链分子的构象弹性理论

研究基于旋转异构态模型、用末端距与构象能描述的链构象分布函数、以及链构象态在体系形变中的消失规则,发展了一个链分子的构象弹性理论.用该理论描述的理想形变行为,支持天然橡胶在大形变时应力陡然上翘归因于链构象变化的观点在物理上的合理性.该理论能够区别不同化学结构高分子所具有的不同形变行为,能够预报高分子形变中熵项与内能项各自的贡献.预报了天然橡胶形变中内能的贡献约为13%, 与实验相符.     

高分子链空间构象分布的复杂性——条件下能量与尺寸的分布

通过高分子链的模型的计算来研究高分子链构象的尺寸与能量的分布。结果表明，高分子的链构象在小尺寸范布居数增多；高分子的链构象在小尺寸范围存在比较稳定的链构象状态；在小尺寸范围比较稳定的链构象多具有类似棒状等非球形结构；高分子的链构象的尺寸与能量的分布显示熵弹性具有不对称性。     

高分子链空间构象分布的复杂性——Θ条件下能量与尺寸的分布

通过高分子链的模型的计算来研究高分子链构象的尺寸与能量的分布．结果表明，高分子的链构象在小尺寸范围布居数增多；高分子的链构象在小尺寸范围存在比较稳定的链构象状态；在小尺寸范围比较稳定的链构象多具有类似棒状等非球形结构；高分子的链构象的尺寸与能量的分布显示熵弹性具有不对称性．     

应用分子图形学、分子力学、量子化学及静电势研究农药分子结构与性能的关系(Ⅲ)——一种获得有机分子优势构象的简单方法

通常可采用分子力学计算来得到有机分子的优势构象,但平常使用分子力学程序,由优化分子的构象得到的优化能,往往并不是分子的最低能量,而与分子的最初输入构象有关,是分子的初始输入构象附近的极小值,这给实际应用带来了困难.目前较为常规的求分子最优几何构象的方法是统计方法(Monte Carlo方法),通过模拟退火(The Simulated Annealing)来处理.开始“温度”较高的分子位于能量较高的位置上,这时分子的构象处于少数几个极小区     

谷胱甘肽分子伞的构象分析及VolSurf表征

使用分子动力学模拟迟火和半经验AMl方法对谷胱甘肽分子伞进行了构象分析 ，结果表明，真空下屏蔽构象和暴露构象的最低能量值相差很小(26.00kJ/mol)。 考虑溶剂效应后，屏蔽构象的能量值最高，暴露构象的能量值最低。屏蔽构象的能 量最低值高于暴露构象的能量最低值89.24kJ/mol，从理论上解释了谷胱甘肽分子 伞在水溶液中呈现暴露构象的原因。利用VolSurf参数分析了分子伞以屏蔽构象穿 透磷脂双分子层的影响因素，结果表明屏蔽构象较小的两亲矩及较大的分子褶皱程 度是其能够穿透细胞膜的主要影响因素，与构象的绝对疏水区域无关。     

Ab initio方法研究2,4—二甲基—1,3—戊二烯结构

用ａｂｉｎｉｔｉｏ方法研究２，４－二甲基－１，３－戊二烯各种构象异构体的结构，找到ｓ－ｔｒａｎｓ和ｓ－ｃｉｓ两种稳定构象，且ｓ－ｔｒａｎｓ更稳定，对稳定构象的几何结构、电荷分布进行了研究，讨论了不同的电子基组对优化几何的影响，并计算了稳定构象的热力学常数，与实验结果进行了比较。     

应用分子图形学,分子力学,量子化学及静电势研究农药分…

应用分子力学程序ＭＭＸ及逐步旋转单键法，探讨了一系列磺酰脲超高效除草剂的优势构象，并应用构象重迭方法研究了它们的构象特征，假设了与受体作用的初步模型。     

O,O‘—2,2’—联苯基,S—苄基二硫代磷酸酯分子的构象研究

本文用ＡＳＥＤ－ＭＯ法研究了Ｏ，Ｏ＇－２，２＇联苯基，Ｓ－苄基二硫代磷酸酯单个分子的构象，得到４种低能构象，分析了常温下４种构象的分布，稳定构象之间的转化以及与晶态分子构象之间的关系。     

谷胱甘肽在水溶液中的构象研究

谷胱甘肽在水溶液中的构象研究韩秀文，屈铭，缪希茄，倪坚毅，胡皆汉（中国科学院大连化学物理研究所，大连１１６０２３）活性小分子多肽对生命体具有特殊及重要作用。因此，研究生命体内活性肽结构的意义很大。小分子多肽在水中构象研究是一个十分活跃的领域，它有利于...     

亮氨酸脑啡肽构象的分子动力学方法研究

采用淬火和模拟退火两种分子动力学的方法对亮氨酸脑啡肽进行了构象搜索，发现了多个Gly－Pheβ－Ⅱ’转角的低能构象．计算结果表明，高温淬火和模拟退火两者结合起来可以有效地寻找低能构象．     

明胶中α、β和γ三种构象的全分析

由文献表明:迄今为止,用十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)测定明胶分子量分布,只能分出<α,α₁,α₂和β组份,而γ及>γ的组份未能检出。也就是说,大约30万以上的分子量组份未能进入凝胶板内(以下简称“入板”)。这对明胶构象的全分析和对明胶质量的正确判断是一个严重的缺陷。 本文主要探讨和研究γ及>γ组份的入板问题。所采取的方法是:控制丙烯酰胺和甲叉丙烯酰胺(交联剂)的相对含量,选择合适的交联度梯度,使之既适用于α和β组份迁移,也能让γ及>γ的组份入板。此外,在小的交联度和大孔径的情况下,还能符合凝胶板对凝胶强度的基本要求。     

蛋白质二级结构的氨基酸紧邻位效应和二肽构象因子

提出了蛋白质二级结构中的氨基酸C端和N端邻位因子以及二肽构象因子. 基于对蛋白质数据库PDB105版全库的分析, 讨论了N端和C端邻位对氨基酸二级结构倾向性的影响, 讨论了二肽序的二级结构倾向性. 发现有些氨基酸的邻位因子对和二肽序对的二级结构构象因子差别较大, 表明这些氨基酸对其N端和C端邻位的影响不对称.     

The stable planar conformation of the γ-butyrolactone ring in solution

<正>The conformations ofγ-butyrolactone ring in solution were deduced on the basis of ~1H NMR spectra of geminal protons of the butyrolactone ring.A series of optically pure(Z)-(-)-4-(1'-alkoxyl-1'-carbalkoxy-methylene)-5(R)[(1R)-menthyloxy]-γ-butyr-olactones with a stable planar conformation of γ-butyrolactone ring were found.     

The histamine H1-receptor antagonist binding site. Part I: Active conformation of cyproheptadine

Summary The active conformation of several histamine H₁-antagonists is investigated. As a template molecule we used the antagonist cyproheptadine, which consists of a piperidylene ring connected to a tricyclic system. The piperidylene moiety is shown to be flexible. The global minimum is a chair conformation but, additionally, a second chair and various boat conformations have to be considered, as their energies are less than 5 kcal/mol above the energy of the global minimum. Two semi-rigid histamine H₁-antagonists, phenindamine and triprolidine, were fitted onto the various conformations of cyproheptadine in order to derive the pharmacologically active conformation of cyproheptadine. At the same time, the active conformation of both phenindamine and triprolidine was derived. It is demonstrated that, within the receptor-bound conformation of cyproheptadine, the piperidylene ring most probably exists in a boat form.     

原卟啉原IX的构象分析

在合理药物设计方法中 ,当靶标酶的三维结构未知时 ,对其底物进行构象分析 ,特别是确定其活性构象 ,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义。我们曾利用距离比较法确定了原卟啉原氧化酶的底物—原卟啉原IX的活性构象 ,本文从构象分析的角度对 4种不同构象的原卟啉原IX分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析 ,结果进一步证实了距离比较法所确定的活性构象更为可靠     

Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide

Summary To interpret differences in the anticholinergic activity among the four steroisomers of 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide (1–4), we performed conformational studies using the semiempirical molecular orbital method. The structures of the global minimum-energy conformations obtained for 1–4, however, could not explain the different activities, particularly in terms of distances between the essential pharmacophores. We thus implemented superimposition studies, using the energetically stable conformations of the most active stereoisomer, 1(2S,4R), as a template. The energy penalties for a conformation change of the less active stereoisomers 2–4 from their global minimum-energy structure to a new conformation, fitting onto the global minimum-energy conformation of 1, appear to account for the differences in the pharmacological potency better than using the other conformations of 1 as a template. We thus presume that the global minimum-energy conformation of 1 is closely related to the bioactive conformation for these anticholinergics, and also that the pharmacological potency is linked to how readily these substances can change their conformations to fit the muscarinic receptor.     

Synthesis and Conformation of cis-1,2-Disubstituted Cyclododecene

Eight 1,2-disubstituted cyclododecenes were synthesized from a-alkoxycarbonyl-cyclododecanone and alkyl chloroformate. Their configuration and conformation determined by IR, NMR spectroscopy and X-ray diffraction analysis showed that the carbon-carbon double bond of all of the synthesized compounds has cis-configuration, and the ring skeleton of their preferred conformation is [lene2333] in solid, and they may adopt two different [lene2333] conformations, which exist in a dynamic equilibrium in solution.     

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010     

群多普利溶液构象的NMR研究

采用1D和2D NMR技术对血管紧张素转化酶抑制剂群多普利在CDCl₃溶液中存在的两种构象进行了结构解析, 并结合分子动力学和密度泛函理论方法对其进行了结构的几何优化和能量计算. 结果表明, 群多普利因分子中酰胺键的旋转而形成反式构象A和顺式构象B, 两种构象的能量差为6.35 kJ/mol, 且顺式构象为该药物的优势构象.