Guosen Yan

Density functional theory studies on molecular structure and IR spectra of 9‐methyladenine: A scaled quantum mechanical force field approach

Density functional theory with the combined Beckes three-parameter exchange functional in combination with the Lee, Yang, and Parr correlation functional (B3LYP) exchange–correlation energy functions using the 6-31G* basis set was applied to study the structures and vibrational infrared (IR) spectra of 9-methyladenine and the related compounds purine and adenine. The calculated force fields were scaled with the scale factors determined from purine. The predicted vibrational frequencies and isotopic shifts of IR bands of adenine and 9-methyladenine were compared with the available observed matrix-isolated IR spectra with a mean deviation of about 6.4 cm−1. The results made it possible to give reliable assignments of the IR spectra of these molecules. This study shows that the scaled density functional force field approach enables, through the transferability of scale factors, good interpretation of vibrational spectra of large molecules.

DFT Study and Monte Carlo Simulation on the Aminolysis of XC(O)OCH3 (X = NH2, H, and CF3) with Monomeric and Dimeric Ammonias.

The aminolysis of substituted methylformates (XC(O)OCH3, X = NH2, H, and CF3) in the gas phase and acetonitrile are investigated by the density functional theory B3LYP/6-311+G(d,p) method and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques. The direct and the ammonia-assisted aminolysis processes are considered, involving the monomeric and dimeric ammonia molecules, respectively. In each case, two different pathways, the concerted and stepwise, are explored. The calculated results show that, for the direct aminolysis, the activation barrier of the concerted path is lower than that of the rate-controlling step of the stepwise process for all three reaction systems. In contrast, for the ammonia-assisted mechanism, the stepwise process is more favorable than the concerted pathway. The substituent effects at the carboxyl C atom of methylformate are discussed. This aminolysis of substituted methylformates is more favored for X = CF3 than for X = H and NH2 in the gas phase for both the direct and the ammonia-assisted processes. Solvent effects of CH3CN on the reaction of HC(O)OCH3 + nNH3 (n = 1, 2) are determined by Monte Carlo simulation. The potential energy profiles along the minimum energy paths in the gas phase and in acetonitrile are obtained. It is shown that CH3CN lowers the energy barriers of all reactions.

Theoretical studies for structures and energetics of Rgn-N2O (Rg=He, Ne, Ar) clusters

Minimum‐energy structures of the Rg2N2O (RgHe, Ne, Ar) clusters have been determined with ab initio MP2 optimization, whereas the minimum‐energy structures of the RgnN2O clusters with n = 3–7 have been obtained with the pairwise additive potentials. Interaction energies and nonadditive three‐body effects of the Rg2N2O ternary complex have been calculated using supermolecule method at MP4 and CCSD(T) levels. It was found from the calculations that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The nonadditive three‐body effects were found to be small for Rg2N2O complexes. Our calculations also indicated that, for HenN2O and NenN2O clusters, the first six He and Ne atoms form the first solvation ring around the middle nitrogen of the N2O monomer, while for ArnN2O, the first five Ar atoms form the first solvation ring.

Ab initio potential energy surface and rovibrational spectra of Ne–N2O

Abstract The intermolecular potential energy surface for Ne–N 2 O has been calculated using the fourth-order Moller–Plesset (MP4) perturbation theory with a large basis set containing bond functions. The MP4 potential is found to have three minima corresponding to the T-shaped and the linear Ne–ONN and Ne–NNO structures. The geometry for the T-shaped configuration is in good agreement with the experimental values. The rovibrational energy levels are calculated. The calculated results show that the MP4 potential supports 27 and 28 vibrational bound states for 20 Ne–N 2 O and 22 Ne–N 2 O complexes, respectively. The calculated transition frequencies are very close to the observed values.

Quantum calculation of highly excited vibrational energy levels of CS2(X) on a new empirical potential energy surface and semiclassical analysis of 1:2 Fermi resonance

We report a refined potential energy function for the ground electronic state of CS2 based on a least-squares fitting to several low-lying experimental vibrational frequencies. Energy levels up to 20,000 cm(-1) have been obtained on this empirical potential using the Lanczos algorithm and potential optimized discrete variable representation. Among them, 329 levels below 10,000 cm(-1) are assigned with approximate normal mode quantum numbers (n1, n(0)2, n3), based on expectation values of one-dimensional (1D) reference Hamiltonians. An effective Hamiltonian is extracted from these assigned levels. The agreement with experimental data, including those of several isotopically substituted species, is excellent. In addition, some Fermi and anharmonic resonances are analyzed. The nearest neighbor level spacing and delta3 distributions indicated that the vibrational spectrum of CS2 is largely regular in the energy range up to 20,000 cm(-1). Semiclassical phase space analysis, including bifurcation analysis of the spectroscopic Hamiltonian, is used to interpret subtle anomalies signaled by expectation values used in normal mode assignments. The meaning of Fermi resonance is clarified by contrasting the semiclassical analysis of CS2 and CO2.

Density functional theory studies on tautomeric stability and infrared spectra of 2-chloroadenine

The tautomeric stability and vibrational IR spectrum of 2-chloroadenine were studied using density functional theory (DFT) at B3LYP/6-31G* level. The amino N(9)H tautomer of 2-chloroadenine was predicted to be most stable. A scaled quantum mechanical (SQM) force field approach was used to calculate the vibrational frequencies of amino N(9)H form of 2-chloroadenine. The force constant scale factors were transferred from those of purine. The mean deviation between the predicted vibrational frequencies and the observed ones is 8.0 cm(-1). The results made it possible to give complete assignments of the IR spectrum of this molecule.

Theoretical Study of the Acid-Promoted Hydrolysis of Oxazolin-5-one : A Microhydration Model

The acid-promoted hydrolysis of 2,4,4-trimethyloxazolin-5-one (TMO) is studied employing the density functional theory (B3LYP) method in conjunction with the 6-31++G(d,p) basis set. Two types of reaction mechanism, N-protonated and O-protonated, are considered, involving protonation at the nitrogen and carbonyl oxygen of TMO to activate the C2 and C5 atoms, respectively, in favor of attack by water molecules. In the N-protonated pathway, the nucleophilic water molecule attacks the activated C2 atom, with a proton transfer from the water molecule to the oxygen atom attached to C2 and the fission of the C2-O bond, leading to a cis ring-opening product (N-acyl-alpha-amino isobutyric acid). While, in the O-protonated pathway, the nucleophilic water molecule attacks the activated carbonyl C5 atom, accompanied by a proton transfer from the water molecule toward the nitrogen atom of oxazole ring and the cleavage of C5-O bond; as a result, a corresponding trans product is generated. The water-assisted hydrolysis reactions are also examined together. A local microhydration model, in which an extra water molecule was added to obtain a continuous H-bond network around the reaction centers, was adopted to mimic the system for the two types of reaction processes. In addition, bulk solvent effect is introduced by use of the conductor-like polarizable continuum model (CPCM). Our computational results in kinetics and thermodynamics clearly manifest that the O-protonated pathway with the nucleophilic attack at the carbonyl C5 atom is more favorable than the N-protonated one, in nice agreement with the available experimental conclusion.

An ab initio potential energy surface of Ne–LiH

Abstract The intermolecular potential energy surface for Ne–LiH is calculated using the fourth-order Moller–Plesset perturbation approach with a large basis set consisting of the midpoint bond function set 3s3p2d. Two local potential minima are found to be located at the linear Ne–LiH ( θ =180°) and Ne–HLi ( θ =0°) geometry. The MP2 potential is also calculated to check the convergence of the potential. In addition, the vibrational energy levels are calculated using the vibrational SCF-CI method. Both MP2 and MP4 potentials support three bound vibrational states for the Ne–LiH system.

STUDY ON PHOTOCHEMISTRY OF CONCERTED 1,J AND I,J SIGMATROPIC REARRANGEMENTS BY THE CLASSICAL PATH METHOD

In this article, a simple and generalized method is developed for investigating nonadiabatic transitions in photochemical sigmatropic rearrangements. To achieve a rapid computation for concerted sigmatropic rearrangements, the many-body treatment developed by Matsen and the Landau-Zener model have been employed to construct the potential energy surfaces for the reaction systems, and to process the nonadiabatic transition probabilities. The nonadiabatic coupling term is evaluated by neglecting the atomic orbital deformation with respect to the reaction coordinate, thus enabling the calculation of coupling terms to be carried out with the topology of the reaction system. It can be seen from the calculations of the nonadiabatic transition for [1,3], [1,4], [1,5], and [3,3] sigmatropic rearrangements that this treatment gives more detailed information than that from the Woodward-Hoffmann rule and the usual molecular theories. The ratio lnP(H)lnP(M) (H = Huckel, M = Mobius) predicts the stereoselectivity of photochemical [i, j] sigmatropic rearrangements including cations, radicals and neutral molecules.

A study of the electronic structure and catalytic properties of the Keggin unit (PMo12O40)3

Abstract Dodecamolybdophosphates, which contain the large cluster anion known as the Keggin unit, have been known to be effective catalysts for many heterogeneous oxidation reactions. SCC-DV-Xα calculations have been performed on the electronic structure of the Keggin anion. According to calculated results, all the component atoms of the anion, P,O p ,O b ,O t , and Mo, have the potential to participate in catalytic reactions, which is strongly supported by many experimental results of K. Eguchi and others.