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Article ; Online: Singular value decomposition analysis of the electron density changes occurring upon electrostatic polarization of water.

Torii, Hajime

RSC advances

2022 Volume 12, Issue 5, Page(s) 2564–2573

Abstract: In-depth elucidation of how molecules are electrically polarized would be one key factor for understanding the properties of those molecules under various thermodynamic and/or spatial conditions. Here this problem is tackled for the case of hydrogen- ... ...

Abstract	In-depth elucidation of how molecules are electrically polarized would be one key factor for understanding the properties of those molecules under various thermodynamic and/or spatial conditions. Here this problem is tackled for the case of hydrogen-bonded water by conducting singular value decomposition of the electron density changes that occur upon electrostatic polarization. It is shown that all those electron density changes are approximately described as linear combinations of ten orthonormal basis "vectors". One main component is the interatomic charge transfer through each OH bond, while some others are characterized as the atomic dipolar polarizations, meaning that both of these components are important for the electrostatic polarization of water. The interaction parameters that reasonably well reproduce the induced dipole moments are derived, which indicate the extent of mixing of the two components in electrostatic polarization.
Language	English
Publishing date	2022-01-19
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra06649h
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Article: Singular value decomposition analysis of the electron density changes occurring upon electrostatic polarization of water

Torii, Hajime

RSC advances. 2022 Jan. 19, v. 12, no. 5

2022

Abstract	In-depth elucidation of how molecules are electrically polarized would be one key factor for understanding the properties of those molecules under various thermodynamic and/or spatial conditions. Here this problem is tackled for the case of hydrogen-bonded water by conducting singular value decomposition of the electron density changes that occur upon electrostatic polarization. It is shown that all those electron density changes are approximately described as linear combinations of ten orthonormal basis “vectors”. One main component is the interatomic charge transfer through each OH bond, while some others are characterized as the atomic dipolar polarizations, meaning that both of these components are important for the electrostatic polarization of water. The interaction parameters that reasonably well reproduce the induced dipole moments are derived, which indicate the extent of mixing of the two components in electrostatic polarization.
Keywords	electrons ; hydrogen bonding ; mixing ; thermodynamics
Language	English
Dates of publication	2022-0119
Size	p. 2564-2573.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/d1ra06649h
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Article ; Online: Substituent Effect and Its Halogen-Atom Dependence of Halogen Bonding Viewed through Electron Density Changes.

Sakai, Takanori / Torii, Hajime

Chemistry, an Asian journal

2023 Volume 18, Issue 3, Page(s) e202201196

Abstract: Elucidating how the halogen-bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely-tuned design of functionally important molecules. Here, this problem is tackled by ...

Abstract	Elucidating how the halogen-bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely-tuned design of functionally important molecules. Here, this problem is tackled by analyzing the electron density differences/changes for variously substituted halobenzenes. It is shown that the anisotropy of the electron distribution around the halogen atom, which is an important factor for halogen-bonding ability, is not much affected by the substituent effect and rather simply depends on the halogen atom, while the partial charge on the halogen atom, which is related to the bond dipole of the C-X bond, is significantly modulated by the substituent effect and gives rise to enhancement of the electrostatic potential on the line extended from the C-X bond. The properties related to the polarization effect are also discussed.
Language	English
Publishing date	2023-01-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2233006-9
ISSN	1861-471X ; 1861-4728
ISSN (online)	1861-471X
ISSN	1861-4728
DOI	10.1002/asia.202201196
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Article ; Online: Asymmetry of the Electrostatic Environment as the Origin of the Symmetry Breaking Effect of the Nitrate Ion in Aqueous Solution.

Torii, Hajime / Watanabe, Kao

The journal of physical chemistry. B

2023 Volume 127, Issue 29, Page(s) 6507–6515

Abstract: Elucidating the mechanism of how vibrational modes are affected by intermolecular interactions is important for a better understanding of the nature of the former as probes of the latter. Here, such an analysis is carried out for the N-O stretching modes ...

Abstract	Elucidating the mechanism of how vibrational modes are affected by intermolecular interactions is important for a better understanding of the nature of the former as probes of the latter. Here, such an analysis is carried out for the N-O stretching modes of the nitrate ion interacting with water, with an emphasis on the symmetry breaking effect. On the basis of theoretical calculations on the structural, vibrational, and electrostatic properties of molecular clusters and spectral simulations for an aqueous solution, a transparent view is demonstrated on the mechanism that modulations of spatially local electrostatic environment give rise to structural and spectroscopic symmetry breaking effect. The electrostatic interaction model constructed here is a seven-parameter model; the use of a single electrostatic parameter, such as the electric field on a single atomic site, is found to be insufficient for quantitative evaluation. It is also shown that the frequency modulations of the N-O stretching modes in aqueous solution occur on a time scale much shorter than 0.1 ps.
Language	English
Publishing date	2023-07-18
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c01977
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Article ; Online: Correlation of the partial charge-transfer and covalent nature of halogen bonding with the THz and IR spectral changes.

Torii, Hajime

Physical chemistry chemical physics : PCCP

2019 Volume 21, Issue 31, Page(s) 17118–17125

Abstract: The electronic structural origin of the THz and IR spectral changes occurring upon halogen-bond formation is examined by employing the technique of electron density analysis. Theoretical calculations and analyses are conducted for the complexes of ... ...

Abstract	The electronic structural origin of the THz and IR spectral changes occurring upon halogen-bond formation is examined by employing the technique of electron density analysis. Theoretical calculations and analyses are conducted for the complexes of pentafluoroiodobenzene (C
MeSH term(s)	Benzene Derivatives/chemistry ; Halogens/chemistry ; Hydrocarbons, Halogenated/chemistry ; Models, Molecular ; Nitrites/chemistry ; Quantum Theory ; Spectrophotometry, Infrared ; Static Electricity
Chemical Substances	Benzene Derivatives ; Halogens ; Hydrocarbons, Halogenated ; Nitrites ; nitryl chloride (UJ70MC62I8)
Language	English
Publishing date	2019-07-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c9cp02747e
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Article ; Online: Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins.

Torii, Hajime

The journal of physical chemistry. B

2018 Volume 122, Issue 1, Page(s) 154–164

Abstract: For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to ... ...

Abstract	For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe
MeSH term(s)	Acetamides/chemistry ; Carbon-13 Magnetic Resonance Spectroscopy ; Coordination Complexes/chemistry ; Ferrous Compounds/chemistry ; Hydrogen Bonding ; Ligands ; Models, Chemical ; Molecular Structure ; Proteins/chemistry ; Static Electricity ; Vibration
Chemical Substances	Acetamides ; Coordination Complexes ; Ferrous Compounds ; Ligands ; Proteins ; N-methylacetamide (V0T777481M)
Language	English
Publishing date	2018--11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.7b10791
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Article ; Online: Characterization of quinolone-resistant and extended-spectrum β-lactamase-producing Escherichia coli derived from sika deer populations of the Nara Prefecture, Japan.

Ikushima, Shiori / Torii, Harumi / Sugiyama, Michiyo / Asai, Tetsuo

The Journal of veterinary medical science

2023 Volume 85, Issue 9, Page(s) 937–941

Abstract: Wildlife in urban areas have the potential to disseminate antimicrobial-resistant bacteria (ARB) across a wider environment. Using antimicrobial-supplemented agar plates, we isolated extended-spectrum β-lactamase-producing Escherichia coli (EEC) and ... ...

Abstract	Wildlife in urban areas have the potential to disseminate antimicrobial-resistant bacteria (ARB) across a wider environment. Using antimicrobial-supplemented agar plates, we isolated extended-spectrum β-lactamase-producing Escherichia coli (EEC) and quinolone-resistant E. coli (QREC) from 144, 23, and 30 deer feces from Nara Park (NP), rural area neighboring NP (RA), and Mt. Odaigahara (MO), respectively. In NP and RA, the prevalence of EEC was 24.3 and 4.3%, respectively; that of QREC was 11.1 and 17.4%, respectively. Neither EEC nor QREC were detected in MO. The pulsotypes of EEC and QREC isolates differed between NP and RA. Our study suggests that deer of the Nara Prefecture are potential carriers of ARB, but long-distance dissemination is unlikely due to limited deer movement.
MeSH term(s)	Animals ; Escherichia coli ; Quinolones/pharmacology ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/veterinary ; Escherichia coli Infections/microbiology ; Japan/epidemiology ; Angiotensin Receptor Antagonists ; beta-Lactamases ; Deer ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests/veterinary
Chemical Substances	Quinolones ; Angiotensin Receptor Antagonists ; beta-Lactamases (EC 3.5.2.6) ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Infective Agents ; Anti-Bacterial Agents
Language	English
Publishing date	2023-07-12
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1071753-5
ISSN	1347-7439 ; 0916-7250
ISSN (online)	1347-7439
ISSN	0916-7250
DOI	10.1292/jvms.23-0069
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Article: Sex differences in the relationship between axial length and dry eye in elderly patients.

Ayaki, Masahiko / Torii, Hidemasa / Yotsukura, Erisa / Negishi, Kazuno

Frontiers in medicine

2023 Volume 10, Page(s) 1170696

Abstract: Purpose: The aim of this study was to explore the association between myopia and dry eye (DE)-related ocular parameters.: Methods: We recruited a total of 460 patients (mean age, 73.6 years; 40.2% men) and performed DE-related, axial length (AL) and ... ...

Abstract	Purpose: The aim of this study was to explore the association between myopia and dry eye (DE)-related ocular parameters. Methods: We recruited a total of 460 patients (mean age, 73.6 years; 40.2% men) and performed DE-related, axial length (AL) and retinal examinations. Statistical analysis revealed a significant sex difference in AL, strip meniscometry value, corneal staining score, corneal endothelial cell density, ganglion cell complex (GCC) thickness, and full macular thickness. AL was strongly age- and sex-dependent, so subsequent analyses were stratified by sex. Results: Among DE-related parameters, strip meniscometry value (ß = -0.167, Conclusion: The current results suggest a relationship between tear production and AL in elderly women and support the hypothesis that there may be a common upstream factor including the parasympathetic nervous system in the association between tear production and AL or DE and myopia.
Language	English
Publishing date	2023-06-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2023.1170696
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Article ; Online: Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide.

Torii, Hajime

Physical chemistry chemical physics : PCCP

2017

Abstract: The intensity generation mechanisms of the far-infrared (far-IR) [or terahertz (THz)] spectrum of liquid formamide, particularly with regard to the behavior of electrons induced by modulations of the hydrogen-bonding conditions of the molecules, are ... ...

Abstract	The intensity generation mechanisms of the far-infrared (far-IR) [or terahertz (THz)] spectrum of liquid formamide, particularly with regard to the behavior of electrons induced by modulations of the hydrogen-bonding conditions of the molecules, are examined theoretically. The theoretical analysis is done in the following two steps. First, density functional theory (DFT) calculations are carried out for the dimers and larger clusters of formamide to analyze the change in the dipole derivative (the square of which is proportional to the IR intensity) induced by hydrogen-bond formation. Then, by using the information derived in the first step, molecular dynamics-based spectral simulations are carried out. It is shown that, upon formation of a hydrogen bond, a change in the dipole derivative is induced along the direction of the hydrogen bond, and is reasonably modeled by the intermolecular charge flux mechanism, where a certain amount of electron density is transferred between molecules according to the modulation of the hydrogen-bond length, similarly to the case of liquid water. This model is in a form that is suitable for use in molecular dynamics-based spectral simulations. From these spectral simulations, it is found that the observed spectral features of the far-IR spectrum of liquid formamide are reasonably reproduced, and that the inclusion of the effect of intermolecular charge flux is essential for it. Contrary to the case of liquid water, the molecular libration band (rather than the molecular translation band) is significantly enhanced by the intermolecular charge flux. It is discussed that this difference is related to the geometrical relation between the hydrogen bonds and the atomic displacements in the molecular translations and librations (rotations). It is considered that, in general, in hydrogen-bonding liquids, modulations of hydrogen-bond lengths occurring upon dynamics of molecules give rise to intermolecular charge fluxes, significantly affecting the dipole derivatives, and hence, the IR intensity distributions in the spectra.
Language	English
Publishing date	2017-06-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c7cp02644g
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Article ; Online: Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride.

Saito, Kento / Torii, Hajime

The journal of physical chemistry. B

2021 Volume 125, Issue 42, Page(s) 11742–11750

Abstract: Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen ...

Abstract	Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line
MeSH term(s)	Fluorine ; Halogens ; Hydrofluoric Acid ; Hydrogen ; Hydrogen Bonding
Chemical Substances	Halogens ; Fluorine (284SYP0193) ; Hydrogen (7YNJ3PO35Z) ; Hydrofluoric Acid (RGL5YE86CZ)
Language	English
Publishing date	2021-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c07211
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