特殊氢方法预测丙氨酸-α-四肽构象稳定性

使用B3LYP/6-31G*方法优化得到了丙氨酸-α-四肽分子的48个稳定构象.定义了丙氨酸-α-多肽中的特殊氢原子,对构象中与特殊氢原子有关的主要非键相互作用进行分析,提出了使用与特殊氢原子有关的非键相互作用来预测多肽构象的相对稳定性,并将之称为特殊氢方法.基于丙氨酸-α-二肽分子的5个构象和三肽分子的7个构象,确定了特殊氢方法中的与特殊氢原子有关的非键相互作用参数.利用特殊氢方法预测丙氨酸-α-四肽分子的48个构象的相对稳定性,与B3LYP/6-31G*方法的相对能量比较,得到了满意的结果.特殊氢方法得到的相对能量(Y)和B3LYP/6-31G*方法得到的相对能量(X)的线性相关方程为Y=0.9296X 2.2041,相关系数R=0.9532,标准偏差为3.0kJ/mol,偏差绝对值≤4.18kJ/mol的构象占87.5%.     

快速确定丙氨酸-α-多肽构象稳定性的新方法

使用B3LYP／6—31G^*方法优化得到了丙氨酸二肽和三肽分子的23个稳定构象．定义了丙氨酸多肽中的特殊氢原子．对构象中与特殊氢原子有关的主要弱相互作用进行了分析,提出了一种快速确定多肽构象稳定性的新方法．确定了相应的弱相互作用参数．将新方法应用于三肽分子构象相对稳定性的预测,得到了满意的结果．     

海藻糖抑制淀粉质多肽42构象转变的分子动力学模拟

应用分子动力学模拟方法研究了海藻糖抑制淀粉质多肽42(Aβ42)构象转变的分子机理.结果表明,海藻糖溶液浓度对Aβ42构象转变具有非常重要的影响.在水和低浓度海藻糖溶液(0.18mol·L-1)中,Aβ42可由初始的α-螺旋结构转变成β-折叠的二级结构;但海藻糖浓度为0.37mol·L-1时即可有效抑制Aβ42的构象转变.这是因为海藻糖利用其优先排阻作用使水分子在多肽周围0.2nm内富集,而其自身却在距离多肽0.4nm的位置附近团聚.另外,海藻糖还可通过降低多肽间的疏水相互作用,减少多肽分子内远距离的接触,有效抑制多肽的疏水塌缩和构象转变.上述分子模拟的结果对于进一步合理设计阿尔茨海默病的高效抑制剂具有非常重要的理论指导意义.     

三螺旋多糖的链结构与功能研究进展

三螺旋多糖是自然界中存在的具有特殊链结构的一类生物大分子,它不仅具有较高的生物活性,而且具有特殊的分子识别能力以及其他多糖无法比拟的功能特性。本文主要概述三螺旋多糖的链结构及其构象转变,分析其变性和复性过程中分子链间的相互作用,阐明三螺旋结构形成和形态变化的科学规律。同时,综述了三螺旋多糖的链构象与其生物活性之间的构效关系,以及基于螺旋构象转变构建的多糖基功能材料的最新研究进展。     

光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

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     

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.     

单核锌双卟啉配合物构象平衡的理论研究及光谱分析

合成了一系列以不同长度柔韧链相连的p/p型单核锌双卟啉配合物。选用Tripos力场,利用分子动力学模拟退火和分子力学构象搜索相结合的方法对该系列双卟啉进行了能量优化和构象分析。理论计算结果表明:该类双卟啉稳定存在的最低能量构象为叠合式,最高能量构象为伸展式,并存在一系列的中间能量构象;双卟啉分子内π-π作用和能量转移与双卟啉存在的两种主要构象密切相关;分析了分子内π-π作用的本质。运用不同光谱测试手段验证了理论计算结果: 利用可见和相应二阶导数吸收光谱研究了双卟啉主要存在的叠合式和伸展式构象,通过红外光谱观察了对双卟啉构象和卟啉环间π-π作用较为敏感的吸收谱带;利用荧光光谱计算了双卟啉的分子内能量转移效率。     

旋光性聚甲基丙烯酸三苯甲酯的合成

<正> 旋光性聚甲基丙烯酸三苯甲酯(PTrMA,A)是一种新型旋光聚合物,其旋光性不是来自结构单元中的手性原子或基因,而是刚性的分子链呈长程单向螺旋构象,使分子链获得手征性的结果.自70年代末问世以来,在改进其合成方法和作为色谱固定相直接拆分手性化合物的应用方面受到人们注意,由于独特的结构,可以设想,如果将它带上特殊     

Loop环对分子内三螺旋DNA稳定性的影响

用分子力学方法研究了 4个分子内三螺旋DNA ( 5′ d(TC) 6 d(T) m d(CT) 6 d(C) n d(AG) 6,m ,n分别为 4,3)的稳定性 ,并与相应的分子间三螺旋d(TC) 6 d(AG) 6·d(CT) 6进行了比较 .结果表明 :Loop环对分子内三螺旋的稳定性影响较小 ,但是Loop上碱基和糖环构象的变化依赖于Loop环的长度 .Loop使分子内三螺旋DNA嘌呤链的碱基堆积作用降低 ,链长增加 .三螺旋DNA的糖环构象大部分是S型 ,同时也存在N型以及其他构象 .     

New approach for representation of molecular surface

A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998     

计算机辅助筛选酪氨酸激酶相关蛋白TRP-2 CTL模拟表位

运用多项式方案、量化基序方案等经典的CTL表位筛选方案, 初步筛选了酪氨酸激酶相关蛋白TRP-2 CTL表位TRP-2_180～188 (SVYDFFVWL)的模拟表位, 以通过表位改造提高其与HLA-A2.1分子结合的能力, 从而提高其免疫原性. 根据打分结果, 合成了4个得分较高的九肽序列, 亲和力实验结果表明所筛选的4个序列较原序列均有较高的亲和力, 但对2位的单突变结果较1和2位双突变结果理想, 进一步运用分子模拟方法对4个序列与HLA-A2.1分子间的相互作用进行了分子模拟分析, 分子模拟结果较好地解释了上述实验现象, 从而为进一步的结构改造提供了理论依据. 本研究提供了一个合理高效的模拟表位筛选方法.     

Method for Smoothing the Boundaries of the Van Der Waals Models of Molecules

A geometrical method is suggested for representing a molecule by a smoothed region. The effective volume and surface area are calculated, which results in more adequate proportionality of interactant molecules compared to the classical van der Waals models.     

A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions

The three-dimensional reference interaction site model integral equation theory (3D-RISM) combined with the ab initio molecular orbital method (3D-RISM-SCF) is applied to a solvated macromolecular system. The solvation structure around a solute molecule is obtained from the 3D-RISM integral equation under the electrostatic potential of the solute molecule, calculated by the ab initio molecular orbital theory. The electrostatic potential should be calculated on each grid point in the three-dimensional real space. Therefore, the calculation of the electrostatic potential is the most time consuming part in this method. In this article, we propose a new procedure to save the computational cost for calculating the electrostatic potential and the solvated fock matrix. The strategy of this procedure is to evaluate the electrostatic potential and the solvated fock matrix in different ways, depending on the distance between solute and solvent. Inside the repulsive cores of solute atoms, it is possible to avoid the calculation of electrostatic potential and solvated Fock matrix by assuming the potential to be infinity. In the region sufficiently far from solute, they are evaluated classically by putting the effective point charge on each atom. In the intermediate region, the electrostatic potential is evaluated directly by integrating the molecular orbitals of the solute molecule. The electronic structure and the energy gradient of Methionine-Enkephalin and solvation structure are estimated by using this procedure in aqueous solution, and are compared with the results from other procedures. The results are compared also with those from the continuum model.     

HLA-A*0201限制性CTL表位肽的三维定量构效关系的研究

运用比较分子力场(CoMFA)和比较分子相似性指数分析(CoMFA)方法研究了50个HLA-A^*0201限制性CTL表位九肽结构与亲和性间的关系,另外15个表位九肽作为预测集用于检验模型的预测能力.结果表明采用CoMSIA得到的构效关系模型(q^2=0.628,r^2=0.997,F=840.419)要明显优于采用CoMFA得到的构效关系模型.在CoMSIA计算中,当引入疏水场时,三维构效关系模型得到明显改善,通过该三维构效关系模型,可较精确地估算预测集中15个CTL表位肽与HLA-A^*0201间的亲和力(r^2pred=0.743).通过分析分子场等值面图在空间的分布,可以观察到表位肽分子周围的立体及疏水特征对表位肽与HLA-A^*0201间结合亲和力的影响,从而为进一步对CTL表位肽进行结构改造并基于此进行治疗性疫苗分子设计提供理论基础.     

DFT study of the conductance of molecular wire:The effect of coupling geometry and intermolecular interaction on the transport properties

The density functional theory (DFT) combining with the non-equilibrium Green functions (NEGF) method is applied to the study of the electronic transport properties for a Di-thiol-benzene (DTB) molecule coupled to two Au(111) surfaces. The dependence of the transport properties on the bias, the coupling geometry of the molecule-electrode interface, and the intermolecular interaction are examined in detail. The results show that the existence of the hydrogen atom at the end of the DTB molecule would significantly decrease the transmission coefficients, and then the differential conductance (dI/dV). By changing the position of the DTB molecule located between two electrodes a maximum value of calculated current is observed. It is also found that the intermolecular interaction will strongly influence the transport properties of the system studied.     

Stochastic molecular optimization using generalized simulated annealing

We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H₂O and H₂O₃) and to polypeptides. The results obtained for H₂O and H₂O₃ using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable α-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an α-helix structure. We obtain this structure simulating all Φ, Ψ pairs using only a few steps, as compared with conventional methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 647–657, 1998     

用密度泛函理论研究NO在H-ZSM-5分子筛不同酸性位的吸附

利用密度泛函理论(DFT),基于7T簇模型,在B3LYP/6-31G(d,p)水平上研究了NO分子在H-ZSM-5分子筛孔道中α,β,γ酸性位的吸附.在计算过程中,首先对H-ZSM-5的α,β,γ酸性位进行优化计算,然后对NO分子η1-N和η1-O两种吸附模式的红外光谱和吸附能进行计算.计算结果表明,NO分子以η1-N模式吸附于H-ZSM-5分子筛酸性位上,不同酸性位对NO分子的吸附能力排序为:α酸性位>β酸性位>γ酸性位.此外,H-ZSM-5分子筛直型孔道更有利于NO分子的吸附和扩散,因而可更有效地促进NO分子催化分解反应的进行.