甲酰胺水溶液的分子动力学模拟

为了解重要的生化模型甲酰胺在水溶液中的微观结构, 采用全原子力场在全浓度范围内对甲酰胺溶液进行了分子动力学模拟, 得到了溶液的径向分布函数, 分析计算了溶质和溶剂分子间的相互作用, 对甲酰胺和水分子的氢键缔合情况进行了分析. 研究发现羰基侧的H原子与水分子能形成C—H…O弱相互作用. 在作者早期的研究中发现, 此相互作用对于阻碍甲酰胺的异构化具有重要意义, 特别是当甲酰胺在溶液中含量增大时, 此相互作用更加不能忽视. 全浓度溶液的模拟表明, 甲酰胺在稀浓度区可以促进水局部结构的增强, 随FM浓度增加, 由水的自身缔合转变为水与FM的交叉缔合, 在FM高浓度区, 两者的交叉缔合将逐渐被甲酰胺自身的线状缔合代替.     

甘油水溶液氢键特性的分子动力学模拟

为了研究低温保护剂溶液的结构和物理化学特性, 以甘油为保护剂, 采用分子动力学方法, 对不同浓度的甘油和水的二元体系进行了模拟. 得到了不同浓度的甘油水溶液在2 ns内的分子动力学运动轨迹, 通过对后1 ns内运动轨迹的分析, 得到了各个原子对的径向分布函数和甘油分子的构型分布. 根据氢键的图形定义, 分析了氢键的结构和动力学特性. 计算了不同浓度下体系中平均每个原子(O和H)和分子(甘油和水)参与氢键个数的百分比分布及其平均值. 同时还计算了所有氢键、水分子之间的氢键以及甘油与水分子之间的氢键的生存周期.     

基于SAFT理论关联醇与DMF体系的1H NMR

混合物核磁共振化学位移可以用不同的化学缔合理论研究,但当形成的缔合体种类很多时,需要很多优化参数.作者从统计缔合流体理论（SAFT）出发,提出了一个能关联混合物核磁共振化学位移,但又不需要假设缔合平衡常数的模型.对于醇与N,N-二甲基甲酰胺（DMF）体系,关联的均方根偏差小于1.01％.讨论了醇与DMF体系和醇与正己烷体系核磁共振化学位移随醇的浓度变化趋势的差异,认为醇与DMF形成比醇的自缔更强的交叉缔合是造成这种变化趋势不同的主要原因.     

分子动力学方法研究聚甲基乙烯基醚／水体系中氢键和准氢键的结构与分布

用分子动力学方法模拟室温下不同浓度的聚甲基乙烯基醚／水体系的微观溶剂化结构．得到的径向分布函数和氢键给体和受体距离分布表明,聚合物与水形成的氢键比水之间形成的氢键短约0．005nm．准氢键C—H…O的数目是范德华作用对的7．2％．我们发现,在各浓度下,水分子并不能均匀地分布在聚合物结构单元上,即使在很稀的溶液（3．3％,质量分数）中,仍然有10％左右的醚氧没有和水分子形成氢键．这说明在溶液中,不但高分子链间有紧密的接触,而且高分子链内的链段间也有紧密的接触,导致链上的一些醚氧不能和水分子有效地接触而形成氢键．准氢键随浓度的变化和氢键的变化趋势类似,但形成准氢键的结构单元数目与形成氢键的结构单元数目比值在0．2附近．文献上用动态DSC测量低分子量聚甲基乙烯基醚（PVME）水溶液的相转变焓发现,在浓度为30％左右有一转折,与本模拟所得出的在浓度为27％左右氢键和准氢键比例的转折相关,这给相转变焓的转折点提供了分子尺度的微观解释．另外,浓度小于54％的溶液中存在“自由水”,在86％的浓溶液中每个结构单元大约与1．56个水分子缔合．     

基于LFHB 理论模型关联和预测醇+惰性溶剂的1H NMR 化学位移

运用含氢键缔合的格子流体状态方程(LFHB), 仅用一个参数关联了一元醇-惰性溶剂共17个体系29套1H NMR化学位移数据. 并且用关联参数成功预测了不同温度下丁醇+环己烷的化学位移. 所得结果与化学缔合理论的结果进行了比较. 对于某些体系在稀浓度范围LFHB的计算氢键缔合度要低于化学缔合理论的结果. 并且分析了LFHB理论中的物理参数和化学参数对于缔合度计算的不同影响.     

葡萄糖水溶液氢键结构和动力分析

利用分子动力学模拟方法研究了不同浓度下葡萄糖水溶液的氢键结构和氢键生存周期. 分析了参与i个氢键(分子内、分子间、所有类型)的葡萄糖分子和水分子的百分比分布. 研究发现存在一个特征数N, 参与N个氢键的分子的比例最高, 当iN时, 参与i个氢键的分子的比例随着浓度的增加而减小. 还分析了不同类型氢键(葡萄糖分子内、葡萄糖分子间、水分子间、葡萄糖分子与水分子间、所有类型)的连续和截断自相关函数, 并计算了对应的氢键生存周期.     

聚N,N-二乙基丙烯酰胺低聚物水溶液的分子动力学研究

对50个单元构成的聚N,N-二乙基丙烯酰胺(PDEA)低聚物的水溶液体系进行了分子动力学的研究,分别模拟了300 K时的伸展链、310 K时的伸展链以及紧缩链与水构成的体系,对溶液中PDEA周围溶剂水分子的分布情况以及水分子形成氢键的情况进行了统计,结果表明在PDEA周围的水产生了比本体水更有序的结构,形成了更多的氢键,这种有序结构维持到第二水合层甚至更远.发生相分离后,PDEA与水分子形成的氢键大部分未被破坏,水合层中每个水分子形成的氢键数也没有明显变化,但水合层(形成有序结构的水分子)内水分子数目的减少使得总的氢键数目减少,从而造成体系能量增加及熵增加.同时还研究了聚合物及水分子的自扩散系数,表明PDEA影响周围水分子结构的同时,对水的动力学性质也产生了很大影响.     

CuCl2和CuSO4的核磁共振系数、粘度系数及其与水分子结构的关系

测定了较低浓度范围内CuCl2、CuSO4水溶液的粘度系数(B)、核磁共振(NMR)系数(B')及其对水17O NMR化学位移的影响, 进一步计算了Cu2+、Cl-、SO2-40的粘度系数及核磁共振系数, 并与文献值进行了比较. 利用17O NMR化学位移、粘度系数和核磁共振系数与水团簇结构和水分子缔合的关系, 分析了CuCl2、CuSO4对水结构的影响. 结果表明, CuCl2和CuSO4均具有促进水分子缔合, 使水团簇加大的作用, 且CuSO4对水的缔合作用大于CuCl2, Cl-对水缔合的破坏作用大于SO2-40 . Cu2+作为顺磁离子, 在核磁共振弛豫过程中, 具有明显的缩短水中质子的自旋-晶格弛豫时间, 使谱线变宽的作用.     

CuCl2和CuSO4的核磁共振系数、粘度系数及其与水分子结构的关系（英文）

测定了较低浓度范围内CuCl2、CuSO4水溶液的粘度系数（B）、核磁共振（NMR）系数（B′）及其对水17ONMR化学位移的影响,进一步计算了Cu2＋、Cl-、SO420-的粘度系数及核磁共振系数,并与文献值进行了比较.利用17ONMR化学位移、粘度系数和核磁共振系数与水团簇结构和水分子缔合的关系,分析了CuCl2、CuSO4对水结构的影响.结果表明,CuCl2和CuSO4均具有促进水分子缔合,使水团簇加大的作用,且CuSO4对水的缔合作用大于CuCl2,Cl-对水缔合的破坏作用大于SO420-.Cu2＋作为顺磁离子,在核磁共振弛豫过程中,具有明显的缩短水中质子的自旋-晶格弛豫时间,使谱线变宽的作用.     

CuCl2和CuSO4的核磁共振系数、粘度系数及其与水分子结构的关系

测定了较低浓度范围内CuCl2、CuSO4水溶液的粘度系数(B)、核磁共振(NMR)系数(B')及其对水17O NMR化学位移的影响,进一步计算了Cu2+、C1-、SO2-4的粘度系数及核磁共振系数,并与文献值进行了比较.利用17O NMR化学位移、粘度系数和核磁共振系数与水团簇结构和水分子缔合的关系,分析了CuCl2、CuSO4对水结构的影响.结果表明,CuCl2和CuSO4均具有促进水分子缔合,使水团簇加大的作用,且CuSO4对水的缔合作用大于CuCl2,Cl-对水缔合的破坏作用大于SO2-4作为顺磁离子,在核磁共振弛豫过程中,具有明显的缩短水中质子的自旋-晶格弛豫时间,使谱线变宽的作用.     

Structure and dynamics of halogenoethanol-water mixtures studied by large-angle X-ray scattering, small-angle neutron scattering, and NMR relaxation

To clarify the structure of solvent clusters formed in halogenoethanol-water mixtures at the molecular level, large-angle X-ray scattering (LAXS) measurements have been made at 298 K on 2,2,2-trifluoroethanol (TFE), 2,2,2-trichloroethanol (TCE), and their aqueous mixtures in the TFE and TCE mole fraction ranges of 0.002 < or = x(TFE) < or = 0.9 and 0.5 < or = x(TCE) < or = 0.9, respectively. The radial distribution functions (RDFs) for TFE-water mixtures have shown that the structural transition from inherent TFE structure to the tetrahedral-like structure of water takes place at x(TFE) approximately 0.2. In the TCE-water mixtures inherent TCE structure remains in the range of 0.5 < or = x(TCE) < or = 1. Small-angle neutron scattering (SANS) experiments have been performed on CF(3)CH(2)OD- (TFE-d(1)-) D(2)O and CF(3)CD(2)OH- (TFE-d(2)-) H(2)O mixtures in the TFE mole fraction range of 0.05 < or = x(TFE) < or = 0.8. The SANS results in terms of the Ornstein-Zernike correlation length have revealed that TFE and water molecules are most heterogeneously mixed with each other in the TFE-water mixture at x(TFE) approximately 0.15, i.e., both TFE clusters and water clusters are most enhanced in the mixture. To evaluate the dynamics of TFE and ethanol (EtOH) molecules in TFE-water and ethanol-water mixtures, respectively, (1)H NMR relaxation rates for the methylene group within alcohol molecules have been measured by using an inversion-recovery method. The alcohol concentration dependence of the relaxation rates for the TFE-water and ethanol-water mixtures has shown a break point at x(TFE) approximately 0.15 and x(EtOH) approximately 0.2, respectively, where the structural transition from alcohol clusters to the tetrahedral-like structure of water takes place. On the basis of the present results, the most likely structure models of solvent clusters predominantly formed in TFE-water and TCE-water mixtures are proposed. In addition, effects of halogenation of the hydrophobic groups on clustering of alcohol molecules are discussed from the present results, together with the previous ones for ethanol-water and 1,1,1,3,3,3-hexafluoro-2-propanol- (HFIP-) water mixtures.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations

An all-atom dimethyl sulfoxide (DMSO) and water model have been used for molecular dy-namics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bondsand weak C—H…O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The sta-ble aggregates of (DMSO)_m·S=O…HW—OW·(H₂O)_n might play a key role in this region.Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.     

Liquid structure of acetic acid-water and trifluoroacetic acid-water mixtures studied by large-angle X-ray scattering and NMR

The structures of acetic acid (AA), trifluoroacetic acid (TFA), and their aqueous mixtures over the entire range of acid mole fraction xA have been investigated by using large-angle X-ray scattering (LAXS) and NMR techniques. The results from the LAXS experiments have shown that acetic acid molecules mainly form a chain structure via hydrogen bonding in the pure liquid. In acetic acid-water mixtures hydrogen bonds of acetic acid-water and water-water gradually increase with decreasing xA, while the chain structure of acetic acid molecules is moderately ruptured. Hydrogen bonds among water molecules are remarkably formed in acetic acid-water mixtures at xA相似文献   

All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactionsof N,N-dimethylacetamide-Water System

N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA-water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H￠ ￠ ￠O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.     

All‐atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol‐water System

All‐atom molecular dynamics (MD) simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol (EtOH)‐water system. The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis. The strong hydrogen bonds and weak C–H···O contacts coexist in the mixtures through the analysis of the radial distribution functions. And the liquid structures in the whole concentration of EtOH‐water mixtures can be classified into three regions by the statistic analysis of the hydrogen‐bonding network in the MD simulations. Moreover, the chemical shifts of the hydrogen atom are in agreement with the statistical results of the average number hydrogen bonds in the MD simulations. Interestingly, the excess relative extent of η_rel^E calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at x_EtOH≈0.18. The excess properties present good agreement with the excess enthalpy in the concentration dependence.     

All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investi-gate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.     

All-atom molecular dynamic simulations and relative NMR spectra study of weak C-H...O contacts in amide-water systems

Amide-water mixtures are studied by all-atom molecular dynamics (MD) simulations and the relative temperature-dependent NMR experiment. The weak C-H...O contacts are found in the amide-water systems theoretically and experimentally. The statistical results of the average numbers of hydrogen bonds indicate that the methyl groups in amide molecules represent different capabilities in forming the weak C-H...O contacts. The statistics also imply that the C-H...O contacts are more obvious in the amide-rich region than those in the water-rich region. The temperature-dependent NMR spectra are also adopted to investigate the weak C-H...O contacts in the amide-water systems. The relative chemical shifts of the methyl groups are in good agreement with the MD simulations.     

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.     

Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum

The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.