光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

光系统Ⅱ抑制剂-顺式氰基丙烯酸酯化合物的三维构效关系和电子结构研究

以距离比较法所获得的顺式氰基丙烯酸酯化合物的活性构象为模板,对39个该类化合物采用比较分子场方法进行了三维构效关系的研究.结果表明,所获得的药效团模型具有很好的预测能力.同时采用量子化学的方法对活性构象模板分子电子结构作了讨论.     

光系统Ⅱ抑制剂: 顺式氰基丙烯酸酯化合物的 三维构效关系的电子结构研究

以距离比较法所获得的顺式氰基丙烯酸酯化合物的活性构象为模板,对39个该类化合物采用比较分子场方法进行了三维构效关系的研究。结果表明,所获得的药效团模型具有很好的预测能力。同时采用量子化学的方法对活性构象模板分子电子结构作了讨论。     

人类免疫缺陷病毒整合酶二酮酸类抑制剂的三维药效团构建

应用遗传算法相似性程序(GASP), 以作用于I型人类免疫缺陷病毒(human immun-odeficiency virus type 1, HIV-1)整合酶(IN)的二酮酸类(diketoacids, DKAs)抑制剂构建药效团模型. 所选训练集分子均具有可靠的类药性特征及DKAs药效团特征. 尝试将抑制剂与药效团叠合后的构象和抑制剂与IN的对接构象进行叠合, 得到药效团模型与分子对接构象中IN残基的相对位置, 并基于抑制剂的药效团模型特征与周围IN氨基酸残基位置的匹配情况进行药效团特征的修改. 所得最优药效团由1个疏水特征、3对氢键特征和1个氢键供体特征组成. 该药效团的命中物质量(goodness of hit, GH)为0.56, 产出率(Y)达63.6%, 假阳性率(FP)为0.41%. 该药效团具有较好的置信度, 产出率较高而假阳性率较低, 可用于数据库搜索发现新的具有DKAs药效团特征的活性化合物, 也可为先导化合物的改造提供帮助.     

基于药效团模型的DHODH抑制剂构效关系研究

利用药效团模型研究二氢乳清酸脱氢酶(Dihydroorotate dehydrogenase,DHODH)抑制剂的构效关系,为DHODH抑制剂的虚拟筛选提供新的方法.以31个具有DHODH抑制活性的化合物为训练集化合物,半数抑制浓度(IC50)范围为7~63000 nmol/L,利用Catalyst/HypoGen算法构建DHODH抑制剂药效团模型,通过对训练集化合物多个构象进行叠合,提取药效团特征及三维空间限制构建药效团模型.利用基于CatScramble的交叉验证方法及评价模型对已知活性化合物的活性预测能力,确定较优药效团模型.模型包含1个氢键受体、3个疏水中心,表征了受体配体相互作用时可能发生的氢键相互作用、疏水相互作用和π-π相互作用,4个药效特征在三维空间的排列概括了DHODH抑制剂产生活性的结构特点.所得较优模型对训练集化合物及测试集化合物的计算活性值与实验活性值的相关系数分别为0.8405和0.8788.利用药效团模型对来源于微生物的系列化合物进行虚拟筛选,筛选出59个预测活性较好的化合物,可作为进一步药物研发的候选化合物.     

虚拟活性化合物的自动生成

虚拟活性化合物的自动生成是从药效团和预先设定的结构碎片出发,通过碎片选择、碎片组装和柔性构象搜索来获得虚拟活性结构。经过对HIV-1蛋白酶抑制剂药效团进行虚拟活性化合物生成,得到了16个虚拟活性化合物,通过构象分析发现生成的化合物满足药效团的限制条件。说明这一方法能够有效的生成虚拟活性结构,与药效团检索结果对比发现生成的虚拟活性结构新颖易于合成。     

酪氨酸激酶抑制剂的柔性原子受体模型方法研究

用柔性原子受体模型方法对一系列嘧啶类衍生物酪氨酸激酶抑制剂进行了3D－ QSAR研究，建立了相关性很好的模型，这些模型对测试集中化合物活性的预测结果 表明其具有较强的预测能力。柔性原子受体模型方法还给出了虚拟的受体模型，表 明了受体和配体之间可能的相互作用，包括两个氢键相互作用、一个疏水作用和一 个硫－芳香相互作用，这与Novartis的药效团模型非常一致。     

药效团检索设计新的HIV-1蛋白酶抑制剂

通过对自建的未开发化合物三维结构库进行药效团检索,得到了4个对HIV-1蛋白酶抑制活化的化合物,通过构象分析发现包含药效团的构象处于优势构象,而且4个结构都含有带两个邻位羟基的苯环和一个间位羰基的药效团以及公共子结构。通过计算发现它们的疏水参数都很小。在考虑满足包含药效团的结构特征和有适中的疏水参数两个因素的前提下,设计出了新的具有潜在抑制HIV-1蛋白酶活性的化合物。它们的结构都比检索得到的四个化合物更为简单,因此易于合成。     

芳基磺酰胺类丙酮酸激酶M2激动剂的基于多复合物的药效团模型和定量构效关系

丙酮酸激酶M2(PKM2)是肿瘤治疗中最具发展潜力的靶点之一. 本文以一系列丙酮酸激酶M2-激动剂复合物的晶体结构为基础, 采用基于多复合物的药效团(MCBP)方法产生了PKM2 的药效团模型. 并使用该药效团模型产生了62个芳基磺酰胺类PKM2激动剂的活性构象和分子叠合, 通过三维定量构效关系(3D-QSAR)方法研究了该类PKM2激动剂与PKM2蛋白的相互作用, 并建立了相关预测模型. 比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA)模型的交互验证相关系数q²分别为0.545 和0.653, 非交互验证相关系数r²分别为0.966和0.987. 本研究为进一步结构优化、设计和合成新型的PKM2激动剂提供了理论依据.     

5-羟色胺(5-HT)和去甲肾上腺素(NE)重摄取抑制剂药效团模型的建立及比较分析

近年来的研究表明, 去甲肾上腺素(NE)能系统和5-羟色胺(5-HT)能系统可能共同参与了抑郁症的发病机制. 采用Catalyst软件的Hypogen方法, 利用22个不同结构类型的5-HT重摄取抑制剂和19个不同结构类型和活性的NE重摄取抑制剂分别建立了5-HT药效团模型和NE药效团模型, 它们的相关系数分别为0.935, 0.844, 这表明所得到的模型能较好地表征重摄取抑制剂化合物的特征; 此外, 我们还选择了四种不同活性的预测集分别对所建立的药效团模型进行检验, 结果表明所建立的药效团模型具有较好的预测能力. 对这两个药效团模型进行了比较分析, 其结果可以为设计高活性的双重5-HT和NE重摄取抑制剂提供依据.     

Single configuration interaction study on conjugated betainic chromophores based on DFT optimized geometries

The structure of a series of heterocyclic betaines was calculated by methods of density functional theory (DFT). The charge distribution and bond characteristics of these compounds were analyzed by Weinhold’s natural bond orbital analysis (NBO) and by natural resonance theory (NRT). In order to probe the aromatic character of the ring fragments, Schleyer’s nucleus-independent chemical shifts (NICSs) were calculated by GIAO-RHF. Ab initio single configuration interaction calculations (SCI) correctly predict intense π→π* transitions at low energies, but the transition energies of the color bands are overestimated. Torsion around the interfragmental bond increases the charge separation between the molecular fragments and the dipole moment. The molecular fragments become increasingly aromatic. The absorption wavelengths increase on torsion while the oscillator strengths decrease.     

反式和顺式含磷稠环6,13-二硫丙基-5,12-二氧-6,13-二硫羰基-6a,7,13a,14-四氮-6,13-二磷杂二苯并(a,h)蒽烷的晶体结构

采用X射线分析测定了标题化合物的晶体结构和分子结构。化合物C_(20)H_(22)-O_2N_4P_2S4(1)为反式构型,M_r=540.63,正交晶系,空间群Pcab,a=7.255(2),b=18.297(3),c=18.576(2),V=2465.9 ~3,Z=4,D_c=1.456g/cm~(-3),最终偏离因子R=0.058,R_ω=0.049;化合物(2)为顺式构型,单斜晶系,空间群Ic,a=14.649(5),b=7.009(2),c=22.694(8),β=100.60(3)°,V=2290.1 ~3,Z=4,D_c=1.643g/cm~(-3),最终偏离因子R=0.061,R_ω=0.065。晶体结构测定结果表明,这对顺反异构体的构象明显不同:反式异构体的分子本身有对称中心且与晶体学对称中心重合,氧,氮,磷杂六员环为椅式构象,磷硫单键为轴向键,磷硫双键为平伏键;顺式异构体的分子本身无对称中心,两个氧氮磷杂六员环分别为椅式和船式构象,环上的磷硫单键为平伏键,磷硫双键为轴向键,与反式异构体恰恰相反。     

Crystal Structure of Trans-2-Amino-3-Cyano-4-(3',4'-Methylenedioxyphenyl)-1-Phenyl-2-Cyclopentene-r-1-ol

1INTRODUCTIONIntheearlyseventiesthreegroupsofinvestigators('--"establishedthatlow--va-lenttitanium,preparedbythereactionofstrongreducingagentsontitaniumtrichlo-rideortitaniumtetrachlorideintetrahydrofuran,canabstractoxygenfromketonesoraldehydes,leadingtotheformationofolefins.Anincreasinginterestinthereac-tioninducedbylow--valenttitaniumreagentsisobservedandalargenumberoffunc-tionalgroupscanbereducedt4--6).However,thereactionoflow-valenttitaniumreagentwith4,4--dicyano--1,3--diaryl--l-butano…     

Ni0-catalyzed cyclotrimerization of 1,3-butadiene: a comprehensive density functional investigation on the origin of the selectivity

A comprehensive theoretical investigation of the mechanism for the Ni(0)-catalyzed cyclotrimerization of 1,3-butadiene by the [Ni(0)(eta(2)-butadiene)(3)] active catalyst complex is presented by employing a gradient-corrected DFT method. All critical elementary processes of the catalytic cycle have been scrutinized, namely, oxidative coupling of two butadienes, butadiene insertion into the allyl-Ni(II) bond, allylic isomerization in both octadienediyl-Ni(II) and dodecatrienediyl-Ni(II) species, and reductive elimination under ring closure. For each of these elementary steps several conceivable routes and also the different stereochemical pathways have been probed. The favorable route for oxidative coupling start from the prevalent [Ni(0)(eta(2)-butadiene)(3)] form of the active catalyst through coupling between the terminal non-coordinated carbon atoms of two reactive eta(2)-butadiene moieties; this is assisted by an ancillary butadiene in eta(2)-mode. The initial eta(3),eta(1)(C(1))-octadienediyl-Ni(II) product is the active precursor for subsequent butadiene insertion, which preferably takes place into the eta(3)-allyl-Ni(II) bond. The insertion is driven by a strong thermodynamic force. Therefore, the dodecatrienediyl-Ni(II) products, with the most favorable bis(eta(3)-allyl),Delta-trans isomers in particular, represent a thermodynamic sink. Commencing from a preestablished equilibrium between the various bis(eta(3)-allyl),Delta-trans forms of the [Ni(II)(dodecatrienediyl)] complex, the major cyclotrimer products, namely all-t-CDT, c,c,t-CDT and c,t,t-CDT, are formed along competing paths by reductive elimination under ring closure, which is shown to be rate-controlling. The all-c-CDT-generating path is completely precluded by both thermodynamic and kinetic factors, giving rise to negligibly populated bis(eta(3)-allyl),Delta-cis precursor isomers. The regulation of the selectivity of the CDT formation as well as the competition between the two reaction channels for generation of C(12)- and C(8)-cycloolefins is elucidated.     

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C−N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a–2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C−N), which is why the six-membered ring lactams C−N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S−H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C−N cleavage in the five-membered ring lactams especially in the 1–2 derivatives (17.58 kcal mol⁻¹). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.     

The angle of twist between the two phenyl rings in the nematic liquid crystal 4-n-pentyl-4'-cyanobiphenyl

The NMR spectrum of the protons in the biphenyl group of 4-n-pentyl-4'-cyanobiphenyl (5CB), was obtained by Sinton et al. (1984, Molec, Phys., 53, 333) and analysed by them to give an angle of twist, φ_min, between the normals to the two phenyl rings of 30 ± 2°. Their analysis made the assumption that V(φ), the potential for rotation about the inter ring bond, is such that only the structures with the minimum energy need be considered when calculating averaged dipolar couplings. Re-analysis of their data by a method which allows for the whole of V(φ) to be sampled when averaging the dipolar couplings yields a value for φ_min of 38.4 ± 0.1°.     

Natural bond orbital analysis and vibrational spectroscopic studies of H-bonded N,N′-diphenylguanidinium nitrate

NIR-FT Raman and FT-IR spectra of the crystallized biologically active molecule N,N′-diphenylguanidinium nitrate (DGN) have been recorded and analyzed using quantum chemical computations based on density functional theory. The extraordinary basicity and strong stability of this novel bioactive compound has been discussed as the consequence of resonance stabilization leading to Y-aromaticity and hydrogen bonding. This peculiar Y-delocalization character of DGN is well reflected in the optimized geometry and bond order (BO) calculations. The observance of the equality of C–N bond lengths in the protonated species indicates delocalization of the π-electron system. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of strong network of inter molecular hydrogen bonds. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of DGN calculated by second order perturbation theory have been studied extensively in comparison with the values of the neutral species. The observed characteristic ring vibrations are well fit with the theoretical values calculated at B3LYP/6-31G* level.     

Modern valence-bond description of the electronic structure of benzocyclobutadiene

The ground state of benzocyclobutadiene, a bicyclic molecule with 8π electrons containing a benzene and a cyclobutadiene ring, is studied by means of modern valence bond (VB) theory in its spin-coupled (SC) form and the complete-active-space self-consistent field (CAS SCF) approach. The CAS SCF wave function is used to optimize the geometry, and SC theory—to obtain a well-correlated and easy to visualize and understand model of the active space hosting the π electrons. It is shown that the π system of the ground state of benzocyclobutadiene can be described with sufficient accuracy as a combination of the π systems of a distorted benzene ring and an isolated double bond. Each of the eight SC orbitals is found to be well-localized about one carbon atom only, with small distortions toward its nearest neighbors. The analysis of the optimal active-space spin-coupling pattern within the SC wave function for benzocyclobutadiene shows unambiguously that this molecule inherits neither the aromatic nor the antiaromatic character of its cyclic components, and it is most appropriate to regard it as nonaromatic. © 1996 John Wiley & Sons, Inc.     

A molecular mechanics force field for the cobalt corrinoids

A force field for the cobalt (III) corrinoids (derivatives of vitamin B₁₂) for use with a modified version of the molecular mechanics program 2(87) has been developed empirically around 19 cobalt corrinoid crystal structures. Bond lengths, bond angles and torsional angles are reproduced with r.m.s. differences of 0.01 Å, 2.4 °, and 4.2 °, respectively, within the standard deviation of the mean of these parameters found in the solid state. The axial ligand occupying the lower coordination site in the cobalamins, 5,6-dimethylbenzimidazole, is shown to have very limited rotational freedom and is constrained by the downward-pointing b and d propionamide side chains of the corrin ring. Strain-energy profiles for rotation of the side chains of the corrin ring show the existence of several local energy minima and this explains the observed variability in the orientations of these side chains in the solid state. The known change in conformation which occurs in the C ring when the e side chain is epimerized from the lower to the upper face of the corrin ring in cyano-13-epicobalamin is correctly predicted, provided the starting conformation of the C ring is unbiased. A study of cyano-8-epicobalamin indicates that an analogous conformational change does not occur in the B ring and the epimerized d side chain assumes an equatorial orientation relative to the corrin ring. Parameters for the Co---C bond in alkylcobalamins were developed and the structure of methyl- and adenosylcobalamin are accurately reproduced. An examination of the strain energy consequences of rotation of the adenosyl ligand about the Co---C bond identifies a number of low-energy conformations at least two of which, in which adenosyl lies over the “southern” and “eastern” portions of the corrin ring, respectively, have been previously deduced from NMR observations. Coordinated neopentyl in neopentylcobalamin is much more hindered to rotation about the Co---C bond and the lowest conformation finds two γ(C) atoms straddling the upwardly projecting C46 methyl group of the corrin.     

Asymmetric annellation effects—IV Dibenzacenes

The asymmetric annellation effects and the shift difference rule are explained on the basis of the two schemes A and B. The asymmetry of the annellation effects in passing from acenes to 1:2-benz-, and 1:2,3:4-dibenzacenes support the scheme B involving the view that the transition of a cyclic conjugated polyene into a benzenoid ring produces a violet spectral shift. Another set of asymmetric annellations is found in the heteronuclear dibenzacenes. This series can be started from ethylene. The merits of a symplified valence bond theory are considered for the interpretation of asymmetric annellation effects. The assumption of two transferable electrons capable of migrating through the rings of an acene leads to two π-electron levels for benzene with 4 π-electrons in two mobile double bonds in the lower level and 2 π-electrons moving freely about the ring and not belonging to any double bond.