Abstract
Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute-solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute-solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute-solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ∼ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 3555-3564 |
| Number of pages | 10 |
| Journal | Journal of Physical Chemistry B |
| Volume | 121 |
| Issue number | 15 |
| DOIs | |
| State | Published - Apr 20 2017 |
Fingerprint
ASJC Scopus subject areas
- Surfaces, Coatings and Films
- Physical and Theoretical Chemistry
- Materials Chemistry
Cite this
Nonpolar Solvation Free Energy from Proximal Distribution Functions. / Ou, Shu Ching; Drake, Justin A.; Pettitt, Bernard.
In: Journal of Physical Chemistry B, Vol. 121, No. 15, 20.04.2017, p. 3555-3564.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Nonpolar Solvation Free Energy from Proximal Distribution Functions
AU - Ou, Shu Ching
AU - Drake, Justin A.
AU - Pettitt, Bernard
PY - 2017/4/20
Y1 - 2017/4/20
N2 - Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute-solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute-solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute-solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ∼ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems.
AB - Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute-solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute-solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute-solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ∼ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems.
UR - http://www.scopus.com/inward/record.url?scp=85020166856&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85020166856&partnerID=8YFLogxK
U2 - 10.1021/acs.jpcb.6b09528
DO - 10.1021/acs.jpcb.6b09528
M3 - Article
C2 - 27992228
AN - SCOPUS:85020166856
VL - 121
SP - 3555
EP - 3564
JO - Journal of Physical Chemistry B Materials
JF - Journal of Physical Chemistry B Materials
SN - 1520-6106
IS - 15
ER -