Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework
| dc.contributor.author | Mukhopadhyay, Abhishek | en |
| dc.contributor.committeechair | Onufriev, Alexey V. | en |
| dc.contributor.committeechair | Mather, William | en |
| dc.contributor.committeemember | Pleimling, Michel J. | en |
| dc.contributor.committeemember | Robinson, Hans D. | en |
| dc.contributor.department | Physics | en |
| dc.date.accessioned | 2016-09-08T06:00:46Z | en |
| dc.date.available | 2016-09-08T06:00:46Z | en |
| dc.date.issued | 2015-03-17 | en |
| dc.description.abstract | One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry -- the asymmetric response of water upon the sign of solute charge -- manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate CHA first into the Born model, and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes -- monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response. | en |
| dc.description.degree | Ph. D. | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:4704 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/72901 | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | biomolecular modeling | en |
| dc.subject | implicit solvation | en |
| dc.subject | bioelectrostatics | en |
| dc.subject | charge hydration asymmetry | en |
| dc.subject | solvation free energy | en |
| dc.title | Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Physics | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | Ph. D. | en |