顺式环十二碳烯的构象

用分子力学法(MMX程序)计算了15-苯基双环[10,3,0]十五碳-1(12)-烯-13-酮,其分子中环十二碳烯部分的构象为能量最低的[l_(ene)2333],与X衍射结果吻合.同时,还计算了15个顺式环十二碳烯的构象,求出了它们的能量及结构参数,讨论了影响构象稳定性的因素.     

含过渡金属和柔性配体催化体系的构象搜索

采用密度泛函理论对含有过渡金属和柔性配体的分子进行优化时,通常只能将初始结构优化到势能面上的局部最小点,而确定反应势能面上各中间体和过渡态的最低能量构象是准确描述一个催化反应最优路径的关键.使用Cr/PCCP体系催化乙烯选择性三聚/四聚反应路径中的关键过渡态(TS1,TS2,TS3)作为分子模型,对基于Tinker软件包和CREST软件包的两种构象搜索方法进行了对比测试.使用两种构象搜索方法均成功找到了三个分子模型的最低能量构象,并且两种方法获得的构象数量总数相差不大.与基于Tinker软件包的构象搜索方法相比,使用CREST软件包进行构象搜索的计算流程更加简单,并且大大减少了计算时间.     

LB膜中NMOB分子构象的研究

利用DFTB3LYP/4-31G^*方法,对2-硝基-5-(N-甲基-N-十八烷基)氨基苯甲酸(NMOB)进行研究。计算结果发现,苯环的5位碳原子、氨基氮原子以及十八烷基链上与其最临近的两个碳原子所组成的两面角(D)约为90ⅲ时,NMOB有最稳构象,在NMOB自交替膜中,NMOB即以这种构象存在;而D=180ⅲ时,体系总能量较最稳构象高出31.57kJ/mol,这种构象存在于NMOB/花生酸镉(CdA)交替膜中,较小的能量差异使NMOB容易在两种构象之间进行转化,在NMOB/花生酸镉(CdA)交替膜中因受到花生酸直立构象紧密排列的诱导作用,NMOB分子以能量相对较高的构象存在。     

联吡啶构象异构的理论研究

采用HF/6-31G*方法,对6种联吡啶构造异构体进行了构象分析.之后采用B3LYP/6-311G**方法对处于势能面上的能量极小构象异构体进行全自由度几何优化和频率分析,并且寻找构象异构化过渡态.采用自洽反应场极化导体模型溶剂理论,探讨了水溶剂对优势构象异构体的几何结构和能量的影响.     

秦岭苦参中苦参碱立体异构体晶体结构研究

从秦岭地区苦参中经过溶剂提取和酸化分离得到一种生物碱盐酸盐结晶1，该 晶体不对称单元含有一对新的苦参碱非对映异构体，绝对构型分别是1S，5S6S， 7R，11R，16S和1S，5S，6S，7R，11R，16R，命名为顺式新苦参碱(cis- neomatrine)和反式新苦参碱(trans-neomatrine)。1的晶体结构(C_(15)H_(24) N_2O·C_(15)H_(24)N_2O·2HCl·5H_2O)属正交晶系，空间群P2_12_12_1, a = 0. 8053(2) nm, b = 1.3464(5) nm, c = 3.0971(9) nm, V = 3.3580(18)nm~3, Z = 4, μ=0.244 mm~(-1), F(000) = 1432, R = 0.0467, wR = 0.1129。顺式新苦参 碱和反式新苦参碱的A环、B环和C环为式构象，D环为半椅式构象，其中A／B为反式 稠合，A／C和B／C为顺式稠合，两种立异构体的区别是顺式新苦参碱的C／D顺式稠 合，反式新苦参碱的C／D反式稠合。     

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…     

间位聚苯及其衍生物的构象与电子结构的理论研究

用分子力学方法(MM)对间位聚苯(PMP)及其衍生物的势能随扭曲角(f)变化规律进行了研究.结果表明，势能曲线上出现四个能量最小值，分别对应于扭曲角f ≈－135°,－45°,45°,135°.进一步对以上构建的全部PMP及其衍生物用分子力场Drieding 2.11进行了分子力学能量优化.最终得到主要的四种构象，其中螺旋构象的能量最低，而且以螺旋构象为优势分布构象.在真实条件下，PMP及其衍生物长链可能采取以上四种构象的混合片段组成.用量子化学方法(GGA-DFT)研究了PMP及其衍生物的电子结构能隙随相邻苯环之间的扭曲角的变化趋势.用量子化学半经验方法(AM1)对四种构象分别进行几何优化，优化结果与分子力学优化结果基本一致，并运用混合密度泛函方法(DFT/B3LYP/6-31G)进一步对AM1优化的构象结构进行更精确的电子结构能隙计算.最终得出影响间位聚苯及其衍生物电子结构能隙的主要因素为连接苯环间扭曲角的大小.     

谷胱甘肽分子伞的构象分析及VolSurf表征

使用分子动力学模拟迟火和半经验AMl方法对谷胱甘肽分子伞进行了构象分析 ，结果表明，真空下屏蔽构象和暴露构象的最低能量值相差很小(26.00kJ/mol)。 考虑溶剂效应后，屏蔽构象的能量值最高，暴露构象的能量值最低。屏蔽构象的能 量最低值高于暴露构象的能量最低值89.24kJ/mol，从理论上解释了谷胱甘肽分子 伞在水溶液中呈现暴露构象的原因。利用VolSurf参数分析了分子伞以屏蔽构象穿 透磷脂双分子层的影响因素，结果表明屏蔽构象较小的两亲矩及较大的分子褶皱程 度是其能够穿透细胞膜的主要影响因素，与构象的绝对疏水区域无关。     

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。     

脯氨酸的构象及性质

用X3LYP法在6-311++G(d, p)和6-311++G(3df, 3pd)基组水平上对脯氨酸15种构象的几何结构、相对能量、电子结构、红外光谱、偶极矩、极化率等性质进行了研究, 并与PBE1PBE/6-311++G(d, p)的结果和文献相比较, 从而得到: (1) 的脯氨酸的15种构象中能量最低的有4种, 不同构象中存在着强弱不同的5种氢键, 其中以N…H—O氢键最强, 并存在特殊的C—H…O=C氢键. 两种方法计算的几何结构数据相近, 均与实验值吻合; (2) 在构象相对能差计算方面, X3LYP具有明显的优势, 用中等基组就可以得到与高水平从头算法和大基组相同的结果, 而PBE1PBE法计算的相对能值则相差较大; (3) 脯氨酸不同构象中偶极矩最大和极化率最小的是最稳定的构象1和2, 两种方法计算的结果一致.     

Calix[4]arene bisphosphite ligands bearing two distal 2,2′-biphenyldioxy or 2,2′-binaphthyldioxy moieties: conformational flexibility and allyl-palladium complexes

Achiral and chiral calix[4]arene bisphosphite ligands (2 and 3) bearing two distal 2,2′-biphenyldioxyphosphinoxy and 2,2′-binaphthyldioxyphosphinoxy moieties, respectively, have been synthesized. Each of these ligands exists in two pairs of interconverting conformations in solution. The partial cone conformer (A) of the (bis)biphenyldioxyphosphinoxy ligand 2 has been separated by fractional crystallization and its structure established by X-ray crystallography. The mechanism of interconversion of the pairs of conformers (A/B and C/D) has been probed by two-dimensional NMR spectroscopy. The ¹H and ³¹P NMR evidence strongly supports a similar kind of exchange mechanism for ligand 3. Freezing of the cone conformer from the interconverting C/D pair of conformers of ligand 2 has been achieved by complexation with (allyl)palladium moieties. The methyl-allyl complex (2d) is moderately effective for catalytic regioselective allylic alkylation of crotyl acetate.     

Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol

The conformations of cis‐ ( 1 ) and trans‐cyclopentane‐1,3‐diol ( 2 ) have been studied by ab initio (Gaussian 98) and molecular mechanics (PCMODEL) calculations and by NMR spectroscopy. The calculations gave two low‐energy conformations for ( 1 ), 1A and 1B , both with axial hydroxyl groups. Two conformations with equatorial hydroxyl groups ( 1C and 1D ) were found but with much higher energy (ca 4.0 kcal mol^?1). Five low‐energy conformers were found for 2 . Four were envelope conformations and one a half‐chair. The complete analysis of the 400 MHz ¹H NMR spectra of 1 in a variety of solvents and 2 in chloroform was performed by extensive decoupling experiments, iterative computer analysis and spectral simulation. This gave all the H,H couplings in the molecule, including in 1 a long‐range ⁴J(H,H) coupling between H‐2cis and H‐4,5cis. The ³J(H,H) couplings were used to determine the conformer populations in these molecules. This was initially achieved using the Haasnoot, de Leeuw and Altona equation. to obtain the conformer couplings. It was found that this equation was not accurate for the C·CH₂·CH₂·C fragment in these molecules and the following equation was derived for this fragment from five‐ and six‐ membered cyclic compounds in fixed conformations: (1) The conformer populations were obtained by calculating the conformer couplings which were then compared with the observed couplings. Compound 1 in benzene solution is an approximately equal mixture of conformers 1A and 1B with small (<4%) amounts of 1C and 1D . In the polar solvents acetone and acetonitrile the populations of 1A and 1B are again equal, with 20% of 1C and <2% of 1D . In 2 the major conformers are 2B and 2D with small amounts of 2C , 2E and 2A . These novel findings are considered with previous data on cyclopentanol and cis‐ and trans‐cyclopentane‐1,2‐diol and it is shown that the axial hydroxyl substituent at the fold of the envelope appears to be a major factor in determining the conformational energies of these compounds. Copyright © 2003 John Wiley & Sons, Ltd.     

Dependence of the L-alanyl-L-alanine conformation on molecular charge determined from ab initio computations and NMR spectra

The l-alanyl-l-alanine (AA) molecule behaves differently in acidic, neutral, and basic environments. Because of its molecular flexibility and strong interaction with the aqueous environment, its behavior has to be deduced from the NMR spectra indirectly, using statistical methods and comparison with ab initio predictions of geometric and spectral parameters. In this study, chemical shifts and indirect spin-spin coupling constants of the AA cation, anion, and zwitterion were measured and compared to values obtained by density functional computations for various conformers of the dipeptide. The accuracy and sensitivity of the quantum methods to the molecular charge was also tested on the (mono)-alanine molecule. Probable AA conformers could be identified at two-dimensional potential energy surfaces and verified by the comparison of the computed parameters with measured NMR data. The results indicate that, whereas the main-chain peptide conformations of the cationic (AA+) and zwitterionic (AAZW) forms are similar, the anion (AA-) adopts also another, approximately equally populated conformer in the aqueous solution. Additionally, the NH2 group can rotate in the two main chain conformations of the anionic form AA-. According to a vibrational quantum analysis of the two-dimensional energy surfaces, higher-energy conformers might exist for all three charged AA forms but cannot be detected directly by NMR spectroscopy because of their small populations and short lifetimes. In accord with previous studies, the NMR parameters, particularly the indirect nuclear spin-spin coupling constants, often provided an excellent probe of a local conformation. Generalization to peptides and proteins, however, has to take into account the environment, molecular charge, and flexibility of the peptide chain.     

Stacking effect of polyfluorene on the chemical shift and electron transport

We investigate the structures, NMR chemical shifts, absorption spectra, frontier molecular orbitals, and transition density matrices of pi-stacked polyfluorenes by ab initio calculations. For F1-F4, we consider two different conformations, syn and anti. The simulated 1H NMR chemical shifts are in good agreement with the previous experiment, and the significantly upfielded chemical shifts explain that the fluorene moieties are stacked on each other. It is found that the relative stability for syn and anti conformers is almost equivalent in B3LYP calculations; however, the syn conformer becomes much more stable than the anti conformer in MP2 calculations, which is consistent with the experimental finding that only the syn conformers are relevant. The vertical detachment energy, which is linearly proportional to the ionization potential, shows the same size dependence as the previous experiment. The electron attachment energy decreases exponentially as the size increases, which implies that the electron transport would be possible even for long chains such as F3 and F4. This was evident from the frontier molecular orbitals (HOMO and LUMO). Also, it is found that the syn conformers are very favorable for electron transport through the pi-stacked fluorene moieties.     

Conformational behavior of cis-2-methoxy, cis-2-methylthio, and cis-2-methylselenocyclohexanol: a theoretical and experimental investigation

Studies on the conformational equilibria of 2-methoxy, 2-methylthio, and 2-methylselenocyclohexanol are reported. Dynamic NMR spectroscopy experiments at 203-210 K were performed, which provided the percentages of each conformer in equilibrium. Theoretical calculations using the B3LYP method and aug-cc-pvdz basis set were applied to determine the differences in energy between the conformers. The analysis of the potential energy surface of each conformer showed the presence of two rotamers. Natural bond orbital analysis provided an explanation of which factors are driving the rotamer and conformer preferences.     

Tryptophol cation conformations studied with ZEKE spectroscopy

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system.     

Ground-state conformational equilibrium and photochemical behavior of syn and anti N,N'-dimethyl-N,N'-di-1-naphthylurea protophanes

The structure, spectroscopy, and photochemistry of N,N'-dimethyl-N,N'-di-1-naphthylurea have been investigated and compared to the properties of the corresponding secondary diarylurea N,N'-di-1-naphthylurea and the tertiary mono arylurea N,N,N'-trimethyl-N'-1-naphthylurea. The crystal structures and solution NMR spectra of the tertiary and secondary dinaphthylureas establish that they adopt folded (E,E) and extended (Z,Z) structures, respectively, both in the solid state and in solution. In solution, the tertiary E,E-dinaphthylurea exists as a mixture of syn and anti conformations separated by a barrier of ca. 14 kcal/mol, as determined by variable-temperature (1)H NMR spectroscopy. Computational exploration of the ground-state potential energy surface suggests that the lowest energy pathway for interconversion of the syn and anti conformers requires concurrent rotation about both the nitrogen-naphthalene and the nitrogen-carbonyl single bonds. The tertiary dinaphthylurea exhibits blue-shifted absorption and red-shifted emission attributed to excitonic interactions between the naphthalene rings. The secondary dinaphthylureas and mono naphthylurea have typical naphthalene-like monomer absorption and fluorescence spectra. Dual exponential fluorescence decay is assigned to the two conformers of the tertiary dinaphthylurea. Nonlinear fitting of the fluorescence decay times provides activation parameters for singlet decay of the two conformers. The decay process is attributed to nonsynchronous naphthalene-naphthalene bonding which, in the case of the syn conformer, results in the formation of a [2+2] intramolecular adduct. The preferred E,E conformation and moderate barrier to conformational isomerization make the tertiary dinaphthylurea an attractive building block for larger self-organizing pi-stacked aromatic arrays.     

The crystal structure of 1,5-bis(3,5-dimethyl-2-hydroxybenzyl)-1,5-diazocan-2,6-dione

The study of the molecular geometry of 1,5-bis(3,5-dimethyl-2-hydroxybenzyl)-1,5-diazocan-2,6-dione (2) as determined by X-ray analysis is reported and compared with that of cyclodi-β-alanyl (3). Interestingly there are 1.5 molecules of 2 in the asymmetric unit, showing the two conformations (1 twist-boat- and 0.5 chair-type) with two parallel aromatic rings (from alternate twist-boat conformers) sandwiching the eight-membered ring of the centrosymmetric chair-type conformation. The twist-boat is shown by pmr spectroscopy to be the only significantly populated conformer at low temperature in deuteriodichloromethane solution.     

Synthesis and Conformational Analysis of the Multidrug Resistance-Reversing Agent Hapalosin and Its Non-N-methyl Analog

Hapalosin was initially synthesized by macrolactonization, and a second synthesis was achieved by cycloamidation. In both syntheses, three of the five stereocenters in hapalosin were established by two Brown allylboration reactions. The synthesis of the non-N-Me analog of hapalosin involved chelation-controlled reduction of a gamma-amino-beta-keto ester and cycloamidation. In CDCl(3) at 25 degrees C, synthetic hapalosin exists as a 2.3:1 mixture of conformers, while its non-N-Me analog exists only as a single conformer. (1)H,(1)H-NOESY and computation reveal that the configuration of the amide bond is responsible for the conformations of the two compounds. The major conformer of hapalosin is found to be an s-cis amide, the minor conformer an s-trans amide, and the non-N-Me analog an s-trans amide. Applying distance constraints to protons that exhibit NOESY correlations, computation shows that the major conformer of hapalosin and the non-N-Me analog have very different conformations. By contrast, the minor conformer of hapalosin and the non-N-Me analog have very similar conformations.     

Synthesis and structural characterization of cis- and trans-fused 4a,5,6,7,8,8a-hexahydro-2H,4H-1,3-benzodithiines and their 2-methyl and 2,2-dimethyl derivatives

Both cis- and trans-fused 4a,5,6,7,8,8a-hexahydro-2H,4H-1,3-benzodithiine together with their 2-methyl and 2,2-dimethyl derivatives were prepared as racemates from the appropriate dithiols obtained via multistep syntheses. The products were characterized by (1)H and (13)C NMR, mass spectrometry, and for two of the cis-fused compounds by X-ray diffraction. (1)H,(1)H vicinal coupling constants indicated that all compounds attain chair-chair conformations as their predominant conformations. All three trans-fused isomers exist in totally biased chair-chair conformations and are essentially conformationally locked, whereas the cis-fused compounds are conformationally mobile and can potentially attain either the S-in or the S-out conformation. The interconversion of the conformers is fast on the NMR time-scale at ambient temperatures, but at 213 K 4ar,5,6,7,8,8ac-hexahydro-1,3-benzodithiine freezes out into a 83:17 mixture of the S-in and S-out forms, respectively. Both 2c-methyl-4ar,5,6,7,8,8ac-hexahydro-1,3-dithiine and the dimethyl derivative adopt almost exclusively the S-in conformer at ambient temperature whereas 2t-methyl-4ar,5,6,7,8,8ac-hexahydro-1,3-dithiine is a 5:1 mixture of the S-out and S-in conformers.