On the possible reaction pathway for the acylation of AChE-catalyzed hydrolysis of ACh: Semiempirical quantum chemical study

The acylation process in the acetylcholinesterase (AChE)-catalyzed hydrolysis of the neurotransmitter, acetylcholine (ACh), has been determined with the semiempirical quantum chemical calculation method AM1 using the model molecules extracted from the X-ray crystal structure of Torpedo Californica AChE. For the sake of identifying the microfeatures of the mechanism of this reaction, two types of possible mechanisms, stepwise mechanism and cooperative mechanisms, were proposed and studied with AM1 methods. All the model molecules for the possible reactants, intermediates, transition states, and products in the reaction pathways of the two mechanisms were obtained. Energy profiles, the structural properties of the transition states, indicate that the acylation of AChE-catalyzed hydrolysis of ACh adopts the cooperative mechanism, i.e., the proton transfer from Ser220 of AChE to His440 occurs simultaneously with the nucleophilic attack of Ser200 to the carbonyl carbon atom of ACh. This result is in agreement with the kinetic data and the secondary isotope effects of AChE-catalyzed reactions. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 515–525, 1998     

Electronic structure and reactivity of guanylthiourea: A quantum chemical study

Electronic structure analysis of guanylthiourea (GTU) and its isomers has been carried out using quantum chemical methods. Two major tautomeric classes (thione and thiol) have been identified on the potential energy (PE) surface. In both the cases conjugation of pi‐electrons and intramolecular H‐bonds have been found to play a stabilizing role. Various isomers of GTU on its PE surface have been analyzed in two different groups (thione and thiol). The interconversion from the most stable thione conformer ( GTU‐1 ) to the most stable thiol conformer ( GTU‐t1 ) was found to take place via bimolecular process which involves protonation at sulfur atom of GTU‐1 followed by subsequent C? N bond rotation and deprotonation. The detailed analysis of the protonation has been carried out in gas phase and aqueous phase (using CPMC model). Sulfur atom (S1) was found to be the preferred protonation site (over N4) in GTU‐1 in gas phase whereas N4 was found to be the preferred site of protonation in aqueous medium. The mechanism of S‐alkylation reaction in GTU has also been studied. The formation of alkylated analogs of thiol isomers (alkylated guanylthiourea) is believed to take place via bimolecular process which involves alkyl cation attack at S atom followed by C? N bond rotation and deprotonation. The reactive intermediate RS(NH₂)C? N? C(NH₂)₂⁺ belongs to the newly identified ^⊕N(←L)₂ class of species and provides the necessary dynamism for easy conversion of thione to thiol. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

平面五元水分子簇的量子化学研究

选用Gaussian03的B3LYP/6-31G(d,p)、DMol3的BLYP/DNP和deMon的BLYP/TZVP等方法计算了甲烷水合物(结构-1)中平面五元水分子簇的结合能和氢键能,作了基组重叠误差(BSSE)和色散能(dispersion)的修正,估算了次级相互作用的贡献.在DMol3程序中使用了大型数值基组DNP,将基组重叠误差降至最低.在Gaussi-an03的B3LYP/6-31G(d,p)计算中,采用平衡法(Counterpoise)校正基组重叠误差.两种计算方法给出了一致的结果,证实了在使用6-31G(d,p)基组时,一对水分子在平衡距离的基组重叠误差高达8 kJ/mol.为估算色散能的贡献,使用了新近发展的包含色散能的密度泛函的DFT程序deMon计算了五元水分子簇.用多种方法计算出了经基组重叠误差和色散能修正的五元水分子簇的分子间结合能和氢键能的较为精确的势能超曲面,为甲烷和其他气体水合物的分子动力学模拟提供了依据.     

Quantum chemical study of oxidation processes in Cu-phthalocyanine

Quantum chemical calculations reproduced quite well the experimental infrared spectra of CuPc and CuNO₃Pc · HNO₃. The agreement in the changes of line intensities during the oxidation supports the idea of ligand oxidation. This result is in agreement with the Mulliken population analysis.     

Quantum chemical investigation on solvation of Ginkgolides

ＧｉｎｋｇｏｉｓａｋｉｎｄｏｆｔｒａｄｉｔｉｏｎａｌＣｈｉｎｅｓｅｈｅｒｂｓｗｈｉｃｈｈａｄｂｅｅｎｕｓｅｄｆｏｒｄｉｓｅａｓｅｔｒｅａｔｍｅｎｔｅｖｅｎｓｉｎｃｅ5000ｙｅａｒｓａｇｏｉｎＣｈｉｎａ.Ｉｎｍｏｄｅｒｎｍｅｄｉｃｉｎｅ,ｇｉｎｇｋｏｈａｓｂｅｅｎｔａｋｅｎａｓａｍｅｄｉｃｉｎｅｓｅｒｉｏｕｓｌｙｄｕｅｔｏｔｈｅｆａｃｔｔｈａｔｉｔｃａｎｂｅｕｓｅｄｔｏｔｒｅａｔａｌｏｔｏｆｄｉｓｅａｓｅｓｓｕｃｈａｓａｓｔｈｍａａｎｄｔｒａｃｈｅｉｔｉｓ.Ｐｈａｒｍａｃｏｌｏｇｉｃａｌｓｃｒｅｅｎｉ…     

Tautomerism of peroxyacetic acid derivatives: a quantum chemical study

The electronic and molecular structures and the relative stabilities of organic peracids X=C(R)-COOH and their cyclic tautomers, dioxiranes

Open image in new window

, with R = Me, CF₃; X = O, NH, were studied using the ab initio Hartree-Fock method and the density functional theory (B3LYP version) as well as at the MP2-MP4 Møller-Plesset levels of perturbation theory. Geometry optimization was performed by the UHF and B3LYP methods with the 6-31G** basis set and at the MP2/cc-pvtz level of theory. The acyclic form of the peracid is more stable than the cyclic dioxirane form irrespective of the nature of the substituent. The energy difference between these tautomers increases as the CF₃ and NH groups are replaced by Me and O, respectively. Parameters of the activation barrier to tautomeric conversion increase in parallel with enhancement of the electron-accepting properties of both substituents. The transition state of tautomeric interconversion, which is topologically similar to the acyclic structure of the carbonyl oxide derivative R(HX)C=O⁺-O^?, was found and characterized taking peroxyacetic acid as an example. The characteristic features of the transition state are an intramolecular “multicenter” H-bond and the charge distribution that is inconsistent with the canonical structure mentioned above. An appropriate reaction coordinate for the transformation of the quasi-tetrahedral dioxirane structure into a planar peroxyacetic acid structure is provided by the dihedral angle. Deprotonated anionic systems are characterized by much smaller differences between the relative stabilities of the open and closed forms of isomers and by much lower activation barriers to isomeric conversions.

     

Quantum chemical study of complexation of trimethylaluminum with chlorine-containing solvents

Complexation of trimethylaluminum with chlorine-containing organic solvents has been studied in an MP2/6-31G(d, tp) approximation. Trimethylaluminum can form complexes with dichloromethane and dichloroethane. For 1:1 and 2:1 complexes, the geometrical and thermodynamic parameters have been determined. For 2:1 complexes, two orientations of trimethylaluminum relative to the chloroalkane molecule are most favorable. Thermodynamic parameters of dimerization and complexation reactions have been studied for reactions of trimethylaluminum with dichloromethane and dichloroethane. For trimethylaluminum, dimerization was found to be preferable to complexation.     

Theoretical studies of sulbactam: Reactions after acylation

DFT methods were used on the model molecular to determine the mechanism of β‐lactamase inhibitor. The results show that the thiazole ring can be opened as well as β‐lactam ring. The thiazole ring‐open product can be formed via β‐lactam ring‐open product or tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. The sulforious form products may be transformed into sulfonyl ones. Water or hydroxyl group in residues on active site will help lower the activation energy of above reactions, and if structure permitted, they also effect the route selection of whole reaction system. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Quantum chemical study of aromatic diamine and dianhydride reactivities in acylation reactions

Semi-empirical calculations of isolated diamines and model anhydrides and of their interaction energy, ΔE, have been made. Reactivity indices of diamines and dianhydrides (atom charges, characteristics of frontier orbitals) have been found. Analysis of the ΔE components has shown that chemical structure of diamines affects mainly electrostatic and charge transfer contributions to ΔE. Chemical structure of diahnydrides influences most significantly charge transfer component. Results of the ΔE calculation have substantiated the choice of reactivity indices.     

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.     

Mechanism and structural aspects of thermal Curtius rearrangement. Quantum chemical study

The electronic and geometric structures of formyl, acetyl, and benzoyl azides were studied and fragments of the potential surfaces for the thermal Curtius rearrangement of these azides into the corresponding isocyanates were calculated by density functional theory at the PBE/TZ2P level. Acyl azides adopt two stable, conformations syn and anti, with respect to the C-N bond. The syn conformers are more stable than their anti analogs. The activation energies of the syn-anti isomerization in the series under study are 9.4, 7.0, and 9.2 kcal mol⁻¹, respectively, and the activation energies of the reverse reaction are 8.5, 6.1, and 2.5 kcal mol⁻¹. The rearrangement of syn-acyl azides is a one-step process, in which elimination of N₂ occurs synchronously with the rearrangement of atoms and bonds to form isocyanates. The activation energies of the rearrangements of syn-HC(O)N₃, syn-MeC(O)N₃, and syn-PhC(O)N₃ are 28.0, 32.9, and 34.5 kcal mol⁻¹, respectively. The rearrangement of the anti conformers of the above-mentioned azides involves the formation of singlet acylnitrene. The activation energies of the latter process are 34.6, 32.9, and 32.3 kcal mol⁻¹, respectively. The activation energies of the rearrangement of acylnitrenes into isocyanates are 20.9, 18.9, and 13.6 kcal mol⁻¹, respectively. The energy characteristics of the process and the structural data for the starting compounds, final products, and transition states provide evidence that the thermal Curtius rearrangement occurs predominantly by a concerted mechanism. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2200–2209, October, 2005.     

Quantum chemical studies on antimalarial of artemisinin (qinghaosu) derivatives

In this paper theoretical studies were performed on artemisinin (qinghaosu) derivatives with semiempirical quantum chemical methods AMI and PM3. The antimalarial activity -logC has an obvious correlation with the net charge of C(16) and bond orders of bonds O(1)-C(10), O(2)-C(6), O(1)-O(2) and O(5)-C(16). According to the calculation results, we derived structure-activity relationship, presented the probable pharmacophore of qinghaosu derivatives and the interaction fashion between the drugs and the plasmodium receptor.     

Quantum chemistry study on the mechanism of the reaction between ozone and 2,3,7,8‐TCDD

Despite of its fundamental importance, the mechanism of the reaction between ozone and dioxins are still lack detailed investigation so far. It is well-known that quantum chemical calculation is a well-established method for investigating chemical reactions. In this article, quantum chemical calculation was employed to investigate the mechanism of the reaction between ozone and dioxins, as exemplified by 2,3,7,8-TCDD. The theoretical study showed that, 2,3,7,8-TCDD was gradually destructed by ozone via six cleavages of the CC bonds. All the six cleavages of the CC bonds were calculated and discussed in detail based on the theoretical calculations by the UB3LYP/6-31G(d) method. At the same time, the energies of stationary points along the reaction process were calculated by the UMP2/6-311g(d,p)//UB3LYP/6-31G(d) method and the activation energy was obtained. The obtained activation energy was 12.25 kcal/mol, which was lower than that of the reaction between benzene and O₃(16.64 kcal/mol). This indicated that, by comparison with benzene, 2,3,7,8-TCDD could be more efficiently destructed by O₃. The reason for this result was also discussed. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Quantum chemical study on the thermal Diels-Alder reaction of cyclohexadiene and methyl crotonate

AM1 molecular orbital method using the unrestricted Hartree-Fock(UHF) calculations has been applied to investigate the thermal reaction of cyclohexadiene and methyl crotonate. The calculated results indicate that the thermal Diels-Alder reaction proceeds to product through the concerted path and two radical pathways.     

Quantum chemical studies on the tautomerism of some potentially tautomeric aminoindazole derivatives

The aqueous phase AM1, PM3, and PM5 calculation data had indicated that when a potentially tautomeric amino group is placed at 3C position of the indazole ring the ring-chain tautomerism becomes feasible. However, when the amino group is placed at 4–7C of the indazole ring only the annular tautomerism was found to be feasible and no effect of amino group to provoke a ring chain tautomerism was observed. On the other hand amino form of 3 amino substituted indazole was found to be predominant over imino forms whereas for the 4–7 amino substituted indazoles imino forms were found to be predominant over amino forms. The attempt to apply soft–hard base and soft nucleophile–electrophile criteria to protonation and tautomerism phenomena was successful.     

取代基咪唑啉与铁原子化学吸附作用能的量子化学计算

用量子化学方法计算了６个咪唑啉型化合物及其与铁原子的化学吸附作用能,探讨了这种作用能与缓蚀性能的关系。得到咪唑啉环上氮与铁的配位键长、双原子作用能以及重叠集居数。研究发现具有ｐ－π共轭体系的咪唑啉以及在环上引入供电子基团或取代芳烃,能增强氮与铁原子的化学吸附作用力。计算结果可为设计性能较好的新型咪唑啉缓蚀剂提供有用的信息。     

[2+2]环加成反应机理的理论研究

[2+2]环加成反应是有机化学中非常重要的一类反应,其机理的研究一直是实验和理论工作者关注的课题之一。本文从理论的角度综述了三类[2+2]环加成反应的反应机理,即简单烯烃或炔烃参与的环加成反应、累积双键体系参与的环加成反应以及稀土钍化合物参与的环加成反应, 得出对于简单的烯烃或炔烃之间的环加成反应一般是按双自由基机理进行,而其他两类反应主要按协同或两性离子方式进行,并且从前线分子轨道作用理论角度分析了产生不同反应机理的原因。     

Quantum chemical metabolism‐based simulation of carcinogenic potency of benzene derivatives

Using an oxenoid model, we investigated dependences of carcinogenic potency of the benzenes C₆H₅‐X on a nature of substituents X. According to the model, a P450 enzyme breaks a dioxygen molecule and generates the oxens, which readily react with substrates. We suggest that a stability of the intermediate OC₆H₆‐X with tetrahedrally coordinated C atom relative to the molecule C₆H₅‐X determines a rate of substrate biotransformation. Using MO LCAO MNDO approach, we calculated the total energies of molecules C₆H₆‐X and arene oxides OC₆H₆‐X. A difference ΔE_min of these values determines activation energy of oxidation reaction. The compounds with the low ΔE_min values are noncarcinogenic. Benzene derivatives with high ΔE_min values belong to carcinogenic compounds series. The carcinogenicity of amino‐ and nitro‐substituted benzenes is also determined by N‐oxidation of amino and reduction of the nitro group. As the phenylhydroxylamines XC₆H₄NHOH and nitrenium ions XC₆OH₄NH⁺ are the common metabolites of the nitro‐ and amino‐substituted benzenes and nitrenium ions XC₆H₄NH⁺ are the ultimate carcinogens, we use the differences ΔE_N = E(XC₆H₄NH⁺) ? E(XC₆H₄NHOH) as the second parameter characterizing the carcinogenic activity of amino‐ and nitro‐substituted benzenes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Theoretical investigation of the decomposition of acyl azides: Molecular orbital treatment

The thermal decomposition of formyl, acetyl, and benzoyl azides to the corresponding isocyanate and nitrogen has been treated theoretically using ab initio molecular orbital calculations at the Møller–Plesset type 2 (MP2)(full)/6‐31G* level. The reaction is stimulated by elongation of N N bond and is followed until the formation of the isocyanate and expulsion of nitrogen. The decomposition of formyl azide proved to be a concerted one‐step reaction without the formation of a nitrene intermediate. In contrast, the conversion of both acetyl and benzoyl azides to the corresponding isocyanate and nitrogen is a two‐step reaction, and a nitrene intermediate is formed. One transition state is located and identified during the course of the conversion of formyl azide, but two transition states are located and identified during the course of the conversion of acetyl and benzoyl azides. The thermodynamic functions, ΔE_r and ΔH_r, of the studied reactions are calculated. The results predict that the ease of conversion of the acyl azide to the isocyanate and nitrogen goes in the order: formyl azide > acetyl azide > benzoyl azide. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Quantum Chemistry Calculation of Quercetin-silver Complex

1 INTRODUCTION Quercetin(3,5,7,3?,4?-pentahydroxyflavone,see Fig. 1) is a kind of flavonol with many pharma-colo- gical actions, such as anti-flammatory, antiviral and antioxidation[1], but its antioxidation is weak. In re- cent years, it has been reported that quercetin can form metallic complexes by combining with some metal ions like copper ion, zinc ion, nickel and rare earth metals, and its antioxidative activity will be stronger than quercetin due to the existence of co- operative ef…