Volume 32; Issue 1

Journal of Computational Chemistry

Volume 32; Issue 1

1

Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength, aromaticity, and excited-state intramolecular proton transfer reaction

Subrata Mahanta, Bijan Kumar Paul, Rupashree Balia Singh, Nikhil Guchhait

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.68 MB

english, 2011

2

From acetylene complexes to vinylidene structures: The GeC2H2 system

Qiang Hao, Andrew C. Simmonett, Yukio Yamaguchi, De-Cai Fang, Henry F. Schaefer III

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 342 KB

english, 2011

3

Optimizing energy functions for protein–protein interface design

Oz Sharabi, Chen Yanover, Ayelet Dekel, Julia M. Shifman

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 473 KB

english, 2011

4

Homology modeling and molecular dynamics simulation studies of human type 1 3β-hydroxysteroid dehydrogenase: Toward the understanding of cofactor specificity

Yongbing Zhao, Jingfa Xiao

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

5

NUPACK: Analysis and design of nucleic acid systems

Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

6

Isomerization of stilbene using enforced geometry optimization

Jon Baker, Krzysztof Wolinski

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 414 KB

english, 2011

7

Parallel implementation of γ-point pseudopotential plane-wave DFT with exact exchange

Eric J. Bylaska, Kiril Tsemekhman, Scott B. Baden, John H. Weare, Hannes Jonsson

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.11 MB

english, 2011

8

Deriving the phylogenetic information from some physicochemical properties of protein sequences computed

Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-Hou Lin

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 185 KB

english, 2011

9

Gabedit—A graphical user interface for computational chemistry softwares

Abdul-Rahman Allouche

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 408 KB

english, 2011

10

Predicting the accuracy of protein–ligand docking on homology models

Annalisa Bordogna, Alessandro Pandini, Laura Bonati

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 739 KB

english, 2011

11

Hydrogen-bond networks in finite ice nanotubes

A. M. Tokmachev, R. Dronskowski

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 255 KB

english, 2011

12

A large decoy set of protein–protein complexes produced by flexible docking

Guillaume Launay, Thomas Simonson

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 804 KB

english, 2011

13

Correlation between thermal conductivity and bond length alternation in carbon nanotubes: A combined reverse nonequilibrium molecular dynamics—Crystal orbital analysis

Mohammad Alaghemandi, Joachim Schulte, Frédéric Leroy, Florian Müller-plathe, Michael C. Böhm

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 410 KB

english, 2011

14

Rapid communication reply to comment on: “Fast determination of the optimal rotational matrix for macromolecular superpositions”

Pu Liu, Dimitris K. Agrafiotis, Douglas L. Theobald

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

15

Comment on “Fast determination of the optimal rotational matrix for macromolecular superpositions” [J. Comp. Chem. 31, 1561 (2010)]

Gerald R. Kneller

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 54 KB

english, 2011

16

Accurate estimation of solvation free energy using polynomial fitting techniques

Conrad Shyu, F. Marty Ytreberg

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 159 KB

english, 2011

17

A CAS study on S-loss and O-loss dissociation mechanisms of the SO2+ ion in the C, D, and E states

Qingyong Meng, Ming-Bao Huang

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 269 KB

english, 2011

18

Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics

Jae In Kim, Sungsoo Na, Kilho Eom

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.44 MB

english, 2011

19

Shape and size effects in π–π interactions: Face-to-face dimers

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 665 KB

english, 2011