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Works (43)

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

Biophysical Journal
2016 | Journal article
DOI: 10.1016/j.bpj.2016.01.002
WOSUID:

WOS:000370763800023
Contributors: Patel, Dhilon S.; Re, Suyong; Wu, Emilia L.; Qi, Yifei; Klebba, Phillip E.; Widmalm, Goeran; Yeom, Min Sun; Sugita, Yuji; Im, Wonpil
Source: Self-asserted source
Suyong Re via ResearcherID

Exploring N-Glycan Conformers: Assessment of Enhanced Sampling Algorithms

Biophysical Journal
2016 | Journal article
WOSUID:

WOS:000375143200237
Contributors: Galvelis, Raimondas; Re, Suyong; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

Journal of Physical Chemistry C
2016 | Journal article
DOI: 10.1021/acs.jpcc.6b08980
WOSUID:

WOS:000386107600043
Contributors: Adhikari, Aniruddha; Re, Suyong; Nishima, Wataru; Ahmed, Mohammed; Nihonyanagi, Satoshi; Klauda, Jeffery B.; Sugita, Yuji; Tahara, Tahei
Source: Self-asserted source
Suyong Re via ResearcherID

Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations (vol 5, pg 4343, 2014)

Journal of Physical Chemistry Letters
2015 | Journal article
DOI: 10.1021/jz502676e
WOSUID:

WOS:000347513700030
Contributors: Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function

International Journal of Quantum Chemistry
2015 | Journal article
DOI: 10.1002/qua.24785
WOSUID:

WOS:000348373700009
Contributors: Miyashita, Naoyuki; Re, Suyong; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase

Journal of Chemical Theory and Computation
2014 | Journal article
DOI: 10.1021/ct5004143
WOSUID:

WOS:000341543000055
Contributors: Komuro, Yasuaki; Re, Suyong; Kobayashi, Chigusa; Muneyuki, Eiro; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Joint Seminar between RIKEN and Glycoinformatics Young Scientist Community

Trends in Glycoscience and Glycotechnology
2014 | Journal article
DOI: 10.4052/tigg.26.71
WOSUID:

WOS:000209630200003
Contributors: Re, Suyong
Source: Self-asserted source
Suyong Re via ResearcherID

Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations

Journal of Physical Chemistry Letters
2014 | Journal article
DOI: 10.1021/jz502299m
WOSUID:

WOS:000346759700020
Contributors: Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Conformational Diversity of N-Glycans in Solution Studied by REMD Simulations

Biophysical Journal
2013 | Journal article
WOSUID:

WOS:000316074301369
Contributors: Sugita, Yuji; Nishima, Wataru; Yamaguchi, Yoshiki; Re, Suyong
Source: Self-asserted source
Suyong Re via ResearcherID

Improved Constrained Optimization Method for Reaction-Path Determination in Quantum Mechanical/Molecular Mechanical Calculations

Biophysical Journal
2013 | Journal article
WOSUID:

WOS:000316074305101
Contributors: Jung, Jaewoon; Re, Suyong; Sugita, Yuji; Ten-no, Seiichiro
Source: Self-asserted source
Suyong Re via ResearcherID

Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations

Journal of Chemical Physics
2013 | Journal article
DOI: 10.1063/1.4775812
WOSUID:

WOS:000314725900007
Contributors: Jung, Jaewoon; Re, Suyong; Sugita, Yuji; Ten-no, Seiichiro
Source: Self-asserted source
Suyong Re via ResearcherID

Interionic Hydration Structures of NaCl in Aqueous Solution: A Combined Study of Quantum Mechanical Cluster Calculations and QM/EFP-MD Simulations

Journal of Physical Chemistry B
2013 | Journal article
DOI: 10.1021/jp308731z
WOSUID:

WOS:000313220600029
Contributors: Ghosh, Manik K.; Re, Suyong; Feig, Michael; Sugita, Yuji; Choi, Cheol Ho
Source: Self-asserted source
Suyong Re via ResearcherID

Multiple Conformers and their Spectroscopic Properties of N-Glycan Predicted using Replica-Exchange Simulations

Biophysical Journal
2013 | Journal article
WOSUID:

WOS:000316074306361
Contributors: Nishima, Wataru; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong
Source: Self-asserted source
Suyong Re via ResearcherID

Solvent Electronic Polarization Effects on Na+-Na+ and Cl--Cl- Pair Associations in Aqueous Solution

Journal of Physical Chemistry B
2013 | Journal article
DOI: 10.1021/jp4049346
WOSUID:

WOS:000323082200016
Contributors: Choi, Cheol Ho; Re, Suyong; Rashid, Mohammad H. O.; Li, Hui; Feig, Michael; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography

Rapid Communications in Mass Spectrometry
2012 | Journal article
DOI: 10.1002/rcm.6412
WOSUID:

WOS:000310872500004
Contributors: Yamaguchi, Yoshiki; Nishima, Wataru; Re, Suyong; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Crystal structure of alpha 5 beta 1 integrin ectodomain: Atomic details of the fibronectin receptor

Journal of Cell Biology
2012 | Journal article
DOI: 10.1083/jcb.201111077
WOSUID:

WOS:000302476600014
Contributors: Nagae, Masamichi; Re, Suyong; Mihara, Emiko; Nogi, Terukazu; Sugita, Yuji; Takagi, Junichi
Source: Self-asserted source
Suyong Re via ResearcherID

Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution

Journal of Physical Chemistry B
2012 | Journal article
DOI: 10.1021/jp212550z
WOSUID:

WOS:000306724100017
Contributors: Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong
Source: Self-asserted source
Suyong Re via ResearcherID

Modulation Mechanism on the Conformational Diversities of Biantennary Complex-Type N-Glycans in Water

Biophysical Journal
2012 | Journal article
WOSUID:

WOS:000321561205197
Contributors: Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiyuki; Sugita, Yiji; Re, Suyong
Source: Self-asserted source
Suyong Re via ResearcherID

Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water

Chemical Physics Letters
2012 | Journal article
DOI: 10.1016/j.cplett.2012.05.014
WOSUID:

WOS:000305802600043
Contributors: Choi, Cheol Ho; Re, Suyong; Feig, Michael; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation

Journal of Computational Chemistry
2011 | Journal article
DOI: 10.1002/jcc.21615
WOSUID:

WOS:000285312300008
Contributors: Re, Suyong; Imai, Takashi; Jung, Jaewoon; Ten-No, Seiichiro; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Modeling the Transition State of Enzyme-catalyzed Phosphoryl Transfer Reaction Using QM/MM Method

Yakugaku Zasshi-Journal of the Pharmaceutical Society of Japan
2011 | Journal article
WOSUID:

WOS:000294527400004
Contributors: Re, Suyong; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

Biophysical Journal
2011 | Journal article
DOI: 10.1016/j.bpj.2011.10.019
WOSUID:

WOS:000297143500002
Contributors: Re, Suyong; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Vibrational Symmetry Breaking of NO3- in Aqueous Solution: NO Asymmetric Stretch Frequency Distribution and Mean Splitting

Journal of Physical Chemistry a
2010 | Journal article
DOI: 10.1021/jp903626t
WOSUID:

WOS:000273672600005
Contributors: Ramesh, Sai G.; Re, Suyong; Boisson, Jean; Hynes, James T.
Source: Self-asserted source
Suyong Re via ResearcherID

A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase

Chemical Physics Letters
2009 | Journal article
DOI: 10.1016/j.cplett.2009.08.068
WOSUID:

WOS:000270423000026
Contributors: Re, Suyong; Jung, Jaewoon; Ten-no, Seiichiro; Sugita, Yuji
Source: Self-asserted source
Suyong Re via ResearcherID

Charge transfer and OH vibrational frequency red shifts in nitrate-water clusters

Journal of Physical Chemistry a
2008 | Journal article
DOI: 10.1021/jp0761012
WOSUID:

WOS:000254883800015
Contributors: Ramesh, Sai G.; Re, Suyong; Hynes, James T.
Source: Self-asserted source
Suyong Re via ResearcherID

PHYS 317-Hydration effects on water reorientation and ionic charge transfer

Abstracts of Papers of the American Chemical Society
2007 | Journal article
WOSUID:

WOS:000207593907513
Contributors: Hynes, James T.; Laage, Damien; Re, Suyong; Ramesh, Sai Ganesh
Source: Self-asserted source
Suyong Re via ResearcherID

Experimental determination of the n(N) -> sigma* (P-O) interaction energy of O-equatorial C-apical phosphoranes bearing a primary amino group

Inorganic Chemistry
2006 | Journal article
DOI: 10.1021/ic0609047
WOSUID:

WOS:000240033700035
Contributors: Adachi, Takahiro; Matsukawa, Shiro; Nakamoto, Masaaki; Kajiyama, Kazumasa; Kojima, Satoshi; Yamamoto, Yohsuke; Akiba, Kin-ya; Re, Suyong; Nagase, Shigeru
Source: Self-asserted source
Suyong Re via ResearcherID

On the ultrafast infrared spectroscopy of anion hydration shell hydrogen bond dynamics

Journal of Physical Chemistry a
2006 | Journal article
DOI: 10.1021/jp064846m
WOSUID:

WOS:000240825800004
Contributors: Nigro, Bruno; Re, Suyong; Laage, Damien; Rey, Rossend; Hynes, James T.
Source: Self-asserted source
Suyong Re via ResearcherID

Interplay of single-wall carbon nanotubes and encapsulated La@C-82, La-2@C-80, and Sc3N@C-80

Physical Review B
2005 | Journal article
DOI: 10.1103/PhysRevB.71.235417
WOSUID:

WOS:000230276800106
Contributors: Lu, J; Nagase, S; Re, SY; Zhang, XW; Yu, DP; Zhang, J; Han, RS; Gao, ZX; Ye, HQ; Zhang, SA et al.
Source: Self-asserted source
Suyong Re via ResearcherID

A bowl-shaped fullerene encapsulates a water into the cage

Journal of the American Chemical Society
2004 | Journal article
DOI: 10.1021/ja038537a
WOSUID:

WOS:000220038800007
Contributors: Iwamatsu, S; Uozaki, T; Kobayashi, K; Re, SY; Nagase, S; Murata, S
Source: Self-asserted source
Suyong Re via ResearcherID

Ab initio molecular orbital investigation of a precursor in ethylene biosynthesis: Proton transfer in a cluster of 1-aminocyclopropane-1-carboxylic acid and water

Journal of Physical Chemistry a
2004 | Journal article
DOI: 10.1021/jp031146y
WOSUID:

WOS:000222125800015
Contributors: Ito, M; Re, S; Tokiwa, H
Source: Self-asserted source
Suyong Re via ResearcherID

How is the CH/pi interaction important for molecular recognition?

Chemical Communications
2004 | Journal article
DOI: 10.1039/b316280j
WOSUID:

WOS:000220663700017
Contributors: Re, S; Nagase, S
Source: Self-asserted source
Suyong Re via ResearcherID

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH- with polychlorinated hydrocarbons CH(4-n)Cln (n=2-4)

Theoretical Chemistry Accounts
2004 | Journal article
DOI: 10.1007/s00214-003-0554-z
WOSUID:

WOS:000221155600001
Contributors: Re, SY; Morokuma, K
Source: Self-asserted source
Suyong Re via ResearcherID

Calculation of packing structure of methanol solid using ab initio lattice energy at the MP2 level

Chemical Physics Letters
2003 | Journal article
DOI: 10.1016/S0009-2614(03)00025-3
WOSUID:

WOS:000181079000013
Contributors: Nagayoshi, K; Kitaura, K; Koseki, S; Re, SY; Kobayashi, K; Choe, YK; Nagase, S
Source: Self-asserted source
Suyong Re via ResearcherID

Theoretical identification of C-20 carbon clusters: Prevalence of the monocyclic isomer and existence of the smallest fullerene and bowl isomer

Physical Review B
2003 | Journal article
DOI: 10.1103/PhysRevB.67.125415
WOSUID:

WOS:000182158000098
Contributors: Lu, J; Re, S; Choe, Y; Nagase, S; Zhou, YS; Han, RS; Peng, LM; Zhang, XW; Zhao, XG
Source: Self-asserted source
Suyong Re via ResearcherID

Characteristic reactions and properties of C-apical O-equatorial (O-cis) spirophosphoranes: Effect of the sigma*(P-O) orbital in the equatorial plane and isolation of a hexacoordinate oxaphosphetane as an intermediate of the Wittig type reaction of 10-P-5 phosphoranes

Journal of the American Chemical Society
2002 | Journal article
DOI: 10.1021/ja026776c
WOSUID:

WOS:000178966700044
Contributors: Matsukawa, S; Kojima, S; Kajiyama, K; Yamamoto, Y; Akiba, K; Re, S; Nagase, S
Source: Self-asserted source
Suyong Re via ResearcherID

Effect of sigma* P-O orbital on structure, stereomutation, and reactivity of C-apical O-equatorial spirophosphoranes

Phosphorus Sulfur and Silicon and the Related Elements
2002 | Journal article
DOI: 10.1080/10426500212284
WOSUID:

WOS:000176800600065
Contributors: Akiba, K; Matsukawa, S; Adachi, T; Yamamoto, Y; Re, SY; Nagase, S
Source: Self-asserted source
Suyong Re via ResearcherID

Molecular geometries, vibrational analysis, bonding and molecular orbitals of the three isomers of [RuCl(qn)(2)NO] (Hqn=2-methyl-8-quinolinol or 2-chloro-8-quinolinol): density functional theory studies

Inorganica Chimica Acta
2002 | Journal article
DOI: 10.1016/S0020-1693(02)01093-9
WOSUID:

WOS:000179283000017
Contributors: Wang, HF; Miki, E; Re, SY; Tokiwa, H
Source: Self-asserted source
Suyong Re via ResearcherID

Enhanced stability of non-proton-transferred clusters of hydrated hydrogen fluoride HF(H2O)(n) (n=1-7): A molecular orbital study

Journal of Physical Chemistry a
2001 | Journal article
DOI: 10.1021/jp011003g
WOSUID:

WOS:000171805000015
Contributors: Re, SY
Source: Self-asserted source
Suyong Re via ResearcherID

ONIOM study of chemical reactions in microsolvation clusters: (H2O)(n)CH3Cl+OH-(H2O)(m) (n+m = 1 and 2)

Journal of Physical Chemistry a
2001 | Journal article
DOI: 10.1021/jp004623a
WOSUID:

WOS:000170152700008
Contributors: Re, S; Morokuma, K
Source: Self-asserted source
Suyong Re via ResearcherID

Coexistence of neutral and ion-pair clusters of hydrated sulfuric acid H2SO4(H2O)n (n=1-5) - A molecular orbital study

Journal of Physical Chemistry a
1999 | Journal article
DOI: 10.1021/jp984759x
WOSUID:

WOS:000080304200030
Contributors: Re, S; Osamura, Y; Morokuma, K
Source: Self-asserted source
Suyong Re via ResearcherID

Size-dependent hydrogen bonds of cluster ions between phenol cation radicals and water molecules: A molecular orbital study

Journal of Physical Chemistry a
1998 | Journal article
DOI: 10.1021/jp980468c
WOSUID:

WOS:000073999900022
Contributors: Re, SY; Osamura, Y
Source: Self-asserted source
Suyong Re via ResearcherID

Structures and stability of hydrated clusters of hydrogen chloride, HCl(H2O)(n), n=1-5

Journal of Chemical Physics
1998 | Journal article
DOI: 10.1063/1.476640
WOSUID:

WOS:000075255500015
Contributors: Re, S; Osamura, Y; Suzuki, Y; Schaefer, HF
Source: Self-asserted source
Suyong Re via ResearcherID
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