Thesis

Modelling of solvation thermodynamics using a combination of reference intercation site model theory and multi-grid numerical methods

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Awarding institution
  • University of Strathclyde
Date of award
  • 2012
Thesis identifier
  • T13390
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Department, School or Faculty
Abstract
  • Solvation Free Energy (SFE) is a fundamental quantity in chemical physics. It describes solvation behavior of substances in liquid media and has many important applications in solution chemistry, biophysics, pharmaceutics, medicine, and environmental sciences. In many applications (for example, screening of drug-candidate databases in a drug-discovery process) it is important to have a fast and accurate method for solvation free energy calculation. In this thesis two new methods for fast and accurate SFE calculations are proposed. The methods combine the theoretical basis of the integral equation theory of liquids with advanced computational techniques. The theoretical part of the methods is based on the Reference Interaction Site Model (RISM) and the three-dimensional RISM (3DRISM) molecular theories and semiempirical models for SFE calculations. The computational part of the methods is based on the multi-grid scheme which drastically increases the computational performance. Additional investigations of speed and accuracy of calculations are performed to determine the optimal parameters of the methods which allow one to calculate the SFE with a required accuracy and minimal computational expenses. The methods are benchmarked on extended sets of small organic and drug-like compounds. It is shown that both (RISM and 3DRISM-based) methods can be successfully used for SFE calculations. It is shown that the parameters of the methods are transferable between different classes of compounds. The average computation time per typical drug-like compound of about 20 atoms is 17 seconds on a single CPU core for the RISM-based method and about 3.5 minutes for more accurate 3DRISM-based method.
Resource Type
DOI
Date Created
  • 2012
Former identifier
  • 989247

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