Coordination and ligand exchange dynamics of solvated metal ions

Recent developments in computer speed and capacity have opened the access to highly accurate molecular dynamics simulations based on quantum mechanically calculated forces for the chemically relevant region around ions in solution (QM/MM formalism). This accuracy, although still extremely consuming (30-300 days of CP time per simulation), is needed for reliable structural details and ligand exchange rates. A large number of main group and transition metal ions have been investigated by this approach, giving very detailed insight into the properties of these ions in solution and allowing to classify the ions by various characteristics. Most first-row transition metal ions have a very stable first hexa-coordinated solvation shell, whose vibrational distortions, however, strongly influence the dynamics of the second shell. The dynamical Jahn-Teller effect - shown to be a femto- and picosecond phenomenon - can strongly influence ligand coordination and exchange dynamics. A large number of ions with very labile solvation shell such as most main group ions, but also transition metal ions, e.g. Ag(I) and Hg(II), can change their coordination within the picosecond scale, leading to an almost simultaneous presence of several species hardly accessible by present experimental techniques. Among these ions, the structure breakers are of particular interest, and it could be shown that there are two types of them, one with a large and very labile first coordination shell such as Cs(I), the other characterised by a small first but an unusually large second solvation shell such as Au(I). Investigations of metal ions coordinated to ammonia ligands have shown that coordination to hetero-atoms can accelerate the ligand exchange reaction rates by several orders of magnitude, e.g. for Cu(II) and Ni(II). Simulations of ions in aqueous ammonia gave a very detailed picture of the complexity of species almost simultaneously present and illustrate the enormous difficulties encountered when trying to fit X-ray or neutron diffraction data for such systems. In general, ligand exchange rates situated in the picosecond range are far below the NMR scale, and as femtosecond laser pulse spectroscopy could not be applied so far to ionic solutions, accurate simulations have become a very important tool to access structure and dynamics of solvated ions. A number of VIDEO clips supplied on the Web as supporting material illustrates the processes occurring in solutions of the metal ions.     

Variational transition state theory without the minimum-energy path

In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions OH+H₂→H₂O+H and C₂H₅→C₂H₄+H are very encouraging. Received: 22 January 1997 / Accepted: 11 March 1997     

超临界NaCl水溶液的分子动力学模拟

采用分子动力学模拟的方法对超临界NaCl水溶液的微观结构进行了研究.模拟发现在所研究超临界条件下,密度的变化比温度的变化对超临界NaCl水溶液的微观结构影响更大.温度及密度对Cl－ H2O径向分布函数的影响比对Na＋ H2O径向分布函数的影响要大.超临界条件下,各gNa＋－Cl－在0.261 nm处出现峰值,表明Na＋、Cl－之间发生了离子的缔合.超临界条件下,随温度增加,缔合作用增强；随密度增加,缔合作用减弱.本文工作为建立可适用于超临界条件下的电解质热力学模型提供了依据.     

Flexibility and Rigidity of Proteins and Protein–Pigment Complexes

Proteins may be rigid or flexible to various degrees as required for optimal function. Flexibility of large parts of a protein, which rearrange or move, is particularly interesting and will be discussed in this article. We differentiate between several categories, although the boundaries between them are diffuse: flexibility of peptide segments, order–disorder transitions of spatially contiguous regions, and domain motions. The domains may be flexibly linked to allow rather unrestricted motions or the motions may be constrained to certain modes. The various categories of large-scale flexibility will be illustrated with the following examples: (1) Small protein proteinase inhibitors are rather rigid molecules which provide binding surfaces complementary to their cognate proteases but show also limited segmental flexibility and adaptation. (2) Large plasma proteinase inhibitors exhibit large conformational changes after interaction with proteases probably for regulatory purposes. (3) Pancreatic serine proteases employ a disorder–order transition of their activation domain as a means to regulate enzymic activity. (4) Immunoglobulins show rather unrestricted and also hinged domain motions in different parts of the molecule probably to allow binding to antigens in different arrangements. (5) Citrate synthase adopts open and closed forms by a hinged domain motion to bind substrates and release products and to perform the catalytic condensation reaction, respectively. (6) Riboflavin synthase, a bifunctional multienzyme complex, catalyzes two consecutive reactions by means of two subunits, α and β. The β-subunits form a shell, in which the α-subunits are enclosed. Diffusional motion of the catalytic intermediates is therefore restricted. In addition, rearrangement of the N-terminal segment occurs during the assembly of the β-subunit. In contrast, rigidity is dominant in the structures of the light-harvesting complexes and the photosynthetic reaction centers involved in photosynthetic light reactions. These are large protein–pigment complexes in which the proteins serve as matrices to hold the pigments in the appropriate conformation and relative arrangement. Since motion would contribute to deactivation of the photoexcited states of the pigments and diminish the efficiency of light-energy and electron transfer, the functional role of rigidity is easy to rationalize for these proteins.     

On hydrogen-bonded complexes: the case of (HF)2

The hydrogen fluoride dimer (HF)₂ is the most completely characterized hydrogen bonded species incorporating a donor molecule and an acceptor molecule. We provide a summary of experimental and theoretical information pertinent to the fundamental and harmonic vibrational frequencies, equilibrium geometry and dissociation energiesD _e andD ₀ as well as a brief critical discussion including some new results on the potential function and current best estimates of experimental quantities.     

时间分辨激光光散射测量系统

自选设计，装配了一套时间分辨的激光光散射测量系统，该系统摄像机，录像机，计算机和自编的软件实现了一体化的数据采集，显示和分析过程，本文给出了该系统的应用实例，球晶的光散射和环氧树脂的固化反应诱导的相分离过程。     

Atomistic Modeling of Silica Based Sol-Gel Processes

Density Functional Theory is used to study water, methanol, ethanol, TMOS, and TEOS molecules and the most important silica clusters participating in sol-gel processes. Calculated bond lengths, bond angles and electric dipole moments compare well with experimental data. The energy of these molecules is reported and used to discuss the energetics of the hydrolysis and condensation reactions. Molecular Dynamics is employed to simulate liquid water, methanol, ethanol, TMOS, TEOS and experimental sol-gel solutions. Calculated densities and enthalpies of vaporisation compare well with experimental data. Preliminary results are presented for MD simulations of sol-gel solutions.     

Study on the Dynamics of Blending of Glucomannan with Carrageenan and Guaran Gum

In order to prove up the interaction between konjac glucomannan (KGM) and other amyloses, by using KGM, guaran gum and carrageenan as materials, their blending in different external conditions was modeled by means of molecular dynamics (MD) method. The result showed that 323 K was a significant turning point for the formation of hydrogen bond, and KGM and guaran gum were just juxtaposed together via intermolecular hydrogen bond; but with the addition of carrageenan, KGM, guaran gum and carrageenan were spirally twisted together, and when their blending proportion is 3:2:9 the combination was the most compact. Moreover, the research result has provided the sequent studies afterwards on amyloses with some references.     

尿液中的纳米微晶及其与尿石形成的关系

尿石症是一种世界范围的常见病和多发病,其主要的矿物成分为草酸钙(CaOxa)等[1-2]。但至今为止,尿石症形成过程中的许多化学及物理问题尚不清楚:尿液中的微晶是怎样生长和聚集?随后又是怎样黏附到尿路细胞膜上而形成结石?正常人与尿石患者尿液中微晶的数量和尺寸等存在什么样的     

How do we know who to include in collaborative research? Toward a method for the identification of experts

Collaborative research, defined as research involving actors participating in the problem situation under study, has an important role in operational research, strategic management and systems thinking. In a recent study, we found that a strong organizational focus incorporated into many soft operational research (OR) approaches is inadequate for studying societal problem situations, which are fragmented and have no clear boundary. Specifically, we failed to find a process of identifying individuals that is capable of representing the perspectives of actors and sufficient for research into societal problem situations. We found no clear terminology accounting for ontological differences between actors, individuals representing them and conceptual representations of acting entities. In response to this gap in the literature, we propose terminology that differentiates among actors (individuals or collective entities in the real world), experts (individuals capable of representing the perspective of an actor) and agents (ideal-typical representations of actors). Based on this terminology, we propose an iterative method to guide the assembly of an expert group to undertake collaborative research into societal problem situations. To demonstrate the application of our method, we present selected insights from our study in an electronic supplement.