Title:
Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions
Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions
| dc.contributor.author | Hohenstein, Edward G. | en_US |
| dc.contributor.author | Parrish, Robert M. | en_US |
| dc.contributor.author | Sherrill, C. David | en_US |
| dc.contributor.author | Turney, Justin M. | en_US |
| dc.contributor.author | Schaefer, Henry F., III | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. Center for Organic Photonics and Electronics | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. Center for Computational Molecular Science and Technology | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. School of Chemistry and Biochemistry | en_US |
| dc.contributor.corporatename | University of Georgia. Center for Computational Quantum Chemistry | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. School of Chemistry and Biochemistry | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. School of Computational Science and Engineering | en_US |
| dc.date.accessioned | 2013-05-29T18:28:38Z | |
| dc.date.available | 2013-05-29T18:28:38Z | |
| dc.date.issued | 2011-11 | |
| dc.description | © 2011 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.3656681 | en_US |
| dc.description | DOI: 10.1063/1.3656681 | en_US |
| dc.description.abstract | Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies. | en_US |
| dc.identifier.citation | Hohenstein, Edward G. and Parrish, Robert M. and Sherrill, C. David and Turney, Justin M. and Schaefer, III, Henry F., "Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions," Journal of Chemical Physics, 135, 17 (November 7 2011) | en_US |
| dc.identifier.doi | 10.1063/1.3656681 | |
| dc.identifier.issn | 0021-9606 | |
| dc.identifier.uri | http://hdl.handle.net/1853/47111 | |
| dc.publisher | Georgia Institute of Technology | en_US |
| dc.publisher.original | American Institute of Physics | en_US |
| dc.subject | Biochemistry | en_US |
| dc.subject | Biology computing | en_US |
| dc.subject | Disperse systems | en_US |
| dc.subject | DNA | en_US |
| dc.subject | Hydrogen bonds | en_US |
| dc.subject | Laplace transforms | en_US |
| dc.subject | Matrix decomposition | en_US |
| dc.subject | Molecular biophysics | en_US |
| dc.subject | Molecular configurations | en_US |
| dc.subject | Perturbation techniques | en_US |
| dc.subject | Physiological models | en_US |
| dc.title | Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions | en_US |
| dc.type | Text | |
| dc.type.genre | Article | |
| dspace.entity.type | Publication | |
| local.contributor.author | Sherrill, C. David | |
| local.contributor.corporatename | Center for Organic Photonics and Electronics | |
| relation.isAuthorOfPublication | 771cfa30-1ff7-4a12-b4c7-4f8e93b4860a | |
| relation.isOrgUnitOfPublication | 43f8dc5f-0678-4f07-b44a-edbf587c338f |
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