Ab initio Studies on polymers

Ab initio crystal orbital calculations have been performed on the infinite all-trans polyene. A structure with r _c=c= 1.346 Å, r _c-c = 1.446 Å, r _c-h = 1.08 Å, and CCC = 125.3 ° was found to be most stable. The most important force constants, the band structure and the density of states were determined as well.     

Au(Ⅰ)电荷转移配合物光谱性质的从头算研究

过渡金属电荷转移配合物的电荷分离是光能转化为电能的光物理过程, 与配合物的电子结构密切相关. 采用从头算方法探索了双核Au(Ⅰ)配合物, cis-[Au2(SHCH2PH2)2]2+(1), cis-[Au2(SHCH2S)2](2) 和cis-[Au2(PH2CH2S)2](3)的电荷转移性质. 采用MP2计算得到基态的Au(Ⅰ)—Au(Ⅰ)距离分别为0.2972, 0.2888和0.2903 nm, 表明Au(Ⅰ)之间存在弱吸引作用; 电子激发使得配合物2和3的金属间的距离缩短了约0.016 nm, 而配合物1仅增长了0.002 nm. CIS方法预测配合物1~3的3A激发态分别产生383, 463和422 nm最低能发射, 具有金属中心(Metal-centered, MC)跃迁和分子内电荷转移(Intramolecular Charge Transfer, ICT)的混合性质.     

光化学反应的从头算研究

光化学反应是最基本也是最重要的物理化学过程之一,在诸多领域有着广泛的应用。由于计算方法的限制以及光化学反应过程的错综复杂性,光化学反应机理的从头算研究是极具挑战性的国际前沿课题之一。本文综述了近20年来羰基化合物光化学反应机理从头算研究的一些进展,总结了羰基化合物电子激发态的特性和光化学反应过程的规律性,为深入研究光化学反应提供一些有用的信息。     

缬氨酸热分解机理的从头算研究

用量子化学从头算方法在RHF/6-21G水平上全优化计算了缬氨酸及其热分解中间产物、产物分子的几何构型,得到其总能量和Mulliken集居数等数据。通过对计算结果的分析,提出了缬氨酸的热分解反应机理。     

CO2与HCN,NH3,H2O分子络合物的从头计算研究

用ab initio能量梯度法(3-21G基组)分别优化CO_2与HCN、NH_3、H_2O_3个分子络合物的平衡几何构型。结果表明HCN、NH_3和H_2O中的N或O原子与CO_2中的C原子之间形成较弱的范德华键,三者的范德华键键长分别为0.2865、0.2775、0.2543nm,稳定化能分别为14.8、27.0、31.2kJ·mol~(-1),3个分子络合物的构型都呈T型,对3个分子络合物的稳定化能的能量分解研究表明它们的形成主要靠静电作用能。     

Ab initio Studies on Intermolecular Interaction of Formamide and Hydroxyacetonitrile Dimers

The structures, the binding energies and the thermodynamic properties of formamide and hydroxyacetonitrile(HAN) dimers have been studied by means of the self-consistent ab initio Hartree-Fock and the second-order Mφller-Plesset correlation energy correction methods. The counterpoise procedure was used to check the basis set superposition error(BSSE) of the binding energies. There exist cyclic structures in a formamide dimer(Ⅰ), a HAN dimer(Ⅱ) and their heterodimer(Ⅲ). The corrected binding energies for dimers Ⅰ, Ⅱ and Ⅲ are respectively -45.53, -45.83 and -43.89 kJ/mol at the MP2/aug-cc-p VDZ//HF/aug-cc-p VDZ level. The change of the Gibbs free energies(ΔG) in the process of Ⅰ Ⅱ→2Ⅲ was predicted to be -2.74 kJ/mol at 298.15 K. Dimer Ⅲ can be spontaneously produced in the mixture of formamide and HAN, which is in agreement with the experimental fact that most cyanohydrins are capable of interacting with dipeptide cyclo-His-Phe(CHP).     

Ab initio calculations on urea

Multiconfiguration wave functions constructed from contracted Gaussian-lobe functions have been found for the ground and valence-excited states of urea. ICSCF molecular orbitals of the excited states were used as the parent configurations for the CI calculations except for the ¹A₁(π → π*) state. The ¹A₁(π → π*) state used as its parent configuration an orthogonal linear combination of natural orbitals obtained from the second root of a three-configuration SCF calculation. The lowest excited states are predicted to be the n π → π* and π → π* triplet states. The lowest singlet state is predicted to be the n π → π* state with an energy in good agreement with the one known UV band at 7.2 eV. The π → π* singlet state is predicted to be about 1.9 eV higher, contrary to several previous assignments which assumed the lowest band was a π → π* amide resonance band. The predicted ionization energy of 9.0 eV makes this and higher states autoionizing.     

Ab initio calculations on porphin

Ab initio SCF calculations are reported for the porphin molecule. The positions of the central protons have been optimized, and the equilibrium geometry is found to be a linear NH ? HN arrangement. The NH vibrational frequencies have been computed and are compared to experimentally measured quantities. Several low ionized states have also been studied in separate spin-restricted SCF calculations. The lowest state is found to have B_1u symmetry with an ionization potential of 8.0 eV.     

Ab initio studies on calicene

Optimum geometries of planar and 90°-twisted C_2v calicene are calculated with single-configuration STO-3G and 3-21-G wavefunctions. The barrier to ring–ring rotation is computed. Bond alternation is pronounced in the planar form and decreases in the twisted form, while dipolar character increases on twisting.     

Ab initio quantum-mechanical calculations on trifluoromethylamine

Extensive ab initio molecular-orbital calculations were carried out on trifluoromethylamine (TFM) to elucidate changes in geometry and electronic structure upon fluorination. The calculations show that the decomposition of CF₃NH₂ is slightly endoenergetic, and the heats of atomization of CF₃NH₂ and CH₃NH₂ show decreased stability of the species upon fluorination. Characteristic of CF₃NH₂ is a highly polar, strong, short CN bond. More limited calculations were carried out on CF₃OH and CH₃OH, and the electronic structure of CF₃OH is found to be generally similar to that of CF₃NH₂. The reduced basicity of the fluorinated amine cannot be ascribed to the inductive effect; the enhanced acidity of the fluorinated alcohol reflects the weakening of the OH bond. No evidence leads to a confirmation of the existence of nitrogen–fluorine hyperconjugation in the fluorinated amine.     

硫代甲酰胺双聚体的量子化学计算

在MP2/6 31G(d)和MP2(FC)/6 311 G(d,p)水平上,对硫代甲酰胺(HC-SNH2)及其3种构型双聚体进行几何全优化计算,经振动频率分析,确认为势能超曲面上的稳定驻点.然后在MP2/6 311 G(2df,2p)水平上进行单点能计算和基组重叠误差(BSSE)校正以获得相互作用能.并利用自然键轨道(NBO)理论和分子中的原子(AIM)理论探讨HCSNH2之间相互作用的本质.     

Ab initio studies on the thermolysis of azetidine

The reaction mechanism of the thermolysis of azetidine to form ethylene and methylen-imine has been studied by ab initio SCF MO method at STO--3G and 3-21G levels. Two possible step-wise pathways are explored. One is the breaking of C--C bond as the first step, while the other is thebreaking of C--N bond. All the stationary points on the potential energy surface (PES) are fully optimiz-ed. MP2 / 3-21G single point calculations on all stationary points and MCSCF / STO-3G computationsfor some stationary points are also carried out. The calculations indicate that azetidine decomposesvia biradicaloid intermediates and the cleavage of C--N bond is preferable to that of C--C bond.     

Ab initio studies of

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.     

Ab initio Ehrenfest dynamics

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.     

Ab initio molecular fragment calculations with pseudopotentials: Model peptide studies

The energetics of rotation about the N? C′(ω); N? C^α(φ), and C^α? C′(?) bonds of the peptide unit have been investigated in the pseudo-FSGO fragment scheme on model compounds formamide and N-methylacetamide. The results indicated that the position of the minimum in ω is in the near vicinity of 0°, i.e., the planar arrangement of the peptide unit. The minimum in φ (C′? N? C^α? H) has been found to be 180° and in ψ(H? C^α? C′? N) to be 60°, in good agreement with PCILO and Gaussian-70 results.     

Ab initio polypeptide structure prediction

The biological activity of a polypeptide strongly depends on its 3D structure. Ab initio prediction of the native structure from the sequence of amino acids has long motivated the development of an optimum energy model such that interactions present in the native conformation are stronger than those present in nonnative conformations and of algorithms capable of finding the basin of lowest free energy among an astronomically large number of possible conformations. Despite recent progress in our understanding of the factors responsible for both polypeptide stability and formation, computer simulations of polypeptide models are still far from being practical software tools for biologists. In this work, state-of-the-art computer simulations aimed at ab initio structure prediction in aqueous solution are reviewed and their strengths and weaknesses are highlighted. Received: 23 June 1999 / Accepted: 20 September 1999 / Published online: 15 December 1999     

Benzooxirene. Ab initio calculations

Ab initio calculations have been performed on benzooxirene, the corresponding oxo carbene (“ketocarbene”), and the transition state linking the two. At the highest level used, QCISD(T)/6-31G^*//MP2(FULL)/6-1G^* with MP2(FULL)/ 6-31G^* zero point energy corrections, the relative energies of the oxirene, the transition state and the carbene are 0, 24.6, and −17.8 kJ mol⁻¹. Correlation energy effects are very important in this system: at the QCISD(T) level the oxirene lies above the carbene, as at the MP4 and HF levels, but at the MP2 level the ordering is reversed. Benzooxirene is probably slightly nonplanar: the HF/6-31G^* geometry is C_2v but the MP2(Fermi contact)/6-31G^* geometry is C_s with a 6-/3-ring coplanarity deviation of about 6.9 °, although in the MP2(FULL)/6-31G^* geometry this is reduced to about 3.1 °.     

Ab initio calculations on blocked Pro-Ala dipeptides

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- -Pro- -Ala-NH₂ and Ac- -Pro- -Ala-NH₂ blocked dipeptides. Th6-31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the H-bond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the -Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the -Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the -Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.