克氏锥虫唾液酸转移酶催化机理的理论研究

克氏锥虫唾液酸转移酶（TcTs）是恰加斯病的致病原,它具有由6个β片构成的桶状催化结构域。该催化结构域集中在酶N端的边缘。本文利用量子力学/分子力学（QM/MM）联用的模型研究了克氏锥虫唾液酸转移酶的催化机理。初始酶和底物复合物模型由蛋白质晶体数据库得到（PDB ID:lSOI）。其中QM部分在半经验模型中由AM1描述,在从头算模型中由B3LYP/6-3lG^*描述。MM部分只取酶的N端结构域,并始终由AMBER力场来描述。QM部分与MM部分成键相互作用边界用pseudo-bond方法处理,将3个重要的氨基酸残基（Glu230,Asp59,Tyr342）的C_β-C_β键作为OM/MM模型中的pseudo-bond。由Nudged Elastic Band（NEB）路径优化方法得到的TcTs半经验的最低能量反应路径中,关键原子间距离沿最低能量路径的变化表明:反应开始后Glu230开始靠近Tyr342,当它们之间的氢键距离由2.9 A缩短为2.4 A时,Tyr342将质子转移给Glu230,增强了Tyr342酚氧负离子的碱性,更有利于Tyr342亲核进攻糖苷键。同时,Asp59作为酸,提供质子给糖苷键断裂后的离去基团。过程中,伴随着唾液酸的单糖糖环从扭曲的船式构象向松弛的椅式构象的转变,从而更有利于稳定生成的共价唾液酸-酶中间产物。对得到的半经验的最低能量反应路径再做B3LYP/6-31G^*/MM模型下的优化,得到反应的能垒约为13.53 kcal/mol,说明该反应路径是合理的。研究结果与实验上通过突变的TcTs_D59A推测的乒乓双置换酸碱催化的机理一致,是对实验结论的有力支持,为TcTs抑制剂的设计和结构修饰提供了理论参考,有助于预防和抗恰加斯病的新药物研发。     

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

The first step of the reaction catalysed by the enzyme citrate synthase is studied here with high level combined quantum mechanical/molecular mechanical (QM/MM) methods (up to the MP2/6-31+G(d)//6-31G(d)/CHARMM level). In the first step of the reaction, acetyl-CoA is deprotonated by Asp375, producing an intermediate, which is the nucleophile for attack on the second substrate, oxaloacetate, prior to hydrolysis of the thioester bond of acetyl-CoA and release of the products. A central question has been whether the nucleophilic intermediate is the enolate of acetyl-CoA, the enol, or an 'enolic' intermediate stabilized by a 'low-barrier' hydrogen bond with His274 at the active site. The imidazole sidechain of His274 is neutral, and donates a hydrogen bond to the carbonyl oxygen of acetyl-CoA in substrate complexes. We have investigated the identity of the nucleophilic intermediate by QM/MM calculations on the substrate (keto), enolate, enol and enolic forms of acetyl-CoA at the active site of citrate synthase. The transition states for proton abstraction from acetyl-CoA by Asp375, and for transfer of the hydrogen bonded proton between His274 and acetyl-CoA have been modelled approximately. The effects of electron correlation are included by MP2/6-31G(d) and MP2/6-31+G(d) calculations on active site geometries produced by QM/MM energy minimization. The results do not support the hypothesis that a low-barrier hydrogen bond is involved in catalysis in citrate synthase, in agreement with earlier calculations. The acetyl-CoA enolate is identified as the only intermediate consistent with the experimental barrier for condensation, stabilized by conventional hydrogen bonds from His274 and a water molecule.     

A combined QM/MM study of the nucleophilic addition reaction of methanethiolate and N-methylacetamide

A combined quantum mechanical (QM) and molecular mechanical (MM) method was used to study the nucleophilic addition reaction of methanethiolate to N-methylacetamide (NMA) in the gas phase and aqueous solution. At the B3LYP/aug-cc-pVDZ//HF/6-31 + G(d) level, the ion-dipole complex was found to be the global minimum on the potential energy surface in the gas phase with a binding energy of 21.2 kcal/mol. The complex has a C-S distance of 4.33 A, and no stabilized tetrahedral intermediate was located. The computed potential of mean force in water shows that solvent effects stabilize the reactants over the tetrahedral adduct by 36.5 kcal/mol, and that the tetrahedral intermediate does not exist for the present reaction in water. The present study provides an initial step for modeling the cysteine protease hydrolysis reactions in enzymes.     

Molecular dynamics and density functional theory studies of substrate binding and catalysis of human brain aspartoacylase

The active-site dynamics of human brain aspartoacylase (hASPA) complexed with its substrate (N-acetyl-l-aspartate) has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach based on the self-consistent charge-density functional tight-binding (SCC-DFTB) model. The Michaelis complex, which is constructed from a recent X-ray structure of the human brain aspartoacylase with a stable tetrahedral intermediate analogue, is reproduced in 1 ns molecular dynamics simulations at 300 K. The simulation shows that the substrate is tightly held in the active site by a hydrogen bond network and the putative nucleophilic water molecule is reasonably close to the nucleophilic center. The catalysis is further modeled with the density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31G(d) level of theory. The DFT calculations indicate the reaction proceeds via a water promoted pathway with Glu178 serving as the general base and general acid. Transition state stabilization for nucleophilic addition is achieved by formations of the weak coordination bond between the substrate carbonyl oxygen atom and the zinc ion as well as of the strong hydrogen bonds between the substrate carbonyl oxygen atom and Arg63.     

QM methods in structure based design: utility in probing protein-ligand interactions

Small changes in ligand structure can lead to large unexpected changes in activity yet it is often not possible to rationalize these effects using empirical modeling techniques, suggesting more effective methods are required. In this study we investigate the use of high level QM methods to study the interactions found within protein-ligand complexes as improved understanding of these could help in the design of new, more active molecules. We study aspects of ligand binding in a set of protein ligand complexes containing ligand efficient, fragment-like inhibitors as these structures are often challenging to determine experimentally. To assess the reliability of our theoretical models we compare the MP2/6-31+G** QM results to the original X-ray coordinates and to QM/MM B3LYP/6-31G*//UFF results which we have previously reported. We also contrast these results with data obtained from an analysis of the distribution of comparable interactions found in (a) high resolution kinase complexes (≤ 1.8?) from the PDB and (b) more generic, small molecule crystal structures from the CSD.     

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

The fragment molecular orbital (FMO) method was applied to quantum chemical calculations of neuramic acid, the natural substrate of the influenza virus neuraminidase, and two of its competitive inhibitors, Oseltamivir (Tamiful^®) and Zanamivir (Relenza^®), to investigate their hydrated structures and energetics. Each of the three ligands was immersed in an explicit water solvent, geometry-optimized by classical MM and QM/MM methods, and subjected to FMO calculations with 2-, 3-, and 4-body corrections under several fragmentation options. The important findings were that QM/MM optimization was preferable to obtain reliable hydrated structures of the ligands, that the 3-body correction was important for quantitative evaluation of the solvation energy, and that the dehydration effect was most remarkable near the hydrophobic sections of the ligands. In addition, the hydration energy calculated by the explicit solvent was compared with the hydration free energy calculated by the implicit solvent via the Poisson-Boltzmann equation, and the two showed a fairly good correlation. These findings will serve as useful information for rapid drug design.     

Structure and adsorption of a basic probe molecule on H-ZSM-5 nanostructured zeolite: an embedded ONIOM study

The adsorption properties of pyridine on H-ZSM-5 zeolites have been investigated by cluster calculations with the ONIOM scheme and with an embedded-ONIOM scheme. The active site has been modeled with cluster sizes of up to 46 tetrahedra. Two different types of pyridine adsorption complexes on the zeolite models are found. If Zeolite is modeled by a small 3T quantum cluster, the adsorption energy of the hydrogen-bonded pyridine complex (Py-Hz), is found to be -18.5kcal/mol. When a larger cluster or the ONIOM models are employed, the optimized geometries show the formation of pyrdinium cation [PyH(+)] bound as an ion-pair complex [PyH(+)][Z(-)]. The calculated energy of formation for this ion-pair complex is -36.8kcal/mol in the ONIOM (B3LYP/6-31G(d,p):UFF) model. Both values are considerably lower than the experimentally estimated heat of adsorption of pyridine in ZSM-5 zeolite of -47.6kcal/mol. Inclusion of the electrostatic effects of the zeolite crystal lattice via the embedded ONIOM model increases the adsorption energy to -44.4kcal/mol. Performing the quantum-chemical treatment at the MP2/6-31G(d,p) level instead of the B3LYP/6-31G(d,p) leads to a slightly lower adsorption energy to -45.9kcal/mol. These data suggest that the embedded ONIOM scheme provides an accurate method of studying the interaction of small organic molecules with zeolites.     

树状分子聚酰胺胺(PAMAM)的量子化学研究

采用传统的Hartree-Fock(HF)从头算和密度泛函B3LYP方法,选择不同的基组水平(3-21G,6-31G*)对以乙二胺为核的1.0代PAMAM分子进行全几何优化,并对结果进行比较,同时与实验值进行对照.结果表明,B3LYP/6-31G*方法得到的结果更可靠.B3LYP/6.31G*计算结果表明,1.0代PAMAM分子构象不完全对称,4个支链基本在一个平面上,伯胺,仲胺和叔胺上的N原子所带负电荷数逐渐减少,HOMO轨道主要集中在核上,核极易发挥供电子作用.     

Computations of model narrow nanotubes closed by fragments of smaller fullerenes and quasi-fullerenes

New type of carbon nanotubes—narrow nanotubes—has recently been observed with diameters of 4–5 Å. It has been postulated that the narrow nanotubes are closed by fullerene fragments of C₂₀ and C₃₆. This paper presents computational results on related model nanotubes with stoichiometries such as C₈₀, C₈₄, C₉₆, C₁₀₈, or C₁₂₀. The computations were carried out at the PM3, AM1, SAM1, HF/3-21G, HF/4-31G, and B3LYP/6-31G^* levels. Two C₃₆ fullerenes were considered, D_6h and D_2d. At the PM3 level and with the C₈₄ nanotube stoichiometry, the D_2d cage closure gave a lower energy (by 185 kcal/mol and a diameter of 5.42 Å). There is another possible candidate, a C₃₂ cage with D_4d symmetry (two four-membered rings). At the PM3 level and with the C₉₆ nanotube stoichiometry, the D_4d closure (with a diameter of 5.43 Å) had energy lower by 210 kcal/mol than that of the D_6h nanotube closure. On the other hand, four-membered rings should not play a significant role for narrow nanotubes with a diameter of 4 Å, where the dodecahedron-related closure should be exclusive. Still narrower nanotubes are briefly discussed.     

Post Hartree-Fock and density functional theory studies on structure and conformational stability of nitrosoethylene and substituted compounds of nitrosoethylene

Post Hartree-Fock and density functional theory (DFT) methods were used to study the different conformers of nitrosoethylene H-CH=CH-NO, and substituted compounds of the nitrosoethylene R-CH=CH-NO (R = Cl, NH2, N(CH3)2, OH, OCH3). The molecules were optimized at MP2/6-31G* level of theory of ab initio and B3LYP/6-31G* and B3PW91/6-31G* levels of theory of DFT. Special emphasis has been given to the effect of substitution of pi-electron donor groups NH2, N(CH3)2, OH, and OCH3, which play a major role in modifying the geometrical parameters of -N=O group by the electronic transmission effects through the central group -CH=CH-. The ability of DFT methods to predict the bond length adjacent to the atoms having lone pair electrons has been discussed. The conformational stabilities have been studied using the relative energies and DFT parameters such as chemical hardness and chemical potential. The role of intra-molecular hydrogen bond on the equilibrium structure has been discussed. The vibrational spectra for the different conformers of the nitrosoethylene and substituted compounds have been generated using the MP2/6-31G* level of theory.     

Electronic structure and nonlinear optical properties of model push-pull polyenes with modified indanone groups: a theoretical investigation

Several model polyenes with modified indanone groups were studied by means of density functional theory (DFT) B3LYP/6-31G*, ab initio HF/3-21G* and semiempirical AM1 methods. We investigated the effect of several substituents upon the relationship between the structure, spatial distribution of the highest occupied and the lowest unoccupied pi-MOs, a concept of the global softness and the global hardness as well as both linear and nonlinear polarizabilities for the set of pi-electron chromophores represented by the short-chain model polyene (butadiene) carrying out p-methoxyphenyl group on the one end and several modified indanone groups on the opposite end of the molecule. As probing endocyclic groups used to modify the structure of indanone the following substituents: > CH2; > C=O; > SO2, > C=CH(NO2) and > C=C(CN)2 were selected. The cubic relationship between the polarizability and the global softness was found. The highest polarizabilities (alpha, beta, gamma) are predicted for the derivatives with > C=C(CN)2 group. It was found that the value of beta depends mainly on the difference between dipole moments in the excited and ground states of the molecules. In the case of > SO2 group the results of AMI calculations significantly deviate from relationships found for other derivatives. Experimental IR and Raman spectra of newly synthesized indandione derivative of cinnamaldehyde were compared with computed ones.     

丙烯酸正丁酯聚合的Diels-Alder反应机理理论研究

本文从理论上对丙烯酸正丁酯(nBA)自引发聚合的Diels-Alder反应机理进行了研究.利用DFT方法在UB3LYP/6-31G*水平上对反应的最低能量路径进行了计算,各驻点能量分别采用MP2/6-311G**和B3LYP/6-311 G(3df;2p)进一步精确计算.结构表明:此Diels-Alder反应仅包括一种途径,即路径(I),另一条途径在热力学不支持.     

最大重迭对称性分子轨道和分子几何参数计算

建立了AMl级别的最大重迭对称性分子轨道计算方案(MOSMO)。采用通常的半经验分子轨道方法AMl级别中完全相同的参数，计算了各种分子的几何参数等。所得计算结果与实验值及HF／6-31G*从头算方法计算结果相符，说明提出的计算方案是可行的。同时，由于提出的计算方案过程简单，更易推广使用到从头算方法难以解决的大分子体系和超分子体系的结构和性质研究。     

Insight into analysis of interactions of GW9508 to wild-type and H86F and H137F GPR40: a combined QM/MM study and pharmacophore modeling

GPR40 is a novel potential target for the treatment of type 2 diabetes. In this work, a two-layered ONIOM based QM/MM approach was employed to study the interactions between GW9508 and GPR40: wild-type, H86F, and H137F mutated systems. The calculated results clearly indicated that His137 is directly involved in ligand recognition through the NH-π interaction with the GW9508. In contrast, His86 is not interacting with the GW9508 in the NH-π interaction. The interaction energies, calculated at the MP2/6-31(d, p) level, were performed to gain more insight into the energetic differences of the wild-type and two mutated systems at the atomistic level. In addition, the obtained pharmacophore model was well consistent with structure-functional requirements for the binding of GPR40 agonists and with per-residue energy decomposition of the ONIOM calculations.     

A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states

A reaction path including transition states is generated for the Silverman mechanism [R.B. Silverman, Chemical model studies for the mechanism of Vitamin K epoxide reductase, J. Am. Chem. Soc. 103 (1981) 5939-5941] of action for Vitamin K epoxide reductase (VKOR) using quantum mechanical methods (B3LYP/6-311G**). VKOR, an essential enzyme in mammalian systems, acts to convert Vitamin K epoxide, formed by Vitamin K carboxylase, to its (initial) quinone form for cellular reuse. This study elaborates on a prior work that focused on the thermodynamics of VKOR [D.W. Deerfield II, C.H. Davis, T. Wymore, D.W. Stafford, L.G. Pedersen, Int. J. Quant. Chem. 106 (2006) 2944-2952]. The geometries of proposed model intermediates and transition states in the mechanism are energy optimized. We find that once a key disulfide bond is broken, the reaction proceeds largely downhill. An important step in the conversion of the epoxide back to the quinone form involves initial protonation of the epoxide oxygen. We find that the source of this proton is likely a free mercapto group rather than a water molecule. The results are consistent with the current view that the widely used drug Warfarin likely acts by blocking binding of Vitamin K at the VKOR active site and thereby effectively blocking the initiating step. These results will be useful for designing more complete QM/MM studies of the enzymatic pathway once three-dimensional structural data is determined and available for VKOR.     

主成分分析-神经网络方法用于硝基苯及其同系物的QSAR研究

运用混合密度泛函理论DFT-B3LYP,以6-31G＊为基组计算35个硝基苯及其同系物电子结构的量化参数,采用主成分分析法对16个量化参数进行预处理,并结合人工神经网络对硝基苯及其同系物的QSAR进行了研究。35个化合物被随机分为两组,即训练集和测试集,其RMS值分别为0．095和0．111。取得了较满意的结果。     

Improved AMBER torsional parameters for the N-N rotational barrier in diacylhydrazines

The structure and rotational barrier for substituted diacylhydrazines are of significant interest given the role this functionality plays in peptidomimetics and ecdysone agonists, the latter of which have application as extremely selective insecticides. Ab initio calculations show that the lowest energy conformations are typically nonplanar with essentially perpendicular nitrogen lone pairs. Molecular mechanics calculations using the AMBER* force field in MacroModel yield minima and rotational barriers that are both quantitatively and qualitatively inconsistent with the ab initio results. In this work the AMBER* N-N rotational barriers for all configurations of the parent, methyl and di-methyl substituted diformylhydrazines have been fitted to MP2/6-31+G** relative energies. The resulting AMBER* torsional parameters have been validated by calculating the rotational barriers for N-t-butyl substituted diformylhydrazine, dibenzoylhydrazine and an azadipeptide. In each case the new AMBER* rotational barriers compare favorably with the corresponding MP2 calculated rotational barriers.     

密度泛函理论和从头计算法研究环戊二烯衍生物气态酸度及其取代基效应

用B3LYP／6-311G(2df,p)／／B3LYP／631 G*和MP2／6-311G(d,p)／／B3LYP／6-31 G*方法准确地预测了9个系列的环戊二烯衍生物(R=CN,CF3,CHO,C283,F,SiH3,H,CH3,OH,NH2)的C-H键的酸度。环戊二烯衍生物气态酸度的范围从284.9 kcal／mol (化合物5a)到357.24kcal／mol(化合物7j),分析取代基的电性、数量以及位置的影响得到了9个QSAR方程。这些数据有助于我们设计以及合成一些有机酸,并有助于深刻理解相关反应中环戊二烯衍生物的性质。     

脂肪胺类化合物脂水分配系数的QSPR研究(英文)

用16种脂肪胺类化合物HF/6-31G**,HF/6-311G**,DFT-B3LYP/6-31G**和DFT-B3LYP/6.311G**全优化计算结构参数:分子最高占用和最低空轨道能(EHOMO和ELUMO),分子次最高占用和次最低空轨道能(ENHOMO和ENLUMO),分子总能量(ET),氢原子所带的最高正电荷(qH+),最负原子的静电荷(q-),分子偶极矩(μ)和分子体积(V),对它们的脂水分配系数(lgKOW)分别进行定量构效关系(QSPR)研究.结果表明:脂肪胺的lgK与分子最低空轨道能(ELUMO),分子的总能量(ET)和分子偶极距(μ)的相关性较好,成功地建立了lgKOW的QSPR方程.特别是基于B3LYP/6-311G**基组建立的方程具有更好的[[预]能力,并通过VIF值和t值对其稳健性进行了检验,结果良好.