Journal of Computational Chemistry

Cover image for Vol. 35 Issue 30

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science


Cover Gallery 2013

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Volume 34, Issue 1
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Volume 34, Issue 1b
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Volume 34, Issue 2
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Volume 34, Issue 2b
FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithmThe role of water in the adsorption of oxygenated aromatics on Pt and PdAppropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methodsVariationally determined electronic states for the theoretical analysis of intramolecular interaction. II. Qualitative nature of the P[BOND]O bond in phosphine oxides
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Volume 34, Issue 3
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Volume 34, Issue 3b
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Volume 34, Issue 4
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Volume 34, Issue 4b
Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuationGlobal and local indices for characterizing biomolecular flexibility and rigidityA nonredundant structure dataset for benchmarking protein-RNA computational dockingTheoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations
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Volume 34, Issue 5
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Volume 34, Issue 5b
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Volume 34, Issue 6
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Volume 34, Issue 6b
Extending Hirshfeld-I to bulk and periodic materialsSolving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approachNatural bond orbital analysis in the ONETEP code: Applications to large protein systemsA detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy
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Volume 34, Issue 7
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Volume 34, Issue 7b
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Volume 34, Issue 8
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Volume 34, Issue 8b
Solvent-driven symmetry of self-assembled nanocrystal superlattices�A computational study(Ala)4-X-(Ala)4 as a model system for the optimization of the ?1 and ?2 amino acid side-chain dihedral empirical force field parametersPICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levelsParameterization of a geometric flow implicit solvation model
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Volume 34, Issue 9
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Volume 34, Issue 9b
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Volume 34, Issue 10
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Volume 34, Issue 10b
Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against mycobacterium tuberculosisA valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force fieldStructure-based redesign of proteins for minimal T-cell epitope contentSpectroscopic fingerprints of toroidal nuclear quantum delocalization via Ab Initio path integral simulations
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Volume 34, Issue 11
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Volume 34, Issue 11b
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Volume 34, Issue 12
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Volume 34, Issue 12b
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machinesTargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemblePDECO: Parallel differential evolution for clusters optimizationUnderstanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of f�rster theory
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Volume 34, Issue 13
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Volume 34, Issue 13b
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Volume 34, Issue 14
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Volume 34, Issue 14b
Parameterization of a reactive force field using a monte carlo algorithmPHI: A powerful new program for the analysis of anisotropic monomeric and exchange-coupled polynuclear d- and f-block complexesGrid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces
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Volume 34, Issue 15
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Volume 34, Issue 15b
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Volume 34, Issue 16
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Volume 34, Issue 16b
Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX typeA partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational spaceNBO 6.0: Natural bond orbital analysis programModeling of phytochrome absorption spectra
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Volume 34, Issue 17
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Volume 34, Issue 17b
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Volume 34, Issue 18
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Volume 34, Issue 18b
Program fullerene�a software package for constructing and analyzing structures of regular fullerenesPhotodeactivation paths in norbornadieneRelating Trp-Glu dipeptide fluorescence to molecular conformation: The role of the discrete chi 1 and chi 2 anglesComputation of magnetic circular dichroism by sum-over-states summations
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Volume 34, Issue 19
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Volume 34, Issue 19b
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Volume 34, Issue 20
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Volume 34, Issue 20b
A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB familyTheoretical characterization and design of small molecule donor material containing naphthodithiophene central unit for efficient organic solar cellsMultiobjective evolutionary algorithm with many tables for purely ab initio protein structure predictionIMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol
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Volume 34, Issue 21
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Volume 34, Issue 21b
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Volume 34, Issue 22
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Volume 34, Issue 22b
Differential geometric analysis of alterations in MH a-helicesPathOpt�A global transition state search approach: Outline of algorithmHigh�quality protein backbone reconstruction from alpha carbons using gaussian mixture models129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent
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Volume 34, Issue 23
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Volume 34, Issue 23b
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Volume 34, Issue 24
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Volume 34, Issue 24b
The performance of density functional and wavefunction-based methods for 2D and 3D structures of Au10A morphometric approach for the accurate solvation thermodynamics of proteins and ligandsComputational gibberellin-binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptorA parallel finite element simulator for ion transport through three-dimensional ion channel systems
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Volume 34, Issue 25
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Volume 34, Issue 25b
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Volume 34, Issue 26
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Volume 34, Issue 26b
GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulationsGALAMOST: GPU-accelerated large-scale molecular simulation toolkitGrcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories1,3-Dipolar cycloadditions of Stone�Wales defective single-walled carbon nanotubes: A theoretical study
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Volume 34, Issue 27
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Volume 34, Issue 27b
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Volume 34, Issue 28
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Volume 34, Issue 28b
Overcoming dissipation in the calculation of standard binding free energies by ligand extractionEfficient optimization of van der Waals parameters from bulk propertiesNuclear quantum effect and temperature dependency on the hydrogen-bonded structure of base pairsElectron density deformations provide new insights into the spectral shift of rhodopsins
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Volume 34, Issue 29
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Volume 34, Issue 29b
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Volume 34, Issue 30
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Volume 34, Issue 30b
Characterization of the polymorphic states of copper(II)-bound A?(1�16) peptides by computational simulationsOptimization of RI-MP2 Auxiliary Basis Functions for 6-31G** and 6-311G** Basis Sets for First-, Second-, and Third-Row ElementsStochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquidsGalaxyDock2: Protein�ligand docking using beta-complex and global optimization
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Volume 34, Issue 31
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Volume 34, Issue 31b
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Volume 34, Issue 32
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Volume 34, Issue 32b
A high-level ab initio study of the N2 + N2 reaction channelAb Initio molecular dynamics study of ethylene adsorption onto Si(001) surface: Short-time fourier transform analysis of structural coordinate autocorrelation functionRapid parameterization of small molecules using the force field toolkitChemical mechanism of surface-enhanced raman scattering spectrum of pyridine adsorbed on Ag cluster: Ab initio molecular dynamics approach

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