海藻糖抑制淀粉质多肽42构象转变的分子动力学模拟

应用分子动力学模拟方法研究了海藻糖抑制淀粉质多肽42(Aβ42)构象转变的分子机理.结果表明,海藻糖溶液浓度对Aβ42构象转变具有非常重要的影响.在水和低浓度海藻糖溶液(0.18mol·L-1)中,Aβ42可由初始的α-螺旋结构转变成β-折叠的二级结构;但海藻糖浓度为0.37mol·L-1时即可有效抑制Aβ42的构象转变.这是因为海藻糖利用其优先排阻作用使水分子在多肽周围0.2nm内富集,而其自身却在距离多肽0.4nm的位置附近团聚.另外,海藻糖还可通过降低多肽间的疏水相互作用,减少多肽分子内远距离的接触,有效抑制多肽的疏水塌缩和构象转变.上述分子模拟的结果对于进一步合理设计阿尔茨海默病的高效抑制剂具有非常重要的理论指导意义.     

拉曼光谱与拉曼效应的量子模型结构分析

散射光谱这种新谱线对应于散射分子中能级的跃迁,为研究分子结构提供了一种重要手段,引起学术界极大兴趣,拉曼也因此荣获1930年诺贝尔物理学奖。并称这种谱线为拉曼光谱。介绍了拉曼光谱的基本原理、拉曼光谱的应用以及其发展,由于拉曼光谱非常弱,实验要求比较高,最后介绍了实验仪器及利用拉曼光谱研究分子的结构。     

A discontinuous Galerkin finite-element method for a 1D prototype of the Boltzmann equation

To develop and analyze new computational techniques for the Boltzmann equation based on model or approximation adaptivity, it is imperative to have disposal of a compliant model problem that displays the essential characteristics of the Boltzmann equation and that admits the extraction of highly accurate reference solutions. For standard collision processes, the Boltzmann equation itself fails to meet the second requirement for d = 2, 3 spatial dimensions, on account of its setting in 2d, while for d = 1 the first requirement is violated because the Boltzmann equation then lacks the convergence-to-equilibrium property that forms the substructure of simplified models. In this article we present a numerical investigation of a new one-dimensional prototype of the Boltzmann equation. The underlying molecular model is endowed with random collisions, which have been fabricated such that the corresponding Boltzmann equation exhibits convergence to Maxwell–Boltzmann equilibrium solutions. The new Boltzmann model is approximated by means of a discontinuous Galerkin (DG) finite-element method. To validate the one-dimensional Boltzmann model, we conduct numerical experiments and compare the results with Monte-Carlo simulations of equivalent molecular-dynamics models.     

Interaction of diethyl aniline methylphosphonate with DNA: Spectroscopic and isothermal titration calorimetry

In this study the diethyl aniline methylphosphonate (DAM) was synthesized, the interaction of DAM with ct-DNA has been investigated by fluorescence spectra, UV spectra, molecular modeling and isothermal titration calorimetry (ITC). The binding constant of DAM to ct-DNA calculated from both isothermal titration calorimetry and fluorescence spectra were found to be in the 10⁴ M⁻¹ range. According to the ethidium bromide displacement studies, UV spectra and isothermal titration calorimetry experimental results, it can be concluded that DAM is an intercalator that can slide into the G-C rich region of ct-DNA. Furthermore, the results obtained from molecular modeling corroborated the experimental results obtanied from spectroscopic and ITC investigations. At the same time, fluorescence spectra suggested that the mechanism of the interaction of DAM to ct-DNA was a static enhancing type. ITC data showed that ct-DNA/DAM binding is enthalpy controlled.     

Measurements of self-broadening and self-pressure-induced shift parameters of the methane spectral lines in the 5556-6166 cm range

The absorption spectra of methane at different path lengths and different pressures for three temperatures 180, 240 and 296 K have been recorded in the 5556-6166 cm⁻¹ region using the Bruker IFS 120 HR and 125 HR high-resolution Fourier transform spectrometers. The multispectrum fitting procedure has been applied to these spectra to recover the spectral line parameters. The main goal of this procedure was the determination of self-broadening and self-pressure-induced shift coefficients and the exponents of their temperature dependences. These parameters have been derived for 406 assigned lines with good values of the signal to noise ratio. The rotational dependence of these parameters is discussed.     

Molecular dynamics simulations on local structure and diffusion in liquid TixAl1−x alloys

The microscopic structure and dynamics of liquid Ti_xAl_1-x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti_0.75Al_0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.     

The comparative study in transport properties of furan, thiophene and selenophene dithiols in nano electronic

The electron transport properties of furan, thiophene and selenophene dithiols based molecular wires through two electrodic systems using non-equilibrium Green’s functions technique (NEGF) are investigated. The electron transport of the above systems is systematically studied by analysis of transmission function, density of states, current–voltage characteristics, and conductance of the systems. The maximum current is occurred at the vicinity of 2.0 V and the values are 90.37, 98.82 and 100.31 μA for furan, thiophene and selenophene dithiols, respectively. These results can be attributed to the molecular projected self consistent Hamiltonian (MPSH) of two electrodic systems with different molecules at different bias voltage and also to quality of resonance of π electrons of heterocyclic ring. We can foresee that the furan, thiophene, and selenophene dithiols can be applied at electronic devices because of switching the high and low current.     

Classical Molecular Dynamics Model for Coupled Two‐Component Plasmas – Ionization Balance and Time Considerations

The dynamic properties of ion‐electron two‐component plasmas (TCP) are studied by using classical molecular dynamics (MD) simulations. There is a variety of time dependent and structural results that MD is able to provide in complement to other methods, e.g., useful micro‐field sequences can be generated. The method deals with some specific difficulties: the mass ratio between ions and electrons enforces very small time‐steps appropriate to follow electrons motion while, ions must move significantly in order to build, self consistently, their spatial structure. This results in expensive simulations. Electron trajectories are trapped and de‐trapped with multiple electron collisions around ions resulting in the occurrence of quasi metastable bound electron states. An analysis of micro‐fields at neutral in a hydrogen plasma reveals the need to consider a complete hierarchy of time scales extended typically over 7 order of magnitude, i.e., from a time‐step: ～10^‐19s, to a time required to obtain statistical averages, ～10^‐11s. In order to extend the MD capabilities in representing real coupled plasmas a classical ionization/recombination process has been implemented allowing to follow the evolution of plasmas involving several ion stages and model the ionization balance. Here again TCP simulations deal with extended time‐scale providing information about relaxation of non equilibrium plasma states (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

分子动力学模拟纯镁熔体凝固过程中结构演化

采用分子动力学模拟方法模拟了在周期性边界条件下由500个原子构成的液态Mg模型系统的凝固过程,分别考察了在5×10^14 K/s、5×10^13 K/s、1×10^13 K/s 、1×10^12 K/s的冷却速率下液态Mg熔体的凝固行为。模拟结果很好地重现了实验值。模拟中原子间作用势采用FS势,结构分析采用径向分布函数、均方位移、系统总能量分析、H-A键对分析技术等方法。结果表明,当冷却速率为5×10^14 K/s时,系统形成以1541键对为主的非晶态结构;当冷却速率分别为5×10^13 K/s、1×10^13 K/s、1×10^12 K/s时,系统形成以1421、1422键对为主的hcp晶态结构;另外,在快速冷却形成非晶的过程中,大部分bcc结构被保留下来,而在慢冷形成晶态的过程中,大部分bcc结构最终演化形成了hcp结构。     

1,3-双(1-苯基-1H-四唑-5-巯基)-乙酰苯腙钳形受体对卤素阴离子的识别机理

采用密度泛函B3LYP(Becke, three-parameter, Lee-Yang-Parr)和HF(Hatree-Fock)方法, 从理论上探讨了1,3-双(1-苯基-1H-四唑-5-巯基)-乙酰苯腙(DAPHZ)钳形受体对卤素阴离子的识别机理,结果发现DAPHZ受体以其钳形结构中的-N-H基团与卤素阴离子间形成双侧红移氢键进行识别. 经BSSE校正后DAPHZ•••F-, DAPHZ•••Cl-和DAPHZ•••Br-体系的分子识别相互作用能ΔECP分别为-327.5,-163.5和-148.3 kJmol-1, 说明钳形DAPHZ受体对F-具有最好的识别能力. 此外, 采用自然键轨道(NBO)计算, 相关H原子化学位移计算及分子中原子(AIM)等理论分析了识别体系中红移氢键的电子结构和性质, 结果表明APHZ受体对卤素阴离子的识别能力的相对顺序为DAPHZ•••F- >> DAPHZ•••Cl- ≈ DAPHZ•••Br-.