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Journal Articles

Annealing effects on hydrogen ordering in KOD-doped ice observed using neutron diffraction

Arakawa, Masashi*; Kagi, Hiroyuki; Fukazawa, Hiroshi

Journal of Molecular Structure, 972(1-3), p.111 - 114, 2010/05

 Times Cited Count:7 Percentile:18.17(Chemistry, Physical)

We measured the neutron powder diffraction of 0.013 M KOD-doped D$$_{2}$$O ice to investigate the formation process of ice XI, a hydrogen-ordered phase of ice Ih. The doped ice Ih transformed to ice XI after annealing at 57 and subsequently at 68 K. The mass fraction of ice XI to that of the doped ice ($$f$$) was estimated using Rietveld analysis for each sample. The $$f$$ value of the doped ice, which had once experienced being ice XI ($$f$$ = 0.23), was larger than that of the doped ice, which had never experienced being ice XI ($$f$$ = 0.14). Results indicate that small hydrogen-ordered domains remained in the ice Ih, which had once trans- formed to ice XI, and accelerated the phase transition from ice Ih to ice XI. Results further suggest that large amounts of ice on icy bodies in our solar system can transform to ice XI, which might be detectable using infrared telescopes or planetary exploration in the near future.

Journal Articles

Multilevel effect on ultrafast isotope-selective vibrational excitations; Quantum optimal control study

Kurosaki, Yuzuru; Yokoyama, Keiichi; Yokoyama, Atsushi

Journal of Molecular Structure; THEOCHEM, 913(1-3), p.38 - 42, 2009/11

Journal Articles

Path-integral molecular dynamics simulations of small hydrated sulfuric acid clusters H$$_2$$SO$$_4$$$$cdot$$(H$$_2$$O)$$_n$$ ($$n$$=1-6) on semiempirical PM6 potential surfaces

Kakizaki, Akira*; Motegi, Haruki*; Yoshikawa, Takehiro*; Takayanagi, Toshiyuki*; Shiga, Motoyuki; Tachikawa, Masanori*

Journal of Molecular Structure; THEOCHEM, 901(1-3), p.1 - 8, 2009/05

Quantum path-integral molecular dynamics simulations for a series of sulfuric acid clusters, H$$_2$$SO$$_4$$$$cdot$$(H$$_2$$O)$$_n$$($$n$$=1-6), were performed using semiempirical PM6 method. It was found that the acid dissociation probability increases with an increase in the cluster size, and that so-called contact-ion-pair structures are dominant in the proton-dissociated clusters. The importance of nuclear quantum effects in the cluster structures and proton-transfer processes is demonstrated.

Journal Articles

Molecular dynamics simulations of small glycine-(H$$_{2}$$O)$$_{it n}$$ ($$n$$=2-7) clusters on semiempirical PM6 potential energy surfaces

Takayanagi, Toshiyuki*; Yoshikawa, Takehiro*; Kakizaki, Akira*; Shiga, Motoyuki; Tachikawa, Masanori*

Journal of Molecular Structure; THEOCHEM, 869(1-3), p.29 - 36, 2008/11

Molecular dynamics simulations based on semiempirical PM6 method was carried out to study statistical structures of glycine-water clusters. We found that zwitterionic form is more stable than neutral form as the cluster size increases. The difference in water solvation structures around the neutral or zwitterionic glycine form is also discussed.

Journal Articles

Hydrogen-atom production channels of acetaldehyde photodissociation; Direct DFT molecular dynamics study

Kurosaki, Yuzuru

Journal of Molecular Structure; THEOCHEM, 850(1-3), p.9 - 16, 2008/02

 Times Cited Count:12 Percentile:32.4(Chemistry, Physical)

Direct density-functional (DFT) molecular-dynamics (MD) calculations have been carried out for the following two hydrogen atom production channels in acetaldehyde photodissociation on the lowest triplet-state (T$$_{1}$$) potential energy surface (PES): CD$$_{3}$$CHO$$rightarrow$$CD$$_{2}$$CHO+D(1); CD$$_{3}$$CHO$$rightarrow$$CD$$_{3}$$CO+H(2). The employed DFT method was B3LYP with the cc-pVDZ basis set. The average product hydrogen kinetic energies estimated from the results of the direct DFT MD calculations were 18.3 and 16.6 kcal mol$$^{-1}$$ for reactions 1 and 2, respectively, and these were half - two thirds of the previously measured values [Kang et al. Chem. Phys. Lett. 434 (2007) 6]. This is because of the low reverse barrier heights predicted at the B3LYP/cc-pVDZ level. The present results for the product hydrogen kinetic energies, however, agree qualitatively with the experimental measurements and strongly supports the mechanisms taking place on the T$$_{1}$$ PES.

Journal Articles

Molecular to ionic transition of BiCl$$_3$$ in LiCl-KCl eutectic melt

Okamoto, Yoshihiro; Yaita, Tsuyoshi; Minato, Kazuo

Journal of Molecular Structure, 749(1-3), p.70 - 73, 2005/07

 Times Cited Count:3 Percentile:7.94(Chemistry, Physical)

The local structures of molten BiCl$$_3$$ and its mixtures in LiCl-KCl eutectic melt were investigated by X-ray absorption fine structure (XAFS) technique. The 1st Bi-Cl correlation in molten pure BiCl$$_3$$ shows covalent nature, since the distance was almost the same as sum of covalent radii of Bi and Cl and the coordination number was almost 3. The similar property was observed also in the mixture of 75% BiCl$$_3$$ with LiCl-KCl eutectic melt. Drastic change was detected in 25% BiCl$$_3$$ mixture melt. The 1st Bi-Cl distance was sum of ionic radii in molten 25% BiCl$$_3$$ melt. The results suggest that BiCl$$_3$$ changes from molecular liquid to ionic by mixing with alkali chlorides.

Journal Articles

Large scale MD simulation of 8-oxoguanine and AP site multiple lesioned DNA molecule combined with biomolecular visualization software

Fujimoto, Hirofumi; Pinak, M.; Nemoto, Toshiyuki*; Sakamoto, Kiyotaka*; Yamada, Kazuyuki*; Hoshi, Yoshiyuki*; Kume, Etsuo

Journal of Molecular Structure; THEOCHEM, 681(1-3), p.1 - 8, 2004/01

We developed the novel system, Fujitsu Bio Molecular Visualization System (F-BMVS), that enables to produce real pictures and an animation by arranging them along a time series of a large scale simulation of biomolecules associated with a molecular dynamics (MD) simulation program. This animation system is used to study the results of molecular dynamics code, AMBER, in order to find structural differences on the lesioned DNA comparing with non-damaged DNA. These structural differences would be a factor that guides a repair enzyme to discriminate a lesion from non-damaged DNA region.

Journal Articles

Local structure of molten LaCl$$_3$$ by K-absorption edge XAFS

Okamoto, Yoshihiro; Shiwaku, Hideaki; Yaita, Tsuyoshi; Narita, Hirokazu; Tanida, Hajime*

Journal of Molecular Structure, 641(1), p.71 - 76, 2002/10

 Times Cited Count:36 Percentile:69.09(Chemistry, Physical)

The local structure of molten LaCl$$_3$$ was investigated by X-ray absorption fine structure(XAFS) of the La K-edge. The nearest La$$^{3+}$$-Cl$$^-$$ distance andcoordination number were 2.89$$pm0.01$$${AA}$ and 7.4$$pm0.5$$ from the curve fitting of the 1st peak in the fourier transform magnitude $$|FT|$$. The coordination number larger than 6 suggests that the local structure of molten LaCl$$_3$$ is not a simple octahedral coordination (LaCl$$_6$$)$$^{3-}$$, but 7-fold (LaCl$$_7$$)$$^{4-}$$ and/or 8-fold (LaCl$$_8$$)$$^{5-}$$ complexes. The 1st La$$^{3+}$$-La$$^{3+}$$ distance, of which correlation was observed as a weak 2nd peak in the $$|FT|$$, was evaluated to be 4.9${AA}$. It suggests that the distorted corner-sharing connection of the complex species is predominant in the melt, inontrast with molten YCl$$_3$$ in which the edge-sharing connection of the 6-fold (YCl$$_6$$)$$^{3-}$$ mainly exists.

Journal Articles

Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA

Ishida, Hisashi

Journal of Biomolecular Structure and Dynamics, 19(5), p.839 - 851, 2002/05

 Times Cited Count:10 Percentile:25.17(Biochemistry & Molecular Biology)

no abstracts in English

Journal Articles

Impact of the 8-oxoguanine on B-DNA molecule; Molecular dynamics study

Pinak, M.

Journal of Molecular Structure; THEOCHEM, 583(1-3), p.189 - 197, 2002/04

The local structural and energetic impact of a mutagenic oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxoG) on a DNA molecule was studied by the method of a molecular dynamics (MD) simulation. The molecule of 8-oxoG was inserted into central part of B-DNA 15-mer d(GCGTCCA'8-oxoG'GTCTACC)$$_{2}$$ replacing the native guanine. The 2-nanosecond MD simulations were performed with the AMBER 5.0 program code at the constant temperature of 310 K ($$sim$$36.5ºC, temperature of human body) for the 8-oxoG lesioned and native DNA molecules. The broken hydrogen bonds resulting in locally collapsed B-DNA structure were observed at the lesion site. The adenine 21 on the complementary strand (separated from 8-oxoG by 1 base pair) is flipped-out of the DNA double helix. Its extrahelical position forms a hole that may favor docking of repair enzyme into DNA during repair process. A strong electrostatic repulsion between nucleotide with the 8-oxoG and neighboring nucleotides contributes to the observed instability of DNA at the lesion.

Journal Articles

Theoretical study on the geometric and electronic structure of the lithium-rich Li$$_{n}$$F$$_{n-1}$$(n=2-5) clusters

Haketa, Naoki*; Yokoyama, Keiichi; Tanaka, Hiromasa*; Kudo, Hiroshi*

Journal of Molecular Structure; THEOCHEM, 577(1), p.55 - 67, 2002/01

no abstracts in English

Journal Articles

Potential energy surface for the C$$_{2}$$H$$_{4}$$ + Cl$$_{2}$$ $$rightarrow$$ C$$_{2}$$H$$_{4}$$Cl + Cl reaction; Ab initio molecular orbital study

Kurosaki, Yuzuru

Journal of Molecular Structure; THEOCHEM, 545(1-3), p.225 - 232, 2001/07

The CASSCF and MRCI calculations with the cc-pVTZ basis set have been carried out for the C$$_{2}$$H$$_{4}$$ + Cl$$_{2}$$ $$rightarrow$$ C$$_{2}$$H$$_{4}$$Cl + Cl reaction. It has been revealed that the reaction has a small barrier from the C$$_{2}$$H$$_{4}$$Cl + Cl side at the CASSCF level of theory, but it has no barrier at the MRCI level. Namely, the C$$_{2}$$H$$_{4}$$Cl + Cl $$rightarrow$$ C$$_{2}$$H$$_{4}$$ + Cl$$_{2}$$ reaction was predicted to be a spontaneous reaction. The result of the MRCI calculation strongly supports the prediction of our previous PMP4(SDTQ) calculation [J. Mol. Struct. (Theochem) 503 (2000) 231].

Journal Articles

Ab initio molecular orbital study of potential energy surface for the H$$_{2}$$NO($$^{2}$$B$$_{1}$$)$$rightarrow$$NO($$^{2}$$$$Pi$$)+H$$_{2}$$ reaction

Kurosaki, Yuzuru*; Takayanagi, Toshiyuki

Journal of Molecular Structure; THEOCHEM, 507(1-3), p.119 - 126, 2000/07

no abstracts in English

Journal Articles

Ab initio molecular orbital study of the C$$_{2}$$H$$_{4}$$+Cl$$_{2}$$$$rightarrow$$C$$_{2}$$H$$_{4}$$Cl$$_{2}$$ reaction

Kurosaki, Yuzuru*

Journal of Molecular Structure; THEOCHEM, 503(3), p.231 - 240, 2000/05

no abstracts in English

Journal Articles

Molecular dynamics of formation of TD lesioned DNA complexed with repair enzyme-onset the enzymetic repair process

Pinak, M.*

Journal of Molecular Structure; THEOCHEM, 499, p.57 - 70, 2000/03

no abstracts in English

Journal Articles

Molecular dynamics of thymine dimer lesioned DNA and of T4 endonuclease V-role of electrostatic energy in recognition process

Pinak, M.*

Journal of Molecular Structure; THEOCHEM, 466, p.219 - 234, 1999/00

no abstracts in English

Journal Articles

Direct ab initio classical trajectory calculations for the N($$^{2}$$D)+CH$$_{4}$$ insertion reaction

Takayanagi, Toshiyuki; Kurosaki, Yuzuru*

Journal of Molecular Structure; THEOCHEM, 492, p.151 - 158, 1999/00

no abstracts in English

Journal Articles

Quantum-mechanical tunneling in the H$$_{2}$$ elimination from 2,3-dimethylbutane cation: (CH$$_{3}$$)$$_{2}$$CHCH(CH$$_{3}$$)$$_{2+}$$$$rightarrow$$(CH$$_{3}$$)$$_{2}$$C=C(CH$$_{3}$$)$$_{2+}$$+H$$_{2}$$; An ab initio molecular orbital study

Kurosaki, Yuzuru*; Takayanagi, Toshiyuki; Miyazaki, Tetsuro*

Journal of Molecular Structure; THEOCHEM, 452, p.209 - 218, 1998/00

no abstracts in English

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