show how one may construct accurate
grids for performing cubature (multidimensional quadrature) with only polynomial scaling
when there is sufficient smoothness. Utilising these efficient grids for electronic structure
provides grid-based methods that scale polynomially while maintaining Full-CI accuracy.
In this presentation the formalism of the approach will be explained and recent results will
be demonstrated.

1294C2-1I

Orbital-Dependent Energy Expressions for Kohn–Sham Potentials
Viktor N. Staroverov
Department of Chemistry, The University of Western Ontario,
London, Ontario N6A 5B7, Canada
Suppose we are given an exchange-correlation Kohn–Sham potential vxc ([ρ]; r)whose parent functional is unknown. One can obtain the energy corresponding
to this potential by integrating vxc ([ρt ]; r) along a path of suitably parametrized
densities ρt (r). If the parent functional exists, then every path yields the same result;
otherwise, the energy is path-dependent. For potentials that are not functional
derivatives (i.e., for most model Kohn–Sham potentials), the path of uniformly scaleddensities, ρt (r) = t3 ρ(tr), usually gives the most sensible results. We explore a
distinctly diﬀerent path in which intermediate densities are constructed by ﬁlling
Kohn–Sham orbitals with fractions of an electron in accordance with the Aufbau
principle,
J−1

J = 1, 2, . . . , N|φi (r)|2 + t|φJ (r)|2 ,ρJt (r) =0t1i=1Here N is the total number of electrons in the system and φi (r) is the spatial partof the ith spin-orbital. Two versions of this method are examined: (i) one in which
the orbitals are found once by solving the N -electron Kohn–Sham equations withvxc ([ρ]; r) and then kept frozen along the entire path; (ii) using relaxed and fully
self-consistent Kohn–Sham orbitals at each point of the path. The frozen-orbital
Aufbau path leads to the following orbital-dependent energy expressionExc [ρ] =

dr

N  1

0

J=1

vxc ([ρJt ]; r) |φJ (r)|2 dt.

The relaxed-orbital path is shown to give the same result as the Janak theorem,
E[ρ] =

N  1

J=1

0

HOMO (J − t) dt,

where E is the total energy and HOMO (J − t) is the highest occupied Kohn–Shamorbital of the (J − t)-electron system. Possible applications of Aufbau paths are
discussed and numerical results for several model potentials are presented.

130

4C2-3C

TDDFT study on quantization behaviors of nonadiabatic couplings inpolyatomic systems
Chunping Hu, Ryo Komakura, Kazuyuki Watanabe
Department of Physics, Tokyo University of Science, Japan
Nonadiabatic couplings (NACs) play a central role in nonadiabatic quantum
simulations. For the efficient computation of NACs, time-dependent density functional
theory (TDDFT) methods have been developed in recent years [1-2], which eliminate
the necessity of constructing many-body wave functions. It was demonstrated that the
TDDFT approach well reproduced the quantization behaviors of NACs near Jahn-Teller
or Renner-Teller intersections, and gave results in an accuracy comparable towave-function based methods. However, preceding studies in the literature are mostly
limited to small three- or four-atom molecules, due to the computational cost. Therefore,
it is necessary to utilize the efficiency of TDDFT to study the quantization behaviors oflarger systems. This is particularly important for Jahn-Teller and Renner-Teller systems,
as the corresponding models are just based on the two-level hypothesis without further
considerations on the different symmetries of intersections.
In the present paper we present extensive calculations on polyatomic Jahn-Teller andRenner-Teller systems by examining the angular NACs between the ground state andthe first excited state, using the TDDFT scheme in Ref. [2]. Taking the sodium clusters(Nan, n d 11 ) as the example (which are well known for the Jahn-Teller distortions inequilibrium geometries), we show that the angular NACs show different quantization
behaviors as the symmetry of conical intersections changes with respect to the atomic
number n. The angular NACs in Na3 (C3v symmetry) converge to the quantized value of
0.5 when the contour radius q around the intersection point is decreased, while results ofother sodium clusters show significant oscillating behaviors, no matter how small thecontour radius q is. In spite of the above differences, the same “geometric phase” with avalue of ȧ can be obtained, by performing the integral of the angular NACs withrespect to the angles on the whole contour. This is consistent with the prediction of the
Jahn-Teller model. On the other hand, calculation examples on the HCnS ( n d 9 )systems show that the angular NACs in the polyatomic Renner-Teller systems arealways 1.0, showing no dependence on the atomic number n, as understood from thefact that the symmetry of the linear atomic chain does not change when n is increased.
[1] C. Hu, H. Hirai and O. Sugino, J. Chem. Phys. 127, 064103 (2007).
[2] C. Hu, O. Sugino, H. Hirai and Y. Tateyama, Phys. Rev. A 82, 062508 (2010).

131

4C3-1I

Embedding as a new perspective on electronic structure theory
Frederick R. Manby,1 P. J. Bygrave,1 C. R. Taylor,1 J. Womack,1
J. D. Goodpaster,2 T. Barnes,2 Thomas F. Miller III2
1
Centre for Computational Chemistry, School of Chemistry,
University of Bristol, Bristol, UK
2
Division of Chemistry and Chemical Engineering,
California Institute of Technology, Pasadena, California, USA
The concept of embedding is at the heart of electronic structure theory: even
Hartree-Fock theory works by considering the quantum mechanics of a single electron embedded in an eﬀective potential that approximately describes interactions
with the environment. Embedding has been used very widely in theoretical chemistry, and common examples of embedding of one kind or another include QM/MM
calculations, polarisable continuum and use of eﬀective core potentials. Here I will
discuss the use of embedding for high-accuracy description of condensed matter, and,more generally as a framework for developing new electronic structure methods.
The work on condensed-matter systems concentrates on various ways to incorporate many-body eﬀects into truncated many-body expansions, and can be used,
for example, in the study of organic crystals.
In more general terms, embedding will be explored as an alternative to inter-paircoupling (which led from the independent-electron pair approximation to coupledcluster theory) and to higher excitation levels.

132

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133

4C3-5C

Large-scale electronic structure calculation with ELSES
and its application to conjugated polymer
T. Hoshi,1,2 S. Nishino,3 S. Yamamoto,4 T. Fujiwara,3 Y. Zempo,5M. Ishida,6 T. Sogabe,7 S.-L. Zhang8,2
1
Department of Applied Mathematics and Physics, Tottori University, Japan
2
Japan Science and Technology Agency, Core Research for Evolutional Science andTechnology (JST-CREST), Japan 3 Center for Research and Development of Higher
Education, University of Tokyo, Japan. 4 School of Computer Science, Tokyo
University of Technology, Japan. 5 Computer and Information Sciences, Hosei
University, Japan. 6 Sumitomo Chemical Co., Ltd, Japan. 7 School of Information
Science and Technology, Aichi Prefecture University, Japan. 8 Department ofComputational Science and Engineering, Nagoya University, Japan
A simulation code ‘ELSES’, Extra-Large-Scale Electronic Structure calculation
code, was developed and realizes large-scale calculations with 103 -107 atoms. [1]Novel linear-algebraic theories, such as multiple Krylov subspace theory, were constructed for ‘order-N ’ algorithms in standard or generalized eigen-value equations.
Tight-binding form Hamiltonians are used. Application studies of metallic and insulating systems were carried out for nanostructured solid, nanowire and liquid.
The present paper focuses on poly-(9,9 dioctyl-ﬂuorene), known as a conjugatedpolymer and a promising material for future light-emitting devices. A previous theory paper [2] drove us to the present large-scale calculations. A molecular dynamics
simulation was carried out and is shown in Fig. 1 (a)-(c). In results, the relation is
discussed between the non-ideal nanostructures with bending and twisting and the
localized π wavefunctions of the highest occupied (HO) and lowest unoccupied (LU)
levels, shown in Fig.1 (d)(e). The above discussion is general and will construct asystematic understanding of related conjugated polymers.
(b)

(c)
(d)

7nm

(a)

(e)

Figure 1: (a)(b)(c) Molecular dynamics simulation of poly-(9,9 dioctyl-ﬂuorene).
The monomer unit is drawn in the inset of (c). (d)(e) A close-up of the resultant
structure with the HO and LU wavefunctions, respectively.
[1] See the web page for references; http://www.elses.jp [2] Y. Zempo, N. Akino,
M. Ishida, M. Ishitobi and Y. Kurita, J. Phys.: Condens. Matter 20, 064231 (2008).

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Kinetic energy and chemical binding
Mike Schmidt1, Klaus Ruedenberg1, Joe Ivanic2
1
Department of Chemistry, Iowa State University, Ames IA 50014, USA
2
Advanced Biomedical Computing Center, NCI-Frederick, Frederick, MD 21702 USA

The H2+ molecule, containing only one electron, is an ideal system forunderstanding what happens when a chemical bond forms. The threeimportant factors in forming this bond, namely the sharing of that electron,
the polarization of atomic orbitals, and the contraction of the atomic
orbitals are not complicated by many-body electron correlations.
Revisiting our old analysis[1] using converged basis sets[2,3] confirms its
correctness. The changes from a hypothetical system "H plus a proton
located at the correct H2+ bond distance" to the exact wavefunction of H2+will be analyzed in terms of these three changes. The analysis uses thevariational principle, and also the virial theorem, since the true H2+ function
must minimize the total energy E=T+V and the ratio |V/T| must be 2. The
results emphasize the importance of kinetic energy changes in causing bondformation. The conventional wisdom that increased electron density at thecenter of a bond causes a lowering of potential energy is demonstrably
false; rather, the ultimate origin of H2+'s lower potential energy iscontraction towards both nuclei.
The insight gained from the study of H2+ will be shown to apply to otherdiatomics. Consideration of H2 introduces e-e repulsions. New results will
be presented for cases such as Be2, B2, C2, N2, O2, and F2, which add thecomplication of inner shells, as well as multiple bonds, non-singlet states,
avoided crossings, or prominent dispersion interactions.
[1] K. Ruedenberg Rev. Mod. Phys. 34, 326(1962)[2] K. Ruedenberg, M. W. Schmidt J.Comput.Chem. 28, 391-410(2006)[3] K. Ruedenberg, M. W. Schmidt J.Phys.Chem.A, 113, 1954-1968(2009).
[4] M. W. Schmidt, K. Ruedenberg, J. Ivanic J.Phys.Chem.A 114, 8687-8696 (2010)135

4C4-3I

Quantum Chemistry Beyond Atomic Orbitals and Slater Determinants
Edward F. Valeev, Florian Bischoﬀ, Liguo Kong, Jinmei Zhang
Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
Atomic orbitals and Slater determinants have supported the development of
accurate quantum chemical theory since 1930s. They both are the pillars of the wellestablished ”technology” of quantum chemistry that is used to rationalize and guidemany experimental studies of today. However, augmenting and/or dismantling bothof these concepts may be necessary for truly predictive electronic structure methods.
First, I will describe our work on the explicitly correlated (R12) electronic structure methods that go beyond purely orbital approximation and describe the correlation of pairs of electrons directly in terms of the interelectronic distances. The
R12 methods attain higher precision (smaller basis set error) than the standard
wave function methods by the virtue of a more eﬃcient description of the Coulomb
correlation at short interelectronic distances. Our focus will be primarily on thedevelopment of R12 methods for modeling multiple electronic states.
In the second part I will discuss methods that do not use atomic orbitals. Atomic
basis sets are ubiquitous in electronic structure studies of molecules and are becoming popular for solids. In search for more universal and robust numerical representations we are exploring adaptive spectral-element basis sets that in principle
allow to compute wave functions with guaranteed high precision. Our focus will beon computing two-electron correlated wave functions in such bases. To make suchcomputations feasible it is essential to use low-rank (separated) representations forboth operators and functions. We will present pilot MP2 computations with suchan approach.

Figure 1: Multiresolution structure of the orbitals of the water molecule. The darkest
volume elements have the highest separation ranks.

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4C4-5C
Why sp2 Nanosilicons Should Not Form: Insight From Quantum Chemistry
E.F.Sheka
Peoples’ Friendship University of Russian Federation, 117198 Moscow, Russia
sheka@icp.ac.ru
Quantum chemistry theory concerns a common essence joining topics that seem absolutely
different at first glance. If radicals are well accepted characteristics for the molecular chemistry,
dangling bonds and magnetic electrons are typical terms for the surface science and magnetism.
However, actually, all the features are of the same origin and are connected with odd electrons ofatoms that form either molecules or surfaces and magnetic solids. The term stands from thedifference between the number of atom valence electrons and that of chemical bonds formed by
the atom. The very fact of the odd electron availability is absolutely necessary for an atomic
system to be peculiar, while not enough. The peculiarity implementation is directly dependent on
the odd electron behavior, mainly, on their coupling. The latter is particularly evident whencomparing basic regularities that govern nanoscience of carbon and silicon. Thus, in the case ofcarbonaceous substances such as ethylene or benzene and to some degree other aromatic
molecules, odd electrons are covalently bonded while silicoethylene as well as siliceous aromatic
molecules do not exist at all. The bare carbon surfaces are nonconductive and nonmagnetic whilesilicon surfaces are conductive and magnetic. sp2 Nanocarbons are both chemical and physicalreality while sp2 nanosilicons do not exist, and so forth.
A unified theoretical and/or computational quantum chemical odd-electron approach has
been suggested [1] making a unified consideration of different nanomaterials on the same
conceptual basis as well as on the same computational footing. The current paper presents theapproach application to the nanoscience of silicon involving electronic structure and magnetic
properties of siliceous sp2 analogues of carbon, such as fullerenes, nanotubes, and graphene, thus
proving the impossibility of their existence [2-4].
References
1. E.F.Sheka. Odd electrons in molecular chemistry, surface science, and solid statemagnetism. Int. Journ. Quant. Chem. 2007, 107, 2935-2955.
2. E.F.Sheka. May silicene exist? arXiv:0901.3663v1, 2009.
3. E.F.Sheka, L.A.Chernozatonskii. Broken spin symmetry approach to chemicalsusceptibility and magnetism of graphenium species. JETP 2010, 110, 123-134.
4. E.F.Sheka. Fullerenes: Nanochemistry, Nanomagnetism, Nanomedicine, Nanophotonics.
CRC Press, Taylor&Francis Group, Boka Raton, 2011.

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