Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

Hohenstein, Edward G.; Parrish, Robert M.; Sherrill, C. David; Turney, Justin M.; Schaefer, Henry F.

doi:doi:10.1063/1.3656681

Volume/Page
Keyword
DOI
Citation
Advanced

Volume: Page/Article:

Search Content Type

article doi:

Citation:

Optimization of a genetic algorithm for searching molecular conformer space

We present two sets of tunings that are broadly applicable to conformer searches of isolated molecules using a genetic algorithm (GA). In order to find the most efficient tunings for the GA, a second GA – a meta-genetic algorithm – was used to tune the first genetic algorithm to reliably find the already known a priori correct answer with minimum computational resources. It is shown that these tunings are appropriate for a variety of molecules with different characteristics, and most importantly...

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale system...

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.

Article Outline

INTRODUCTION
THEORETICAL METHODS
1. Symmetry-adapted perturbation theory
2. Density fitting
3. Laplace transform techniques
4. Generalized two-electron integrals
5. Coupled-perturbed Hartree-Fock equations
6. Exchange-dispersion evaluation
RESULTS AND DISCUSSION
1. Timings
2. Accuracy of approximate energy denominators
3. Application to intercalator complexes
CONCLUSIONS

RELATED DATABASES

To view database links for this article, you need to log in.

KEYWORDS and PACS

Keywords

biochemistry, biology computing, disperse systems, DNA, hydrogen bonds, Laplace transforms, matrix decomposition, molecular biophysics, molecular configurations, perturbation techniques, physiological models

PACS

87.15.R-

Reactions and kinetics
02.30.Uu

Integral transforms
36.20.Hb

Configuration (bonds, dimensions)
87.14.gk

DNA
87.15.A-

Theory, modeling, and computer simulation
87.15.Fh

Bonding; mechanisms of bond breakage

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.3656681

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef

American Institute of Physics

Figures (3) Tables (2)

Access to article objects (figures, tables, multimedia) requires a subscription; log in to view available files.
(Access to supplementary files, where available, is free for this journal.)