Lyudmila V. Slipchenko, PhD , Purdue University
- the effective fragment potential (EFP) method in GAMESS has been extended to allow flexible fragments; initial benchmarks show that the flexible fragment potentials accurately reproduce torsional barriers in ethane and other alkanes and alcohols. The more detailed benchmarks on conformational space of polypeptides are underway. A manuscript describing this work is prepared for publication in JPCB.
- mixing in water-TBA solutions at different concentrations of TBA have been investigated by EFP-MD. Structural characteristics of these solutions are compared to available neutron scattering data. There is a nice agreement between the EFP and experimental radial distribution functions (RDF) in terms of both heights of the peaks and relative intensities of different components. We found that for these mixtures, EFP performs better than the GROMOS96 force field often used for simulations of alcohol solutions. A manuscript describing the investigation of incomplete mixing in water-TBA solutions is submitted to JPCB: M. Hands and L.V. Slipchenko, Intermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-Tert-Butanol Mixtures, J. Phys. Chem. B, submitted (2011).
- the effective fragment library is populated with molecules from S22 dataset for non-covalent interactions. The library is available within the GAMESS and Q-CHEM distributions. The accuracy of EFP for S22 dataset is benchmarked against the highly accurate CCSD(T)/CBS and SAPT (symmetry adapted perturbation theory) data. While EFP provides very good accuracy (mean absolute deviation with respect to CCSD(T)/CBS is 0.9 kcal/mol) the analysis of the specific interaction-energy terms (electrostatic, polarization, dispersion, exchange-repulsion) reveals that the remaining deficiencies in EFP come from electrostatic and polarization terms, mainly due to insufficient description of short-range charge-penetration effects. A manuscript describing this work is submitted to JCTC: J.C. Flick, D. Kosenkov, E.G. Hohenstein, C.D. Sherrill, and L.V. Slipchenko, Accurate Prediction of Non-covalent Interaction Energies with the Effective Fragment Potential method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set, J. Chem Theory Comp., submitted (2011).
- interactions between benzene and water were investigated using EFP and classical molecular dynamics, in collaboration with experimental group of Prof. Ben-Amotz at Purdue. The focus of this study is on characterizing pi-hydrogen bonds of benzene in liquid water in terms of their orientational and energetic preferences. An exciting conclusion of this project is that the conversion of a water-water hydrogen bond to a benzene-water pi-hydrogen bond is endothermic but the pi-H bonds are stabilized by entropy. A manuscript is submitted to JACS: K.P. Gierszal, J.G. Davis, M.D. Hands, D.S. Wilcox, L.V. Slipchenko, and D. Ben-Amotz, pi-Hydrogen Bonding in Liquid Water, J. Amer. Chem. Soc., submitted (2011).
- EFP was applied to characterize the pi-pi interactions in complexes of benzene with pyridine and DNA base pairs. Two papers are published: Q.A. Smith, M.S. Gordon*, and L.V. Slipchenko, Benzene-Pyridine Interactions Predicted by the Effective Fragment Potential Method, J. Phys. Chem. A, 115 (18), 4598–4609 (2011); Q.A. Smith, M.S. Gordon*, and L.V. Slipchenko, Effective Fragment Potential Study of the Interaction of DNA Bases, J. Phys. Chem. A, in press (2011) DOI: 10.1021/jp2047954.
- we explore strategies for improved performance of EFP by developing algorithms for faster and more accurate exchange-repulsion and charge-transfer terms. We have developed pilot codes for the on-the-fly parameterization of these energy terms; initial benchmarks are promising. The detailed optimization of the parameterization procedures is underway.
Additionally, several more developments, significantly extending the applicability of the EFP method, have been conducted. These include development of QM/EFP interface of the EFP code with configuration interaction singles with perturbative doubles [CIS(D)] method and time-dependent density functional theory. A papers describing analysis of solvatochromic shifts and photodynamics of para-nitroanyline by using new CIS(D)/EFP is published: D. Kosenkov and L.V. Slipchenko, Solvent Effects on the Electronic Transitions of p-Nitroaniline: A QM/EFP Study, J. Phys. Chem. A, 115 (4), 392-401 (2011).
Research within this project has the following impact:
- development of the EFP method and its application to chemical/biological processes in solvents and environments is the main direction of Dr. Slipchenko’s research. Particular tasks fulfilled within the project (preparing the EFP library with improved EFP potentials, development of “flexible” fragments and scripts for analyzing and streamlining EFP-MD simulations) will be extremely useful for many future EFP-related projects;
- five papers have been published, three manuscripts have been submitted to journals, and several more are in preparation;
- participating graduate students Levi Haupert, Frank Emmert, and Mike Hands as well as undergraduate students Stephanie Thompson and Joanna Flick got expertise in performing ab initio computations and running classical and EFP Monte-Carlo and molecular dynamics simulations. Graduate students Mike Hands and Frank Emmert got expertise in developing perl and python scripts for analyzing MD data. Graduate student Levi Haupert got expertise in developing GAMESS codes. Undergraduate student Joanna Flick got expertise in programming in Java and C++ for visualizing EFP input and output files in WebMO visual software.
- Prof. Slipchenko presented results related to this project at several national and international conferences, including the ACS national meeting in Anaheim. Graduate student Mike Hands attended the Gordon research conference on “Dynamics at Surfaces” where he presented a poster describing his work on interactions of ions with alcohols and water. Undergraduate student Joanna Flick presented her work on accuracy of EFP potentials for the S22 dataset at the ACS national meeting in Denver.