Why calcium inhibits magnesium-dependent enzyme phosphoserine phosphatase? A theoretical study

Mechanisms for the formation of the Schiff base from acetaldehyde and butylamine, glycine and phosphatidylethanolamine based on Dmol3/DFT calculations were realized. For the case of phosphatidylethanolamine, calculations were done under periodic boundary conditions, in an amine-phospholipid monolayer model with two molecules of phosphatidylethanolamine by cell. All models contained explicit aqueous solvent. In the three cases, a neutral amino group is used to model the nucleophilic attack on the carbonyl group of acetaldehyde, and water molecules form hydrogen bond networks. These networks were involved in the reactions by performing as proton-transfer carriers, important in some steps of reactions, and stabilizing reaction intermediates. In all the studied reactions, they take place in two steps, namely: (1) formation of a carbinolamine and (2) its dehydration to the Schiff base, being the dehydration the rate-determining step of the process, consistent with available experimental evidence for similar reactions. The main difference between the studied reactions is found in the value for relative free energy for the intermediates and transition states in the second step; these values are lower in the cases of glycine and phosphatidylethanolamine in comparison with butylamine, due the influence of their molecular environments. Based on the results, the aminophospholipid surface environment and carboxylic group of glycine may boost Schiff base formation via a neighboring catalyst effect.     

一维C_(36)聚合物的C_(36)分子间的电-声相互作用

在用半经验自洽场晶体轨道方法计算能带结构的基础上，并在平均场近似和形变势理论框架下，研究了四种一维线性 C36聚合物模型的 C36分子间电 声耦合常数及其对超导相变和金属 绝缘体相变的影响 .计算结果表明，一维线性 C36聚合物的 C36分子间电 声耦合常数极小，对超导相变和金属 绝缘体相变的影响可以完全忽略 .     

Theoretical Study of the Low-Lying Excited States of Butoxy Radicals and Non-Radiative Decay Routes

The potential energy surfaces for the butoxy radical dissociation into R·＋O on the six low-lying electronic states have been determined with the combined CASSCF and MR-CI methods. The isomerization reactions between the different conformers of 1- and 2-butoxy radicals at the X and B states have been also investigated with the MP2, B3LYP, and CASSCF methods. The non-radiative decay mechanisms of butoxy radicals at the B state have been characterized with the computed potential energy surfaces and intersections. Supported by recent LIF experimental results, it was predicted that the t-butoxy radical would predissociate via the B/C intersection. As to 1- and 2-butoxy radicals, the relative energies of the transition states for the isomerization reactions between conformers at the B state are much lower than those of the B/C intersections, resulting in the predominance of the isomerization in the decay of the B state for 1- and 2-butoxy radicals.     

CH自由基与O2反应的从头算研究

采用量子化学从头算法（UMP2／6－31G**水平），从理论上研究了CH＋O2反应的两个主要通道.根据计算所得的反应诸途径（连接反应物Cn＋）及两个通道的最终产物）讨论了复杂的反应机理．发现反应过程涉及O2的第一激发态1△g，且沿反应途径有势能面相交，反应途径中包括多个中间体及过渡态．     

钙调素离子选择性的理论研究

通过分子动力学模拟计算研究了Ca2+, Mg2+, K+, Na+与钙调素形成复合物的结构和能量特征. 计算得到了结合不同离子后的钙调素结构差异, 阐明了钙调素对这几种离子具有不同结合性质的结构和动力学原因. 其中, Ca2+与钙调素EF-hand基序中侧链残基上的氧原子形成配位键, 从而使其复合物的结构有较大的改变, 而和Ca2+同一主族, 性质相似的Mg2+及不同主族的Na+和K+, 它们与钙调素的结合能力比Ca2+与钙调素的弱许多, 对钙调素结构的影响也较小, 由此推测钙调素与Ca2+的结合机制和钙调素对Ca2+具有选择性的原因是由离子与钙调素中EF-hand基序的结合强度和构型共同决定的.     

硫代乙酰胺光化学反应机理的理论研究

用B3LYP, MP2和CASSCF方法, 采用cc-pVDZ和6-31++G**基组, 研究了硫代乙酰胺在基态和最低三态上消除硫化氢以及其它光解离反应, 并考虑了单个溶剂分子参与反应对质子迁移反应的影响, 得到了消除硫化氢反应的反应机理, 计算结果可以很好地解释实验结果. 进而用CASSCF方法计算了第一激发单态上的各驻点, 以及各交叉点. 计算结果表明, 在S1和T1态上发生除分子内转动以外的化学反应的可能性比较小, 当分子被激发到S2态上时, 将通过S2/S1交叉点到S1态, 在S1态上的分子有两条途径去活化, 通过S1/S0交叉点到热基态, 通过S1/T1交叉点系间窜越到T1态. 因而得出CH3CSNH2发生光解离反应的可能性不大. 基于此, 可将硫代酰胺结构引入蛋白或多肽中, 有望在不破坏分子整体结构的情况下对其进行光化学研究.     

Quantum chemical study on the mechanism of the consecutive addition of HCN to aminoacetonitrile

MINDO/3 method has been used to study the mechanism of the consecutive addition ofHCN to aminoacetonitrile.The results obtained for the first three steps show that the reaction isexothermic,and step I is the rate determining step.     

四苯基卟啉质子化结构变化的理论研究(Ⅱ)——五氟苯基及吡咯环上氟的取代基效应

卟啉的衍生物在DNA螺旋中的嵌入并堆积具有高选择性.为考察5,10,15,20-四(五氟苯基)卟啉(TF₅-PPH₂)和2,3,7,8,12,13,17,18-八氟-5,10,15,20-四(五氟苯基)卟啉(F₂₈TPPH₂)中F取代基对质子化卟啉结构的影响,在四苯基卟啉研究的基础上,用半经验的AM₁MO方法,并进行合理的对称性限制,计算了TF₅-PPH₂和F₂₈TPPH₂及其质子化二酸(TF₅-PPH₄²⁺)和(F₂₈TPPH₄²⁺)的几种可能的构型.结果表明,由于F取代基的影响,质子化过程中的结构、键电荷布居和前线分子轨道均有明显的变化,二者的质子化二酸与溶液质子的快速交换作用也都变得更加困难.