Biomedical subjects

Yuriko Aoki

Publications and source records attributed to Yuriko Aoki.

12 recordsLinked to original sources

PubMed2006

Search for suitable approximation methods for fullerene structure and relative stability studies: case study with C50.

Local density approximation (LDA), several popular general gradient approximation (GGA), hybrid module based density functional theoretical methods: SVWN, BLYP, PBE, HCTH, B3LYP, PBE1PBE, B1LYP, and BHandHLYP, and some nonstandard hybrid methods are applied in geometry prediction for C60 and C70. HCTH with 3-21G basis set is found to be one of the best methods for fullerene structural prediction. In the predictions of relative stability of C50 isomers, PM3 is an efficient method in the first step for sorting out the most stable isomers. HCTH with 3-21G predicts very good geometries for C50, similar to the performance of B3LYP6-31G(d). The gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital from the predictions of all the density functional theory methods has the following descending order: E(gap)(half-and-half hybrid)>E(gap)(B3LYP)>E(gap)(HCTH)(GGA)>E(gap)(SVWN)(LDA).

Journal Article↗

PubMed2006

Effect of the complexant shape on the large first hyperpolarizability of alkalides Li+(NH3)4M-.

The effect of complexant shape effect on the first hyperpolarizability beta(0) of alkalides Li(+)(NH(3))(4)M(-) (M=Li, Na, K) was explored. At the MP2/6-311++G level, Li(+)(NH(3))(4)M(-) (M=Li, Na, K) have considerable beta(0) values due to excess electrons from chemical doping and charge transfer. By comparison with the alkalides Li(+)(calix[4]pyrrole)M(-), a complexant shape effect in Li(+)(NH(3))(4)M(-) is detected. The beta(0) values of Li(+)(NH(3))(4)M(-) with the "smaller", inorganic, T(d)-symmetric (NH(3))(4) complexant are more than four times larger than those of Li(+)(calix[4]pyrrole)M(-) with the "larger", organic C(4v)-symmetric calix[4]pyrrole complexant. The ratios of the beta(0) values of Li(+)(NH(3))(4)M(-) and Li(+)(calix[4]pyrrole)M(-) are 6.57 (M=Li ), 6.55 (M=Na), and 5.17 (M=K). In the Li(+)(NH(3))(4)M(-) systems, the NBO charge and oscillator strength are found to monotonically depend on the atomic number of the alkali metal anion. The order of the NBO charges of the alkali anions M(-) is -0.667 (M=Li )>-0.644 (M=Na)>-0.514 (M=K), while the order of the oscillator strengths in the crucial transition is 0.351 (M=Li )<0.360 (M=Na)<0.467 (M=K). This indicates that complexant shape effects are strong, and consequently the beta(0) values of Li(+)(NH(3))(4)M(-) are found to be beta(0)=70 295 (M=Li )<96 780 (M=Na)<185 805 a.u. (M=K). This work reveals that the use of a high-symmetry complexant is an important factor that should be taken into account when enhancing the first hyperpolarizability of alkalides by chemical doping.

Journal Article↗

PubMed2006

Binary clusters AuPt and Au6Pt: structure and reactivity within density functional theory.

Within density functional theory with the general gradient approximation for the exchange and correlation, the bimetallic clusters AuPt and Au(6)Pt have been studied for their structure and reactivity. The bond strength of AuPt lies between those of Au(2) and Pt(2), and it is closer to that of Au(2). The Pt atom is the reactive center in both AuPt and AuPt(+) according to electronic structure analysis. AuPt(+) is more stable than AuPt. Au(6)Pt prefers electronic states with low multiplicity. The most stable conformation of Au(6)Pt is a singlet and has quasi-planar hexagonal frame with Pt lying at the hexagonal center. The doping of Pt in Au cluster enhances the chemical regioselectivity of the Au cluster. The Pt atom essentially serves as electron donor and the Au atoms bonded to the Pt atom acts as electron acceptor in Au(6)Pt. The lowest triplet of edge-capped rhombus Au(6)Pt clusters is readily accessible with very small singlet-triplet energy gap (0.32 eV). O(2) prefers to adsorb on Au and CO prefers to adsorb on Pt. O(2) and CO have stronger adsorption on AuPt than they do on Au(6)Pt. CO has a much stronger adsorption on AuPt bimetallic cluster than O(2) does. The adsorption of CO on Pt modifies the geometry of AuPt bimetallic clusters.

Journal Article↗

PubMed2006

Ab initio MO analysis of interaction paths between radicals in ferromagnetic organic systems.

Interaction path analyses for pi-conjugated organic systems were performed at the ab initio molecular orbital level to examine the relationship between inter-radical interactions and the high-spin stability of the system. It was found that the high-spin stability results from through-bond interactions between radicals, not from through-space interactions, in relation to the stabilization of a low-spin state due to the effects of electron correlation. L(ij)(min) value for estimating the mixing of nonbonding molecular orbitals well predicted the relationship between the through-bond interactions and the high-spin stability. Furthermore, molecular orbital calculations revealed that the all-trans type interaction path between radicals produces long-range exchange interactions, and the additivity of high-spin stability is observed by keeping short-range through-bond interaction paths.

Journal Article↗

PubMed2006

Nonlinear optical properties of alkalides Li+(calix[4]pyrrole)M- (M = Li, Na, and K): alkali anion atomic number dependence.

A new type of alkalide compound, Li+(calix[4]pyrrole)M- (M = Li, Na, and K), is presented in theory, which may be stable at room temperature. It has been shown by our calculations that the first hyperpolarizability (beta) is considerably large by means of the density functional theory method. The beta values are determined at the B3LYP/6-311++G level (for the alkali atoms the 6-311++G(3df) basis set is employed) as 8.9 x 103, 1.0 x 104, and 2.4 x 104 au for M = Li, Na, and K, respectively. These beta values are much larger than that of electride Li+(calix[4]pyrrole)e- (beta = 7.3 x 103 au) by a factor of 1.2 to 3.4. Comparing to the cryptand calix[4]pyrrole, the beta values of Li+(calix[4]pyrrole)M- are enhanced by 20-60 times. It is revealed, for the first time, that the beta value of alkalide compounds depends on the atomic number of the alkali anion, and it can be enhanced by choosing the akali anions with larger atomic numbers. The alkali anion in the alkalide compound decreases the transition energy and also increases the oscillator strength of the main transition, consequently the beta value is enhanced. This study proposes such a novel way to synthesize and design new NLO materials by using the alkali atom with a larger atomic number to create an anion in alkalide compounds.

Journal Article↗

PubMed2006

Royal crown-shaped electride Li3-N3-Be containing two superatoms: new knowledge on aromaticity.

The structure and aromaticity of a royal crown-shaped molecule Li(3)-N(3)-Be are studied at the CCSD(T)/aug-cc-pVDZ level. This molecule is a charge-separated system and can be denoted as Li(3) (2+)N(3) (3-)Be(+). It is found that the Li(3) (2+) ring exhibits aromaticity mainly because the Li(3) (2+) ring can share the pi-electron with the N(3) (-3) ring. The 4n+2 electron counter rule can be satisfied for the Li(3) (2+) subunit if the shared pi valence electron of N(3) (3-) subunit is also taken into account. This new knowledge on aromaticity of a ring from the interactions between subunits is revealed first time in this paper. Li(3)-N(3)-Be can be also regarded as a molecule containing two superatoms (Li(3) and N(3)), which may be named as a "superomolecule." Li(3)-N(3)-Be is a new metal-nonmetal-metal type sandwich complex. The N(3) (3-) trianion in the middle repulses the electron clouds of the two metal subunits (mainly to the Li(3) superatom) to generate an excess electron, and thus Li(3)-N(3)-Be is also an electride. This phenomenon of the repulsion results in: (a) the HOMO energy level increased, (b) the electron cloud in HOMO distended, (c) the area of the negative NICS value extended, and (d) the VIE value lowered. So the superomolecule Li(3)-N(3)-Be is not only a new metal-nonmetal-metal type sandwich complex but also a new type electride, which comes from the interaction between the alkali superatom (Li(3)) and the nonmetal superatom (N(3)).

Journal Article↗

PubMed2006

Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems.

Current state of development of the elongation method originally proposed by Imamura is presented. Recent progress in methodology, including geometry optimization and employment of the fast multiple method, is highlighted. The accuracy and efficiency of the elongation method as compared to exact canonical Hartree-Fock and Kohn-Sham approaches are discussed. Potential applications are illustrated by wide range of calculations for model systems. The elongation calculations are demonstrated to be much more efficient compared to the conventional ones with high accuracy maintained. The elongation CPU time is shown by the model calculations as linear or sub-linear scaling for quasi-one-dimensional systems. Future work of development into post-Hartree-Fock methodologies are pointed out.

Journal Article↗

PubMed2005

Bimetallic clusters Pt6Au: geometric and electronic structures within density functional theory.

Within density functional theory at the general gradient approximation for exchange and correlation (BPW91) and the relativistic 19-electron Los Alamos National Laboratory effective core pseudopotentials and basis sets (3s3p2d), the geometric and electronic structures of Pt(6)Au bimetallic clusters have been studied in detail in comparison with Pt(7). A total of 38 conformations for Pt(6)Au are located. The most stable conformation for Pt(6)Au is a sextet with an edge- and face-capped trigonal bipyramid, in which the Au atom caps an edge of the trigonal bipyramid. Pt(6)Au, in general, prefers a three-dimensional geometry and high spin electronic state with multireference character. The electronic impact of the doping of Au in Pt clusters on the overall chemical activity of the doped bimetallic cluster is not as significant as that of the doping of Pt in Au clusters; however, the doping of Au lowers the chemical activity, thus enhancing the chemoselectivity in the gas phase, of PtAu bimetallic clusters.

Journal Article↗

PubMed2005

Ab initio MO study on [3 + 2] annulation using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates and its through-space/bond interaction analysis.

Ab initio through-space/bond interaction analysis was applied to [3 + 2] annulation based on Brook rearrangement using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates. An uncertain reaction mechanism, wherein a bulky cyclopentenol with large substituents on the same side of the five-membered ring was obtained as a major product, can be explained by the low activation energy of its reaction pathway. Intramolecular orbital interactions related to the carbanion generated by Brook rearrangement preferentially provide the stabilization of the reaction pathway to the bulky cyclopentenol (major product) compared with that provided to the non-bulky cyclopentenol (minor product). In addition, ab initio molecular orbital calculations suggest the existence of an E/Z conformational inversion after Brook rearrangement. This result accurately explains the loss of the E/Z stereochemical integrity in the starting materials of the experiment.

Journal Article↗

PubMed2004

A new localization scheme for the elongation method.

A different localization scheme for the elongation method is developed based on regional molecular orbitals. This scheme is more efficient and more accurate than the previous one especially for covalently bonded systems with strongly delocalized pi electrons. Ab initio test calculations have been performed on three model systems: water chains, polyglycine, and cationic cyanine chains. The dependence on the size of the starting clusters and the effect of the basis set are investigated. Our results are compared with conventional ab initio calculations and it is found in all cases that the error per added unit levels off to a satisfactorily small value as long as the starting cluster is sufficiently large.

Journal Article↗

PubMed2003

Novel strategy for molecular imprinting of phenolic compounds utilizing disulfide templates.

A molecularly imprinted polymer was synthesized by using allyl phenyl disulfide as a template. The mixture of allyl phenyl disulfide, divinylbenzene, and 2,2'-azobis(isobutyronitrile) in chloroform was polymerized by UV irradiation for 24 h at 5 degrees C and further 3 h at 80 degrees C. The disulfide bonds of the resulting polymer were reductively cleaved by NaBH(4) in methanol to give thiol groups in the binding sites. The polymer selectively recognized phenol rather than thiophenol. In chromatographic study using polymer-packed columns, the retention factor of the IP for phenol was 5.60 and that of a reference polymer was 4.20. The higher retention for phenol was supported by ab initio calculation.

Disulfides↗

PubMed2003

Interpretation of enantioresolution in nordeoxycholic acid channels based on the four-location model.

Nordeoxycholic acid (NDCA) forms three kinds of host frameworks, M1, M2, and M3, with channels where aliphatic alcohols (1-7) are accommodated. (13)C-NMR studies clarified that racemic alcohols 1- or 2-6 are enclosed in the M1- or M2-type channel with lower than 15% enantiomeric excess, respectively, while 3-methyl-2-pentanol (7) is done in the M3-type with 47% ee. These inclusion phenomena can be explained due to the Difference Fourier maps of electron densities of their enantiomers in the channels. In addition, analysis of the manner of packing indicates that four locations in the channels should be fixed for the enantioresolution of the alcohols. These results support the four-location model, which has been proposed by Mesecar et al.(20) with respect to enantioresolution on protein surfaces.

Deoxycholic Acid↗