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.     

Dielectric Properties of Solutions Isomorphous with Water

The dielectric properties of aqueous solutions of ammonia, hydrogen fluoride, hydrogen peroxide, and ammonium halides are determined by the number of hydrogen bonds formed by the solute species with the molecules forming the water framework. For such solutions, the product of the concentration coefficient of the dielectric permittivity by the ratio of the number of hydrogen bonds per solute molecule and per water molecule is constant. In aqueous solutions with a water-like structure, the mechanism of the dielectric polarization is the same as in pure water (proton-activation mechanism) and is determined by proton fluctuations on the line of hydrogen bonds.__________Translated from Zhurnal Obshchei Khimii, Vol. 75, No. 1, 2005, pp. 39–45.Original Russian Text Copyright © 2005 by Potapov, Parkhomenko.     

Intermolecular-medium and intramolecular-weak hydrogen bonding chains in the crystals of chiral trifluoromethylated amino alcohols

A structural feature of hydrogen bonding chains found in the crystals of trifluoromethylated amino alcohols is reported. Hydrogen bondings of 3-(N,N-dialkylamino)-1,1,1-trifluoro-2-propanols construct chiral spiral hydrogen bonding chains. Lone pairs on the nitrogen atoms of the amino alcohols participate in two hydrogen bondings. Detailed structural analysis of the hydrogen bonds of the 3-(N,N-dimethylamino)-1,1,1-trifluoro-2-propanol suggested that the chain built up with alternating intermolecular-medium and intramolecular-weak hydrogen bonds. The medium intermolecular hydrogen bond, which transfers a proton from the hydroxy group to the amino nitrogen, would make a tentative zwitterionic form of the molecule. Then, electrostatic attraction between the charges in the zwitterion centers induced a weak intramolecular hydrogen bond.     

Structural Study of Methane Hydrate

The authors present a structural study of methane hydrate by using MP2 calculations and the QTAIM method. Two different structures are analyzed for the empty clathrate molecule. Both structures exhibit 30 hydrogen bonds and they differ in the position of the 10 O–H bonds that are not involved in hydrogen bonds. As the available space in the middle of the structure, where the guest could be located, is the same in both cases, most stable molecule is considered to be filled with methane. We also try to establish similarities and differences between methane occupied and empty units by analyzing geometrical and density charge properties, particularly what is related to the hydrogen bonds among water molecules in the clathrate. Our results allow us to conclude that the introduction of methane does not vary the main structural properties of this molecule.     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

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.     

单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Study of molecular behavior in a water nanocluster: size and temperature effect

Temperature and size effects on the behavior of nanoscale water molecule clusters are investigated by molecular dynamics simulations. The flexible three-centered (F3C) water potential is used to model the inter- and intramolecular interactions of the water molecule. The differences between the structural properties for the surface region and those for the interior region of the cluster are also investigated. It is found that as the temperature rises, the average number of hydrogen bonds per water molecule decreases, but the ratio of surface water molecules increases. After comparing the water densities in interior regions and the average number of hydrogen bonds in those regions, we find there is no apparent size effect on water molecules in the interior region, whereas the size of the water cluster has a significant influence on the behavior of water molecules at the surface region.     

Reconsideration on hydrogen bond strengthening or cleavage of photoexcited coumarin 102 in aqueous solvent: a DFT/TDDFT study

In this work, the excited-state hydrogen bonding dynamics of photoexcited coumarin 102 in aqueous solvent is reconsidered. The electronically excited states of the hydrogen bonded complexes formed by coumarin 102 (C102) chromophore and the hydrogen donating water solvent have been investigated using the time-dependent density functional theory method. Two intermolecular hydrogen bonds between C102 and water molecules are considered. The previous works (Wells et al., J Phys Chem A 2008, 112, 2511) have proposed that one intermolecular hydrogen bond would be strengthened and the other one would be cleaved upon photoexcitation to the electronically excited states. However, our theoretical calculations have demonstrated that both the two intermolecular hydrogen bonds between C102 solute and H(2)O solvent molecules are significantly strengthened in electronically excited states by comparison with those in ground state. Hence, we have confirmed again that intermolecular hydrogen bonds between C102 chromophore and aqueous solvents are strengthened not cleaved upon electronic excitation, which is in accordance with Zhao's works.     

Dependence of the number of hydrogen bonds per water molecule on its distance to a hydrophobic surface and a thereupon-based model for hydrophobic attraction

A water molecule in the vicinity of a hydrophobic surface forms fewer hydrogen bonds than a bulk molecule because the surface restricts the space available for other water molecules necessary for its hydrogen-bonding. In this vicinity, the number of hydrogen bonds per water molecule depends on its distance to the surface. Considering the number of hydrogen bonds per bulk water molecule (available experimentally) as the only reference quantity, we propose an improved probabilistic approach to water hydrogen-bonding that allows one to obtain an analytic expression for this dependence. (The original version of this approach [Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 130, 124713 (2009)] provides the number of hydrogen bonds per water molecule in the vicinity of a hydrophobic surface as an average over all possible locations and orientations of the molecule.) This function (the number of hydrogen bonds per water molecule versus its distance to a hydrophobic surface) can be used to develop analytic models for the effect of hydrogen-bonding on the hydration of hydrophobic particles and their solvent-mediated interaction. Presenting a model for the latter, we also examine the temperature effect on the solvent-mediated interaction of two parallel hydrophobic plates.     

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.     

A first‐principles investigation of the hydrogen bond interaction and the sensitive characters in cis‐1,3,4,6‐tetranitrooctahydroimidazo‐[4,5‐d]imidazole

A theoretical study of structural and electronic properties of cis‐1,3,4,6‐tetranitrooctahydroimidazo‐[4,5‐d]imidazole (BCHMX) crystal is performed using density functional theory. The band structure, the total density of states, the atomic orbit projected density of states (PDOS) of C, N, O, and H, and Mulliken population analysis are discussed. The study by analyzing the PDOS shows that the structure of BCHMX crystal possesses C? H···O intra‐ and intermolecular hydrogen bonding. There are hydrogen bonds between H₃‐1s and O₅‐2p orbits, H₂‐1s and O₆‐2p orbits of intramolecules and between H₂‐1s and O₁‐2p orbits of intermolecules. The reasons for the smaller impact sensitivity compared with β‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocane and 1,3,5‐trinitro‐1,3,5‐triazinane are also explored from the band gap in the crystal and the weakest bond dissociation energy in single molecule. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structural studies on the hydration of L-glutamic acid in solution

A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.     

Structural and energetic consequences of the formation of intramolecular hydrogen bonds

Formation of intramolecular hydrogen bonds leads to structural modifications in the whole molecule, which are discussed on the basis of B3LYP/6-31G(d,p) calculations. The energy and the structure of various hydrogen-bonded and open conformers are considered for two groups of ortho-substituted phenols–N-dimethylaminomethylphenols (Mannich bases) and N-methylbenzylideneamines (Schiff bases). The energy of intramolecular hydrogen bond formation in Mannich bases was corrected for non-bonded interactions within the molecules, based on a thermodynamic cycle. Structural data were used to estimate the fraction of the ortho-quinoid (keto) form in particular tautomers. It is shown that proton transfer in Schiff bases leads to an increase of this fraction to about 40%, while opening of the hydrogen bond in the proton transferred form increases the keto fraction to 70%.     

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.     

4-羟甲基吡啶－水红移氢键的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-311++G**基函数对4-羟甲基吡啶与水形成的1:1和1:2（摩尔比）氢键复合物进行了理论计算研究,分别得到稳定的4-羟甲基吡啶－H₂O和4-羟甲基吡啶－(H₂O)₂氢键复合物3个和8个。经基组重叠误差和零点振动能校正后,最稳定的1:1和1:2氢键复合物的相互作用能分别为-20.536和-44.246 kJ/mol。振动分析显示O-H···N(O)氢键的形成使复合物中O-H键对称伸缩振动频率红移(减小)。自然键轨道分析表明,4-羟甲基吡啶与水形成最稳定的1:1和1:2氢键复合物时,分子间电荷转移分别为0.02642 e 和0.03813 e 。含时密度泛函理论TD-B3LYP/ 6-311++G**计算显示,相对于4-羟甲基吡啶单体分子,氢键H-OH···N和H-OH···OH的形成分别使最大吸收光谱波长兰移8~16纳米和红移4~11纳米。     

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.     

A study of the hydrogen bond by means of comparative calculations

The nature of the hydrogen bond is investigated by means of a comparative analysis of some hydrogen bonded and hydrogen-like bonded systems. It is concluded that the hydrogen bond is determined by electrostatic interaction between the proton and the region of high electron density in the neighbour molecule.     

Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions

Molecular dynamics simulations of dilute and concentrated aqueous NaCl solutions are carried out to investigate the changes of the hydrogen bonded structures in the vicinity of ions for different ion concentrations. An analysis of the hydrogen bond population in the first and second solvation shells of the ions and in the bulk water is done. Although essentially no effect of ions on the hydrogen bonding is observed beyond the first solvation shell of the ions for the dilute solutions, for the concentrated solutions a noticeable change in the average number of water-water hydrogen bonds is observed in the second solvation shells of the ions and even beyond. However, the changes in the average number of hydrogen bonds are found to be relatively less when both water-water and ion-water hydrogen bonds are counted. Thus, the changes in the total number of hydrogen bonds per water are not very dramatic beyond the first solvation shell even for concentrated solutions.