Misako Aida

An ab initio molecular orbital study on the characteristics of 8-hydroxyguanine.

To investigate the mechanism by which the 8-hydroxyguanine residue in DNA affects the fidelity of DNA replication, the intrinsic properties of this modified base were investigated using an ab initio molecular orbital method. The most stable 8-hydroxyguanine form was revealed to be 6,8-diketo. The addition of an oxygen atom to the 8 position of a guanine base was shown to change the electrostatic potential of the molecule entirely and to give it a negative character. This effect may influence the local structure of 8-hydroxyguanine-containing DNA and the interaction with DNA polymerase, thereby resulting in infidelity of DNA replication.

An ab initio molecular orbital study on the sequence-dependency of DNA conformation: An evaluation of intra- and inter-strand stacking interaction energy

The various nearest neighbor stacking interaction energies of stacked base pairs in the DNA double helix are calculated for both A- and B-type conformations using an ab initio molecular orbital method. It is demonstrated that the sequence-dependent conformational preference for A- or B-type results from the stacking interaction. In particular, the base sequence showing the highest preference for an A-type conformation is revealed as GC/GC, and the one with the next highest preference, AT/AT; for a B-type conformation, the respective sequences are CG/CG and CA/TG. The overall conformation of a DNA fragment is not determined by these particular sequences only but is influenced by all base pair steps. An intrinsically favorable conformation is predicted from the constituent stacking interaction.

Raman scattering tensors of tyrosine

Polarized Raman scattering measurements have been made of a single crystal of L-tyrosine by the use of a Raman microscope with the 488.0-nm exciting beam from an argon ion laser. The L-tyrosine crystal belongs to the space group P2(1)2(1)2(1) (orthorhombic), and Raman scattering intensities corresponding to the aa, bb, cc, ab and ac components of the crystal Raman tensor have been determined for each prominent Raman band. A similar set of measurements has been made of L-tyrosine-d4, in which four hydrogen atoms on the benzene ring are replaced by deuterium atoms. The effects of NH3-->ND3 and OH-->OD on the Raman spectrum have also been examined. In addition, depolarization ratios of some bands of L-tyrosine in aqueous solutions of pH 13 and pH 1 were examined. For comparison with these experimental results, on the other hand, ab initio molecular orbital calculations have been made of the normal modes of vibration and their associated polarizability oscillations of the L-tyrosine molecule. On the basis of these experimental data and by referring to the results of the calculations, discussions have been presented on the Raman tensors associated to some Raman bands, including those at 829 cm-1 (benzene ring breathing), 642 cm-1 (benzene ring deformation), and 432 cm-1 (C alpha-C beta-C gamma bending).

Ab initio molecular dynamics simulations on the hydrolysis of methyl chloride with explicit consideration of three water molecules

Ab initio molecular dynamics (MD) simulations were performed on the hydrolysis of methyl chloride (CH3Cl) with explicit consideration of three water molecules to understand the dynamics of the reaction and the role of solvent molecules in SN2 reactions in solution. The simulations clearly showed the existence and dynamical characteristics of two nearly concerted proton transfers involving the attacking water molecule and the solvent water molecules on the way to formation of the products. Observation of these proton transfers points clearly to the need for an explicit quantum chemical treatment of at least a few solvent water molecules to describe methyl chloride solvolysis.

A polarizable mixed Hamiltonian model of electronic structure for micro-solvated excited states. I. Energy and gradients formulation and application to formaldehyde (1A2)

We describe an efficient implementation of a polarizable mixed Hamiltonian model of electronic structure that combines Hartree–Fock, Kohn–Sham, or multiconfiguration quantum-chemical wave functions with a polarizable and flexible molecular mechanics potential of water, and that is applicable to micro-solvated electronic excited states. We adopt a direct algorithm for the calculation of the polarization response of the solvent subsystem. The strategy facilitates the calculation of the energy of the system and of the forces with respect to the solute coordinates and the solvent coordinates, including for excited states. This capability opens the way to the determination of optimized, transition structures, force constants, and intrinsic reaction pathways for the solute–solvent system, and to molecular dynamics calculations to account for finite temperature effects. As an illustration we characterize the structure and energy of micro-solvated formaldehyde H2CO in its ground state and in its 1(π*←n) excited s...

Enumeration of topology-distinct structures of hydrogen bonded water clusters

Abstract We present a graph theoretical procedure to generate all the topology-distinct structures for water clusters. The hydrogen bond matrix (H-B matrix) is defined and used to enumerate the topology-distinct structures. The generated hydrogen bond matrices are used as the theoretical framework to obtain all the topology-distinct local minima for (H 2 O) n ( n ⩽4); each of the local minima is different in the topology of the hydrogen bonding pattern.

Vibrational modes in thymine molecule from an ab initio MO calculation

Abstract Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

One transition state leading to two product states: ab initio molecular dynamics simulations of the reaction of formaldehyde radical anion and methyl chloride

Ab initio molecular dynamics (MD) simulations for the reaction of formaldehyde radical anion and methyl chloride indicate that trajectories starting from a well-characterized single transition state reach either an electron-transfer (ET) product or a C-substituted SN2 product. The two kinds of trajectories have different characteristics. Trajectories which lead to the SN2 product state are simple, with C–C bond formation and C–Cl bond breaking essentially completed within 50 fs. By contrast, trajectories leading to the ET product are more complex with a sudden electron reorganization taking place around 15–30 fs; the major bonding changes and electron and spin reorganization are completed after 250 fs.

An ab initio MO study on the disulfide bond: properties concerning the characteristic S-S dihedral angle

The characteristics of disulfide groups concerning the S-S dihedral angle are represented by ab initio SCF calculations using the split-valence 6-31G(*) basis set. It is shown that the hyperconjugation between the S-H bond and the electron pair on the other sulfur plays an important role in determining the characteristic S-S dihedral angle. The S 3d orbitals do not participate in such characteristics. The nature of the S-S bond is compared with that of the O-O bond. The S-S bond length varies largely depending on the S-S dihedral angle. This is related to the frequency-conformation correlation of the disulfide group.

Chiral sum frequency spectroscopy of thin films of porphyrin J-aggregates.

Thin films of chiral porphyrin J-aggregates have been studied by vibrationally and electronically doubly resonant sum frequency generation (SFG) spectroscopy. It was revealed that the chiral supramolecular structures of porphyrin aggregates in solutions were retained in the thin film samples, and their chirality was determined by using chiral vibrational SFG spectroscopy. Electronic resonance profiles of some vibrational bands in achiral and chiral SFG were different from each other, and both were distinct from electronic absorption spectra. To account for these peculiar profiles, we have proposed interference effects of Raman tensor components in achiral and chiral SFG susceptibilities, which is analogous to that of resonance Raman scattering.