Molecular Surface Areas with TRIFORCE
Coming Soon!
Information
| Date: | 5 August 2014 |
| Funding: | NIH, OSU, AGAUR |
| Category: | Methodology |
| With: | Nils J. D. Drechsel, Ken A. Dill, Jordi Villà–Freixa |
Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion
Coming Soon!
Information
| Date: | 7 November 2014 |
| Funding: | NIH, OSU |
| Category: | Methodology |
| With: | Libo Li, Ken A. Dill |
Alcohols in Free Energy Calculations
In this project, we develop a simple optimization strategy for incorporating experimental dielectric response information of neat liquids in classical molecular models of alcohol. Using optimizations of methanol, we determine simple and transferable hydroxyl modulation rules that correct the dielectric behavior of arbitrary molecule containing hydroxyl groups. In addition to improvements in calculated static dielectric constants, we found this to lead to significant improvement in the calculated hydration free energy values for a wide variety of small molecule alcohol models. Check out the article by clicking View Project.
Information
| Date: | 19 June 2014 |
| Funding: | NIH, OSU |
| Category: | Modeling |
| With: | Karisa L. Wymer, David L. Mobley |
Effective Interactions Between Solvated Ions
From a systematic series of particle pair Potential of Mean Force (PMF) calculations we develop a rapid interpolation scheme that we call i-PMF. We show that it is capable of capturing the full set of PMFs for arbitrary combinations of ion sizes ranging from 2 to 5.5 Å. The advantage of the interpolation process is computational cost. Whereas it can take 100 hours to simulate each PMF with explicit molecular dynamics, we can compute an equivalently accurate i-PMF in seconds. A companion web application for i-PMF is available at dillgroup.io if you want to play with the tool.
This work (along with a work we published in 2009) was also highlighted in a recent ACS virtual issue on ion pairing advances: Ion Pairing: From Water Clusters to the Aqueous Bulk. Cited works are said to exemplify "current progress in experimental and computational approaches to ion pairing in cluster and bulk aqueous systems with important practical implications, in particular, for biological problems." Nice!
Information
| Date: | 17 July 2014 |
| Funding: | NIH, ALCC, ARRS |
| Category: | Methodology |
| With: | Miha Lukšič, Ken A. Dill |
Molecular Solvation with a Field Variant of Semi-Explicit Assembly
Here we present a field variant of the Semi-Explicit Assembly (SEA) model for molecular solvation. The original form of SEA can saturate its solvation response, leaving it with under-predicted hydration free energies for charge-dense solutes, like monatomic or molecular ions. This new version of SEA implements an adaptive solvation surface boundary and a polar charging free energy surface that can be uniquely accessed as a function of electric field and solvation surface curvature. We show that this new approach is quantitatively predictive with full explicit solvent hydration free energies non-polar, polar, and charged molecular solutes. We also show it can quantitatively predict hydration of amino acid dipeptides, providing a route to accurate assessment of hydration for larger biomolecule solutes.
Information
| Date: | 19 June 2014 |
| Funding: | NIH |
| Category: | Methodology |
| With: | Libo Li, Ken A. Dill |