Biomedical subjects

Hua-Gen Yu

Publications and source records attributed to Hua-Gen Yu.

9 recordsLinked to original sources

PubMed2006

A rigorous full-dimensional quantum dynamics calculation of the vibrational energies of H3O-2.

The vibrational energy levels of the H(3)O-(2) anion have been calculated using a rigorous quantum dynamics method based on an accurate ab initio potential energy surface. The eigenvalue problem is solved using the two-layer Lanczos iterative diagonalization algorithm in a mixed grid/nondirect product basis set, where the system Hamiltonian is expressed in a set of orthogonal polyspherical coordinates. The lowest 312 vibrational energy levels in each inversion symmetry, together with a comparison of fundamental frequencies with previous quantum dynamics calculations, are reported. Finally, a statistical analysis of nearest level spacing distribution is carried out, revealing a strongly chaotic nature.

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PubMed2006

A clue to the diffuse structure in ultraviolet spectra of the GeCl2 A-X transition.

Geometries, harmonic vibrational frequencies, and relative electronic energies of the two low-lying electronic states of the GeCl(2) dimer have been calculated at the CIS(D) method with a cc-pVTZ basis set. Minima corresponding to three isomers on the ground-state potential energy surface have been characterized. The most stable dimer has a dissociation energy of 0.74 eV and has a trans-(GeCl(2))(2) structure. There is also a related, less stable, cis minimum. A third, C(i) symmetry, isomer has a binding energy of 0.31 eV. It is found that this C(i) isomer has substantial dipole transition strength to the first excited singlet state of the dimer with a vertical excitation energy of 3.33 eV. The transition energy (T(0)) between this C(i) isomer and the van der Waals complex on the singlet excited state is predicted to be 4.007 eV, or a 1104 cm(-1) blueshift with respect to that of the GeCl(2) A-X transition. This finding may explain the diffuse structure which has been observed in the ultraviolet laser-induced fluorescence spectra of GeCl(2).

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PubMed2006

Quantum molecular dynamics study of the reaction of O2 with HOCO.

The reaction of O2 with HOCO has been studied by using an ab initio direct dynamics method based on the UB3PW91 density functional theory. Results show that the reaction can occur via two mechanisms: direct hydrogen abstraction and an addition reaction through a short-lived HOC(O)O2 intermediate. The lifetime of the intermediate is predicted to be 660 +/- 30 fs. Although it is an activated reaction, the activation energy is only 0.71 kcal/mol. At room temperature, the obtained thermal rate coefficient is 2.1 x 10(-12) cm3 molecule(-1) s(-1), which is in good agreement with the experimental results.

Carbon Dioxide↗

PubMed2006

Hot bands in jet-cooled and ambient temperature spectra of chloromethylene.

Rotationally resolved spectra of several bands lying to the red of the origin of the A(1)A" - X (1)A' band system of chloromethylene (HCCl), were recorded by laser absorption spectroscopy in ambient temperature and jet-cooled samples. The radical was made by excimer laser photolysis of dibromochloromethane, diluted in inert gas, at 193 nm. The jet-cooled sample showed efficient rotational but less vibrational cooling. Analysis showed that the observed bands originate in the (upsilon(1),upsilon(2),upsilon(3)) = (010), (001), and (011) vibrational levels of the ground electronic state of the radical, while the upper-state levels involved were (000), (010), (001), and (011). Vibrational energies and rotational constants describing the rotational levels in the lower-state vibrational levels were determined by fitting to combination differences. The analysis also resulted in a reevaluation of the C-Cl stretching frequency in the excited state and we find E(001)' = 13 206.57 or 926.17 cm(-1) above the A(1)A" (000) rotationless level for HC(35)Cl. Scaled ab initio potential energy surfaces for the A and X states were used to compute the transition moment surface and thereby the relative intensities of different vibronic transitions, providing additional support for the assignments and permitting the prediction of the shorter wavelength spectrum. All the observed upper state levels showed some degree of perturbation in their rotational energy levels, particularly in K(a) = 1, presumably due to coupling with near-resonant vibrationally excited levels of the ground electronic state. Transitions originating in the low-lying a(3)A" were also predicted to occur in the same wavelength region, but could not be identified in the spectra.

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PubMed2005

Direct ab initio dynamics study of the OH + HOCO reaction.

The reaction between OH and HOCO has been examined using the coupled-cluster method to locate and optimize the critical points on the ground-state potential energy surface. The energetics are refined using the coupled-cluster method with basis set extrapolation to the complete basis set (CBS) limit. Results show that the OH + HOCO reaction produces H2O + CO2 as final products and the reaction passes through an HOC(O)OH intermediate. In addition, the OH + HOCO reaction has been studied using a direct dynamics method with a dual-level ab initio theory. Dynamics calculations show that hydrogen bonding plays an important role during the initial stages of the reaction. The thermal rate constant is estimated over the temperature range 250-800 K. The OH + HOCO reaction is found to be nearly temperature-independent at lower temperatures, and at 300 K, the thermal rate constant is predicted to be 1.03 x 10(-11) cm3 molecule(-1) s(-1). In addition, there may be an indication of a small peak in the rate constant at a temperature between 300 and 400 K.

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PubMed2005

A coherent discrete variable representation method for multidimensional systems in physics.

A coherent discrete variable representation (ZDVR) is proposed for constructing a multidimensional potential-optimized DVR basis. The multidimensional quadrature pivots are obtained by diagonalizing a complex coordinate operator matrix in a finite basis set, which is spanned by the lowest eigenstates of a two-dimensional reference Hamiltonian. Here a c-norm condition is used in the diagonalization procedure. The orthonormal eigenvectors define a collocation matrix connecting the localized ZDVR basis functions and the finite basis set. The method is applied to two vibrational models for computing the lowest bound states. Results show that the ZDVR method provides exponential convergence and accurate energies. Finally, a zeroth-order approximation method is also derived.

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PubMed2005

Ab initio and direct dynamics studies of the reaction of singlet methylene with acetylene and the lifetime of the cyclopropene complex.

The energetics of the (1)CH(2) + C(2)H(2) --> H + C(3)H(3) reaction are accurately calculated using an extrapolated coupled-cluster/complete basis set (CBS) method based on the cc-pVDZ, cc-pVTZ, and cc-pVQZ basis sets. The reaction enthalpy (0 K) is predicted to be -20.33 kcal/mol. This reaction has no classical barrier in either the entrance or exit channel. However, there are several stable intermediates-cyclopropene (c-C(3)H(4)), allene (CH(2)CCH(2)), and propyne (CH(3)CCH)-along the minimum energy path. These intermediates with zero-point energy corrections lie below the reactants by 87.11 (c-C(3)H(4)), 109.69 (CH(2)CCH(2)), and 110.78 kcal/mol (CH(3)CCH). The vibrationally adiabatic ground-state (VAG) barrier height for c-C(3)H(4) isomerization to allene is obtained as 45.2 kcal/mol, and to propyne as 37.2 kcal/mol. In addition, the (1)CH(2) + C(2)H(2) reaction is investigated utilizing the dual-level "scaling all correlation" (SAC) ab initio method of Truhlar et al., i.e., the UCCSD(SAC)/cc-pVDZ theory. Results show that the reaction occurs via long-lived complexes. The lifetime of the cyclopropene intermediate is obtained as 3.2 +/- 0.4 ps. It is found that the intermediate propyne can be formed directly from reactants through the insertion of (1)CH(2) into a C-H bond of C(2)H(2). However, compared to the major mechanism in which the propyne is produced through a ring-opening of the cyclopropene complex, this reaction pathway is much less favorable. Finally, the theoretical thermal rate constant exhibits a negative temperature dependence, which is in excellent agreement with the previous results. The temperature dependence is consistent with the earlier RRKM results but weaker than the experimental observations at high temperatures.

Journal Article↗

PubMed2004

Converged quantum dynamics calculations of vibrational energies of CH4 and CH3D using an ab initio potential.

Exact variational calculations of vibrational energies of CH4 and CH3D are carried out using a two-layer Lanczos algorithm based on the ab initio potential energy surface of D. W. Schwenke and H. Partridge, Spectrochim. Acta, Part A 57, 887 (2001). The convergence of the calculated vibrational energies is discussed in detail. In addition, we report all well converged vibrational energy levels up to 6600 cm(-1) for CH4, and those up to 5000 cm(-1) for CH3D, respectively. These results clearly outperform previous theoretical calculations. And a comparison with experimental results available is also made.

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PubMed2004

Full-dimensional quantum calculations of vibrational spectra of six-atom molecules. I. Theory and numerical results.

Two quantum mechanical Hamiltonians have been derived in orthogonal polyspherical coordinates, which can be formed by Jacobi and/or Radau vectors etc., for the study of the vibrational spectra of six-atom molecules. The Hamiltonians are expressed in an explicit Hermitian form in the spatial representation. Their matrix representations are described in both full discrete variable representation (DVR) and mixed DVR/nondirect product finite basis representation (FBR) bases. The two-layer Lanczos iteration algorithm [H.-G. Yu, J. Chem. Phys. 117, 8190 (2002)] is employed to solve the eigenvalue problem of the system. A strategy regarding how to carry out the Hamiltonian-vector products for a high-dimensional problem is discussed. By exploiting the inversion symmetry of molecules, a unitary sequential 1D matrix-vector multiplication algorithm is proposed to perform the action of the Hamiltonian on the wavefunction in a symmetrically adapted DVR or FBR basis in the azimuthal angular variables. An application to the vibrational energy levels of the molecular hydrogen trimer (H2)3 in full dimension (12D) is presented. Results show that the rigid-H2 approximation can underestimate the binding energy of the trimer by 27%. Finally, it is demonstrated that the two-layer Lanczos algorithm is also capable of computing the eigenvectors of the system with minor effort.

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