International Journal of Quantum Chemistry

Cover image for Vol. 113 Issue 4

Special Issue: Seventh Congress of the International Society for Theoretical Chemical Physics

15 February 2013

Volume 113, Issue 4

Pages i–iv, 393–618

Issue edited by: Hiromi Nakai, Kazunari Yoshizawa, Koji Ando, Takahito Nakajima, Erkki J. Brändas

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Computations of Chemical Reactions and Dynamics
    4. Computations of Structures, Properties and Functions of Complex Systems
    5. Computational Biochemistry and Biophysics
    6. Computational Meso- and Nano-Science
    1. You have free access to this content
      Cover Image, Volume 113, Issue 4 (pages i–ii)

      Article first published online: 22 JAN 2013 | DOI: 10.1002/qua.24384

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      Quartz is ubiquitous in the Earth's crust and its interaction with water is a crucial part in many environmental and geochemical processes. First principle molecular dynamics simulations are used by Mia Ledyastuti, Yunfeng Liang, and Toshifumi Matsuoka on page 401 to understand the formation mechanism and structure of defects in crystalline and amorphous silica. When interacting with water, germinal silanol species dominate the silica surface. The hydroxylation mechanism, the formation of the siloxane bridge Si[BOND]O[BOND]Si, and the peroxy Si[BOND]O[BOND]O[BOND]Si and Si[BOND]O[BOND]O[BOND]H defects of quartz in an aqueous environment are also revealed in detail in this work.

    2. You have free access to this content
      Inside Cover, Volume 113, Issue 4 (pages iii–iv)

      Article first published online: 22 JAN 2013 | DOI: 10.1002/qua.24385

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      The use of DNA as a molecular wire is explored by Peng Xie, Hiroyuki Teramae, Kai Liu, and Yuriko Aoki in the article on page 489. This theoretical investigation focuses in detail on the influence of the base composition and base sequence on the DNA conductivity, highlighting the role of the special guanine base in the charge transfer process, in which it can form an electron loss center.

  2. Computations of Chemical Reactions and Dynamics

    1. Top of page
    2. Cover Image
    3. Computations of Chemical Reactions and Dynamics
    4. Computations of Structures, Properties and Functions of Complex Systems
    5. Computational Biochemistry and Biophysics
    6. Computational Meso- and Nano-Science
    1. Theoretical study on the reaction mechanism of formation of 3,5-diacetyl-1,4-dihydrolutidine (pages 393–396)

      Hiroyuki Teramae and Yasuko Y. Maruo

      Article first published online: 7 APR 2012 | DOI: 10.1002/qua.24105

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      The reaction to form the lutidine derivative (3,5-diacetyl-1,4-dihydrolutidine) from pentane-2,4-dione is used for the explicit detection of the concentration of the formaldehyde. This study reports the reaction path of the formation of lutidine derivative with the ab initio molecular orbital method at HF/3-21G, HF/6-31G(d,p), and MP2/6-31G(d,p) levels.

    2. Temperature dependence of self-assembled molecular capsules consisting of gear-shaped amphiphile molecules with molecular dynamics simulations (pages 397–400)

      Jun Koseki, Yukiumi Kita, Shuichi Hiraoka, Umpei Nagashima and Masanori Tachikawa

      Article first published online: 7 APR 2012 | DOI: 10.1002/qua.24108

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      Molecular dynamics simulations were used to theoretically analyze dynamical properties of two kinds of self-assembled hexameric capsules consisting of gear-shaped methylated (1) or demethylated (2) molecules. Analyzing the temperature dependence of internal volumes of hexameric capsules, it was found that the disassembly temperatures of 16 capsule, 340 K, is higher than that of 26 capsule, 210 K. The large disassembly temperature difference is consistent with the corresponding experimental result that 16 is stable, whereas 2 exists as a monomer in aqueous methanol.

    3. The first-principles molecular dynamics study of quartz–water interface (pages 401–412)

      Mia Ledyastuti, Yunfeng Liang and Toshifumi Matsuoka

      Article first published online: 23 APR 2012 | DOI: 10.1002/qua.24138

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      The ability to understand the formation mechanism and structure of defects in crystalline and amorphous silica is of fundamental importance in earth sciences. This can be achieved by first–principles molecular dynamics. In the case of the interaction between water and quartz, it is found that germinal silanol species dominate the surface.

    4. Quantum chemical insights into the dissociation of nitric acid on the surface of aqueous electrolytes (pages 413–417)

      Himanshu Mishra, Robert J. Nielsen, Shinichi Enami, Michael R. Hoffmann, Agustín J. Colussi and William A. Goddard III

      Article first published online: 31 MAY 2012 | DOI: 10.1002/qua.24151

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      Dissociation of nitric acid at the surface of aqueous electrolytes pertains to vital atmospheric phenomena, but the underlying mechanisms remain uncertain. Quantum mechanical calculations are reported showing that interfacial anions catalyze proton transfer from HNO3(g) to the surface of water. Catalysis arises from the electrostatic reorganization of interfacial water molecules in the presence of anions.

    5. Density functional theory studies on the addition and abstraction reactions of OH radicals with terephthalate dianions (pages 418–422)

      Nobuaki Tanaka, Shigeo Itoh and Hiromasa Nishikiori

      Article first published online: 13 FEB 2012 | DOI: 10.1002/qua.24022

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      The addition and abstraction reactions of OH radicals with terephthalate dianions are investigated by density functional theory calculations that include solvent effects. For the addition reactions, those targeting the ipso- and ortho-carbons are predicted to be exoergic. The H-atom abstraction reaction is also predicted to be exoergic. On the basis of the rate constants calculated by means of the transition state theory, the H-atom abstraction reaction is determined to be the thermochemically favored path.

  3. Computations of Structures, Properties and Functions of Complex Systems

    1. Top of page
    2. Cover Image
    3. Computations of Chemical Reactions and Dynamics
    4. Computations of Structures, Properties and Functions of Complex Systems
    5. Computational Biochemistry and Biophysics
    6. Computational Meso- and Nano-Science
    1. Electronic structures and molecular structures of polyynes (pages 423–427)

      Akira Imamura and Yuriko Aoki

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24244

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      Polyynes have two types of π systems which are perpendicular to each other and compete to form double bonds. Different types of symmetric and antisymmetric combinations between neighboring π orbitals in these molecules cause different bond alternations, depending on the length of the carbon chain and type of end group. sp2 carbon atoms in both end groups yield equi-bond structures, leading to small HOMO–LUMO gaps.

    2. Mechanism of the aerobic oxidation of methanol to formic acid on Au8: A DFT study (pages 428–436)

      Sangita Karanjit, Karan Bobuatong, Ryoichi Fukuda, Masahiro Ehara and Hidehiro Sakurai

      Article first published online: 10 MAR 2012 | DOI: 10.1002/qua.24056

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      Under mild conditions, gold nanoparticles are known to be active for the selective oxidation of alcohols to carbonyl compounds. Density functional theory calculations suggests that the reaction mechanism of the aerobic oxidation of methanol to formic acid on Au8 clusters is a stepwise process, with the hydrogen abstraction of the methoxy species as rate-determining step.

    3. Theoretical investigation for the stability of the concave-bound cyclopentadienyl iron complex of sumanene (pages 437–442)

      Mitsutaka Okumura, Yasuyuki Nakanishi, Keiji Kinoshita, Satoru Yamada, Yasutaka Kitagawa, Takashi Kawakami, Shunsuke Yamanaka, Toru Amaya and Toshikazu Hirao

      Article first published online: 19 MAR 2012 | DOI: 10.1002/qua.24057

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      When metals interact with curved carbon π-surfaces they show a clear preference to binding to the convex side rather than the concave one. However, stereoselectivity of iron complexes for the concave surface of sumanene can be achieved with the selection of appropriate counterions.

    4. Oxygen activation and dissociation on h-BN supported Au atoms (pages 443–452)

      Min Gao, Andrey Lyalin and Tetsuya Taketsugu

      Article first published online: 27 MAR 2012 | DOI: 10.1002/qua.24066

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      Gold clusters possess unique catalytic activity in various oxidation reactions by molecular oxygen. Among the factors that influence this activity the cluster size and the interaction with the support are the most important. The effect of a so-called “inert” support, like hexagonal boron nitride (h-BN), on the molecular and dissociative adsorption of O2 is discussed in this article on the basis of the results of density functional theory calculations.

  4. Computational Biochemistry and Biophysics

    1. Top of page
    2. Cover Image
    3. Computations of Chemical Reactions and Dynamics
    4. Computations of Structures, Properties and Functions of Complex Systems
    5. Computational Biochemistry and Biophysics
    6. Computational Meso- and Nano-Science
    1. The nature of chemical bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II: Jahn-Teller distortion and its suppression by Ca doping in cubane structures (pages 453–473)

      K. Yamaguchi, S. Yamanaka, H. Isobe, T. Saito, K. Kanda, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya, M. Okumura, H. Nakamura, M. Shoji and Y. Yoshioka

      Article first published online: 17 JUL 2012 | DOI: 10.1002/qua.24280

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      While the roles of manganese ions in the CaMn4O5 cluster of oxygen evolving complex of photosystem II have been investigated in relation to the molecular mechanism of water splitting reaction, not much attention has been given so far to the Ca ion. By replacing Mn ions with Ca (or Sr) ion in the cubane structure it is found that Ca-doping suppresses Jahn-Teller effects for Mn ions.

    2. Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach (pages 474–478)

      Xichen Li, Eduardo M. Sproviero, Ulf Ryde, Victor S. Batista and Guangju Chen

      Article first published online: 22 MAY 2012 | DOI: 10.1002/qua.24143

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      The oxygen-evolving complex (OEC) of photosystem II, containing a Mn4Ca cluster at its core, is the only natural system that can form O2 from water and sunlight. Quantum mechanical calculations based on a cluster model have suggested a possible structure and mechanism for OEC. In this article, the theoretically obtained structure is further refined and combined with a fit to polarized extended X-ray absorption fine structure data.

    3. Computational modeling of standard reduction potentials of B12 cofactors (pages 479–488)

      Manoj Kumar, Wlodzimierz Galezowski and Pawel M. Kozlowski

      Article first published online: 22 MAY 2012 | DOI: 10.1002/qua.24155

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      The cleavage of the Co–C bond constitutes the key catalytic step of B12-dependent enzymes containing cobalamins as cofactor. As the weakening of that bond is related to the one-electron reduction of the cofactor, it becomes fundamental to achieve a detailed understanding of the redox properties of such enzymes. DFT calculations find the reduction potential of cobalamins to be directly correlated with the energy of their lowest unoccupied molecular orbitals.

    4. Electronic states of mixed base pairs systems of dna and the effect of base composition and sequences on the band structures using screw axis translational symmetry (pages 489–496)

      Peng Xie, Hiroyuki Teramae, Kai Liu and Yuriko Aoki

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24199

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      DNA molecule has the potential use as a molecular wire due to its unique overlapping orbitals of DNA base pairs. To further understand the charge transfer mechanism of DNA, this article used some theoretical findings to discuss the importance of base guanine (G) in the charge transfer process, and the effect of base sequences on the DNA conductivity.

    5. Theoretical studies of electrostatic effect of protein environment on electronic structures and chemical indices of the active site of oxygenated and deoxygenated hemerythrin (pages 497–503)

      Yu Takano, Kizashi Yamaguchi and Haruki Nakamura

      Article first published online: 7 APR 2012 | DOI: 10.1002/qua.24107

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      This is a report on the electrostatic effect of the protein environment on the electronic structures of the active site of hemerythrin (Hr) using hybrid density functional calculations. The electrostatic effects hardly affect the shape and symmetry of the singly occupied molecular orbitals but enhance the orbital interaction between the active core of Hr and oxygen molecule, suggesting that the protein environment intensifies the intrinsic ability of the active site and to express biological functions.

    6. A quantum chemistry study of Ds–Pa unnatural DNA base pair (pages 504–509)

      Takao Otsuka and Tsuyoshi Miyazaki

      Article first published online: 9 APR 2012 | DOI: 10.1002/qua.24094

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      There have been many attempts to generate new genetic alphabets to DNA. The unnatural Ds–Pa base pair shows a remarkable success in this direction and has a great chemical and biological potential. This article elucidates the intermolecule interactions of the pair using quantum chemistry calculations.

    7. Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor (pages 510–517)

      Patchreenart Saparpakorn, Masato Kobayashi, Supa Hannongbua and Hiromi Nakai

      Article first published online: 5 JUN 2012 | DOI: 10.1002/qua.24164

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      MK-4965 is a promising new drug that inhibits HIV-1 RTs and some of its most important mutants. Better insight into the binding modes of MK-4965 to HIV-1 RTs is obtained using divide-and-conquer based Hartree–Fock (HF) and second-order Møller–Plesset perturbation theory calculations. As they identify the main interaction between the two systems, these calculations offer a useful guide to the design of future, more efficient, HIV-1 RTs inhibitors.

    8. Comparison of a simulated λ Cro dimer conformational ensemble to its NMR models (pages 518–524)

      Logan S. Ahlstrom and Osamu Miyashita

      Article first published online: 21 FEB 2012 | DOI: 10.1002/qua.24029

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      Protein structures solved by X-ray crystallography and NMR represent just snapshots of the conformational ensemble, whereas proteins are dynamic and change conformations to function. The dynamical information achievable through molecular simulation can enhance the knowledge of experimentally solved structures by reconstructing the protein conformational ensemble in solution. In this study, simulation is used to reconcile differences in the experimentally solved structures of the λ Cro dimer, with particular emphasis on the NMR models.

    9. Full geometry optimizations of the mixed-valence CaMn4O4X(H2O)4 (X=OH or O) cluster in OEC of PS II: Degree of symmetry breaking of the labile Mn-X-Mn bond revealed by several hybrid DFT calculations (pages 525–541)

      K. Yamaguchi, H. Isobe, S. Yamanaka, T. Saito, K. Kanda, M. Shoji, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya and M. Okumura

      Article first published online: 13 APR 2012 | DOI: 10.1002/qua.24117

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      Several hybrid DFT methods were applied to full geometry optimizations of the CaMn4O4X(H2O)4 (X[DOUBLE BOND]OH1− (1) or O2− (2)) cluster in the OEC of PSII. The computational results for 2 indicated reduction of the Mn3_;Mn4 distance with the deprotonation of the bridging oxo group. The results for 1 are not inconsistent with an experimental proposal based on the new XRD structure, namely a protonated μ3-oxygen at the internal O(57) site of the cluster in the S1 state.

    10. Absorption and emission properties of various substituted cinnamic acids and cinnamates, based on TDDFT investigation (pages 542–554)

      Malinee Promkatkaew, Songwut Suramitr, Thitinun Karpkird, Masahiro Ehara and Supa Hannongbua

      Article first published online: 4 JUN 2012 | DOI: 10.1002/qua.24169

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      Cinnamates are widely used as UVA and UVB absorbers in commercial sunscreens. Their absorption properties and photochemical stability can be tuned by substitution at the molecule's aromatic ring. Time-dependent density functional theory is used in this study to aid the design of novel UVB blocking molecules by selecting the substituted methyl-cinnamate and cinnamic acid among different candidates with the desired photochemical and photophysical behavior.

    11. Molecular Dynamics simulations of azanaphthoquinone annelated pyrrole derivatives as anticancer agent in DNA duplex (pages 555–562)

      Auradee Punkvang, Pornpan Pungpo, Pharit Kamsri, Dararat Kasamsri, Apinya Srisupan, Patchreenart Saparpakorn, Supa Hannongbua, Peter Wolschann, Supakit Prueksaaroon and Nipawan Pongprom

      Article first published online: 7 APR 2012 | DOI: 10.1002/qua.24120

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      Currently, the cancer treatment using the existing drugs that act as topoisomerase II inhibitors is limited by their cardiotoxicity and drug resistance, leaving an open problem. This report provides an insight into the binding behavior of azanaphthoquinone annelated pyrrole derivatives acting as the novel DNA intercalating agents in the DNA duplex fragment, which is fruitful guideline for further development of novel DNA intercalating agents.

    12. Excitation energy transfer in GFP-X-CFP model peptides (X = amino acids): Direct Versus through-bridge energy transfers (pages 563–568)

      Tsutomu Kawatsu and Jun-ya Hasegawa

      Article first published online: 23 FEB 2012 | DOI: 10.1002/qua.24027

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      The role of the bridging protein media has been investigated using the quantum chemical calculations for the excitation energy transfer (EET) electronic coupling. A model peptide is adopted connecting cyan and green fluorescent protein chromophores (CFPc and GFPc), a CFPc-X-GFPc model, and the X (amino acids) dependence is examined. The major part of the EET coupling element arises from the direct interaction between CFPc and GFPc. The through-X interactions vary for the type of residues.

    13. Probable polybasic residues inserted into the cleavage site of the highly pathogenic avian influenza A/H5N1 hemagglutinin: Speculation of the next outbreak in humans (pages 569–573)

      Nopporn Kaiyawet, Thanyada Rungrotmongkol and Supot Hannongbua

      Article first published online: 4 APR 2012 | DOI: 10.1002/qua.24099

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      Avian influenza outbreaks over the past few years have captured the world's attention on possibility of bird to human transmission. This report proposes the possible insertion amino acid sequences at the HA cleavage site, which are speculated for new strains of highly pathogenic (to humans) avian influenza virus A/H5N1 that may cause the next outbreak.

    14. Quantum chemical study on molecular-level affinity of DJ-1 binding compounds (pages 574–579)

      Yasuhiro Shigemitsu

      Article first published online: 13 APR 2012 | DOI: 10.1002/qua.24132

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      A quantitative prediction of a ligand–receptor binding free energy has been a challenging task and an ultimate goal for in silico drug design. This article reports the performance of several modern computational techniques applied to the estimation of the binding energies of DJ-1, a key small protein to Parkinson's disease, with the three inhibitor candidates. The detailed mode of ligand–receptor interactions is also studied by means of fragment-based decomposition analysis.

  5. Computational Meso- and Nano-Science

    1. Top of page
    2. Cover Image
    3. Computations of Chemical Reactions and Dynamics
    4. Computations of Structures, Properties and Functions of Complex Systems
    5. Computational Biochemistry and Biophysics
    6. Computational Meso- and Nano-Science
    1. Interfacial dipole and band bending in model pentacene/C60 heterojunctions (pages 580–584)

      Julien Idé, Sébastien Mothy, Adrien Savoyant, Alain Fritsch, Philippe Aurel, Raphaël Méreau, Laurent Ducasse, Jérôme Cornil, David Beljonne and Frédéric Castet

      Article first published online: 7 FEB 2012 | DOI: 10.1002/qua.24006

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      Understanding of the mechanism governing the free charge carrier generation in organic photovoltaic cells is a hot issue in organic electronics. Devices combining electron-donating and electron-accepting organic materials can yield very high internal conversion efficiencies provided the energy levels of the two materials are properly tuned. In this article quantum chemical results are presented that further illustrate how the intrinsic band bending at the pentacene7sol;C60 model heterojunction can be tuned by the relative orientation of the molecules in the vicinity of the interface.

    2. Diradicalology in third-order nonlinear optical systems: Second hyperpolarizabilities of acetylene-linked phenalenyl-based superpolyenes (pages 585–591)

      Masayoshi Nakano, Ryohei Kishi, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Shu Minamide, Yudai Inoue, Taishi Yamada, Soichi Ito, Shabbir Muhammad, Yasuteru Shigeta, Takashi Kubo and Benoît Champagne

      Article first published online: 23 FEB 2012 | DOI: 10.1002/qua.24035

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      Third order non-linear optical properties of open-shell singlet systems are strongly correlated with their diradical characters. As such these properties can be controlled as a function of the diradical characters, a concept that it is referred to as “diradicalology”. In this work “diradicalology” is explored for a series of open-shell superpolyene systems, composed of acetylene-linked phenalenyl radicals.

    3. Comparative study of diradical characters and third-order nonlinear optical properties of linear/cyclic acenes versus phenylenes (pages 592–598)

      Shabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Shu Minamide, Ryohei Kishi, Yasuteru Shigeta and Masayoshi Nakano

      Article first published online: 16 MAR 2012 | DOI: 10.1002/qua.24032

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      A comparative study of the effect of diradical character on third-order NLO polarizabilities (γzzzz) of open-shell acenes versus closed-shell phenylene counterparts has been performed using the LC-UBLYP method. The γzzzz values of acenes with intermediate diradical characters are larger than those of closed-shell phenylenes, which are attributed to the open-shell singlet configurations of linear/cyclic acenes. A relationship among the architectures, diradical characters and γzzzz values of different acenes and phenylenes has been revealed.

    4. A theoretical study on the hydrogen transport mechanism in SrTiO3 perovskite. II. Scandium doping at titanium site (pages 599–604)

      Taku Onishi and Trygve Helgaker

      Article first published online: 29 MAR 2012 | DOI: 10.1002/qua.24086

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      Cubic SrTiO3 perovskite shows high proton conductivity, which is further enhanced by nitrogen-doping. The substitution of a titanium center with a trivalent cation such as scandium (Sc3+) yields an oxygen vacancy, as in the case of N-doping. The proton-conduction mechanism in Sc-doped SrTiO3 perovskite is studied in this article by means of density functional theory. It is found that the scandium-doping has no energetic advantage in the activation energy for proton-conduction.

    5. Antidot effects on the open-shell characters and second hyperpolarizabilities of rectangular graphene nanoflakes (pages 605–611)

      Kyohei Yoneda, Shu Minamide, Taishi Yamada, Soichi Ito, Takuya Minami, Ryohei Kishi, Yasuteru Shigeta and Masayoshi Nakano

      Article first published online: 7 APR 2012 | DOI: 10.1002/qua.24089

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      For rectangular graphene nanoflakes (GNFs) with/without antidot structure, the open-shell characters (yi) and second hyperpolarizabilities (γ) are investigated using the LC-UBLYP method. The antidot GNF is found to display intermediate yi values in contrast to the perfect one, which is regarded as a pure tetraradical system. The intermediate open-shell character of the antidot GNF turns out to cause the enhancement of the γ value, despite of the decrease in the number of π-electrons.

    6. Why sp2-like nanosilicons should not form: Insight from quantum chemistry (pages 612–618)

      E. F. Sheka

      Article first published online: 29 MAR 2012 | DOI: 10.1002/qua.24081

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      The creation of unpaired electrons in due course results from the C[DOUBLE BOND]C bond stretching until breaking. The blue box in the lower left corner marks the interval of the C[DOUBLE BOND]C bond lengths characteristic for sp2 nanocarbons according to the relevant numbers of unpaired electrons. The low amount of the latter explain a partial radicalization of the species. The longer length of Si[DOUBLE BOND]Si bonds and larger relevant numbers of unpaired electrons reveal a complete radicalization of the sp2 nanosilicons.

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