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Parallel synthesis method of the electronic structures for proteins/nucleic acids and the development of the analytic system of their structures and functions

Research Project

Project/Area Number 14340185
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionKYUSHU UNIVERSITY (2004-2005)
Hiroshima University (2002-2003)

Principal Investigator

AOKI Yuriko  Kyushu University, Faculty of Engineering Sciences, Professor, 大学院・総合理工学研究院, 教授 (10211690)

Co-Investigator(Kenkyū-buntansha) NAKA Kazunari  Hiroshima University, Faculty of Science, Research associate, 大学院・理学研究科, 助手 (30314727)
TAKEDA Kunio  Okayama Science University, Faculty of Engineering, Professor, 工学部, 教授 (10113193)
IMAMURA Akira  Hiroshima Kokusaigakuin University, President, 学長 (70076991)
GU Feng Long  Kyushu University, Faculty of Engineering Sciences, Researcher, 大学院・総合理工学研究院, 特任助教授 (80404036)
MAKOWSKI Marcin  Kyushu University, Faculty of Engineering Sciences, Researcher, 大学院・総合理工学研究院, 特任助手 (90404045)
茂木 孝一  九州大学, 大学院・総合理工学研究院, 助手 (30304835)
Project Period (FY) 2002 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥13,900,000 (Direct Cost: ¥13,900,000)
Fiscal Year 2005: ¥2,000,000 (Direct Cost: ¥2,000,000)
Fiscal Year 2004: ¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 2003: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2002: ¥4,400,000 (Direct Cost: ¥4,400,000)
KeywordsElongation method / parallel synthesis / Peptides / collagen triple helix / electronic states / Order-N method / total energy / quantum chemistry / エネルギー勾配法 / 高分子 / 階層的合成法 / 電子状態 / MOPAC / ポリエチレン / ポリシラン / 局在化分子軌道 / 構造転移
Research Abstract

In this work, some new improvements of the elongation method will be addressed. The elongation calculations are demonstrated to be much more efficient compared to the conventional one with high accuracy. The elongation CPU time is shown as linear or sub-linear scaling for quasi-one-dimensional systems. Parallel calculations were also succeeded in our systems.
In the elongation method, after we obtain the electronic structure of the starting cluster, we localize the canonical molecular orbitals into regional localized molecular orbitals so that any polymer chain can be built up by adding a monomer unit to this starting cluster step by step. By this fashion, any random polymer can be theoretically synthesized by the elongation method using parallel CPUs.
One can see from our publications that the elongation method can reproduce very high accuracy in total energy with much of CPU time savings compared to the conventional one. The model systems cover non-bonded water chain, weakly bonded system (polyethylene), and very delocalized polymer (polyacetylene). It can be seen that all these models, the elongation method can provide chemical accuracy for the energy compared to the conventional one. The differences can be given to be less than 10^<-8>Hartree/atom.
The advantages of the elongation method are also highlighted for larger conducting polymers like polyparaphenylene, polydiacetylene, polythiophene and their substituted systems as well as polypeptides like collagen triple helix. As this system is very large for any conventional treatment and the elongation treatment guarantees the accuracy and also gains much CPU time saving.

Report

(5 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • Research Products

    (43 results)

All 2006 2005 2004 Other

All Journal Article (31 results) Publications (12 results)

  • [Journal Article] Elongation method for linear scaling SCF calculations of polymers2006

    • Author(s)
      J.Korchowiec et al.
    • Journal Title

      Journal Chemical Modeling in Science and Engineering (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Elongation method and supermolecule approach for the calculation of nonlinear susceptibilities.Application to the 3-methyl-4-nitropyridine 1-oxide and 2-Methyl-4-nitroaniline crystals2006

    • Author(s)
      F.L.Gu et al.
    • Journal Title

      Journal Chemical Modeling in Science and Engineering (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Nonlinear Optical Properties of Alkalides Li+(calix[4]pyrrole)M-(M=Li,Na and Kl) : Alkali Anion Atomic Number Dependence2006

    • Author(s)
      W.Chen et al.
    • Journal Title

      J.Am.Chem.Soc.Communication 128

      Pages: 1072-1073

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Molecular design of a p-conjugated single-chain electronically conductive polymer2006

    • Author(s)
      A.Imamura et al.
    • Journal Title

      Int.J.Quantum Chem 106

      Pages: 1924-1933

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Royal-crown-shaped electride Li3-N3-Be containing two superatoms : new knowledge on aromaticity2006

    • Author(s)
      Z.Li et al.
    • Journal Title

      J.Comp.Chem (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Elongation Method for Polymers and its Application to Nonlinear Optics, in Atoms, Molecules and Clusters in Electric Fields : Theoretical Approaches to the Calculation of Electric Polarizabilities2006

    • Author(s)
      Feng Long Gu, Akira Imamura, Yuriko Aoki
    • Journal Title

      Imperial College Press(edited by G.Maroulis) (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Shape effect on the large first hyperpolarizability of alkalide systems : Li+(NH3)4M-(M=Li, Na and K)2006

    • Author(s)
      Y.-Q.Jing, Z.-R.Li, D.Wu, Y.Li, B.-Q.Wang, F.L.Gu, Y.Aoki
    • Journal Title

      Chem Phys Chem (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Effciency and accuracy of the elongation method as applied to the electronic structures of large systems2006

    • Author(s)
      M.Makowski, J.Korchowiecc, F.L.Gu, Y.Aoki
    • Journal Title

      J.Comp.Chem. (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Binary Clusters AuPt and Au6Pt : Structure and Reactivity within Density Functional Theory2006

    • Author(s)
      W.Q.Tian, M.Ge, F-.L.Gu, T.Yamada, Y.Aoki
    • Journal Title

      J.Phys.Chem.A (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Elongation method and supermolecule approach for the calculation of nonlinear susceptibilities. Application to the 3-methyl-4-nitropyridine 1-oxide and 2-Methyl-4-nitroaniline crystals2006

    • Author(s)
      F.L.Gu, M.Guillaume, E.Botek, B.Champagne, F.Castet, L.Ducasse, Y.Aoki
    • Journal Title

      Journal Chemical Modeling in Science and Engineering (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Elongation method for linear scaling SCF calculations of polymers2006

    • Author(s)
      J.Korchowiec, F.L.Gu, Y.Aoki
    • Journal Title

      Journal Chemical Modeling in Science and Engineering (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Analytical Method for Predicting Ferromagnetic Properties of Benzyl-Radical Polymers Based on NBMO Theory2006

    • Author(s)
      Y.Orimoto, Y.Aoki
    • Journal Title

      J.Chem.Theor.Comp. 2(3)

      Pages: 786-796

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Ab Initio MO Analysis of Interaction Paths between Radicals in Ferromagnetic Organic Systems2006

    • Author(s)
      Y.Orimoto, T.Imai, K.Naka, Y.Aoki
    • Journal Title

      J.Phys.Chem.A 110(17)

      Pages: 5803-5808

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Royal-crown-shaped electride Li3-N3-Be containing two superatoms : new knowledge on aromaticity2006

    • Author(s)
      Z.-R.Li, F.-F.Wang, D.Wu, Y.Li, W.Chen, X.-Y.Sun, F.L.Gu, Y.Aoki
    • Journal Title

      J.Comp.Chem. 27

      Pages: 986-993

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Nonlinear Optical Properties of Alkalides Li+(calix[4]pyrrole)M-(M=Li, Na and Kl) : Alkali Anion Atomic Number Dependence2006

    • Author(s)
      W.Chen, Z.Li, C.Sun, F.L.Gu, Y.Aoki
    • Journal Title

      J.Am.Chem.Soc.Communication 128

      Pages: 1072-1073

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Molecular design of pi-conjugated single-chain electronically conductive polymer2006

    • Author(s)
      A.Imamura, Y.Aoki
    • Journal Title

      Int.J.Quantum Chem. 106

      Pages: 1924-1933

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Quantum-Chemical Approach to the Solvatochromic Transition in Polysilane Derivatives2006

    • Author(s)
      Y.Orimoto, Y.Aoki
    • Journal Title

      J.Polym.Sci.Part B : Polymer Physics 44(1)

      Pages: 119-133

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Elongation method and supermolecule approach for the calculation of nonlinear susceptibilities. Application to the 3-methyl-4-nitropyridine 1-oxide and 2-Methyl-4-nitroaniline crystals2006

    • Author(s)
      F.L.Gu et al.
    • Journal Title

      Journal Chemical Modeling in Science and Engineering (in press)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Nonlinear Optical Properties of Alkalides Li+(calix[4]pyrrole)M-(M=Li, Na and Kl) : Alkali Anion Atomic Number Dependence2006

    • Author(s)
      W.Chen et al.
    • Journal Title

      J.Am.Chem.Soc.Communication 128

      Pages: 1072-1073

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Molecular design of a p-conjugated single-chain electronically conductive polymer2006

    • Author(s)
      A.Imamura et al.
    • Journal Title

      Int.J Quantum Chem (in press)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Elongation Method with Cut-off Technique for Linear SCF Scaling2005

    • Author(s)
      J.Korchowiec et al.
    • Journal Title

      Int.J.Quantum Chem 102

      Pages: 785-794

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] NBO-Based CI/MP Through-Space/Bond Interaction Analysis and its Application to Stereoelectronic Effects in SN2 Reactions2005

    • Author(s)
      Y.Orimoto, K.Naka, Y.Aoki
    • Journal Title

      Int.J.Quantum Chem (in press)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Elongation Method with Cut-off Technique for Linear SCF Scaling2005

    • Author(s)
      J.Korchowiec, F.L.Gu, A.Imamura, B.Kirtman, Y.Aoki
    • Journal Title

      Int.J.Quantum Chem. 102

      Pages: 785-794

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Calculation of Static(Hyper)Polarizabilities for p-Conjugated Donor/Acceptor Molecules and Block Co-Polymers by the Elongation Finite-Field Method2004

    • Author(s)
      S.Ohnishi, F.L.Gu, K.Naka, A.Imamura, B.Kirtman, Y.Aoki
    • Journal Title

      J.Phys.Chem.A 108

      Pages: 8478-8484

    • Related Report
      2004 Annual Research Report
  • [Journal Article] A new localization scheme for the elongation method2004

    • Author(s)
      F.L.Gu, Y.Aoki, J.Korchowiec, A.Imamura, B.Kirtman
    • Journal Title

      J.Chem.Phys. 121

      Pages: 10385-10391

    • Related Report
      2004 Annual Research Report
  • [Journal Article] An analytical molecular orbital approach in Tetrathiafulvalene Tetracyanoquinodimethane(TTF-TCNQ)2004

    • Author(s)
      T.Tada, Y.Aoki, A.Imamura
    • Journal Title

      Mol.Phys. 102

      Pages: 1891-1901

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Study on the optical and magnetic properties of C_<48>N_<12> azafullerene isomers2004

    • Author(s)
      F.L.Gu, Z.Chen, H.Jiao, W.Q.Tian, Y.Aoki, W.Thiel, P.R.Schleyer
    • Journal Title

      Phys.Chem.Chem.Phys. 6

      Pages: 4566-4570

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Elongation Method at Semi-empirical and ab initio Levels for Large Systems2004

    • Author(s)
      Y.Aoki, F.L.Gu, J.Korchowiec
    • Journal Title

      Lecture Series on Computer and Computational Sciences and Engineering 2004

      Pages: 775-778

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Evaluation of Nonlinear Susceptibilities of 3-Methyl-4-nitropyridine 1-oxide Crystal : An Application of the Elongation Method to Nonlinear Optical Properties2004

    • Author(s)
      F.L.Gu, B.Champagne, Y.Aoki
    • Journal Title

      Lecture Series on Computer and Computational Sciences and Engineering 2004

      Pages: 779-782

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 水素結合型アンモニアワイヤーに沿ったプロトン移動2004

    • Author(s)
      青木
    • Journal Title

      高分子 53(7)

      Pages: 512-512

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 高分子にみられる協同現象的構造移転反応に対するミクロな立場からの解析2004

    • Author(s)
      折本, 青木
    • Journal Title

      高分子加工 53(10)

      Pages: 435-441

    • Related Report
      2004 Annual Research Report
  • [Publications] Y.Kawabata, T.Itaya, K.Ueda, H.Ochiai, Y.Aoki, A.Imamura: "Novel-Type Charge-Transfer Complex Formation between Indoxyl Sulfate and Anthraquinonesulfonate Ions in an Aqueous Polyelectrolyte Solution"Polymer Journal. 35(1). 50-55 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] F.L.Gu, Y.Aoki, A.Imamura, D.M.Bishop, B.Kirtman: "Application of the Elongation Method to Nonlinear Optical Properties : Finite Field Approach for Calculating Static Electric (Hyper)polarizabilities"Molecular Physics. 101(10). 1487-1494 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] B.Champagne, D.Jacquemin, F.L.Gu, Y.Aoki, B.Kirtman, D.M.Bishop: "Pseudo Linear-Dependence Dependence and Long-Range Interaction Effects on the Polarizability and Hyperpolarizabilities of Stereoregular Polymers"Chem.Phys.Lett.. 373(5-6). 539-549 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Y.Kawabata, T.Itaya, K.Ueda, Y.Aoki, A.Imamura: "A Theoretical Treatment of Charge-Transfer Interaction in an Aqueous Solution of Polyelectrolyte"Polymer Journal. 35(7). 573-577 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Y.Orimoto, Y.Aoki: "Ab initio MP2 TS/TB Analysis of an Enhanced Hyperpolarizability βvalue by Considering the Effect of Electron Correlations in Donor-σ-Acceptor Systems"Phys.Rev.A. 68(6). 063808 1-063808 6 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] T.Tada, Y.Aoki, A.Imamura: "An analytical Molecular Orbital Approach in Tetrathiafulvalene Tetracyano-Quinodimethane (TTF-TCNQ)"Molecular Physics. (掲載予定).

    • Related Report
      2003 Annual Research Report
  • [Publications] T.Tada, Y.Aoki: "Efficient ab initio molecular-orbital approach to quasi-one-dimensional molecular crystals based on neighboring-interaction-localized molecular orbitals"Phys. Rev. B. 65. 1131131-1131134 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] F.L.Gu, Y.Aoki, D.M.Bishop: "Crystal orbital calculation of coupled-perturbed Hartree-Fock dynamic (hyper) polarizabilities for polydiacetylene and polybutatriene"J. Chem. Phys.. 117. 385-395 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Y.Aoki, T.Tada, Y.Orimoto: "poly(para-phenylene) with the end structure of CH_2-(C_6H_4)_n-provides nearly zero band gaps in long chains with n>6"Phys. Rev. B.. 66. 1931041-1931044 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Y.Orimoto, Y.Aoki: "pure Through-Bond State in Organic Molecules for Analysis of the Relationship Between Intramolecular Interactions and Total Energy"Int. J. Quantum Chem.. 92. 355-366 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Y.Orimoto, Y.Aoki: "Important Role of Si Main Chain for Solvatochromism in Poly[bis(4-propoxybutyl) silylene]"J. Polym. Sci. Part A : Polymer Chemistry. 41. 483-486 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] F.L.Gu, Y.Aoki, A.Imamura, D.M.Bishop, B.Kirtman: "Application of the elongation method to nonlinear optical properties : finite field approach for calculating static electric(hyper) polarizabilities"Mol. Phys.. (印刷中).

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2021-04-07  

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