基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性（英文）

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别.尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用.量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述.但是在分子模拟中采用量子化学方法则太昂贵了.近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境.在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的.随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息.本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性.计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性.并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

利用电子结构数据拟合H2分子的电子壳模型势函数参数

电子壳模型势函数在离子晶体的原子级计算机模拟中有广泛应用,其势参数主要通过拟合晶体的实验数据或电子结构数据得到.提出了通过拟合双原子分子的量子化学从头计算电子结构数据来获得该势函数的方法,并由H2分子的电子结构数据建立了H原子间的电子壳模型势函数.此外,还应用该势函数对H+2分子离子进行了计算.该势函数拟合方案更适合于共价键型的分子.     

高压下金属铌熔化曲线的分子动力学模拟

铌作为一种高熔点的金属,广泛应用于制作合金材料. 铌的高温高压熔化曲线对于铌基合金的实际应用具有重要影响,但目前还未被成功研究. 本文中,我们采用铌目前已有的嵌入原子相互作用势函数（EAM）,通过经典的分子动力学方法,模拟了铌的熔化曲线. 两相法和改进Z方法的熔化曲线几乎完全一致,与Z方法的结果稍有差异. 我们也比较了尺寸效应对铌熔化曲线的影响. 我们认为,铌的现有的势函数描述其高压特性时不再适合,后续需要构建精确的温度和压强依赖的相互作用势函数来研究铌的高压特性.     

利用电子结构数据拟合H2分子的电子壳模型势函数参数

电子壳模型势函数在离子晶体的原子级计算机模拟中有广泛应用,其势参数主要通过拟合晶体的实验数据或电子结构数据得到.提出了通过拟合双原子分子的量子化学从头计算电子结构数据来获得该势函数的方法,并由H₂分子的电子结构数据建立了H原子间的电子壳模型势函数.此外,还应用该势函数对H⁺₂分子离子进行了计算.该势函数拟合方案更适合于共价键型的分子. 关键词： 电子壳模型势 参数拟合 共价键 2分子')" href="#">H₂分子     

He-NO碰撞体系分波截面的理论计算

首先用Huxley势函数拟合在RCCSD(T)/aug-cc-pVTZ bf理论水平下计算的He-NO相互作用能数据,从而得到了He原子与NO分子相互作用各向异性势;然后用密耦近似方法计算了He-NO碰撞体系的总分波截面、弹性分波截面和非弹性分波截面,并总结了分波截面的变化规律.计算结果表明,拟合势较好地描述了He-NO系统相互作用的各向异性特征,利用碰撞体系分子间势的量子化学从头计算结果,可解决势能参数难以确定的问题,对进一步研究原子与分子碰撞机理有一定参考价值.     

天然色素苏木精与蛋白质纤维之间的相互作用

通过量子化学计算方法在密度泛函理论B 3LYP/6-31G*水平上对天然色素与蛋白质纤维之间的相互作用的相关性质进行了系统研究。对含有不同官能团的蛋白质纤维分子片段、苏木分子以及它们所构成的二元相互作用体系的几何构型进行了优化和频率分析;得到了含有不同官能团的蛋白质纤维分子片段和苏木分子之间的相互作用能和热力学数据,以及NBO电荷转移情况;通过AIM分析界定了含有不同官能团的蛋白质纤维分子片段和苏木分子之间的相互作用性质。计算结果表明,利用苏木对蛋白质纤维进行染色时,如果染液偏酸性,则苏木主要与蛋白质纤维中的氨基发生作用;如果染液偏碱性,则苏木主要与蛋白质纤维中的羧基发生作用。相对来说,在碱性条件下染色时,蛋白质纤维与苏木相互作用的结构更稳定。     

稀有气体二聚体解析势能函数的高精度拟合

原子间相互作用势的计算是原子分子物理研究领域的重要组成部分,它的精确计算为新型材料的研究奠定了理论基础;同时也为密度泛函等方法的评价、测试提供了标准对比数据。本文首先以最近所发表的NgD×15基准集为基础,在相同的计算方法下补充了其它点的一系列数据;以此为标准利用最小二乘法对He2—Rn2体系的相互作用势函数进行了拟合;从而得到了高精度全部同核稀有气体二聚体相互作用势函数的解析式。同时以CCSD(T)/ aug-cc-pV5Z-{6s6p6d3f2g1h}计算结果为标准与Gordon的MGCD84数据库中现有数据He2-Kr2体系进行了比较;总体发现本文的计算精度是非常高的,也证明了拟合结果的可靠性;并且给出了目前量子化学方法难以计算的近核区相互作用势数值。     

用核磁共振方法研究金属离子与蛋白质的相互作用

许多蛋白质含有金属离子,金属离子对蛋白质发挥生物学功能起着很大的作用. 金属离子与蛋白质的相互作用以及参与蛋白质功能调节的方式各种各样：有些金属离子高度专一性地与蛋白质紧密结合,对蛋白质发挥生物学功能起着关键性的作用;有些金属离子只是作为蛋白质发挥功能的辅助因子而瞬态地与蛋白质松散结合. 本文简要介绍目前国际上用NMR方法研究抗磁金属离子和顺磁金属离子与蛋白质相互作用的进展,并具体介绍了NMR方法在钙调蛋白、锌指蛋白、朊病毒蛋白等金属离子蛋白研究上的应用.     

He-HBr体系各向异性势及非弹性散射截面的理论研究

首先用BFW势函数形式拟合在CCSD(T)/aug-cc-pVQZ理论水平下计算的He-HBr相互作用能数据,得到了He原子与HBr分子各向异性势;并与ESMSV势进行比较,验证了拟合势的可靠性;然后采用公认的精确度较高的CC近似方法计算了He-HBr碰撞体系能量在150meV下He原子和HBr分子碰撞的转动激发微分截面和分波截面,总结了该碰撞体系非弹性散射截面的变化规律.研究表明:①拟合势较好地描述了He-HBr系统相互作用的各向异性特征;利用碰撞体系分子间势的量子化学从头计算结果,可解决势能参数难以确定的问题.②低激发态被激发的几率要远远大于高激发态被激发的几率;激发态越高,大角散射的几率越大.③尾部效应仅在低激发态中产生,高激发态不产生尾部效应.     

He-HF体系各向异性势及分波散射截面的研究

用BFW势函数拟合在CCSD(T)/aug-cc-pVQZ理论水平下计算的He-HF相互作用能数据,获得了He原子与HF分子相互作用的各向异性势,并与已知的势模型进行比较,验证了拟合势的可靠性;然后采用密耦方法计算了He-HF体系在不同碰撞能量下的分波散射截面,总结了分波散射截面的变化趋势.研究表明:①拟合势不但表达形式简洁,而且较好地描述了He-HF系统相互作用的各向异性特征.②入射粒子的能量越高,得到收敛的分波截面所需的分波数越多,量子效应越不显著,尾部效应也越弱;尾部效应仅在低激发态中产生,高激发态不产生尾部效应.     

Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH~- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gasphase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH~- + CO_2→ HCO_3~- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH~- to CO_2 results in the breaking of the OH~- solvation shell and the forming of the CO_2 solvation shell. The loss of hydrogen bonds in the OH~-solvation shell without being compensated by the formation of hydrogen bonds in the CO_2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD(T)/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.     

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACT

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

O~++H_2→OH~++H反应的动力学研究

采用含时量子波包方法结合二阶分裂算符传播子对初始态为(v=0, j=0)的O~++H_2→OH~++H反应体系在0.01—1.00 eV的碰撞能范围内进行了态分辨理论水平上的动力学计算.对反应概率、积分截面、微分截面以及固定初始态的热速率常数等动力学信息进行了计算并与文献报道的实验和理论结果进行了比较.结果表明本文的理论结果与实验结果十分符合.从微分截面的散射信息可知,在低碰撞能范围内,插入反应机制在反应中占据主导地位.随着碰撞能的增加,反应机制逐渐由插入机制变为抽取反应机制.     

On the nature of the SO4/Ag(111) and SO4/Au(111) surface bonding

The nature of sulfate-Ag(111) and sulfate-Au(111) surface bonding has been investigated at the SCF + MP2 level of theory. Convergence of binding energy with cluster size is investigated and, unlike neutral adsorbates, large clusters are required in order to obtain reliable binding energies. In the most stable adsorption mode, sulfate binds to the surface via three oxygen atoms (C_3v symmetry) with a binding energy of 159.3 kcal/mol on Ag(111) and 143.9 kcal/mol on Au(111). The geometry of adsorbed sulfate was optimized at the SCF level. While the bond length between sulfur and the oxygens coordinated to the surface increases, the sulfur-uncoordinated oxygen bond length decreases. This weakening and strengthening of the bonds, respectively, is consistent with bond order conservation in adsorbates on metal surfaces. Although a charge transfer of 0.4 electrons towards the metal is observed, the adsorbate remains very much sulfate-like. The molecular orbital analysis indicates that there is also some charge back-donation towards unoccupied orbitals of sulfate. This results in an increased electron density around sulfur as revealed in the electron density difference maps. Analysis of the Laplacian of the charge density of free sulfate provides a suitable framework to understand the nature of the different charge transfer processes and allows us to establish some similarities with the CO- and SO₂-metal bondings.     

Ce3+对Er3+/Yb3+共掺氟磷酸盐玻璃光谱性质的影响

研究了能量接受离子Ce³⁺对Er³⁺上转换发光强度以及Er³⁺在1.5μm附近波段发光性能参数的影响，并从能量匹配及能级结构角度出发对Er³⁺/Ce³⁺间的能量转移机制进行了分析.分析认为，⁴I_11/2能级的Er³⁺通过无辐射能量转移把能量传递给²F_5/2能级的Ce³⁺关键词： 氟磷酸盐玻璃 光谱性质 光纤放大器 3+和Ce³⁺')" href="#">Er³⁺和Ce³⁺     

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method has been widely used in predicting the binding affinity among ligands, proteins, and nucleic acids. However, the accuracy of the predicted binding energy by the standard MM/PBSA is not always good, especially in highly charged systems. In this work, we take the protein-nucleic acid complexes as an example, and showed that the use of screening electrostatic energy (instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA. In particular, the Pearson correlation coefficient of dataset II in the modified MM/PBSA (i.e., screening MM/PBSA) is about 0.52, much better than that (< 0.33) in the standard MM/PBSA. Further, we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA. The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.     

O-与CH3CN反应机理的密度泛函理论研究

采用G3MP2B3方法研究了氧负离子与乙腈反应的势能剖面.在(U)B3LYP/6-31+G(d,p)理论水平下分别优化了该反应势能面上反应物、产物、中间体和过渡态的分子结构,采用G3MP2B3方法校正了这些关键点的能量. 势能面上的各个反应路径均通过针对过渡态的內禀反应坐标理论计算加以确定. 分别考察了四个可能的热力学产物通道,即质子转移、氢原子转移、H₂⁺转移和双分子亲核取代反应途径. 其中,经H₂⁺转移生成H₂O的反应通道为该反应的主要产物通道.