分子组装机器：纳米工厂

在2016年获得诺贝尔化学奖后,分子机器作为最具应用前景的化学领域之一而广受关注。从属于其中的分子组装机器是一种能在微观尺度上精确控制化学反应的机器,又可称为纳米工厂。本文对纳米工厂的设计思路进行简要综述,结合工作原理与实际表现分析近年来相关的研究成果,并对其研究前景与面临的诸多挑战加以陈述与总结。     

Front Cover: Dynamic Covalent Chemistry for Synthesis and Co-conformational Control of Mechanically Interlocked Molecules (Eur. J. Org. Chem. 8/2023)

Mechanically interlocked molecules have found extensive applications in areas all across the physical sciences, from materials to catalysis and sensing. However, introducing mechanical bonds and entanglements at the molecular level is still a significant challenge due to the inherent restriction in entropy needed to preorganize strands before interlocking. Over the last decade, dynamic covalent chemistry has emerged as one of the most efficient methods of forming rotaxanes, catenanes and molecular knots. By using reversible bonds such as imines, disulfides and boronate esters, one can use the inherent error-correction in these linkages to form interlocked architectures with high fidelity and often in excellent yields. This review reports on recent advances in the use of dynamic covalent chemistry to make mechanically interlocked molecules, systematically surveying clipping, capping and templating approaches with dynamic bonds. Furthermore, it is also discussed how dynamic bonds can be used to control motion, co-conformational expression and catalytic activity in mechanically interlocked molecular machinery.     

Molecular design of ambipolar redox-active open-shell molecules: Principles and implementations

The mini-review highlights key structural features and provides guidelines for the molecular design of ambipolar redox-active frameworks, which are of interest for the fabrication of all-organic ‘poleless’ batteries and semiconductors. Open-shell molecules that can form at least three relatively stable redox states (i.e. cationic, neutral, and anionic) are discussed. The efficiency of the suggested strategies is supported by the representative examples taken from the recent publications.     

Li<Superscript><Emphasis Type="Bold">+</Emphasis></Superscript> Transport Mechanism in Oligo(Ethylene Oxide)s Compared to Carbonates

Molecular dynamics simulations have been performed on oligo(ethylene oxide)s of various molecular weights doped with the lithium bis(trifluoromethanesulfonyl)imide salt (LiTFSI) in order to explore the mechanism of Li⁺ transport in materials covering the range from liquid electrolytes to prototypes for high molecular weight poly(ethylene oxide)-based polymer electrolytes. Good agreement between MD simulations and experiments is observed for the conductivity of electrolytes as a function of molecular weight. Unlike Li⁺ transport in liquid ethylene carbonate (EC) that comes from approximately equal contributions of vehicular Li⁺ motion (motion together with solvent) and Li⁺ diffusion by solvent exchange, Li⁺ transport in oligoethers was found to occur predominantly by vehicular motion. The slow solvent exchange of Li⁺ in oligo(ethylene oxide)s highlights why high molecular weight amorphous polymer electrolytes with oligo(ethylene oxide)s solvating groups suffer from poor Li⁺ transport. Ion complexation and correlation of cation and anion motion is examined for oligoethers and compared with that in EC.     

光学单分子方法探测蛋白质的功能

过去20年中, 光学单分子探测的方法已经发展成为许多领域、特别是生物学领域研究的强有力工具. 单分子探测不仅能够给出物理量的平均值, 还可以给出有关分布的信息, 也能对一个分子的轨迹进行追踪. 这些独特的性质使单分子探测不仅仅在平衡体系, 如蛋白折叠、酶反应动力学、膜表面动力学等研究中发挥作用, 而且对非平衡体系的探测更具有其它方法无法比拟的优势, 同时单分子探测在生物活体中追踪分子时也有关键作用.     

几种自组装拉胀分子网络的分子模拟

报道了几种蜈蚣形、双足蜈蚣形聚合物 ,以及单箭头、双箭头形小分子通过氢键自组装形成拉胀分子网络的分子设计 .分子力学计算结果表明这些自组装分子网络靠氢键相互作用规则排列 ,具有类似倒插蜂窝网络结构 ,所设计的聚合物、小分子的合成较之以往报道的二维网络结构的合成简便易行 ,为真正分子水平意义上的拉胀结构的实现提供了新的思路和指导     

Dithienylethene-Based Single Molecular Photothermal Linear Actuator

By employing a mechanically controllable break junction technique, we have realized an ideal single molecular linear actuator based on dithienylethene (DTE) based molecular architecture, which undergoes reversible photothermal isomerization when subjected to UV irradiation under ambient conditions. As a result, open form (compressed, UV OFF) and closed form (elongated, UV ON) of dithienylethene-based molecular junctions are achieved. Interestingly, the mechanical actuation is achieved without changing the conductance of the molecular junction around the Fermi level over several cycles, which is an essential property required for an ideal single molecular actuator. Our study demonstrates a unique example of achieving a perfect balance between tunneling width and barrier height change upon photothermal isomerization, resulting in no change in conductance but a change in the molecular length, which results in mechanical actuation at the single molecular level.     

基于24-冠-8大环化合物构筑的人工分子器件和分子机器

简要阐述了分子器件和分子机器的相关概念,按照调控方式分类综述了基于24冠8的准轮烷、轮烷和索烃大环化合物构筑的分子器件和分子机器等在超分子领域的研究进展并对研究前景作了展望.     

Sub-structure-based screening and molecular docking studies of potential enteroviruses inhibitors

Rhinoviruses (RV), especially Human rhinovirus (HRVs) have been accepted as the most common cause for upper respiratory tract infections (URTIs). Pleconaril, a broad spectrum anti-rhinoviral compound, has been used as a drug of choice for URTIs for over a decade. Unfortunately, for various complications associated with this drug, it was rejected, and a replacement is highly desirable. In silico screening and prediction methods such as sub-structure search and molecular docking have been widely used to identify alternative compounds. In our study, we have utilised sub-structure search to narrow down our quest in finding relevant chemical compounds. Molecular docking studies were then used to study their binding interaction at the molecular level. Interestingly, we have identified 3 residues that is worth further investigation in upcoming molecular dynamics simulation systems of their contribution in stable interaction.     

Molecular Machines: How Motion and Other Functions of Living Organisms Can Result from Reversible Chemical Changes

Certain model proteins dramatically fold and become more ordered on raising the temperature. When the temperature is raised to drive folding and assembly, these model proteins can lift weights and perform work; they can produce motion. The temperature of warm-blooded animals, however, is kept constant. Therefore, motion cannot result from a change in temperature. In this case, a free energy change, caused, for example, by an increase in the concentration of a chemical, can lower the temperature at which the protein folding and assembly transition occurs from above to below physiological temperature. Raising the concentration of a chemical isothermally has indeed been shown to result in motion and the efficient performance of work. These model proteins and the mechanism they reveal provide insight into the molecular basis for diverse biological functions; they are models for the molecular machines that comprise the living organism, and they provide a new class of materials for both medical and nonmedical applications.     

Molecular design of ambipolar redox-active molecules II: closed-shell systems

This mini-review highlights key structural features that should be taken into account when creating ambipolar redox-active closed-shell metal-free molecules. This type of compound is strongly required for the fabrication of all-organic ‘poleless’ batteries and semiconductors. The suggested strategies aimed at stabilization of both oxidized (cationic) and reduced (anionic) redox-states are based on the comprehensive analysis of the most successful structures taken from the recent publications.     

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.     

Structure,Dynamics and Properties of Materials with Polymers Having Complex Architectures

Various non-linear highly branched polymers such as multiarm stars, block copolymer micelles and bottlebrush-like polymers have been studied in order to analyze their intramolecular structure and effects of spatial ordering resulting from their specific macromolecular architecture. These polymers constitute a class of compact macromolecules which, due to the high intramolecular density, interact strongly, excluding each other in space. Investigations of the structure and dynamics in such systems, using various experimental methods as well as computer simulations, have been performed. Small angle X-ray scattering is used to characterize the structure and mechanical spectroscopy is used for the detection of the dynamic behavior of the systems. Simulations have been performed using the cooperative motion algorithm with lattice polymers equivalent to the considered macromolecules. Results of both experiments and the simulation seem to support the concept of slow structural cooperative rearrangements controlling the flow in such systems. The effects are analogous to those related to flow in low molecular liquids but take place on another size scale. The new slow relaxation processes creates new super soft-states which are characterized by shear modulus plateau lower than 10⁴ Pa.     

Recent studies of docking and molecular dynamics simulation for liquid‐phase enantioseparations

Liquid‐phase enantioseparations have been fruitfully applied in several fields of science. Various applications along with technical and theoretical advancements contributed to increase significantly the knowledge in this area. Nowadays, chromatographic techniques, in particular HPLC on chiral stationary phase, are considered as mature technologies. In the last thirty years, CE has been also recognized as one of the most versatile technique for analytical scale separation of enantiomers. Despite the huge number of papers published in these fields, understanding mechanistic details of the stereoselective interaction between selector and selectand is still an open issue, in particular for high‐molecular weight chiral selectors like polysaccharide derivatives. With the ever growing improvement of computer facilities, hardware and software, computational techniques have become a basic tool in enantioseparation science. In this field, molecular docking and dynamics simulations proved to be extremely adaptable to model and visualize at molecular level the spatial proximity of interacting molecules in order to predict retention, selectivity, enantiomer elution order, and profile noncovalent interaction patterns underlying the recognition process. On this basis, topics and trends in using docking and molecular dynamics as theoretical complement of experimental LC and CE chiral separations are described herein. The basic concepts of these computational strategies and seminal studies performed over time are presented, with a specific focus on literature published between 2015 and November 2018. A systematic compilation of all published literature has not been attempted.     

Tuneable fluorescent marker appended to β-cyclodextrin: a pH-driven molecular switch

The photophysical properties of a pH dependent molecular switch based on pyridin-4-yl indolizin β-cyclodextrin 1 in water are described. The reversibility phenomena of fluorescent emission is attributed to a molecular motion of enclosed fluorescent moiety to inside/outside location.     

STUDY OF THE MOLECULAR MOTION IN POLYEPICHLOROHYDRIN BY HIGH RESOLUTION NMR

The molecular motion in polyepichlorohydrin (PEPCH), in solution and bulk, was studied by high resolution NMR by means of line width, spin-lattice relaxation time T_1 and nuclear Overhauser effect NOE. The results show that the VJGM model can describe the main chain motion of PEPCH in solution perfectly. In bulk state, the relationship between the line width and the temperature is consistent with WLF equation, but that between the high frequency molecular motion correlation time (in T_1 scale ) and temperature is consistent with Arrhenius equation. The motion parameters of PEPCH in both states were calculated. The internal rotation motion of side—CH_2Cl group was analyzed by using equal three-site jump and diffusion internal rotation model in both states.     

Recent theoretical studies of water oxidation in photosystem II

In the present mini-review, computational work over the past decade on water oxidation in photosystem II (PSII) is summarized. The size of the chemical model used for the oxygen evolving complex (OEC) has during this time increased from the initial 20 atoms to the present day 220 atoms. The electronic structure methods used have during the same period only undergone minor improvements. It is concluded that the results have now reached a high level of convergence and the predictions for both the structure of the OEC and the O-O bond formation mechanism are most probably of higher accuracy than presently available from experiments.     

Coca‐Chaos

The wobbling of a pop bottle is investigated by a molecular dynamics simulation, and is shown to display chaotic behaviour. This is one of the simplest commonly available objects to show this behaviour, and is an excellent example for demonstrating the phenomenon. The reason for the chaotic motion is the fact that the bottle stands on five feet, the importance of this being that the number of feet must be odd. The smoothness of the motion is interrupted whenever the bottle moves from one foot to another, but we show by considering a related “executive toy” that the chaotic behaviour is not a result of these motion discontinuities.     

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.