氢键缔合体的分子力场和振动光谱的研究

氢键缔合体的分子力场和振动光谱的研究孙泽民，王丰，唐作华，鄢国森（四川大学化学系，成都，６１００６４）关键词氢键，力常数，振动频率氢键缔合体的结构在一定程度上受单体间氢键作用的影响，而振动光谱对分子结构及其坏境的变化极为敏感，故其在探讨分子间氢键方面...     

Theoretical Study on Gas Phase Reactions of OH Hydrogen-Abstraction from Formyl Fluoride with Di erent Catalysts

The mechanisms and kinetics of the gas phase reactions that the hydrogen atom in formyl uoride (FCHO) abstracted by OH in the presence of water, formic acid (FA), or sulfuric acid (SA) are theoretically investigated at the CCSD(T)/6-311++G(3df, 3pd)//M06-2X/6-311++G(3df, 3pd) level of theory. The calculated results show that the barriers of the transition states involving catalysts are lowered to -2.89, -6.25, and -7.76 kcal/mol from 3.64 kcal/mol with respect to the separate reactants, respectively, which re ects that those catalysts play an important role in reducing the barrier of the hydrogen abstraction reaction of FCHO with OH. Additionally, using conventional transition state theory with Eckart tun-neling correction, the kinetic data demonstrate that the entrance channel X FCHO+OH (X=H₂O, FA, or SA) is signi cantly more favorable than the pathway X OH+FCHO. More-over, the rate constants of the reactions of FCHO with OH radical with H₂O, FA, or SA introduced are computed to be smaller than that of the naked OH+FCHO reaction because the concentration of the formed X FCHO or X OH complex is quite low in the atmosphere.     

鸟嘌呤与氨基酸残基体系的极化力场

发展了应用于鸟嘌呤G和氨基酸残基体系的浮动电荷力场, 该力场明确定义了孤对电子和键的电荷和位置, 通过电荷随着环境的浮动来体现极化效应; 通过氢键拟合函数k_HB描绘了氢键键能. 应用量子化学方法, 对G与氨基酸残基体系从氢键、 几何结构及电荷分布3个方面展开计算及分析, 并以其为基准, 确定参数发展了适用于G与氨基酸残基氢键体系的ABEEMσπ PFF. 采用3种不同力场模拟目标分子的结构和性质. 模拟结果表明, 发展的ABEEMσπ PFF与量子化学方法具有最好的一致性, 可用于模拟生物大分子体系.     

Crystal Engineering of Multiple-component Organic Compound:Organic co-Crystals of the Functional Groups of Carboxyl and Amino with Persistent Hydrogen Bonding Motifs

Three small organic molecular co-crystal compounds (C₃N₆H₆)·(C₆H₁₀O₄)·H₂O(1), C₃H₈N₂O(3) and (H₄btec)₂·(4,4'-bipy)(4)(H₄btec=1,2,4,5-benzenetetracarboxylic acid, 4,4'-bipy=4,4'-bipyridine) and one coordination supramolecular compound [Mn(C₂O₄)(H₂O)₂]·C₆H₁₁NO₂(2) were synthesized by hydrothermal reaction. They were characterized by elemental analysis, infrared(IR) spectroscopy and single crystal X-ray diffraction(XRD). Structural analyses reveal that these 2D or 3D supramolecular networks of the compounds were formed by C―H···O, N―H···O, N―H···N, O―H···O and O―H···N hydrogen bonds. Therein, the functional groups of ―COOH, ―NH₂ and ―OH play important roles in constructing supramolecular architectures.     

油纸复合介质中水分子扩散行为的分子动力学模拟

对不同温度下水分子在油纸复合介质中的扩散行为进行了分子动力学模拟研究. 通过分析水分子与纤维素形成的氢键发现, 油中的水分子在模拟过程中会逐渐扩散到纤维素内并与之形成氢键, 而纤维素内的水分子则与纤维素形成氢键后被束缚于纤维素中. 通过分析水分子的扩散系数发现, 由于油和纤维素的极性不同, 使得水分子在油和纤维素两种单介质中的扩散行为有较大差别, 而在复合介质中的扩散系数受水分子在油和纤维素中的比例影响较大, 两者表现出很强的相关性. 水分子和两介质的相互作用与两介质的极性也存在很大的关系, 且不同温度下水分子与两介质的相互作用能和水分子在油和纤维素中的比例也表现出了较强的相关性. 不同温度下水分子的不同分布弱化了温度对扩散系数的影响.     

Supramolecular Assemblies of Three New Metronidazole Derivatives Constructed with Various Dihydroxy-benzoic Acids via Hydrogen Bonds

Metronidazole(MTZ) is an important antibiotic, which has been widely applied to cure protozoal and bacterial diseases for human beings or animals. Herein, three novel drug supramolecular crystals constructed by MTZ with 2,5-dihydroxy-benzoic acid(2,5-DHBA)(1), 2,6-dihydroxy-benzoic acid(2,6-DHBA)(2) and 3,5-dihydroxy-benzoic acid(3,5-DHBA)(3), respectively, have been discovered. The hydrogen bonds of N-H···O(O-H···N), C-H···O and O-H···O play important roles in the 3D supramolecular framework formation for crystals 1-3. Interestingly, due to the vary locations of the substituent groups, the two-dimensional layers in crystals 1 or 2 are constructed via intermolecular hydrogen bonds between MTZ and 2,5-DHBA or 2,6-DHBA, while in crystal 3 water molecules play a significant role except the intermolecular hydrogen bonds between MTZ and 3,5-DHBA. In addition, five synthons of I R₂²(8), II R₃³(9) in crystal 1, III R₁²(4), IV R₂²(8) in crystal 2 and V R₂²(7) in crystal 3 formed through various hydrogen bonds are founded in this work. Systematic studies of syntheses, crystal structures and thermal analysis are reported.     

Characterization on the Mean Molar Absorptivity of Amino Acids in Microbial Lipopeptides

The molar absorption coefficients of each of 14 kinds of amino acids were determined by the spectrophotometric method, and the mean molar absorption coefficients of 37 different mixtures of each with amino acid composition exactly equivalent to that of the peptide chain of the corresponding lipopeptide were determined based on calculation or experimental. The significance of the results is that the mean molar absorption coefficients strongly demonstrate the regular patterns, though different amino acids bear quite different molar absorption coefficients.     

Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods

Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.     

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to nonnative local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.     

A Correlation of the Drag Force Coefficient on a Sphere with Interface Slip at Low and Intermediate Reynolds Numbers

The hydrodynamics of a sphere with interface slip has been numerically investigated for flows of Reynolds number ranging 0 < Re ≤ 75. A simple correlation of the drag force coefficient in the present of interface slip has been derived based on our numerical simulations. The correlation takes the slip coefficient and Reynolds number as two input parameters. By comparing results found in the literature, we believe that the present correlation is more accurate; it provides a source for future experiment study and for numerical simulations of large multi-particle system where the interface slip is important.     

以芳香族多羧酸为配体的Ni(II)配位超分子的研制及光诱导下的表面电子行为

采用水热方法合成了2个Ni(II)配合物[Ni3(btc)2(H2O)14]·4H2O(1)和[Ni2(btec)(bipy)2(H2O)6]·2H2O(2), (H3btc=1,3,5-benzenetricarboxylic acid, H4btec=1,2,4,5-benzenetetracarboxylic acid, bipy=2,2'-bipyridyl). 通过X射线单晶衍射(XRD)、红外光谱(IR)、紫外-可见-近红外吸收光谱(UV-Vis-NIR)对化合物进行了表征. 结果表明, 化合物(1)是由2个均苯三甲酸根桥连的三核Ni(II)离子的化合物, 而化合物(2)是由1个均苯四甲酸根桥连的双核化合物, 分子中bipy分子作为端基配体. 分子中大量的水分子和羧酸根的存在使2个化合物分别被连成具有三维(3D)和二维(2D)结构的配位超分子化合物. 着重研究了化合物的表面光电压光谱(SPS), 并将其与UV-Vis-NIR吸收光谱进行了分析和对比, 发现SPS 中表面光伏响应带与UV-Vis-NIR 吸收光谱的吸收峰在数量和位置上都是一一对应的. 此外, 对比2个化合物的表面光电压光谱可以看出,配合物的结构及中心金属的配位微环境对其表面光伏响应带的强度、位置和形状均有一定影响.     

Theoretical Studies on Complexes of Calcium Ion with Amino Acids

The complexes formed by calcium ion and 12 common amino acids were investigated systematically in the gas phase at the level of MP2/6-311＋＋G（d,p）//MP2/6-3 1G（d,p）.The results show that the salt-bridge structure is the most preferred motif for Ca2＋ binding aliphatic amino acids without heteroatom in the side chain,while charge-solvated（CS） structure is the most preferred motif for Ca2＋ binding other amino acids except for glutamine and lysine.IR spectra of Gln-Ca2＋ and Asn-Ca2＋ complexes were calculated and compared well with the available experiments.From the study in aqueous solution,the bidentate salt-bridge structure was determined to be the most favorable for all the twenty kinds of amino acids to chelate Ca2＋ to both the oxygen atoms of the negatively carboxylate group in the backbone.     

Matrix IR studies on hydrogen-bonded complexes of hydrogen chloride and hydrogen bromide with ketene

Infrared spectra of matrices codeposited Ar/HX (X=Cl, Br) with Ar/H₂CCO mixtures have been examined. Isotopic substitutions (HX, DX, H₂CCO, D₂CCO) showed that ketene formed the 1:1 hydrogen-bonded complex with HX. The HX stretching modes were observed at 2684 cm⁻¹ in the H₂CCO–HCl complex and at 2384 cm⁻¹ in the H₂CCO–HBr complex. The ν₁ modes of the ketene submolecules were shifted to low frequency and the ν₉ modes to high frequency. It was proposed for the structure of the complex that the acid proton is bonded to the C=C pi electron system.     

分光光度法研究氨基酸与四氯苯醌形成的荷移配合物

本文用分光光度法研究了5种氨基酸与四氯苯醌形成的荷移配合物.通过对影响配合物形成因素的研究,确立了以四氯苯醌形成荷移配合物的方法测定氨基酸的最佳反应条件,测定了反应平衡常数.讨论了配合物的组成.     

One‐Step Synthesis of Racemic α‐Amino Acids from Aldehydes,Amine Components,and Gaseous CO2 by the Aid of a Bismetal Reagent

α‐Amino acids are essential resources for human life and are highly useful as building blocks for organic synthesis. The core framework of an α‐amino acid can be divided into three basic components: an aldehyde, an amine, and carbon dioxide (CO₂). We report herein that a one‐step synthesis of α‐amino acids has been successfully achieved from these three basic and inexpensive chemicals with a single operation, in which the mixture of an aldehyde, a sulfonamide, and gaseous CO₂ was heated at 100 °C in the presence of Bu₃Sn‐SnBu₃ and CsF. In this one‐pot sequential protocol, two important intermediates (imine and α‐amino stannane) are involved and the stannyl anion generated in situ plays a crucial role, particularly for the efficient stannylation of the imine in the presence of proton sources and for promoting retrostannylation of the undesired α‐alkoxy stannane owing to its high stability and tolerance of the presence of proton sources. This methodology enabled the synthesis of a wide range of racemic arylglycine derivatives in high yields.     

甲醛与乙醛,甲醚,硝基甲烷相互作用的从头算研究

用6-31G、全构型优化,研究了甲醛与乙醛、甲醚、硝基甲烷的相互作用。结果表明所有超分子稳定构型都包含2个C—H—O氢键的平面环状结构。H—O距离为0.228～0.264 nm,作用能为—19～—24 kJ/mol,与二聚水的作用能接近。稳定性主要取决于甲基上取代基Y吸电子能力以及环状结构中氢键张力。STO-3G不很适用于研究这类分子的相互作用。     

镧(Ⅲ)-氨基酸配合物的温度滴定量热法研究

稀土配合物因其特有的性质而日益受到人们的重视 [1] .对于稀土与氨基酸配合物的已有研究 [2 ,3] ,但尚未见到关于镧 ( )与不同种氨基酸配合反应的较系统的报道 .文献 [2 ,3]大多采用 p H电位法或其它非热化学方法 ,且大多只得到反应的平衡常数 ,而用滴定量热法直接测定其配合常数和反应焓变的研究尚未见报道 .用滴定热量法可同时测定配合反应的焓变和熵变 [4 ] ,而且在滴定量热过程中 ,反应体系基本上是一封闭体系 ,除了对体系的温度进行监测外 ,对反应体系没有其它任何干扰 ,因而可以减少外界因素的影响 ,从而减少测定的误差 .本文用滴…     

一种基于多羧基荧光共轭聚电解质的氨基酸检测新方法

基于多羧基荧光共轭聚电解质PPE-(COOK)₄, 发展了一种检测半胱氨酸(Cys)和组氨酸(His)的简便方法. 该方法以PPE-(COOK)₄与Cu²⁺所构成的猝灭体系为基础, 当体系中存在半胱氨酸或组氨酸时, PPE-(COOK)₄/Cu²⁺体系的荧光恢复, 从而实现对上述氨基酸的测定. 由于PPE-(COOK)₄具有类似四乙酸乙二胺(EDTA)的螯状侧链结构, 使其在磷酸盐缓冲液(PBS, 10 mmol/L, pH=7.4)中对Cu²⁺具有超高的灵敏度和选择性, 因此可以借助各种金属掩蔽离子来提高氨基酸检测的特异性. 实验结果表明, 在PPE-(COOK)₄/Cu²⁺体系中引入Ni²⁺或Hg²⁺后, 可分别实现对半胱氨酸和组氨酸的特异性检测, 线性范围分别为1~5和0.5~2.5 μmol/L, 检出限分别为0.15和0.04 μmol/L.