MOPAC 的输入文件格式及其输入输出文件管理系统的开发

简介了广为全计算化学程序MOPAC的输入文件格式及基产生文件的种类,用事例阐述了MOPAC输入文件中各部分代码的含义,指出并纠正了著名的ChemOffice中的组件Chem3D在图形显示方面的错误,从使用的方便性和实用性方面考虑,开发了一个MOPAC输入输出文件管理系统,提高了工作效率和计算结果的可靠性。     

A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process

BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer’s disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.     

染料分子结构与颜色关系的量子化学分析

文章运用MOPAC半经验量化程序,对部分染料分子结构进行计算,然后将结果和事实相对照与比较,从而分析染料分子结构与颜色的关系,并从中总结出一些规律。     

Molecular modeling of the octacoordinated tetracarbonato-Nd(Ⅲ),[Nd(CO3)4]5-,complex and its nonacoordinated fluoro- and aquo-adducts

Theoretical investigation on the structures of the octacoordinated[Nd(CO3)4]5- and the nonacoordinated[Nd(CO3)4·OH2]5- complexes,using the SPARKLE parameters of the lanthanides within MOPAC,revealed that they possessed dodecahedral and square antiprismatic structures respectively with an average Nd-O distance of 0.249 nm.These structures and the Nd-O distances agreed well with those experimentally found in the crystal structures.Replacing the water molecule with a fluoride ion or a mondentatecarbonato ligand resulted in a nonacoordimted distorted square antiprismatic structures where the trans-carbonato groups were twisted.The corresponding decacoordinated structures with two fluoride ions or a bidentatecarbonato group,[Nd(CO3)4·F2]7- and[Nd(CO3)5]7.were also investigated.In both cases considerable twisting of the transcarbonato groups was observed.     

4-氨基联苯系的致癌活性研究

在SGI工作站上运用MOPAC程序的PM3方法对4-氨基联苯系的几组化合物进行了计算，借用氨基亚氮阳离子与环上环氧化物的双官能团烷化作用观点，得出了该组化合物致癌活性的机理，与实验依据较为符合，从而建立了良好的量化构效关系．     

Comparison between the theoretical models and experimental structures of some oc tacoordinated Ln(Ⅲ)-bis-dipyridyl-bis-dichloroacetato-diaquo complexes and their phenanthroline analogues

The title complexes were modeled using the semiempirical MOPAC and the newly developed SPARKLE paramerters of the lanthanides. The calculated bond dis tances and angles agreed well with those found from crystal structure measuremen ts. This technique allows us to screen a large number of molecules and get struc tural information within a very short time.     

丙烯碳酸酯在石墨阳极上反常分解的MOPAC解释（英文）

应用半经验分子轨道计算绝对速率理论 ,研究了乙烯和丙烯碳酸酯 (EC ,PC)分解的反应机理 ,推断了丙烯碳酸酯在石墨阳极上反常分解行为。还原出来的自由基的二次聚合反应 ,被认为是这一速率的决定因素。PC的二聚速率远慢于EC ,这就导致PC的反常分解行为     

Molecular dynamics simulations of nanosheets of polymeric carbon nitride and comparison with experimental observations

A computational study of the properties of polymeric carbon nitride using molecular dynamics is presented. The analysis of ideal infinite-extent sheets permits to evaluate the effect of temperature on the network of hydrogen bonds responsible for the linkage of the material. The weakening of this binding mechanism at sufficiently high temperatures, together with the inter-layer interactions characteristic of this type of 2D materials, is shown to determine the conformation properties of polymeric carbon nitride at the nanoscale. The results obtained from the simulation of finite samples in the canonical ensemble at varying temperatures are consistent with those from the characterization of our experimentally synthesized samples. Hydrogen bonding between adjacent polymer ribbons leads this process and is the cause of the typical crumpled structure of this material.     

5,6-O-苯亚甲基-L-抗坏血酸和5,6-O-苯亚甲基-D-异抗坏血酸的合成

采用N,N-二甲基乙酰胺(DMAc)为溶剂、对甲苯磺酸(TsOH)为催化剂、环己烷为带水剂,苯甲醛与L-抗坏血酸反应生成(顺)-5,6-O-苯亚甲基-L-抗坏血酸和(反)-5,6-O-苯亚甲基-L-抗坏血酸,与D-异抗坏血酸反应生成(顺)-5,6-O-苯亚甲基-D-异抗坏血酸和(反)-5,6-O-苯亚甲基-D-异抗坏血酸.1HNMR数据表明,两个反应所得到的顺反异构体均为不等量.应用Chemoffice 9.0的3D模块中半经验分子轨道(MOPAC)程序计算的结果表明,两个反应顺式异构体最稳定构象的能量均比反式异构体最稳定构象的能量低,优势产物均可能以顺式异构体为主.以5,6-O-苯亚甲基-D-异抗坏血酸合成为例,用正交实验法优化了合成反应条件.     

Boron ions B interaction with Si(100) and Ge(100) surfaces

The goal of this work is simulation of possible structures, formed by boron ions (B⁺) during adsorption on Si(100) and Ge(100) surfaces. Calculations were carried out using a semi-empirical method, known as the Modified Neglect of Differential Overlap method (MNDO). The surface was simulated using of Si₄₉(Ge₄₉) and Si₆₃(Ge₆₃) clusters. Results of quantum-chemical calculations the boron ion (B⁺) interaction with Si(100) − 2 × 1 and Ge(100) − 2 × 1 surfaces are presented and show adsorption barriers for boron ions and migration barriers of adsorbed boron ion (during migration along surface dimer row and along surface dimer).