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1

Structures and stability of hydrated clusters of hydrogen chloride, HCl(H[sub 2]O)[sub n], n=1–5

Re, Suyong, Osamura, Yoshihiro, Suzuki, Youhei, Schaefer, Henry F.

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 382 KB

english, 1998

2

carbon clusters: Prevalence of the monocyclic isomer and existence of the smallest fullerene and bowl isomer

Lu, Jing, Re, Suyong, Choe, Yoong-kee, Nagase, Shigeru, Zhou, Yunsong, Han, Rushan, Peng, Lianmao, Zhang, Xinwei, Zhao, Xiangeng

Journal:

Physical Review B

Year:

2003

Language:

english

File:

PDF, 363 KB

english, 2003

3

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

RE, Suyong, SUGITA, Yuji

Journal:

YAKUGAKU ZASSHI

Year:

2011

Language:

english

File:

PDF, 1.90 MB

english, 2011

4

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation

Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-No, Yuji Sugita

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 2.79 MB

english, 2011

5

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

Suyong Re, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita

Journal:

Chemical Physics Letters

Year:

2009

Language:

english

File:

PDF, 798 KB

english, 2009

6

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

Kanade Nagayoshi, Kazuo Kitaura, Shiro Koseki, Suyong Re, Kaoru Kobayashi, Yoong-Kee Choe, Shigeru Nagase

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 315 KB

english, 2003

7

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

Hongfei Wang, Eiichi Miki, Suyong Re, Hiroaki Tokiwa

Journal:

Inorganica Chimica Acta

Year:

2002

Language:

english

File:

PDF, 200 KB

english, 2002

8

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)

Suyong Re, Keiji Morokuma

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2004

Language:

english

File:

PDF, 525 KB

english, 2004

9

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

Cheol Ho Choi, Suyong Re, Michael Feig, Yuji Sugita

Journal:

Chemical Physics Letters

Year:

2012

Language:

english

File:

PDF, 600 KB

english, 2012

10

Size-Dependent Hydrogen Bonds of Cluster Ions between Phenol Cation Radicals and Water Molecules: A Molecular Orbital Study

Re, Suyong, Osamura, Yoshihiro

Journal:

Journal of Physical Chemistry A

Year:

1998

Language:

english

File:

PDF, 343 KB

english, 1998

11

A Bowl-Shaped Fullerene Encapsulates a Water into the Cage

Iwamatsu, Sho-ichi, Uozaki, Takashi, Kobayashi, Kaoru, Re, Suyong, Nagase, Shigeru, Murata, Shizuaki

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 85 KB

english, 2004

12

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

Nishima, Wataru, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji, Re, Suyong

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 543 KB

english, 2012

13

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

Yamaguchi, Yoshiki, Nishima, Wataru, Re, Suyong, Sugita, Yuji

Journal:

Rapid Communications in Mass Spectrometry

Year:

2012

Language:

english

File:

PDF, 1.30 MB

english, 2012

14

Conformational flexibility of N-glycans in solution studied by REMD simulations

Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita

Journal:

Biophysical Reviews

Year:

2012

Language:

english

File:

PDF, 659 KB

english, 2012

15

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

Re, Suyong, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 381 KB

english, 2011

16

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

Ghosh, Manik K., Re, Suyong, Feig, Michael, Sugita, Yuji, Choi, Cheol Ho

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

17

ONIOM Study of Chemical Reactions in Microsolvation Clusters: (H 2 O) n CH 3 Cl + OH - (H 2 O) m ( n + m = 1 and 2)

Re, Suyong, Morokuma, Keiji

Journal:

Journal of Physical Chemistry A

Year:

2001

Language:

english

File:

PDF, 312 KB

english, 2001

18

Enhanced Stability of Non-Proton-Transferred Clusters of Hydrated Hydrogen Fluoride HF(H 2 O) n ( n = 1−7): A Molecular Orbital Study

Journal:

Journal of Physical Chemistry A

Year:

2001

Language:

english

File:

PDF, 265 KB

english, 2001

19

Experimental Determination of the n N → σ* P-O Interaction Energy of O-Equatorial C-Apical Phosphoranes Bearing a Primary Amino Group

Adachi, Takahiro, Matsukawa, Shiro, Nakamoto, Masaaki, Kajiyama, Kazumasa, Kojima, Satoshi, Yamamoto, Yohsuke, Akiba, Kin-ya, Re, Suyong, Nagase, Shigeru

Journal:

Inorganic Chemistry

Year:

2006

Language:

english

File:

PDF, 317 KB

english, 2006

20

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

Sugita, Yuji, Nishima, Wataru, Yamaguchi, Yoshiki, Re, Suyong

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

21

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

Jung, Jaewoon, Re, Suyong, Sugita, Yuji, Ten-no, Seiichiro

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 34 KB

english, 2013

22

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

Nishima, Wataru, Yamaguchi, Yoshiki, Sugita, Yuji, Re, Suyong

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 57 KB

english, 2013

23

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

Nishima, Wataru, Miyashita, Naoyuki, Yamaguchi, Yoshiyuki, Sugita, Yiji, Re, Suyong

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 61 KB

english, 2012

24

Coexistence of Neutral and Ion-Pair Clusters of Hydrated Sulfuric Acid H 2 SO 4 (H 2 O) n ( n = 1−5)A Molecular Orbital Study

Re, Suyong, Osamura, Yoshihiro, Morokuma, Keiji

Journal:

Journal of Physical Chemistry A

Year:

1999

Language:

english

File:

PDF, 340 KB

english, 1999

25

Charge Transfer and OH Vibrational Frequency Red Shifts in Nitrate−Water Clusters

Ramesh, Sai G., Re, Suyong, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2008

Language:

english

File:

PDF, 161 KB

english, 2008

26

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

Choi, Cheol Ho, Re, Suyong, Rashid, Mohammad H. O., Li, Hui, Feig, Michael, Sugita, Yuji

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 942 KB

english, 2013

27

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca 2+ -ATPase

Komuro, Yasuaki, Re, Suyong, Kobayashi, Chigusa, Muneyuki, Eiro, Sugita, Yuji

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.97 MB

english, 2014

28

Characteristic Reactions and Properties of C -Apical O -Equatorial ( O-cis ) Spirophosphoranes: Effect of the σ* 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

Matsukawa, Shiro, Kojima, Satoshi, Kajiyama, Kazumasa, Yamamoto, Yohsuke, Akiba, Kin-ya, Re, Suyong, Nagase, Shigeru

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 785 KB

english, 2002

29

Vibrational Symmetry Breaking of NO 3− in Aqueous Solution: NO Asymmetric Stretch Frequency Distribution and Mean Splitting †

Ramesh, Sai G., Re, Suyong, Boisson, Jean, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

30

On the Ultrafast Infrared Spectroscopy of Anion Hydration Shell Hydrogen Bond Dynamics

Nigro, Bruno, Re, Suyong, Laage, Damien, Rey, Rossend, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2006

Language:

english

File:

PDF, 126 KB

english, 2006

31

Ab Initio Molecular Orbital Investigation of a Precursor in Ethylene Biosynthesis: Proton Transfer in a Cluster of 1-Aminocyclopropane-1-carboxylic Acid and Water

Ito, Mika, Re, Suyong, Tokiwa, Hiroaki

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 258 KB

english, 2004

32

Effect of σ* P--O Orbital on Structure, Stereomutation, and Reactivity of C -Apical O -Equatorial Spirophosphoranes

Akiba, Kin-ya, Matsukawa, Shiro, Adachi, Takahiro, Yamamoto, Yohsuke, Re, Suyong, Nagase, Shigeru

Journal:

Phosphorus Sulfur and Silicon and the Related Elements

Year:

2002

Language:

english

File:

PDF, 143 KB

english, 2002

33

How is the CH/? interaction important for molecular recognition?Electronic supplementary information (ESI) available: optimized cartesian coordinates. See http://www.rsc.org/suppdata/cc/b3/b316280j/

Re, Suyong, Nagase, Shigeru

Journal:

Chemical Communications

Year:

2004

Language:

english

File:

PDF, 304 KB

english, 2004

34

, and

Lu, Jing, Nagase, Shigeru, Re, Suyong, Zhang, Xinwei, Yu, Dapeng, Zhang, Jin, Han, Rushan, Gao, Zhengxiang, Ye, Hengqiang, Zhang, Shuang, Peng, Lianmao

Journal:

Physical Review B

Year:

2005

Language:

english

File:

PDF, 703 KB

english, 2005

35

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

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 3.24 MB

english, 2014

36

REIN: Replica-exchange INterface for simulating protein dynamics and function

Miyashita, Naoyuki, Re, Suyong, Sugita, Yuji

Journal:

International Journal of Quantum Chemistry

Year:

2015

Language:

english

File:

PDF, 805 KB

english, 2015

37

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

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

The Journal of Physical Chemistry Letters

Year:

2015

File:

PDF, 121 KB

2015

38

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

Jung, Jaewoon, Re, Suyong, Sugita, Yuji, Ten-no, Seiichiro

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 2.85 MB

english, 2013

39

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

Patel, Dhilon S., Re, Suyong, Wu, Emilia L., Qi, Yifei, Klebba, Phillip E., Widmalm, Göran, Yeom, Min Sun, Sugita, Yuji, Im, Wonpil

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 2.30 MB

english, 2016

40

Exploring N-Glycan Conformers: Assessment of Enhanced Sampling Algorithms

Galvelis, Raimondas, Re, Suyong, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 40 KB

english, 2016

41

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

Adhikari, Aniruddha, Re, Suyong, Nishima, Wataru, Ahmed, Mohammed, Nihonyanagi, Satoshi, Klauda, Jeffery B., Sugita, Yuji, Tahara, Tahei

Journal:

The Journal of Physical Chemistry C

Year:

2016

Language:

english

File:

PDF, 1.67 MB

english, 2016

42

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics

Galvelis, Raimondas, Re, Suyong, Sugita, Yuji

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.80 MB

english, 2017

43

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

Re, Suyong, Watabe, Shigehisa, Nishima, Wataru, Muneyuki, Eiro, Yamaguchi, Yoshiki, MacKerell, Alexander D., Sugita, Yuji

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.86 MB

english, 2018

44

3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Re, Suyong, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 242 KB

english, 2011

45

3C1148 New implementation of the reaction path determination in the QM/MM method(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Jung, Jaewoon, Re, Suyong, Sugita, Yuji, Ten-no, Seiichiro

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 260 KB

english, 2011

46

1PT212 Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution(The 50th Annual Meeting of the Biophysical Society of Japan)

Nishima, Wataru, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji, Suyong, Re

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 213 KB

english, 2012

47

3P049 Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans(01A. Protein: Structure,Poster)

Re, Suyong, Watabe, Shigehisa, Nishima, Wataru, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

48

3P111 Molecular dynamics simulations of SR Ca^-ATPase using improved ATP force field(03. Membrane proteins,Poster)

Komuro, Yasuaki, Kobayashi, Chigusa, Re, Suyong, Muneyuki, Eiro, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 695 KB

english, 2013

49

3E1110 Replica-exchange interface program (REIN)(Proteins:Structure,Oral Presentation)

Miyashita, Naoyuki, Re, Suyong, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 210 KB

english, 2012

50

1P204 Structure and orientation of hydrating water molecules at phospholipid/water interface revealed by molecular dynamics simulation(13A. Biological & Artificial membrane: Structure & Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 694 KB

english, 2014