Biomedical subjects

Yosuke Kanai

Publications and source records attributed to Yosuke Kanai.

5 recordsLinked to original sources

PubMed2006

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers.

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.

Journal Article↗

PubMed2006

Competing mechanisms in the optically activated functionalization of the hydrogen-terminated Si(111) surface.

Recent experiments have shown that organic monolayers on silicon surfaces can be formed through the optically activated surface reaction of H-terminated Si surfaces with terminally unsaturated organic molecules (Eves et al. J. Am. Chem. Soc. 2004, 126, 14318; Sun et al. J. Am. Chem. Soc. 2005, 127, 2514). Possible mechanisms for the formation of this monolayer involve the abstraction of a H atom either at the same attachment site of the molecule (Path A) or from a neighboring site (Path B). Using periodic Density Functional Theory calculations together with an efficient method for finding reaction pathways, we examine both optically activated reaction mechanisms for an alkene and an aldehyde reacting with H-Si(111). Our results show that while Path A is energetically more favorable its significant barrier is likely to limit its viability. Path B on the other hand encounters a much lower H atom abstraction barrier and appears to be more viable.

Journal Article↗

PubMed2005

Role of molecular conjugation in the surface radical reaction of aldehydes with H-Si(111): first principles study.

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).

Journal Article↗

PubMed2005

A theoretical study of biotin chemisorption on Si-SiC(001) surfaces.

Biotin is a promising candidate for functionalization of semiconducting surfaces, given its strong, unmatched affinity to specific proteins such as streptavidin and avidin. Using density functional theory, we have carried out a theoretical investigation of the structural and electronic properties of biotin chemisorbed on a biocompatible substrate; in particular we have considered the clean and hydroxylated Si-SiC(001) surfaces. Our calculations show that, upon chemisorption, biotin retains the electronic properties responsible for its strong affinity to proteins. While the electronic states of the hydroxylated surface undergo negligible changes in the presence of the molecule, those of the clean surface are considerably affected.

Adsorption↗

PubMed2004

Surface reaction of alkynes and alkenes with H-Si(111): a density functional theory study.

Recent experiments on the addition of alkene and alkyne molecules to H-terminated silicon surfaces have provided evidence for a surface chain reaction initiated at isolated Si dangling bonds and involving an intermediate carbon radical state, which, after abstraction of a hydrogen atom from a neighboring Si-H unit, transforms into a stable adsorbed species plus a new Si dangling bond. Using periodic density functional theory (DFT) calculations, together with an efficient method for determining reaction pathways, we have studied the initial steps of this chain reaction for a few different terminal alkynes and alkenes interacting with an isolated Si dangling bond on an otherwise H-saturated Si(111) surface. Calculated minimum energy pathways (MEPs) indicate that the chain mechanism is viable in the case of C(2)H(2), whereas for C(2)H(4) the stabilization of the intermediate state is so small and the barrier for H-abstraction so (relatively) large that the molecule is more likely to desorb than to form a stable adsorbed species. For phenylacetylene and styrene, stabilization of the intermediate state and decrease of the H-abstraction barrier take place. While a stable adsorbed species exists in both cases, the overall heat of adsorption is larger for the alkyne molecules.

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