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.     

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%.     

白藜芦醇清理羟基自由基夺氢机理的量子化学研究

在DFT方法的B3LYP/6-31G水平下, 对反式白藜芦醇分子的所有可能构象进行了优化, 并对最稳定构象进行了自然键轨道分析. 键级数据表明, 白藜芦醇清理羟基自由基最活泼反应位点应为其单羟基环上的羟基, 对产物白藜芦醇自由基的优化结果表明, 单羟基环氧自由基的稳定性最高. 在B3LYP/6-31G水平下寻找白藜芦醇单羟基环羟基清理羟基自由基的过渡态, 频率分析结果表明只存在一个虚频. 对该过渡态结构进行内禀反应坐标反应路径解析(IRC), 结果表明, 过渡态沿反应坐标方向分别指向反应物络合物和产物络合物, 反应通道各个能量驻点显示反应物与反应物络合物的能量差为E1=173.5193 kJ/mol, 反应物络合物与过渡态、反应物络合物与产物的能量差分别为Ea=16.5143 kJ/mol, E2=51.8799 kJ/mol. 可见反应物的能量远高于过渡态及产物, 因此, 反应物络合物的形成应是整个反应的驱动力.     

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。     

DOPA醌在Cu（100）表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

F+CH_3OH碰撞反应机机理和反应势能面

以MP2（full）/6-311 + +g(d,p)水平上详细研究了氟原子与甲醇抽氢反应的 多通道反应机理，得到了各条通道中涉及的驻点的构型和振动频率及其能量，给出 了两张完整的反应势能面，结果表明，氟原子从C原子上抽氢时有一条明显的最低 能量通道，而从氧原子上抽氢时要涉及多条分支通道和多个驻点构型，给出了各分 支通道势能面示意图，结果表明以形成五元环状过渡态通道为优势通道，计算得到 经途径1生成CH_2OH时反应放热170.62kJ/mol，经分支途径6生成CH_3O自由基时反 应放热119.4 kJ/mol，此结果与实验值一致。     

F+CH_3OH碰撞反应机机理和反应势能面

以MP2（full）/6-311 + +g(d,p)水平上详细研究了氟原子与甲醇抽氢反应的 多通道反应机理，得到了各条通道中涉及的驻点的构型和振动频率及其能量，给出 了两张完整的反应势能面，结果表明，氟原子从C原子上抽氢时有一条明显的最低 能量通道，而从氧原子上抽氢时要涉及多条分支通道和多个驻点构型，给出了各分 支通道势能面示意图，结果表明以形成五元环状过渡态通道为优势通道，计算得到 经途径1生成CH_2OH时反应放热170.62kJ/mol，经分支途径6生成CH_3O自由基时反 应放热119.4 kJ/mol，此结果与实验值一致。     

采用动态NMR对8-C-glucosyl-prunetin构象研究

采用动态NMR方法,对从海南黄檀中分得的8-C-glucosyl-prunetin及其它7位 上羟基烷基化了的8－C苷异黄酮的构象进行了研究。结果表明,在8－C苷异黄酮中 ,当7位上羟基烷基化了时,由于1"-C(sp~3)-8C(sp~2)单键旋转受阻,产生两种构 象异构体。同时,借助分子力场（MM）计算方法,确定了8-C-glucosyl-prunetin 两种构象异构栓中的优势构象,即为1"-H与7－OCH_3位于同侧。由低能量构象转化 为高能量构象所需活化能为75.66 kJ/mol。这一结果与动态NMR实验计算的71. 48kJ/mol活化自由能数值相符。     

α-环糊精包合物中环己烷构象平衡的PM3研究

用PM3分子轨道方法研究了α-环糊精的包合作用对环己烷构象平衡的影响。发现α-环糊精的包合作用可以改变环己烷的构象平衡。计算结果表明,虽然环己烷的椅式构象比船式构象稳定18.5 kJ*mol-1, 但在α-环糊精的包合物中,船式环己烷包合物比椅式环己烷包合物稳定4.4 kJ*mol-1。因此,超分子体系中客体分子的构象平衡不能简单地从其游离态的构象平衡外推得到,而应该考虑在超分子体系中分子间相互作用对构象的影响。     

石杉碱甲-AChE复合物中石杉碱甲的结构特征: 量子化学研究

在运用量子化学从头计算方法(HF/4-31G)结合点电荷模型方法对AChE-HupA复合物活性位点的410个原子和1929个点电荷进行理论计算的基础上, 比较了石杉碱甲分子在形成复合物前后的结构变化特征。发现复合物中石杉碱甲分子构象并非能量最低构象, 它的能量比HF/4-31G全优化得到的构象的能量高91.8kj/mol。和单分子状态相比, 形成复合物后季铵基和内酰胺基的N-H, C=O键的键长变长、键强减弱, 其总原子净电荷也发生了明显的变化。且这些基团的空间取向都有不同程度的改变, C(8)-N(21)键的旋转达20ⅲ。这些信息将有益于设计新的AChE抑制剂。     

α-单取代环十二酮构象间相互转换的理论研究

在CVFF力场下,DMSO氛围中,通过分子动力学常温模拟研究α-单取代环十二酮的构象,常温优势构象为α-边外取代[3333]-2-酮,环骨架为[3333],羰基位于C2位置,取代基位于α-边外向位.动态分析带有不同取代基的α角顺取代和α-边外取代[3333]-2-酮构象的相互转化的结果表明,它们的转换路径基本一致,转换能垒随着取代基体积的增大而升高.氯和溴取代环十二酮转换过程中最高能垒分别为43.9和44.3kJ/mol,相应的构象为α-边外取代[31233]-2-酮;甲基、乙基和叔丁基取代环十二酮最高转换能垒达53.9kJ/mol,相应的构象为α-边外取代[31233]-2-酮;存在活泼质子的氨基和羟基环十二酮转换能垒中最高能量构象为α-边外取代[31323]-1-酮;苯硫基和苄基取代环十二酮除出现α-边外取代[3333]-2-酮构象外,转换过程中还出现了较α-角顺取代[3333]-2-酮构象更稳定的α-边外取代[4233]-3-酮构象.     

The distribution and conformation of very long-chain plant wax components in a lipid bilayer

Plant wax contains long-chain alkanes and related components which are transported to the surface of the plant by specialized ABC transporter proteins. Here, we determine the distribution and conformation of three wax components, nonacosane, nonacosan-15-one, and nonacosan-15-ol, using unbiased and umbrella sampling molecular dynamics simulations. The molecules all partitioned to the center of the bilayer, with a free-energy difference of -70 kJ/mol between bulk water and the center of the bilayer for the alkane and -55 kJ/mol for the two more-polar molecules. All of the wax molecules were highly mobile in the bilayer, freely moving between opposite leaflets on a time scale of a few nanoseconds. Nonacosan-15-one and nonacosan-15-ol folded double to expose their hydrophilic group to the solvent, whereas nonacosane alternated between orientations spanning the full bilayer and orientations in the center of the bilayer.     

HSCCS自由基势能面的理论研究

在CCSD(T)/6-311G(d,f)//MP2/6-311G(d,f) ZPE水平下,计算得到含有8个异构体和11个过渡态的HSCCS自由基体系势能面,讨论了异构体的结构与稳定性及异构体之间的异构化过程.结果表明异构体m1的能量最低,除m1以外,异构体m2和m3的能量也比较低,在MP2水平上,过渡态TS1的能量比异构体m2仅高3.9kJ/mol,而在CCSD(T)水平上,TS1的能量比m2低14.6 kJ/mol,这说明异构体m2可以迅速转化为能量更低的m1.异构体m3的能量比异构体m1高49.99 kJ/mol,可以推断,在合适的实验条件下可以观测到异构体m1.     

Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop

The potential of mean force (PMF) of a phospholipid in a bilayer is a key thermodynamic property that describes the energetic cost of localized lipid defects. We have calculated the PMF by umbrella sampling using molecular dynamics simulations. The profile has a deep minimum at the equilibrium position in the bilayer and steeply rises for displacements both deeper into the bilayer and moving away from the bilayer. As the lipid loses contact with the bilayer, the profile abruptly flattens without a significant barrier. The calculated free energy difference of 80 kJ/mol between the minimum of the PMF and the value in water agrees well with the free energy difference calculated from the experimentally measured critical micelle concentration. Significant water/lipid defects form when a lipid is forced into the bilayer interior, in the form of a small water pore that spans the membrane. The energy required to form such a water pore is also found to be 80 kJ/mol. On the basis of this energy, we estimate the lipid flip-flop rate and permeability rate of sodium ions. The resulting rates are in good agreement with experimental measurements, suggesting lipid flip-flop and basal permeability of ions are pore mediated.     

MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation

The binding of xylotetraose in different conformations to the active site of endo-1,4-beta-xylanase II (XynII) from Trichoderma reesei was studied using molecular dynamics (MD) simulations and free energy analyses employing the MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Surface Area) method. MD simulations of 1 ns were done for the substrate xylotetraose having the reactive sugar, which is bound in the -1 subsite of XynII in the 4C1 (chair) and 2So (skew boat) ground state conformations, and for the transition state of the XynII catalysed hydrolysis of the beta-glycosidic linkage. According to the simulations and free energy analysis, XynII binds the substrate with the -1 sugar in the 2So conformation 59.8 kJ mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. The reactive 2So conformation resembles closely the reaction transition state and has the breaking glycosidic bond in a pseudo-axial orientation ready for facile bond cleavage. The transition state was calculated to be bound 77.1 kJ mol(-1) tighter than the 4C1 ground state conformation. The molecular mechanical interaction energy between the enzyme and the reactive pyranoside unit at the -1 subsite was 75.7 kJ mol(-1) more favorable for the binding of the 2So conformation than the 2C1 conformation, explaining the clearly tighter binding of the reactive structure The results of this study indicate that in the Michaelis complex XynII, a member of the family 11 xylanase, the substrate is bound in a skew boat conformation and in the catalytic reaction, the -1 sugar proceeds from the 4C1 conformation through 2So to the transition state with the -1 sugar in the 2,5B conformation.     

THEORETICAL STUDIES ON CARBENES AND CARBENOIDS (Ⅳ) ——ISOMERIZATIONS AND DECOMPOSITIONS OF CARBENOIDS H_2C=CLiCl AND H_2CLiCl

The isomerizations and decompositions of carbenoids H_2C=CLiCl and H_2CLiCl have been studied by use of HF/STO-3G gradient method. Three equilibrium structures of H_2C=CLiCl were obtained, in which the linear structure has the lowest energy and the askew substituted structure was the next. It is found that the decomposition of H_2C=CLiCl undergoes a concerted FBW rearrangement and the inversion barrier of its askew substituted structure is 36 kJ/mol. For H_2CLiCl, the askew substituted structure, extending all valences of the carbon into a single hemisphere, is the lowest energy and its inversion barrier is 87 kJ/mol. The discussions on the factors concerned with the structural stabilities are given in this paper.     

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.     

Chair, boat and twist conformation of dodecamethylcyclohexasilane and undecamethylcyclohexasilane: a combined DFT and Raman spectroscopic study.

The conformations of dodecamethylcyclohexasilane Si6Me12 and undecamethylcyclohexasilane Si6Me11H have been investigated by ab initio calculations employing the B3LYP density functional with a 6-31+G(d) basis set. Local minima as well as transition structures were calculated with imposed symmetry constraints. For Si6Me12, three unique minima, which correspond to the chair, twist and boat conformations were located with relative zero-point-vibration-corrected energies of 0.0, 7.8 and 11.4 kJ mol(-1). A half-chair conformation with four coplanar silicon atoms connects the chair and twisted minima via an energy barrier of 16.0 and 8.2 kJ mol(-1), respectively. A second transition structure with a barrier of 3.9/0.3 kJ mol(-1) connects the twist with the boat structure. Solution Raman spectra of Si6(CH3)12 and Si6(CD3)12 fully corroborate these results. Below -40 degrees C, the symmetric SiSi ring breathing vibration is a single line, which develops a shoulder (originating from the twist conformer) at longer wavelengths whose intensity increases with increasing temperature. From a Van't Hoff plot, the chair/twist enthalpy difference is 6.6+/-1.5 kJ mol(-1) for Si6(CH3)12 and 6.0+/-1.5 kJ mol(-1) for Si6(CD3)12, which is in reasonable agreement with the ab initio results. Due to the low barrier, the boat conformation cannot be observed, because either the lowest torsional vibration level lies above it or a rapid interconversion between the twist and boat conformations occurs, resulting in averaged Raman spectra. For Si6Me11H, six local minima were located. The chair with the hydrogen atom in the axial position (axial chair) is the global minimum, followed by the equatorial chair (+1.9 kJ mol(-1)) and the three twist conformers (+5.3, +8.0 and +8.1 kJ mol(-1)). The highest local minimum (+11.9 kJ mol(-1)) is a C(s) symmetric boat with the hydrogen atom in the equatorial position. Two possible pathways for the chair-to-chair interconversion with barriers of 13.9 and 14.5 kJ mol(-1) have been investigated. The solution Raman spectra in the SiSi ring breathing region clearly show that below -50 degrees C only the axial and equatorial chairs are present, with an experimental deltaH-value of 0.46 kJ mol(-1). With increasing temperature a shoulder develops which is attributed to the combined twist conformers. The experimental deltaH-value is 6.9 kJ mol(-1), in good agreement with the ab initio results. Due to the low interconversion barriers, the various twist conformers cannot be detected separately.     

磷酸铝分子筛骨架结构及其稳定性的模拟计算(Ⅱ)──骨架结构中各类键长、键角的取值及其分布

应用晶格能极小化技术计算了19种磷酸铝分子筛的骨架晶格能. 从计算结果发现这些磷酸铝分子筛彼此间的晶格能相差很小,而与磷酸铝致密相块磷铝矿(Berlinite)相差48～127kJ/mol. 据此可以解释磷酸铝分子筛骨架结构的多样性和相似性. XRD数据表明在它们的结构中包含很短的AI－O键(0. 1478nm)、P－O键(0. 1348nm)和很长的AI－O键(0. 1942nm)、P－O键(0. 1678nm),O－T－O键角有大的分布范围(O－AI－O键角为98. 62°～122. 27°和O－P一O键角为92. 36°～122. 86°),平均AI-O一P键角在153°左右,并且具有更大的分布范围(114°～180°). 量子化学AMI计算结果表明,在AI-O一P键角由114°变化至180°而引起的能量改变很小(仅22. 97kJ/mol),当AI一O一P键角为137. 74°时能量最低.