有机分子识别和聚集体组装中的非共价键协同作用

综述了近年来不同的非共价键作用力包括分子间氢键、供体-受体相互作用、π-π堆积作用、静电作用、疏溶剂作用和金属-配体配位作用等的协同作用在有机分子识别和有序聚集体组装研究中的应用.     

过渡金属络合物自旋哈密顿算符的理论分析

利用不可约张量方法讨论了过渡金属络合物自旋哈密顿。在考虑自旋轨作用、电子与其它电子旋轨作用、自旋-自旋偶极作用、Fermi作用和外磁场作用的近似下,得到了由分子参量表示的自旋哈密顿参量。在原子轨道近似下,近似地计算了红宝石的g因子,结果与实验符合得相当好,表明用本法解释过渡金属络合物的ESR谱是成功的。     

蛋白质相互作用预测、设计与调控

蛋白质相互作用是生命活动在分子水平上的基本事件. 蛋白质相互作用的三维图像可以给出关键生命活动过程的分子细节. 了解蛋白质相互作用的原理有助于揭示生命活动的机制, 并在此基础上开展有重要价值的蛋白质设计. 本文对于蛋白质相互作用预测、设计和调控研究的近期进展进行了总结归纳, 介绍了作者实验室在相关领域的研究进展, 并对今后的研究方向进行了展望. 主要包括: (1) 蛋白质相互作用网络、蛋白质相互作用机制和蛋白质复合物结构计算分析; (2) 基于序列、结合位点以及复合物结构的蛋白质相互作用预测; (3)蛋白质相互作用设计方法; (4) 利用化学分子调控蛋白质相互作用的方法; (5) 针对蛋白质相互作用的蛋白质药物设计方法.     

Ultrasonic investigation of molecular interaction of thyroxine and anti-tuberculosis drugs and DFT studies

The strength of molecular interaction between thyroxine hormone (THY) and two widely used anti-tuberculosis (ATB) drugs, ethambutol(ETH) and rifampicin(RIF) is assessed through ultrasonic at various blend compositions of the hormone and drugs. Ultrasonic study is carried out at three different temperatures (303 ​K, 310 ​K and 313 ​K). The trend in acoustical properties with blend ratio is used to establish the molecular interaction between thyroxine and ATB drugs. The main aim of this study is to identify the blend ratios and the temperature at which the hormone-drug interaction is significant in aqueous medium. DFT analysis is carried out to understand the type of interaction. The results obtained in DFT analysis of the complexes of thyroxine and drug molecules support the experimental observations. Both studies suggest that THY-RIF interaction is stronger than ETH-THY interaction.     

Factors Affecting Preparation of Molecularly Imprinted Polymer and Methods on Finding Template-Monomer Interaction as the Key of Selective Properties of the Materials

Molecular imprinting is a technique for creating artificial recognition sites on polymer matrices that complement the template in terms of size, shape, and spatial arrangement of functional groups. The main advantage of Molecularly Imprinted Polymers (MIP) as the polymer for use with a molecular imprinting technique is that they have high selectivity and affinity for the target molecules used in the molding process. The components of a Molecularly Imprinted Polymer are template, functional monomer, cross-linker, solvent, and initiator. Many things determine the success of a Molecularly Imprinted Polymer, but the Molecularly Imprinted Polymer component and the interaction between template-monomers are the most critical factors. This review will discuss how to find the interaction between template and monomer in Molecularly Imprinted Polymer before polymerization and after polymerization and choose the suitable component for MIP development. Computer simulation, UV-Vis spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), Proton-Nuclear Magnetic Resonance (¹H-NMR) are generally used to determine the type and strength of intermolecular interaction on pre-polymerization stage. In turn, Suspended State Saturation Transfer Difference High Resolution/Magic Angle Spinning (STD HR/MAS) NMR, Raman Spectroscopy, and Surface-Enhanced Raman Scattering (SERS) and Fluorescence Spectroscopy are used to detect chemical interaction after polymerization. Hydrogen bonding is the type of interaction that is becoming a focus to find on all methods as this interaction strongly contributes to the affinity of molecularly imprinted polymers (MIPs).     

The electrostatical molecular potential — A tool for the prediction of electrostatic molecular interaction properties

Starting from the molecular potential we get, by using elementary electrostatics, information about energetically favoured regions for interaction with ions and dipoles around H₂O and H₂CO. The molecule-dipole interaction is represented by the electric field patterns.     

含氢键吡啶合钴(Ⅱ)配合物的晶体结构和磁交换作用

合成了含水配合物［Co(py)₄Cl₂］·H₂O。分析了其单晶结构并与已知的无水配合物Co(py)₄Cl₂作了比较。发现结晶水的存在使含水配合物晶胞及分子对称性下降,由4方晶系I4₁/acd空间群变为单斜晶系P2₁/n空间群。并且水分子通过氢键作用把［Co(py)₄Cl₂］联接成一维长链。用Curie-Weiss定律,零场分裂磁化率公式加分子场校正磁化率公式拟合变温磁化率数据,发现分子间存在弱的反铁磁性交换作用。用Fisher一维线性链模型磁化率公式拟合,得出其氢键链内交换常数约为-1.03K。     

桥基原子对金属—金属作用的影响

本文借助EHMO法得到的Mulliken集居数和经验公式,讨论了过渡金属原子簇分子构型的稳定性和桥基与金属原子形成的平面距离D对其稳定性的影响。指出可用D值与实验上得到的距离d值的差别,判断过渡金属原子簇化合物金属—金属作用的强弱。     

微扰分子轨道法在有机化学中的应用

经Dewar, Hoffmann, Epiotis, Houk, Wolfe和Kost等理论化学家的努力,PMO理论已经成为研究影响分子构型、构象和(立体专一性和区域专一性)反应产物的结构因素的一个有效的手段。Epiotis的非键轨道作用理论已经使有机化学家认识到, 一个拥挤的构象或过渡态不一定是一个能量上不利的状态。π轨道作用的分析表明, 共轭基团间的作用在本质上是相斥的, 全平面构象不是共轭效应最大的构象。WSW-like法不仅为定量PMO法提供了一组完整的、具有正确集据数的轨道基组, 而且它还成功地将轨道作用能转化为原子作用能。     

Molecular Dynamics Simulation Study of ClF in Water: Halogen Bonding Interaction in Liquid

Does the halogen bonding interaction co-exist in liquid when it competes with the hydrogen bonding interaction? The classical molecular dynamics simulations for the solvation properties of ClF molecule in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio interaction energy calculations for the pre-reactive H₂O…ClF complex. We find that the halogen bonding interactions occur between O and Cl atoms and have the comparable strength and population with respect to the hydrogen bonding interactions of Cl…H.     

基于分子模拟和光谱法分析漆酶与甲酚的相互作用

该文运用计算模拟与光谱法研究了甲酚与漆酶的相互作用。首先,计算模拟表明漆酶与3种甲酚同分异构体都能发生相互作用,分子对接研究结果表明漆酶与甲酚同分异构体能以氢键和疏水作用力相结合,且结合位点相似。通过分子动力学模拟比较漆酶结合甲酚前后残基的柔性差异,验证了分子对接结合位点的可靠性。其次,选取计算模拟中结果较好的间甲酚,利用光谱法探究间甲酚与漆酶的荧光猝灭机制及结合前后漆酶二级结构的变化。荧光猝灭实验证实漆酶与间甲酚间是形成非荧光复合物的静态猝灭,与分子对接结果一致。红外光谱研究结果表明,漆酶与间甲酚结合后二级结构发生变化,其内部的β-转角和β-反向平行结构向β-折叠、无规则卷曲和α-螺旋结构转化,这与分子动力学模拟结果相呼应。该研究为利用漆酶转化环境中甲酚污染物提供了理论基础与数据支持。     

分子动力学模拟研究[Bmim][PF_6]+水+醇三元体系的微观结构和分子间相互作用(英文)

研究离子液体体系的微观结构和分子间相互作用具有重要意义.本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF6])+水+乙醇和[Bmim][PF6]+水+异丙醇三元体系进行了分子模拟研究,计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能,并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能.在此基础上,研究了溶液体系的微观结构、分子间相互作用和相行为.结果表明,水倾向于与离子液体阴离子和阳离子极性部分作用,醇倾向于与阴离子和阳离子非极性部分作用;库仑力主导阴离子-溶剂相互作用,色散力主导阳离子-溶剂相互作用,阴阳离子的缔合状态对色散力影响较小,对库仑力的影响非常显著.     

分子动力学模拟研究[Bmim][PF6]+水+醇三元体系的微观结构和分子间相互作用

研究离子液体体系的微观结构和分子间相互作用具有重要意义. 本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF₆])+水+乙醇和[Bmim][PF₆]+水+异丙醇三元体系进行了分子模拟研究, 计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能, 并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能. 在此基础上, 研究了溶液体系的微观结构、分子间相互作用和相行为. 结果表明, 水倾向于与离子液体阴离子和阳离子极性部分作用, 醇倾向于与阴离子和阳离子非极性部分作用; 库仑力主导阴离子-溶剂相互作用, 色散力主导阳离子-溶剂相互作用, 阴阳离子的缔合状态对色散力影响较小, 对库仑力的影响非常显著.     

Hydration forces near charged interfaces in terms of effective ion potentials

Experiments and simulations provide detailed information on the structure and interaction of charged interfaces in aqueous solutions. In order to understand this information in terms of general principles it is favourable to use effective potentials, which describe the interaction of ions and surfaces in the presence of solvent. Effective potentials are derived from molecular simulations and are capable of discerning ion-specific behaviour. We argue that short-range interactions in aqueous solutions involve two characteristic lengths, the range of the interaction and the spatial periodicity, both about 2.5 ± 0.5 Å.     

分子磁交换机理研究进展

概述了分子磁交换的机理研究及其进展。介绍了直接交换、超交换和双交换三种作用机理及基于自旋密度分析的自旋极化和自旋离域作用机制，并对今后分子磁性的理论研究作了展望。     

Theoretical analyses of the host–guest interaction within chlorine hydrate

The host–guest interaction is necessary for the stabilization of hydrates. Using Density Function Theory methods, the host–guest interaction within an unconventional chlorine hydrate was investigated, in combination with typical noncovalent analyses. The host–guest interaction energy was predicted to be as high as 17.51 kcal/mol, which was stronger than the typical van der Waals (vdW) interaction, due to an involvement of up to 20 Cl…O interactions. Polarization and dispersion energies made up the main contribution to the total interaction energy. Further visualization of the host–guest interaction validated, together with the general Cl…O interaction, another vdW interaction between the guest‐Cl atom and the five‐membered H₂O cluster. Isosurfaces associated with two patterns of vdW interactions yielded a better “fit” in shape, suggesting their cooperativity in stabilizing the steric configuration. The σ‐region on the guest‐Cl atom was verified to regulate the electron redistribution over the molecular space. These results are useful for understanding specific halogen behavior, and the origin and nature of host–guest interaction in hydrates. © 2013 Wiley Periodicals, Inc.     

6-羟基石松碱与乙酰胆碱酯酶的相互作用

目前治疗阿尔茨海默症(Alzheimer’s disease,AD)的主要药物为乙酰胆碱酯酶抑制剂(AChEI).为探讨石松碱类化合物对AChE的抑制作用,以6-羟基石松碱(6-hydroxylycopodine,HLD)为对象,应用核磁共振、分子对接、酶活性测定、分子动力学模拟及自由能分析,研究了HLD与AChE的相互作用.研究发现6-羟基石松碱对乙酰胆碱酯酶具有混合型抑制作用,其结合作用主要来自氢键和范德华作用.     

Molecular Spectroscopic Study on the Interaction between Heparin and Neutral Red

The interaction between heparin and neutral red was investigated by molecular spectroscopic methods. The change of all spectra suggested that positively charged neutral red had interacted with negatively charged heparin. The study of influence factors indicated that electrostatic force and hydrophobic bond might be involved in the interaction. The total binding number per disaccharide unit and intrinsic binding constant were obtained using Scatchard model.     

Molecular integrals over the gauge-including atomic orbitals. II. The Breit-Pauli interaction

Each accompanying coordinate expansion (ACE) formula is derived for each of the orbit-orbit interaction, the spin-orbit coupling, the spin-spin coupling, and the contact interaction integrals over the gauge-including atomic orbitals (GIAOs) by the use of the solid harmonic gradient (SHG) operator. Each ACE formula is the general formula derived at the first time for each of the above molecular integrals over GIAOs. These molecular integrals are arising in the Breit-Pauli two-electron interaction for a relativistic calculation. We may conclude that we can derive a certain ACE formula for any kind of molecular integral over solid harmonic Gaussian-type orbitals by using the SHG operator. The present ACE formulas will be useful, for example, for a calculation of a molecule in a uniform magnetic field, for a relativistic calculation, and so on, with the GIAO as a basis function.     

Computer simulation studies on the interactions between nanoparticles and cell membrane

In recent times,nanoparticles(NPs)have received intense attention not only due to their potential applications as a candidate for drug delivery,but also because of their undesirable effects on human health.Although extensive experimental studies have been carried out in literature in order to understand the interaction between NPs and a plasma membrane,much less is known about the molecular details of the interaction mechanisms and pathways.As complimentary tools,coarse grained molecular dynamics(CGMD)and dissipative particle dynamics(DPD)simulations have been extensively used on the interaction mechanism and evolution pathway.In the present review we summarize computer simulation studies on the NP-membrane interaction,which developed over the last few years,and particularly evaluate the results from the DPD technique.Those studies undoubtedly deepen our understanding of the NP-membrane interaction mechanisms and provide a design guideline for new NPs.