An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.
An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first prinn class="Chemical">ciples. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amidehydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.
Authors: Graeme M Day; Timothy G Cooper; Aurora J Cruz-Cabeza; Katarzyna E Hejczyk; Herman L Ammon; Stephan X M Boerrigter; Jeffrey S Tan; Raffaele G Della Valle; Elisabetta Venuti; Jovan Jose; Shridhar R Gadre; Gautam R Desiraju; Tejender S Thakur; Bouke P van Eijck; Julio C Facelli; Victor E Bazterra; Marta B Ferraro; Detlef W M Hofmann; Marcus A Neumann; Frank J J Leusen; John Kendrick; Sarah L Price; Alston J Misquitta; Panagiotis G Karamertzanis; Gareth W A Welch; Harold A Scheraga; Yelena A Arnautova; Martin U Schmidt; Jacco van de Streek; Alexandra K Wolf; Bernd Schweizer Journal: Acta Crystallogr B Date: 2009-03-16
Authors: Courtney E Cox; Jeremy R Phifer; Larissa Ferreira da Silva; Gabriel Gonçalves Nogueira; Ryan T Ley; Elizabeth J O'Loughlin; Ana Karolyne Pereira Barbosa; Brett T Rygelski; Andrew S Paluch Journal: J Comput Aided Mol Des Date: 2017-01-28 Impact factor: 3.686
Authors: Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks Journal: J Chem Phys Date: 2017-10-28 Impact factor: 3.488
Authors: Shuai Liu; Shannon Cao; Kevin Hoang; Kayla L Young; Andrew S Paluch; David L Mobley Journal: J Chem Theory Comput Date: 2016-03-02 Impact factor: 6.006
Authors: Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder Journal: J Chem Theory Comput Date: 2018-09-19 Impact factor: 6.006