122 results on '"Satoko Hayashi"'
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2. Dynamic and Static Nature of Br4σ(4c–6e) and Se2Br5σ(7c–10e) in the Selenanthrene System and Related Species Elucidated by QTAIM Dual Functional Analysis with QC Calculations
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Satoko Hayashi, Waro Nakanishi, and Taro Nishide
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Article Subject ,Functional analysis ,010405 organic chemistry ,Hydrogen bond ,Chemistry ,Organic Chemistry ,Structure (category theory) ,Charge (physics) ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Adduct ,Dual (category theory) ,Inorganic Chemistry ,Trigonal bipyramidal molecular geometry ,Chemical physics ,TP248.13-248.65 ,Biotechnology ,QD146-197 - Abstract
The nature of Br4σ(4c–6e) of the BBr-∗-ABr-∗-ABr-∗-BBr form is elucidated for SeC12H8(Br)SeBr---Br-Br---BrSe(Br)C12H8Se, the selenanthrene system, and the models with QTAIM dual functional analysis (QTAIM-DFA). Asterisks (∗) are employed to emphasize the existence of bond critical points on the interactions in question. Data from the fully optimized structure correspond to the static nature of interactions. In our treatment, data from the perturbed structures, around the fully optimized structure, are employed for the analysis, in addition to those from the fully optimized one, which represent the dynamic nature of interactions. The ABr-∗-ABr and ABr-∗-BBr interactions are predicted to have the CT-TBP (trigonal bipyramidal adduct formation through charge transfer) nature and the typical hydrogen bond nature, respectively. The nature of Se2Br5σ(7c–10e) is also clarified typically, employing an anionic model of [Br-Se(C4H4Se)-Br---Br---Br-Se(C4H4Se)-Br]−, the 1,4-diselenin system, rather than (BrSeC12H8)Br---Se---Br-Br---Br-Se(C12H8Se)-Br, the selenanthrene system.
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- 2020
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3. Intrinsic Dynamic and Static Nature of π···π Interactions in Fused Benzene-Type Helicenes and Dimers, Elucidated with QTAIM Dual Functional Analysis
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Taro Nishide and Satoko Hayashi
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Chemistry ,General Chemical Engineering ,ab initio calculations ,nonbonded interactions ,General Materials Science ,polycyclic aromatic hydrocarbon (PAH) ,QD1-999 ,quantum theory of atoms-in-molecules (QTAIM) - Abstract
The intrinsic dynamic and static nature of the π···π interactions between the phenyl groups in proximity of helicenes 3–12 are elucidated with the quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA). The π···π interactions appear in C-∗-C, H-∗-H, and C-∗-H, with the asterisks indicating the existence of bond critical points (BCPs) on the interactions. The interactions of 3–12 are all predicted to have a p-CS/vdW nature (vdW nature of the pure closed-shell interaction), except for 2Cbay-∗-7Cbay of 10, which has a p-CS/t-HBnc nature (typical-HBs with no covalency). (See the text for definition of the numbers of C and the bay and cape areas). The natures of the interactions are similarly elucidated between the components of helicene dimers 6:6 and 7:7 with QTAIM-DFA, which have a p-CS/vdW nature. The characteristic electronic structures of helicenes are clarified through the natures predicted with QTAIM-DFA. Some bond paths (BPs) in helicenes appeared or disappeared, depending on the calculation methods. The static nature of Ccape-∗-Ccape is very similar to that of Cbay-∗-Cbay in 9–12, whereas the dynamic nature of Ccape-∗-Ccape appears to be very different from that of Cbay-∗-Cbay. The results will be a guide to design the helicene-containing materials of high functionality.
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- 2022
4. Thermal stimulation at 39°C facilitates the fusion and elongation of C2C12 myoblasts
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Satoko Hayashi and Shinichi Yonekura
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Fever ,Cell Fusion ,Myoblasts ,Mice ,03 medical and health sciences ,Myoblast fusion ,medicine ,Animals ,Myocyte ,Cells, Cultured ,030304 developmental biology ,0303 health sciences ,Fusion ,Chemistry ,Myogenesis ,0402 animal and dairy science ,Skeletal muscle ,Cell Differentiation ,04 agricultural and veterinary sciences ,General Medicine ,040201 dairy & animal science ,Cell biology ,medicine.anatomical_structure ,Elongation ,General Agricultural and Biological Sciences ,Nucleus ,C2C12 - Abstract
The aim of this study was to determine the effect of thermal stimulation at 39°C on the fusion and elongation of skeletal muscle cells. During a 5 day differentiation process of C2C12 cells, nine groups subjected to varying lengths of thermal stimulation at 39°C were established. Afterward, all groups were immunostained using anti-muscle heavy-chain antibody to test for myotube formation. Quantification of the myotube area demonstrated a significant increase in the group subjected to thermal stimulation at 39°C during the latter half of the differentiation compared with the control group, but the fusion index was significantly higher in the group that received hyperthermic treatment during the first half of the differentiation period. Moreover, the longitudinal length of myotubes was significantly increased in the groups that were subjected to thermal stimulation at 39°C during the latter half of the differentiation period. The distance between the center of myotubes and the nucleus farthest away from the center was substantially extended in the group receiving thermal stimulation at 39°C only on the fourth day of the differentiation. Together, these results demonstrate that thermal stimulation at 39°C facilitates myoblast fusion and elongation.
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- 2019
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5. Behavior of Multi-HBs in Acetic Acid Dimer and Related Species: QTAIM Dual Functional Analysis Employing Perturbed Structures Generated Using Coordinates from Compliance Force Constants
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Satoko Hayashi, Waro Nakanishi, and Taro Nishide
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Force constant ,Acetic acid ,chemistry.chemical_compound ,chemistry ,Functional analysis ,Computational chemistry ,Hydrogen bond ,Dimer ,Thio ,General Chemistry ,Acetamide - Abstract
The dynamic and static nature of each hydrogen bond (HB) in acetic acid dimer (1), acetamide dimer (2a), thio- and seleno-derivatives of 2a (2b and 2c, respectively), and acetic acid–acetamide mixe...
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- 2019
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6. Nature of the E⋯E′ interactions (E, E′ = O, S, Se, and Te) at naphthalene 1,8-positions with fine details of the structures: experimental and theoretical investigations
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Taro Nishide, Satoko Hayashi, Manabu Uegaito, Mao Minoura, Waro Nakanishi, Eiichiro Tanaka, Norihiro Tokitoh, and Takahiro Sasamori
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Chemistry ,Hydrogen bond ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Acceptor ,Catalysis ,0104 chemical sciences ,Crystal ,chemistry.chemical_compound ,Crystallography ,Atomic orbital ,Materials Chemistry ,Order (group theory) ,0210 nano-technology ,Conformational isomerism ,Naphthalene ,Natural bond orbital - Abstract
The intrinsic dynamic and static natures of the E⋯E′ interactions at the 1,8-positions of 1-(MeE)–8-(MeE′)C10H6 [1a–1f (E ≠ E′) and 1g–1j (E = E′)] were elucidated with QTAIM-DFA, after structural determination of 1-(PhE)–8-(PhE′)C10H6 (3a–3f), where (E, E′: x) = (O, S: a), (O, Se: b), (O, Te: c), (S, Se: d), (S, Te: e), (Se, Te: f), (O, O: g), (S, S: h), (Se, Se: i) and (Te, Te: j) (χE ≥ χE′). While the AB structures are confirmed for 3a, 3b and 3d–3f, which consist of the np(E)⋯σ*(E′–CPh) interactions, the structure was BB for 3c, where the E–CR/E′–CR (R = Ph) bond is perpendicular to the naphthyl plane in A and it is placed on the plane in B. While the AB structures are determined by the p(E)–π(Ph) conjugations, the BB structure is by the crystal packing effect. The BA structure with np(E′)⋯σ*(E–CPh) was not detected. While the nature of a typical hydrogen bond with covalency was predicted for BB, AA and BA, with the CT-MC (molecular complex formation through charge transfer) nature for AB in 1e and 1f (R = Me for E–CR/E′–CR), the CT-MC nature was predicted for all conformers of 1j, for example. NBO analysis for 1a–1f revealed that the acceptor orbitals contribute much more than the donor orbitals and the order is σ*(O–CMe
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- 2019
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7. Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters, with the Structural Feature Elucidated by QTAIM Dual-Functional Analysis and MO Calculations
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Waro Nakanishi, Satoko Hayashi, Taro Nishide, and Eiichiro Tanaka
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chemistry.chemical_classification ,Physics ,Halogen bond ,Functional analysis ,Hydrogen bond ,ab initio calculations ,Pharmaceutical Science ,Organic chemistry ,structures ,Symmetry (physics) ,Article ,Analytical Chemistry ,quantum theory of atoms-in-molecules (QTAIM) ,QD241-441 ,chemistry ,Chemistry (miscellaneous) ,Ab initio quantum chemistry methods ,Chemical physics ,Critical point (thermodynamics) ,Drug Discovery ,Molecular Medicine ,Non-covalent interactions ,Physical and Theoretical Chemistry ,Natural bond orbital ,bromide - Abstract
The intrinsic dynamic and static nature of noncovalent Br-∗-Br interactions in neutral polybromine clusters is elucidated for Br4–Br12, applying QTAIM dual-functional analysis (QTAIM-DFA). The asterisk (∗) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Data from the fully optimized structures correspond to the static nature of the interactions. The intrinsic dynamic nature originates from those of the perturbed structures generated using the coordinates derived from the compliance constants for the interactions and the fully optimized structures. The noncovalent Br-∗-Br interactions in the L-shaped clusters of the Cs symmetry are predicted to have the typical hydrogen bond nature without covalency, although the first ones in the sequences have the vdW nature. The L-shaped clusters are stabilized by the n(Br)→σ*(Br–Br) interactions. The compliance constants for the corresponding noncovalent interactions are strongly correlated to the E(2) values based on NBO. Indeed, the MO energies seem not to contribute to stabilizing Br4 (C2h) and Br4 (D2d), but the core potentials stabilize them, relative to the case of 2Br2, this is possibly due to the reduced nuclear–electron distances, on average, for the dimers.
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- 2021
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8. Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters with the Structural Feature, Elucidated by QTAIM Dual Functional Analysis and MO Calculations
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Eiichiro Tanaka, Satoko Hayashi, Taro Nishide, and Waro Nakanishi
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analytical_chemistry ,Physics ,chemistry.chemical_classification ,Halogen bond ,Functional analysis ,chemistry ,Ab initio quantum chemistry methods ,Chemical physics ,Critical point (thermodynamics) ,Hydrogen bond ,Non-covalent interactions ,Symmetry (physics) ,Natural bond orbital - Abstract
The intrinsic dynamic and static nature of the non-covalent Br-*-Br interactions in the neutral polybromine clusters is elucidated for Br4–Br12, applying QTAIM dual functional analysis (QTAIM-DFA). The asterisk (*) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Data from the fully optimized structures correspond to the static nature of interactions. The intrinsic dynamic nature is originated from those of the perturbed structures generated using the coordinates derived from the compliance constants for the interactions and the fully optimized structures. The non-covalent Br-*-Br interactions in the L-shaped clusters of the Cs symmetry are predicted to have the typical hydrogen bond nature without covalency, although the first ones in the sequences have the vdW nature. The L-shaped clusters are stabilized by the n(Br)->σ*(Br–Br) interactions. The compliance constants for the corresponding non-covalent interactions are strongly correlated to the E(2) values based on NBO. Indeed, the MO energies seem not contribute to stabilize Br4 (C2h) and Br4 (D2d), but the core potentials stabilize them, relative to the case of 2Br2, maybe due to the reduced nuclear-electron distances in the average for the dimmers.
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- 2021
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9. Insulin-like growth factor-1 induces IRE1-XBP1-dependent endoplasmic reticulum biogenesis in bovine mammary epithelial cells
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Makoto Miyaji, Hiroshi Ishizaki, Satoko Hayashi, Mst Mamuna Sharmin, Satoshi Haga, Hiroki Matsuyama, and Shinichi Yonekura
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XBP1 ,Chemistry ,Endoplasmic reticulum ,Endoribonuclease activity ,Mammary gland ,Epithelial Cells ,mTORC1 ,Protein Serine-Threonine Kinases ,Endoplasmic Reticulum ,Cell biology ,medicine.anatomical_structure ,Pregnancy ,Gene expression ,Endoribonucleases ,Genetics ,medicine ,Unfolded protein response ,Animals ,Animal Science and Zoology ,Cattle ,Female ,Insulin-Like Growth Factor I ,Food Science ,Insulin-like growth factor 1 receptor - Abstract
Insulin-like growth factor-1 (IGF-1) plays a key role in proliferation and galactopoiesis in mammary epithelial cells (MEC), but its definitive functions on endoplasmic reticulum (ER) during protein synthesis remain unknown. The present study aimed to elucidate the effects of IGF-1 on ER biogenesis in MEC in vitro and examined the expression of ER biogenesis-associated genes in the mammary gland during early lactation. We treated mammary alveolar cells–large T antigen cells (immortalized bovine MEC line established via stable transfection with simian virus-40 large T-antigen) with IGF-1 and examined ER biogenesis using the fluorescence intensity of an ER tracker and quantitative real-time PCR. We found IGF-1 significantly increased ER tracker staining and upregulated mRNA levels of ER biogenesis-related genes, such as CHKA (choline kinase α), PCYT1A (choline-phosphate cytidylyltransferase A), and SURF4 (surfeit locus protein 4). We focused on unfolded protein response to explore molecular mechanisms by which IGF-1 induces ER biogenesis. We found IGF-1 significantly increased mRNA levels of the XBP1 splicing form (XBP1s). Based on western blot analysis, IGF-1 induced the expression of (inositol-requiring kinase 1 α) protein, upstream of XBP1s, and phosphorylated-IRE1α. The inhibition of IRE1 endoribonuclease activity with 4-methylumbelliferone 8-carbaldehyde (4μ8C) significantly suppressed the increase in ER tracker fluorescence and ER biogenesis-related gene expression induced by IGF-1. Also, IGF-1–induced XBP1s and ER biogenesis-associated gene expression was inhibited by rapamycin, an inhibitor of mTORC1 (mammalian target of rapamycin complex 1), indicating that IRE1-XBP1 activation by IGF-1 is mediated by mTORC1. Moreover, to clarify the expression of XBP1s and ER biogenesis-associated genes expression under normal physiological conditions, mammary gland tissue from biopsies of dairy cows during late gestation and lactation were analyzed. In vivo data highlighted the significant increases in the mRNA levels of XBP1s and ER biogenesis-related genes in mammary gland tissue immediately after calving through 6 wk of lactation. The mRNA levels of IGF1R (IGF-1 receptor) in mammary glands increased during 6 wk of lactation. Therefore, the present study indicated for the first time that IGF-1 induces ER biogenesis by activating the IRE1-XBP1 axis under the regulation of mTORC1 in bovine MEC line.
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- 2021
10. Behaviour of the XH-*-π and YX-*-π interactions (X, Y = F, Cl, Br and I) in the coronene π-system, as elucidated by QTAIM dual functional analysis with QC calculations
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Waro Nakanishi, Yuji Sugibayashi, and Satoko Hayashi
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Physics ,Electron energy ,Functional analysis ,010405 organic chemistry ,General Chemical Engineering ,General Chemistry ,010402 general chemistry ,Curvature ,01 natural sciences ,Potential energy ,Coronene ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,chemistry ,Polar coordinate system ,Open shell - Abstract
The dynamic and static nature of XH-*-π and YX-*-π in the coronene π-system (π(C24H12)) is elucidated by QTAIM dual functional analysis, where * emphasizes the presence of bond critical points (BCPs) in the interactions. The nature of the interactions is elucidated by analysing the plots of the total electron energy densities Hb(rc) versus Hb(rc) − Vb(rc)/2 [=(ħ2/8m)∇2ρb(rc)] for the interactions at BCPs, where Vb(rc) are the potential energy densities at the BCPs. The data for the perturbed structures around the fully optimized structures are employed for the plots in addition to those of the fully optimized structures. The plots are analysed using the polar coordinate of (R, θ) for the data of the fully optimized structures, while those containing the perturbed structures are analysed using (θp, κp), where θp corresponds to the tangent line of each plot and κp is the curvature. Whereas (R, θ) show the static nature, (θp, κp) represent the dynamic nature of the interactions. All interactions in X–H-*-π(C24H12) (X = F, Cl, Br and I) and Y–X-*-π(C24H12) (Y–X = F–F, Cl–Cl, Br–Br, I–I, F–Cl, F–Br and F–I) are classified by pure CS (closed shell) interactions and are characterized as having the vdW nature, except for X–H = F–H and Y–X = F–Cl, F–Br and F–I, which show the typical-HB nature without covalency. The structural features of the complexes are also discussed.
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- 2018
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11. Linear Multiselenium Interactions in Dicationic Oligomers of 1,5‐(Diselena)canes: Behavior of Se mc σ( m c c‐ n e e) (6≤ m c ≤16) Elucidated with QTAIM Dual Functional Analysis
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Waro Nakanishi, Kengo Nagata, Satoko Hayashi, and Taro Nishide
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Physics ,Dimer ,Trimer ,General Chemistry ,Type (model theory) ,Cover Profile ,Crystallography ,chemistry.chemical_compound ,chemistry ,Group (periodic table) ,Ab initio quantum chemistry methods ,Cover (algebra) ,Molecular graph ,Histone octamer - Abstract
Invited for this month's cover picture is the group of Dr. Satoko Hayashi at Faculty of Systems Engineering and Chemistry at Wakayama University. The cover picture shows the linear Se(16) σ(16c–30e) interactions, illustrated by the molecular graph type on the optimized structure of the dicationic octamer of 1,5‐(diselena)cane. HOMO‐1 of ψ(462) is drawn on the structure, which is located predominantly on the Se atoms. The optimized structure is stable, due to the nice engagement between the (CH(2))(3) moieties. The contour maps of ρ(r) are also drawn on the molecular C (s) planes of the dicationic dimer and trimer to demonstrate clearly the existence of the interactions between Se atoms. Read the full text of their Full Paper at 10.1002/open.202100017.
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- 2021
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12. Relativistic Effect on 1 J (M,C) in Me4 M, Me3 M− , Ph4 M, and Ph3 M− (M=Pb, Sn, Ge, Si, and/or C): Role of s-Type Lone Pair Orbitals in the Distinct Effect for the Anionic Species
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Satoko Hayashi, Waro Nakanishi, Masaichi Saito, and Taro Nishide
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Coupling constant ,Carbon group ,Fermi contact interaction ,010304 chemical physics ,Chemistry ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Crystallography ,Atomic orbital ,Ab initio quantum chemistry methods ,0103 physical sciences ,Physical and Theoretical Chemistry ,Atomic physics ,Relativistic quantum chemistry ,Lone pair - Abstract
Indirect one-bond nuclear spin-spin couplings between M and C [1 J(M,C)] in Me4 M, Me3 M- , Ph4 M, and Ph3 M- (M=Pb, Sn, Ge, Si, C) are analyzed with consideration of the relativistic effect and by employing Slater-type basis sets. The evaluated total values 1 JTL (M,C) reproduced the observed values with some systematic calculation errors. Fermi contact terms 1 JFC (M,C) contribute predominantly to 1 JTL (M,C) (≈99 %). A distinct relativistic effect on 1 J(Pb,C) is predicted for Me3 Pb- and Ph3 Pb- . The mechanisms for the distinct effect are elucidated by using the comparison between Me3 Pb- and Me4 Pb as an example. The contributions to 1 JFC (M,C) [or 1 JSD+FC (M,C), where SD denotes the spin-dipolar term] are decomposed into those of occupied orbitals and occupied-to-unoccupied transitions. The s-type lone-pair orbitals are demonstrated to contribute to the distinct relativistic effect on 1 J(Pb,C) of Me3 Pb- (and Ph3 Pb- ). The results are in sharp contrast to the cases of 1 J(M,C) for M atoms lighter than Pb, such as Si, and are explained by the s character of the M-C bonds. This treatment enables visualization and clear recognition the origin of the nuclear couplings for the species exhibiting a relativistic effect.
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- 2017
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13. Nature ofE2X2σ(4c–6e) of theX---E—E---Xtype at naphthalene 1,8-positions and model, elucidated by X-ray crystallographic analysis and QC calculations with the QTAIM approach
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Satoko Hayashi, Takahiro Sasamori, Yutaka Tsubomoto, Waro Nakanishi, and Norihiro Tokitoh
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010405 organic chemistry ,Chemistry ,Hydrogen bond ,Metals and Alloys ,X-ray ,Shell (structure) ,010402 general chemistry ,01 natural sciences ,Potential energy ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Crystallography ,Covalent bond ,Ab initio quantum chemistry methods ,Materials Chemistry ,Open shell ,Natural bond orbital - Abstract
The nature ofE2X2σ(4c–6e) of theX-*-E-*-E-*-Xtype is elucidated for 1-(8-XC10H6)E–E(C10H6X-8′)-1′ [(1)E,X= S, Cl; (2) S, Br; (3) Se, Cl; (4) Se, Br] after structural determination of (1), (3) and (4), together with modelA[MeX---E(H)—E(H)---XMe (E= S and Se;X= Cl and Br)]. The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied. The total electron energy densitiesHb(rc) are plottedversus Hb(rc) –Vb(rc)/2 for the interactions at the bond critical points (BCPs; *), whereVb(rc) show the potential energy densities at the BCPs. Data for the perturbed structures around the fully optimized structures are employed for the plots, in addition to those of the fully optimized structures. The plots were analysed using the polar coordinate (R, θ) representation of the data of the fully optimized structures. Data containing the perturbed structures were analysed by (θp, κp), where θpcorresponds to the tangent line of the plot and κpis the curvature. Whereas (R, θ) shows the static nature, (θp, κp) represents the dynamic nature of interactions.E-*-Eare all classified as shared shell (S) interactions for (1)–(4) and as weak covalent (Cov-w) in nature (S/Cov-w). The nature ofpureCS (closed shell)/typical-HB (hydrogen bond) with no covalency is predicted forE-*-Xin (1) and (3),regularCS/typical-HB nature with covalency is predicted for (4), and an intermediate nature is predicted for (2). The NBO energies evaluated forE-*-Xin (1)–(4) are substantially larger than those in modelAdue the shortened length at the naphthalene 1,8-positions. The nature ofE2X2of σ(4c–6e) is well elucidatedviaQTAIM-DFA.
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- 2017
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14. Behavior of Intramolecular π-π Interactions with Doubly Degenerated Bond Paths Between Carbon Atoms in Opposite Benzene Rings of Diethenodihydronaphthalenes by QTAIM Approach
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Satoko Hayashi, Waro Nakanishi, Kohei Matsuiwa, Yutaka Tsubomoto, and Yuji Sugibayashi
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Ethylene ,010405 organic chemistry ,Hydrogen bond ,General Chemistry ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,0104 chemical sciences ,symbols.namesake ,chemistry.chemical_compound ,Crystallography ,chemistry ,Computational chemistry ,Ab initio quantum chemistry methods ,Intramolecular force ,symbols ,van der Waals force ,Benzene ,Open shell - Abstract
Dynamic and static nature of intramolecular π-π interactions between ethylene moieties in diethenodihydronaphthanaphtalene (1 b) and derivatives (2 b–12 b) are elucidated by employing QTAIM-DFA (QTAIM dual functional analysis). During the course of the investigations, doubly degenerated bond paths were detected between carbon atoms in opposite benzene rings of dibenzo-derivative of 1 b with an etheno-bridge on the backside (11 b). It must be very curious, since one BP should correspond to an interaction between two carbon atoms. Intramolecular π-π interactions in 1 b–12 b are all classified by the pure CS (closed shell) interactions. The interactions between ethylene groups, with no substituents as in 1 b–8 b, are predicted to have the van der Waals (vdW) nature. Those for 9 b–12 b have the hydrogen bond (HB) nature with no covalency, where the ethylene moieties are included in one or two benzene ring(s), except for 10 b, if evaluated with MP2/6-311G(3d). The character in 10 b is close to the borderline area between the vdW and HB nature with no covalency, although should be the vdW type. The interactions in 2 b–12 b evaluated with MP2/6-311G(3d) are predicted to be somewhat stronger than the case with MP2/6-311G(d), as a whole.
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- 2017
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15. Extracts of citrus Sudachi peel attenuate body weight gain in C57BL/6 mice fed a high-fat diet
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Yuka Minatogawa, Mariko Nakamoto, Hitomi Kobayashi, Tohru Sakai, Mami Mitani, Satoko Hayashi, Yoshitaka Nii, and Emi Shuto
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0301 basic medicine ,C57BL/6 ,030109 nutrition & dietetics ,biology ,Chemistry ,Insulin ,medicine.medical_treatment ,Citrus sudachi ,Adipose tissue ,General Medicine ,030204 cardiovascular system & hematology ,biology.organism_classification ,medicine.disease ,Body weight ,Obesity ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Fat diet ,medicine ,Sudachi ,Food science - Abstract
Citrus Sudachi is the special local product of Tokushima Prefecture, and over 98% of Sudachi consumed in Japan every year is produced in Tokushima Prefecture. In this study, we evaluated the function of sudachi peel extract (SPE) using an animal model of obesity. C57BL/6 mice were fed a high-fat diet containing 1% SPE powder. Treatment with SPE significantly decreased body weight compared to that of mice fed a high-fat diet. A significant difference in body weight was observed between the control and SPE groups from 7 weeks after the start of the experiment, the significant difference continued until the end of the 14-week experiment. Reduction of blood glucose levels following insulin administration in SPE-treated mice was grater than that in control mice. Determination of mRNA expression in adipose tissue showed that the expression level of TNF-α in the SPE group was significantly decreased compared to that on the control group. These results suggest that SPE potentially has the ability to attenuate body weight gain. J. Med. Invest. 64: 20-23, February, 2017.
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- 2017
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16. Behavior of interactions between hydrogen chalcogenides and an anthracene π-system elucidated by QTAIM dual functional analysis with QC calculations
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Yuji Sugibayashi, Satoko Hayashi, and Waro Nakanishi
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Quantum chemical ,Anthracene ,Functional analysis ,Hydrogen ,010405 organic chemistry ,Hydrogen bond ,General Chemical Engineering ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Curvature ,01 natural sciences ,0104 chemical sciences ,Chalcogen ,Crystallography ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Open shell - Abstract
The nature of EH2-*-π(C14H10) interactions (E = O, S, Se and Te) of an anthracene system was elucidated by applying QTAIM dual functional analysis (QTAIM-DFA) after clarification of the structural features with quantum chemical (QC) calculations. π-HB (hydrogen bond) interactions were detected for E = O, S, Se and Te, whereas π-EB (chalcogen bond) interactions were observed for E = O in (EH2)-*-π(C14H10), where the bond paths connected H in EH2 to C14H10 in π-HB, and they connected E in EH2 to C10H8 in π-EB. The QTAIM-DFA parameters of (R, θ) and (θp, κp) were evaluated for the interactions via analysing the plots of Hb(rc) versus Hb(rc) − Vb(rc)/2 for the interactions at the bond critical points. Data obtained from the perturbed structures around the fully optimized structures were employed for the plots, in addition to the fully optimized structures. Data obtained from the fully optimized structures were analysed using (R, θ), which corresponded to the static nature, and those obtained from the perturbed structures were analysed using (θp, κp), which represented the dynamic nature of the interactions, where θp corresponds to the tangent line of the plot and κp is the curvature. The θ and θp values are less than 90° for all the interactions examined, except for the iH-*-11C(π) interaction in TeH2-*-C14H10 (C1: IIBAtc), where iH is located closer to the centre of C14H10. Therefore, the interactions examined were predicted to have vdW nature, appeared in the pure-CS (closed shell) interaction region, although iH-*-11C(π) was predicted to have the pure-CS/typical-HB nature without covalency. Additionally, the π-HB interaction seems to be slightly stronger than π-EB in (OH2)-*-π(C14H10).
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- 2017
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17. Effects of fatty acids on inducing endoplasmic reticulum stress in bovine mammary epithelial cells
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Moeko Mizusawa, Satoko Hayashi, Shotaro Sakata, Shinichi Yonekura, Mst Mamuna Sharmin, and Wataru Arai
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Linolenic acid ,Cell Survival ,Linoleic acid ,Apoptosis ,Endoplasmic Reticulum ,Butyric acid ,Palmitic acid ,chemistry.chemical_compound ,Mammary Glands, Animal ,Genetics ,Palmitoleic acid ,Animals ,chemistry.chemical_classification ,Fatty Acids ,Fatty acid ,Cell Differentiation ,Epithelial Cells ,Endoplasmic Reticulum Stress ,Oleic acid ,chemistry ,Biochemistry ,Animal Science and Zoology ,Cattle ,Female ,Stearic acid ,Food Science - Abstract
Fatty acids play important roles in the regulation of endoplasmic reticulum (ER) stress-induced apoptosis in different cells. Currently, the effects of fatty acids on bovine mammary epithelial cells (MEC) remain unknown. Our study examined bovine MEC viability and measured unfolded protein response (UPR)-related gene and protein expressions following fatty acid treatments. To evaluate the role of fatty acids, we treated MAC-T cells (a line of MEC) with 100 to 400 μM of saturated (palmitic and stearic acid) and unsaturated (palmitoleic, oleic, linoleic, and linolenic acid) fatty acids and 1 to 5 mM of short- and medium-chain fatty acids (acetic, propionic, butyric, and octanoic acid). Thereafter, we determined UPR-related gene expression using quantitative real-time PCR. Palmitic acid stimulated expression of XBP1s, ATF4, ATF6A, and C/EBP homologous protein (CHOP). Stearic acid increased expression of XBP1s and CHOP and decreased expression of ATF4 and ATF6A. Results of Western blot analysis and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that palmitic and stearic acid reduced MAC-T cell viability and induced extreme ER stress by increasing the protein expression of ER stress markers, such as phospho-PKR-like endoplasmic reticulum kinase, phospho-eIF2α, cleaved CASP-3, and CHOP. Among unsaturated long-chain fatty acids, palmitoleic acid increased expression of ATF4 and ATF6A. Oleic acid increased expression of XBP1s, ATF4, and ATF6A. Linoleic and linolenic acids increased expression of XBP1s, ATF4, and ATF6A but decreased expression of XBP1s and ATF6A at the highest dose. Although palmitoleic, oleic, and linoleic acid decreased CHOP expression, only palmitoleic acid increased MAC-T cell viability. Therefore, unsaturated long-chain fatty acids did not induce severe ER stress. Acetic, propionic, and butyric acids decreased expression of ATF4, ATF6A, and CHOP and increased XBP1s expression. Although only octanoic acid increased ATF4 and ATF6A expressions, it lowered expression of XBP1s and CHOP. Although fatty acid treatment did not increase the levels of ER stress proteins, butyric and octanoic acids reduced cell viability, possibly because of early differentiation. These results suggest that saturated fatty acids play important roles in MEC viability by inducing severe ER stress compared with unsaturated fatty acids. In addition, acetic and propionic acids (short- and medium-chain fatty acids) reduced ER stress. Therefore, the present study reflects the new insight that serum fatty acid concentration plays an important role in maintaining the lactation physiology of dairy cows.
- Published
- 2019
18. Nature of intramolecular O-H⋯π interactions as elucidated by QTAIM dual functional analysis with QC calculations
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Satoko Hayashi, Taro Nishide, and Waro Nakanishi
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Functional analysis ,Hydrogen bond ,Chemistry ,General Chemical Engineering ,Intermolecular force ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Crystallography ,Intramolecular force ,0210 nano-technology ,Open shell ,Conformational isomerism ,Natural bond orbital - Abstract
The intrinsic dynamic and static nature of intramolecular OH–*–π interactions is elucidated using a QTAIM dual functional analysis (QTAIM-DFA) after clarifying the structural features. Asterisks (*) are employed to emphasize the presence of bond critical points (BCPs) on the bond paths (BPs), which correspond to the interactions in question. Data from the fully optimized structures correspond to the static nature of the interactions. In our treatment, data from the perturbed structures, which are based around the fully optimized structure, are employed for the analysis in addition to those from the fully optimized structure, which represent the dynamic nature of the interaction. Seven intramolecular OH–*–C(π) interactions were detected in six-membered rings, with six BPs and BCPs for each, among the 72 conformers of the species examined here (1–15). The interactions are predicted to have a vdW or t-HBnc (typical hydrogen bonds with no covalency) nature, which appeared in the pure closed shell region. They appear to be stronger than the corresponding intermolecular interactions. Nine BPs with BCPs were also detected for the intramolecular O–*–X interactions (X = C(π) and H(π), joined to C(π)) in the 5–7-membered rings. The E(2) values of the interactions, as obtained by NBO, are discussed in relation to the stabilities of the conformers and the BPs with BCPs.
- Published
- 2019
19. Behavior of Halogen Bonds of the Y−X⋅⋅⋅π Type (X, Y=F, Cl, Br, I) in the Benzene π System, Elucidated by Using a Quantum Theory of Atoms in Molecules Dual-Functional Analysis
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Satoko Hayashi, Waro Nakanishi, and Yuji Sugibayashi
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010405 organic chemistry ,Chemistry ,Bent molecular geometry ,Atoms in molecules ,010402 general chemistry ,01 natural sciences ,Quantum chemistry ,Potential energy ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,symbols.namesake ,Ab initio quantum chemistry methods ,Quantum mechanics ,Halogen ,symbols ,Pi interaction ,Physical and Theoretical Chemistry ,van der Waals force - Abstract
The nature of halogen bonds of the Y-X-✶-π(C6 H6 ) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual-functional analysis (QTAIM-DFA), which we proposed recently. Asterisks (✶) emphasize the presence of bond-critical points (BCPs) in the interactions in question. Total electron energy densities, Hb (rc ), are plotted versus Hb (rc )-Vb (rc )/2 [=(ħ(2) /8m)∇(2) ρb (rc )] for the interactions in QTAIM-DFA, in which Vb (rc ) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θp , κp ) for those that contained the perturbed structures; θp corresponds to the tangent line of the plot and κp is the curvature. Whereas (R, θ) corresponds to the static nature, (θp , κp ) represents the dynamic nature of the interactions. All interactions in Y-X-✶-π(C6 H6 ) are classified by pure closed-shell interactions and characterized to have vdW nature, except for Y-I-✶-π(C6 H6 ) (Y=F, Cl, Br) and F-Br-✶-π(C6 H6 ), which have typical hydrogen-bond nature without covalency. I-I-✶-π(C6 H6 ) has a borderline nature between the two. Y-F-✶-π(C6 H6 ) (Y=Br, I) were optimized as bent forms, in which Y-✶-π interactions were detected. The Y-✶-π interactions in the bent forms are predicted to be substantially weaker than those in the linear F-Y-✶-π(C6 H6 ) forms.
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- 2016
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20. Nature of S2Se2 σ(4c–6e) at naphthalene 1,8-positions and models, elucidated by QTAIM dual functional analysis
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Waro Nakanishi, Yutaka Tsubomoto, and Satoko Hayashi
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010405 organic chemistry ,Chemistry ,Hydrogen bond ,General Chemical Engineering ,Hypervalent molecule ,Shell (structure) ,General Chemistry ,010402 general chemistry ,Curvature ,01 natural sciences ,Potential energy ,0104 chemical sciences ,Crystallography ,Covalent bond ,Computational chemistry ,Polar coordinate system ,Open shell - Abstract
The nature of extended hypervalent interactions of the BE–*–AE–*–AE–*–BE type is elucidated for 1-(8-MeBEC10H6)AE–AE(C10H6BEMe-8′)-1′, (1 (AE, BE) = (S, S), 2 (S, Se), 3 (Se, S) and 4 (Se, Se)) and models A–D, BR2BE⋯(AR)AE–AE(AR)⋯BEBR2 (AR, BR = H and Me). QTAIM dual functional analysis, which we proposed recently, is applied to the analysis. Total electron energy densities Hb(rc) are plotted versus Hb(rc) − Vb(rc)/2 for the interactions at bond critical points (BCPs; *), where Vb(rc) show potential energy densities at BCPs. Data for the perturbed structures around the fully optimized structures are employed for the plots, in addition to those of the fully optimized ones. While the data for the fully optimized structures are analysed by the polar coordinate (R, θ) representation, those containing the perturbed structures are by (θp, κp): θp corresponds to the tangent line for the plot and κp is the curvature. While (R, θ) show the static nature, (θp, κp) represent the dynamic nature of interactions. All AE–*–AE interactions in 1–4 and models A–D are classified by the shard shell interactions and have the character of a weak covalent nature. The AE–*–BE interactions in 1–4 are all classified by the regular closed shell interactions. They are predicted to have the typical HB (hydrogen bond) nature with covalency for 1 and 2 but the nature of the molecular complex formation through CT for 3 and 4. The AE–*–BE interactions in models A–D are predicted to be weaker than those in 1–4.
- Published
- 2016
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21. Quantum chemical calculations with the AIM approach applied to the π-interactions between hydrogen chalcogenides and naphthalene
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Waro Nakanishi, Satoko Hayashi, and Yuji Sugibayashi
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Quantum chemical ,Hydrogen ,010405 organic chemistry ,Chemistry ,General Chemical Engineering ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Adduct ,chemistry.chemical_compound ,Crystallography ,Computational chemistry ,Open shell ,Naphthalene - Abstract
The nature of the π–interactions in the 1 : 1 and 2 : 1 adducts of EH2 with the naphthalene π-system (E = O, S, Se and/or Te) is elucidated by applying QTAIM-DFA (QTAIM dual functional analysis). The H–*–π interactions are detected in EH2–*–π(C10H8) and (EH2)2–*–π(C10H8) for E = S, Se and Te, whereas E–*–π interactions are in OH2–*–π(C10H8), (OH2)2–*–π(C10H8) and HE–H–*–π(C10H8) (denoted by HHE–*–C10H8) (E = S, Se and Te). Asterisks * emphasize the existence of bond critical points (BCPs) on the interactions in question. Hb(rc) are plotted versus Hb(rc) − Vb(rc)/2 at the BCPs in QTAIM-DFA. Plots for the fully optimized structures are analyzed using the polar coordinate (R, θ) representation. Those containing the perturbed structures are by (θp, κp): θp corresponds to the tangent line of the plot and κp is the curvature. While (R, θ) describe the static nature, (θp, κp) represent the dynamic nature of interactions. The θ and θp values are less than 90° for all interactions in question, examined in this work, except for θp = 90.6° for HHTe–*–π(C10H8). Therefore, all interactions examined are classified by the pure-CS (closed shell) interactions and predicted to have vdW-nature, except for HHTe–*–π(C10H8), which should have the character of the typical HB-nature without covalency. The π–EB interaction in HHS–*–C10H8 is predicted to have the border character between the vdW-nature and the typical HB-nature without covalency, since θp = 89.8°. The nature of four interactions appeared between 2H in TeH2 and C10H8 in TeH2–*–π(C10H8) is also clarified well using QTAIM-DFA.
- Published
- 2016
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22. TRPV4 Increases the Expression of Tight Junction Protein-Encoding Genes via XBP1 in Mammary Epithelial Cells
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Moeko Mizusawa, Aminul Islam, Shinichi Yonekura, Mst Mamuna Sharmin, and Satoko Hayashi
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0301 basic medicine ,XBP1 ,UPR ,mammary gland development ,Occludin ,Article ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Zoology ,Gene expression ,lcsh:QL1-991 ,Gene knockdown ,lcsh:Veterinary medicine ,General Veterinary ,Tight junction ,Chemistry ,Cell growth ,CLDN3 ,Cell biology ,030104 developmental biology ,HC11 mouse mammary epithelial cell ,TRPV4 ,030220 oncology & carcinogenesis ,Unfolded protein response ,lcsh:SF600-1100 ,Animal Science and Zoology - Abstract
Mild heat stress (39 °, C&ndash, 40 °, C) can positively regulate cell proliferation and differentiation. Indeed, mild heat treatment at 39 °, C enhances the less-permeable tight junctions (TJs) formation and milk production in mammary epithelial cells. However, the molecular mechanisms of this response have not yet been delineated. In this study, the involvement of temperature-sensitive transient receptor potential vanilloid 4 (TRPV4) in the increase of &beta, casein and TJ protein-encoding gene expression in response to mild heat treatment (39 °, C) has been explored using HCll mouse mammary epithelial cells. Severe heat treatment (41 °, C) induced the transcriptional level of Chop (C/EBP homologous protein, proapoptotic marker) and reduced the cell viability. It is speculated that the difference in unfolded protein response (UPR) gene expression upon stimulation at 39 °, C vs. 41 °, C controls cell survival vs. cell death. The accumulation of Trpv4 mRNA was significantly higher in 39 °, C heat treatment cells. The &beta, casein, Zo-1 (zona occludens-1), Ocln (occludin), and Cldn3 (claudin 3) transcript levels were significantly increased in response to the addition of a selective TRPV4 channel agonist (GSK1016790A) at 37 °, C. TRPV4 stimulation with GSK1016790A also increased the X-box-binding protein 1 splicing form (Xbp1s) at the transcript level. The increase in the mRNA levels of &beta, casein, Zo-1, Ocln, and Cldn3 in response to 39 °, C heat treatment was suppressed by XBP1 knockdown. Moreover, the transcript level of Trpv4 was significantly increased at Day 15 of gestation, and its expression declined after 1 day of lactation. TRPV4 is activated not only by temperature but also by mechanical forces, such as cell stretching and shear stress, which guide mammary epithelial development in a normal mammary gland. These findings provide new insights of the possible function of TRPV4 in mammary gland development.
- Published
- 2020
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23. Behavior of the E–E’ Bonds (E, E’ = S and Se) in Glutathione Disulfide and Derivatives Elucidated by Quantum Chemical Calculations with the Quantum Theory of Atoms-in-Molecules Approach
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Satoko Hayashi, Yutaka Tsubomoto, and Waro Nakanishi
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Models, Molecular ,Molecular Conformation ,Pharmaceutical Science ,010402 general chemistry ,01 natural sciences ,Redox ,Article ,Antioxidants ,Catalysis ,Analytical Chemistry ,lcsh:QD241-441 ,chemistry.chemical_compound ,lcsh:Organic chemistry ,Ab initio quantum chemistry methods ,Quantum mechanics ,Drug Discovery ,Physical and Theoretical Chemistry ,Conformational isomerism ,Glutathione Peroxidase ,Glutathione Disulfide ,010405 organic chemistry ,ab initio calculations ,Organic Chemistry ,Atoms in molecules ,Potential energy ,Monte-Carlo method ,quantum theory of atoms-in-molecules (QTAIM) ,glutathione dichalcogenides ,0104 chemical sciences ,chemistry ,Chemistry (miscellaneous) ,Covalent bond ,Intramolecular force ,Molecular Medicine ,Glutathione disulfide ,Quantum Theory ,Thermodynamics - Abstract
The nature of the E–E’ bonds (E, E’ = S and Se) in glutathione disulfide (1) and derivatives 2–3, respectively, was elucidated by applying quantum theory of atoms-in-molecules (QTAIM) dual functional analysis (QTAIM-DFA), to clarify the basic contribution of E–E’ in the biological redox process, such as the glutathione peroxidase process. Five most stable conformers a–e were obtained, after applying the Monte-Carlo method then structural optimizations. In QTAIM-DFA, total electron energy densities Hb(rc) are plotted versus Hb(rc) − Vb(rc)/2 at bond critical points (BCPs), where Vb(rc) are potential energy densities at BCPs. Data from the fully optimized structures correspond to the static nature. Those containing perturbed structures around the fully optimized one in the plot represent the dynamic nature of interactions. The behavior of E–E’ was examined carefully. Whereas E–E’ in 1a–3e were all predicted to have the weak covalent nature of the shared shell interactions, two different types of S–S were detected in 1, depending on the conformational properties. Contributions from the intramolecular non-covalent interactions to stabilize the conformers were evaluated. An inverse relationship was observed between the stability of a conformer and the strength of E–E’ in the conformer, of which reason was discussed.
- Published
- 2018
24. Transannular E···E′ Interactions in Neutral, Radical Cationic, and Dicationic Forms of cyclo-[E(CH2CH2CH2)2E′] (E, E′ = S, Se, Te, and O) with Structural Feature: Dynamic and Static Behavior of E···E′ Elucidated by QTAIM Dual Functional Analysis
- Author
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Kohei Matsuiwa, Waro Nakanishi, Nozomu Nishizawa, and Satoko Hayashi
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Crystallography ,Functional analysis ,Covalent bond ,Chemistry ,Organic Chemistry ,Cationic polymerization ,Order (group theory) ,Static behavior - Abstract
The nature of the transannular E-∗-E' interactions in neutral, radical cationic, and dicationic forms of cyclo-E(CH2CH2CH2)2E' (1) (E, E' = S, Se, Te, and O) (1, 1(•+), and 1(2+), respectively) is elucidated by applying QTAIM dual functional analysis (QTAIM-DFA). Hb(rc) are plotted versus Hb(rc) - Vb(rc)/2 for the data of E-∗-E' at BCPs in QTAIM-DFA, where ∗ emphasizes the existence of BCP. Plots for the fully optimized structures are analyzed by the polar coordinate (R, θ) representation. Those containing the perturbed structures are by (θp, κp): θp corresponds to the tangent line of the plot, and κp is the curvature. While (R, θ) describes the static nature, (θp, κp) represents the dynamic nature of interactions. The nature is well-specified by (R, θ) and (θp, κp). E-∗-E' becomes stronger in the order of 1 < 1(•+) < 1(2+), except for O-∗-O. While E-∗-E' (E, E' = S, Se, and Te) in 1(2+) are characterized as weak covalent bonds, except for S-∗-Te (MC nature through CT) and Se-∗-Te (TBP nature through CT), O-∗-E' seems more complex. The behavior of E-∗-E' in 1(2+) is very close to that of cyclo-E(CH2CH2CH2)E' (E, E' = S, Se, Te, and O), except for O-∗-O.
- Published
- 2015
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25. Basic Concept and Applications of AIM Dual Functional Analysis: For Better Understanding and Explanation of Experimental Results Related to Interactions
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Waro Nakanishi and Satoko Hayashi
- Subjects
Theoretical computer science ,Chemistry ,Organic Chemistry ,DUAL (cognitive architecture) ,Functional analysis (psychology) - Published
- 2015
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26. Linear Four-Chalcogen Interactions in Radical Cationic and Dicationic Dimers of 1,5-(Dichalcogena)canes: Nature of the Interactions Elucidated by QTAIM Dual Functional Analysis with QC Calculations
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Shota Otsuki, Kengo Nagata, Satoko Hayashi, and Waro Nakanishi
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Electron energy ,Functional analysis ,010405 organic chemistry ,Chemistry ,Hypervalent molecule ,Cationic polymerization ,Electron ,010402 general chemistry ,01 natural sciences ,Potential energy ,0104 chemical sciences ,Crystallography ,Chalcogen ,Computational chemistry ,Physical and Theoretical Chemistry - Abstract
The dynamic and static nature of extended hypervalent interactions of the BE···AE···AE···BE type are elucidated for four center–seven electron interactions (4c–7e) in the radical cationic dimers (1·+) and 4c–6e in the dicationic dimers (12+) of 1,5-(dichalcogena)canes (2: AE(CH2CH2CH2)2BE: AE, BE = S, Se, Te, and O). The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied for the analysis. Total electron energy densities Hb(rc) are plotted versus Hb(rc) – Vb(rc)/2 [= (ℏ2/8m)∇2ρb(rc)] at bond critical points (BCPs) of the interactions, where Vb(rc) values show potential energy densities at BCPs. Data from the fully optimized structures correspond to the static nature of the interactions. Those from the perturbed structures around the fully optimized ones are also plotted, in addition to those of the fully optimized ones, which represent the dynamic nature of interactions. The BE···AE–AE···BE interactions in 12+ are stronger than the corresponding ones in 1·+, respectively. ...
- Published
- 2017
27. Dynamic and Static Behavior of E-E' Bonds in Neutral and Charged Forms of HEE'H, MeEE'Me, andCyclo-1,2-EE'(CH2)3(E, E' = O, S, Se, and Te) Elucidated by AIM Dual Functional Analysis
- Author
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Satoko Hayashi, Hiroaki Miza, Kohei Matsuiwa, and Waro Nakanishi
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Crystallography ,Functional analysis ,Chemistry ,Stereochemistry ,General Chemistry ,Polar coordinate system ,Curvature ,Static behavior ,Charged species - Abstract
The nature of the E-*-E' bonds in neutral, monoanionic, monocationic, and dicationic forms of HEE'H (1), MeEE'Me (2), and cyclo-1,2-EE'(CH2)3 (3) (E, E' = O, S, Se, Te) is investigated by applying AIM (atoms-in-molecules method) dual functional analysis. Hb(rc) are plotted versus Hb(rc) – Vb(rc)/2 for the data of E-*-E' at bond critical points (BCPs) of fully optimized structures and perturbed structures around the fully optimized ones. Plots for the fully optimized structures are analyzed by the polar coordinate (R, θ) representation. The (θp, κp) parameters are derived from those of the perturbed structures: θp corresponds to the tangent line of each plot, and κp is the curvature. While (R, θ) correspond to the static nature, (θp, κp) represent the dynamic nature of interactions. The nature of E-*-E' in the neutral and charged species is classified by comparing their θ and θp values with those of the standard interactions as a reference. Data for E-*-E' in the neutral forms of 1–3 appear in the shared-shell (SS) region (180° < θ), except for MeS-*-TeMe (2c), which does in the regular closed-shell (CS) region (90° < θ < 180°). The E–E' bonds in the monoanionic forms of 1–3 become much longer and weakened. Therefore, data of the monoanionic forms appear in the regular CS. On the other hand, the strengths of E-*-E' in the mono- and dicationic forms are almost equal to those in the neutral forms of 1–3 in the plots, irrespective of the shorter E-*-E' lengths in the cationic forms, relative to the neutral forms.
- Published
- 2014
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28. Aromatic Selenoic, Selenothioic, and Diselenoic Acid Salts: Isolation, Characterization, and 77Se NMR Spectra, Together with Theoretical Elucidation
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Daisuke Nishi, Waro Nakanishi, Satoko Hayashi, and Toshiaki Murai
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NMR spectra database ,Chemistry ,Organic chemistry ,General Chemistry ,Isolation (microbiology) ,Characterization (materials science) - Abstract
To systematically elucidate molecular and electronic structures of aromatic selenoic acid salts and their heavier congeners, they were synthesized by reacting selenoic, selenothioic, and diselenoic...
- Published
- 2014
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29. Relativistic effects on the 125Te and 33S NMR chemical shifts of various tellurium and sulfur species, together with 77Se of selenium congeners, in the framework of a zeroth-order regular approximation: applicability to tellurium compounds
- Author
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Waro Nakanishi, Kohei Matsuiwa, and Satoko Hayashi
- Subjects
chemistry ,General Chemical Engineering ,Chemical shift ,chemistry.chemical_element ,General Chemistry ,Electron ,Atomic physics ,Relativistic quantum chemistry ,Tellurium ,Polarization (waves) ,Sulfur ,Selenium ,Zeroth order - Abstract
The relativistic effects on absolute magnetic shielding tensors [σ(Z: Z = Te, Se and S)] are explicitly evaluated for various tellurium, selenium and sulfur species using the DFT(BLYP)-GIAO method. Calculations of σ(Te), σ(Se) and σ(S) are performed under the spin–orbit ZORA relativistic (Rlt-so) and nonrelativistic (Non) conditions with the Slater-type basis sets of the quadruple zeta all electron with four polarization functions (QZ4Pae). Structures optimized at the MP2 level under nonrelativistic conditions are employed for the evaluations. While the range of the relativistic effects on the total shielding tensors for Te (Δσt(Te)Rlt-so = σt(Te)Rlt-so − σd+p(Te)Non) is predicted to be −55 to 658 ppm, that for Δσt(S) is predicted to be 5 to 32 ppm, except for Me2SBr2 (TBP), where Δσt(S)Rlt-so = −29 ppm. The range for Δσt(Se) is 2 to 153 ppm. The magnitudes of the relativistic effects on σt(Te), σt(Se) and σt(S) are about 25 : 5 : 1. The applicability of σt(Te)Rlt-so to analyze δ(Te)obsd is also examined, mainly with the OPBE//OPBE method under the spin–orbit ZORA relativistic conditions with QZ4Pae, in addition to the above method.
- Published
- 2014
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30. Applications of Normal Coordinates of Internal Vibrations to Generate Perturbed Structures: Dynamic Behavior of Weak to Strong Interactions Elucidated by Atoms-in-Molecules Dual Functional Analysis
- Author
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Masayuki Kitamoto, Waro Nakanishi, Kohei Matsuiwa, and Satoko Hayashi
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Vibration ,Functional analysis ,Chemistry ,Atoms in molecules ,Normal coordinates ,General Chemistry ,Physics::Chemical Physics ,Molecular physics ,Dual (category theory) - Abstract
Normal coordinates of internal vibrations (NIV) are employed to generate the perturbed structures necessary in the atoms-in-molecules (AIM) dual functional analysis for a wide range of weak to stro...
- Published
- 2012
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31. Unusual Saddle-like Structure of (2-MeOC6H4CS)2S: Theoretical Studies and Comparison with its Oxygen Isologues
- Author
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Yuka Kito, Shinzi Kato, Satoko Hayashi, Masaru Ishida, Osamu Niyomura, Masahiro Ebihara, and Waro Nakanishi
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Chemistry ,chemistry.chemical_element ,Photochemistry ,Sulfur ,Inorganic Chemistry ,Crystallography ,chemistry.chemical_compound ,symbols.namesake ,Intramolecular force ,X-ray crystallography ,symbols ,Moiety ,Molecule ,Van der Waals radius ,HOMO/LUMO ,Derivative (chemistry) - Abstract
Compound (2-MeOC6H4CS)2S (1) showed an unusual saddle structure in which the –C(=S)–S–C(=S)– moiety is planar and two benzene rings lie a face-to-face and the distances (3.07 A) between the central sulfur atom and two 2-methoxy oxygen atoms are within the sum of van der Waals radii of the both atoms. However, the results of MO calculation at the B3LYP/6-311+G(2d, p) level showed no orbital interaction between both atoms. From the results of the calculations at the MP2 level, it was deduced that the crystal packing effect is important for such densely packed crystal, due to its less effective volume. On the other hand, the para-methoxy derivative (4-MeOC6H4CS)2S (2) in which the two methoxy oxygen atoms are not able to contact with the central sulfur atom shows an L-shaped structure in which the –C(=S)–S–C(=S)– moiety is not planar. The –C(=O)–S–C(=S)– moiety in compound (2-MeOC6H4CO)(2-MeOC6H4CS)S (3b) shows an L-shaped structure, though the two methoxy oxygen atoms are in intramolecular contact with the central sulfur atom. The deep blue to green colors of compounds 1 and 2 and the deep violet color of compound 3b are due to transitions of the lone-pair electrons in the HOMO (ψ87) of the thiocarbonyl sulfur atom to the LUMO (ψ89)and of those in the HOMO (ψ83) of the thiocarbonyl sulfur atom to the LUMO (ψ85), respectively.
- Published
- 2012
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32. Dynamic and Static Behaviors of N–Z–N σ(3c–4e) (Z = S, Se, and Te) Interactions: Atoms-in-Molecules Dual Functional Analysis with High-Resolution X-ray Diffraction Determination of Electron Densities for 2-(2-Pyridylimino)-2H-1,2,4-thiadiazolo[2,3-a]pyridine
- Author
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Satoko Hayashi, Mateusz B. Pitak, Waro Nakanishi, Simon J. Coles, and Michael B. Hursthouse
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chemistry.chemical_compound ,Crystallography ,chemistry ,Covalent bond ,Pyridine ,Atoms in molecules ,X-ray crystallography ,Charge density ,Molecule ,Moiety ,Physical and Theoretical Chemistry ,Adduct - Abstract
The structure of 2-(2-pyridylimino)-2H-1,2,4-thiadiazolo[2,3-a]pyridine (NSN) indicates that the molecule has a planar geometry with a linear N···S···N linkage, creating a tetracyclic structure of the formal C2v symmetry. To clarify the nature of the NSN σ(3c–4e) bonding, together with the related NSeN and NTeN, the dynamic and static behaviors are investigated by applying atoms-in-molecules (AIM) dual functional analysis to both the fully optimized and perturbed structures. The structures were optimized computationally, retaining C2v symmetry. All bond critical points are detected as expected and exhibited on both sides of the N···Z···N moiety which supports the formation of NZN σ(3c–4e). It is confirmed that N···S···N is of the covalent nature close to Me2S+-∗-Cl or Me2Se+-∗-Br, whereas N···Se···N and N···Te···N have the (regular) CS nature close to the CT adducts of Me2S(-∗-Cl)2 (TBP) and Me2Se-∗-Br2 (MC), respectively. An experimental high-resolution charge density determination has been performed on ...
- Published
- 2011
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33. Relativistic Effect on 77Se NMR Chemical Shifts of Various Selenium Species in the Framework of Zeroth-Order Regular Approximation
- Author
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Masahiko Hada, Yoshifumi Katsura, Waro Nakanishi, and Satoko Hayashi
- Subjects
Magnetic Resonance Spectroscopy ,Chemical shift ,Analytical chemistry ,chemistry.chemical_element ,Electron ,Polarization (waves) ,Selenium ,Paramagnetism ,chemistry ,Computational chemistry ,Electromagnetic shielding ,Diamagnetism ,Physical and Theoretical Chemistry ,Relativistic quantum chemistry - Abstract
The relativistic effects on absolute magnetic shielding tensors (σ(Se)) are explicitly evaluated for various selenium species (40 species) with the DFT(BLYP)-GIAO method. Calculations are performed under relativistic and nonrelativistic conditions with the Slater-type basis sets in ADF 2010 in the framework of ZORA, employing the optimized structures under nonrelativistic conditions at B3LYP of Gaussian 03. Quadruple zeta all electron with four polarization functions (QZ4Pae) are mainly applied to evaluate σ(Se). Ranges of the effect on diamagnetic (σ(d)(Se)), paramagnetic shielding tensors (σ(p)(Se)), and σ(d+p)(Se) (= σ(d)(Se) + σ(p)(Se)) are -24 to -20 ppm, -115 to -3 ppm, and -136 to -26 ppm, respectively. The spin-orbit terms (σ(so)(Se)) are evaluated to be 92-225 ppm with QZ4Pae, which clarifies the effect on total shielding tensors (σ(t)(Se) = σ(d+p)(Se) + σ(so)(Se)) to be -8 to 152 ppm, at the spin-orbit ZORA level. The calculated σ(t)(Se) values reproduced well the observed values.
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- 2011
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34. Highly Regioselective Amination of Unactivated Alkanes by Hypervalent Sulfonylimino-λ 3 -Bromane
- Author
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Waro Nakanishi, Takao Kaneaki, Masahito Ochiai, Kazunori Miyamoto, and Satoko Hayashi
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Alkane ,chemistry.chemical_classification ,Multidisciplinary ,Concerted reaction ,Imine ,Hypervalent molecule ,Regioselectivity ,Carbon–hydrogen bond activation ,Medicinal chemistry ,chemistry.chemical_compound ,chemistry ,Kinetic isotope effect ,Organic chemistry ,Amination - Abstract
Amination of alkanes has generally required metal catalysts and/or high temperatures. Here we report that simple exposure of a broad range of alkanes to N-triflylimino-λ3-bromane 1 at ambient temperature results in C–H insertion of the nitrogen functionality to afford triflyl-substituted amines in moderate to high yields. Marked selectivity for tertiary over secondary C–H bonds was observed; primary (methyl) C–H bonds were inert. Addition of hexafluoroisopropanol to inhibit decomposition of 1 dramatically improved the C–H amination efficiencies. Second-order kinetics, activation parameters (negative activation entropy), deuterium isotope effects, and theoretical calculations suggest a concerted asynchronous bimolecular transition state for the metal-free C–H amination event.
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- 2011
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35. How do weak Z-X-X and stronger X-Z-X interactions affect NMR chemical shifts of chalcogenide dihalides, R2Z·X2? Theoretical background on the structural prediction of R2Z·X2 through chemical shifts in solutions
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Satoko Hayashi, Waro Nakanishi, Takahito Nakai, and Akito Tanioku
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Bromine ,Chalcogenide ,Stereochemistry ,Chemical shift ,Heteroatom ,chemistry.chemical_element ,General Chemistry ,Adduct ,Paramagnetism ,chemistry.chemical_compound ,Bipyramid ,chemistry ,Physical chemistry ,Diamagnetism - Abstract
The mechanism is clarified for the high applicability of criteria to distinguish molecular complexes (MC) from pseudo-trigonal bipyramidal adducts (TBP) of chalcogenide dihalogens in solutions, based on the NMR chemical shifts. The criteria are theoretically investigated employing MC and TBP of MeSeMe (1), EtSeEt (3), PhSePh (7), PhSPh (8), and PhSeH (22) with chlorine and/or bromine. The adducts of (CH2CH)2Se (26), H2C(CHCH)2Se (27), and H2C(CHCH)2S (28) are also investigated. Behaviors of total absolute magnetic tensors (σt) for the atoms in question are analyzed separately by the diamagnetic and paramagnetic terms, which well support the observed NMR chemical shifts of the MC and TBP adducts in solutions. As a result, the criteria are thoroughly supported on the basis of theoretical background and the mechanism of criteria is clarified with the diamagnetic and paramagnetic terms. The results shed light on the specific effect of weak ZXX and stronger XZX interactions on the NMR chemical shifts of the adducts, R2Z·X2. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:446–456, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20707
- Published
- 2011
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36. Photoinduced Regio- and Stereoselective Introduction of Phenylchalcogeno Moieties to Ethynylferrocene
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Jun Tohoma, Waro Nakanishi, Kiichi Hirata, Akihiro Nomoto, Satoko Hayashi, Akiya Ogawa, Takuma Ikeda, Takuya Fujiyama, and Kiyomi Kakiuchi
- Subjects
chemistry.chemical_compound ,chemistry ,Diphenyl ditelluride ,Stereoselectivity ,General Chemistry ,Medicinal chemistry ,Diphenyl diselenide - Abstract
Upon photoirradiation, diphenyl diselenide and diphenyl ditelluride reacted with ethynylferrocene to afford the corresponding bischalcogenated vinylferrocenes. Regio- and stereoselectivities were d...
- Published
- 2014
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37. Behavior of I4 σ(4c-6e) in tellurolane system and related species, elucidated by QTAIM dual functional analysis with QC calculations
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Waro Nakanishi, Satoko Hayashi, and Taro Nishide
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Functional analysis ,010405 organic chemistry ,Chemical physics ,Chemistry ,General Chemistry ,DUAL (cognitive architecture) ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences - Published
- 2018
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38. Hypervalent λ3-Bromane Strategy for Baeyer−Villiger Oxidation: Selective Transformation of Primary Aliphatic and Aromatic Aldehydes to Formates, Which is Missing in the Classical Baeyer−Villiger Oxidation
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Waro Nakanishi, Satoko Hayashi, Akira Yoshimura, Masahito Ochiai, and Kazunori Miyamoto
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Aldehydes ,Formates ,Chemistry ,Methyl formate ,Hypervalent molecule ,General Chemistry ,Hydrocarbons, Aromatic ,Biochemistry ,Catalysis ,Reductive elimination ,Hydrocarbons, Brominated ,Baeyer–Villiger oxidation ,Benzaldehyde ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Octanal ,Criegee intermediate ,Organic chemistry ,Hydrate ,Oxidation-Reduction - Abstract
A conceptually distinct, modern strategy for Baeyer-Villiger oxidation (BVO) was developed. Our novel method involves initial hydration of water to carbonyl compounds, followed by ligand exchange of hypervalent aryl-lambda(3)-bromane on bromane(III) with the resulting hydrate, yielding a new type of activated Criegee intermediate. The intermediate undergoes BV rearrangement and produces an ester via facile reductive elimination of an aryl-lambda(3)-bromanyl group, because of the hypernucleofugality. The novel strategy makes it possible to induce selectively the BV rearrangement of straight chain primary aliphatic as well as aromatic aldehydes, which is missing in the classical BVO: for instance, octanal and benzaldehyde afforded rearranged formate esters with high selectivity (95%) under our conditions, while the attempted classical BVO produced only carboxylic acids. This firmly establishes the powerful nature of new methodology for BVO.
- Published
- 2010
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39. Dynamic Behaviors of Interactions: Application of Normal Coordinates of Internal Vibrations to AIM Dual Functional Analysis
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Waro Nakanishi and Satoko Hayashi
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Vibration ,Functional analysis ,Chemistry ,Normal coordinates ,Polar ,Tangent ,Physical and Theoretical Chemistry ,Curvature ,Kappa ,Mathematical physics - Abstract
A method to evaluate the dynamic nature of interactions is proposed based on the AIM dual functional analysis. Normal coordinates of internal vibrations (NIV) are employed to generate the perturbed structures necessary for the analysis. H(b)(r(c)) are plotted versus H(b)(r(c))-V(b)(r(c))/2 [= (variant Planck's over 2pi(2)/8m)nabla(2)rho(b)(r(c))] at bond critical points for the purpose. The plots are represented by the polar (R, theta) coordinate. Each plot for an interaction shows a specific curve, which is expressed by (theta(p), kappa(p)): theta(p) corresponds to the tangent line for the plot from the y-direction, and kappa(p) is the curvature. Although (R, theta) values correspond to the static nature of interactions, (theta(p), kappa(p)) values show the dynamic nature. The applicability of NIV is examined exemplified by the charge-transfer interactions as the first step to analyze the dynamic behaviors of interactions with NIV. The (theta(p), kappa(p)) values evaluated with NIV are very close to those obtained by the partial-optimization method (POM), where the distances or angles in question are fixed suitably, if the internal vibrations are substantially located on the interactions in question. The magnitudes of differences in theta(p) and kappa(p) between those evaluated with NIV and POM are < or = 2 degrees and < or = 2 au(-1), respectively, for usual interactions. The treatment is demonstrated to be applicable to a wide range of interactions.
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- 2010
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40. P(O, S, Se, and Te)–π(Ar) Conjugations as Factors to Control Fine Structures of 1-(Chalcogena)naphthalenes
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Satoko Hayashi, Waro Nakanishi, and Takahito Nakai
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Inorganic Chemistry ,Chalcogen ,Crystallography ,Stereochemistry ,Chemistry ,Organic Chemistry ,Biochemistry ,Lone pair ,Nmr data - Abstract
The p(Z)–π(Ar) conjugation as the factors to control the fine structures of organic chalcogen compounds are investigated. The structures of 1-(arylchalcogena)naphthalenes [1-(p-YC6H4Z)C10H7, 1-ArZNap; 1 (Z = O) and 2 (Z = S)] are determined by the X-ray crystallographic analysis. The structures of 1, 2, and 1-ArTeNap (4) are also determined in solutions, together with 1-ArSeNap (3), employing the NMR data of 9-(arylselanyl)anthracenes (5) and 1-(arylselanyl)anthraquinones (6). NMR data of 5 and 6 can be used as the standard of the A and B structures, respectively, for all Y examined in solutions: The Se–CAr bond in 5 (A) is placed almost perpendicular to the anthryl plane in A, and the bond is located on the plane in 6 (B). Structures of 1–4 are A if Y are electronically accepting groups such as Y = Cl, but they are B with Y of donating groups such as Y = OMe both in crystals and solutions. It is interesting that δ(Ci: 1–4) are hardly affected from the conformation around the Z–CAr bonds, whereas δ(H: 1–4...
- Published
- 2010
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41. Atoms-in-Molecules Dual Functional Analysis of Weak to Strong Interactions
- Author
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Waro Nakanishi and Satoko Hayashi
- Subjects
Functional analysis ,Chemical physics ,Chemistry ,Organic Chemistry ,Atoms in molecules ,Dual (category theory) - Published
- 2010
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42. How Are Non-Bonded G···Z (Z = O, S, and Se) Distances at Benzene 1,2-, Naphthalene 1,8-, and Anthracene 1,8,9-Positions Controlled? An Approach to Causality in Weak Interactions
- Author
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Satoko Hayashi and Waro Nakanishi
- Subjects
Causality (physics) ,chemistry.chemical_compound ,Crystallography ,Anthracene ,Reflection (mathematics) ,Chemistry ,Stereochemistry ,Plane (geometry) ,Order (group theory) ,General Chemistry ,Benzene ,Anthraquinone ,Naphthalene - Abstract
Mechanisms operating in weak interactions are sometimes quite different from those in strong ones. Factors to control the non-bonded G···Z (Z = O, S, and Se) distances at naphthalene 1,8-positions in 8-G-1-RZC 10 H 6 are analyzed as an example to clarify the causality of weak interactions. Structures around Z in 8-G-1-RZC 10 H 6 are well explained by three types, A, B, and C, where the Z―CR bond is perpendicular to the naphthyl plane in A, it is placed on the plane in B, and C is intermediate between A and B. The r(Z...Z) distances in 1,8-(RZ) 2 C 10 H 6 are observed to increase in an order of BB < CC < AB < AA. It seems difficult to explain the sequence based on the magnitudes of the closed-shell Z···Z interactions, since the BB interaction must not be so strong especially for Z of heavier atoms. The mechanism to control the r(Z···Z) distances is demonstrated to be the reflection from the repulsive interactions between R and H at the 2-position in 1,8-(RZ) 2 C 10 H 6 . Similar phenomena are also detected in the observed and calculated results at the benzene 1,2-, anthracene 1,8,9-, and anthraquinone 1,8,9-positions, which are explained based on the mechanism. Proposed idea and mechanism will help us to understand what happens in such weak interactions.
- Published
- 2009
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43. Evidence for Effective p(Z)−π(Ar) Conjugations (Z = S, Se, and Te, as Well as Z = O) in 9-(Arylchalcogenyl)triptycenes: Experimental and Theoretical Investigations
- Author
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Mao Minoura, Waro Nakanishi, Satoko Hayashi, and Takashi Nakamoto
- Subjects
Crystallography ,Chemistry ,Stereochemistry ,Organic Chemistry ,X-ray crystallography ,Proton NMR ,Molecule ,Activation energy ,Resonance (chemistry) ,Ground state ,Transition state ,Spectral line - Abstract
The p(Z)-pi(Ar) conjugations must operate fully in the ground states of 9-(arylchalcogenyl)triptycenes (p-YC(6)H(4)ZTpc:1 (Z = O), 2 (Z = S), 3 (Z = Se), and 4 (Z = Te)), where the p-YC(6)H(4) group is placed in the bisected area between two phenyl planes of the triptycyl group with the parallel orientation. The ground-state geometries, which we call (A: pl), are confirmed by X-ray analysis. However, the conjugations never operate in the transition states between (A: pl) and/or the topomeric structures (A': pl'), where the Z-C(Tpc) bond is perpendicular to the plane. The site-exchange processes correlate to the conjugations. Temperature-dependent (1)H NMR spectra are analyzed for 2 and 3 to demonstrate the effective p(Z)-pi(Ar) conjugations. The activation energies for the interconversion between (A: pl) and (A': pl') (GR: gear process) were obtained for 2 (DeltaG(GR)(2)) and 3 (DeltaG(GR)(3)). DeltaG(GR)(3) correlate well with DeltaG(GR)(2), and DeltaG(GR)(2) are well analyzed by the Hammett-type dual parameters. DeltaG(GR)(2) and DeltaG(GR)(3) are demonstrated to be controlled by the resonance interaction of the p(Z)-pi(C(6)H(4))-p(Y) conjugations. QC calculations are performed on the ground and exited states of 1-4, which clarify the effective p(Z)-pi(C(6)H(4))-p(Y) conjugations for Z of heavier atoms.
- Published
- 2009
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44. H/D Isotope Effect on 77Se NMR Chemical Shifts in 8-Methyl-1-(arylselanyl)naphthalenes and Related Selenides: Nonbonded C─H—Se Through-Space Versus Through-Bond Mechanisms
- Author
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Kentaro Yamane, Satoko Hayashi, and Waro Nakanishi
- Subjects
Stereochemistry ,Chemical shift ,Organic Chemistry ,Biochemistry ,Inorganic Chemistry ,Crystallography ,symbols.namesake ,chemistry.chemical_compound ,Reflection (mathematics) ,chemistry ,Ab initio quantum chemistry methods ,Kinetic isotope effect ,symbols ,Van der Waals radius ,Conformational isomerism ,Naphthalene ,Natural bond orbital - Abstract
77Se NMR chemical shifts of methyl-d 3 derivatives of 8-methyl-1-(phenylselanyl) naphthalene ( 1 ) and 8-methyl-1-(p-anisylselanyl)naphthalene ( 2 ) are observed 0.25 and 0.20 ppm upfield from 1 and 2 , respectively. The observations must be the reflection of the nonbonded interactions of the C─H—Se 3c–4e type in 1 and 2 . The mechanism is elucidated by means of crystallographic and theoretical investigations. The nonbonded distance between Se and C Me (2.989 A) is observed to be shorter than the sum of the van der Waals radii of the two by 0.91 A in 2 . 1 and 2 may be in equilibrium between conformers A and B in solution, where Se─C i is perpendicular to the naphthyl plane in A and it is on the plane in B . Natural bond orbital (NBO) analysis on 1 revealed that the nonbonded n p (Se)—σ *(C─H) interaction contributes in A , whereas nonbonded n s (Se)—σ *(C─H) and double σ (C─H)—σ *(Se–C) interactions operate in B .
- Published
- 2009
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45. How does non-covalent Se⋯SeO interaction stabilize selenoxides at naphthalene 1,8-positions: structural and theoretical investigations
- Author
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Józef Drabowicz, Satoko Hayashi, Atsushi Furuta, Waro Nakanishi, Takahiro Sasamori, and Norihiro Tokitoh
- Subjects
chemistry.chemical_compound ,Crystallography ,chemistry ,Stereochemistry ,Non covalent ,Materials Chemistry ,General Chemistry ,Lone pair ,Racemization ,Catalysis ,Bond cleavage ,Naphthalene - Abstract
Bis-selenides(LL), such as 8-[MeSe(X)]-1-[MeSe(Z)]C10H6 (1(LL)), 8-[EtSe(X)]-1-[EtSe(Z)]C10H6 (2(LL)), 8-[p-YC6H4Se(X)]-1-[MeSe(Z)]C10H6 (3(LL)) and 8-[p-YC6H4Se(X)]-1-[p-YC6H4Se(Z)]C10H6 (4(LL)) were oxidized with ozone at 0 °C, where (X, Z) = (lone pair, lone pair) for LL. Bis-selenoxides, 1(OO), 3(OO) and 4(OO) where (X, Z) = (oxygen, oxygen), were obtained in the oxidation of 1(LL), 3(LL) and 4(LL), respectively, via corresponding selenide-selenoxides, 1(LO), 3(LO) and 4(LO), respectively. A facile Se–C bond cleavage was observed in 2(LL). The structures of 1(LO) and 1(OO) were determined by the X-ray analysis. Three Se⋯SeO atoms in 1(LO) and four OSe⋯SeO atoms in 1(OO) align linearly. While the non-covalent Se⋯SeO 3c–4e interaction operates to stabilize 1(LO), the non-covalent OSe⋯SeO 4c–4e interaction would not stabilize 1(OO). The 3c–4e interaction must play an important role to control the stereochemistry of selenoxides. The 8-G-1-[MeSe(OH)2]C10H6 (n(OH·OH)) are the key intermediates in the racemization of 8-G-1-[MeSe(O)]C10H6 (n(O)) in solutions, where G = SeMe (1), H (5), F (6), Cl (7) and Br (8). Energies of n(OH·OH), relative to n(O), are evaluated based on the theoretical calculations. G of SeMe is demonstrated to operate most effectively to protect from racemization of selenoxides among n = 1 and 5–8, since the relative energies for G of cis- and trans-SeMe are largest.
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- 2009
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46. Fine Structures of 8-G-1-(p-YC6H4C ≡ CSe)C10H6(G = H, Cl, and Br) in Crystals and Solutions: Ethynyl Influence and Y- and G-Dependences
- Author
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Satoko Hayashi, Kentaro Yamane, and Waro Nakanishi
- Subjects
Inorganic Chemistry ,Crystallography ,Chemistry ,Organic Chemistry ,Biochemistry - Abstract
Fine structures of 8-G-1-(p-YC6H4C ≡ CSe)C10H6[1(G = H) and2(G = Cl): Y = H (a), OMe (b), Me (c), F (d), Cl (e), CN (f), andNO2(g)] are determined by the X-ray analysis. Structures of1,2, and3(G = Br) are calledAif each Se–Cspbond is perpendicular to the naphthyl plane, whereas they areBwhen the bond is placed on the plane. Structures are observed asAfor1a–cbearing Y of nonacceptors, whereas they areBfor1e–gwith Y of strong acceptors. The change in the structures of1e–gversus those of1a–cis called Y-dependence in1. The Y-dependence is very specific in1relative to 1-(p-YC6H4Se)C10H7(4) due to the ethynyl group: the Y-dependence in1is almost inverse to the case of4due to the ethynyl group. We call the specific effect “Ethynyl Influence.” Structures of2are observed asB: theA-type structure of1bchanges dramatically toBof2bby G = Cl at the 8-position, which is called G-dependence. The structures of2and3are examined in solutions based on the NMR parameters.
- Published
- 2009
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47. Analysis of One-Bond Se-Se Nuclear Couplings in Diselenides and 1,2-Diselenoles on the Basis of Molecular Orbital Theory: Torsional Angular Dependence, Electron Density Influence, and Origin inJ1(Se, Se)
- Author
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Satoko Hayashi, Waro Nakanishi, and Akito Tanioku
- Subjects
Inorganic Chemistry ,Electron density ,Basis (linear algebra) ,Chemistry ,Computational chemistry ,Organic Chemistry ,Molecular orbital ,Angular dependence ,Molecular orbital theory ,Biochemistry ,Molecular physics - Abstract
Nuclear couplings for the Se-Se bonds,J1(Se, Se), are analyzed on the basis of the molecular orbital (MO) theory. The values are calculated by employing the tripleζbasis sets of the Slater type at the DFT level.J1(Se, Se)are calculated modeled by MeSeSeMe (1a), which shows the typical torsional angular dependence onϕ(CMeSeSeCMe). The dependence explains well the observedJ1(Se, Se)obsdof small values (≤64 Hz) forRSeSeR′(1) (simple derivatives of1a) and large values (330–380 Hz) observed for 4-substituted naphto[1,8-c,d]-1,2-diselenoles (2) which correspond tosymperiplanardiselenides.J1(Se, Se :2) becomes larger as the electron density on Se increases. The paramagnetic spin-orbit terms contribute predominantly. The contributions are evaluated separately from each MO(ψi)and eachψi→ψatransition, whereψiandψaare occupied and unoccupied MO's, respectively. The separate evaluation enables us to recognize and visualize the origin and the mechanism of the couplings.
- Published
- 2009
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48. Noncovalent Z···Z (Z=O, S, Se, and Te) Interactions: How Do They Operate to Control Fine Structures of 1,8-Dichalcogene-Substituted Naphthalenes?
- Author
-
Waro Nakanishi and Satoko Hayashi
- Subjects
Crystallography ,chemistry.chemical_compound ,Chemistry ,Stereochemistry ,General Chemistry ,Homonuclear molecule ,Naphthalene - Abstract
Homonuclear Z···Z (Z=O, S, Se, and Te) interactions are investigated employing naphthalene 1,8-positions in 1,8-(MeZ)2C10H6 (1a–1d: Z=O (a), S (b), Se (c), and Te (d)), 1-MeZ-8-PhZC10H6 (2a–2c), an...
- Published
- 2008
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49. Fine structures of 8-G-1-(arylethynylselanyl)naphthalenes (G = H, Cl, Br): Factors to control the linear alignment of five G⋯Se–C C–CAr atoms in crystals and the behavior in solution
- Author
-
Kentaro Yamane, Satoko Hayashi, Takahiro Sasamori, Waro Nakanishi, and Norihiro Tokitoh
- Subjects
Inorganic Chemistry ,NMR spectra database ,Quantum chemical ,Crystallography ,chemistry.chemical_compound ,Chemistry ,Stereochemistry ,Aryl ,Materials Chemistry ,Physical and Theoretical Chemistry ,Lone pair - Abstract
8-G-1-(p-YC6H4C CSe)C10H6 [2 (G = Cl) and 3 (G = Br): Y = H (a), OMe (b), Me (c), F (d), Cl (e), CN (f) and NO2 (g)] have been prepared and the NMR spectra measured, in addition to 1 (G = H). Structures have been determined by X-ray crystallographic analysis for 2b, 2e and 2g, which are all type B (B), where the Se–Csp bond is placed in the naphthyl plane in B. The type is classified as A if the Se–Csp bond is perpendicular to the naphthyl plane. Structures around the p-YC6H4 (Ar) group are pd (perpendicular) for Y = OMe (2b) and Cl (2e) and pl (planar) for Y = NO2 (2g), where the Se–CNap bond is placed in the aryl plane in pl and perpendicular to the plane in pd. The 1b (A: pd) structure changes dramatically on going to 2b (B: pd) with G = Cl at the 8-position. The effect is called the G-dependence in 2. The G-dependence arises from the energy lowering effect of the np(Cl)⋯σ∗(Se–Csp) 3c–4e interaction. Structures are both (B: pd) for 1e and 2e and both (B: pl) for 1g and 2g. One may realize that the structures are unchanged by G = Cl in place of G = H for Y = Cl and NO2 at a first glance. However, the B structures in 2e and 2g must be much more stabilized by the G-dependence of the np(Cl)⋯σ∗(Se–Csp) 3c–4e interaction or the G⋯Se–Csp–Csp–Csp2 5c–6e type interaction. The structures of 2 and 3 are examined in solution based on the NMR parameters. The results show that 2 and 3 behave very similarly to each other and the structures are predominantly B, with some equilibrium between pd and pl around the aryl groups in solution. Quantum chemical calculations support the observations.
- Published
- 2008
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50. 77Se NMR Chemical Shifts of 9-(Arylselanyl)triptycenes: New Standard for Planar Structures of ArSeR and Applications to Determine the Structures in Solutions
- Author
-
Waro Nakanishi, Satoko Hayashi, and Takashi Nakamoto
- Subjects
Anions ,Anthracenes ,Magnetic Resonance Spectroscopy ,Chemistry ,Stereochemistry ,Chemical shift ,Organic Chemistry ,Chemistry, Organic ,Molecular Conformation ,Benzene ,Stereoisomerism ,Naphthalenes ,Quinone ,Selenium ,Crystallography ,Planar ,Models, Chemical ,Halogen ,Quantum Theory ,Molecule ,Chemical solution ,Anthraquinone Derivatives ,Software - Abstract
A set of new delta(Se) parameters is proposed as a standard for the planar (pl) orientational effect of p-YC(6)H(4) (Ar) in ArSeR, employing 9-(arylselanyl)triptycenes (1: p-YC(6)H(4)SeTpc). The Se-C(R) bond in ArSeR is placed on the Ar plane in pl and it is perpendicular to the plane in pd. Large upfield shifts are observed for Y = NMe(2), OMe, and Me (-22 to -6 ppm) and large downfield shifts for Y = COOEt, CN, and NO(2) (19-37 ppm), relative to Y = H, with small upfield and moderate downfield shifts by Y of halogens (-1 ppm for Y = F and 4 ppm for Y = Cl and Br). This must be the result of the p(Se)-pi(C(6)H(4))-p(Y) conjugation in 1 (pl). While the character of delta(Se) in 1 (pl) is very similar to that in 9-(arylselanyl)anthracenes (2 (pl)), it is very different from that of 1-(arylselanyl)anthraquinones (3 (pd)). Sets of delta(Se) of 1 and 2 must serve as the standard for pl and that of 3 does for pd in solutions. Structures of various ArSeR in solutions are determined from the viewpoint of the orientational effect based on the standard delta(Se) of 1-3. While the structure of 2-methyl-1-(arylselanyl)naphthalenes is concluded to be all pl in solutions, those of 8-chloro- and 8-bromo-1-(arylselanyl)naphthalenes are all pd, except for Y = COOEt, CN, and NO(2): The equilibrium between pd and pl contributes to those with Y = COOEt, CN, and NO(2). The structure of 1-(arylselanyl)naphthalenes changes depending on Y. The structures of ArSeMe and ArSeCOPh are shown to be pl and pd, respectively, in solutions. Those of ArSePh and ArSeAr seem to change depending on Y. delta(Se) of 1-3 are demonstrated to serve as the standard to determine the structures in solutions. The rules of thumb derived from the characters in delta(Se) for 1-3 are very useful to determine the structures of ArSeR in solutions, in addition to the analysis based on the plots.
- Published
- 2008
- Full Text
- View/download PDF
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