分子模拟方法在聚合物性质研究中的应用

综述了四种常用的分子模拟方法：即量子力学方法、分子力学方法、蒙特卡洛方法和分子动力学方法在聚合物性质研究中的应用。四种方法各有优势,共同与计算机模拟成为密不可分的组成部分。     

并行计算在分子模拟中的应用

简要介绍了并行计算机的发展背景,结合网络中心搭建的Linux cluster并行机说明了此类并行机的基本架 构。对三款常用的并行分子模拟软件进行了评述,比较了不同架构并行机的运行效率。对其中一款软件在此并行 机上进行了实测,并对并行机和分子模拟软件的发展进行了合理的预测。     

分子模拟技术在气体膜分离研究中的应用

回顾了分子模拟技术在气体膜分离领域的应用，介绍了各种模拟方法的特点，阐述了具体的应用范围、存在的问题及发展趋势。表明分子模拟在定性分析气体与膜材料的亲和性、预测渗透系数和分离因子方面有一定价值，但离定量预测和分析还有一定距离，非平衡分子动力学是适用于气体膜分离研究的方法，其研究还处于初期阶段。     

分子模拟在聚合物膜研究中的应用

简要回顾了近15年来分子模拟在各种聚合物膜研究中的应用,分析了它为宏观实验现象提供的新解释以及给聚合物膜的改性和设计研究工作带来的新思路,同时也对当前计算条件下模拟中存在的问题进行了探讨。     

定量构效关系在化合物性质研究中的应用

概述了定量构效关系（QSPR/QSAR）的基本原理以及定量构效关系在化合物性质研究中的应用,重点介绍了定量构效关系在化合物毒性、水溶性和LogPow等方面的应用。     

分子模拟参数在三维定量构效关系（3D—QSAR）中的应用

分子是否相似,这在很早以前已成为设计生物活性物质及考虑结构变化时的一个重要依据。以天然物质及现有的活性化合物为先导物,从中寻求新的类似物,此即为众所周知并广泛应用的模拟合成。“相似的化合物显示相似的活性”,以此为前提进行新化合物的合成亦取得不少成果。然而在这里,认识生物体分子及其类似性则至关重要,人们从结构式所设想的类似性往往并非一致。从传统的生物等价性(bioisosterism)考虑,由对生物方面相似性的认识而积累的有关经验来指导医药、农药的合成无疑是一个方向,但还难以达到定性的标准。     

分子模拟在化工应用中的若干问题及思考

随着高技术学科的飞速进步,化工学科在多年来已形成的理论和实验研究之外,又产生了一种完全独立而新颖的研究手段——分子模拟.目前化学工业受关注的新技术涉及聚合物、电解质等复杂物质,临界、超临界等复杂状态,界面、膜、溶液等复杂现象.实现化学工业从产品到过程设计完全自动化,在这些方面除了准确的物性数据外,更要对各种复杂现象的机理有深刻了解.分子模拟被认为是实现这一目标的关键技术之一.本文以分子动力学为主,结合计算量子化学,对分子模拟在化工应用中的若干问题进行讨论.     

分子模拟技术在分子筛的吸附扩散研究中的应用

二分子模拟是近年发展起来的一门新兴计算化学技术.简要介绍了分子模拟技术的基本原理及其优点和缺点,重点阐述了分子模拟中的Monte Carlo分子模拟和分子动力学模拟两种方法及其在分子筛的吸附扩散研究中的应用.同时介绍了这两种组合方法的应用,最后展望了分子模拟技术的发展方向.     

分子模拟在纳米材料改性聚合物中的应用

介绍了近年来国内外分子模拟研究纳米改性聚合物材料的部分工作,主要包括纳米材料的结构模拟,力学性能的模拟,改性剂相互作用的模拟以及聚合物基纳米复合材料界面作用的模拟。     

分子模拟在SBS改性沥青中的应用

利用分子模拟技术对SBS改性剂与沥青之间的相溶机理进行了研究.选用一种有代表性的基质沥青构建了其三维无定形单元平均结构, 然后采用分子力学(MM) 和分子动力学(MD) 方法在不同温度下进行模拟,得到能量最低也即最稳定的构象.经过对分子运动轨迹数据的分析,计算出不同温度下的无定形模型的内聚能密度（CED）,进而计算出溶解度参数.研究发现,从模拟数据来看：在110 ℃低温共熔态,线形SBS在沥青中的溶解性很差,然而在加了少量的硫以后,情况大为改善;而星形SBS在沥青中的溶解性较好,加入少量硫以后效果不明显.在150 ℃高温共熔态,线形和星形SBS与沥青均能很好地互溶,此结论验证了实验结果,同时数据也很接近.     

Towards more realistic computational modeling of homogenous catalysis by density functional theory: combined QM/MM and ab initio molecular dynamics

The combined quantum mechanics/molecular mechanics (QM/MM) and the ab initio molecular dynamics methods (AIMD) are fast emerging as viable computational molecular modeling tools. Both methods allow for the incorporation of effects that are often ignored in high level calculations, but may be critical to the real chemistry of the simulated system. In the combined QM/MM method part of the system, say the active site, is treated quantum mechanically whereas the remainder of the system is treated with a faster molecular mechanics force field. This allows high level calculations to be performed where the effects of the environment are incorporated in a computationally tractable manner. With the ab initio molecular dynamics methods, the system is simulated at a finite temperature with no empirical force field. Rather, the forces at each time step are determined with a full electronic structure calculation at the density functional level. Thus, simulations of chemical reactions can be performed where finite temperature effects are realistically represented. In this paper a brief introduction to both methods is given. The methods are further demonstrated with specific applications to modeling homogenous catalytic processes at the molecular level. These applications are our latest efforts to build more realistic computational models of catalytic systems at the density functional level.     

Predicted Incorporation of Non‐native Substrates by a Polyketide Synthase Yields Bioactive Natural Product Derivatives

The polyether ionophore monensin is biosynthesized by a polyketide synthase that delivers a mixture of monensins A and B by the incorporation of ethyl‐ or methyl‐malonyl‐CoA at its fifth module. Here we present the first computational model of the fifth acyltransferase domain (AT5_mon) of this polyketide synthase, thus affording an investigation of the basis of the relaxed specificity in AT5_mon, insights into the activation for the nucleophilic attack on the substrate, and prediction of the incorporation of synthetic malonic acid building blocks by this enzyme. Our predictions are supported by experimental studies, including the isolation of a predicted derivative of the monensin precursor premonensin. The incorporation of non‐native building blocks was found to alter the ratio of premonensins A and B. The bioactivity of the natural product derivatives was investigated and revealed binding to prenyl‐binding protein. We thus show the potential of engineered biosynthetic polyketides as a source of ligands for biological macromolecules.     

Molecular Dynamics Simulation of Tryptophan Hydroxylase-1: Binding Modes and Free Energy Analysis to Phenylalanine Derivative Inhibitors

Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1) is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD) simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.     

The cooperative effect between active site ionized groups and water desolvation controls the alteration of acid/base catalysis in serine proteases

What is the driving force that alters the catalytic function of His57 in serine proteases between general base and general acid in each step along the enzymatic reaction? The stable tetrahedral complexes (TC) of chymotrypsin with trifluoromethyl ketone transition state analogue inhibitors are topologically similar to the catalytic transition state. Therefore, they can serve as a good model to study the enzyme catalytic reaction. We used DFT quantum mechanical calculations to analyze the effect of solvation and of polar factors in the active site of chymotrypsin on the pK_a of the catalytic histidine in FE (the free enzyme), EI (the noncovalent enzyme inhibitor complex), and TC. We demonstrated that the acid/base alteration is controlled by the charged groups in the active site—the catalytic Asp102 carboxylate and the oxyanion. The effect of these groups on the catalytic His is modulated by water solvation of the active site.