3-(3′-吡啶基)-6-芳基-1，2，4-三唑并[3，4-b]-1，3，4-噻二唑衍生物基态和激发态性质

用密度泛函B3LYP方法对3-(3'-吡啶基)-6-芳基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑衍生物(芳基为苯基、3-吡啶基和苯乙烯基)进行基态几何构型全优化,计算分子的电离势I_p和电子亲和势E_A等相关能量,并用Zerner间略微分重叠(ZINDO)和含时密度泛函(TDDFT)方法计算吸收光谱,用单组态相互作用方法(CIS)优化三种化合物分子的S_1激发态结构,分析其能量与发射光谱的关系,计算溶剂中分子的吸收和发射光谱,并与实验结果对照.计算结果表明,从3-(3'-吡啶基)-6-苯基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑分子(化合物A)到3-(3'-吡啶基)-6-(3'-吡啶基)-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑分子(化合物B)以及3-(3'-吡啶基)-6-对乙烯苯基-1,2,4-三唑并[3,4-b]- 1,3,4-噻二唑分子(化合物C)的电子亲和势依次增大,愈来愈容易接受电子,吸收光谱和发射光谱红移.     

PPAR激动剂的定向设计、虚拟筛选及合成

过氧化物酶体增殖因子活化受体(PPAR)是核受体超家族的一员.基于受体结构的药物分子设计与组合化学策略相结合,构建了过氧化物酶体增殖因子活化受体(PPAR)激动剂的虚拟化合物库.将已知小分子配体(GW409544)与PPAR晶体复合物进行剥离,得到受体的活性构象,并利用此活性受体分子与虚拟库中小分子进行对接和虚拟筛选,得到理论上结合较强的化合物,并对这些化合物进行合成,共合成9个新化合物.活性筛选结果显示化合物对PPAR具有一定的亲和力,其中有三个化合物显示出对PPARα,PPARγ的双重激动作用,从而指导新活性化合物的设计和合成.     

配体活性构象搜寻方法及其应用研究——Ⅰ.搜寻方法及凝血酶抑制剂活性构象的搜寻

在综合系统构象搜寻和配体-生物大分子对接(Dock)方法的基础上,发展了根据受体活性部位三维结构搜寻配体活性构象的搜寻方法BCSPL.用此方法搜寻了凝血酶抑制剂PPACK的活性构象,结果与晶体结构非常吻合,又用此方法搜寻了膦酰肽类和二肽、三肽类凝血酶抑制剂与人体α凝血酶结合时的活性构象,并在此基础上用分子力学计算了抑制剂与凝血酶的结合能,结果表明结合能与活性有很好的相关性,计算结果能合理地解释抑制剂与凝血酶的相互作用方式及结构与活性的关系.     

3-(3’-吡啶基)-6-芳基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑衍生物基态和激发态性质

用密度泛函B3LYP方法对3-(3’-吡啶基)-6-芳基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑衍生物(芳基为苯基、3-吡啶基和苯乙烯基)进行基态几何构型全优化, 计算分子的电离势IP和电子亲和势EA等相关能量, 并用Zerner间略微分重叠(ZINDO)和含时密度泛函(TDDFT)方法计算吸收光谱, 用单组态相互作用方法(CIS)优化三种化合物分子的S1激发态结构, 分析其能量与发射光谱的关系, 计算溶剂中分子的吸收和发射光谱, 并与实验结果对照. 计算结果表明, 从3-(3’-吡啶基)-6-苯基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑分子(化合物A)到3-(3’-吡啶基)-6-(3’-吡啶基)-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑分子(化合物B)以及3-(3’-吡啶基)-6-对乙烯苯基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑分子(化合物C)的电子亲和势依次增大, 愈来愈容易接受电子, 吸收光谱和发射光谱红移.     

计算机化学模拟—分子构象识别的新方法

简介了几种利用计算机图形技术研究化合物分子构象的新方法。重点介绍了分子力学计算方法中的系统搜索、随机搜索方法和分子动力学计算方法中的模拟淬火、模拟退火等新技术 ,为药物分子设计中受体与配体分子构象的识别提供了合理可行的方法。     

芬太尼类化合物与阿片μ受体相互作用的分子对接与分子动力学模拟

采用分子对接和分子动力学(MD)模拟方法研究了芬太尼类化合物与阿片μ受体的相互作用机制.先用AutoDock4.0程序将芬太尼类化合物对接到同源模建的阿片μ受体结构中,再用GROMACS程序包在水溶液体系中分别对12个芬太尼激动剂和阿片μ受体蛋白复合物进行了MD模拟研究,优化对接复合物的结构,最后利用MM-PBSA方法,在APBS程序中计算芬太尼类衍生物与阿片μ受体的结合自由能,计算出的受体配合物结合常数(Ki)与其实验值吻合较好,并预测了化合物的活性排序.结果表明,复合物蛋白结构与空载受体蛋白结构有较大差异,特别是胞内区IL2、IL3和跨膜区段TM4骨架构象变化较大,不同的化合物对受体结构影响也有差异,活性较好的化合物会增加蛋白特定区域结构的柔性.芬太尼类化合物可能是通过和受体结合后诱导阿片μ受体构象转变为活性构象,引起一系列的信号传导激活G蛋白,从而引发生理效应.     

柔性原子受性模型（FLARM）

柔性原子受体模型(Flexible Atom Receptor Model, FLARM)方法使用了改进 的遗传算法(IGA)，比传统的受体模型方法具有更快的计算速度；FLARM受体模型中 的原子空间坐标在遗传演化过程中是可变的，避免了不合适的起始位点对模型的影 响；另外，FLARM用增加空原子权重的方法，可以生成不完全封闭的、允许有大段 空区域的受体模型，这样的模型能更好地模拟实际受体的结构，并且容易和药效团 模型找到对应关系。我们用FLARM方法分别计算了甾类化合物体系的CBG蛋白亲和性 和1,1,3-三氧-2H,4H-噻吩并[3,4-e] [1,2,4]噻二嗪衍生物(TTD)体系的抗HIV-1活 性，计算结果表明FLARM生成的虚拟受体模型对配体分子的活性具有较高的预测能 力，在此虚拟受体模型的基础上还可以进一步分析虚拟受体分子与配体分子的相互 作用机制，对真实受体分子结构的活性位点进行初步预测。     

基于分子对接的苯丙素甙（PPGs）类化合物的虚拟筛选和合理设计

采用虚拟化合物生成法对抗肿瘤的苯丙素甙(PPGs)类化合物进行了配体受体对 接研究。以三种不同的骨架结构为基础分别生成了五十个虚拟苯丙素甙(PPGs)类化 合物，并将它们与端粒DNA受体进行分子对接，分析已知结构的对接结果，通过虚 拟筛选的方法得到了一批与受体相互作用能较高并且复合物能量较低的新的有潜力 的活性化合物。该方法可以弥补分子对接研究中，只能计算药物与受体的相互作用 ，无法有效设计新化合物的不足。这种方法在基于结构的药物分子设计中具有重要 的意义。     

含过渡金属和柔性配体催化体系的构象搜索

采用密度泛函理论对含有过渡金属和柔性配体的分子进行优化时,通常只能将初始结构优化到势能面上的局部最小点,而确定反应势能面上各中间体和过渡态的最低能量构象是准确描述一个催化反应最优路径的关键.使用Cr/PCCP体系催化乙烯选择性三聚/四聚反应路径中的关键过渡态(TS1,TS2,TS3)作为分子模型,对基于Tinker软件包和CREST软件包的两种构象搜索方法进行了对比测试.使用两种构象搜索方法均成功找到了三个分子模型的最低能量构象,并且两种方法获得的构象数量总数相差不大.与基于Tinker软件包的构象搜索方法相比,使用CREST软件包进行构象搜索的计算流程更加简单,并且大大减少了计算时间.     

DFT方法研究基于脲及硫脲衍生物的阴离子受体

采用密度泛函理论(DFT)模拟了两个基于脲和硫脲衍生物的受体分子对卤素阴离子的识别过程.结构优化表明基于脲衍生物的受体分子1最稳定构象为"反反"构象,分子内部形成稳定的C~α-H…O=C分子内氢键;而基于硫脲衍生物的受体分子2,不能形成分子内氢键,最稳定构象为"反顺"构象.受体1、2与卤素阴离子F~-、Cl~-可形成稳定的双氢键复合物,在此过程中,受体2经历了由"反顺"构象到"反反"构象的异构化过程.结构和能量分析表明,1、2受体分子与F~-离子间的氢键强度远大于其与Cl~-离子间的氢键;另一方面,受体2与阴离子间的氢键明显强于受体1,这是由于硫脲基N-H键具有更强的酸性.此外,对受体分子、氢键复合物及去质子化产物的吸收光谱计算结果表明,受体与F~-离子作用可产生明显的吸收光谱红移,而与Cl~-离子的作用对光谱影响较小.     

A Modiˉed Molecular Structural Mechanics Method for Analysis of Carbon Nanotubes

A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young's modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young's moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young's moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.     

Determination of extremely localized molecular orbitals in the framework of density functional theory

Extremely localized molecular orbitals are rigorously localized on only a preselected set of atoms and do not have any tails outside the localization region. The importance of these orbitals lies in their ability to be transferred from one molecule to another one. A new algorithm to determine extremely localized molecular orbitals in the framework of the density functional theory method is presented. This could also be a valuable tool in the quantum mechanics/molecular mechanics methodology where localized molecular orbitals are used to describe covalent bonds across the frontier region. The present approach is used to build up the electron density of thymopentin, a polypeptide constituted by five residues, starting from extremely localized molecular orbitals determined on a set of model molecules. The results obtained confirm good transferability properties for these orbitals.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (−)-menthyl acrylate revisited with the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method

The construction of the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method is detailed. This method is specifically devoted to the study of the reactivity of large chemical systems in solution. The solvent, modeled by a polarizable continuum, surrounds the whole solute molecule. Solute–solvent interactions are taken into account by means of the self-consistent reaction field approach. The solute system is treated by both quantum and molecular mechanics, the former being principally applied to the reactive part, i.e., the part undertaking bond forming or breaking, the latter being reserved for the ancillary encumbering groups. The connection between the molecular mechanics and the quantum mechanics part is accomplished by a strictly localized bond orbital that remains frozen within the local self-consistent field framework. As a test system, the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate is studied for the first time with steric interactions and electrostatic solvent effects taken into account simultaneously. The results indicate that the coupling of both interactions leads to conclusions that could not have been guessed from separate calculations.Proceedings of the 11th International Congress of Quantum chemistry satellite meeting in honour of Jean-Louis Rivail     

Studies on molecular interactions of β-cyclodextrin and antiulcer agent

The search for the lowest energy conformation of complex {β-cyclodextrin (β-CD)+chlorambucil} were carried out by molecular mechanics method. Theoretical calculations of molecular interactions of complex were carried out using the molecular orbital method. The correlation between energy changes and molecular structures are discussed. The large interaction energies calculated by the molecular orbital method bears out the inclusion phenomenon.     

磷在P-ZSM-5沸石中存在的形态

用密度泛函理论和ONIOM (our own N-layer integrated molecular orbital molecular mechanics)方法研究磷改性的ZSM-5沸石中含磷基团的可能存在形态. 计算的反应焓和自由能数据表明P-ZSM-5沸石中以磷进入骨架和在骨架外的形成磷酸根离子对是合理的稳定结构. 而且, 计算结果表明离子对模型F和G更适合在室温下存在, 磷进入骨架的酸性结构C'在高温下更稳定, 而磷进入骨架的结构C对温度变化不敏感. 计算得到的²⁷Al, ³¹P, ²⁹Si化学位移、酸性的变化趋势和结构参数与相关实验数据吻合.     

An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.     

Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations

Massively parallel divide-and-conquer density functional tight-binding (DC-DFTB) molecular dynamics and metadynamics simulations are efficient approaches for describing various chemical reactions and dynamic processes of large complex systems via quantum mechanics. In this study, DC-DFTB simulations were combined with multi-replica techniques. Specifically, multiple walkers metadynamics, replica exchange molecular dynamics, and parallel tempering metadynamics methods were implemented hierarchically into the in-house Dcdftbmd program. Test simulations in an aqueous phase of the internal rotation of formamide and conformational changes of dialanine showed that the newly developed extensions increase the sampling efficiency and the exploration capabilities in DC-DFTB configuration space.     

Multiple grid methods for classical molecular dynamics

Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.     

New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces

A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.     

顺式环十二碳烯的构象

用分子力学法(MMX程序)计算了15-苯基双环[10,3,0]十五碳-1(12)-烯-13-酮,其分子中环十二碳烯部分的构象为能量最低的[l_(ene)2333],与X衍射结果吻合.同时,还计算了15个顺式环十二碳烯的构象,求出了它们的能量及结构参数,讨论了影响构象稳定性的因素.