应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

Sr2+和Ba2+水分子体系结构和结合能的从头算和ABEEM/MM研究

应用从头算方法和ABEEM/MM浮动电荷分子力场, 研究了水合碱土离子团簇Sr²⁺/Ba²⁺(H₂O)_n (n=1-6), 构建了离子-水相互作用的ABEEM/MM势能函数, 获得了水合离子团簇的稳定结构, 计算了结合能. 计算结果表明, ABEEM/MM方法的结果和从头算方法的结果有很好的一致性. 进一步应用ABEEM/MM对Sr²⁺和Ba²⁺水溶液进行了分子动力学模拟. 对Sr²⁺水溶液, 得到的Sr²⁺-水中氧原子的径向分布函数的第一和第二最高峰分别位于0.257和0.464 nm处, 第一和第二水合层的配位水分子数分别为9.2和11.4; 对Ba²⁺水溶液, 得到的Ba²⁺与水中氧原子的径向分布函数的第一和第二最高峰分别位于0.269和0.467 nm处, 第一和第二水合层的配位水分子数分别为9.9和12.4. 这与实验值或其它理论模拟结果有较好的一致性. 对比外层的水分子, 金属离子的极化作用使得溶液中第一水合层中水分子的O―H键长增长, HOH键角减小.     

环多肽晶体的浮动电荷极化力场模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对五种环多肽晶体进行了研究. 与传统力场相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理地体现了分子中的电荷分布. 相对其他极化力场模型, 具有计算量较小的特点. 该模型下计算得到的环多肽分子单元相对实验测得的结构的原子位置、氢键长度和二面角的均方根偏差分别为0.009 nm、0.013 nm和5.16°, 能够很好地重复实验结果. 总体上, 其结果优于或相当于其他力场模型, 适用于对实际蛋白质体系的模拟和研究.     

微过氧化物酶水溶液的ABEEM/MM动力学模拟

应用原子-键电负性均衡浮动电荷分子力场(ABEEM/MM), 对微过氧化物酶水溶液进行了分子动力学模拟. 研究了水溶液对微过氧化物酶的结构, 血红素的皱裂构象以及轴配体咪唑基的取向的影响. 结果表明, 在水溶液中微过氧化物酶的骨架氨基酸是稳定的, 而血红素的皱裂构象在水分子的作用下趋于平面. 与血红素轴配体咪唑基键连的组氨酸决定着咪唑基的空间取向, 而咪唑基与血红素侧链的丙酸基的静电作用对其取向仅起次要作用.     

精密从头算与ABEEM／MM模型对水团簇（H2O）11 9种低能结构的计算

用精密从头算方法研究了(H2O)11的9种低能异构体的性质,包括优化的几何结构、结合能、偶极矩和氢键个数等,并且得出了515-a是(H2O)11的全局最低能结构.同时,也用ABEEM/MM(atom bond electronegativity equalization method/molecular mechanics)模型研究了这些性质,与从头算的结果进行了比较,得到了相符合的结果.这显示了ABEEM/MM模型在描述中等大小的水分子团簇结构上是成功的.     

An investigation of crambin and BPTI based on ABEEM/MM model

Molecular dynamics simulation studies on crambin,BPTI(298 K,in vacuo) have been performed by ABEEM/MM method. Some structural properties were discussed.The results show fair consistency with those from X-ray experiment,Moreover, ABEEM/MM model can properly describe the interactions of hydrogen bond of protein systems.     

应用QM与ABEEM/MM结合的方法研究NAMI-A的结构性质

应用量子力学(QM)与ABEEM浮动电荷力场(ABEEM/MM)相结合的方法研究了抗癌药物NAMI-A在水溶液中的结构性质. 所有的结构优化都是在DFT的B3LYP方法下采用6-31G(d,p)和LanL2DZ基组完成的, 没有加入任何限制性条件. 结果表明, 优化得到的NAMI-A构型受不同环境及方法的影响均有变化. 与气相中得到的构型相比, QM/MM迭代优化得到构型要比PCM的构型变化更明显. QM/MM (ABEEM/MM)迭代优化得到的NAMI-A构型比QM/MM (OPLS-AA)的变化要小. 总之, 溶剂通过极化效应对NAMI-A结构、电荷分布及径向分布函数等性质均有影响, 客观地处理极化效应才能正确地反映QM区的性质.     

水合氢离子团簇从头算和ABEEM/MM的理论研究

应用高水平的从头计算方法和ABEEM/MM模型, 研究了水合氢离子团簇H3O＋(H2O)n (n＝1～6), 优化得到了低能构象, 探讨了其结合能和稳定性, 显示出H3O＋(H2O)3局域结构的优势存在．对H3O＋(H2O)6VIa团簇的ABEEM电荷分布进行分析, 表明第一水合层水分子与水合氢离子之间的氢键相互作用要明显强于与第二水层水分子的氢键相互作用. 研究结果表明, ABEEM/MM方法计算的结果和从头算得到的结果存在很好的一致性.     

ABEEM/MM浮动电荷力场应用于血红素结构的研究

运用拟合的参数, 应用ABEEM/MM浮动电荷力场对血红素分子结构进行了模拟. 结果表明, 该力场与CHARMM力场相比, 能更好地模拟晶体结构. 计算的ruffing构象能与B3LYP/6-31G*计算结果的线性相关系数在0.98以上, 同时表明血红素分子中twist-angle对ruffing构象具有明显影响. ABEEM/MM力场计算的细胞色素c552中血红素分子的电荷分布与CHARMM固定电荷力场的比较, 更准确地反映了血红素分子的电荷分布以及极化现象.     

ABEEM浮动电荷分子力场在含离子体系中的发展和应用

离子水合及生物分子体系内离子选择性的微观作用机制是人们长期探索的重要课题,其难点在于如何合理精确地描述上述体系内的离子-水、离子-生物分子等各种相互作用.本文主要总结近年来原子-键电负性均衡浮动电荷分子力场（ABEEM/MM）在含离子体系中的发展和应用,包括离子水溶液、金属蛋白、离子-核酸碱基体系的研究.我们优选相关参数,构建上述体系的势能函数,并对气相水合离子团簇、离子水溶液、金属蛋白、离子-核酸碱基体系进行研究,模拟其结构、活性、热力学和动力学等性质.研究和比较结果表明,我们的ABEEM浮动电荷力场总体上优于其它力场方法,其精度可达到或接近高水平从头计算MP2方法.这为进一步探讨生物分子体系内的离子选择性、金属酶及其它含离子体系的结构和性质奠定了基础.     

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.     

血红素近轴侧基氢键的ABEEM/MM分子动力学模拟

应用ABEEM/MM浮动电荷力场对鲸鱼肌红蛋白及突变体进行了分子动力学模拟. 结果表明, 血红素近轴侧基不存在稳定的双氢键, 该氢键对轴配体咪唑的取向不起决定性作用, 而咪唑的取向与键联的组氨酸有密切联系. 同时表明, 血红素轴配体的柔性与其邻近的氨基酸和咪唑体积有关.     

Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM

Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.     

Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method

Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states. The Ru-N-O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°–138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru-N-O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first-step hydrolysates. The activation free energies of the nitrosylation reactions show that the H₂O-NO exchange reaction of [RuCl₄(Im)(H₂O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO–H₂O exchange reaction of [RuCl₃(NO)(Im)(DMSO)] is faster than that of [RuCl₃(H₂O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.     

应用ABEEM/MM模型研究水分子团簇(H2O)n (n=11～16)的性质

应用ABEEM/MM 模型计算了较大的水分子团簇(H2O)n (n=11~16)的各种性质,如：优化的几何构型, 氢键个数, 结合能, 稳定性, ABEEM 电荷分布, 偶极矩, 以及结构参数、平均氢键个数和强度, 增加的团簇结合能等.结果表明,从立方体结构到笼状结构的过渡出现在n=12的水分子团簇中,随着类似于笼状结构特点的不断增强,五元环的富集程度有所增加.     

Application of the ABEEM/MM model in studying the properties of the water clusters(H_2O)_n(n=7-10)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters(H2O) n(n = 7-10) ,such as optimized geometries,the hydrogen bonds number,cluster interaction en-ergies,stabilities,ABEEM charge distributions,dipole moments,structural parameters,and so on,and to describe the transition reflected by the hexamer region from two-dimensional(from dimer to pen-tamer) to three-dimensional structures(for clusters larger than the hexamer) .     

精密从头算与ABEEM/MM模型对水团簇(H2O)11 9种低能结构的计算

用精密从头算方法研究了(H2O)11的9种低能异构体的性质, 包括优化的几何结构、结合能、偶极矩和氢键个数等, 并且得出了515-a是(H2O)11的全局最低能结构. 同时, 也用ABEEM/MM(atom bond electronegativity equalization method/molecular mechanics) 模型研究了这些性质, 与从头算的结果进行了比较, 得到了相符合的结果. 这显示了ABEEM/MM模型在描述中等大小的水分子团簇结构上是成功的.     

Application of the ABEEM/MM model in studying the properties of the water clusters (H2O)n (n= 7- 1O)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters (H2O)n(n = 7-10), such as optimized geometries, the hydrogen bonds number, cluster interaction energies, stabilities, ABEEM charge distributions, dipole moments, structural parameters, and so on, and to describe the transition reflected by the hexamer region from two-dimensional (from dimer to pentamer) to three-dimensional structures (for clusters larger than the hexamer).     

Application of the ABEEM/MM model in studying the properties of the water clusters (H2O) n ( n =7?10)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters (H₂O) _n (n = 7−10), such as optimized geometries, the hydrogen bonds number, cluster interaction energies, stabilities, ABEEM charge distributions, dipole moments, structural parameters, and so on, and to describe the transition reflected by the hexamer region from two-dimensional (from dimer to pentamer) to three-dimensional structures (for clusters larger than the hexamer). Supported by the National Natural Science Foundation of China (Grant No. 20373021)     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.