A density functional theory and quantum theory of atoms in molecules study on hydrogen bonding interaction between paracetamol and water molecules

To consider the hydrogen bonding interactions between paracetamol and water molecules, probable complexes of paracetamol from three active sites (carbonyl oxygen atom, hydroxyl oxygen atom, and nitrogen atom) with H₂O molecule were formed. The optimized geometries and total energies have been obtained at the B3PW91/6-31+G(d, p) level of theory. Comparison of hydrogen bond lengths and the energies of complexes showed hydrogen bond that form between the oxygen atom of the carbonyl group and hydrogen atom is stronger than others. Moreover, an increase in the number of hydrogen bonds increases stability of paracetamol-water complexes. At the end, the QTAIM was applied to explain the nature of the hydrogen bonds and confirm the more stability by complexation.     

The concentration effect on the ‘hydrophobic’ and ‘hydrophilic’ behaviour around DMSO in dilute aqueous DMSO solutions. A computer simulation study

We have carried out a molecular dynamics study of dimethyl sulfoxide (DMSO) in water at 298 K at two different densities by simulating two different concentrations: 0.055 and 0.19 mole fraction. We have found an enhancement in the structure of water, an effect that becomes more pronounced as the concentration of DMSO increases. At both concentrations there is a well-defined hydration structure around the oxygen atom of DMSO, which is able to establish strong hydrogen bonds with surrounding water molecules. An increase in the concentration of DMSO depletes the solution of bulk water molecules, reducing the number of hydrogen bonds that water can have in the immediate vicinity of DMSO but increasing the strength of the hydrogen bonds made between the oxygen atom of DMSO and water. There is clear evidence of ‘hydrophobic’ hydration around the methyl groups of DMSO, which is enhanced as the concentration of DMSO increases.     

Al quadrupole interaction in zeolites loaded with probe molecules—a quantum-chemical study of trends in electric field gradients and chemical bonds in clusters

The electric field gradient (EFG) has been calculated in zeolite clusters at the aluminium site surrounded by four SiO₄ tetrahedra. Density functional theory (DFT) with the 6-31G^{* *} basis set has been employed. Formation of a Brønsted acid site by protonation of one oxygen atom of the A1O₄ tetrahedron perturbs the coordination of aluminium, i.e., the corresponding Al-O bond is considerably weaker than in the unprotonated case. This leads to a large EFG, and the calculated quadrupole coupling constant (QCC) for ²⁷Al is 18.2 MHz. Different probe molecules were adsorbed on the Brønsted site. The hydrogen bond formed between the acid proton and the probe molecule weakens the zeolitic O---H bond. For conservation of the overall bond order of the oxygen atom, its bonds to the neighboring tetrahedral atoms (Si, Al) become stronger. As a consequence, the perturbation of the AlO₄ tetrahedron and the EFG at the aluminium position decrease depending on the strength of the hydrogen bond. Perturbation of an oxygen atom of the AlO₄ tetrahedron by accepting a hydrogen bond from the base molecule also affects the corresponding AlO---O bond order. A linear correlation is found between the calculated QCC constants for ²⁷Al and the AlO---O bond orders of the oxygen atoms which are perturbed by protonation or by hydrogen bonds. A geometrical shear strain parameter and a simple electrostatic point charge model are less successful at predicting the trends in EFG which clearly shows the importance of the chemical bonds. Published by Elsevier Science B.V.     

Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

The basic result of carboxylic group that the oxygen atom of the -OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N—H… O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, α-oxalic acid and β-oxalic acid, also were looked into in terms of hydrogen bonding and packing.     

Comparison of hydrogen and halogen bonds between dimethyl sulfoxide and hypohalous acid: competition and cooperativity

A theoretical study of the complexes formed between dimethyl sulfoxide (DMSO) and hypohalous acid (HOX, X = Cl, Br, and I) has been carried out at the MP2/aug-cc-pVTZ level. For each HOX, four minima binary complexes were found, two mainly with an OH???O hydrogen bond and the other two with an OX???O halogen bond. The hydrogen-bonded complexes are more stable than the halogen-bonded analogues for HOCl and HOBr, while both types of complexes have similar stability in the iodine case. A red shift was found for the associated H–O and X–O bond stretch vibrations and a small blue shift for the distant bonds. As the oxygen of DMSO simultaneously binds with two HOCl molecules, the corresponding interactions are weakened with diminutive effect. This diminutive effect is the largest in the complexes with two OH???O hydrogen bonds but the smallest in those with two OCl???O halogen bonds.     

用激光拉曼光谱研究液态乙醇的水合作用过程

为研究室温下乙醇-水二元混合物内部的分子间缔合情形,测得了不同体积配比溶液的拉曼光谱,发现位于2 800~3 050 cm-1波数区间的C—H伸缩振动频率随乙醇中加入水量的增加整体呈现蓝移趋势,而位于1 048 cm-1附近的CO伸缩振动频率的变化规律却与此相反。分析认为,这种现象主要由溶液内部分子间发生的不同水合作用所致,并据此阐明了液态乙醇的水合作用过程:水分子首先与纯乙醇中的自缔合短链发生氢键缔合作用,形成了含有较多乙醇分子数的乙醇水合团簇,直到溶液中水的体积含量达到50%时,乙醇的水合作用达到暂时饱和;而当水的体积含量继续增加到70%以后,水分子致使原有乙醇水合团簇解离形成较小尺寸的团簇,并与解离点位上的乙醇分子羟基发生进一步水合作用;而后,当水体积含量增至一定程度后,还会导致乙醇分子疏水基CH基团与水分子间形成弱氢键C—H…O。     

碳纳米胶囊中水分子的分子动力学研究

采用分子动力学方法研究了不同温度下碳纳米胶囊中水分子及其氢键的聚集密度分布,讨论了水分子内部键角及其取向规律.计算结果表明,由于碳纳米胶囊的束缚作用,水分子主要聚集在与胶囊形状相似的三个薄层中,随着温度的升高,聚集密度峰均会展宽并向管壁移动.氢键的分布规律与水分子聚集密度类似并对其取向角分布有明显影响.与通常情况不同,在1000K高温时仍存在相当数量的氢键.在3100 K附近,碳纳米胶囊发生破裂,溢出少量水分子后自动愈合.     

Structure and dynamics of ordered water in a thick nanofilm on ionic surfaces

The structure and dynamics of water in a thick film on an ionic surface are studied by molecular dynamic simulations. We find that there is a dense monolayer of water molecules in the vicinity of the surface. Water molecules within this layer not only show an upright hydrogen-down orientation, but also an upright hydrogen-up orientation. Thus, water molecules in this layer can form hydrogen bonds with water molecules in the next layer. Therefore, the two-dimensional hydrogen bond network of the first layer is disrupted, mainly due to the O atoms in this layer, which are affected by the next layer and are unstable. Moreover, these water molecules exhibit delayed dynamic behavior with relatively long residence time compared with those bulk-like molecules in the other layers. Our study should be helpful to further understand the influence of water film thickness on the interfacial water at the solid-liquid interface.     

Monomer structures of water adsorbed on p(2 x 2)-Ni(111)-O surface at 25 and 140 K studied by surface X-ray diffraction

The structures of a monomeric water molecule adsorbed on p(2 x 2)-Ni(111)-O surface were determined by difference Fourier calculations. At temperatures of 25 K, water molecules chemisorb predominantly at 2 x 2 oxygen atom sites, forming an OH---O(ad) (2 x 2) hydrogen bond. A 2 x 2 oxygen atom (O(ad)) is surrounded by one to three monomeric water molecules, which take statistically disordered positions with threefold symmetry. At temperatures of 140 K, monomeric water molecules occupy a top site of Ni atoms via an oxygen lone pair and are stabilized as a singleton molecule on the surface.     

Molecular Dynamics Study on Microstructure of Potassium Dihydrogen Phosphates Solution

用分子动力学模拟方法研究了不同温度下磷酸二氢钾(KDP)水溶液的内能和微结构. 水分子被看作简单点电荷模型,磷酸二氢根被看作七节点模型. 另外系统地研究了溶液的内能和径向分布函数. 在饱和温度附近,局域粒子数密度有很大的波动;饱和溶液的比热要比不饱和溶液的比热高表明溶液在低于饱和温度的过程中经历了结晶过程;水中的氧原子跟磷酸二氢根中的氢原子的径向分布函数表明二者之间形成很强的氢键结构;在KDP水溶液中,钾阳离子跟磷酸二氢根中的氧原子有很强的相互作用,并且在饱和溶液中形成的离子对数量更多.     

Surface defects on ZnO nanowires: implications for design of sensors

Surface defects are commonly believed to be fundamentally important to gas-sensor performance. We examine the effect of gas coverage and ethanol orientation on its adsorption on the stoichiometric and oxygen deficient (101(-)0) nanowire surface. Our density functional theory calculations show that ethanol adsorbs in multiple stable configurations at coverages between 1/4 and 1 ML, highlighting the ability of ZnO to detect ethanol. Ethanol prefers to bind to a surface Zn via the adsorbate oxygen atom and, if a surface oxygen atom is in close proximity, the molecule is further stabilized by formation of a hydrogen bond between the hydrogen of the hydroxyl group and the surface oxygen. Two primary adsorption configurations were identified and have different binding strengths that could be distinguished experimentally by the magnitude of their OH stretching frequency. Our findings show that ethanol adsorbed on the oxygen deficient ZnO(101(-)0) surface has a reduced binding strength. This is due to either the lack of a hydrogen bond (due to a deficiency in surface oxygen) or to surface reconstruction that occurs on the defect surface that weakens the hydrogen bond interaction. This reduced binding on the oxygen deficient surface is in contrast to the defect enhanced gas-sensor interaction for other gases. Despite this difference, ethanol still acts as a reducing gas, donating electrons to the surface and decreasing the band gap. We show that multiple adsorbed ethanol molecules prefer to be orientated parallel to each other to facilitate the hydrogen bonding to the defect-free surface for enhanced interaction.     

Quantum-Chemical Investigation of the Intermolecular Interaction Effect on the Spectral-Luminescent and Physical-Chemical Properties of Certain 8-Azasteroid Class Molecules

The effect of hydrogen bonds on the spectral-luminescent and proton-acceptor properties of 8-azagone-12,17-dione and its 2,3-dimethoxy substituent is examined. The method of molecular electrostatic potential is used for choosing a spatial model for complexes with the 1:2 mixture ratio. Hydrogen bonding of oxygen atoms of C and D cycles of both molecules with water molecules is shown to affect but slightly the spectral-luminescent properties. The effect of hydrogen bonds on the proton-acceptor properties of molecules both in the ground and fluorescent states is most pronounced: the proton-acceptor properties of oxygen atoms of the C, D, and methoxy groups decrease, particularly in the fluorescent state, while the same properties of the nitrogen atom increase. We can assume on the basis of these facts that the role of the nitrogen atom in the intermolecular interaction is increased when it is in the S ₁ state.     

Hydrogen-bond dynamics near a micellar surface: origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.     

Noncovalent Hydrogen Isotope Effects in Paramagnetic Molecules

Zero-point energies (ZPE) of intermolecular, non-bonded vibrations and isotope effects, induced by noncovalent interactions, are computed for paramagnetic molecules. They appear to be not significant for complexation of HO₂ and oxygen with C–H bonds and results to isotope effect, which deviates from unit by 5–10%. However, ZPE and isotope effects in complexes of HO₂ and nitroxyl radicals with water are larger and reach 50–70%. The largest effect, about 12, is found for complexation of hydrogen atom with water. Complexation of nitroxyl and peroxy radicals by hydrogen bonds is accompanied by transfer of spin density of unpaired electron from radical to the ligand molecules and induces high field paramagnetic shifts of the ligand NMR lines. It evidences that the spin transfer via intermolecular bonds occurs by mechanism of spin polarization.     

Theoretical investigation of hydrogen atom transfer in the hydrated C–G base pair

Hydrogen atom transfer and the related electronic rearrangement in the hydrated C–G base pair have been studied in order to understand the role of the hydrogen bonds between the bases and those with the water molecules in these processes. The modification of hydrogen transfer due to the first shell and bulk hydration has been analysed. The different structures, when the hydrogen atom moves in a H-bond or in another bond, have been studied. Two naïve schemes, where the water molecules are only indirectly or directly involved in the hydrogen atom transfer, have been considered. The results support the idea that the actual mechanisms are more complex than these schemes. Hydration modifies the potential energy curves of both tautomers and zwitterionic structures, but does not generate new stable structures (minimum PES) of these types. We find a new stable structure due to both a reorganization of the two down water molecules and other global changes of the system. This new system is generated from a zwitterionic structure. The charges, during hydrogen transfer, of the hydrogen donor and of the hydrogen acceptor part of the base pair and of the hydrogen atoms between the bases have been determined and their modifications, due to the first shell and bulk hydration, have been analysed. The qualitative and quantitative behavior has been studied.     

Correlations among hydrogen bonds in liquid water

By performing computer simulations of water with the TIP5P potential we show that structures formed by two or more hydrogen bonds affect the dynamical and static properties of water, especially in the vicinity of freezing temperature. In particular, the short time correlation between two coupled hydrogen bonds cannot be predicted assuming the statistical independence of the single hydrogen bonds. This introduces an additional relaxation time of approximately 9 ps close to the freezing point. We also find that the time persistence of structures formed by several hydrogen bonds (the first solvation shell) correlates with the local density, which is smaller around water molecules with a long-living environment.     

Molecular mechanism of gelation upon the addition of water to a solution of poly(acrylonitrile) in dimethylsulfoxide

The solidification of a solution of poly(acrylonitrile) (PAN) in dimethylsulfoxide (DMSO) upon introduction of water into the solution is studied by Raman spectroscopy. In the absence of water, DMSO molecules are found to produce dipole-dipole bonds with PAN molecules. Upon the introduction of water, DMSO molecules produce hydrogen bonds with it and bands at 1005 and 1015 cm⁻¹ appear in the Raman spectrum, which are assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. Simultaneously, water molecules produce hydrogen bonds with PAN molecules: R-C≡N...H-O-H...N≡C-R, where R is the carbon skeleton of a PAN molecule. Accordingly, a band at 2250 cm⁻¹ arises in the Raman spectrum, which is assigned to the valence vibrations of C≡N bonds producing hydrogen bonds with a water molecule. When the water content is low and the DMSO concentration is high, the length of the hydrogen bonds varies in wide limits and the band at 2250 cm⁻¹ is wide. As the water content rises, DMSO molecules come out of PAN, the variation of the hydrogen bond length in it decreases (the band at 2250 cm⁻¹ narrows), and a high-viscosity system (gel) arises that consists of PAN molecules bonded to water molecules via “equally strong” hydrogen bonds.     

单个钛原子储氢能力和储氢机制的第一性原理研究

采用基于密度泛函理论的第一性原理方法研究了单个过渡金属钛原子吸附氢分子的物理机制. 研究表明,单个钛原子最多能吸附8对氢分子,吸附结构为对称的两个类金字塔型结构, 其平均吸附能为- 0.28 eV.通过计算轨道能级和差分电荷密度分布,分析决定吸附结构、 吸附能大小以及吸附氢分子数目的内在物理机制.研究表明,钛原子的4s电子转移到3d轨道上, 从而产生较强的极化电场,导致氢分子极化,钛原子通过静电极化作用吸附氢分子. 本文的研究将对设计高密度储氢材料有一定的指导作用.     

Interaction of hydrogen molecules on Ni-doped single-walled carbon nanotube

Adsorption of hydrogen molecules on an Ni-doped (8,0) single-walled carbon nanotube (SWNT) is investigated by using first-principles density functional calculations. The result shows that a single Ni atom adsorbed on the bridge site of the tube could cannot dissociate the H₂, however it can chemisorb three H₂ at most, with the average binding energy per H₂ suitable for the hydrogen storage at the room temperature. More H₂ would physisorb around an Ni atom weakly. As for the SWNT with an Ni dimer adsorbed, we find that when the H₂ approaches the Ni--Ni bond, it dissociates without overcoming any barrier and makes bonds with Ni atom.     

木犀草素和鸟嘌呤间相互作用的理论研究

采用密度泛函理论中的B3LYP方法对木犀草素和鸟嘌呤之间的相互作用和机理进行研究,分别找到了十八种木犀草素和鸟嘌呤复合物. 结果表明这些复合物是通过氢键相互作用而稳定存在的. 利用分子中的原子理论(AIM)和自然键轨道理论(NBO)对体系中的氢键进行研究. 通过基组重叠误差校正的复合物间的相互作用能为6.04～56.94 kJ/mol,计算结果表明在木犀草素-鸟嘌呤复合物中有很强的氢键相互作用. 比较了木犀草素和四个DNA碱基间的相互作 用,发现木犀草素-胸腺嘧啶是最强的,木犀草素-腺嘌呤是最弱的.