Biomedical subjects

Hiroto Tachikawa

Publications and source records attributed to Hiroto Tachikawa.

12 recordsLinked to original sources

PubMed2006

Diffusion dynamics of the li atom on amorphous carbon: A direct molecular orbital-molecular dynamics study.

Direct molecular orbital-molecular dynamics (MO-MD) calculation was applied to diffusion processes of the Li atom on a model surface of amorphous carbon and compared with the diffusion mechanism of Li+ ion. A carbon sheet composed of C96H24 was used as the model surface. The total energy and energy gradient on the full dimensional potential energy surface of the LiC96H24 system were calculated at each time step in the trajectory calculation. The optimized structure, where the Li atom is located at the center of mass of the model surface, was used as the initial structure at time zero. Simulation temperatures were chosen in the range of 200-1250 K. The dynamics calculations showed that the Li atom vibrates around the initial position below 250 K, and it moves above 300 K. At middle temperature, the Li atom translates freely on the surface. At higher temperature (1000 K), the Li atom moves from the center to edge region of the model surface and is trapped in the edge. The activation energy calculated for the Li atom is larger than that for the Li+ ion. This difference is due to the fact that the Li atom diffuses together with an unpaired electron on the carbon surface. The diffusion mechanism of the Li atom was discussed on the basis of the theoretical results.

Journal Article↗

PubMed2006

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach.

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.

Journal Article↗

PubMed2006

Direct observation and reactions of Cl3 radical.

The broad absorption of Cl3 radical was observed between 1150 and 1350 nm using cavity ring-down spectroscopy at 213-265 K and 50-200 Torr with He, N2, Ar, or SF6 diluents. The absorption intensity of Cl3 increased at lower temperature and higher pressure. SF6 was the most efficient diluent gas. The temperature dependent equilibrium constants for Cl3 formation from Cl+Cl2 were theoretically calculated at the MP4SDQ6-311+G(d) level. Observed decay time profiles of Cl3 and the pressure dependence of Cl3 formation are explained by the equilibrium reaction and a decay reaction of Cl+Cl3.

Journal Article↗

PubMed2006

Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl.

Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.

Journal Article↗

PubMed2006

Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study.

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

Journal Article↗

PubMed2005

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study.

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.

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PubMed2005

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bR: a TD-DFT study.

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin have been investigated by means of time-dependent density functional theory. The residues around PSBR are replaced by the point charges on atoms. The structures of PSBR and residues are referred from X-ray data. The atomic charges on the each residue were calculated the B3LYP/6-311G(d,p) level. The excitation energy of PSBR perturbed by the point charges on atoms of each residue was calculated at the B3LYP/6-31G(d,p) level. A total of 23 residues and five water molecules around PSBR were considered in the calculations. The large spectral shifts were caused by the Asp212 and Asp85. The origin of the spectral shifts was discussed on the basis of theoretical results.

Bacteriorhodopsins↗

PubMed2005

Experimental and theoretical studies on the organic-inorganic hybrid compound: aluminum-NTCDA Co-deposited film.

Electronic absorption, Fourier transform-infrared (FT-IR), and electron spin resonance spectra of aluminum-naphthalene tetracarboxylic dianhydlide (Al-NTCDA) co-deposited film have been measured at room temperature, and hybrid density functional theory (DFT) calculations have been carried out in order to elucidate the electronic states for the ground and low-lying excited states of the complexes. After the interaction of NTCDA with Al atom, the new electronic transition bands were appeared at near-IR region. The C=O stretching modes of NTCDA are red-shifted by the interaction with Al. From the DFT calculations, it was found that the electronic state of the complex at the ground state is characterized by a slight charge-transfer state expressed by (Al(4))(delta+)(NTCDA)(delta-). The binding of Al to NTCDA is strong. The C=O double-bond character of NTCDA is changed to C-O single-bond-like character by the strong interaction of Al to the C=O bond. This is the origin of the red-shift of the FT-IR spectrum. The electronic states of organic-inorganic hybrid material were discussed on the basis of theoretical results.

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PubMed2005

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions.

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.

Acetylcholinesterase↗

PubMed2004

TD-DFT calculations of the potential energy curves for the trans-cis photo-isomerization of protonated Schiff base of retinal.

One-dimensional potential energy curves for the isomerization of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin (bR), i.e., isomerization from all-trans- to 13-cis-forms, have been calculated by means of time-dependent density functional theory (TD-DFT) calculations, in order to elucidate the mechanism of initial step in photo-absorption. The transition state of the isomerization in the first excited state is located at theta(13-14)=58 degrees , where theta(13-14) means twist angle around the C(13)=C(14) double bond of PSBR The potential barrier is formed by the avoided crossing between S(1) (B(u)-like) and S(2) (A(g)-like) states. The mechanism of the isomerization was discussed on the basis of theoretical results.

Energy Transfer↗

PubMed2004

Hydrogen atom formation from the photodissociation of water ice at 193 nm.

The TOF spectra of photofragment hydrogen atoms from the 193 nm photodissociation of amorphous ice at 90-140 K have been measured. The spectra consist of both a fast and a slow components that are characterized by average translational energies of 2k(B)T(trans)=0.39+/-0.04 eV (2300+/-200 K) and 0.02 eV (120+/-20 K), respectively. The incident laser power dependency of the hydrogen atom production suggests one-photon process. The electronic excitation energy of a branched cluster, (H(2)O)(6+1), has been theoretically calculated, where (H(2)O)(6+1) is a (H(2)O)(6) cyclic cluster attached by a water molecule with the hydrogen bond. The photoabsorption of this branched cluster is expected to appear at around 200 nm. The source of the hydrogen atoms is attributed to the photodissociation of the ice surface that is attached by water molecules with the hydrogen bond. Atmospheric implications are estimated for the photodissociation of the ice particles (Noctilucent clouds) at 190-230 nm in the region between 80 and 85 km altitude.

Journal Article↗

PubMed2003

Ozone-water 1:1 complexes O3-H2O: an ab initio study.

Ab initio MO calculations have been carried out for the ozone-water 1:1 complexes in order to elucidate the structures and electronic state of the complexes. The QCISD calculations indicated that three structures are obtained as stable forms of O(3)-H(2)O. The most stable structure of O(3)-H(2)O has C(s) symmetry where the central oxygen of O(3) and all atoms of H(2)O are located on the molecular C(s) plane. The dipole of H(2)O orients toward the central oxygen atom of O(3) (i.e., dipole orientation form). The other two forms are cis and trans forms of O(3)-H(2)O where all atoms are located on the molecular plane, and a hydrogen of H(2)O binds to one of the terminal oxygen atoms of O(3) by a hydrogen bond. The binding energies of O(3) to H(2)O for dipole, cis, and trans forms are calculated to be 2.39, 2.27, and 2.30 kcal/mol, respectively, at the QCISD(T)/6-311++G(3df,3pd)//QCISD/6-311++G((d,p) level. The dipole orientation form is more stable in energy than the cis and trans forms. Rotational constants for the dipole orientation form are calculated to be A = 11.897, B = 4.177, and C = 3.318 GHz which are in good agreement with the experimental values (A = 11.961, B = 4.174, and C = 3.265 GHz). The electronic states of O(3)-H(2)O were discussed on the basis of theoretical results.

Journal Article↗