分子力场发展的新趋势

分子模拟中的力场方法是用来精确计算分子结构和能量的计算方法,它通过原子核的位置来计算体系能量。最初的分子力场都是针对某一特定体系的,它们的许多参数要由观测数据拟合得到。当时要建立新的分子力场是十分困难的,因为实验归属振动谱带需要花费大量的时间。所以此后大多数工作者都致力于发展涵盖尽可能多体系的“求全”型分子力场,这种趋势一直延续至今。但是随着各个学科研究的不断深入,所需要研究的体系越来越复杂,要求的精度也越来越高。在保证相当精度的条件下,“求全”型的分子力场要想涵盖所有需要研究的体系常常是十分困难的事情。2003年问世的Direct Force Field软件包能够便捷的建立针对某一特定分子体系,并且有相当精度的分子力场。它的出现为分子力场从“求全”转为向“求精”发展提供了可能。     

分子组装机器：纳米工厂

Molecular machines have attracted significant attentions as one of the most promising aspects of chemistry for their potential applications ever since receiving the 2016 Nobel Prize in Chemistry. The molecular assembler, also called the nanofactory, is a novel type of molecular machines that are capable of controlling the chemical reactions precisely at the microscopic level. As an analog to the macroscopic factories, nanofactories are comprised of a "transporting" part, the molecular walkers, and an "assembling" part, the molecular robotic arms. In this review, we provide a brief introduction of the research progress in recent years together with analysis on the principles of designing, constructing and operating molecular assemblers. We also summarize the prospects and challenges in the research area of molecular assemblers.     

I/V characteristics of a molecular switch

We present a study of the conduction properties of a class of aromatic compounds, whose conformation can be modulated with a transverse electric field, with strong effects on the molecular transport properties. The theoretical method includes the molecule–electrode interaction in a simple, although effective way: the coupling matrix elements are considered independent from the energy of the continuum spectrum of the lead. This results in a simple expression for the molecular Green’s function with a significant simplification in the expression of the transmission function. The effects of the voltage bias on the electronic molecular density is included through a uniform effective electric field. A simplified but accurate method for the evaluation of the molecular response to the field, which spares lengthy computations for each value of the voltage, is presented. The proposed method is calibrated on the widely studied benzene-1,4-dithiol molecule. The calculations on the selected molecular wire (a tetracyano derivative of 4,4′-di(mercaptoethynyl)tolan) show that conductivity is low for perpendicular rings, whereas conduction is allowed for the planar conformation, which corresponds to the equilibrium geometry in the absence of the transverse electric field.     

浅谈2016年诺贝尔化学奖:分子机器

2016年诺贝尔化学奖颁给了Jean-Pierre Sauvage、Fraser Stoddart和Ben Feringa,以表彰他们在设计与合成分子机器领域的卓越贡献.分子机器是模拟自然界的生物大分子机器或宏观机器的分子,科学家通过精巧的设计,利用有机合成反应构建这些内部能相对运动的分子,实现从分子层面的精确控制.本次诺贝尔化学奖颁给了尚无实际应用的分子机器,给未来带来了无限可能.     

Interfacial nanoarchitectonics for molecular manipulation and molecular machine operation

The nanoarchitectonics concept enables us to produce functional systems and materials from nanoscale units through nanotechnological approaches together with the processes including chemical syntheses, atom/molecule manipulations, self-assemblies, self-organizations, field-induced material regulations, and bio-related processes. Especially, manipulations of molecules (molecular machines) and sophisticated organization would be attractive targets in interfacial nanoarchitectonics. In this short review, we introduce several typical examples on manipulations of functional molecules and molecular machines at interfacial media. The examples are classified roughly according to driving forces of manipulations; (i) manipulations through chemical reactions and interactions; (ii) light-driven manipulations; (iii) electrically controlled manipulations; (iv) mechanical manipulations. Future possibilities of molecular manipulations at interfaces such as usages in biological systems are discussed in perspective section.     

卟啉超分子化合物在分子器件中的应用

分子电子器件已成为近年来的一个研究热点，卟啉类化合物因为光敏性好、性能稳定、易于修饰等优点成为分子器件研究的理想模型化合物。本文着重介绍了它在分子器件中的最新应用进展。     

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.     

分子纳米磁体的研究进展及应用

分子磁学主要研究无机配合物以及有机自由基的电子结构和磁性之间的关系。近些年发展起来的分子纳米磁体可以在单分子尺度上实现磁双稳态,独立作为一个磁功能单元,可能突破尺寸对传统磁性材料的制约,有望实现超高密度磁存储。分子纳米磁体中清晰的量子态也为量子退相干研究提供了化学调控的手段,这将为量子计算机提供物质基础。本文简要介绍了分子纳米磁体的概念和特征,并对研究进展进行了简要综述。     

Towards an understanding of the molecular basis of hydrophobicity

Summary The modern view is stressed that the structuring of water around nonpolar solutes, a process called hydrophobic hydration, actually favors the solubility of nonpolar solutes in water, its associated positive free energy of transfer arising from the enthalpic input required to create a cavity in water to accommodate the solute. The results of a series of molecular dynamics simulations of methane in SPC/E water at different temperatures are reported. These results show the existence of a larger fraction of broken hydrogen bonds in the hydration-shell water of the nonpolar solutes with respect to the bulk water, the difference increasing with a rise in temperature. This supports Muller's modified hydration-shell hydrogen-bond model predictions, where hydration-shell water molecules have lower free energies of hydrogen-bond breaking than those in the bulk.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27 September 1, 1995.     

分子印迹整体柱的制备、分类与应用

分子印迹整体柱在分离科学领域获得广泛应用,能够用于萃取分离有机小分子、特异性识别金属离子和蛋白质分离。本文综述了分子印迹整体柱的印迹策略、材料分类与应用,重点介绍了新型的分子印迹整体柱,并从特异性、分离效率、快速检测等方面讨论了分子印迹整体柱目前面临的挑战,展望了其发展前景和方向。     

Synthesis of covalently bonded nanostructure from two porphyrin molecular wires leading to a molecular tube

Molecular wire, diacetylene-linked porphyrin dimer 6 having terminal alkenes, was synthesized. Porphyrin dimer 6 formed the 1:1 double-stranded ladder complex with 1,4-diazabicyclo[2.2.2]octane (DABCO). The co-planar stacked two porphyrin molecular wires in the ladder complex were connected by olefin metathesis in the presence of the Grubbs catalyst in order to make a covalently bonded tubular nanostructure. The obtained molecular tube 7 was characterized by ¹H, ¹³C NMR spectroscopy, and MALDI-TOF MS spectrometry.     

The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs

Summary Atom assignment onto 3D molecular graphs is a combinatoric problem in discrete space. If atoms are to be placed efficiently on molecular graphs produced in drug binding sites, the assignment must be optimized. An algorithm, based on simulated annealing, is presented for efficient optimization of fragment placement. Extensive tests of the method have been performed on five ligands taken from the Protein Data Bank. The algorithm is presented with the ligand graph and the electrostatic potential as input. Self placement of molecular fragments was monitored as an objective test. A hydrogen-bond option was also included, to enable the user to highlight specific needs. The algorithm performed well in the optimization, with successful replications. In some cases, a modification was necessary to reduce the tendency to give multiple halogenated structures. This optimization procedure should prove useful for automated de novo drug design.     

Time-efficient flexible superposition of medium-sized molecules

We present an efficient algorithm for the structural alignment of medium-sized organic molecules. The algorithm has been developed for applications in 3D QSAR and in receptor modeling. The method assumes one of the molecules, the reference ligand, to be presented in the conformation that it adopts inside the receptor pocket. The second molecule, the test ligand, is considered to be flexible, and is assumed to be given in an arbitrary low-energy conformation. Ligand flexibility is modeled by decomposing the test ligand into molecular fragments, such that ring systems are completely contained in a single fragment. Conformations of fragments and torsional angles of single bonds are taken from a small finite set, which depends on the fragment and bond, respectively. The algorithm superimposes a distinguished base fragment of the test ligand onto a suitable region of the reference ligand and then attaches the remaining fragments of the test ligand in a step-by-step fashion. During this process, a scoring function is optimized that encompasses bonding terms and terms accounting for steric overlap as well as for similarity of chemical properties of both ligands. The algorithm has been implemented in the FLEXS system. To validate the quality of the produced results, we have selected a number of examples for which the mutual superposition of two ligands is experimentally given by the comparison of the binding geometries known from the crystal structures of their corresponding protein–ligand complexes. On more than two-thirds of the test examples the algorithm produces rms deviations of the predicted versus the observed conformation of the test ligand below 1.5 Å. The run time of the algorithm on a single problem instance is a few minutes on a common-day workstation. The overall goal of this research is to drastically reduce run times, while limiting the inaccuracies of the model and the computation to a tolerable level.     

外电场作用下寡聚苯分子导线的性质

利用Hartree-Fock 方法在6-31G*水平上对聚苯分子进行了计算研究. 分别从几何构型、分子轨道空间分布和分子轨道能级三个方面讨论了外电场对寡聚苯分子导线的影响, 给出了分子导线的性质与外电场的关系. 进一步, 连接硫原子于聚苯分子的两端, 并共价结合在金电极上. 利用非平衡格林函数方法对其在0-2.0 V 偏压下电子输运特征进行了深入研究.     

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.     

The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity

Summary Three previous papers in this series have outlined an optimization method for atom assignment in drug design using fragment placement. In this paper the procedure is rigorously tested on a selection of five ligand-protein co-crystals. The algorithm is presented with the molecular graph of the ligand, and the electrostatic/hydrophobic potential of the site, with the aim of creating a placement on the molecular graph which is as electrostatically complementary or hydrophobically similar to the site as possible. Various designer options were tested, including, where appropriate, hydrogen bonding and a restricted number of halogens. In most cases, the placement obtained was at least as good as the native ligand, if not significantly better.     

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.     

Molecular dynamics on distributed memory (MIMD) parallel computers

Summary Several algorithms are described that have been applied to molecular dynamics simulations and their merits discussed. The subject matter is confined to distributed (MIMD) algorithms. A simple mathematical model is used to illustrate the performance characteristics of a parallel MD algorithm.     

Unified synthesis of diverse building blocks for application in the discovery of bioactive small molecules

The synthesis of large numbers of diverse molecular scaffolds with controlled molecular properties is a significant challenge in synthetic organic chemistry. A modular unified synthesis was developed, and was exploited in the synthesis of sixteen diverse three-dimensional scaffolds. The approach exploited two cyclisation precursors to be converted, using a toolkit of cyclisation reactions, into spirocyclic and fused-ring scaffolds. Remarkably, Pd-catalysed aminoarylation of substituted N-Boc-hex-5-enylamine cyclisation precursors to yield N-Boc piperidine-containing scaffolds was successful which was ascribed to a significant Thorpe−Ingold effect. Computational property analysis showed that the decorated scaffolds are shape-diverse, and enable diverse lead-like chemical space to be targeted.