水与乙醇分子在金管内吸附作用的分子动力学研究

使用分子动力学研究了乙醇与水分子在纳米金管内按照不同比例混合时的吸附现象,并利用径向密度分布函数及水和乙醇分子所形成的平均氢键数来探讨纳米限制效应.结果表明,径向密度分布函数和氢键数目受纳米金管影响较大.另外,水与金管之间的作用力比乙醇与金管之间的大,导致水分子形成的平均氢键数不同于乙醇分子的.     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

高岭石-水体系中水分子结构的分子动力学模拟

以Hendricks模型为初始结构, 利用CLAYFF力场对高岭石-水体系进行无晶体学限制的分子动力学模拟. 结果表明, 层间水有三种类型: I型类似于Costanzo提出的“洞水”分子, 其HH矢量(水分子中从一个氢原子位置指向另一个氢原子位置的方向矢量)平行于(001)平面, 而C2轴稍微倾斜于(001)面法线; II型类似于“连接水”, 一个氢氧键指向临近的层间四面体氧形成氢键, 另一个氢氧键与(001)面近似平行; III型水分子在层间近似保持为竖直状, 一个氢与层间四面体氧形成氢键, 而另一个氢与对面层的羟基氧形成氢键. 高岭石羟基氢沿(001)晶面法线的浓度曲线显示一部分羟基指向变为近似平行于(001)面, 羟基氧因此能够暴露出来与层间水分子氢形成氢键. 此外, 模拟中还观察到部分II型水分子氧偏离于层间的平均位置而更靠近四面体层, 这和Costanzo的实验结果一致, 可能是X射线谱图中(002)弱衍射峰出现的原因.     

水与受质子溶剂氢键作用的IR研究

一般认为,水与受质子溶剂通过氢键作用形成1:1和1:2缔合物: H_2O+S?H_2O.S (1) H_2O.S+S?H_2O._2S (2)文献报道了通过NMR和IR光谱等方法求得的各种有机溶剂与水作用的K_(11)和K_(12)值.S.O.Paul等观察了水在受质子溶剂中的IR谱图,将OH伸缩振动区域的吸收峰分解为四个峰并分别指定为1:1和对称1:2缔合物中水的吸收峰.对于二氧六环,四个峰位置分别为:Ⅰ.3653cm~(-1);Ⅱ.3622cm~(-1);Ⅲ.3580cm~(-1);Ⅳ.3509cm~(-1),指定峰Ⅰ、Ⅳ分别为1:1缔合物的非氢键合和氢键合OH伸缩振动吸收,峰Ⅱ、Ⅲ分别为对称1:2缔合物的反对称和     

水-甲醇体系的Monte Carlo分子膜拟

本文应用Monte Carlo分子膜拟方法对水、甲醇水-甲醇的1:1混合物、甲醇无限稀释时的水溶液和水无限稀释时的甲醇溶液等五个体系进行了研究。采用TIP分子位能函数, 得到了上述体系的热力学性质、原子径向分布函数、分子氢键配位数分布。并以Monte Carlo分子模拟获得的结构函数与X射线衍射实验结果进行了比较。     

水-甲醇体系的Monte Carlo分子膜拟

本文应用Monte Carlo分子膜拟方法对水、甲醇水-甲醇的1:1混合物、甲醇无限稀释时的水溶液和水无限稀释时的甲醇溶液等五个体系进行了研究。采用TIP分子位能函数, 得到了上述体系的热力学性质、原子径向分布函数、分子氢键配位数分布。并以Monte Carlo分子模拟获得的结构函数与X射线衍射实验结果进行了比较。     

用氢键连接形成的超分子晶体

通常的氢键发生在F、O、N原子上的氢原子与F、O、N之间,但在某些特殊情况下,C—H也具有形成氢键的能力,例如Cl3C—H与丙酮的氧原子或水的氧原子之间的氢键.炔基氢也具有形成氢键的能力.早在1989年,国际化学竞赛就出过一个实验题,测量丙酮与三氯甲烷形成氢键的热效应.     

二甲基亚砜防冻机理的拉曼光谱分析

采用拉曼光谱对不同体积比的二甲基亚砜(DMSO)水溶液进行测量, 并利用Origin 7.5对水的光谱带进行分峰, 求得拉曼光谱峰面积比值. 应用混合模型对实验结果进行了分析, 分析结果表明, 防冻剂二甲基亚砜与水混合时, 其SO基团与水分子的OH基团形成氢键(SO…H—O), 有效地阻止了四面体结构冰的生成, 并证实了二甲基亚砜与水的体积比为1∶1时, 防冻效果最佳.     

Structure of methanol confined in MCM-41 investigated by large-angle X-ray scattering technique

Large-angle X-ray scattering (LAXS) measurements over a temperature range from 223 to 298 K have been made on methanol confined in mesoporous silica MCM-41 with two different pore diameters, 28 A (C14) and 21 A (C10), under both monolayer and capillary-condensed adsorption conditions. To compare the structure of methanol in the MCM-41 pores with that of bulk methanol, X-ray scattering intensities for bulk methanol in the same temperature range have also been measured. The radial distribution functions (RDFs) for the monolayer methanol samples showed that methanol molecules are strongly hydrogen bonded to the silanol groups on the MCM-41 surface, resulting in no significant change in the structure of adsorbed methanol with respect to the pore size and temperature. On the other hand, the RDFs for the capillary-condensed methanol samples showed that hydrogen-bonded chains of methanol molecules are formed in both pores. However, the distance and number of hydrogen bonds estimated from the RDFs suggested that hydrogen bonds between methanol molecules in the pores are significantly distorted or partly disrupted. It has been found that the hydrogen bonds are more distorted in the smaller pores of MCM-41. With decreasing temperature, however, the hydrogen-bonded chains of methanol in the pores were gradually ordered. A comparison of the present results on methanol in MCM-41 pores with those on water in the same pores revealed that the structural change with temperature is less significant for confined methanol than for confined water.     

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.     

Solute-solvent friction kernels and solution properties of methyl oxazoline-phenyl oxazoline (MeOx-PhOx) copolymers in binary ethanol-water mixtures

Solvent mixtures often alter the solubility of polymeric substances. Statistical copolymers made from 2-methyl-2-oxazoline (MeOx) and 2-phenyl-2-oxazoline (PhOx) are known for their varying solubilities in pure ethanol, pure water and in binary mixtures of ethanol-water. Constrained Molecular Dynamics (MD) simulations have been carried out with an aim to explain the varying solubilities of the statistical MeOx-PhOx copolymers. The solute-solvent dynamic friction kernels calculated through constrained MD simulations corroborate the solubility pattern in these copolymers. The solvation characteristics have been analyzed in terms of the solute-solvent radial distribution functions (RDFs). The ethanol-soluble MeOx-PhOx copolymers exhibit characteristic solute-composition dependence in the dynamic solute-solvent friction kernels, indicating the strength of the solute-solvent correlations. The aggressive solvation by the ethanol molecules in the binary solvent mixtures has been brought out by the O(solute)-H(ethanol) RDFs which exhibit a characteristic dependence on the ethanol content in the solvent composition. The corresponding O(solute)-H(water) RDFs are devoid of any such composition dependence. For all the MeOx-PhOx copolymers, the O-site solvation is strongly dominated by the water molecules and the N-sites are solvated equally by both ethanol and water molecules.     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Molecular dynamics study of the tautomeric equilibrium in the 4-nitro- and 2,4,6-trichloro derivatives of 2-(N,N-dialkyloaminomethyl)phenol

 Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. Received: 26 April 2002 / Accepted: 9 September 2002 / Published online: 31 March 2003     

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.     

Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models

Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.     

Effect of the polarity of functional groups (-H, -OH, and -COOH) on the structure of a solvent near single-wall carbon nanopipes

The effect of the functionalization of carbon nanopipes on the structure of a phase separation nanopipe solvent at 300 K was performed using molecular dynamics. Radial distribution functions, ranged radial distribution functions, self-diffusion coefficients, coordination numbers, and the number of hydrogen bonds for the investigated systems were obtained. The influence of the polarity of functional groups on the structure of water near nanopipes was established.