Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

氢键在现代化学中的作用

在各种分子间相互作用中,氢键占有很特殊的地位,被称作为超分子化学中的万能相互作用。讨论了氢键在超分子、自组装、分子识别、晶体工程、材料化学和催化过程等现代化学领域中的作用。     

纯水溶液中的氢键交换反应路径

利用分子动力学模拟方法对纯水溶液的氢键转化动力学性质进行了深入的微观探讨,溶液中非氢键构型为寿命较短(0.1～0.2 ps)的过渡态构型,我们发现氢键交换通过两种过渡构型完成,氢键角度扭曲激发后与氢键第一壳层水分子沿路径1交换,氢键径向拉伸激发后与氢键第二壳层水分子沿路径2交换,过渡态路径的选择具有温度依赖性.氢键转化需在旧氢键受体氢键过量和新氢键受体氢键不足,同时满足交换反应空间结构要求下才能完成.氢键交换反应对水分子平动和转动行为起着决定作用.     

两个新的氢键诱导液晶化合物的合成

通过４－丁氧基苯甲酸（４ＢＡ０与两个手性取代的苯乙烯基吡啶（ＶＳＺ及ＬＳＺ）间的氢键作用合成了２个新的液晶化合物，用ＤＳＣ、偏光显微镜研究了其液晶行为，并由红外光谱证实了分子间氢键的存在，形成的复合物４ＢＡ－ＶＳＺ具有手性近晶Ｃ相。     

The Role of Hydrogen Bond in Catalytic Triad of Serine Proteases

In order to investigate the origin of catalytic power for serine proteases, the role of the hydrogen bond in the catalytic triad was studied in the proteolysis process of the peptides chymotrypsin inhibitor 2 (CI2), MCTI-A, and a hexapeptide (SUB), respectively. We first calculated the free energy profile of the proton transfer between His and Asp residues of the catalytic triad in the enzyme-substrate state and transition state by employing QM/MM molecular dynamics simulations. The results show that a low-barrier hydrogen bond (LBHB) only forms in the transition state of the acylation of CI2, while it is a normal hydrogen bond in the acylation of MCTI-A or SUB. In addition, the change of the hydrogen bond strength is much larger in CI2 and SUB systems than in MCTI-A system, which decreases the acylation energy barrier significantly for CI2 and SUB. Clearly, a LBHB formed in the transition state region helps accelerate the acylation reaction. But to our surprise, a normal hydrogen bond can also help to decrease the energy barrier. The key to reducing the reaction barrier is the increment of hydrogen bond strength in the transition state state, whether it is a LBHB or not. Our studies cast new light on the role of the hydrogen bond in the catalytic triad, and help to understand the catalytic triad of serine proteases.     

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.     

Studies on Hydrogen Bonding Network Structures of Konjac Glucomannan

In this paper, the hydrogen bonding network models of konjac glucomannan （KGM） are predicted in the approach of molecular dynamics （MD）. These models have been proved by experiments whose results are consistent with those from simulation. The results show that the hydrogen bonding network structures of KGM are stable and the key linking points of hydrogen bonding network are at the O（6） and O（2） positions on KGM ring. Moreover, acety has significant influence on hydrogen bonding network and hydrogen bonding network structures are more stable after deacetylation.     

X-ray diffraction investigation of siloxanes. I. Effects of organic substituents at the silicon atoms on the structure of acyclic trisiloxane-1,5-diols and on formation of different hydrogen bond systems

The molecular and crystal structure of four acyclic trisiloxane compounds, which differ in substituents at the silicon atoms (Ph-phenyl, mPh-methoxyphenyl, 2mPh-dimethoxyphenyl), was investigated by X-ray diffraction analysis. Due to intermolecular hydrogen bonding between the oxygen atoms of the diol fragments, the crystal structure of 1,1,5,5-tetramethyl-3,3-diphenyl-1,3,5-trisiloxane-1,5-diol (C₁₆H₂₄O₄Si₃) (I) is a double chain architecture with hydrogen-bonded dimeric motifs of C(8)R ₄ ⁴ (12) type in graph set representation. In 1,1,5,5-tetramethyl-3,3-(2-methoxybenzo)-1,3,5-trisiloxane-1,5-diol (C₁₈H₂₈O₆Si₃) (II) and 1,1,5,5-tetramethyl-3,3-(2,6-dimethoxybenzo)-1,3,5-trisiloxane-1,5-diol (C₂₀H₃₂O₈Si₃) (III), a double chain structure with a graph set R ₃ ³ (8)D ₃ ³ (10) is formed. In contrast to I–III, 1,1,3,3,5,5-hexaphenyl-1,3,5-trisiloxane-1,5-diol (C₃₆H₃₂O₄Si₃) (IV) has an intramolecular hydrogen bond S(8). The independent molecules are joined by O-H...O intermolecular hydrogen bonds into centrosymmetrical dimers; the system of hydrogen bonds in general may be described as S(8)R ₄ ⁴ (8).     

燃料电池用聚合物质子交换膜的研究进展

质子交换膜（PEM）是质子交换膜燃料电池的核心组件之一,具有隔绝阴阳极、提供质子传递通道和阻止燃料渗透的作用. 商业化应用的全氟磺酸PEM存在燃料渗透严重、高温条件下导电性差和成本高的问题,开发性能优良的聚合物PEM显得很有必要. 本文讨论了近年来聚合物PEM的研究进展,分别从聚合物的主链、支链和交联结构角度介绍了分子结构对薄膜相分离、质子导电性、稳定性和电池性能等性能的影响,并讨论了聚合物分子结构设计方面存在的问题,最后对燃料电池用聚合物PEM在未来的发展方向进行了展望.     

Energetic Ordering of Hydrogen Bond Strengths in Methanol-Water Clusters: Insights via Molecular Tailoring Approach

In this work, we examine the strength of various types of individual hydrogen bond (HB) in mixed methanol-water M_nW_m, (n+m=2 to 7) clusters, with an aim to understand the relative order of their strength, using our recently proposed molecular tailoring-based approach (MTA). Among all the types of HB, it is observed that the O_M−H…O_W HBs are the strongest (6.9 to 12.4 kcal mol⁻¹). The next ones are O_M−H…O_M HBs (6.5 to 11.6 kcal mol⁻¹). The O_W−H…O_W (0.2 to 10.9 kcal mol⁻¹) and O_W−H…O_M HBs (0.3 to 10.3 kcal mol⁻¹) are the weakest ones. This energetic ordering of HBs is seen to be different from the respective HB energies in the dimer i. e., O_M−H…O_M (5.0 to 6.0 kcal mol⁻¹)>O_W−H…O_M (1.5 to 6.0 kcal mol⁻¹)>O_M−H…O_W (3.8 to 5.6 kcal mol⁻¹)>O_W−H…O_W (1.2 to 5.0 kcal mol⁻¹). The plausible reason for the difference in the HB energy ordering may be attributed to the increase or decrease in HB strengths due to the formation of cooperative or anti-cooperative HB networks. For instance, the cooperativity contribution towards the different types of HB follows: O_M−H…O_W (2.4 to 8.6 kcal mol⁻¹)>O_M−H…O_M (1.3 to 6.3 kcal mol⁻¹)>O_W−H…O_W (−1.0 to 6.5 kcal mol⁻¹)>O_W−H…O_M (−1.2 to 5.3 kcal mol⁻¹). This ordering of cooperativity contribution is similar to the HB energy ordering obtained by the MTA-based method. It is emphasized here that, the interplay between the cooperative and anti-cooperative contributions are indispensable for the correct energetic ordering of these HBs.     

含有氢键供体大环化合物的构筑及其功能研究进展

含有氢键供体基团构筑的大环化合物因其结构中具有可以提供氢键供体的N—H基团,可以为大环化合物的主客体化学提供额外的分子间作用力,在分子识别、自组装以及超分子催化等领域被广泛应用.综述了近十年基于(硫)脲键、酰胺键构筑的大环化合物的合成方法及其在分子识别中的最新研究进展.为今后此类大环化合物的合成及应用提供参考.     

氢键活化的苯环上C-F键的亲核取代反应研究

以2,4,5-三氟苯乙酮在氢化钠作用下与碳酸二乙酯反应制得3,4-二氟-6-乙氧基苯甲酰乙酸乙酯(2);2经对甲基苯磺酸催化水解脱羧,合成3,4-二氟-6-乙氧基苯乙酮(3)路线为模型,研究了苯环上C-F键的亲核取代反应.实验结果证明,在形成分子内氢键的活化作用下,苯环上的C-F键能够被烷氧负离子亲核取代.2和3的结构经1H NMR, 19F NMR和MS表征.     

Synthesis, Characterization and Fluorescence of a One-dimensional Cadmium（Ⅱ） Compound Involving Covalent and Hydrogen Bonds

1 INTRODUCTION The rational design and synthesis of new metal- organic coordination polymers have generated con- siderable interest in supramolecular chemistry and material science owing to their intriguing structural diversities and potential applications as functional materials[1～3]. Molecular self-assembly has been pro- ved to be an efficient way to construct various inte- resting coordination polymers[4～6]. The coordina- tion covalent bond, hydrogen bond or other mole- cular interact…     

Synthesis, Characterization and Fluorescence of a One-dimensional Cadmium( Ⅱ ) Compound Involving Covalent and Hydrogen Bonds

The title compound [Cd(Hq)2(Hdpa)2] (Hq = 8-hydroxyquinoline, H2dpa = diphenic acid) has been synthesized and characterized by single-crystal X-ray diffraction analysis. It crystallizes in monoclinic, space group C2/c with a = 20.6880(5), b = 14.2584(4), c = 13.4776(4) (A), β = 113.434(2)°, C46H28Cd1N2O10, Mr = 881.10, V = 3647.68(17) (A)3, Z = 4, Dc = 1.604 g/cm3, F(000) = 1784,μ = 0.668 mm-1, the final R = 0.0576 and wR = 0.1157 for 2631 observed reflections with I ＞2σ(Ⅰ). The centrosymmetric Cd(Ⅱ) ion is six-coordinated in a slightly distorted octahedral geometry.The intermolecular hydrogen bonds extend the mononuclear structure into a one-dimensional supramolecular framework. The fluorescence spectrum of the compound exhibits intense emission at 520 nm when excited at 330 nm in solid state at room temperature.     

Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.     

Bond detectors for molecular dynamics simulations,Part I: Hydrogen bonds

Charge sensitivity analysis in AMBER force‐field resolution has been used in quest for detectors of hydrogen bonds (HBs). The process of HB formation was investigated on ab initio classical trajectories (B3LYP/6‐31G*) of different nucleobase pairs. Several charge sensitivities, namely: electronegativity, hardness, Fukui function (FF), and polarization matrix, were analyzed. The global and constrained equilibria were considered. It was demonstrated that FF indices and polarization matrix elements are good detectors of HB formation. © 2013 Wiley Periodicals, Inc.     

Ab Initio Study of H-Bond Dynamics in Three-Component Crystals Comprising (DABCOH+)n Polycationic Chains

In this work, the dynamic character of hydrogen-bond (H-bond) networks in two three-component crystals comprising polycationic chains was described. The first studied system was 1,4-diazabicyclo[2.2.2]octan-1-ium (DABCOH⁺) sulfamate monohydrate, known for its large negative linear compressibility. The second analyzed material was the newly obtained polar salt co-crystal: 1,4-diazabicyclo[2.2.2]octan-1-ium sulfamate urea. X-ray diffraction measurements enabled us to study the H-bond systems in both crystals using the graph set analysis. Obtained structures served as the initial models for Born-Oppenheimer molecular dynamics computations. A detailed study of intermolecular interactions and power spectra was conducted. The analysis of time and space correlations between the changes in H-bonds enabled the detection of proton transfer occurring in both systems at 300 K. Further study of those dynamic phenomena was done using the Energy Decomposition Analysis for selected trajectory fragments. Our work should improve the understanding of dielectric and ferroelectric properties of hybrid organic-inorganic materials.     

2-羟基吡啶与水氢键作用的理论研究

本文采用量子化学的Hatree-Fock方法和密度泛函理论(DFT)的B3LYP方法,在6-31G(d)水平上,研究了2-羟基吡啶分子(Hy)及其酮式互变异构体2(1H)-吡啶酮(Py)与水的相互作用。考察它们之间在形成Hy…H2O,Py…H2O,Hy…Hy,Py…Py和Hy…Py等复合物前后的能量变化和分子结构参数变化特点。计算结果表明,在这些复合物中都形成了较强的氢键作用,在水合物中,Py与水形成复合物时能量降低较多,与实验结果一致。经过零点振动能(ZPVE)和基组叠加误差(BSSE)校正后的复合物离解能分别为38.3,40.8,73.0,82.7和71.1 kJ/mol(B3LYP/6-31G(d)),水合物的离解能远小于二聚体复合物,而酮式结构的二聚体的离解能最大。