Osamu Takahashi

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Organization: Hiroshima University
Department: Department of Chemistry
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Co-reporter:Osamu Takahashi, Mathias P. Ljungberg, and Lars G. M. Pettersson
The Journal of Physical Chemistry B December 14, 2017 Volume 121(Issue 49) pp:11163-11163
Publication Date(Web):November 21, 2017
DOI:10.1021/acs.jpcb.7b09262
The X-ray emission spectrum of liquid ethanol was calculated using density functional theory and a semiclassical approximation to the Kramers–Heisenberg formula including core-hole-induced dynamics. Our spectrum agrees well with the experimental spectrum. We found that the intensity ratio between the two peaks at 526 and 527 eV assigned as 10a′ and 3a″ depends not only on the hydrogen bonding network around the target molecule but also on the intramolecular conformation. This effect is absent in liquid methanol and demonstrates the high sensitivity of X-ray emission to molecular structure. The dependence of spectral features on hydrogen-bonding as well as on dynamical effects following core excitation are also discussed.
Co-reporter:Naohiro Nishida, Yuka Horikawa, Takashi Tokushima, Osamu Takahashi
Journal of Electron Spectroscopy and Related Phenomena 2017 Volume 220(Volume 220) pp:
Publication Date(Web):1 October 2017
DOI:10.1016/j.elspec.2016.12.006
•We reproduced an XES spectrum of carbonate and bicarbonate ions in aqueous solutions.•An ab initio MD simulation reproduced the solute-solvent model.•Theoretical data provided electronic and molecular structure information.We perform theoretical calculations to reproduce the site-selective X-ray emission spectroscopy (XES) spectrum for carbonate and bicarbonate ions in aqueous solution at the oxygen K-edge. We perform structure sampling, and using an ab initio molecular dynamics simulation, we reproduce the solute-solvent model. Relative XES peak intensities with core-hole excited state molecular dynamics simulations are calculated using density functional theory. A comparison of several models shows that a cluster model with surrounding water can describe the experimental XES spectra, and these calculations provide electronic and molecular structure information in an aqueous solution.
Co-reporter:Yuji Kohno, Kazuki Mori, Reiko I. Hiyoshi, Osamu Takahashi, Kazuyoshi Ueda
Chemical Physics 2016 Volume 472() pp:163-172
Publication Date(Web):15 June 2016
DOI:10.1016/j.chemphys.2016.04.002

Highlights

MD calculations were performed for TATB crystal with high pressure.

Cell parameters were consistent with the previous experiments and calculations.

Intra- and inter hydrogen bonds were maintained with pressure.

A unique structural change was observed in the range of 2.0 to 4.0 GPa.

Difference TATB with DATB was discussed.

Co-reporter:Naohiro Nishida, Takashi Tokushima, Osamu Takahashi
Chemical Physics Letters 2016 Volume 649() pp:156-161
Publication Date(Web):April 2016
DOI:10.1016/j.cplett.2016.02.063

Highlights

We observed two types of X-ray emission spectra in aqueous acetic acid.

We reproduced the X-ray emission spectra via theoretical calculations.

Theoretical data gave us electronic and molecular structure information.

Co-reporter:Osamu Takahashi, Mai Kimoto, Lars G.M. Pettersson
Chemical Physics 2015 s 450–451() pp: 109-114
Publication Date(Web):1–15 April 2015
DOI:10.1016/j.chemphys.2015.01.012
•Theoretical procedure of XNCD spectra was developed with DFT.•XNCD spectra of alanine and serine were calculated.•Cluster models representing the solid phase were also applied.X-ray natural circular dichroism (XNCD) spectra of alanine and serine were calculated at the C, N, and O K-edges within the framework of density functional theory. Basis set and gauge dependence of d-alanine were examined as a test case. XNCD spectra of crystalline d-alanine and l-serine were obtained using cluster models of increasing size. The absolute intensities of the XNCD spectra were found to be reduced in the solid phase compared to the gas phase monomers, suggesting that a monomer model is not necessarily a good representation of the solid phase.
Co-reporter:Yasuhiro Ohkubo, Akio Kawano, Miho Orimoto, Osamu Takahashi, Katsuyoshi Yamasaki
Chemical Physics Letters 2014 Volume 592() pp:64-68
Publication Date(Web):30 January 2014
DOI:10.1016/j.cplett.2013.12.004
Co-reporter:Osamu Takahashi, Kiyoshi Ueda
Chemical Physics 2014 440() pp: 64-68
Publication Date(Web):31 August 2014
DOI:10.1016/j.chemphys.2014.06.007
•Double ionization potentials were calculated by HF and DFT.•C60, dicyano molecules, and disilyl compounds were studied.•DFT was confirmed as a valid method to estimate DIPs.•The origin of different behaviors in interatomic relaxation energies is discussed.The double ionization energies of two-site double core-hole states were calculated for several systems: C60, dicyano molecules, and disilyl compounds. For C60, the interatomic relaxation energy decreases from positive to negative values with increasing core-hole distances. For dicyano molecules, the interatomic relaxation energy increases monotonically from a negative value toward zero with an increase in the carbon chain length. For disilyl compounds, the energy first decreases from positive to negative and then approaches zero with an increase in the carbon chain length. The results based on density functional theory agree with those based on Hartree–Fock theory for all systems, illustrating similar tendencies and confirming the validity of using density functional theory for calculations of double core-hole states. The origin of the different behaviors in interatomic relaxation energies is also discussed.Graphical abstract
Co-reporter:Osamu Takahashi, Yuji Kohno, Kazuyoshi Ueda and Motohiro Nishio  
New Journal of Chemistry 2013 vol. 37(Issue 3) pp:843-849
Publication Date(Web):14 Dec 2012
DOI:10.1039/C2NJ40955K
Introduction of methyl group(s) at bridgehead carbons at positions 10 and 5 of steroidal 1,3-dienes has been known to influence the Cotton effect of the π–π* transition at ca. 260 nm. Thus the positive sign of the circular dichroism (CD) curve of 5α-estra-1,3-dien-17β-ol becomes negative in 5α-androsta-1,3-dien-17β-ol, even though the helical sense of the diene chromophore remains practically unchanged. In order to investigate the effect of methyl substitution on the CD of 1,3-diene steroids, we carried out time dependent density functional theory (TD-DFT) calculations at the M06-2X/6-311++G(d,p)//MP2/6-31G(d,p) level. It has been shown that replacement of the bridgehead hydrogen by a methyl group greatly influenced the sign and amplitude of CD spectra of the π–π* transition. We suggest that the change in the CD curves by methyl substitution originates from CH/π hydrogen bonds between the diene π-system and a CH3 group homoallylic to it.
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Shin-ichi Nagaoka, Kiyoshi Ueda
Chemical Physics Letters 2011 Volume 518() pp:44-48
Publication Date(Web):15 December 2011
DOI:10.1016/j.cplett.2011.11.006

Abstract

We calculated ionization potentials (IPs) to create single core–hole states and double ionization potentials (DIPs) to create double core–hole (DCH) states for a series of trihalosilyl–trimethylsilyl molecules bridged with hydrocarbons. From the calculated DIPs, IPs, and the hole–hole repulsion energies, we extracted the excess relaxation energies for the creation of DCHs at a single atomic site and interatomic relaxation energies for the creation of DCHs at two different sites. These excess and interatomic relaxation energies depend solely on the chemical environment around the atom(s) with core hole(s). We found that the interatomic relaxation is almost blocked by a dimethylene group (–CH2CH2–).

Co-reporter:Osamu Takahashi, Motomichi Tashiro, Masahiro Ehara, Katsuyoshi Yamasaki, Kiyoshi Ueda
Chemical Physics 2011 Volume 384(1–3) pp:28-35
Publication Date(Web):16 June 2011
DOI:10.1016/j.chemphys.2011.04.015

Abstract

We have investigated the K–2, K–1L–1, and L–2 double core hole (DCH) states of the SiX4 (X = H, F, Cl, and CH3) molecules using the CASSCF and DFT methods aiming at the DCH electron spectroscopy. The Si 1s IPs and DIPs of the present molecules and the generalized relaxation energies are compared and analyzed. The values extracted from the excess relaxation energy agree well with the generalized relaxation energy. The effect of the substituents (H, F, Cl, and CH3) surrounding the central Si atom is examined. The present results illustrate that the DCH electron spectroscopy for K–2, K–1L–1, and L–2 DCH states is useful for the chemical analysis.

Co-reporter:Osamu Takahashi, Motomichi Tashiro, Masahiro Ehara, Katsuyoshi Yamasaki, and Kiyoshi Ueda
The Journal of Physical Chemistry A 2011 Volume 115(Issue 44) pp:12070-12082
Publication Date(Web):September 26, 2011
DOI:10.1021/jp205923m
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.
Co-reporter:Osamu Takahashi, Yuji Kohno, and Motohiro Nishio
Chemical Reviews 2010 Volume 110(Issue 10) pp:6049
Publication Date(Web):June 15, 2010
DOI:10.1021/cr100072x
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Kazuyoshi Ueda, Hiroko Suezawa, Motohiro Nishio
Carbohydrate Research 2009 Volume 344(Issue 10) pp:1225-1229
Publication Date(Web):6 July 2009
DOI:10.1016/j.carres.2009.04.011
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 CH3O–CH2–X (X = OH, OCH3, F, Cl, Br, CN, CCH, C6H5, 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/π hydrogen bonds play an important role in stabilizing the gauche conformation of these compounds.
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Kazuyoshi Ueda, Hiroko Suezawa, Motohiro Nishio
Tetrahedron 2009 65(17) pp: 3525-3528
Publication Date(Web):
DOI:10.1016/j.tet.2009.02.014
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Youji Kurihara, Kazuyoshi Ueda, Yoji Umezawa, Hiroko Suezawa, Motohiro Nishio
Tetrahedron 2009 65(27) pp: 5443
Publication Date(Web):
DOI:10.1016/j.tet.2009.04.067
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Ryuta Ohtaki, Kazuyoshi Ueda, Hiroko Suezawa, Yoji Umezawa, Motohiro Nishio
Carbohydrate Research 2007 Volume 342(Issue 9) pp:1202-1209
Publication Date(Web):2 July 2007
DOI:10.1016/j.carres.2007.02.032
Ab initio MO calculations were carried out at the MP2/6-311++G(d,p) level to investigate the conformational energy of 2-substituted oxanes and 1,3-dioxanes. It has been found that the Gibbs free energies of the axial conformers are smaller than those of the corresponding equatorial conformers in every case when the 2-substituent Z is electron withdrawing (OCH3, F, Cl, Br). The difference in Gibbs energy between the equatorial and axial conformers ΔGeq–ax increases from Z = OCH3 to F, Cl, and then to Br. In the axial conformers, the interatomic distance between Z and the axial C–H, separated by four covalent bonds, has been found to be appreciably shorter than the van der Waals distance, suggesting the importance of the five-membered CH/n (CH/O or CH/halogen) hydrogen bond in stabilizing these conformations. Natural bonding orbital (NBO) charges of the relevant atoms have been shown to be different between the two conformers: more positive for H and more negative for C in the axial conformers than in the corresponding equatorial conformers. In view of the above findings, we suggest that the CH/n hydrogen bond plays an important role in stabilizing the axial conformation in 2-substituted oxanes and 1,3-dioxanes, and by implication, in the anomeric effect in carbohydrate chemistry.
Co-reporter:Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Kazuyoshi Ueda, Hiroko Suezawa, Motohiro Nishio
Chemical Physics Letters 2007 Volume 440(1–3) pp:64-69
Publication Date(Web):25 May 2007
DOI:10.1016/j.cplett.2007.04.013
Ab initio MO calculations were carried out to investigate the conformational preference of n-propyl halides, isobutyl halides, sec-butyl halides, and n-butyl halides. It has been found in most cases that the conformer in which a methyl group is close to the halogen atom is favored. The distance between the halogen atom and one of the hydrogens in the interacting CH3 group has been shown, in every case, to be shorter than the van der Waals distance. Natural bond orbital (NBO) charges have given results consistent with this finding. We suggest that the CH/n hydrogen bond contributes in determining the conformation of these molecules.Ab initio MO calculations were carried out to investigate the conformational preference of n-propyl halides, isobutyl halides, sec-butyl halides, and n-butyl halides. It has been found in most cases that the conformer in which a methyl group is close to the halogen atom is favored.
Co-reporter:Osamu Takahashi Dr.;Katsuyoshi Yamasaki ;Yuji Kohno Dr.;Kazuyoshi Ueda ;Hiroko Suezawa Dr.;Motohiro Nishio Dr.
Chemistry – An Asian Journal 2006 Volume 1(Issue 6) pp:
Publication Date(Web):23 NOV 2006
DOI:10.1002/asia.200600204

Ab initio molecular-orbital (MO) calculations were carried out, at the MP2/6-311++G(d,p)//MP2/6-31G(d) level, to investigate the conformational Gibbs energy of alkyl 1-cyclohexylethyl ketones, cyclo-C6H11CHCH3COR (R=Me, Et, iPr, and tBu). In each case, one of the equatorial conformations was shown to be the most stable. Conformers with the axial CHCH3COR group were also shown to be present in an appreciable concentration. Short CH⋅⋅⋅CO and CH⋅⋅⋅OC distances were found in each stable conformation. The result was interpreted on the grounds of CH⋅⋅⋅π(CO) and CH⋅⋅⋅O hydrogen bonds, which stabilize the geometry of the molecule. The ratio of the diastereomeric secondary alcohols produced in the nucleophilic addition to cyclo-C6H11CHCH3COR was estimated on the basis of the conformer distribution. The calculated result was consistent with the experimental data previously reported: the gradual increase in the product ratio (major/minor) along the series was followed by a drop at R=tBu. The energy of the diastereomeric transition states in the addition of LiH to cyclo-C6H11CHCH3COR was also calculated for R=Me and tBu. The product ratio did not differ significantly in going from R=Me to tBu in the case of the aliphatic ketones. This is compatible with the above result calculated on the basis of the conformer distribution. Thus, the mechanism of the π-facial selection can be explained in terms of the simple premise that the geometry of the transition state resembles the ground-state conformation of the substrates and that the nucleophilic reagent approaches from the less-hindered side of the carbonyl π face.

Co-reporter:Osamu Takahashi;Ko Saito;Yuji Kohno;Hiroko Suezawa;Shinji Ishihara;Motohiro Nishio
European Journal of Organic Chemistry 2004 Volume 2004(Issue 11) pp:
Publication Date(Web):12 MAY 2004
DOI:10.1002/ejoc.200300801

Ab initio MO calculations were carried out for the conformations of a series of alkyl-substituted benzyl alcohols C6H5CH2CHOH−R (R = CH3, C2H5, iPr, tBu) at the MP2/6-311G(d,p)//MP2/6-31G(d) level. It was found that the conformation where the OH group is gauche to the phenyl group is the most stable. The geometry where both the OH and R groups are close to phenyl is the second most stable. This finding has been interpreted on the grounds of the attractive OH/π and CH/π hydrogen bonds and a repulsive van der Waals interaction between vicinal CH groups. NMR nuclear Overhauser effects, spin-coupling data, and IR spectroscopic data are consistent with the conclusion given by the MO calculations. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Co-reporter:Osamu Takahashi Dr.;Yuji Kohno Dr.;Ko Saito ;Motohiro Nishio Dr.
Chemistry - A European Journal 2003 Volume 9(Issue 3) pp:
Publication Date(Web):29 JAN 2003
DOI:10.1002/chem.200390084

Ab initio MO calculations were carried out to examine the conformational energies of various benzylic compounds C6H5CH2XR (X=O, CH2, CO, S, SO, SO2; R=CH3, C2H5, iC3H7, tC4H9) at the MP2/6-311G(d,p)//MP2/6-31G(d) level. Rotamers with R/Ph in gauche relationship are generally more stable than the R/Ph anti rotamers. In these stable geometries, the interatomic distance in the interaction of α- or β-CH in the alkyl group and the ipso-carbon atom of the phenyl ring is short. The computational results are consistent with experimental data from supersonic molecular jet spectroscopy on 3-n-propyltoluene and NMR and crystallographic data on structurally related ketones, sulfoxides, and sulfones. In view of this, the alkyl/phenyl-congested conformation of these compounds has been suggested to be a general phenomenon, rather than an exception. The attractive CH/π interaction has been suggested to be a dominant factor in determining the conformation of simple aralkyl compounds.

Co-reporter:Osamu Takahashi
Computational and Theoretical Chemistry (15 February 2017) Volume 1102() pp:
Publication Date(Web):15 February 2017
DOI:10.1016/j.comptc.2017.01.007
•Relativistic corrections with single- and double-core vacancies were estimated.•The sixth-order Douglas-Kroll-Hess Hamiltonian were applied.•Basis set dependence for the corrections is also discussed.Relativistic corrections with single- and double-core vacancies at the K-, L1-, and L23-edges from Li to Kr were estimated using the restricted active space self-consistent field method with fairly large basis sets based on the spin-free part of the sixth-order Douglas-Kroll-Hess Hamiltonian. Our estimations for Ne, Ar, and Kr are consistent with the previously reported values. Estimated corrections for all edges were fitted by a power law and are consistent with previous reports. The basis set dependence for the corrections is also discussed. The relativistic corrections for nine small molecules are estimated, and we found that the relativistic corrections for atoms are a good approximation for molecules. The present results are useful for the future study to predict the single and double core-electron binding energies correctly.
Silane, trifluoro[2-(trimethylsilyl)ethyl]-
2,4,6,8,10-Dodecapentaynedinitrile
2,4,6,8-Decatetraynedinitrile
2,4,6-Octatriynedinitrile
DISILANE, 1,1,1-TRIFLUORO-2,2,2-TRIMETHYL-
Formic acid, nitro-
CARBONOFLUORIDIC ACID
Silane, trichloro[2-(trimethylsilyl)ethyl]-
1,1,1-trichloro-2,2,2-trimethyldisilane
2-Butenedinitrile