Katsuyoshi Yamasaki

The origin of the generalized anomeric effect: possibility of CH/n and CH/pi hydrogen bonds

Ab initio MO calculations were carried out at the MP4/6-311++G(3df,3pd)//MP2/6-311++G(3df,3pd) level to investigate the conformational Gibbs energy of a series of methyl ethers CH(3)O-CH(2)-X (X=OH, OCH(3), F, Cl, Br, CN, C triple bond CH, C(6)H(5), CHO). It was found that the Gibbs energy of the gauche conformers is lower in every case than that of the corresponding anti conformers. In the more stable gauche conformers, the interatomic distance between X and the hydrogen atom was shorter than the sum of the van der Waals radii. The natural bonding orbital (NBO) charges of group X were more negative in the gauche conformers than in the anti conformers. We suggest that the CH/n and CH/pi hydrogen bonds play an important role in stabilizing the gauche conformation of these compounds.

Theoretical molecular double-core-hole spectroscopy of nucleobases.

Double-core-hole (DCH) spectra have been investigated for pyrimidine, purine, the RNA/DNA nucleobases, and formamide, using the density functional theory (DFT) method. DCH spectra of formamide were also examined by the complete-active-space self-consistent-field (CASSCF) method. All possible single- and two-site DCH (ssDCH and tsDCH) states of the nucleobases were calculated. The generalized relaxation energy and interatomic generalized relaxation energy were evaluated from the energy differences between ssDCH and single-core-hole (SCH) states and between tsDCH and SCH states, respectively. The generalized relaxation energy is correlated to natural bond orbital charge, whereas the interatomic generalized relaxation energy is correlated to the interatomic distance between the core holes at two sites. The present analysis using DCH spectroscopy demonstrates that the method is useful for the chemical analysis of large molecular systems.

Acceleration of the Reaction OH + CO → H + CO2 by Vibrational Excitation of OH

The collision complex formed from a vibrationally excited reactant undergoes redissociation to the reactant, intramolecular vibrational relaxation (randomization of vibrational energy), or chemical reaction to the products. If attractive interaction between the reactants is large, efficient vibrational relaxation in the complex prevents redissociation to the reactants with the initial vibrational energy, and the complex decomposes to the reactants with low vibrational energy or converts to the products. In this paper, we have studied the branching ratios between the intramolecular vibrational relaxation and chemical reaction of an adduct HO(v)-CO formed from OH(X(2)Π(i)) in different vibrational levels v = 0-4 and CO. OH(v = 0-4) generated in a gaseous mixture of O(3)/H(2)/CO/He irradiated at 266 nm was detected with laser-induced fluorescence (LIF) via the A(2)Σ(+)-X(2)Π(i) transition, and H atoms were probed by the two-photon excited LIF technique. From the kinetic analysis of the time-resolved LIF intensities of OH(v) and H, we have found that the intramolecular vibrational relaxation is mainly governed by a single quantum change, HO(v)-CO → HO(v-1)-CO, followed by redissociation to OH(v-1) and CO. With the vibrational quantum number v, chemical process from the adduct to H + CO(2) is accelerated, and vibrational relaxation is decelerated. The countertrend is elucidated by the competition between chemical reaction and vibrational relaxation in the adduct HOCO.

Photoemission cross sections for CH radicals produced by collisions of He(23S) atoms with CH3X (X=H, Cl, Br, I)

Photoemission cross sections (σem) for the A–X, B–X, and C–X bands of CH resulting from the He(23S)+CH3X (X=H, Cl, Br, I) reaction have been studied in the relative collision energy (ER) of 120–210 meV. Formation cross sections (σ) for CH(A, B, C) were evaluated from the σem’s taking account of predissociation. A good correlation was found between the sum of the σ’s for CH and the dipole-induced dipole interaction of He(2 3S) with targets. The σem’s from methane increase with ER, while those from methyl halides decrease with increasing ER. The positive energy dependence for methane implies that effective potentials leading to CH are repulsive, whereas attractive potentials play a dominant role in the reaction of He(2 3S) with methyl halides. Model potentials between CH3Cl and He*(Li) calculated using ab initio molecular orbital methods indicate that He(2 3S) approaches CH3Cl not from CH3 side but from Cl side.

Molecular dynamics studies of the structural change in 1,3-diamino-2,4,6-trinitrobenzene (DATB) in the crystalline state under high pressure.

Molecular dynamics (MD) calculations were performed to reveal the effect of high pressure on the crystal of 1,3-diamino-2,4,6-trinitrobenzene (DATB). The coordinates of the individual atoms in the DATB crystal structure were obtained using X-ray diffraction analysis. The primary simulation cell consists of 54 molecules in a monoclinic cell, corresponding to 27 unit cells obtained by replicating the experimentally determined unit cell. The pressure dependence of intermolecular distance concerning hydrogen bonds in the DATB crystal was investigated in the range of 1 atm to 25.0 GPa by increasing the pressure at every 0.5 GPa. Intermolecular distances of the hydrogen bonds between the nitro and amino groups decrease with increasing pressure up to 25.0 GPa, except in the range of 7.5 to 8.5 GPa. A unique structural change in the DATB crystal occurred at approximately 7.5 GPa. Intermolecular distances began to remarkably increase at 7.5 GPa and kept increasing until 8.5 GPa. To clarify the origin of this strange behavior, we used the same pressure regions as those above to analyze the changes in the dihedral angles defined by the plane of the nitro or amino group and by the aromatic rings of hydrogen bonds. The results showed a strong correlation between the increment of the intermolecular distances and the changes in the dihedral angles for these groups. Moreover, when the pressure dependence of the crystal parameter was analyzed, it was found that the a-axis length did not change despite the change in the lengths of the other two axes. The direction of the a axis corresponds to the direction of intermolecular hydrogen bond networks in the crystal. The results of the present MD calculations explained our previous results for Raman spectra measurements. Further analysis showed that these hydrogen bonds play an important role in stabilizing the energy change of the crystal system.

Efficient vibrational relaxation of O2(X 3Σ−g, ν = 8) by collisions with CF4

A laser flash photolysis–laser-induced fluorescence (LIF) technique has been employed to study the relaxation kinetics of vibrationally excited O2(X 3Σ−g). The time-resolved LIF excited B 3Σ−u–X 3Σ−g system has been recorded and analyzed by the integrated-profiles method. The rate coefficient for vibrational relaxation of O2(X 3Σ−g, ν = 8) by collisions with CF4, [1.4 ± 0.3(2σ)] × 10−11 cm3 molecule−1 s−1, indicates that CF4 is an efficient relaxant of O2(X 3Σ−g) and that the propensity rule for O2 relaxation suggested by Mack et al. (J. A. Mack, K. Mikulecky and A. M. Wodtke, J. Chem. Phys., 1996, 105, 4105) has been observed experimentally.

Importance of the CH/π hydrogen bond in the enhancement of CD amplitude of exomethylene steroids

Introduction of an axial methyl group to a bridgehead carbon has been known to enhance the circular dichroism (CD) amplitude of exomethylene steroids such as 4- and 6-methylene-5α-estrane, at ca. 200 nm (π/π* transition). To investigate the effect of a methyl group on the rotational strength of these steroids, time-dependent density functional theory (DFT) calculations were carried out at the M06-2X/6-311++G(d,p)//MP2/6-31G(d,p) level. It has been shown that the replacement of the bridgehead hydrogen atom at position 10 of these steroids by a methyl group influenced the CD amplitude at the π/π* transition. Analysis of natural bonding orbital (NBO) charges of relevant atoms has provided data consistent with this finding. In view of this, we suggest that the enhancement of the CD amplitude by methyl substitution β to the carbon-carbon double bond originates from the CH/π hydrogen bond occurring between CH groups and the π-system.

Kinetic study of vibrational energy transfer from a wide range of vibrational levels of O2(X(3)Sigma(g)-, v = 6-12) to CF4.

A wide range of vibrational levels of O2(X(3)Sigma(g)(-), v = 6-13) generated in the ultraviolet photolysis of O3 was selectively detected by the laser-induced fluorescence (LIF) technique. The time-resolved LIF-excited B(3)Sigma(u)(-)-X(3)Sigma(g)(-) system in the presence of CF4 has been recorded and analyzed by the integrated profiles method (IPM). The IPM permitted us to determine the rate coefficients k(v)(CF4) for vibrational relaxation of O2(X(3)Sigma(g)(-), v = 6-12) by collisions with CF4. Energy transfer from O2 (v = 6-12) to CF4 is surprisingly efficient compared to that of other polyatomic relaxation partners studied so far. The k(v)(CF4) increases with vibrational quantum number v from [1.5 +/- 0.2(2sigma)] x 10(-12) for v = 6 to [7.3 +/- 1.5(2sigma)] x 10(-11) for v = 12, indicating that the infrared-active nu3 vibrational mode of CF4 mainly governs the energy transfer with O2(X(3)Sigma(g)(-), v = 6-12). The correlation between the rate coefficients and fundamental infrared intensities has been discussed based on a comparison of the efficiency of energy transfer by several collision partners.

He*(2 3S) Penning ionization of H2S. I. Theoretical Franck–Condon factors for the H2S(X̃ 1A1,v′=0)→H2S+(X̃ 2B1,à 2A1) ionization and H2S+(ÖX̃) transition

In order to elucidate the ionization dynamics, in particular the vibrational distribution, of H2S+(A) produced by the Penning ionization of H2S with He*(2 3S) atoms, the Franck–Condon factors (FCFs) were presented for the H2S(X)→H2S+(X,A) ionization and the H2S+(A–X) transition, and Einstein’s A coefficients were presented for the latter transition. The FCFs were obtained by quantum vibrational calculations using the global potential energy surfaces (PESs) of H2S(X 1A1) and H2S+(X 2B1,A 2A1,B 2B2) electronic states. The global PESs were determined by the multireference configuration interaction calculations with the Davidson correction and the interpolant moving least squares method combined with the Shepard interpolation. The obtained FCFs exhibit that the H2S+(X) state primarily populates the vibrational ground state since its equilibrium geometry is almost equal to that of H2S(X), while the bending mode (ν2) is strongly enhanced for the H2S+(A) state; the maximum in the population is around ν2=...

Vibrational energies for the X̃1 A1, Ã1 B1, and B̃1 A1 states of SiH2/SiD2 and related transition probabilities based on global potential energy surfaces

Transition probabilities were evaluated for the XA11-AB11 and AB11-BA11 systems of SiH2 and SiD2 to analyze the X→A→B photoexcitation. The Franck–Condon factors (FCFs) and Einstein’s B coefficients were computed by quantum vibrational calculations using the three-dimensional potential energy surfaces (PESs) of the SiH2(XA11,AB11,BA11) electronic states and the electronic transition moments for the X-A, X-B, and A-B system. The global PESs were determined by the multireference configuration interaction calculations with the Davidson correction and the interpolant moving least-squares method combined with the Shepard interpolation. The obtained FCFs for the X-A and A-B systems exhibit that the bending mode is strongly enhanced in the excitation since the equilibrium bond angle greatly varies with the three states; the barrier to linearity is evaluated to be 21 900cm−1 for the X state, 6400cm−1 for the A state, and 230–240cm−1 for the B state. The theoretical lifetimes for the pure ben...