A central partition of molecular conformational space. IV. Extracting information from the graph of cells

In previous works (Gabarro-Arpa, J. Math. Chem. 42 (2006) 691–706) a procedure was described for dividing the 3 × N-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells or G, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: (1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone, whose faces are determined empirically from a set of relations between the coordinates of the molecule, (2nd) it is also shown that this cone can be decomposed into a set of smaller cones, (3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.     

Synthesis,Structure, and Optical Properties of Terminally Sulfur‐Functionalized Core‐Substituted Naphthalene‐Bisimide Dyes

The synthesis, characterization, and optical properties of a series of new 2,6‐disubstituted naphthalene‐bisimide dyes as molecular rods comprising terminal AcS groups is reported. The first series of dyes ( 1 – 3 ), comprising phenylhetero (Ph‐X) core substituents, cover a broad range of the VIS spectrum, ranging from yellow ( 2 ) over red ( 3 ) to blue ( 1 ). The second series of dyes contains benzylhetero (Bn‐X) core substituents ( 4 – 7 ). For the same heteroatom connecting the substituent to the naphthalene core, both series were found to display comparable colors. For the second series, the colors were blue ( 4 ), red ( 5 ), and violet ( 6, 7 ). The Ph‐X‐substituted dyes 1 – 3 are nonfluorescent, in contrast to the Bn‐X‐substituted compounds 4 – 7 . This rich variety of optical features that can be adjusted by rather small alterations of the core substituents makes these structurally very comparable molecular rods ideal candidates for optically triggered molecular‐transport investigations. Also, thanks to the terminal AcS groups, these compounds can be placed between nobel‐metal electrodes for optically triggered transport experiments.     

Apicidin选择性抑制ClassⅠ HDACs分子动力学研究

采用模拟方法研究组蛋白脱乙酰酶抑制剂(Apicidin)选择性抑制组蛋白去乙酰化酶(Histone deacetylases, HDACs)中的HDAC1和HDAC8. 通过HDAC8晶体结构同源模建HDAC1三维结构模型, 将Apicidin分别与HDAC1和HDAC8对接并进行分子动力学模拟, 结果表明, HDAC1活性口袋入口处的Arg270是Apicidin-HDAC1形成稳定结构的重要因素; HDAC1中Tyr303及His178与Apicidin形成2个持续存在的氢键, 而在HDAC8中未发现, 这是Apicidin选择性抑制HDAC1高于HDAC8的另一重要原因.     

反相液相色谱中温度对蛋白分子构象变化的新表征

液相色谱中溶质计量置换保留模型的Ｚ值可用来对反相高效液相色谱中热变蛋白的分子构象进行表片。发现在异丙醇－甲酸４４％（Ｖ／Ｖ）－水体系为流动相对完全变性蛋白的Ｚ值随温度升高而降低。且Ｚ值与绝对温度例数（１／Ｔ）成正比，因此蛋白分子构象变化可用Ｚ对１／Ｔ作图所得两条直线的斜率差值来表征，差值愈大，蛋白分子构象变化愈甚。该两直线的交点即为蛋白分子构象的突变温度。与通常采用的１ｇＫ＇对１／Ｔ的作图相比，用     

自旋交叉配合现象与分子电子器件

自旋交叉配合物在热、压力或光诱导自旋交叉现象的同时会伴随着其它一些协同效应，比如配合物颜色的改革、存在着大的热滞后效应等，这些协同效应是单个分子或分子集合体作为热开关、光开关和信息存储元件材料的基础。因此，自旋交叉配合物是开发新型的热开关、光开关和信息存储元件材料的理想分子体系。本文概述了自旋交叉现象的研究历史、现状和未来的发展趋势。讨论了影响配合物自旋交叉性质的各种内在的和外部的因素，总结了目前用于研究自旋交叉现象的各种现代测试技术。最后，展望了自旋交叉配合物在分子电子器件方面的应用前景。     

A preliminary step toward molecular spring driven by cooperative guest binding

A macrocyclic host molecule that comprised two different rotating modules, cerium(IV) bis(porphyrinate)s and ferrocenyl rotating units, exhibiting contraction/expansion motion was synthesized, which can be regarded as a prototype of artificial molecular spring driven by cooperative guest binding in 1:6 stoichiometry.     

Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules

Summary This paper outlines an application of the theory of simulated annealing to molecular matching problems. Three cooling schedules are examined: linear, exponential and dynamic cooling. The objective function is the sum of the elements of the difference distance matrix between the two molecules generated by continual reordering of one molecule. Extensive tests of the algorithms have been performed on random coordinate data together with two related protein structures. Combinatorial problems, inherent in the assignment of atom correspondences, are effectively overcome by simulated annealing. The algorithms outlined here can readily optimize molecular matching problems with 150 atoms.     

The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity

Summary The fragment placement method has been successfully extended to the problem of envelope-directed design. The atom assignment paradigm was based on molecular similarity between two molecular structures. A composite supersurface is defined to form the surface onto which the molecular fields are projected. The assignment process is then determined by using molecular similarity in the objective function to be optimized. In principle, this procedure is closely similar to that outlined in the previous paper for site-directed design. The rationale has been extensively tested on two benzodiazepine antagonists believed to bind to the same site.     

降冰片烯开环易位聚合反应的分子量及分子量分布控制

使用Grubbs催化剂催化降冰片烯单体进行开环易位聚合反应, 研究了催化剂搅拌溶解时间、聚合反应的溶剂极性和三苯基膦的加入等反应条件对降冰片烯单体ROMP反应分子量及分子量分布的影响, 从而得到降冰片烯ROMP反应的最佳条件.     

新型Schiff碱分子钳对中性分子的识别性能研究

采用差紫外光谱法考察了3种新型Schiff碱分子钳对一系列二苯甲酮、芳香二胺的识别性能.测定了主客体间的结合常数(Ka)和自由能变化(ΔG0).结果表明,分子钳对所考察的客体显示良好的识别作用,主客体间形成1:1型超分子配合物.讨论了识别作用的推动力与形状、大小匹配和几何互补等因素对形成主客体配合物的影响,并利用核磁氢谱与计算机模拟作为辅助手段对主要的实验结果与现象进行了解释.     

共聚高分子混合物的分子热力学模型

以硬球链流体的分子热力学模型为基础 ,引入方阱位能相互作用的贡献 ,建立了共聚高分子混合物的分子热力学模型 .模型中具有物理意义的链节参数 (链节数、链节直径和链节间的相互作用能 )由纯物质的pVT关系拟合得到 ,而用来校正交叉作用能和交叉碰撞直径的可调参数需由液液平衡的实验数据回归得到 .采用了相对简单的处理方法来确定这些可调参数 .对所选共聚高分子混合物的共存曲线、互溶窗和互溶图等相行为的关联结果令人满意 .     

1,8-二巯基芘分子电学特性的理论研究

Based on the first principle,electrical properties of a molecular junction consisting of pyrene-1,8-dithiol molecule and gold surface have been investigated. The cluster of three gold atoms is used to simulate the gold surface. Density functional theory is employed to obtain the electronic structures of the molecule and the extended molecule. Then the frontier orbital theory and the perturbation theory are used to determine the interaction energy between the molecule and the gold surface quantitatively. The elastic Green function method is applied to study the current-voltage properties of the molecular junction. Numerical results show that the sulfur atoms can be chemically absorbed on the gold surface and the bonding between the molecule and gold is mainly covalent-typed. The fermienergy of the extended molecular system lies between the HOMO and the LUMO and closer to the HOMO of the system. When the external applied bias is lower than 1 V,there is a current gap for the molecular junction. With the increasing of the bias,the conductance of the junction exhibits plateaus. These electrical properties are closely related with the electronic structures of the molecular junction. The extended molecular orbits have great contribution to the charge transport. Localized molecular orbits give little contribution to the current while charge transport is taken place by tunneling.     

Hydrogen bonding in molecular recognition by HIV-1 protease

Molecular recognition of the cleavage sites of the substrates by HIV-1 protease is analyzed in terms of hydrogen bonding. Crystal structures of an inactive enzyme complexed with six different substrates were used as reference structures. Applying molecular mechanics calculations it can be shown that the interaction energies between the real substrate and the enzyme are larger than with other peptides. From the analysis, it can be concluded that water molecules are essential in the recognition process. Moreover, the hydrogen bonds between the protease and various substrates are characterized in detail.     

The role played by head–tail configuration on the molecular weight distribution of α-cyclodextrin tubes

Supramolecular complexes consisting of cyclic molecules, such as cyclodextrins (CD), and polymeric chains have attracted considerable attention, being addressed in literature as novel molecular assembly. The so-called molecular tube (MT), synthesized by cross-linking adjacent α-CD in a polyrotaxane, is expected to act as host for large molecules in inclusion processes. In addition, these tubes can also be used as building-blocks in the formulation of novel materials. Molecular tubes constructed with α-cyclodextrin are obtained as a mixture containing entities with various molecular weights, and the molecular features determining the tube size distribution are not completely understood. In this paper, we propose the use of a statistical procedure based on binary numbers to examine the MT formation process. A complete analysis of the distinct orientations between cyclodextrin’s units was made and, in the light of the approximations of our model, we pointed out, on quantitative basis, that the molecular weight distribution of α-cyclodextrin MTs can be explained assuming imperfections in the cross-linking process due to the existence of head-to-tail (HT) arrangements in the polyrotaxanes employed in synthesis.     

用定量结构性质关系预测表面活性剂的浊点

用结构、电子、空间和热力学等性质为描述符，建立了宏观性质非离子表面活性剂浊点与微观结构之间的定量结构性质关系. 这些描述符包括辛醇/水分配系数lgP、分子表面积A、相对分子质量Mr、偶极矩μ-y和μ-z.通过49个非离子表面活性剂浊点的实验数值与五个性质之间的关系式，成功地预测了其他非离子表面活性剂的浊点.     

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues

Summary Continuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1--mercaptopropionic acid]-arginine-vasopressin ([Mpa¹]-AVP), [1-(-mercapto-,-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp]-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths]-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa¹]-AVP and [Cpp¹-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths¹]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.     

蛋白质-RNA相互作用界面预测与设计

蛋白质-RNA之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一. 结构生物学家利用实验手段可以得到蛋白质-RNA复合物的三维结构, 通过原子水平的晶体结构来解释蛋白质与RNA的识别过程. 但实验取得蛋白质-RNA的复合物结构非常困难, 耗钱、耗时, 同时受限于其相互作用强度. 因而利用理论的方法对蛋白质-RNA相互作用界面进行预测与设计在生物医学研究中十分重要. 本文主要综述了近期蛋白质-RNA相互作用界面预测与设计方面的进展, 包括以下几个方面: (1) 蛋白质-RNA分子对接算法以及对接前后存在的构象变化的处理; (2) 蛋白质-RNA 识别机制的研究; (3) 基于蛋白质-RNA 相互作用界面的分子设计. 蛋白质-RNA分子对接算法逐步完善将有助于我们对大量未知功能的蛋白质与RNA进行功能注释, 而基于生物大分子相互作用界面的分子设计将在药物设计领域中有广阔的应用前景.     

Properties of large organic molecules on metal surfaces

The adsorption of large organic molecules on surfaces has recently been the subject of intensive investigation, both because of the molecules’ intrinsic physical and chemical properties, and for prospective applications in the emerging field of nanotechnology. Certain complex molecules are considered good candidates as basic building blocks for molecular electronics and nanomechanical devices. In general, molecular ordering on a surface is controlled by a delicate balance between intermolecular forces and molecule–substrate interactions. Under certain conditions, these interactions can be controlled to some extent, and sometimes even tuned by the appropriate choice of substrate material and symmetry. Several studies have indicated that, upon molecular adsorption, surfaces do not always behave as static templates, but may rearrange dramatically to accommodate different molecular species. In this context, it has been demonstrated that the scanning tunnelling microscope (STM) is a very powerful tool for exploring the atomic-scale realm of surfaces, and for investigating adsorbate–surface interactions. By means of high-resolution, fast-scanning STM unprecedented new insight was recently achieved into a number of fundamental processes related to the interaction of largish molecules with surfaces such as molecular diffusion, bonding of adsorbates on surfaces, and molecular self-assembly. In addition to the normal imaging mode, the STM tip can also be employed to manipulate single atoms and molecules in a bottom–up fashion, collectively or one at a time. In this way, molecule-induced surface restructuring processes can be revealed directly and nanostructures can be engineered with atomic precision to study surface quantum phenomena of fundamental interest. Here we will present a short review of some recent results, several of which were obtained by our group, in which several features of the complex interaction between large organic molecules and metal surfaces were revealed. The focus is on experiments performed using STM and other complementary surface-sensitive techniques.     

The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties

Summary This paper is the first of a series which examines the problems of atom assignment in automated de novo drug design. In subsequent papers, a combinatoric optimization method for fragment placement onto 3D molecular graphs is provided. Molecules are built from molecular graphs by placing fragments onto the graph. Here we examine the transferability of atomic residual charge, by fragment placement, with respect to the electrostatic potential. This transferability has been tested on 478 molecular structures extracted from the Cambridge Structural Database. The correlation found between the electrostatic potential computed from composite fragments and that computed for the whole molecule was encouraging, except for extended conjugated systems.     

The atom assignment problem in automated de novo drug design. 2. A method for molecular graph and fragment perception

Summary If atom assignment onto 3D molecular graphs is to be optimized, an efficient scheme for placement must be developed. The strategy adopted in this paper is to analyze the molecular graphs in terms of cyclical and non-cyclical nodes; the latter are further divided into terminal and non-terminal nodes. Molecular fragments, from a fragments database, are described in a similar way. A canonical numbering scheme for the fragments and the local subgraph of the molecular graph enables fragments to be placed efficiently onto the molecular graph. Further optimization is achieved by placing similar fragments into bins using a hashing scheme based on the canonical numbering. The graph perception algorithm is illustrated in detail.