Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.15, 74-76, by J-STAGE]
<Title:> Grid Inhomogeneous Solvation Theoryを用いた血液凝固因子Xaの水和サイト解析
<Author(s):> 佐藤　博之, 松浦　東
<Corresponding author E-Mill:> shryk(at)jp.fujitsu.com
<Abstract:> The hydration structure in the active site of human coagulation factor Xa (fXa) was investigated from the viewpoint of excess free energy. Water distribution in the active site of fXa was calculated using partly constrained molecular dynamics (MD) simulation. Then the free energy of the distribution was evaluated using grid inhomogeneous solvation theory (GIST). The analyzed excess free energy shows excellent correlation to the experimental binding affinity of known ligands only if the side chain fluctuation of the active site of fXa was taken into account. This result indicates that the side chain fluctuation generated by partly constrained MD has an important role for identifying the appropriate hydration structure, and that GIST in combination with partly constrained MD provides useful information for assessing the protein-ligand binding affinity.
<Keywords:> Hydration structure, Partly constraind MD, GIST, Binding affinity, Excess free energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 57-59, by J-STAGE]
<Title:> Armchair α-Graphyne NanotubeのHOMO-LUMO Gapのチューブ長依存性
<Author(s):> 森川　大, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> 13st309e(at)shinshu-u.ac.jp
<Abstract:> Graphyne nanotubes (GNTs) are new carbon-based nanotubes and have a structure similar to the carbon nanotubes (CNTs). In the GNTs, armchair α-GNT is the highest resemblance to armchair CNT, and algebraic structure counts (ASC) are equal. This correspondence suggests that the HOMO-LUMO gaps in the finite-length armchair α-GNT oscillate with the increase of the tube length in the same fashion as the oscillation of HOMO-LUMO gaps in finite-length armchair CNT. In this work, the tube length dependences of the HOMO-LUMO gaps in the finite-length armchair α-GNT were examined by means of the H ckel method and density functional theory (DFT). It was found that the HOMO-LUMO gaps in armchair α-GNT oscillate as functions of the tube length with the period of 3.
<Keywords:> Graphyne nanotube, Carbon nanotube, Algebraic structure count, Kekul structure, HOMO-LUMO gap
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 60-62, by J-STAGE]
<Title:> ホモ/ヘテロダイマー系分子間振動の粗視化による分子間/分子内剛性の定量化
<Author(s):> 磯貝　実, 北條　博彦
<Corresponding author E-Mill:> houjou(at)iis.u-tokyo.ac.jp
<Abstract:> We have developed a method for quantifying the intermolecular forces in supramolecular systems by modifying our original method of coarse-graining intermolecular vibrations. We evaluated the true and apparent intermolecular stiffness constants for 21 dimers composed of formic acid-, acetic acid-, trichloroacetic acid-, formamide-, formamidine- or urea-monomer. In this method, the atomic displacement vectors of a dimer were projected onto a subspace spanned by bases corresponding to 12 relative translational and rotational motions and several intramolecular vibrations that are coupled with intermolecular vibrations. The intermolecular stiffness constants showed moderate linearity with the corresponding dimerization energies. The apparent stiffness constant can be explained by a mechanical model using inter- and intramolecular stiffness constants of the constituent monomers.
<Keywords:> Intermolecular forces, Normal mode analysis, Coarse graining, Principal component analysis, Hydrogen bond, Terahertz spectroscopy
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0039/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 63-65, by J-STAGE]
<Title:> 量子化学計算情報を記述子とした機械学習に基づく反応予測手法の開発
<Author(s):> 藤波　美起登, 清野　淳司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We have developed a novel reaction prediction system, which uses machine learning with quantum chemical descriptors. Numerical assessments of the system were performed on basic polar and radical organic chemical reactions. The accuracy of the present system was close to that of a previous system having machine learning with topological information, which is termed ReactionPredictor.
<Keywords:> Reaction prediction system, Quantum chemical descriptor, Machine learning, Neural network, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 66-67, by J-STAGE]
<Title:> 化学・生命科学系の理学教育における3Dプリンタの活用事例
<Author(s):> 望月　祐志, 中村　昇太, 山中　正浩, 山田　康之, 工藤　光子, 常盤　広明, 川上　勝, 北本　俊二
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> Recently, technologies and applications of 3D-printers have attracted practical interests in the contexts of manufacturing and research developments. In contrast, the educational usages have still been underway. In this Letter, we report a variety of demonstrative 3D-printed molecular models used for education of chemistry and biology in our faculty of Science.
<Keywords:> Science Education, 3D-printers, On-demand molecular models, DNA, Proteins, Catalysts, Orbital lobes
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 68-70, by J-STAGE]
<Title:> Implementation of Efficient Two-component Relativistic Method Using Local Unitary Transformation to GAMESS Program
<Author(s):> Yuya NAKAJIMA, Junji SEINO, Michael W. SCHMIDT, Hiromi NAKAI
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> This Letter provides an implementation of an efficient and accurate relativistic method based on the infinite-order two-component scheme with the local unitary transformation (LUT-IOTC) to the GAMESS program. The sample input and major capabilities in GAMESS are shown as well as the accuracies and efficiencies in energy and analytical energy gradient calculations. The scheme realizes calculations of molecules containing heavy elements with four-component relativistic accuracy and the non-relativistic computational cost.
<Keywords:> Relativistic effect, Linear-scaling, Infinite order Douglas Kroll Hess transformation, Divide-and-conquer method, Local unitary transformation
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 15-15, by J-STAGE]
<Title:> 計算化学連携講座 於:都立戸山高等学校
<Author(s):> 内田　希
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_foreword_15_3/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 49-50, by J-STAGE]
<Title:> [Mg(DMF)₆]²⁺の構造に及ぼす結晶中の陰 イオンの効果
<Author(s):> 山　博史, 伊藤　美咲, 三橋　了爾, 御厨　正博
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> In a crystal, an octahedral magnesium(II) complex cation, [Mg(DMF)₆]²⁺ (DMF: N,N-dimethylformamide), was found to exist as a C₂ conformer, which was thought to be energetically unfavorable. In order to find the reason for this, structural analysis was conducted on the basis of semi-empirical PM6 method and density functional theory method. The C₂ conformer was not found to be stable in a vacuum; however, it was found to be stabilized when surrounded by four tetraphenyl borate anions like the crystal structure.
<Keywords:> マグネシウム錯体, DMF錯体, 結晶構造, 配座異性体, 密度汎関数法
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 51-52, by J-STAGE]
<Title:> ペプトイド類のフラグメント分子軌道計算
<Author(s):> 川田　修太郎, 坂口　正貴, 米倉　伊吹, 奥脇　弘次, 望月　祐志, 福澤　薫
<Corresponding author E-Mill:> kawada(at)rikkyo.ac.jp
<Abstract:> Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.
<Keywords:> Peptoid, Fragment Molecular Orbital Method, Nanobiotechnology, Self-assembling, Crystallization
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0032/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 53-54, by J-STAGE]
<Title:> 軟X線分光法による炭酸水溶液の電子状態と構造
<Author(s):> 西田　尚大, 堀川　裕加, 徳島　高, 高橋　修
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp
<Abstract:> We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of carbonate in the liquid phase at the oxygen K-edge. Structure sampling as a cluster model was performed from a snapshot of the first principles molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. Theoretical XES spectra for CO₃^2- and HCO₃^– were well reproduced experimentally and that for H₂CO₃ was predicted.
<Keywords:> Soft X-ray absorption spectroscopy, soft X-ray emission spectroscopy, carbonate, DFT, meta-dynamics method
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0030/_article/-char/ja/