この解説では,最近達成されたヘムタンパク質の全電子計算について紹介し,大次元固有値問題の困難とその解決方法について述べる。開発したProteinDFというプログラムもその並列化もオブジェクト指向プログラミングというソフトウエア工学の技法の上に成立している。この技法の効果と普及の必要性を説明する。

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ホームページを始めとするマークアップ式の構造化文書が注目を集めている。この方式を化学のドキュメンテーションに応用するにはその目的にみあった化学構造式の表現方法が必要である。著者らは, すでに文書中に化学構造式情報を埋め込むための線形化学表現XyMNotationを提案している^[1] 。この方式による入力コードは, IUPAC命名法を参考に単純な規則を取り入れたため, 文字列のテキスト情報としても, 化学構造式を化学者に理解可能なものである。本稿ではXyMNotationを印刷・出版に応用した例として, XyMTeXの開発についてのべる。さらにインターネットブラウザーでの活用例として, XyMJavaの開発について概略をのべる。

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The He, Li, and Li⁺ penetrations of the benzene ring are discussed from density functional theory (DFT) computations and intrinsic reaction coordinate (IRC) analyses. The high activation energy of more than 200 kcal/mol for the He penetration appears to derive mainly from the electrostatic repulsion between the benzene ring and the He atom. The activation energies decrease in the sequence of He > Li > Li⁺. The activation barrier for the Li⁺ penetration (160 kcal/mol) may be overcome under high-temperature and high-pressure conditions. If it occurs in preparing lithium intercalation graphite, we must change our concept of “staging” in graphite intercalation compounds.

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The conformations of phenol, anisole and guaiacol, especially solvent effect on the intra-molecular hydrogen bond were computed with semi-empirical molecular orbital calculation, MOPAC2000. Solvent effect on the conformations of phenol and anisole appears minimal. However, the optimum conformation of guaiacol was transformed from cis- to trans-forms by increase of specific conductivity of the solvent. This effect would be due to the break of intra-molecular hydrogen bond between phenolic hydroxyl and methoxyl groups caused by perturbation from polar solvents.

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The rate constants were experimentally obtained for the oxidative reaction of three monolignols (p-coumaryl, coniferyl and sinapyl alcohol) and four similar forms of 3-mono- or 3, 5-disubstituted p-coumaryl alcohols (3-ethoxy-, 3-propoxy-, 3-methyl- and 3, 5-dimethyl-p-coumaryl alcohol) by using horseradish peroxidase (HRP) -H₂O₂ as the oxidant. To investigate the factor determining reaction rate of each substrate, the molecular volume and the highest occupied molecular orbital (HOMO) energy were applied. The molecular volume was obtained by using optimum conformation data with MOPAC2000. And the HOMO energy was calculated with MOPAC2000 under four conditions, i.e., when the phenolic hydroxyl form of each compound is either neutral or anion, and when each substrate is at polar or nonpolar milieu.
We infer that the reason why 3, 5-disubstituted p-coumaryl alcohol deviates from the profiles of others was due to local steric hindrance and distortion effect of the substituted groups. In assuming anion/water, the reaction rates of substrates correlated with HOMO energies excluding 3, 5-disubstituted p-coumaryl alcohols. In alternate form and milieu, no suitable relationship between HOMO energies and reaction rates was obtained. From these results, we suggest that the rate-determining step in the oxidative reaction for 3-substituted p-coumaryl alcohol is where one electron is withdrawn by oxidized HRP under anion/water condition.

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