ArticleThe journal of physical chemistry. A2010
Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers.
Article in The journal of physical chemistry. A, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.The Journal of chemical physics · 2025Article
- Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water.Scientific reports · 2022Article
- Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.The Journal of chemical physics · 2021Article
- Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?Nanomaterials (Basel, Switzerland) · 2021Review
- Psi4 1.4: Open-source software for high-throughput quantum chemistry.The Journal of chemical physics · 2020Article
- The influence of water potential in simulation: a catabolite activator protein case study.Journal of molecular modeling · 2019Article
- Polarizable embedding for simulating redox potentials of biomolecules.Physical chemistry chemical physics : PCCP · 2019Article
- Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.Journal of chemical theory and computation · 2017Article
- Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.The journal of physical chemistry. A · 2015Article
- First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate.The journal of physical chemistry. B · 2012Article
- The effective fragment molecular orbital method for fragments connected by covalent bonds.PloS one · 2012Article
- Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk.The journal of physical chemistry. A · 2011Article
- Fragme∩t: An Open-Source Framework for Multiscale Quantum Chemistry Based on Fragmentation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
9 authors.
Funding
Abstract
The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.
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