由NMR获取原子间距离约束计算蛋白质三维结构

提出一种以核磁共振(NMR)技术获取蛋白质分子多肽链中原于对(主要是H-H对)的距离约束,来计算蛋白质在溶液中的三维结构的方法。这种方法把肽平面之间的二面角当作独立变量,通过从局部到整体逐渐最优化的方法使适当构造的目标函数最小,计算出这些二面角,以及主链每个残基上六种原子N、H^N、C^α、H^α、C'、O的空间坐标.本方法已编写成计算程序DISNMA,并以碱性胰蛋白酶抑制剂(BPTI)为标准结构,得到了很好的验证.     

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.     

一种获取三肽构象系综的可靠量子化学方法

三肽是蛋白质的基本组成模块, 具有重要生理功能. 解析其结构对于更大的肽及蛋白质研究具有重要意义. 基于二面角组合规则, 结合键旋转手段, 提出一种获取三肽构象系综的从头算量子化学方法. 使用该方法对八个目标三肽的势能面进行彻底搜索, 将所得结果与以前的预测方法及蛋白质数据库(PDB) 提取的结构进行比较.结果表明, 新方法搜索到了最完整的三肽构象系综. 此外证明了 PDB 结构存在缺陷, 遗漏了大部分中低能区的重要构象. 将新获取的三肽结构用于红外光谱研究, 理论结果与实验数据符合得更精准.     

表面增强拉曼光谱对于蛋白质二级结构的酰胺III谱带表征

本文利用斜角沉积法制备银纳米棒阵列基底用于蛋白质二级结构的检测,结合酰胺Ⅲ谱带光谱分析,建立了一种基于表面增强拉曼光谱(SERS)蛋白质二级结构的表征方法.用这种方法获得了两种典型蛋白质(溶菌酶和细胞色素C)的SERS信号.通过分析蛋白质骨架酰胺Ⅲ的光谱,研究了浓度对蛋白质折叠状态的影响.结果表明在一定范围内随着浓度的增加,溶菌酶的α-螺旋结构和β-折叠结构成分增加,而细胞色素C的二级结构基本保持不变.     

振动激发对H+CH反应矢量性质的影响

基于从头算势能面CH2(1A'),用准经典轨线(QCT)方法研究了不同振动激发(v=0-3)下反应H+CH→H2+C(1D)的动力学性质.在质心坐标系下计算了四个极化微分反应截面(PDDCDs),计算并讨论了描述k-j'矢量相关的P(θr)分布函数和描述k-k-'j'三矢量相关的二面角分布P(φr).研究结果表明势能面上的深势阱和不同的振动态对产物分子H2有重要影响.     

表面增强拉曼光谱对于蛋白质二级结构的酰胺Ⅲ谱带表征（英文）

本文利用斜角沉积法制备银纳米棒阵列基底用于蛋白质二级结构的检测,结合酰胺Ⅲ谱带光谱分析,建立了一种基于表面增强拉曼光谱(SERS)蛋白质二级结构的表征方法.用这种方法获得了两种典型蛋白质(溶菌酶和细胞色素C)的SERS信号.通过分析蛋白质骨架酰胺Ⅲ的光谱,研究了浓度对蛋白质折叠状态的影响.结果表明在一定范围内随着浓度的增加,溶菌酶的α-螺旋结构和β-折叠结构成分增加,而细胞色素C的二级结构基本保持不变.     

H+H2反应截面的全量子力学研究

利用全量子力学耦合通道扭曲波近似(CCDWA)方法和三种势能面计算了H+H2(vα=0,jα=0)→H2(vβ,jβ)+H碰撞的反应截面,并与准经典弹道计算结果及公认较好的计算结果作了比较.研究表明:在相同的势能面下利用CCDWA方法得到的截面和公认较好的计算结果符合很好,而准经典弹道计算的反应截面误差较大. 关键词： 反应散射 势能面 反应截面     

多巴胺DA分子的构象异构及其一水复合物的结构与性质研究

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T1: H15O7C1C6], C2-O8 [二面角T2: H16O8C2C3]和C9-C10 [二面角T3: 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LP1(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-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.     

XY(H,Li,Na)分子基态的结构与势能函数

运用群论及原子分子反应静力学方法,推导了XY(H,Li,Na)分子基态的电子态及相应的离解极限.并采用密度泛函方法(B3LYP)和二次组态相互作用方法(QCISD)优化计算了XY(H,Li,Na)分子基态的平衡结构、振动频率和离解能.使用QCISD/6-311++G(3df,3pd)方法,对XY(H,Li,Na)分子基态进行了单点能扫描计算,采用最小二乘法拟合Murrell-Sorbie函数得到了相应的势能函数和与该基态相对应的光谱常数(Be,αe,ωe和ωexe),计算结果与实验数据符合得相当好.     

金岛膜表面二硫双琥珀酰亚胺基丙酸酯分子吸附行为的表面增强红外光谱分析

二硫双琥珀酰亚胺基丙酸酯(dithiobis-succinimidyl propionate,DTSP)是一种重要的同源双功能偶联分子,广泛地应用于蛋白质在载体表面的共价固定。研究利用表面增强红外光谱分析了DTSP分子在真空蒸镀金岛膜表面的吸附特性。首先通过密度泛函理论对吸附于金表面的DTSP分子进行了结构优化,计算了该分子的振动模式和红外强度。表面增强红外吸收和变角偏振反射吸收测量结果表明TSP分子在金表面有序排列,其五元杂环平面与金表面法线成65°左右的二面角。此外,表面增强红外光谱还成功地监测到了TSP分子和Nα′,Nα″二(羧甲基)-L-赖氨酸在金表面的实时组装过程。     

An icosahedral quasicrystalline model for amorphous semiconductors

In the first article of this series an icosahedral quasicrystal with a tetracoordinated decoration of atoms was introduced as a model for amorphous semiconductors. The electronic structure is one of its most interesting features. Based upon a LCAO tight binding scheme with five orbitals sp³s* per atom the electronic density of states (DOS) is calculated by use of the recursion method. Various effects of the specific geometry on the DOS are investigated, including the topology of the tetracoordinated network, the corresponding dihedral angles, bond angles, bond lengths, and dangling bonds. These geometrical parameters are treated separately and therefore reveal their distinct influences on the DOS. The resulting effects are discussed regarding the DOS as a whole, while details are provided about variations of the outer band edges, shifts of maxima and first moments of uppermost valence band and lowest conduction band, and — most important — changes in the central gap. The properties of single wave functions are subject of the third article in this series.     

Simultaneous observation of oxygen uptake curves and electronic states during room-temperature oxidation on Si(0 0 1) surfaces by real-time ultraviolet photoelectron spectroscopy

Ultraviolet photoelectron spectroscopy was used to measure the oxygen uptake, changes in work function due to the surface dipole layer of adsorbed-oxygen atoms, Δ?_SDL, and changes in band bending due to the defect-related midgap state, ΔBB, simultaneously during oxidation on Si(0 0 1) surface at room-temperature, RT, under an O₂ pressure of 1.3 × 10⁻⁵ Pa. The oxygen dosage dependence of Δ?_SDL revealed that dissociatively adsorbed-oxygen atoms occupy preferentially dimer backbond sites at the initial stage of Langmuir-type adsorption, which is associated with a rapid increase of ΔBB. When raising temperature to ∼600 °C, such preferential occupation of the dimer backbond sites by oxygen atoms is less significant and ΔBB becomes smaller in magnitude. The observed relation between Δ?_SDL and ΔBB indicates that point defects (emitted Si atoms + vacancies) are more frequently generated by oxygen atoms diffusing to the dimer backbond sites at lower temperature in RT −600 °C.     

Peculiarities of the spectral-angular distribution of transition radiation from a relativistic particle in a dihedral angle

The spatial distributions of transition radiation from relativistic particles entering and exiting the edge of a dihedral angle formed by perfectly conducting flat surfaces have been investigated. The angular distributions of the radiation intensity in dihedral angles with various opening angles have been calculated. The angular distributions of forward radiation (when the particle exits the dihedral angle) and backward radiation (when the particle enters the dihedral angle) are shown to differ significantly.     

New method for calculating reflected wave fronts of acute retroreflectors with tuned dihedral angle

An acute retroreflector having dihedral angles of 45, 60 and 90 deg exactly reflects incident rays in the opposite direction. Beam pattern or wave front of the reflected light of the acute retroreflector can be controlled by tuning dihedral angles. We present here a new method for calculating the reflected wave front of the acute retroreflector, in which the wave front is calculated with high accuracy and in a shorter calculation time than by the conventional ray trace method.     

碳纳米管封装表面异构Si20融化的结构演变

采用分子动力学方法模拟一种硅的特殊结构（表面异构的硅十二面体结构）填充到扶手型单壁纳米管组成的复合结构的加热过程，通过可视化，键角分布，二面角分布等分析方法来研究这种结构在碳纳米管中的稳定性和结构演变情况。研究发现这种结构在碳纳米管中是非常稳定的，并且随着温度的升高，硅纳米团簇的四面体结构开始减少，近邻原子数目有所增加，但不超过8个。该复合结构是由二十个四面体组成的正十二面体，通过模拟分析可知这种结构具有相当高的稳定性，一部分原因是正四面体的单臂纳米管比较稳定，对十二面体结构的硅起了一定的保护作用；另一部分原因是Si20的正十二面体本身具有较高稳定度，这一点我们通过可视化软件发现这种团簇是缩成一团而并不是从中间裂开观察得到。     

Geometric symmetry modulated spin polarization of electron transport in graphene-like zigzag FeB<Subscript>2</Subscript> nanoribbons

Due to electron deficiency, the graphene-like honeycomb structure of boron is unstable. By introducing Fe atoms, it is reported that FeB₂ monolayer has excellent dynamic and thermal stabilities at room temperature. Based on first-principles calculations, the spin-dependent transport of zigzag FeB₂ nanoribbons (ZFeB₂NRs) under ferromagnetic state (FM) is investigated. It is found that, around the Fermi level, FeB-terminated (or FeFe-terminated) ZFeB₂NRs exhibit completely spin-polarized (or spin-unpolarized) transmission, and BB-terminated configurations exhibit completely unpolarized or partially polarized transmission. Further analysis shows that, the hinge dihedral angle has a switching effect on the transport channels, and the spin polarization of the transmission is determined by the symmetry of the distribution of hinge dihedral angles along the transverse direction of the ribbon, where symmetric/asymmetric distribution induces spin-unpolarized/polarized transmission. Moreover, such a symmetry effect is found to be robust to the width of the ribbon, showing great application potential. Our findings may throw light on the development of B-based spintronic devices.     

The molecular structures and electron distributions of the 1,8-bis-(dimethylamino)-naphthalenes,studied by density functional and ab initio MP2 calculations

The equilibrium structure of 1,8-bis-(dimethylamino)-naphthalene (DMAN), has been investigated in some detail; only one minimum energy conformer was found, although a saddle point, close to the structure of a previously claimed second conformer (J. Am. Chem. Soc., 120, 4840 (1998)), was also identified. Alternative apparent minima are attributed to artefacts when small bases are used. Equilibrium structures of members of the DMAN series with chloro-, bromo-, nitro- and methoxy-substituents in the ortho(2,7-) and para(4,5-) positions, as well as 4-nitro-DMAN were also determined, and compared with crystallographic and previous theoretical data. There are close correlations between calculated and observed values for bond lengths, angles and dihedral angles across the known compounds, and this enables additional correlation with other members of the series where no experimental data so far exists. The MP2 and DFT methods used, with a triple zeta basis set including polarization (TZVP), lead to very similar results but the dihedral angles in particular show more variation. Substituent effects on the bond lengths and angles in the ring geometry are relatively small, and the intrinsic pattern of short αβ-bonds in the naphthalene system is largely preserved, but the C₃C₄ bond is shorter than that for C₁C₂. Steric effects arising from interaction of 1,8- and 2,7-substituents on the naphthalene ring leads to significant twisting of the naphthalene skeleton. In addition, considerable in-plane and out-of-plane bending of the substituents from the naphthalene ring system is apparent. The effect of adjacent substituents upon the dihedral angle between the dimethylamino-groups and the ring is also apparent. The ground state molecular electronic properties have been determined and compared with experiment. The electron distribution in the B3LYP methods lead to markedly higher dipole moments than the MP2 ones, and the latter are regarded as more reliable.     

13C direct detected COCO-TOCSY: a tool for sequence specific assignment and structure determination in protonless NMR experiments

A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in (13)C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles phi as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D(9K), a 75 amino acid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49 [Formula: see text] values were measured and related to backbone phi angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, (4)J(CC) and (5)J(CC), could be measured. This constitutes an unprecedented case for proteins of medium and small size.     

用一维和二维核磁共振波谱研究吗啡和可待因的分子构型

用360MHz超导核磁共振波谱仪测定了吗啡(morphine)和可待因(codeine)的质子耦合常数。用二维J-谱验证了一维质子谱的J-耦合。用一系列改性的Karplus公式计算了二面角(dihedral sngles),估算了吗啡和可待因的分子构型(configuration)。