吡啶并嘧啶类衍生物抗癌活性与电子结构关系的量子化学研究

采用量子化学密度泛函理论(DFT)方法,在B3LYP/6-31G*基组水平上对吡啶并嘧啶类衍生物进行了几何构型优化和电子结构计算。根据计算结果分析了吡啶并嘧啶类衍生物抗癌活性与电子结构的构效关系,结果表明:吡啶并嘧啶类衍生物抗癌活性与最低空轨道的能量,分子的偶极矩、苯环上5位碳原子的电荷密度及苯环上总电荷密度相关。     

基于过氧键裂解的青蒿素抗疟机制量子化学研基于过氧键裂解的青蒿素抗疟机制量子化学研究

目的研究青蒿素类衍生物的抗疟作用机制。方法电子结构计算在B3LYP/6-31G*水平进行，反应路径计算在HF/STO-3G水平进行。结果过氧桥键是青蒿素类化合物的活性中心，在Fe^{2+影响下过氧键逐渐裂解，两个氧原子与Fe2+以共价键结合形成环状加成产物。结论青蒿素类衍生物可与亚铁血红素形成加成产物。}     

氨基和亚氨基化合物量子化学参数与氢键酸度的相关性研究

应用 Gaussian98W程序分别在 B3 L YP/6-3 11G* *和 HF/6-3 11G* * ( I原子用 3 -2 1G* *基组 )水平优化了 67个氨基和亚氨基化合物的几何结构 ,计算了氨基或亚氨基氢和氮原子的净电荷 QH和 QN、前线分子轨道能级 EHOMO和 ELUMO、系统总能ET和偶极矩 D等量子化学参数。为阐明这些参数与实验氢键酸度∑ αH2 的关系 ,将所得 B3 LYP和 HF两个参数集对 ∑αH2 进行了主成分回归 ( PCR)和逐步回归 ( SWR)分析 ,结果表明 ,B3 L YP高精度参数集的回归模型其拟合优度和预测值均好于 HF的 ;PCR模型预测值与实验值吻合较好 ,而 SWR所建模型因存在多重共线性问题 ,预测值并不可靠。     

棘球蚴病化学药物研究：苯并咪唑类化合物的合成

用3,4-二氨基取代苯分别与氰基氨基甲酸甲酯及取代苯甲醛作用,合成了5(6)-(取代氨基甲酰)苯并咪唑-2-氨基甲酸甲酯(Ⅰ_1～22)和2-取代苯基-5(6)-取代苯并咪唑(Ⅱ_1～12)。经感染棘球蚴的小鼠试验,多数化合物对棘球蚴有不同程度的作用,其中化合物Ⅰ_(10,19)及Ⅱ_1较强,但均不如甲苯咪唑。     

2-烃硫基苯并咪唑的合成及其抗寄生虫活性

苯并咪唑类化合物具有广泛的抗寄生虫病活性,特别是其2-烃硫基取代物有较强的驱虫作用,其中三氯苯达唑(肝蛭净,triclo-bendazole)已经上市,因此我们设计合成了以下八类化合物:1,2-烃硫基-5(6)-丙硫基苯并咪唑(Ⅸ);2,2-烃硫基-5(6)-丙亚砜基苯并咪唑(Ⅹ);3,2-烃硫基-5-(6)-丙砜基苯并咪唑(Ⅺ);4, 2-烃硫基-5(6)-氯苯并咪唑(Ⅻ);5,2-烃硫基-5(6)-苯硫基苯并咪唑■; 6, 2-烃硫基-5(6)-苯甲酰苯并咪唑■; 7,2-烃硫基-5(6)-丙氧基苯并咪唑■;8,2-(对卤亚苄基)噻唑并[3, 2-a]苯并咪唑-3(2 H)-酮■。     

糖苷键水解过渡态类似物-2-(对甲氧苯基)-亚氨基哌啶的电子结构

以糖苷键水解过渡态类似物为半抗原诱发的单克隆抗体,具有像酶那样催化适当底物的作用。本文用Ami法计算研究了2-(对甲氧苯基)-亚氨基哌啶-糖苷键水解过渡类似物电子结构。根据前线轨道特征和电荷分布讨论了此化合物的电子结构,发现其分子活性中心位于C_6和C_9。     

量化参数在抗HIV黄酮类化合物毒性的构效关系中的应用

目的　定量描述具有抗艾滋病毒HIV活性的33种黄酮类化合物的结构与毒性的构效关系。方法　在B3LYP/ 6 -31G 的水平上计算了该类化合物1 4个量子化学参数,并通过逐步回归分析(SRA)进行变量筛选,得到5个重要的量子化学参数,分别是分子最低空轨道能量(ELUMO)、分子硬度(η)、分子极化率(α)、偶极距(μ)和7号碳原子上的净电荷Q7。然后分别采用主成分回归(PCR)和偏最小二乘回归(PLS)方法,通过留一法交叉验证选择潜变量个数,建立具有较好预测能力的定量构效关系(QSAR)模型。结果　两个模型均具有较好的预测能力,但PLS方法得到的模型优于PCR方法,具有更强的预测能力。结论　从建立的QSAR模型可看出各个参数对其毒性的影响,通过改变取代基可降低其毒性,并指导抗HIV低毒性药物的结构设计和研究开发。     

喜树碱衍生物抗肿瘤活性定量构效关系的DFT研究

采用量子化学密度泛函理论(DFT)方法,对喜树碱7位取代衍生物进行几何构型优化和电子结构计算,根据计算结果分析其抗肿瘤活性与电子结构的定量构效关系。结果表明,喜树碱7位取代衍生物抗肿瘤活性与分子总能量、8位和6位碳原子电荷密度及B环总电荷密度相关,其中影响最大的是8位碳原子电荷密度数值。     

氯苯类化合物的电子结构与其对水生物发光细菌毒性关系

应用CNDO/2量子化学方法计算了 11个氯苯类化合物的电子结构 ,并结合相关分析和逐步回归分析方法 ,探讨了氯苯类化合物电子结构与其对发光细菌 (microtox)半致死量负对数 (EC50 )之间的定量关系 ,得到分子最低空轨道 (LUMO)和最高占据轨道 (HOMO)的能量差 (DELH)与EC50 之间的线性方程 :EC50 =9.6 3- 0 .52 9DELH　R =0 .937。结果表明 :DELH值越小 ,即化合物接受电子的能力越强 ,则氯苯化合物对发光细菌的毒性越大 ,据此可预测氯苯化合物的毒性     

6-取代氨基-L-D4G/ddG-5'-单磷酸酯的合成与抗HIV活性研究

目的前期工作发现一些碱基6位胺取代2',3'-双脱氧-2',3'-双脱氢鸟苷(D4G)和2',3'-双脱氧鸟苷(dd G)在体外实验中表现出良好的抗HIV活性,而碱基6位胺取代的L-D4G/dd G却无活性。推测其活性缺失可能与代谢过程中单磷酸化限速步骤有关。鉴于此,作者设计合成了L-D4G/dd G-5'-单磷酸酯,并对其抗HIV活性进行评价。方法本文以L-四乙酰核糖和6-氯-鸟嘌呤为原料,按已有合成方法合成中间体L-6-氯-2',3'-双脱氧-2',3'-双脱氢鸟苷,然后经磷酸酯化、胺取代、催化氢化等反应合成目标化合物。在假病毒评价体系中,以依法韦仑为阳性对照,对目标化合物进行抗HIV活性评价。结果合成了6个L-D4G/dd G-5'-单磷酸酯,抗HIV体外活性评价结果表明,与没有抗病毒活性的前体结构相比,化合物3a、3c、4a、4c的病毒抑制率有所提高。结论作为潜在的核苷抗病毒药物,L-D4G/dd G单磷酸酯前药的结构优化具有进一步深入研究的意义。     

Assignment of the absolute configuration at the sulfur atom of thioridazine metabolites by the analysis of their chiroptical properties: The case of thioridazine 2-sulfoxide

Thioridazine (THD) is a commonly prescribed phenotiazine neuroleptic drug, which is extensively biotransformed in the organism producing as main metabolites sulfoxides and a sulfone by sulfur oxidation. Significant differences have been observed in the activity of the THD enantiomers as well as for its main metabolites, and enantioselectivity phenomena have been proved in the metabolic pathway. Here the assignment of the absolute configuration at the sulfur atom of enantiomeric THD-2-sulfoxide (THD-2-SO) has been carried out by circular dichroism (CD) spectroscopy. The stereoisomers were separated by HPLC on Chiralpak AS column, recording the CD spectra for the two collected enantiomeric fractions. The theoretical electronic CD spectrum has been obtained by the TDDFT/B3LYP/6-31G*, as Boltzmann averaging of the contributions calculated for the most stable conformations of the drug. The comparison of the simulated and experimental spectra allowed the absolute configuration at the sulfur atom of the four THD-2-SO stereoisomers to be assigned. The developed method should be useful for a reliable correlation between stereochemistry and activity and/or toxicity.     

Nitrosative guanine deamination: ab initio study of deglycation of N-protonated 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazoles

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazoles (1) (R at N1) have been discussed as possible intermediates in nitrosative guanine deamination, which are formed by dediazoniation and deprotonation of guaninediazonium ion. The parent system 1 (R = H) and its N1 derivatives 2 (R = Me) and 3 (R = MOM) are considered here. Protonation of 1-3, respectively, may occur either at the cyano-N to form cations 4 (R = H), 6 (R = Me), and 8 (R = MOM) or at the imino-N to form cations 5 (R = H), 7 (R = Me), and 9 (R = MOM), respectively. This protonation is the first step in the acid-catalyzed water addition to form 5-cyanoimino-imidazole-4-carboxylic acid, which then leads to oxanosine. There also exists the option of a substitution reaction by water at the R group of 6-9, and this dealkylation forms N-[4-(oxomethylene)-imidazol-5-yl]carbodiimide (10) and N-[4-(oxomethylene)-imidazol-5-yl]cyanamide (11). In the case of DNA, the R group is a deoxyribose sugar, and attack by water leads to deglycation. To explore this reaction option, the S(N)1 and S(N)2 reactions of 6-9 with water were studied at the MP2/6-31G*//RHF/6-31G* and CCSD/6-31G*//RHF/6-31G* levels, with the inclusion of implicit solvation at the IPCM(MP2/6-31G*)//RHF/6-31G* level, and the electron density distributions of tautomers 1, 10, and 11 were analyzed. The low barriers determined for the MOM transfer show that the deglycation could occur at room temperature but that the process cannot compete with water addition.     

Assessing the protonation state of drug molecules: the case of aztreonam

Herein we examine the viability of physicochemical approaches based on standard computational chemistry tools to characterize the structure and energetics of flexible drug molecules with various titratable sites. We focus on the case of the monobactam antibiotic aztreonam, whose structure and physicochemical properties have been ascribed to several tautomeric forms, although it is still unclear which protonation states are responsible for its biological activity. First, we experimentally determined the pKa values for aztreonam over the pH range 0.8-7.0 using both 1H NMR and 13C NMR spectroscopy. Second, we carried out quantum chemical calculations on snapshots extracted from classical molecular dynamics simulations. Various levels of approximation were used in the energy calculations: ONIOM(HF/3-21G*:AMBER) for geometry relaxation, B3LYP/6-31+G** for electronic and electrostatic solvation energies, and molecular mechanics for attractive dispersion energy. The value of the free energy of solvation of a proton was treated as a parameter and chosen to give the best match between calculated and experimental pKa values for small molecules. Overall, this computational scheme can give satisfactory results in the pKa calculations for drug molecules.     

Theoretical study of the SNV reaction of trichloroethylene (TCE) and CH3S- as a model for glutathione conjugation of TCE

Trichloroethylene (TCE), a major environmental pollutant, is activated to mutagenic and nephrotoxic intermediates through a glutathione (GSH) conjugation pathway. Three product isomers of GSH-TCE conjugation, having potentially different toxicities, are theoretically possible: cis- or trans-S-(1, 2-dichlorovinyl)glutathione (cis- or trans-1,2-DCVG, respectively) or 2,2-DCVG. This study involved application of ab initio molecular orbital theory to computing potential energy profiles (PEPs) and predicting product outcome of the reaction of CH3S- with TCE as a model for GSH-TCE conjugation in biological systems. A goal of this study was to determine the extent to which a body of chemical knowledge pertaining to nucleophilic vinylic substitution (SNV) reactions, of which the GSH-TCE conjugation is a representative example, is relevant to this biological conjugation problem. PEPs were computed for all studied species at the HF/6-31+G level of theory; electron correlation effects were estimated at the MP2/6-31+G and MP4/6-31+G levels, and the influence of solvation was estimated using the PS-GVB solvation model. Multiple proposed reaction pathways were considered, including conjugation at the C1 or C2 site on TCE, by in-plane (sigma) or out-of-plane (pi) approach of the nucleophile. Some aspects of the MP2 and HF PEPs were found to differ significantly. However, on the basis of comparison of activation barriers, calculations at all levels of theory predict preference for C2 conjugation over C1 conjugation and formation of the trans-1,2-DCVM product over the cis-1,2-DCVM product. These predictions are consistent with GSH-TCE conjugation results from in vivo experiments. In contrast, relative product energies appear to be a poor indicator of the product outcome for this system. Hence, theoretical consideration of the reaction chemistry in the vicinity of the site of nucleophilic addition appears to be necessary and sufficient to predict the outcome of the enzyme-mediated GSH-TCE conjugation.     

Electronic structure and UV spectrum of fenofibrate in solutions

The structure and UV spectra of fenofibrate have been evaluated in gas phase and in solutions using time dependent density functional theory (TDDFT) method at the B3LYP/6-31G(d), B3LYP/6-311G(d,p) and B3LYP/6-311++G(d,p) levels. The solvent effects have been taken into account based on the polarizable continuum model (PCM). The computed results appear that the introduction of dielectric medium has slight effect on the molecular geometry of fenofibrate. There is one allowed excited state presenting the strongest oscillator strength in the UV region, which is associated with the HOMO-->LUMO and HOMO-1-->LUMO transition both in gas phase and in solutions. The prediction of the lambda(max) in THF, ethanol and DMSO is 285 nm, 286 nm and 287 nm, respectively, which are in a good agreement with experimental data of 284 nm, 285 nm and 288 nm.The results demonstrate that TDDFT-PCM is a useful tool for study of the electronic absorption in solutions.     

Early Prediction of Pharmaceutical Oxidation Pathways by Computational Chemistry and Forced Degradation

PURPOSE: To show, using a model study, how electronic structure theory can be applied in combination with LC/UV/MS/MS for the prediction and identification of oxidative degradants. METHODS: The benzyloxazole 1, was used to represent an active pharmaceutical ingredient for oxidative forced degradation studies. Bond dissociation energies (BDEs) calculated at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level with isodesmic corrections were used to predict sites of autoxidation. In addition, frontier molecular orbital (FMO) theory at the Hartree-Fock level was used to predict sites of peroxide oxidation and electron transfer. Compound 1 was then subjected to autoxidation and H2O2 forced degradation as well as formal stability conditions. Samples were analyzed by LC/UV/MS/MS and degradation products proposed. RESULTS: The computational BDEs and FMO analysis of 1 was consistent with the LC/UV/MS/MS data and allowed for structural proposals, which were confirmed by LC/MS/NMR. The autoxidation conditions yielded a number of degradants not observed under peroxide degradation while formal stability conditions gave both peroxide and autoxidation degradants. CONCLUSIONS: Electronic structure methods were successfully applied in combination with LC/UV/MS/MS to predict degradation pathways and assist in spectral identification. The degradation and excipient stability studies highlight the importance of including both peroxide and autoxidation conditions in forced degradation studies.