水和甲醇混合溶剂氢键相互作用及对高分子链溶解能力的理论研究

用密度泛函理论对水和甲醇混合溶剂体系的氢键结构进行了详细研究.通过构象和频率分析发现在水团簇中五聚体和六聚体环状结构最为稳定,同时发现一个全新的特征,即甲醇分子能与水五聚体和六聚体形成双氢键.根据各相互作用的稳定化能,分析了水和甲醇混合溶剂对PNIPAM溶解能力的影响,并对实验现象给予了合理解释.     

聚偏二氯乙烯构象分布的理论研究

在MP2/6-311++G**水平下, 对2,2,4,4-四氯戊烷与2,2,4,4,6,6-六氯庚烷旋转异构体构象进行几何优化和能量计算. 结果表明, 对于2,2,4,4-四氯戊烷, 采用gauche-gauche排列的旋转异构体的能量较低; 2,2,4,4,6,6-六氯庚烷旋转异构体中, 采用trans-gauche-trans-gauche排列的构象能量较低. 反之, 完全采用trans-trans排列的旋转异构体构象能量较高, 不稳定. 通过比较模型分子不同旋转异构体构象的能量差值可以得到一级和二级特征的相互作用能差, 进而计算统计权重参数. 在此基础上, 应用计算得到的模型分子的几何构型与统计权重参数, 分别构建针对—CH2—和—CCl2—中心的聚偏二氯乙烯的6态旋转异构态模型. 通过旋转异构态模型可以计算聚偏二氯乙烯分子中各种构象的分布.     

DME构象的ADF研究

用ＡＤＦ方法对游离状态下的１,２－二甲氧基乙烷（ＤＭＥ）的构象进行了研究。结果表明,能量最低的３种构象ｔｇｇ,’ｔｇｔ,ｔｔｔ的能量相近,其中ｔｔｔ不是能量最低的构象,而且说明ＤＭＥ在气态、液态、固态和游离状态下分别采用哪种构象为最优构象,除了与构象的能量有关外,还受分子间相互作用及分子的对称性是否适合于紧密堆积的影响。     

密码子与反密码子的识别和相互作用

本文根据经验的多原子分子间相互作用势研究了氨基酸的遗传密码子与反密码子的相互识别。我们以RNA12的几何构型为理论模型,计算了RNA12上互补碱基间,非互补碱基间和碱基三联体间的相互作用能,并对碱基异构体参与的非互补碱基配对的相互作用能函数进行了自选尺度拟牛顿法的最优化处理.研究结果可归纳如下:1.从分子间相互作用能的角度阐明了氨基酸遗传密码子与反密码子配对的wobble学说。并指出,当存在一定自由度时密码子的第三个碱基U能与反密码子中碱基G、I的醇式异构体配对,而密码子的第三个碱基A能以顺式构象与反密码子中碱基I配对,并求得它们的最优配位模式。2.现有的大多数密码子和反密码子间的识别关系可由它们之间的相互作用能来说明,从而进一步阐明了密码子与反密码子中碱基间直接的物理的相互作用在密码子与反密码子的高度专一性识别过程中起着重要的作用。     

胰岛素分子相互作用能的计算

胰岛素分子间的相互作用是人们所关心的一个课题,它对探讨胰岛素及其类似物与受休的相互作用和它们在溶液中的行为有着重要的意义,本文在前文工作的基础上,计算了两个胰岛素分子在不同距离和不同取向时的相互作用能,并试图对上述问题的研究提供线索。 我们从胰岛素两聚体的晶体结构数据出发,找出两个单体分子相距最近的三对点,求其中点坐标,在过该三点的平面上作一条垂线,作为分子间平移和转动的参考轴,固     

X射线单晶衍射研究系列功能七元杂环桥联联苯构象

含有七元杂环桥联联苯的π-共轭聚合物是重要的宽禁带光电材料, 其发光性质决定于两苯环间扭曲角. 利用X射线单晶衍射仪确定了系列功能的七元杂环桥联联苯化合物的晶体结构, 比较了桥联原子, 6,6位取代基及分子间弱氢键对这类桥联联苯扭曲构象的影响. 桥联键是—CH2—O—CH2—和—CH2—S—CH2—的七元杂环桥联联苯两苯环间的扭曲角分别为39°和51°, 在6,6位上含有不同取代基的双氧桥联七元杂环桥联联苯的扭曲角存在5°的差异. 在双氧桥联的七元杂环桥联联苯的二聚物中, 桥联的氧原子与非桥联的苯亚基-苯亚基2,2’位置上的两个氢原子之间形成的氢键网络结构导致中心联苯呈现平面构象, 但氢键并没有改变桥联联苯的构象. 七元杂环桥联联苯的构象主要由桥联原子决定, 同时分子间相互作用亦能轻微调控这类桥联联苯的扭曲角.     

溶剂沸点对聚(3-己基噻吩)薄膜内链结构与分子取向的影响

以聚(3-己基噻吩)(P3HT)为研究对象,借助荧光相关光谱、紫外-可见光谱和掠角红外光谱考察了溶剂性质对旋涂膜内P3HT的链结构与分子取向的影响。结果表明:溶液中P3HT的分子链构象受溶解度的影响,当P3HT溶解在溶解性好的良溶剂中时,链构象更伸展;固体薄膜内P3HT的物理结构却不受其在溶剂中溶解度大小的影响而具有沸点依赖性,溶解在高沸点溶剂中的P3HT旋涂后,薄膜内P3HT主链平面性与π-π相互作用均得到提高;此外,溶剂沸点的增加导致分子取向由"面朝上"方式转变为"边朝上"方式。     

3.0分辨率[L-Met]~(B0)牛胰岛素的晶体结构研究

基于[L-Met]_(BO)牛胰岛素(LMBBI)晶体的对称性和分子密堆积法的基本原理,确定了只使用一维的旋转和一维的平移即可确定分子在晶胞中的位置和取向的结构测定方案,依据此方案,使分子置换法的旋转函数的计算和用R因子搜索法精化旋转平移位置的计算大大简化。运用生物大分子刚体修正技术对模型进行了初步精化,用能量极小化的立体化学制约的最小二乘修正技术并辅以差值Fourier图人工分析对模型进行了调整和精化。在最终的电子密度图上,B链N端加长的L-Met在独立区两个分子中的表现比较清晰,相对于三方二锌猪胰岛素分子,B链N端的构象发生了较大的变化。     

N-苄叉基-2-氨基噻唑及其类似物的构象和分子内的扭曲驱动力

确定了N-苄叉基-2-氨基噻唑(2a)和N-对硝基苄叉基-2-氨基噻唑(2b)的晶体结构.结合已报道的N-对硝基苄叉基-2-氨基嘧啶(1a),N-对硝基苄叉基-2-氨基吡啶(1b)和N-苄叉基-3-氨基吡啶(2c)的晶体结构,利用AM1,RHF,DFT方法和6-311G,6-311G^**基组,优化每个分子的22个旋转构象(θ=0°～90°).由DFT法所得到的最优构象的扭角θ(1a,22°;1b,0°;1c,42°;2a、2b:0°)与实验值(1a,26°;1b,20°;1c,46°;2a,8.8°;2b,3.8°)最接近.尽管分子最优构象扭角的差异很大,但总电子能最稳定的构象都在θ=±42°附近.在任一分子、任何电子态中,离域的π体系总是失稳定的,全平面构象不是π体系最稳定的构象.无论是离域的还是定域的π体系,它们均倾向于扭曲的几何构象.π电子的离域是分子扭曲的驱动力之一.与经典观点相反,非键原子间的核排斥作用是分子扭曲的阻力,而不是动力.     

白鲢鱼胰岛素的晶体结构测定

本文继用旋转函数方法对白鲢鱼胰岛素分子在P2_12_12_1晶胞中的取向分析之后,以已知的二锌猪胰岛素分子为模型,应用平移函数及R因子搜索方法,确定了白鲢鱼胰岛素六聚体在晶胞中的位置。在这样得到的模型晶胞中,分子的堆积合理。利用现有的3.5衍射数据,对该模型进行了初步的约束参数最小二乘修正。用修正过的原子参数算得的电子密度图上,未投入修正的多肽链片段有相应的表现。     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Cyclization and catenation directed by molecular self-assembly

We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene pi-pi stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N,N'-(2-(2-(2-(2-thioacetylethoxy)ethoxy)ethoxy)ethyl)perylenetetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of complex concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.     

Proton nuclear magnetic resonance study on the aromatic amino acid-guanine nucleotide system: effect of base methylation on the stacking interaction with tyrosine and phenylalanine

The stacking interactions of tyrosine methylester (TyrOMe)-guanosine-5'-monophosphate (GMP), TyrOMe-7-methylguanosine-5'-monophosphate (m7GMP), phenylalanine methylester (PheOMe)-GMP and PheOMe-m7GMP pairs in neutral buffer solution have been studied by proton nuclear magnetic resonance (1H-NMR). The H8 proton signal of GMP showed no noticeable temperature dependence, while the signals of other protons showed usual dependences arising from the ring stacking interaction with aromatic amino acids. The results can be interpreted in terms of the intramolecular C-H ... O hydrogen bonding and ring stacking. Complex formations in 1:1 molar ratio were deduced for all pairs from their Job plots. The association constant for each pair was obtained by analysis of the Scatchard plot. Further, the van't Hoff plot provided thermodynamic parameters of the complex structure. The analyses of these data suggested that albeit the N-quaternization of GMP strengthens the stacking interaction with aromatic amino acid, the bulky methyl group in m7GMP facilitates the dissociation from the amino acid with small environmental change. The possible conformations of GMP and m7GMP in the interaction states are discussed on the basis of the coupling constants.     

Efficient interstrand excess electron transfer in PNA:DNA hybrids

PNA:DNA strands were prepared containing a flavin electron donor and a thymine dimer acceptor, which gives a strand break upon single electron reduction. With these constructs, it was confirmed that an excess electron transfer through the base stack can be efficient in an interstrand fashion. The effect of an increased distance, a changed sequence, and stacking was explored.     

Biochemical steps in visual transduction: roles for nucleotides and calcium ions

Abstract— Recent studies from this laboratory permit the suggestion of a scheme for describing molecular mechanisms which may regulate excitation and adaptation in amphibian rod photoreceptor cells. The experiments have studied several chemical changes which occur upon illumination of isolated rod outer segments: (1) activation of cyclic GMP phosphodiesterase which is sensitive to calcium concentration, (2) a resulting rapid drop in cyclic GMP levels which has stoichiometry and time course appropriate for the internal transmitter presumed to mediate between photon absorption in the disc membrane system and the permeability decrease in the plasma membrane, (3) a dephosphorylation of two small proteins whose phosphorylation is controlled by cyclic GMP levels, and (4) a slower hydrolysis of GTP which may drive efflux of calcium from the outer segment. It is suggested that the rapid decrease in sodium conductance which follows illumination is caused by the dephosphorylation of the two small proteins, with their dephosphorylation being controlled by the cyclic GMP decrease. In a slower reaction light activates a GTP-dependent extrusion of calcium from the cytoplasmic space. This lowering of internal calcium causes desensitization of the light-sensitive phosphodiesterase enzyme responsible for the cyclic GMP decrease, so that its intensity-response function now resembles that of the light-adapted rod photoreceptor. Thus, changes in plasma membrane conductance are regulated by cyclic GMP, and the sensitivity of the system is controlled by slower calcium movements which set the light-sensitivity of the phosphodiesterase enzyme. Finally, the light-initiated phosphorylation of rhodopsin also appears to play a role, with phosphorylated rhodopsin causing desensitization of the phosphodiesterase enzyme.     

Molecular structures of dicarboxylated viologens on a Cu(100) surface during an ongoing charge transfer reaction

Molecular structures of dicarboxylated viologens (1,1'-bis (7-carboxyheptyl)-4,4'-bipyridinium dibromide molecules, V-(C(7)-COOH)(2)) on a Cu(100) surface are studied by means of in situ scanning tunneling microscopy (STM) in combination with cyclic voltammetry (CV). Self-assembled monolayers of adsorbed dicarboxylated viologens form during an ongoing charge transfer reaction. Mainly six structures of the organic molecules are observed, including a dot array, metastable phases, stripe patterns, a closed stacking stripe pattern, chloride desorption, and a dimer phase. The molecular structural models for all the structures have been successfully established. The carboxylated viologen molecules in the dicationic state prefer the face-on configuration on the surface and form the dot array phase. The other phases are shown by the radical state of the viologens. The metastable phases show two forms: cluster-like and stripe pattern-like structures. Main features of the metastable phases are face-to-face configurations of the radical viologens in π-stacking form between neighboring parallel bipyridiniums. Hydrogen bonding is considered to be the major factor in constructing the network of the stripe pattern. At a more negative potential, the bilayers of the stripe pattern transform to be a monolayer of the closed stacking stripe pattern because of the enhanced electrostatic force. The closed stacking stripe pattern is stable on the surface until chloride desorption. As the chloride anions desorb from the Cu(100) surface, the disordered dimers transform to an ordered dimer phase on a Cu(100)-1×1 surface due to the hydrogen bonding between neighboring dimer rows.     

Direct observation of mixed-valence and radical cation dimer states of tetrathiafulvalene in solution at room temperature: association and dissociation of molecular clip dimers under oxidative control

We have observed the mixed-valence and radical cation dimer states of a glycoluril-based molecular clip with tetrathiafulvalene (TTF) sidewalls at low concentration (1 mM) at room temperature. This molecular clip has four consecutive anodic steps in its cyclic voltammogram, which suggests a sequential oxidation of these TTF sidewalls to generate species existing in several distinct charge states: neutral monomers, mixed-valence dimers, radical cation dimers, and fully oxidized tetracationic monomers. The observation of characteristic NIR spectroscopic absorption bands at approximately 1650 and 830 nm in spectroelectrochemistry experiments supports the presence of intermediary mixed-valence and radical cation dimers, respectively, during the oxidation process. The stacking of four TTF radical cations in the dimer led to the appearance of a charge-transfer band at approximately 946 nm. Nanoelectrospray ionization mass spectrometry was used to verify the tricationic state and confirm the existence of other different charged dimers during the oxidation of the molecular clip.     

Structure of Cyclic Aryl Thioester Dimer Based on o-Phthaloyl Dichloride and Bis(4-mercaptophenyl) Sulfide

IntroductionTheadvantageofmacrocyclicoligomersasprecursorsforthepreparationofhighperformancepolymersviaring openingpolymerization (ROP)hassparkedmuchinterestintheareaofadvancedthermoplasticcomposites.1 3Andaseriesofcyclicoligomerssuchascarbonates,4 arylesters ,5,6 ethers,7amides8andsulfides9,10 hasbeensuccessfullysynthesized .Recently ,Nishikuboetal.11reportedakindofnovelmacro cyclicoligomerscontainingthioestergroupspreparedbycon densationofbis(4 mercaptophenyl)sulfidewitharomaticaciddichlo…     

Structure of Cyclic Aryl Thiosester Dimer Based on o—Phthaloyl Dichloride and Bis（4—mercaptophenyl）Sulfide

A Cyclic aryl thioester dimer was prepared by the reaction of o-phthaloyl dichloride and bis(4-mercaptophenyl)sulfide in good yield under pseudo-high dilution conditions via interfacial polycondensation.The structure of the cyclic dimer was confirmed by a conmbination of MALDI-TOF-Ms,FTIR,gel permeation chromatography and NMR analyses.The X-ray diffraction study of the single crystal of cyclic thioester dimer obtained form two sotutions reveals no severe internal strain on the cyclic structure.