Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomer's β-sheets would be involved in interaction area and the side chains on two β-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the two β-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two     

1，4二环己基取代六元瓜环与Na(Ⅰ)自组装实体的合成与晶体结构

A novel complex of a new 1,4-dicyclohexyl cucurbituril(DCYQ[6]) with sodium(Ⅰ) ion was synthesized, and the crystal structure was determined by X-ray diffraction technique. In this self-assembled entity both the cavity interaction of DCYQ[6] included a nitrate anion and the portal interaction of the dipole carbonyls of DCYQ[6] with sodium cations lead to form self assembled molecular capsules. The crystal structure of the entity shows a packing of the self assembled molecular capsules connected by hydrogen bonds of water molecules. CCDC: 271400.     

Molecular imprinting of protein by coordinate interaction

In this article,a novel strong interaction by forming complex between bovine serum albumin(BSA) and copper ion was utilized for the preparation of molecular imprinted hydrogel in aqueous solution.Results show that the inclusion of copper ion in preparation can bridge the template BSA and functional monomers together and improve the imprinting effect compared to the polymer made without copper ion added.High selectivity factor and large adsorption capacity are also observed for the obtained BSA-imprinted ...     

CLOUD POINT CURVES OF POLY(ETHYLENE GLYCOL)/POLY(PROPYLENE GLYCOL) MIXTURES AND THEIR THERMODYNAMIC EXPLANATION

In the study of poly(ethylene glycol) (PEG) and poly(propylene glycol) (PPG) mixtures not only a bimodal shape but also a reverse trend of the dependence on molecular weight of the cloud point curves were observed.This trend indicates that the miscibility of the studied mixtures decreases as the molecular weight of one component decreases. The excess volumes of the mixtures show that the interaction parameter between two components decreases at first and increases after passing a minimum as the concentration of one component increases. This supports the explanation of Koningsveld on the bimodal shape of cloud point curves. Based on a binary interaction model a formula was derived revealing that the interaction between PPG and the end group of PEG and the hydrogen bonding interaction between ether and hydroxy end group inner or inter PEG molecules are not favorable for mixing. The latter interaction is an "attractive" force in PEG molecules. The two interactions are responsible for the observed abnormal dependence.     

DFT Study of Thiophene Adsorption on the Pd（111） and Pt（111） Surfaces

Thiophene adsorption on the(111) surfaces of Pd and Pt have been investigated by density functional theory.The results indicate that the adsorption at the hollow sites is the most stable.To our interest,the molecular plane of thiophene ring is distorted with C=C bond being elongated to 1.450  and C-C bond being shortened to 1.347 ,and the C-H bonds tilt 13.91～44.05o away from this plane.Furthermore,analysis on population and density of states verified the calculated adsorption geometries.Finally,charge analysis suggests that thiophene molecule is an electron acceptor,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.     

PHASE SEPARATION IN BIMODAL MOLECULAR WEIGHT HIGH DENSITY POLYETHYLENE WITH DIFFERING BRANCH CONTENTS BY MOLECULAR DYNAMICS AND MESODYN SIMULATION

The phase behavior of bimodal molecular weight high density polyethylene(BHDPE) in solid state was investigated.Hildebrand solubility parameters(δ) were calculated for the models of blends of higher molecular weight branch polyethylene(HBPE) with different branch contents and lower molecular weight linear polyethylene(LLPE),by using molecular dynamics(MD) simulations.These 3 values were then used to calculate the corresponding Flory-Huggins interaction parameter(x) between HBPE and LLPE models.In order t...     

Allyl chloride/AlCl_3/ether cationic initiating systems for polymerization of 1,3-pentadiene

Various ethers were used to mediate the polymerizations of 1,3-pentadiene (PD) initiated by AlCl3 and by allyl chloride (AllyCl)/AlCl3. The introduction of the ethers exert considerable effects on polymer yield and molecular weight due to its interaction with the propagating carbocation. The carbocation reactivity is reduced by this interaction which is subject to the ether's nucleophilicity determined by the steric hindrance of groups adjacent to oxygen. The reduction of carbocation reactivity gives rise to a decrease of polymer yield owing to inhibition of propagation but results in an augmentation of molecular weight due to suppression of various side reactions such as terminations. By using suitably nucleophilic ethers such as diphenyl ether, the polymerization can be mediated to give an high molecular weight polymer in high yield.     

The Synthesis of a New Dumbbell-shaped Compound of Bis-4,4''''-bipyridine Bridged by 2,2''''-Bipyridine

Molecular machine is a new born research field1-5, Stoddart and co-workers firstly reported a molecular shuttles in 19916. In molecular machine a cyclic (bead) moves back and forth like a shuttles between two or more groups (station) having noncovalent interaction with a bead. Dumbbell-shaped component is the key intermediate for the synthesis of molecular machines7. One of the approaches for control movement of the bead is based on coordination reaction intrigue. In our protocol, a ligand…     

Theoretical Characterization of Chiral Carbon Nanotube Encapsulating Ellipsoidal C70

The molecular orientation of ellipsoidal C70 in carbon nanotubes is carefully studied by first principles calculations. Using （14, 7） single-wall carbon nanotube （SWCNT） as a prototype material, we explored that the weak chemical interaction between SWCNT and C70 was the crucial factor to determine the molecular orientation. However, the small energy difference makes the distinguishment of two possible molecular orientations difficult. By simulating scanning tunneling microscope images and optical properties, we found that local electronic states sensitively depended on the molecular orientation of ellipsoidal C70, which provided a practical way of using scanning tunneling microscope to recognize the molecular orientation of ellipsoidal C70.     

High-throughput Screening: Synthesis of a Novel Fluorescent Microspheres

As one of efficient analytes, fluorescent microspheres have shown much usability on many biochemical and biomedical processes. Recent applications with fluorescent microspheres have included cytokine quantitation, single nucleotide polymorphism genotyping, phosphorylated protein detection, and characterization of the molecular interaction of nuclear receptors. These, coupled with the rapid advances in molecular biology and synthesis techniques of drugs, have presented a basis for drug screenin…     

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.     

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。     

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.     

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。     

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。