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.

Studies on the Conformations and Hydrogen Bonding of ACE Inhibitory Tripeptide VEF by All-atom Molecular Dynamics Simulations and Molecular Docking

Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-accessible surface, and root-mean-square deviations are used to characterize the properties of VEF in aqueous solution. The VEF molecule is highly flexible in water and conformations can shift between the extended and folded states. The VEF molecule exists in extended state mostly in aqueous solution and the conformations bonded with ACE are also the extended ones. The findings indicate that MD simulations have a good agreement with the molecular docking analysis.

Formation Sites and Microscopic Conformation Study on the Konjac Glucomannan Molecular Helices

In this work, the formation sites, helical parameters and hydrogen bond positions of Konjac glucomannan molecular helices were investigated using molecular dynamic simulation method. To our interest, the KGM chain is mainly composed by local left and right helix struetttres. The formation sites of KGM chain might locate at the chain-segments containing acetyl groups, and the left helix is the favorable conformation of KGM. Temperature-dependent molecule conformation study indicates that the right helix is dominant when the temperature is lower than 343 K, above which, however, the left helix is dominating （right helix disappears）. In addition, intramolecular hydrogen bonds in the left helix can be found at the -OH groups on C（2）, C（4） and C（6） of mannose residues; comparably, the intramolecular hydrogen bonds in the right helix can be mainly observed at the -OH groups on C（4） and C（6） of the mannose residues and C（3） of the glucose residues. In conclusion, molecular dynamic simulation is an efficient method for the microscopic conformation study of glucomannan molecular helices.

Hydrogen Bond Networks' QSAR and Topologica Analysis of Konjac Glucomannan Chains

Based on the knot theory and researching of network structures of glucomannan molecules, the polysaccharides were analyzed. The link prediction analysis is to further reveal the interactions between polysaccharides, to elaborate QSAR of polysaccharides, and to analyze the network conformation relationships among polysaccharides. We made a classification for glucomannan molecules based on the related domestic and international theories, and investigated their network structures and application prospects. The knot theory and the link predictions not only simplify the glucomannan microscopic descriptions but also play a guiding role in predicting and regulating the structures.

Intramolecular Resonance-assisted Hydrogen Bonds in N-Salicylidene-anilines

In the crystal structures of N-salicylidene-anilines, the ortho-OH group with the central N atom forms a planar six-membered ring through intramolecular hydrogen bonds (Fig. 1). The pseudo-aromatic ring is coplanar with its attached phenyl ring. The resonance strengthens the H-bond through proton transfer between the O and N atoms (Fig. 1, I II): dCO and dCC become shorter and dCN longer significantly. The d1～d6 are also changed regularly. According to the geometries obtained from X-ray analysis and retrieved from the Cambridge Structural Database (CSD, version 5.21)[1], we believe that the main resonance, at least in solid state, is the molecular keto form (II, Fig. 1) instead of the zwitterionic one (III, Fig. 1).

Helical Conformation Tunability via Hydrogen Bonding in Supramolecular Frameworks

Hydrogen-bonded molecules and their dynamics are significantly important in chemistry and biology due to their widespread functionality.Besides their natural abundance and diversity,applications of molecules with dynamic conformations in artificial networks allow information storage and molecular motor design on the nanometer scale.Here,we report hydrogen-bonded molecular networks with tunable helical conformation on metal surfaces.The dynamics of helical conformation in two-dimensional hydrogenbond networks are triggered and resolved by scanning probe microscopy at the single-molecule level.In combinationwith theoretical calculations,the surfacespecific hydrogen bonds are identified as the origin of the dynamic helical conformation.Our results provide a distinctive access to molecular architecture with tunable helical conformation driven by hydrogenbond interaction on surfaces.

Peptoids with aliphatic sidechains as helical structures without hydrogen bonds and collagen/ inverse-collagen type structures

Aliphatic homo-polypeptoids of NAla, NVal, NIle and NLeu both in the presence and absence of protecting groups adopt helical structures without hydrogen bonds with Φ, Ψ values of ~ 0, ± 90° with trans amide bonds. These structures are stabilized by carbonyl-carbonyl interactions and characterized by ~ 3.16 residues per turn with a pitch of ~ 6.13 ?. It has been shown that like polyvaline and polyleucine peptides, poly-peptoids can also be exploited for the construction of potential surfactant like molecules by incorporating charged amino acid residues at the N terminal. A single-handed template with Φ, Ψ values of ~ 0, 90° can be attained by incorporating L-leu or L-val at the C-terminal of poly-NIle. Analysis of the simulation results in water as a function of time reveals that the opening of helical structures without hydrogen bonds takes place at sub-picosecond time scale starting from the N-terminal. This leads to the formation of collagen or inverse-collagen type structures (Φ, Ψ ~ -60, 145° and 60, -145° respectively) stabilized by interactions of water molecules with the backbone carbonyl groups.

Molecular Dynamics Simulation of Glucomannan Solution

The method of molecular dynamics simulation is carried out to simulate the KGM segment in solution, investigate the stable conformation and compute its energy, and discuss the effect of the change of hydrogen bond on its structure and energy. The results show that the structure of KGM segment can be optimized by molecular simulation method and the most stable conformation can be found, indicating the hydrogen bond is the main factor influencing the conformation and property of KGM.

Studies on the Effect of Structure to Property Stability of Glucomannan

The effect of pH value on the kinds and number of Glucomannan hydrogen bonds was studied by experiments and molecular dynamics simulation, and that of the pH change on property and hydrogen bond was also analyzed. Ultimately, the impact of hydrogen bond change on its structure and property was discussed. The results of experiment and simulation were consistent with each other. In experiment, when pH〉7, peak strength of 1720 cm^-1 v-acetyl is reduced and peak of V-OH is widened; and in simulation, the function of hydrogen bond of KGM increases, the number of hydrogen bonds increases by 19 and two kinds of hydrogen bonds are formed. Potential energy reduces by 443.1 kJ/mol. Acetylate is an important group to affect the gel intensity which can be improved by the hydrogen bond interaction.

Gas Phase Conformations of Tetrapeptide Glycine-Phenylalanine- Glycine-Glycine

Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti- cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) The phenolic hydrogen of HBMC forms hydrogen bond with the neighbouring nitrogen,which is its striticture basis of possessing photosensitizing activity.

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Substituted polyglycolides having two asymmetric centers are attractive alternatives to materials derived from petroleum because of their biocompatibility and biodegradability. The conformational behavior of various substituted polyglycolides has been investigated by both quantum mechanical and molecular dynamics approaches. Polymethylglycolide (polylactide) and polyphenylmethylglycolide in RS or SR forms are predicted to adopt 27 ribbon type structures with φ, ψ values of ±30, ±50 or +30 or +50 respectively stabilised by carbonyl-carbonyl interactions. Isopropylglycolide and isobutyl-glycolide having branching at β & γ positions respectively in their side chains can be realized in all SS form with φ, ψ values lying in right handed helical region. In addition to carbonyl-carbonyl interactions, the hydrophobic interactions between the side chains in isopropylgly-colide the C-H-O interactions also contributes to the stability. With cyclic side chains directly attached to Cα of backbone, polyphenylglycolide (polymandelide) and polycyclohexylglycolide are found to adopt left handed helical structure without hydrogen bonds in RR form, stabilised by stacking interactions and hydrophobic interactions respectively. In all the forms of polyphenylglycolide & polycyclohexylglycolide, the cyclic side chains are found to be locked into unfavourable gauche plus conformation. The stability of substituted polyglycolides has been analyzed in terms of various interactions. The carbonyl-carbonyl interactions in all the conformations of all forms of substituted polyglycolides are found to be of highly shielded parallel motif with only one short carbon-oxygen interaction. Simulation studies of substituted polyglycolides in water give a good insight of the approach of water molecules to the backbone.

Transition metal coordination polymers with flexible dicarboxylate ligand:Synthesis,characterization,and photoluminescence property

Under solvothermal conditions,six new coordination polymers(CPs)[Mn(L)(phen)(H_(2)O)]_(n)(1),[Co(L)(phen)(H_(2)O)]_(n)(2),[Cu(L)(phen)(H_(2)O)]_(n)(3),[Zn_(2)(L)_(2)(phen)2(H_(2)O)]_(n)(4),[Zn(L)(phen)]_(n)(5),and[Cd(L)(phen)2]_(n)(6)were synthesized by reactions of dicarboxylate ligand 2,2'-(1,2-phenylenebis(methylene))bis(sulfanediyl)dinobutyric acid(H_(2)L)and 1,10-phenanthroline(phen)with the corresponding metal salts.Complexes 1-6 have been structurally characterized by single-crystal X-ray diffraction analyses,elemental analysis,IR,thermogravimetric analysis,and powder X-ray diffraction.The structures of 1-6 are 1D chains,which are further connected by hydrogen bonding interac-tions to form 3D supramolecular structures.Among them,1 and 2 are isomorphic with L2-of syn-conformation,while L2-shows anti-conformation in 3-6.In addition,the solid-state photoluminescence property of 4-6 was investigated.

3-芳胺甲烯基-6-烷基(芳基)-5,6-二氢-2H-吡喃-2,4-二酮的合成及其杀菌活性的研究

以５，６－二氢－６－烷基（芳基）－２Ｈ－吡喃－２，４－二酮（１）、芳胺（２）和原甲酸三乙酯进行缩合反应，合成了２０ 个３－芳胺甲烯基－６－烷基（芳基）－５，６－二氢－２Ｈ－吡喃－２，４－二酮（３）． 由于分子内氢键的形成， 化合物３ 由一对构象异构体４ 和５ 组成． 生物活性初步测定结果表明，

苯甲酰脲类昆虫生长调节剂——伏虫隆的合成及单晶结构研究

合成得到苯甲酰脲类昆虫生长调节剂Ｎ－（３，５－二氯－２，４－二氟）－Ｎ′－（２，６－二氟苯甲酰基）脲（ｔｒｉｆｌｕｂｅｎｚｕｒｏｎ，伏虫隆），并对其单晶结构进行了测定和研究，发现其属于三斜晶，Ｚ＝６，且在一个晶胞中有三个具有不同构像的伏虫隆分子，而作为其活性元的脲桥以分子内氢键形成了一个稳定的六员环。

单嘧磺隆除草剂的晶体构象-活性构象转换的密度泛函理论研究

应用密度泛函理论在B3LYP/6-31G(d)水平上对新型除草剂单嘧磺隆绕脲桥部分两个C—N键的内旋转势能面进行计算,然后对势能面上的驻点进行构型优化和过渡态搜索,得到单嘧磺隆4种稳定构象和构象转换过程所涉及的8个过渡态结构.研究结果表明,单嘧磺隆晶体构象-活性构象转换过程中涉及4种稳定构象和8条转换途径,脲桥部分NH基团与嘧啶环上N原子所形成的分子内氢键对于构象的稳定性及转换过程起着十分重要的作用.应用极化连续介质溶剂模型(PCM)在B3LYP/6-31++G(d,p)水平下进行溶剂化效应计算,结果表明单嘧磺隆从晶体构象转换成活性构象主要是在水相中进行的.

多巴胺DA分子的构象异构及其一水复合物的结构与性质

采用密度泛函B3LYP/6-31+G~#方法对多巴胺DA的构象异构及其稳定性进行了研究.结果表明,势能面上存在6种稳定构象和8种构象转换过渡态,构象之间主要通过C1—O7[二面角T_1:H15O7C1C6],C2—O8[二面角T_2:H16O8C2C3]和C9一C10[二面角T_3;N11C10C9C5]单键旋转而相互转化.频率及NBO分析表明,分子内存在红移O…H-O及蓝移N…H—C两类氢键,氢键中电子转移类型均为LP_1(X)→σ~#(H—Y)[X=O,N;Y=O,C],二级稳定化能E^((2))对稳定构象有3.6 kJ·mol^(-1)～9.3 kJ·mol^(-1)的稳定化贡献.分子中的原子理论(AIM)分析表明,构象中O…H一O及N…H—C键的电子密度ρ(r)和Laplacian量▽~2ρ(r)分别在0.0094～0.0171和0.0307～0.0798之间.采用极化连续模型(polarized continuum model,PCM)对体系进行了溶剂化效应计算,结果表明,DA的构象转换主要在水相中进行.应用静电势模型(electrostatic potential map,EPM)对构象的活性位点进行了预测,并以此研究了多巴胺一水复合物的结构与性质.

单嘧磺隆晶体-活性构象转换的分子动力学模拟

应用分子动力学模拟方法对单嘧磺隆在水、正辛醇和正辛烷3种不同溶剂中的构象行为、单嘧磺隆与3种溶剂之间的相互作用能及氢键相互作用进行了计算研究.计算结果表明,在3种不同的溶剂中,单嘧磺隆的优势构象不同;其构象转换过程,特别是转换成活性构象的过程主要发生在水溶液中;与溶剂分子间的相互作用是分子构象行为的决定因素;单嘧磺隆的脲桥部分可以和含氢键接受体的溶剂形成氢键,分子间与分子内氢键的竞争可能是从晶体构象转换成活性构象的主要驱动力.

喜树碱药效构象及分子内氢键对抗肿瘤活性的影响

喜树碱类抗肿瘤药物是临床广泛使用的DNA拓扑异构酶Ⅰ (topoisomeraseⅠ ,TopoⅠ )的特异性抑制剂。为从原子水平阐明喜树碱的作用模式 ,设计结构新颖、活性更高、毒性更低的TopoⅠ抑制剂 ,本研究采用abinitio方法RHF/ 3 2 1G对喜树碱分子构象空间进行了系统研究 ,并与半经验量化AM1、PM 3方法比较 ,所得构象均采用密度泛函方法B3LYP/ 6 31G(d)计算单点能 ,并进行频率检查验证。结果发现 ,A型构象可形成分子内氢键 ,较B型构象能量更低 ,为喜树碱药效构象。喜树碱E环形成分子内氢键 ,能量约为 2 9 31kJ/mol,这是该分子发挥药效的结构基础 ,同时使得它易于受溶剂水影响而裂解 ,生成无活性的羧酸盐形式。本研究还表明 ,喜树碱与TopoⅠ DNA复合物作用 ,需破坏分子内氢键 ,能量补偿较大 。

杯[4]吡咯在不同溶液中的分子动力学模拟研究

运用分子动力学 (MD)模拟方法对杯 [4]吡咯与不同溶剂之间的相互作用能、杯 [4]吡咯在不同溶液中的构象变化以及杯 [4]吡咯与溶剂分子之间的氢键相互作用进行了计算研究 .模拟发现 ,杯 [4]吡咯与不同溶剂间的相互作用能受溶剂分子偶极矩和杯 [4]吡咯 -溶剂分子间氢键相互作用影响 .杯 [4]吡咯在不同溶液中的构象发生翻转的主导因素是杯 [4]吡咯与溶剂分子间形成氢键相互作用 ,溶剂分子的偶极矩不是杯 [4]吡咯发生构象转化的主要因素 .