Quantum Topological Studies on the Molecular Complexes-CO_2-NCH and CO_2-OH_2

Topological properties of charge distribution for the title complexes and their constituent are analyzed by using ab initio calculations at 3-21G basis set. The results obtained are compared with those originated from ab initio and energy decomposition method. It has been determined that the title molecular complexes are T-shaped. The characteristics of the bonds and the changes originated from the formation of the complexes are discussed.     

Theoretical studies on the reaction path and dynamics of the reaction CH_3+H_2O→CH_4+OH

The reaction path, the dynamical properties along the reaction path and CVT rate constants are computed by the ab initio MO method, the reaction path Hamiltonian theory and the variational transition state theory. The results show that the effect of the electron correlation energy on activation barrier is large, the recrossing and tunneling effects exist in the reaction.     

Ab initio Studies on the Fe-S Protein Model Complexes

In this paper, ab initio calculations of the iron-sulfur protein model complexes have been completed on Fe_2S_2(SH)_2~(n-) and Fe_4S_4(SH)_4~(n-)(n=2, 3). The results indicate that the occupied terminal sulfur characteristic orbitals are found in the front orbital site and the energy levels of the occupied Fe 3d-like orbitals appear internally below the S-H bonding orbitals in the valence band. Although the energy sequence is different from what was reported in literature, our results are in agreement with the relevant experimental facts. We have discussed the reason that variations of the active sites are produced by various oxidation levels. The action mechanism of the Fe-S proteins as electron carriers in the biological processes is also explored preliminarily.     

Theoretical studies of the reactions of O(~3p) with halogenated methyl (Ⅰ)——Reaction mechanism of the O(~3p) CH_2Cl reaction

The reaction of O(~3P) with CH_2Cl radical has been studied using ab initio molecular orbital theory. G2 (MP2) method is used to calculate the geometrical parameters, vibrational frequencies and energies of various stationary points on the potential energy surface. The reaction mechanism is revealed. The addition of O(~3P) with CH_2Cl leads to the formation of an energy rich intermediate OCH_2Cl which can subsequently undergo decomposition or isomerization to the final products. The calculated heat of reaction for each channel is in agreement with the experimental value. The production of H CHClO and Cl CH_2O are predicted to be the major channels. The overall rate constants are calculated using transition state theory on the basis of ab initio data. The rate constant is pressure independent and exhibits negative temperature dependence at lower temperatures, in accordance with the experimental results.     

Theoretical studies on the structures and reactivity of stannylenoids I.The structures and isomerization of stannylenoid H_2SnLiF

The structures of singlet stannylenoid H2SnLiF have been examined by ab initio MO theory. Four equilibrium states and three transition states of isomerization reaction are located. The calculation shows that the p-complex 1 is the most stable and experimentally detectable. The other three species, three-membered ring 2, o-complex 3 and tetrahedron 4, are also local minima on the potential energy surface, but are higher in energy.     

Theoretical Studies on Structures and Properties of Endohedral Fullerenes Complexes： XHn@C32（X=F,O, N,C; n=l-4）

Theoretical studies on structures and properties of endohedral fullerene complexes formed by encapsulating small molecules of HF, H20, NH3, and CH4 in a C32 fullerene cage, were carried out by ab initio method. Current calculations reveal that these processes to encase them in fullerene are energetically unfavorable because of the small cavity size of C32. The red shift in the F-H stretching frequency indicates the potential existence of hydrogen bonding between the HF molecule and the carbon cage.     

A MOLECULAR ORBITAL STUDY ON ADENOSINE PHOSPHATES

AMP, ADP and ATP are calculated using the CNDO method, and ATP is studied by an ab initio calculation.The essential features of the electronic structure of these molecules are described in detail. Their ionization potentials, dipole moments and bond orders are given.The interaction between ATP with metal ions and enzyme molecules is discussed.     

Dynamical studies of the reaction H~++He+He→HHe~++He

The classical trajectory method is employed to calculate the rate coefficient kr for the reaction H++He+He-HHe++He at the temperatures ranging 200-350 K, based on an ab initio potential energy surface. The results show that kr is strongly dependent on the temperature, which can be well fitted by the function kr=ATDr-3 with A=4.192x10-31 cm6/s and the reaction dimension Dr=2.706. The product molecules HHe+ are found in high vibrational states.     

Ab initio study of the complexes of first-row transition-metal ions with CH, CH_2, and CH_3

The geometries and bonding characteristics of the complexes of the first-row transition-metal ions with CH, CH_2 and CH_3 were investigated by ab initio molecular orbital theory. MCH~ and MCH_2~ are linear and coplanar, re spectively. Both of them are with obvious treble or double bond characteristics, but these multiple bonds are mostly "im perfect". The calculated bond dissociation energies of C--M~ , C=M~ and C≡M~ are mostly close to the experi mental values, and appear in similar periodic trends from Sc to Zn.     

Topological studies on IRC paths of the isomerization reaction of silicon methyl-nitrene

On the basis of kinetic study of isomerization reaction of H_3Si-N, ab initio (RHF, UHF/6-31G) calculations on some points of the singlet and triplet reaction paths were carried out. The breakage and formation of chemical bond in the reaction are discussed. The calculated results show that there is a transitional structure of three-membered ring on each of reaction paths. A 'structural transition region' and a 'structural transition state' in both of studied reaction are found. Our previous conclusion that the structure transition state (STS) always appears before the energy transition state (ETS) in endothermic reaction and after ETS in exothermic reaction is further confirmed. The relationship between the change of spin density distribution and the structural transition state are investigated.     

分子间相互作用的研究——-价轨道模型势从头算能量分解法

研究分子间相互作用是了解液体,固体性质和结构以及气体性质的关键,也是研究化学和生物化学催化机制及化学反应途径的重要方面.因此,近几年来这个领域的理论和实验研究引起了人们广泛的兴趣并取得了长足的进步.特别值得指出的是Morokuma等提出的基于单行列式从头算的能量分解法,较好地解决了很多体系中分子间相互作用的本质问题,受到了理论化学界的普遍重视.但是这种方法很费计算机时间,对于较大的体系,特别是含有重原子的体系,应用受到了限制.因此简化这种方法,使它能够比较容     

Would the pseudocoordination centre method be appropriate to describe the geometries of lanthanide complexes?

The correct prediction of the ground-state geometries of lanthanide complexes is an important step in the development of efficient light conversion molecular devices (LCMD). Considering this, we evaluate here the capability of semiempirical approaches and ab initio effective core potential (ECP) methodology in reproducing the coordination polyhedron geometries of lanthanide complexes. Initially, we compare the facility of two semiempirical approaches: Pseudocoordination centre method (PCC) and Sparkle model. In the first step, we considered only high-quality crystallographic structures and included 633 complexes, and in the last step, we compare the capability of two semiempirical approaches with ab initio/ECP calculations. Because this last methodology was found to be computationally very demanding, we further used a subset containing 91 high-quality crystallographic structures. A total of 91 ab initio full geometry optimizations were performed. Our results suggest that only the semiempirical Sparkle model (hundreds of times faster) present accuracy similar to what can be obtained by present-day ab initio/ECP full geometry optimization calculations on such lanthanide complexes. In addition, it further indicates that the PCC approach has a poor prediction related to the coordination polyhedron geometries of lanthanide complexes.     

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations

We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.     

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.     

Infrared spectra of the complexes of trifluoroethene with dimethyl ether, acetone, and oxirane: a cryosolution study

Infrared spectra of solutions of trifluoroethene and dimethyl ether, acetone, or oxirane in liquid krypton and liquid argon have been studied. For each Lewis base the formation of a 1:1 complex with the Lewis acid was observed. The C-H stretching of trifluoroethene being perturbed by a strong Fermi resonance, the complexes with trifuloroethene-d were also investigated and showed that in each case the hydrogen bond between the acid and base is of the traditional, red-shifting type. The structures of the complexes were investigated using ab initio calculations. These indicate that with dimethyl ether and acetone two different isomeres can be formed, but with a single one detected in the solution in each case. The Fermi resonance in the complex with unlabeled trifluoroethene is discussed using data derived form ab initio potential and dipole hypersurface calculations. The complexation enthalpies of the complexes were obtained from temperature dependent studies of the solutions and are discussed in relation to the ab initio complexation energies and Monte Carlo free energy perturbation calculations of solvent effects.     

Ab initio calculation of anisotropic magnetic properties of complexes. I. Unique definition of pseudospin Hamiltonians and their derivation

A methodology for the rigorous nonperturbative derivation of magnetic pseudospin Hamiltonians of mononuclear complexes and fragments based on ab initio calculations of their electronic structure is described. It is supposed that the spin-orbit coupling and other relativistic effects are already taken fully into account at the stage of quantum chemistry calculations of complexes. The methodology is based on the establishment of the correspondence between the ab initio wave functions of the chosen manifold of multielectronic states and the pseudospin eigenfunctions, which allows to define the pseudospin Hamiltonians in the unique way. Working expressions are derived for the pseudospin Zeeman and zero-field splitting Hamiltonian corresponding to arbitrary pseudospins. The proposed calculation methodology, already implemented in the SINGLE_ANISO module of the MOLCAS-7.6 quantum chemistry package, is applied for a first-principles evaluation of pseudospin Hamiltonians of several complexes exhibiting weak, moderate, and very strong spin-orbit coupling effects.     

One- and three-parameter density functional theory and high level ab initio theory study of the CH+CH disproportionation reaction

Complete basis set (CBS) ab initio computational studies were performed with the target being to explore the CH+CH potential energy surface. Several closed and open shell intermediates were located on the potential energy surface. Computed enthalpies for the branching reactions, as well as heats of formation are in excellent agreement. Although CBS computed energies are of high quality, this computational study is not capable of predicting the branching product ratio due to fact that neither the MP2 nor the 6-311G(2d,2p) basis set are sufficient to locate the reactant complexes and the transition state structures for the hydrogen and carbon transfer reactions in the reaction complexes. To properly explore the CH+CH potential energy surface a much higher ab initio theory level is required.     

The influence of the Jahn-Teller effect and of heteroligands on the reactivity of Cu2+

Experimentally hardly accessible Jahn-Teller inversions and the influence of heteroligands on the reactivity of Cu2+ are characterized by ab initio QM/MM MD simulations of Cu2+ ion and its amino complexes in water.