Internal dynamics of flexible molecules: Cyclohexane

Summary The international motions of a single cyclohexane molecule are studied by molecular dynamics calculations. Classical trajectories are calculated by integrating Newton's equation of motion. The potential functions used are essentially the same as in Allinger's MM2 program which is widely applied for calculations on conformational energies of organic molecules.Geometries and relative energies are reported for all stable low energy conformers and some transition states of cyclohexane. Vibrational frequencies of classical oscillations of individual bonds — computed for ethane as reference system — are close to the experimental values.Two trajectories of the molecular dynamics of cyclohexane were simulated. In the first we were able to follow the process of ring inversion: chair twisted forms inverted chair. The reaction path is analysed in detail and compared with static approaches. The second trajectory shows the correlated reorientation of the possible twisted forms alone. This process is known as pseudorotation.Dedicated to Prof. Dr. Karl Schlögl     

Theoretical studies on the reaction path and dynamics of the reaction CH_3+H_2O→CH_4+OH

The reaction path, the dynamical properties along the reaction path and CVT rate constants are computed by the ab initio MO method, the reaction path Hamiltonian theory and the variational transition state theory. The results show that the effect of the electron correlation energy on activation barrier is large, the recrossing and tunneling effects exist in the reaction.     

Atomistic Simulation Study of Calcium,Phosphate and Fluoride Ion Association to the Teleopeptide‐Tails of Collagen – Initial Steps to Biomineral Formation

The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.     

Ward's identity in critical dynamics

We consider the relaxation of an order-parameter fluctuation of wave numberk in a system undergoing a second-order phase transition. In general, close to the critical point, wherek ^{–1 –1} (the correlation length) the relaxation rate has a linear dependence on/k of the form (k, ) = (k, 0)x(1–a/k). In analogy with the use of Ward's identity in elementary particle physics, we show that the numerical coefficienta is readily calculated by means of a mass insertion. We demonstrate, furthermore, that this initial linear drop is the main feature of the full/k dependence of the scaling functionR ^–x (k,), wherex is the dynamic critical exponent andR=(k²+ ²)^1/2 is the distance variable.     

用计算模拟方法研究Al_3P_4O_(16)~(3-)计量比的二维层状磷酸铝中的有机胺模板能力

将快速 Monte Carlo方法与分子动力学方法相结合 ,研究了不同种类有机分子在 Al3P4 O3- 1 6 计量比的二维层状磷酸铝形成中的模板能力 .依据主 -客体之间非键相互作用能 (包括范德华能、氢键能和库仑能 ) ,可合理地解释已知实验现象 ,并能有效地预测出适于形成某一特定无机层结构的有机胺模板剂 .通过选择理论预测的有机胺分子作为模板剂 ,成功地合成了二维层状磷酸铝化合物 Al3P4 O1 6 · 1 .5 H3NC6 H1 0 NH3.     

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate.     

Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT     

Influence of static and dynamical structural changes on ultrafast processes mediated by conical intersections

The technological needs imposed by the exponential miniaturization trend of conventional electronic devices has drawn attention towards the development of smaller and faster devices like ultrafast molecular switches. In recent years molecular switches emerge again in the focus of active and innovative research with state-of-the-art optical tools recording their dynamics in real time. Still many questions about the underlying microscopic mechanism are left open, including potential factors that effect the switching process in either way, improve or worsen it. Due to the complexity of such molecules it is difficult to obtain a global answer from experiment alone. On the other side molecular switches are generally too large for a complete quantum chemical and quantum dynamical calculation. In our group we therefore developed an ab initio based modular model to handle the laser induced quantum dynamics in molecular switches like fulgides. It enables us to study the effect of internal molecular coupling and of the molecular response to external fields. We can investigate the related wave packet dynamics, the switching efficiency and the controllability. Our results focus on the laser induced ring opening in fulgides, which equals one direction of the switching process. Presented are the influence of a conical intersection seam and of time-dependent potentials, mimicking the mean interaction with the environment. Furthermore the relation of controllability and the wave packet's momentum is studied and the influence of potential barriers on the switching dynamics is shown.     

Considerations on the recognition of the D1 receptor by agonists

Summary A model of the mechanism for recognition of the D1 receptor has been developed. Conformational analysis for 10 agonists from diverse chemical families was carried out as a first step toward the characterization of the bioactive form. First, maximum structural overlap of the features common to all ligands allowed a simple identification of the candidate bioactive form for each ligand. At a second level of characterization, steric and electronic properties were computed for all accessible structures to analyze those properties that may modulate receptor recognition.     

金属Cu低指数表面熔化行为的分子动力学模

采用Mishin镶嵌原子势, 通过分子动力学方法模拟了金属Cu的低指数表面在不同温度的表面熔化行为, 分析了熔化过程中系统结构组态的变化以及固-液界面迁移情况. 金属Cu的(100)和(110)表面在低于熔点发生预熔化, 而(111)表面存在明显的过热现象. 准液体层的厚度随温度升高而增加, 热稳定性与表面的密排顺序一致, 按(111)、(100)、(110)顺序增大. 当温度高于热力学熔点时, 固液界面的移动速度与温度成正比, 外推得到热力学熔点约为1360～1380 K, 与实验结果1358 K吻合良好. 动力学系数定义为界面移动速度与过热程度的比值, 表现为明显的各向异性: k100=39 cm•s−1•K−1, k110=29 cm•s−1•K−1, k111=20 cm•s−1•K−1. k100与k110之间的比例符合collision-limited理论, (111)密排面有与其它低指数表面不同的熔化方式.