共查询到20条相似文献,搜索用时 15 毫秒
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Alexey Aleksandrov 《Journal of computational chemistry》2019,40(32):2834-2842
Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox-active isoalloxazine system, which is capable of one- and two-electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water–solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin-containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc. 相似文献
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Henrique S. Fernandes Nuno M. F. S. A. Cerqueira Srgio F. Sousa Andr Melo 《Molecules (Basel, Switzerland)》2022,27(17)
The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand–protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store. 相似文献
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An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 ?. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems. 相似文献
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聚合物银纹化的分子机理 总被引:2,自引:0,他引:2
本文综述了近年来有关聚合物银纹化分子机理方面研究的进展情况。内容包括银纹的起源、生长、断裂过程以及各种结构关系对银纹的影响,并对几种典型的聚合物银纹形态进行了描述。 相似文献
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Abstract Molecular Mechanics calculation (Allinger's force field and MM2 1985 program) was successfully applied for the structure-reactivity studies of organophosphorus compounds in our laboratory. 相似文献
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Theasymmetrycatalysisisanimportantchemicalreactionwidelyusedinbiology,pharmacyalldagriculture.Itispreferredtoenantioselectivehydrogenationofmethylpyruvate(MP)oversuppoFtedplatiniumnanoclusters.Cinchonidine(CD)isamodifier,aco-catalysttothereaction.Withoutthemodifier,therewouldbenoenantioselectivitytothehydrogenationofpyruvate.Inordertoobtainbetterunderstandingofthemechanismofthereaction,especiallytheroleofthemoditler,thepresentstudybymolecularmodelinghasbeenperformedandtheresultsarereportedhe… 相似文献
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Enantiorecognitionisameasureofthediscriminationabilitybetweenenantiomericmolecules.Itisoffundamentalsignificanceinmanyareasofthechemicalandbiologicalsciences,italsoplaysanimportantroleinseparationofenantiomersbychromatography.Althoughtheintermolecularforces(hydrogenbonding,multipolarassociation,dispersionforces,chargetransfercomplexation,hydrophobicassociation.etc.)havebeenthoroughlystudiedandarewelldocumented,buthowtheseforcespreciselyworkinconcerttopromoteintermolecularactionisnotclearyet'.T… 相似文献
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A New Method for Studying Foaminess 总被引:1,自引:0,他引:1
A new method is proposed for studying the foaminess of surfactant solutions. The method is based on the determination of the stability of the foam monolayer in contact with the solution surface. Data on the foaminess of an aqueous sodium dodecyl sulfate solution are reported. 相似文献
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Dr. Michael A. L. Limb Dr. Reynier Suardíaz Dr. Ian M. Grant Prof. Adrian J. Mulholland 《Chemistry (Weinheim an der Bergstrasse, Germany)》2019,25(3):764-768
Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on lysozyme show significant distortion of the bound saccharide is required to facilitate the catalytic reaction. 相似文献
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杯芳烃构象的分子力学研究 总被引:2,自引:0,他引:2
杯芳烃是对位取代的苯酚与甲醛反应得到的环状缩合物,由于其独特的结构和易于衍生化的特点而受到广泛的关注[1].杯芳烃中苯酚单元由亚甲基相连,由于酚羟基端可经杯中央翻转而产生多种构象异构体.杯[4]芳烃有4种典型构象:杯式、部分杯式、1,2-交替式和1,... 相似文献
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