Journal Of Computational Chemistry
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- Wiley from 1980
A DFT study on Cu(I) coordination in Cu-ZSM-5: Effects of the functional choice and tuning of the ONIOM approach.
The coordination of Cu(+) at the T1 and T7 positions of the M7 ring of Cu-ZSM-5, and the interaction of NO with coordinated Cu(+) were investigated by means of DFT/ONIOM calculations. The B3LYP, BLYP, PBE1PBE, PBE, M06, and M062X functionals with the def2-TZVP (def2-QZVP for Cu) basis set were used...
Cover image, volume 36, issue 5.
On page 273 (DOI: 10.1002/jcc.23800), Dmitry Zuev, Eugene Vecharynski, Chao Yang, Natalie Orms, and Anna I. Krylov report on new iterative diagonalization algorithms targeting interior eigenstates of large matrices, which enable calculations of highly excited states within equation-of-motion coupled...
Cover image, volume 35, issue 28.
On page 2070 (DOI: 10.1002/jcc.23733), Martin Andersson and Susan L. S. Stipp report the prediction of the free energy of hydration for 40 mono- and multivalent cations and anions using density functional theory and the implicit solvent model COSMO-RS. No significant systematic errors for mono- and...
Cover image, volume 33, issue 26.
A HOBDI (4-hydroxybenzylidene-1,2-dimethylimidazolinone) solute molecule in aqueous solution was used as one of the test systems to validate the newly implemented quantum-chemical/molecular-mechanical (QM/MM) functionality of the GROMOS (Groningen Molecular Simulation) software for (...
Inside cover, volume 33, issue 24.
As presented by Chuan Li, Lin Li, Jie Zhang, and Emil Alexov on page 1960, the image shows the distribution of electrostatic field mapped onto the surface of the adeno-associated virus, PDB ID 3KIC. The structural file, after a standard protonation, contains approximately 484,500 ato...
Automatic analysis of computed catalytic cycles.
We present the AUTOF program that allows the user to apply the complete model in a black box fashion. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011. Copyright © 2010 Wiley Periodicals, Inc....
The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α-alkenoyl ketene-(S,S)-acetals: Hydrogen bonding and elect...
A density functional theory (DFT) study was performed to elucidate the mechanism for the [5 + 1] benzannulation of nitroethane and α-alkenoyl ketene-(S,S)-acetals. The calculation results are consistent with experimental findings, showing that the reaction proceeds via deprotonation of nitroethane,...
Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material.
We investigated the electronic structure and microscopic charge transport properties of the cyanated bithiophene-functionalized DPP molecule (compound 1). First, we analyzed in detail the partition of the total relaxation (polaron) energy into the contributions from each vibrational mode and the inf...
How does a hydrocarbon staple affect peptide hydrophobicity?
Water is essential for the proper folding of proteins and the assembly of protein-protein/ligand complexes. How water regulates complex formation depends on the chemical and topological details of the interface. The dynamics of water in the interdomain region between an E3 ubiquitin ligase (MDM2) an...
Melting of icosahedral nickel clusters under hydrostatic pressure.
The thermal stabilities and melting behavior of icosahedral nickel clusters under hydrostatic pressure have been studied by constant-pressure molecular dynamics simulation. The potential energy and Lindemann index are calculated. The overall melting temperature exhibits a strong dependence on pressu...