Journal of Computational Chemistry
Copyright © 2013 Wiley Periodicals, Inc., A Wiley Company
Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner
Impact Factor: 4.583
ISI Journal Citation Reports © Ranking: 2011: 26/154 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- Analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment
Neil Qiang Su, Igor Ying Zhang and Xin Xu
Article first published online: 16 MAY 2013 | DOI: 10.1002/jcc.23312
The XYG3-type doubly hybrid (xDH) functionals are nonvariational in both the hybrid density functional part and the second-order perturbation part, each of which requires formally a coupled-perturbed Kohn–Sham equation to be solved for analytic gradients. An implementation is reported here which combines the two parts by defining a total Lagrangian such that only a single set of the Z-vector equations need to be solved. Test calculations are provided to demonstrate the satisfactory performance of the xDH functionals for geometry optimizations.
- Nonfitting protein–ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors
Li Rao, Igor Ying Zhang, Wenping Guo, Li Feng, Eric Meggers and Xin Xu
Article first published online: 16 MAY 2013 | DOI: 10.1002/jcc.23303
Accurate theoretical estimation of protein–ligand interaction is vitally important for the rational design of an effective drug. In this work, we have developed a nonfitting protein–ligand interaction scoring function based on divide and conquer strategy and first-principles methods. Good correlations on applications to cyclin-dependent kinase 2 and p21-activated kinase 1 inhibitor databases are found between the calculated scores and the experimental inhibitor efficacies with the square of correlation coefficient R2 of 0.76–0.89.
- XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC-CI combined with dipped adcluster model
Atsushi Ishikawa and Hiroshi Nakatsuji
Article first published online: 16 MAY 2013 | DOI: 10.1002/jcc.23324
O1s core-electron binding energies of electrophilic and nucleophilic oxygens important for olefin epoxidation on silver surface were investigated by the symmetry-adapted-cluster configuration-interaction (SAC-CI) method combined with the dipped adcluster model (DAM). The experimental information and our theoretical results indicate that Oelec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that Onuc is the one on the reconstructed added-row site of Ag(110).
- Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities
Ireneusz W. Bulik, Robert Zaleśny, Wojciech Bartkowiak, Josep M. Luis, Bernard Kirtman, Gustavo E. Scuseria, Aggelos Avramopoulos, Heribert Reis and Manthos G. Papadopoulos
Article first published online: 16 MAY 2013 | DOI: 10.1002/jcc.23316
A set of exchange-correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM-B3LYP, LC-BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of polymethineimine oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the MP2 and CCSD methods.
- Corrected small basis set Hartree-Fock method for large systems
Rebecca Sure and Stefan Grimme
Article first published online: 14 MAY 2013 | DOI: 10.1002/jcc.23317
A newly developed HF-3c quantum chemical protocol combines a Hartree- Fock/small basis set calculation with three physically plausible atom-pair wise correction terms. It yields good results for non-covalent interactions, geometries of organic molecules, supramolecular complexes and small proteins. For most test cases its accuracy approaches DFT-D3/large basis set quality, but obtained at a tiny fraction of computational cost and can hence be applied to large molecular systems as an alternative to semiempirical methods.