空间距离在三维分子相似度计算中的应用

采用Tripos公司的MOPAC模块计算分子的空间距离,所得距离矩阵用带有约束条件的空间距离方法计算分子的相似度,同时通过4组化合物的计算,与纯空间距离方法进行比较,得到了较为满意的结果。     

褪黑激素受体拮抗剂的三维定量构效关系研究

采用两种分子场分析方法即比较分子场分析法（CoMFA）和比较分子相似因子分析法（CoMSIA）进行了37个褪黑激素受体拮抗剂的构效关系研究.计算结果表明，两种方法得到的构效关系模型都具有较好的预测能力.在计算中，还考察了不同格点距离和电荷计算方法对构效关系模型的影响.通过分析分子场等值面图在空间的分布，可以观察到叠合分子周围分子场特征对化合物活性的影响，为设计新的褪黑激素拮抗剂提供了一些理论依据.     

GEMC和GDI方法计算流体气液相平衡的比较

考察采用TraPPE联合原子和OPLS全原子力场两种分子力场, Gibbs系综蒙特卡罗(GEMC)方法和Gibbs-Duhem积分(GDI)方法计算流体气液相平衡的适用性、计算速度、计算精度等问题. 结果表明, 在采用全原子力场情况下, GDI方法比GEMC方法极大地节省了计算时间. 从计算结果来看, 两种方法各有适用范围, 在使用时可互为补充. 在给定力场的前提下, 两种方法所得到的液相密度、蒸发焓、临界温度和临界密度相差不大, 而当力场中的缺陷导致蒸发焓的计算不够准确时, 两种计算方法得到的气体的压力和密度明显不同,进而导致预测的临界压力也明显不同.     

几种苄基哌嗪衍生物13C NMR的计算研究

本文分别采用量子化学从头算Hatree-Fock方法和密度泛函B3LYP方法在6-311G++基组水平下对几种苄基哌嚷衍生物的13C NMR作了计算研究.结果表明两种方法计算得到的各苄基哌嗪衍生物中C原子化学位移的计算值与实验值之间均近似存在线性关系,其中采用考虑了电子相关作用的密度泛函方法计算时,各化合物中碳原子的化...     

萜类化合物的QSRR研究及其在结构鉴定中的应用

采用顶空固相微萃取(SPME)-气相色谱质谱(GC-MS)联用技术分析石香薷和腊梅鲜花中的萜类化合物, 通过保留指数与质谱解析相结合, 分别对化合物进行结构鉴定, 共鉴定出17种单萜化合物, 30种倍半萜化合物. 采用遗传算法(GFA)分别对单萜及倍半萜化合物建立定量结构-色谱保留关系(QSRR)预测模型, 并对该模型进行显著性及预测能力的检测. 同时, 利用计算所得到的模型分别对随机选取的几个萜类化合物进行保留指数预测. 结果表明: 计算保留指数与预测保留指数接近, 模型预测性能较好. 该研究为各种单萜化合物及倍半萜化合物保留指数的预测提供了一种有效手段, 同时, 为建立有效的GC-MS定性方法提供了一定的依据.     

手性有机化合物构效关系的量子拓扑学研究

在拓扑化学理论基础上, 从手性分子中成键原子的结构特征和手性原子所处的局部化学微环境出发, 应用密度泛函理论(DFT), 在B3LYP/6-31＋G(d)水平上计算所得距离代替传统二维距离, 结合分子中各原子的支化度, 应用原子的平衡电负性对分子图进行着色, 并引入手性校正因子进行校正, 得到新型的手性拓扑指数w₁和w₂. 采用偏最小二乘回归法建立了18种手性羟基酸和氨基酸的薄层色谱保留指数R_M的定量结构-保留拓扑模型, 并用这种模型对R_M进行预测, 结果表明预测结果和实验值吻合较好. 同时对拓扑模型采用留一交叉检验法(leave-one-out cross-validation, LOO-CV)和外检验相结合的方法进行测试, 测试结果显示模型具有良好稳定性和较强的预测能力.     

基于原子表面的蛋白质水合自由能预测模型

提出了一种计算蛋白质水合自由能的简化模型（SAWSA 2）.模型把蛋白质分子中的原子分为20种不同的原子类型,通过每类原子的溶剂可及化表面以及相应的溶剂化参数,就可以得到分子的水合自由能.不同原子类型的溶剂化参数通过110个蛋白质分子水合自由能拟合得到,水合自由能的标准值采用了基于求解Possion-Boltzmann方程（PB）以及分子表面计算（SA） 相结合的方法.采用得到的模型,预测了20个蛋白质分子的水合自由能,预测值的相对值和绝对值都能和PB/SA的计算值很好地吻合,大大优于两种已报导的水合自由能模型.     

化学环境编码与分子相似度计算

分子相似度方法主要用于药物分子设计中先导化合物的选取及化合物物理、化学性质的预测,这种方法所依据的原理是：相似的化合物结构将具有相似的化学及物理性质［‘,’1．将已知具有某种性质的化合物的结构（常称为探针化合物）与诸多化合物进行比较,由此得到与之相似的化合物,这种邻近化合物有可能在分子设计中做先导化合物．近年来已报道过多种化合物相似度的计算方法,可粗略的归为以下几类：（l）结构碎片法［‘’‘j;（2）拓扑指数法卜·“;（3）量子化学方法［’,’j．本文提出一种新的化学环境编码方法,该方法有别于结构碎片…     

利用样本成分耗散物的非线性化学指纹图谱原理及相似度计算与评价

在恒温恒压条件下,以丙酮和样本中底物作为主要耗散物的不同成分的样本对非线性化学反应机理产生不同影响,从而引起反应体系电位-时间曲线形状不同变化为特征的B-Z化学振荡体系为例,就非线性化学指纹图谱原理进行了详细研究和讨论,并提出了计算非线性化学指纹图谱系统相似度的通用方法.利用系统相似度和欧氏距离、相关系数及夹角余弦对不同生产批次古汉养生精和18种其他样本的非线性化学指纹图谱的相似度进行了计算与分析.结果表明,相关系数和夹角余弦都不能用来作为评价非线性化指纹图谱相似度的指标.利用欧氏距离公式计算指纹图谱的非参数型相似度时,能正确反映指纹图谱的特征差异,但用其计算参数型相似度时,则有时不能正确反映样本非线性化学指纹图谱特征差异的相对程度.系统相似度能最真实反映样本指纹图谱之间差异程度,是4种相似度计算方法中最好的,可用于非线性化学指纹图谱相似度计算与评价.成功提出了一种经济、简便、易行和有效的鉴别样本真伪与评价其质量的科学方法.     

N—O键解离焓的密度泛函理论研究

在高精度计算方法G3和G3B3的基础上,比较了密度泛函理论(DFT)十几种方法对N—O键解离焓(BDE)相对于实验值的计算精度,发现用B3P86方法计算15种化合物N—O键的BDE,均方根误差最小,仅为6.36kJ·mol-1,计算值与实验值的线性相关系数为0.991.在此基础上,用该方法分别计算了非芳香化合物及芳香化合物的N—O键BDE.通过自然键轨道分析,发现部分N—O键的BDE与N—O键的键长、原子电荷密度及键级之间存在定量关系.此外,在B3P86方法的基础上预测了几种典型的杂环芳香化合物N—O键BDE值.     

Potential energy distribution study of infrared frequencies of methylamine and methylphosphine

Normal mode assignments of the IR frequencies of methylamine and methylphosphine and their deuterated isotopomers are determined based on calculated potential energy distributions. The PED for each frequency is found using Kim’s Correspondence Rules of unified group theory and the program MOLVIB. The predominant motion of each PED is used to name the corresponding vibrational frequency. We compare our results with literature values. Our IR frequency assignments show generally good agreement with experiment and other calculations although there are some differences. We observe no differences in the principal component of normal mode PEDs across different levels of theory with the same basis set. We observe a few differences at the same level of theory with different basis sets.     

Prediction of vibrational frequencies of UO2(2+) at the CCSD(T) level

Electronic structure calculations at the coupled cluster (CCSD(T)) and density functional theory levels with relativistic effective core potentials and large basis sets were used to predict the isolated uranyl ion frequencies. The effects of anharmonicity and spin-orbit corrections on the harmonic frequencies were calculated. The anharmonic effects are larger than the spin-orbit corrections, but both are small. The anharmonic effects decreased all the frequencies, whereas the spin-orbit corrections increased the stretches and decreased the bend. Overall, these two corrections decreased the harmonic asymmetric stretch frequency by 6 cm-1, the symmetric stretch by 3 cm-1, and the bend by 3 cm-1. The best calculated values for UO22+ for the asymmetric stretch, symmetric stretch, and bend were 1113, 1032, and 174 cm-1, respectively. The separation between the asymmetric and the symmetric stretch band origins was predicted to be 81 cm-1, which is consistent with experimental trends for substituted uranyls in solution and in the solid state. The anharmonic vibrational frequencies of the isoelectronic ThO2 molecule also were calculated and compared to experiment to calibrate the UO22+ results.     

Criteria for determining the hydrogen-bond structures of a tyrosine side chain by fourier transform infrared spectroscopy: density functional theory analyses of model hydrogen-bonded complexes of p-cresol

Fourier transform infrared (FTIR) spectroscopy is a powerful method to investigate the structures of key Tyr residues involved in various protein reactions. In this study, we have performed density functional theory (DFT) calculations for various hydrogen-bonded complexes of p-cresol, a simple model of a Tyr side chain, in different hydrogen-bond forms to develop explicit criteria for determining the hydrogen-bond structures of Tyr using FTIR spectroscopy. The CO stretching (nuCO) and COH bending (deltaCOH) vibrations were focused as markers and calculated results were compared with experimental data of p-cresol and Tyr. The calculated and experimental nuCO frequencies appeared at 1280-1260, 1260-1250, 1255-1235, and 1240-1220 cm-(1) in the hydrogen-bond donor, free, donor-acceptor, and acceptor forms, respectively. These frequencies, which showed little overlap between the individual hydrogen-bond forms, had a negative linear correlation with the CO lengths in optimized geometries. The deltaCOH frequencies were found at 1255-1210 cm-(1) in the donor form, while the free and acceptor forms showed relatively low deltaCOH frequencies at 1185-1165 and 1190-1160 cm-(1), respectively. In the donor-acceptor form, the vibrational mode with a considerable deltaCOH contribution was found at 1280-1255 cm-(1) with a weak IR intensity. This frequency and the nuCO frequency in the donor-acceptor form are similar to the nuCO and deltaCOH frequencies, respectively, of the donor form, making it difficult to discriminate the two forms. These two forms can be clearly distinguished by detecting a strong nuCO(D) band in p-cresol-OD or Tyr-OD, in which the deltaCOD vibration largely downshifts to approximately 1000 cm-(1). The nuCO(D) frequency of the donor-acceptor form was found at 1260-1240 cm-(1), while that of the donor form was at 1270-1255 cm-(1). Practically, plotting the frequency of the lower-frequency strong IR band (nuCO of the donor-acceptor form or deltaCOH of the donor form) of undeuterated species against the nuCO(D) frequency is convenient for accurate discrimination. Because the donor form shows a positive linear correlation between deltaCOH and nuCO(D) frequencies, the two forms exhibited distinct areas in this plot. The effects of hydrogen-bond interactions on other potential IR and Raman markers are also discussed.     

Plasmon frequencies of cube shaped metal clusters

The plasmon frequencies of a cube shaped metal cluster are calculated by two different methods. Unlike the spherical cluster, which has a single plasmon frequency, $\omega _p /\sqrt 3 $ , the cube has a series of optically active plasmon frequencies. The two dominant peaks appear at frequencies which are considerably lower than that of a spherical cluster.     

DFT方法研究间苯二酚-甲醛气凝胶单体分子性质与振动频率

用B3LYP密度泛函方法在6-311G**基组水平上计算了单元、二元羟甲基间苯二酚的分子体积和振动频率,通过理论计算与实验结果的比较,探讨了间苯二酚-甲醛气凝胶形成的微观机理,具体分析了各振动模式的归属和同位素取代对振动频率的影响.     

Correlation of the thermal stability and the decomposition kinetics of six different vegetal fibers

The thermal degradation behavior of six different vegetal fibers was studied using thermogravimetry under nitrogen atmosphere at four different heating rates (5, 10, 20 and 40 °C min^?1). The degradation models Kissinger, Friedman and Flynn–Wall–Ozawa methods were used to determine the apparent activation energy and the frequency factor of these fibers. Furthermore, the solid state degradation mechanisms were determined using Criado’s method. Additionally, X-ray diffraction and Fourier transform infrared (FTIR) spectroscopy were analyzed to corroborate the obtained results. The results indicated that the apparent calculated activation energies can be more closely related to the exponential dependence of the rate of heterogeneous reactions than to the, necessary “energy”, which is commonly used. The Criado’s master curves indicated two different degradation mechanisms for the fibers: diffusion followed by random nucleation. The results also indicated that the crystallinity index as calculated by X-ray diffraction and determinated by FTIR does not necessarily represent higher thermal stability as noted by the thermogravimetric analysis curves. The thermal behavior and the degradation mechanism did not show to be influenced by the lignocellulosic components of the fibers, exception for buriti and sisal. This behavior was attributed to higher extractive content.     

Ar-matrix IR spectra of 5-halouracils interpreted by means of DFT calculations

The infrared low-temperature Ar-matrix spectra of 5-halouracils and unsubstituted uracil were measured and interpreted in terms of the spectra calculated at the DFT/B3PW91/6-311G level followed by a potential energy distribution (PED) analysis. For the PED analysis, the sets of halouracil mode definitions were constructed so that dissimilarities in the interpretations of the different spectra were minimized. Anharmonic frequency calculations enabled more light to be shed on the Fermi resonance (FR) phenomena occurring in the nu(C=O) stretching vibrations region. For each halouracil vibrational spectrum, several FRs manifest themselves in the nu(C=O) stretching vibrations region. We show that the most frequent components participating in these resonances are the nu(C(4)=O(10)) frequency, a beta(N-H) mode frequency, and a beta(C=O) mode frequency. The experimental nu(N-H) frequencies are reproduced by the calculated anharmonic frequencies better than by the scaled harmonic ones, and the nu(C=O) frequencies respond in the opposite manner. The experimental frequencies located below 1500 cm(-1) are reproduced equally well by the two kinds of calculations.     

Ab initio studies on the vibrational spectra and conformational isomerism of 2,4-dimethyl-1,3-pentadiene

Ab initio was used to study the structure of various conformational isomers and their vibrational spectra of 2,4-dimethyl-1,3-pentadiene (2,4-PD) in detail. Two stable conformations, s-trans and s-cis, were found in which s-trans is more stable. The geometry of stable conformations and charge distributions were studied, and the effect of different basis sets on geometry optimization is discussed. The results of complete optimization indicate that molecular skeleton is nearly in a plane, its largest deviation is only 0.3 degrees. Therefore, it is reasonable and available to hypothesis that the molecule has Cs symmetry. The thermal dynamics conformations were calculated and compared with experimental values. DeltaH(o) between two conformations of 2,4-PD measured from experiment is 4.36 kJ/mol, deltaS(o) is 2.56 J/mol K., calculated results are slightly different from experimental ones. Vibrational frequencies of 2,4-PD conformers have been studied by ab initio molecular orbital calculations using different basis set. The calculated vibrational frequencies are analyzed and compared with the experimental spectra.     

丙酮酸分子结构与振动光谱的密度泛函理论研究

用密度泛函方法BLYP、B3LYP和从头算Hartree-Fock(HF)方法在6-31G*基组水平上对丙酮酸分子的几何结构（甲基的重叠式和交错式两种构象）和振动光谱分别进行了优化和计算,并给出了各种频率所对应的红外强度及拉曼活性,对光谱进行了指认。结果表明：在丙酮酸分子的两种构象中,重叠式比较稳定*B3LYP计算得到的构型参数与实验结果比较一致;在振动频率的计算中,BLYP未标度力场所计算的非CH3伸缩振动基频预测值和实验值的平均绝对偏差为10.4cm-1;而HF标度力场的平均绝对偏差为17.9cm-1。说明两者的结果与实验观测频率比较吻合,但B3LYP的频率计算值偏差（38.3cm-1）较大。根据振动频率的势能分布和红外光谱强度对此分子的振动基频进行了理论归属。     

Structure and vibrational assignment of the enol form of 1,1,1-trifluoro-2,4-pentanedione

Molecular structure of 1,1,1-trifluoro-pentane-2,4-dione, known as trifluoro-acetylacetone (TFAA), has been investigated by means of Density Functional Theory (DFT) calculations and the results were compared with those of acetylacetone (AA) and hexafluoro-acetylacetone (HFAA). The harmonic vibrational frequencies of both stable cis-enol forms were calculated at B3LYP level of theory using 6-31G** and 6-311++G** basis sets. We also calculated the anharmonic frequencies at B3LYP/6-31G** level of theory for both stable cis-enol isomers. The calculated frequencies, Raman and IR intensities, and depolarization ratios were compared with the experimental results. The energy difference between the two stable cis-enol forms, calculated at B3LYP/6-311++G**, is only 5.89 kJ/mol. The observed vibrational frequencies and Raman and IR intensities are in excellent agreement with the corresponding values calculated for the most stable conformation, 2TFAA. According to the theoretical calculations, the hydrogen bond strength for the most stable conformer is 57 kJ/mol, about 9.5kJ/mol less than that of AA and about 14.5 kJ/mol more than that of HFAA. These hydrogen bond strengths are consistent with the frequency shifts for OH/OD stretching and OH/OD out-of-plane bending modes upon substitution of CH(3) groups with CF(3) groups. By comparing the vibrational spectra of both theoretical and experimental data, it was concluded that 2TFAA is the dominant isomer.