全原子分子动力学模拟结合核磁共振波谱研究N-甘氨酰甘氨酸水溶液的结构和弱相互作用

采用分子动力学模拟方法结合核磁共振化学位移系统研究了甘氨酰甘氨酸水溶液体系饱和溶解度范围的弱相互作用. 径向分布函数表明体系中不同类型的原子显示出形成氢键的不同能力. 氢键网络分析发现了不同氢键所能形成的分子簇结构. 随温度变化核磁共振化学位移值用于研究形成氢键的变化情况,并和模拟得到的结果进行比较,模拟和实验结果得到了较好的吻合.     

Studies on the structures and interactions of glutathione in aqueous solution by molecular dynamics simulations and NMR spectroscopy

All-atom molecular simulations and temperature-dependent NMR have been used to investigate the conformations and hydrogen bonds of glutathione (GSH) in aqueous solution. The simulations start from three different initial conformations. The properties are characterized by intramolecular distances, radius of gyration, root-mean-square deviation, and solvent-accessible surface. GSH is highly flexible in aqueous solutions in the simulations. Moreover, conformations can covert between “extended” and “folded” states. Interestingly, the two different hydrogen atoms in cysteine (H_N2) and glycin (H_N3) show different capabilities in forming NH?OW hydrogen bonds. The temperature-dependent NMR results of the different amide hydrogen atoms also show agreements with the MD simulations. Competing formation of GSH hydrogen-bonding interactions in aqueous solutions leads to hydrogen-bonding networks and the distribution of conformations. These changes will affect the activity of GSH under physiological conditions.     

Tautomeric populations of the charged species of 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) studied with computer simulations and cluster expansions

Correct net charge and protonation pattern in the polyamine backbone is one of the major factors that define the interactions of this class of compounds. 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) is a isosteric charge deficient analogue of naturally occurring spermine (Spm) with different biological features. The tautomeric populations of each SpmTrien charge state were estimated with computer simulations, molecular dynamics (MD) and quantum mechanical calculations, and cluster expansions separately. In the computer simulations, tautomeric populations of each charge state were obtained by constrained least‐squares fitting the theoretically calculated (GIAO B3LYP/6‐311 + G**) ¹⁵ N NMR chemical shieldings of SpmTrien tautomers to the experimentally measured chemical shifts. Theoretical chemical shieldings were calculated for water complexes of SpmTrien obtained from MD simulations in explicit water. Both methods gave highly similar realistic results. SpmTrien has many major populations of tautomers at biologically relevant charge states of three (+3) and four (+4) thus enabling a large variety of structures for specific ionic interactions. Copyright © 2013 John Wiley & Sons, Ltd.     

NMR chemical shift study of the methanol—benzene-d6 system

The OH proton chemical shifts of methanol referred to the CH₃ proton in the methanol — benzene-d₆ system have been measured from room temperature up to the supercritical region. MD simulations have also been performed at the same composition as experiment at 575 K. The chemical shift results in the supercritical region are in good agreement with those of pure methanol at the same density within experimental errors. The results of NMR and MD simulation suggest that the hydrogen-bonded structure of methanol is practically not affected by addition of benzene molecules.     

Quantum cluster equilibrium theory of liquids: temperature dependent chemical shifts,quadrupole coupling constants and vibrational frequencies in liquid ethanol

Temperature dependent NMR chemical shifts for hydrogen and oxygen, NMR quadrupole coupling constants for deuterium and vibrational frequencies for the OH bond of liquid ethanol are calculated for the temperature range 250 to 350 K using the ab initio quantum cluster equilibrium method and compared with experimental measurements. The calculated NMR chemical shifts, quadrupole coupling constants and infrared vibrational frequencies are in good agreement with experimental measurements. The results indicate that cyclic tetramer and pentamer structures rather than linear structures are the principal components of liquid ethanol.     

固体丁酸类代谢物13C化学位移的结构依赖性

丁酸类代谢物广泛存在于动物、植物和微生物中,且具有多种重要的生理功能,但它们的固体核磁共振参数、分子动力学性质及其结构依赖性并未得到清楚的认识. 该文使用高分辨交叉极化与魔角旋转核磁共振（¹³C CPMAS）实验技术,分析了一系列固体丁酸类代谢物的¹³C化学位移, 发现了这些代谢物的¹³C化学位移与其分子结构的一些相关性规律. 另外还发现,固体丁酸类代谢物与其在溶液中的¹³C化学位移有显著的差异. 这些代谢物中甲基参与的疏水作用以及羟基、氨基和羧基参与的氢键作用均对其化学位移大小有重要的影响. 上述结果为认识代谢物的结构和功能以及功能对结构的依赖性提供了重要信息.     

Theoretical analysis of solvent effects on nitrogen NMR chemical shifts in oxazoles and oxadiazoles

Using quantum chemistry methods we have evaluated the solvent effects on the ¹⁴N NMR chemical shifts in five oxa- and oxadiazoles dissolved in twelve solvents. These solvents differ in their polarity with the dielectric constants varying from 2 to 80. Moreover, three of them have a hydrogen-bond donor character. All possible hydrogen-bonding in the water solution with the oxygen and nitrogen (hydrogen-acceptor) centers in oxazoles (2) and oxadiazoles (3) have been considered in our studies. It has been shown that both the pure solvent and hydrogen-bonding effects are significant and result in ¹⁴N magnetic shielding increase. In water solutions the pure solvent effect is larger than the hydrogen-bonding effect. In addition, the solvent effect has been analyzed in terms of its direct and indirect contributions. It should be emphasized that our theoretical results for ¹⁴N chemical shifts in oxa- and oxadiazoles remain in a very good agreement with the accurate experimental data.     

Hydrogen bond dynamical properties of adsorbed liquid water monolayers with various TiO2 interfaces

Equilibrium classical molecular dynamics (MD) simulations have been performed to investigate the hydrogen-bonding kinetics of water in contact with rutile-(110), rutile-(101), rutile-(100), and anatase-(101) surfaces at room temperature (300?K). It was observed that anatase-(101) exhibits the longest-lived hydrogen bonds in terms of overall persistence, followed closely by rutile-(110). The relaxation times, defined as the integral of the autocorrelation of the hydrogen bond persistence function, were also longer for these two cases, while decay of the autocorrelation function was slower. The increased number and overall persistence of hydrogen bonds in the adsorbed water monolayers at these surfaces, particularly for anatase-(101), may serve to promote possible water photolysis activity thereon.     

高压下液态硝基甲烷的分子动力学模拟

 对高压下液态硝基甲烷的性质进行经典和基于第一性原理计算的Car-Parrinello分子动力学（CPMD）模拟。利用经典势的分子动力学（MD）模拟研究了高压压缩状态下液态硝基甲烷的结构和热力学性质,得到了高达14.2 GPa压力下的理论Hugoniot数据。对于一些热力学函数,如总能和粒子速度,经典势模拟给出了很好的总趋势,基本特征和实验观测一致。但是在给定的密度下,经典模拟预言的Hugoniot压力偏高。在几个选定的密度下,进行了CPMD模拟,得到了二体相关函数、速度自相关函数、振动光谱和其它的热力学性质,并与经典模拟结果进行了比较。对二体相关函数的分析表明经典势的短程部分的刚性可能太强,从而导致了比实验值高的理论压力值。对于某些二体相关函数,CPMD模拟和经典模拟结果差别很大,可以归结为量子效应。当压力增高时,量子模拟得到的振动光谱向高频部分移动的现象与实验观测相符合。     

Molecular dynamics simulations of the chiral recognition mechanism for a polysaccharide chiral stationary phase in enantiomeric chromatographic separations

We use explicit-solvent fully atomistic molecular dynamics (MD) simulations, permitting all the interactions between the atoms constituting the polymeric chiral stationary phase (CSP), the solvent molecules and the drug molecule enantiomers, to better understand the chiral recognition mechanism that makes chromatographic separation possible. Using amylose tris(3,5-dimethylphenyl carbamate) (ADMPC) as prototype, three solvent systems, and ten racemates as solutes, we seek a molecular dynamics average quantity that could serve as a metric that predicts which of the two enantiomers will elute first and also correlates with the ratio of retention times for enantiomers. To better understand the molecular dynamic chiral recognition that provides the discrimination which results in the separation of enantiomers by high performance liquid chromatography, we examine the differences in hydrogen bonding lifetimes in various donor–acceptor pairs between the drugs and the ADMPC, and map out the differences in ring-ring interactions between the drugs and the ADMPC. Several MD average quantities related to hydrogen-bonding lifetimes correlate with the ratio of retention times for the enantiomers. One of these quantities provides a prediction of the correct elution order 90% of the time, and the ratios of these quantities for the enantiomers provide linear correlation (0.85 coefficient) with experimental separation factors.     

Molecular dynamics investigation of water adsorption on rutile surfaces

Born-Oppenheimer molecular dynamics (MD) simulations were performed in the framework of the semi-empirical molecular orbital method MSINDO to study water adsorption on rutile surfaces. Monolayer and doublelayer water coverage was considered on the rutile (1 1 0) and (1 0 0) surfaces and the adsorbate structures were determined. Vibrational density of states of hydrogen atoms were calculated by constant temperature MD simulations at 100 K. These were used to interpret the experimental vibrational spectrum by assigning all peaks to the particular types of hydrogen atoms.     

A theoretical forecast of the hydrogen bond changes in the electronic excited state for BN and its derivatives

The relationship between electronic spectral shifts and hydrogen-bonding dynamics in electronically excited states of the hydrogen-bonded complex is put forward. Hydrogen bond strengthening will induce a redshift of the corresponding electronic spectra, while hydrogen bond weakening will cause a blueshift. Time-dependent density function theory (TDDFT) was used to study the excitation energies in both singlet and triplet electronically excited states of Benzonitrile (BN), 4-aminobenzonitrile (ABN), and 4-dimethylaminobenzonitrile (DMABN) in methanol solvents. Only the intermolecular hydrogen bond C≡N...H-O was involved in our system. A fairly accurate forecast of the hydrogen bond changes in lowlying electronically excited states were presented in light of a very thorough consideration of their related electronic spectra. The deduction we used to depict the trend of the hydrogen bond changes in excited states could help others understand hydrogen-bonding dynamics more effectively.     

Influence of stress state on the evolution of misfit dislocation networks in a Ni‐based single crystal superalloy

The structural evolution of interfacial dislocation networks in a Ni‐based single crystal superalloy under various stress states was simulated by molecular dynamics (MD). From the simulation, we found that the dislocation network exhibits different deformation and damage mechanisms under various stress states. The square dislocation network at the (100) phase interface is the easiest to damage under a [100] uniaxial load, but more difficult to damage when multi‐axial loads are applied. This suggests that the application of a [100] direction axial load is the key factor for the damage of the square dislocation network, which leads to failure of the Ni‐based single crystal superalloy under the [100] axial centrifugal load. Moreover, based on MD simulations, the effects of the stress state on γ′ rafting were explored. The results indicate that the morphology of γ′ raft depends on the damage structures of the dislocation network under various stress states.     

相对化学位移值：获得CH基团中氢原子精确化学位移值的一种简单方法

为了解决CH基团中氢原子的精确化学位移值的问题,引入相对化学位移值概念．内标法和外标法用于测量全浓度范围的N-甲基乙酰胺水溶液．对于同一个分子来说,选择分子内某个基团的氢原子化 学位移作为一个标准值,得到的其它基团氢原子相对化学位移值随温度和浓度的变化是和测试方法无关的．     

Molecular dynamics simulations of mechanical properties of epoxy-amine: Cross-linker type and degree of conversion effects

Molecular dynamics (MD) simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines. The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simulated under the polymer consistent force field (PCFF). Three types of curing agents (rigidity1,3-phenylenediamine (1,3-P), 4,4-diaminodiphenylmethane (DDM), and phenol-formaldehyde-ethylenediamine (PFE)) with different numbers of active sites are selected in the simulations. We focus on the effects of the cross-linkers on thermo-mechanical properties such as density, glass transition temperature (T_g), elastic constants, and strength. Our simulations show a significant increase in the T_g, Young's modulus and yield stress with the increase in the degree of conversion. The simulation results reveal that the mechanical properties of thermosetting polymers are strongly dependent on the molecular structures of the cross-linker and network topological properties, such as end-to-end distance, crosslinking density and degree of conversion.     

Free vibration analysis of multi-layer graphene nanoribbons incorporating interlayer shear effect via molecular dynamics simulations and nonlocal elasticity

Free vibration of cantilever multi-layer graphene nanoribbons (MLGNRs) with interlayer shear effect is investigated using molecular dynamics simulations (MD) and nonlocal elasticity. Because of similarity of MLGNRs to sandwich structures, sandwich formulations are expressed in the nonlocal form. By comparing the first two frequencies of MLGNRs with various layers and lengths obtained using MD simulations with those of the nonlocal sandwich formulation; the nonlocal parameter is calibrated to match the results of two methods. The results reveal that the calibrated nonlocal parameter for predicting the second frequencies is dependent on the number of MLGNR layers, and it increases by increasing the number of layers.     

Chemical Shift and Its Uses as an Electronic Parameter in Structure-Activity Correlations

Apparent correlations are found between the N-H chemical shifts of congeneric series of compounds and the dipole moments of the molecules, such as lactams and thiolactams, cyclic ureas and thioureas. When there is a high degree of correlation, either the N-H chemical shift or the dipole moment of the molecule can be used as an electronic parameter in correlating the biological activity with the chemical structure. In a series of substituted salicylaldehydes the Hammett σ constant gives better correlation with the biological activity than the O-H chemical shift. This is probably due to the anisotropic effect of the substituent besides the electronic effect. Other factors affecting the N-H chemical shift, e.g. intramolecular hydrogen-bonding of nitrosoureas and the deshielding effect of a benzene ring, in o-phenyleneureas are also presented. In spite of the limitations, the chemical shifts of many compounds can be obtained very easily, therefore, their uses in structure-activity correlations deserve further investigation.     

The strong OHO hydrogen bond. How much covalency?

In the strong OHO hydrogen bond of the phosphoric acid–urea 1?:?1 complex the proton shifts gradually with temperature from the donor towards the acceptor atom, passing through the center of the hydrogen bond at around 315?K. The AIM parameters were evaluated for the published neutron structures at different temperatures. The values of the electron density, its Laplacian, and the energy densities at both the critical points between the proton and the oxygen atoms in the OHO hydrogen bond were correlated with the OH and HO distances. Changes in the AIM parameters of the strong hydrogen bond were compared with those of the weak NHO bond in this complex.     

Studies on ground and excited state prototropic equilibria of 2-fluorenaldehyde 2-pyridylhydrazone

The ground and excited state pK values of 2-fluorenaldehyde 2-pyridylhydrazone obtained from variations in fluorescence intensity with pH are reported. The two acid-base equilibria are separately treated by instrumental and chemical means. Absorption and fluorescence spectral shifts are employed to show that solute-solvent interactions through hydrogen-bonding are responsible for the disagreement between the excited state pK values obtained from Förster cycle calculations and from fluorimetric titration measurements.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.