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涉及芳香族氨基酸的CH/π相互作用:CHARMM色氨酸力场的优化

CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field.

作者信息

Macias Alba T, Mackerell Alexander D

机构信息

Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA.

出版信息

J Comput Chem. 2005 Nov 15;26(14):1452-63. doi: 10.1002/jcc.20281.

DOI:10.1002/jcc.20281
PMID:16088926
Abstract

High-level ab initio calculations have been carried out to study weak CH/pi interactions and as a check of the CHARMM force field for aromatic amino acids. Comparisons with published data indicate that the MP2/cc-pVTZ level of theory is suitable for calculations of CH/pi interaction, including the T-shape benzene dimer. This level of theory was, therefore, applied to investigate CH/pi interactions between ethene or cis-2-butene and benzene in a variety of orientations. In addition, complexes between ethene and a series of model compounds (toluene, methylindole and p-cresol) representing the aromatic amino acids were studied motivated by the presence of CH/pi interactions in biological systems. Ab initio binding energies were compared to the binding energies obtained with the CHARMM22 force field. In the majority of orientations, CHARMM22 reproduces the preferred binding modes, with excellent agreement for the benzene dimer. Small discrepancies found in the calculations involving methylindole along with a survey of published thermodynamic data for the aromatic amino acids prompted additional optimization of the tryptophan force field. Partial atomic charges, Lennard-Jones parameters, and force constants were improved to obtain better intra- and intermolecular properties, with significant improvements obtained in the reproduction of experimental heats of sublimation for indole and free energies of aqueous solvation for methylindole.

摘要

已进行高水平的从头算计算来研究弱CH/π相互作用,并以此检验用于芳香族氨基酸的CHARMM力场。与已发表数据的比较表明,MP2/cc-pVTZ理论水平适用于CH/π相互作用的计算,包括T形苯二聚体。因此,该理论水平被用于研究乙烯或顺-2-丁烯与苯在各种取向时的CH/π相互作用。此外,受生物系统中存在CH/π相互作用的启发,研究了乙烯与一系列代表芳香族氨基酸的模型化合物(甲苯、甲基吲哚和对甲酚)之间的复合物。将从头算结合能与用CHARMM22力场获得的结合能进行了比较。在大多数取向中,CHARMM22再现了优选的结合模式,与苯二聚体的结果高度吻合。在涉及甲基吲哚的计算中发现的小差异以及对已发表的芳香族氨基酸热力学数据的调查促使对色氨酸力场进行进一步优化。改进了部分原子电荷、 Lennard-Jones参数和力常数,以获得更好的分子内和分子间性质,在吲哚升华热的实验再现以及甲基吲哚水合自由能方面有显著改进。

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