应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

(HAlNH)n(n=2～3)环状化合物的结构特征

用自洽场理论(HF)和密度泛函理论(DFT)的B3LYP方法,在6-31G*的水平上对化合物(HAlNH)2和(HAlNH)3的几何结构进行优化,并分别与环丁二烯C4H4和苯分子C6H6的结构和成键方式进行比较.以B3LYP/STO-3G方法讨论其分子轨道波函数(ψ).结果表明C4H4和(HAlNH)2均为D2h对称,前者为长方形结构,形成两个孤立的π键;而后者为菱形结构,形成一个π44键.C6H6和(HAlNH)3分子点群分别为D6h和D3h,并均形成一个π66键.成键原子对分子轨道的贡献不同,其中C原子是完全等价的,而Al和N原子各不相同,N原子比Al的贡献要大得多.     

吲哚与亚烷基丙二酸二甲脂Michael加成反应机理的从头算研究

在HF/6-31G(d)水平下, 对吲哚(A)与亚烷基丙二酸二甲脂(B)的Michael加成反应的机理进行了从头算理论研究. 计算结果表明, 该反应的机理为: A＋B→分子复合物→TS1→IM→TS2→产物. 其中第一阶段由复合物经过渡态TS1生成中间体IM, 是C—C键的形成阶段, 该阶段的活化能垒较后一阶段要大, 是该反应的决速步骤; 第二阶段由IM经过渡态TS2生成产物, 完成H迁移和C—H键的形成. 反应过程中, 底物分子中离域化的π键电子的相互作用, 促进了 C—C新键的形成, 同时吲哚的共轭体系遭到部分破坏, 而体系经H迁移使新的C—H键形成后, 吲哚环的共轭体系又得到了恢复. 在MP2/6-311＋G(d,p)水平下, 分别考虑乙醇和1,2-二氯乙烷的溶剂化效应, 单点能计算结果显示, 质子化溶剂对反应的影响较大, 不仅降低了反应的能垒, 且溶剂质子有可能参与了H迁移和C—H键的形成过程, 这一结论与实验结果一致.     

苯酚-酰胺系列氢键复合物从头计算研究

运用G94W量子化学程序包,在HF/6-31G基组水平上对酰胺(DMF,DMA,HCONH2,HCONHCH3andCH3CONH2)与苯酚形成的系列氢键复合物(看作超分子)进行从头计算研究。根据计算结果探讨复合物的稳定性、施体和受体间的电荷转移及几何参数变化等规律。结果表明苯酚与上述一系列酰胺都可形成稳定的氢键复合物,其稳定性次序为CH3CONH2～HCONHCH3＞HCONH2＞DMA＞DMF。结果还表明形成氢键复合物的过程包含着电荷转移,电荷由供体酰胺转移到受体苯酚中,酰胺中C=O键长和苯酚中的O-H键长都明显有规律性地变长。计算结果与实验规律相符。     

单嘧磺隆除草剂的晶体构象-活性构象转换的密度泛函理论研究

应用密度泛函理论在B3LYP/6-31G(d)水平上对新型除草剂单嘧磺隆绕脲桥部分两个C—N键的内旋转势能面进行计算, 然后对势能面上的驻点进行构型优化和过渡态搜索, 得到单嘧磺隆4种稳定构象和构象转换过程所涉及的8个过渡态结构. 研究结果表明, 单嘧磺隆晶体构象-活性构象转换过程中涉及4种稳定构象和8条转换途径, 脲桥部分NH基团与嘧啶环上N原子所形成的分子内氢键对于构象的稳定性及转换过程起着十分重要的作用. 应用极化连续介质溶剂模型(PCM)在B3LYP/6-31＋＋G(d, p)水平下进行溶剂化效应计算, 结果表明单嘧磺隆从晶体构象转换成活性构象主要是在水相中进行的.     

碱(土)金属离子与2-(3′-羟基-2′-吡啶基)苯并噁唑阳离子-π复合物及其分子内质子转移过程的理论研究

采用密度泛函B3LYP方法,在6-311++G(d,p)基组水平上对碱(土)金属离子(Li+,Na+,K+,Be2+,Mg2+和Ca2+)与2-(3’-羟基-2’-吡啶基)苯并噁唑(HPyBO)的36种阳离子-π复合物的初始构型进行了几何全优化,并计算了其相互作用能.结果表明,碱(土)金属离子与HPyBO复合物有较强的阳离子-π相互作用,部分复合物甚至达到了化学键的强度.相对能量的变化表明碱(土)金属离子的作用能改变HPyBO分子内质子转移过程的能垒,甚至可以导致优势构型反转.当考虑水的溶剂效应后,各质子转移异构体的相对能量及质子转移的能垒均有一定程度的改变.另外,应用分子中的原子(AIM)方法对复合物分子内氢键的键临界点性质进行了分析.     

电场作用下分子导线的理论研究

摘要利用从头计算法分别在HF/6-31G, HF/6-31G*, HF/6-31G**, HF/6-31+G, HF/6-31++G, HF/6-31+G*, HF/6-31+G**, HF/D95+*, B3LYP/6-31G*和B3LYP/6-31+G*水平上计算了5个单体的聚乙炔分子导线, 从几何构型、 SCF能量和分子轨道能级三个方面讨论了外电场对分子导线的影响, 给出了聚乙炔分子导线性质与外电场变化的定量关系.     

甲亚胺1,1-脱氢反应途径的量子拓扑研究

根据甲亚胺(H2C=NH)1,1-脱氢生成CNH的IRC途径,用ab inito4-31G基组计算了反应进程中的各点,着重从量子拓扑学的角度讨论了化学键的性质、强度、原子的电子集居等诸拓扑指标的变化,直观、清晰、定量地描述了H(1)-C键断裂,H(1)-H(2)键形成及从母体脱除的协同非同步过程.该方面的研究未见文献报道.     

(HAlNH)n(n=2～3)环状化合物的结构特征

用自洽场理论 (HF)和密度泛函理论 (DFT)的B3LYP方法 ,在 6 31G 的水平上对化合物(HAlNH) 2 和 (HAlNH) 3 的几何结构进行优化 ,并分别与环丁二烯C4 H4 和苯分子C6H6的结构和成键方式进行比较。以B3LYP STO 3G方法讨论其分子轨道波函数 (Ψ)。结果表明 :C4 H4 和 (HAlNH) 2 均为D2h对称 ,前者为长方形结构 ,形成两个孤立的π键 ;而后者为菱形结构 ,形成一个π44键。C6H6和 (HAlNH) 3分子点群分别为D6h和D3h,并均形成一个π66键。成键原子对分子轨道的贡献不同 ,其中C原子是完全等价的 ,而Al和N原子各不相同 ,N原子比Al的贡献要大得多     

卡宾与醚C-H键插入反应的理论研究——(Ⅰ)卡宾与二甲醚的插入反应

用量子化学从头计算方法在MP2/6-31G(d)水平上计算了单重态的CH₂与二甲醚中C-H键插入反应的过程,并在MP₄/6-31G(d)水平上计算了反应物、过渡态和产物的能量。反应仅具有一个8.1kJ/mol的早期势垒,反应过程是卡宾的一个亲电-亲核过程,在插入过程中,卡宾空的p轨道和占有一对孤电子的σ轨道分别指向C-H键的H原子和C原子。     

How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.     

Gas-phase structures of acetyl peroxynitrate and trifluoroacetyl peroxynitrate

The molecular structures and conformational properties of acetyl peroxynitrate (PAN, CH3C(O)OONO2) and trifluoroacetyl peroxynitrate (FPAN, CF3C(O)OONO2) were investigated in the gas phase by electron diffraction (GED), microwave spectroscopy (MW), and quantum chemical methods (HF/3-21G, HF/6-31G*, MP2/6-31G*, B3PW91/6-31G*, and B3PW91/6-311+G*). All experimental and theoretical methods show the syn conformer (C=O bond of acetyl group syn to O-O bond) to be strongly predominant relative to the anti conformer. The O-NO2 bonds are extremely long, 1.492(7) A in PAN and 1.526(10) A in FPAN, which correlates with their low bond energy and the easy formation of CX3C(O)OO* and *NO2 radicals in the atmosphere. The O-O bonds (1.418(12) A in PAN and 1.408(8) A in FPAN) are shorter than that in hydrogen peroxide (1.464 A). In both compounds the C-O-O-N dihedral angle is close to 85 degrees.     

胺类分子在LiMOR分子筛中吸附的量子化学研究

 采用量子化学方法(ONIOM,B3LYP/6-31G(d,p):HF/3-21G)研究了锂型丝光沸石(LiMOR)的结构及其对胺类分子的吸附性能. 在校正基组迭加误差的基础上计算得到氨、甲胺、二甲胺和三甲胺分子的吸附热分别为117.6,132.7,122.2和106.0 kJ/mol,表明胺分子在LiMOR分子筛上吸附强度的次序为三甲胺＜氨＜二甲胺＜甲胺. 通过结构优化得到了吸附复合物的平衡几何参数、电子结构数据以及N-H键伸缩振动频率,胺分子与分子筛之间的主要作用力为氮上的孤对电子和锂离子之间的静电作用力,胺分子与分子筛骨架氧之间的弱氢键作用对其吸附有一定的稳定作用.     

胺对锂电池电解液中小分子的稳定作用

用密度泛函理论(DFT)方法在PBE0/6-31+G(d, p)水平上对乙胺、乙二胺分别与电解液中的小分子H2O、HF分子间的相互作用进行理论计算, 并在PBE/TZP 水平上利用能量分解分析(EDA)方法对胺与HF、H2O 结合的II-1、II-2、III-1和III-2模型进行计算分析. 结果表明, 胺类物质都能与HF、H2O形成N…H—F(O)、F(O)…H—N或F(O)…H—C的稳定氢键. 但HF与胺类物质形成的氢键比H2O与胺形成的氢键强, 故胺类物质在电解液中优先稳定HF. 乙二胺与HF、H2O结合的稳定性比乙胺强. 乙胺、乙二胺与HF(H2O)形成的最稳定构型均由F(O)—H…N 和F(O)…H—C 氢键结合形成.     

Microsolvation of formamide: a rotational study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.     

Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation

The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.     

Molecular structure of 2,5-dihydropyrrole (C4NH7), obtained by gas-phase electron diffraction and theoretical calculations

The structure of 2,5-dihydropyrrole (C4NH7) has been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing third-order M?ller-Plesset (MP3) level of theory and the 6-311+G(d,p) basis set. Several theoretical calculations were performed. From theoretical calculations using MP3/6-311+G(d,p) evidence was obtained for the presence of an axial (63%) (N-H bond axial to the CNC plane) and an equatorial conformer (37%) (N-H bond equatorial to the CNC plane). The five-membered ring was found to be puckered with the CNC plane inclined at 21.8 (38) degrees to the plane of the four carbon atoms.     

甲醛与甲酰胺相互作用的从头算研究

The optimizations geometries and vibrational frequencies of H2CO,HCONH2 and acquired 3 complexes between H2CO?HCONH2 have been calculated by using the ab initio method at the MP2/6-31G（ d）and MP2 （FC）/6-311++G（d,p）level. The non-minimum structures with negative vibrational frequencies are excluded. The lowest energy conformer of these complexes is a cyclic structure with N - H?O and C - H?O hydrogen bonds in a common plane. No significant changes are observed in the geometries of the monomers in their complexed state. The most characteristic geometrical properties of the complex are the lengthening of the contacting N-H bonds by 0.4-1.1 pm,and the general shortening of the contacting C-H bonds by 0.3-0.4 pm with respect to the monomers. The interaction energies of complexes have been corrected by the basis set superposition error （BSSE）using the full Boys-Bernardi counterpoise correction scheme. The corrected complex interaction energies of 3 structures at MP2/6-311++G（2df,3p）/ / MP2（FC）/6-311++G（d,p）level are -29.94, -16.10 and -18.45 kJ/mol,respectively. The interaction energies indicate that C - H?O is a weak hydrogen bond. The results of natural bond orbital population analysis reveals that there is only a small charge-transfer in the process of forming the complexes. The results of natural bond orbital analysis and atom in the molecule scheme appear quite significant in view of their importance for understanding the mechanisms of intermolecular interaction leading to hydrogen bonding. The results of molecular interaction energy decomposition analysis show that the electrostatic interaction plays an essential role in stabilizing the H2CO?HCONH2 complexes.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

The conformers of phenylglycine

The neutral form of the unnatural amino acid phenylglycine was vaporized by laser ablation, and the presence of two conformers was detected in a supersonic expansion by Fourier transform microwave spectroscopy. Both conformers were unequivocally identified by comparison of their experimental rotational and quadrupole coupling constants with those calculated ab initio. The most stable conformer is stabilized by intramolecular hydrogen bonds N-H...O=C, N-H...pi (with the closest C-C bond in the aromatic ring), and a cis-COOH interaction. The other conformer exhibits a O-H...N hydrogen bond between the hydrogen atom of the hydroxyl group and the lone pair at the nitrogen atom.