导致乙烷的交叉型构象是超共轭作用而不是空间阻碍

在国内外现行的有机化学和结构化学教科书中 ,对乙烷分子的构象问题都是认为 :由于两个ＣＨ3基团可以按Ｃ—Ｃ单键为轴进行旋转 ,使Ｃ原子上的Ｈ原子在空间的相对位置发生变化 ,出现各种构象异构体。在其中势能最高的为重叠型构象 ,如图 1 (ａ)所示 ;势能最低的为交叉型构象 ,如图 1 (ｂ)所示。这两种构象的能量差 ,即转动势垒为 1 2 .1ｋＪ/ｍｏｌ。为什么重叠型构象的能量较高 ,一般认为是由于两个Ｃ原子的Ｈ原子最近的距离为 2 2 7ｐｍ ,短于Ｈ原子的范德华半径之和 (即 2 40 ｐｍ)产生排斥力 ,而出现空间阻碍效应。而在交叉型构象中 ,两…     

Walsh-及π-轨道间的作用——环丙基取代苯类的光电子谱研究

本文对环丙基取代苯类系列化合物的光电子谱进行了分析和讨论,由于构象问题使得谱的解释变得复杂,但六环丙基苯(12)可能是个例外。现已证明在π-体系和环丙基之间无论是平分交叉构象,还是垂直构象都有明显的作用,其交叉项比值B(e_A,2p)/B(e_S,2p)≈1.4,不象传统的Walsh轨道所预料的那么大,文中阐述的由STO-3G模型导出的定域键轨道是一个更为合用、更具有启发性的模型。     

维甲化合物与维甲X受体相互作用模拟及QSAR研究

用分子对接确定了一系列RXR激动剂与受体的作用方式,与X衍射测得的晶体复合物中9-cis-RA的作用方式相近。对接后的配体-受体复和物经分子力学优化后更接近药效构象,两者相互作用能与活性具有一定的相关性,相关系数R^2=0.64。用活性构象建立的CoMFA模型比低能构象建立的CoMFA模型有更高的可信度,其交叉验证相关系q^2=0.791,非交叉验证相关系数γ^2=0.988,绝对误差SE=0.099,f6,33=456.8。     

q~2引导构象选择CoMFA方法研究HIV－1RT抑制剂

对未知受体结构的药物设计其主导方法CoMFA来说，柔性目标分子的多种构象 造成了问题的复杂性。本文介绍交叉验证参数R~2(q~2)引导的构象选择CoMFA方法 ，选择化合物的最佳构象。将一组47个HIV－1 RT抑制剂进行有、无构象选择的 CoMFA分析来作评价。根据化合物的活性、毒性、选择性指数（毒性／活性比）等 实验数据得到的模型，其交叉验证参数q~2为0.7以上，非交叉验证的相应参数为0. 94以上，最后，还经过试验集化合物验证该模型的预测能力，置信度（1－α）＞ 0.99。     

联苯桥联的PPV齐聚物基态构型、电子能级和吸收光谱的理论研究

用密度泛函方法对联苯桥联的PPV齐聚物(TSB)的反式结构进行全优化,得到基态分子的最优几何构型和电子能级,并用ZINDO和TD-DFT方法分别计算其吸收光谱,分析了不同类型的端位取代基团对前线分子轨道能量和能隙的影响. 结果表明,联苯桥联后的PPV齐聚物在结构上形成了链间交叉链内扭曲的构象,这种交叉扭曲的构象降低了分子的对称性,减弱了共轭分子在固体中的π-π堆积作用,这可能是减少荧光猝灭效应,提高固体发光器件效率的重要原因.     

5-芳基乙内酰脲类化合物在Pirkle型色谱柱上拆分的CoMFA研究

用比较分子场分析法(CoMFA)研究了5-芳基乙内酰脲类化合物定量结构-保留关 系。本研究林构象搜索所得的低能结构出发构建化合物分子的构象，并进行了全空 间搜索。得到了较好的模型CoMFA的交叉验证回归系数q~2为0.764，模型的线性回 归系数r~2为0.962)。这些方程不仅有助于推测被识别剂和识别剂之间的结合方式 ，还可以定量地预测结构相近的类似物的拆分可能性，为设计合成新的识别剂和被 识别剂都提供了一定的理论依据。     

一种确定反应中间态几何特征和能量的综合性方法

通过综合使用传统的过渡态优化算法、数学统计工具以及人工神经网络算法(ANN)找到一种不依赖于反应物起始构象而得到化学反应中过渡态结构和能量的方法. 在两个反应物互相接近的过程中, 每一步的几何构象都对应着一个系统能量值. 本研究的目的是尽可能地收集处在反应能量面上的这种能量点值. 通过采用几何参数作为自变量对势能面进行模拟研究, 得到了势能面上对应过渡态结构的一阶鞍点. 采用乙醛负离子和甲醛作为反应物, 对经典的醛醇缩合反应中的亲核进攻步骤进行了研究. 对内禀反应坐标(IRC)路径的计算是从反应物的三组不同起始构象出发, 最终获得了反应势能面上的96个点. 本研究中的势能面采用人工神经网络算法进行模拟研究, 并利用交叉验证方法评估得到的结果, 避免了采用人工神经网络算法时过度拟合情况的发生.     

基于5-芳基乙内酰脲类化合物的CoMFA和HQSAR研究

用CoMFA和HQSAR两种QSAR方法研究了50个乙内酰脲类分子的定量构效关系.本研究从构象搜索所得的低能结构出发构建化合物分子的构象, 建立CoMFA模型,并进行了全空间搜索. HQSAR本质上是一种二维的QSAR方法,与CoMFA方法相比,该方法在数据处理方面,比CoMFA方法快捷,并且可重复性好.两种方法均得到了较好分析结果, CoMFA的交叉验证相关系数q2 值为0.815, HQSAR的q2值为0.893.这些方程有力地说明了该类分子在(R,R)-N-3,5-dinitrobenzoyl-1,2-diamine型手性固定相上拆分过程中的影响因素,对今后类似拆分的实验研究提供了理论支持.     

取代环己酮还原立体选择性的过渡态理论解释

对于取代环已酮还原产物的立体选择性,仅通过还原试剂的动力学条件和生成产物的热力学稳定性进行预测是不准确的,需要考虑反应过程中存在的其他因素。采用过渡态理论可以对取代环已酮还原产物的立体选择性进行更全面、更准确的预测。一方面,还原试剂进攻羰基形成过渡态时,表现出决定立体选择性的空间位阻效应和电子效应;另一方面,反应物优势构象,即形成过渡态时的扭转应变和相对于标准对交叉构象偏转角的大小对产物的立体选择性也不容忽视。本文从过渡态形成过程中所体现的空间位阻、电子效应和构象三方面进行讨论,阐述了取代环已酮还原产物的立体选择性。     

1,6-二(对甲氧苯基)十二甲基六硅烷的合成及结构

采用1,6-二氯十二甲基六硅烷与对溴苯甲醚的格氏试剂反应制得了标题化合物。对其进行了结构分析。X射线衍射分析表明,该晶体属单斜晶系,分子是中心对称的,化合物呈交叉锯齿型稳定构象。     

取代冠醚的异构体计数

采用图论方法对取代冠醚的构造、构型以及手性构型和非手性构型进行计数。为了便于计数，取代冠醚的构型、手性构型和非手性构型的计数采用平面模型，并利用Ｐｏｌｙａ计数定理求出其计数母函数，最后使用计算机计算，结果列表给出。     

The numbers of chiral and achiral alkanes and monosubstituted alkanes

Whereas the theory for the enumeration of the optical isomers of the lakyl radicals and the alkanes has long been understood, this is not the case for the corresponding archiral isomers. We present for the first time recurrence formulae for counting the number of archiral isomers of the alkyl radicals and the alkanes. For chiral and archiral alkanes and monosubstituted alkanes, numerical results up to C₁₄ are tabulated.After presenting the history of the problem and the necessary definitions, we proceed to derive functional equations on the various generating functions, which readily yield the more explicit recurrence formulae usefule for numerical calculations. In the process, we first re-derive Pólya's expression for planted steric trees using his classical enumeration theorem. This result is then extended to the enumeration of free steric trees using the now standard tree-counting method due to Otter and known as a dissimilarity characteristic equation.By definition, a steric tree is a quartic tree (all points having degree 1 or 4) in which the four neighbors of every carbon point are given a tetrahedral configuration. Building on the methods of the first two authors for counting chiral and archiral trees in the plane, we obtain the formula for counting achiral steric trees, thus setting a problem first enunciated by van't Hoff and Le Bel in 1874.     

Carbonyles tres decales par rapport a l'eclipse dans les aldehydes et les cetones aliphatiques satures: analyse conformationnelle theorique

The theoretical conformational analysis of two series of molecules HCOR, MeCOR is treated. Spectroscopic data [15] have indicated the existence of non-eclipsed conformations which become more important with increasing steric hindrance of the group R.All the methods used (semi-empirical quantum methods, P.C.I.L.O., I.N.D.O., C.N.D.O./2, and the Liquori empirical potential method) lead to the following stable conformations: with the carbonyl group exclusively eclipsed for slightly substituted R (R = Me, Et, tBu); with the carbonyl eclipsed and also staggered (? ? 60°) for moderately substituted compounds (MeCOPr, MeCOiBu, MeCOCiPr(Me)₂) (low rotational barriers permitting equilibria between eclipsed and staggered conformations); with the carbonyl exclusively staggered (? ? 60°) for more hindered compounds (MeCOCH₂tBu, MeCOCH(tBu)Me, MeCOC(Me),tBu, MeCOCH(tBu)₂).Contradictory results are obtained for certain compounds (iPrCOMe, tBuCH₂CHO for example) : the calculated changeover from eclipsed to staggered conformations differentiates the semi-empirical methods from the empirical potential method used.     

Enumeration of Isomers of Acyclic Saturated Hydroxyl Ethers

In this paper, we present generating functions for counting constitutional isomers and stereo isomers of acyclic saturated compounds consisting of O, C and H for the first time, and obtain the numbers of constitutional isomers and stereo isomers of acyclic saturated hydroxyl ethers. The numerical results are tabulated.     

Effects of anharmonicities on radiationless transitions in large molecules

A new computational method to account for the effect of anharmonicities on non-radiative decay rates of large molecules in the statistical limit is given by using expansions of the generating functions which have been used successfully in multiphonon processes. This method is free from the ambiguity which, as in previous conventional methods, arises from the factorization which separates the decay rate into a product of an electronic term, a Franck-Condon factor and a density of final states. The rate expression is asymmetric with respect to the sign of the displacement of the accepting modes. Actual calculations are performed for a model molecule which closely resembles benzene. The numerical data for the decay rate exceed the results of the harmonic approximation by about two orders of magnitude.     

Catalytic olefination reaction of carbonyl compounds. A study on stereoselectivity of alkene formation

The mechanism of formation of alkene stereoisomers in the catalytic olefination reaction of carbonyl compounds was studied. 4-Chlorobenzaldehyde hydrazone 1 stereoselectively reacts with a number of F-, Cl-, Br-, and I-containing polyhaloalkanes in the presence of catalytic amounts of CuCl to give -substituted styrenes 2 with the more thermodynamically stable alkene isomer being the major product. A model for the formation of the stereoisomers of alkenes 2 in the olefination reaction is proposed. Stereoselectivity of the reaction is determined by elimination of copper(ii) halides from the lowest-lying conformers of organocopper intermediates II. According to quantum-chemical calculations, the elimination should involve the staggered conformations with antiperiplanar arrangement of C—Hal and C—Cu bonds and proceed by the E2 anti-elimination mechanism. The results of quantum-chemical calculations are in good agreement with the experimental E/Z alkene isomer ratios.     

A theoretical study of the staggered and eclipsed forms of the dinuclear complex Mn Re(CO)10

Two possible conformers of the dinuclear complex Mn Re(CO)10, each of C(4v) symmetry, with eclipsed and staggered conformations, have been analyzed theoretically. Using both the B3LYP and BP86 density functionals we find that the staggered form is lower in energy. A determination of the B3LYP potential energy surface as a function of the Mn-Re distance is presented for both conformers. The computed bond lengths, bond angles, and rotational constant for the staggered conformation compare favorably with the results from microwave experiments. The harmonic frequencies for the staggered structure have been determined using several basis sets, with both analytical and finite difference methods. These unscaled vibrational frequencies, together with their intensities for both infrared and Raman activity, are used to assign the three most intense experimental IR and Raman bands, and in particular, the nu(CO) region. The lowest A(2) vibration was calculated to occur at 41 cm(-1) in the staggered conformer; this frequency becomes imaginary in the (saddle point) eclipsed form. Several fundamentals remain to be observed experimentally.     

Semiempirical quantum-chemical calculations on the conformations of methyl formate and methyl thiolformate

The cis, trans, and gauche conformations of the methyl esters of formic and thiolformic acids have been investigated by different semiempirical methods. Total geometry optimization (CNDO/2, MINDO/3) and bond angle optimization (PCILO, NDDO) have been performed for the O-alkyl ester. The S-alkyl ester has been studied by the MINDO/3 method at the total geometry optimization level and by CNDO/2 and PCILO methods at the bond angle optimization level. The influence of sulphur d orbitals on the optimized molecular geometry as well as on the magnitude and direction of the dipole moment vector has been investigated in the CNDO/2 framework. The total energy differences of the conformers are compared to the experimental and ab initio results. CNDO/2 and NDDO energy partitioning have been performed to obtain information on the origin of the cis—trans energy difference and of the rotation barrier. The extent of the lone-pair delocalization has been studied in the different conformations using localized molecular orbitals. Calculations have been performed on the staggered and eclipsed positions of the methyl group in the planar conformations of both esters.     

Generating conformational transition paths with low potential-energy barriers for proteins

The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.     

Are there atomic orbitals in a molecule?

Effective atomic orbitals (AOs) have been calculated by the method of the "fuzzy atoms" analysis by using the numerical molecular orbitals (MOs) obtained from plane-wave DFT calculation, i.e., without introducing any atom-centered functions. The results show that in the case of nonhypervalent atoms there are as many effective AOs with non-negligible occupation numbers, as many orbitals are in the classical minimal basis set of the given atom. This means that, for nonhypervalent systems, it is possible to present the MOs as sums of effective atomic orbitals that resemble very much the atomic minimal basis orbitals of the individual atoms (or their hybrids). For hypervalent atoms some additional orbitals basically of d-type are also of some importance; they are necessary to describe the back-donation to these positive atoms. It appears that the d-type orbitals play a similar role also for strongly positive carbon atoms. The method employed here is also useful to decide whether the use of polarization functions of a given type is a matter of conceptual importance or has only a numerical effect.