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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments
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Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments

机译：基于有效片段势技术的量子力学和分子力学方法对生物分子系统的建模：柔性片段的建议

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摘要

Development and applications of a new approach to hybrid quantum mechanical and molecular mechanical (QM/MM) theory based on the effective fragment potential (EFP) technique for modeling properties and reactivity of large molecular systems of biochemical significance are described. It is shown that a restriction of frozen internal coordinates of effective fragments in the original formulation of the theory (Gordon, M. S.; Freitag, M. A.; Bandyopadhyay, P.; Jensen, J. H.; Kairys, V.; Stevens, W. J. J. Phys. Chem. A 2001, 105, 293) can be removed by introducing a set of small EFs and replacing the EFP-EFP interactions by the customary MM force fields. The concept of effective fragments is also utilized to solve the QM/MM boundary problem across covalent bonds. The buffer fragment, which is common for both subsystems, is introduced and treated specially when energy and energy gradients are computed. An analysis of conformations of dipeptide-water complexes, as well as of dipepties with His and Lys residues, confirms the reliability of the theory. By using the Hartree-Fock and MP2 quantum chemistry methods with the OPLS-AA molecular mechanical force fields, we calculated the energy difference between the enzyme-substrate complex and the first tetrahedral intermediate for the model active site of the serine protease catalytic system. In another example, the multiconfigurational complete active space self-consistent field (CASSCF) method was used to model the homolytic dissociation of the peptide helix over the central C-N bonds. Finally, the potentials of internal rotation of the water dimer considered. In all cases, an importance of the peptide environment from MM subsystems on the computed properties of the quantum parts is demonstrated.
机译：描述了一种基于有效片段势（EFP）技术的混合量子力学和分子力学（QM / MM）理论的新方法的开发和应用，该方法可对具有生物化学意义的大分子系统的性质和反应性进行建模。结果表明，在理论的原始公式中有效片段的冻结内部坐标受到限制（戈登，MS; Freitag，MA; Bandyopadhyay，P .; Jensen，JH; Kairys，V .; Stevens，WJJ Phys。可以通过引入一组小型EF并用常规MM力场代替EFP-EFP相互作用来删除2001、105、293）。有效片段的概念也用于解决跨共价键的QM / MM边界问题。在计算能量和能量梯度时，将引入和处理两个子系统通用的缓冲区片段。对二肽-水复合物以及带有His和Lys残基的二肽的构象的分析证实了该理论的可靠性。通过使用具有OPLS-AA分子机械力场的Hartree-Fock和MP2量子化学方法，我们为丝氨酸蛋白酶催化系统的模型活性位点计算了酶-底物复合物与第一个四面体中间体之间的能量差。在另一个例子中，使用多构型完全活性空间自洽场（CASSCF）方法来模拟肽螺旋在中心C-N键上的均质解离。最后，考虑了水二聚体内部旋转的可能性。在所有情况下，都证明了MM子系统的肽环境对量子部分的计算性质的重要性。

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