An ab initio MO study on the thymine dimer and its radical cation

Ab initio SCF calculations with the 6-31G basis set for the thymine dimer (cys-syn form) and the thymine dimer radical cation are reported. The fusion of the thymine bases at the C5 and C6 positions involves the formation of a cyclobutane ring with puckering. The puckering causes a notable difference in the electronic structures of the two bases of the thymine dimer. The density of the HOMO orbital of the thymine dimer is localized on the O2, N1, and C6 atoms of both thymine rings, with the higher density on one of the rings. The HOMO orbital has a bonding character on the C6(SINGLEBOND)C6 bond. In the thymine dimer radical cation, the unpaired electron is localized mainly on the lengthened C6(SINGLEBOND)C6 bond with the higher density on one of the C6 atoms and to a lesser extent on the N1 atoms of both rings. © 1996 John Wiley & Sons, Inc.     

An ab initio study of the reaction of ammonium ion with hydride ion and lithium hydride

Both the abstraction and substitution mechanisms for the reaction of NH⁺₄ with H^? and the abstraction mechanisms for the reaction with LiH in the gas phase have been investigated by theoretical methods. LiH results to be a better reagent and reactions with and without scrambling are competitive in accordance with experimental findings.     

Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study

The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.     

Interaction between thymine dimer and flavin-adenine dinucleotide: a DFT and direct ab initio molecular dynamics study

The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.     

Hydrated carbonium ions as possible nitrosamine metabolites: An ab initio study

Various isomers of CH₃(H₂O) (where n = 1–3) have been studied using self-consistent field gradient techniques. The calculations have largely employed a split valence (4-21G) basis set, although the effects of polarization functions and electron correlation have been considered for a model system. A mechanism for the formation of CH₃OH from CH₃(H₂O), involving linear hydration chains, is proposed, and the relevance of the results to the various proposed pathways for the decomposition of nitrosamine metabolites is discussed.     

An ab initio study of formamide

Calculated energy and molecular properties of the ground and low-energy excited states of formamide are presented at the ground state geometry. Satisfactory results are obtained except for the ¹* energy which remains too high by 1 eV (which is nevertheless a large improvement over previous calculations). The predicted triplet energies lie at 5.4 eV (³ n*) and 5.8 eV (³*).     

Possible gas-phase ion pairs in amine-HCl complexes. An ab initio theoretical study

Ab initio MO calculations were performed for complexes between HCl and NH₃, CH₃NH₂, (CH₃)₂NH and (CH₃) ₃N. SCF geometry optimization for the latter three complexes gives double-minimum potential surfaces, which become single- minimum surfaces when electron correlation is considered. It is proposed that (CH₃)₃NHCl may be an ion pair in the gas phase.     

An ab initio study of the proton transfer and tautomerization processes in hydroxycarbene

We have investigated the hydrogen-bonded complexes formed by hydroxycarbene in trans configuration at MP2 and CCSD computational levels. In addition, these complexes have been used as starting point in the potential tautomerization of hydroxycarbene to produce formaldehyde. The presence of molecules that can be involved in the tautomerization significantly reduces its barrier. The electron density of the different structures obtained has been analyzed with the Atoms in Molecules methodology.     

Evolution of intermolecular structure and dynamics in supercritical carbon dioxide with pressure: an ab initio molecular dynamics study

The effect of pressure on supercritical carbon dioxide (scCO2) has been characterized by using Car-Parrinello molecular dynamics simulations. Structural and dynamical properties along an isotherm of 318.15 K and at pressures ranging from 190 to 5000 bar have been obtained. Intermolecular pair correlation functions and three-dimensional atomic probability density map calculations indicate that the local environment of a central CO2 molecule becomes more structured with increasing pressure. The closest neighbors are predominantly oriented in a distorted T-shaped geometry while neighbors separated by larger distances are likely oriented in a slipped parallel arrangement. The structure of scCO2 at high densities has been compared with that of crystalline CO2. The probability distributions of intramolecular distances narrow down with increasing pressure. A marginal but non-negligible effect of pressure on the instantaneous intramolecular OCO angle is observed, lending credence to the idea that intermolecular interactions between CO2 molecules in an inhomogeneous near neighbor environment could contribute to the observed instantaneous molecular dipole moment. The extent of deviation from a perfect linear geometry of the carbon dioxide molecule decreases with increasing pressure. Time constants derived from reorientational time correlation functions of the molecular backbone compare well with experimental data. Within the range of thermodynamic conditions explored here, no significant changes are observed in the frequencies of intramolecular vibrational modes. However, a blue shift is observed in the low-frequency cage rattling mode with increasing pressure.     

An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree‐Fock level in conjunction with Dunning double‐ζ plus polarization function basis sets. The simulation predicts an average H? Cl bond distance of 1.28 Å, which is in good agreement with the experimental value. The H_HCl···O_w and Cl_HCl···H_w distances of 1.84 and 3.51 Å were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure‐making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Characterization of dynamics and reactivities of solvated ions by ab initio simulations

Based on a systematic investigation of trajectories of ab initio quantum mechanical/molecular mechanical simulations of numerous cations in water a standardized procedure for the evaluation of mean ligand residence times is proposed. For the characterization of reactivity and structure-breaking/structure-forming properties of the ions a measure is derived from the mean residence times calculated with different time limits. It is shown that ab initio simulations can provide much insight into ultrafast dynamics that are presently not easily accessible by experiment.     

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate.     

An ab initio study of ascorbic acid

The conformations of ascorbic acid and its singly ionized analog are found to agree with the X-ray structures. The calculations are discussed in terms of the known chemistry of ascorbic acid and its metabolites.     

Glycine interaction with carbon nanotubes: an ab initio study

The interaction of the glycine radical on the side walls of both armchair and zigzag single walled carbon nanotubes is investigated by density functional theory. It is found that the interaction potential of the N-centered glycine radical with the tubes has a minimum of 16.9 (armchair) and 20.2 (zigzag) kcal/mol with respect to the dissociation products. In contrast, the C-centered radical, which is 22.7 kcal/mol lower in energy than the N-centered radical, does not form stable complexes with both types of carbon nanotubes.     

An ab initio study of pyruvic acid

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Möller-Plesset level of theory using the 6-311++G^** basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.     

Neutral hydrolyses of carbon disulfide: An ab initio study of water catalysis

The water-catalyzed hydrolysis reaction of carbon disulfide (CS(2)) has been investigated at the levels of HF and MP2 with the basis set of 6-311++G(d,p) using the combined supramolecular/continuum models, in which up to six water molecules are involved in the hydrolysis and the effect of water bulk solvent is taken into account according to the polarizable continuum model (PCM). The activation Gibbs free energies in water solution, DeltaG(sol) (not equal) (298 K), for the rate-determining steps of one up to six water hydrolyses are 247.9, 184.2, 152.3, 141.8, 134.4, and 118.9 kJ/mol, respectively. The most favorable hydrolysis path of CS(2) involves a sort of eight-membered ring transition structure formed by six water molecules, among which three water molecules are not involved in the proton transfer, two near to the nonreactive sulfur atom, and one below the parent carbon disulfide. This suggests that the hydrolysis of CS(2) can be mediated with the water molecule(s) and be significantly facilitated by the cooperative effects of the water molecule(s) in the nonreactive region. The catalytic effects of water molecule(s) due to the alleviation of ring strain in the proton transfer process may result from the synergistic effects of rehybridization and charge reorganization from the prereaction complex to the rate-determining transition state structure induced by water molecule(s). PCM solvation models could significantly lower the rate-determining activation Gibbs free energies by 20-38 kJ/mol when two up to six explicit water molecules involved in the neutral hydrolysis of CS(2).     

三硝基苯-对位取代苯酚负离子荷移复合物从头算研究

运用G94W量子化学程序,在HF/3-21G基组水平上对三硝基苯-对位取代苯酚(取代基:CH~3O-,CH~3-,Cl-)负离子的电荷转移复合物进行从头计算。把电荷转移复合物看成一个超分子,研究该系列复合物的稳定性、电荷转移及几何构型等规律。计算结果表明,苯酚负离子供电中心O沿一倾角指向三硝基苯中的任意相邻两个硝基之间的C位置上,复合物的稳定性按对位取代苯酚取代基CH~3O-,CH~3-,Cl-的次序减小,与实验规律相一致。计算结果还表明,形成该系列复合物具有明显的电荷转移,其稳定性与电荷转移量有关等。