title: How Molecular Conformational Changes Affect Changes in Free Energy.
abstract: A simple quantitative relationship between the molecular conformational changes and the corresponding changes in the free energy is presented. The change in free energy is the sum of that part of the enthalpic change that is due to the externally applied work (perturbation) and of that part of the entropic change, termed dissipative entropy, that is related to the conformational changes. The dissipative entropy is equivalent to the relative entropy, a concept from information theory, between the distributions of the conformations in the initial and the final states. The remaining change in entropy (nondissipative) cancels exactly with the remaining enthalpic change. The calculation of the dissipative entropy is demonstrated to pose the main difficulty in free energy computation. The straightforward decomposition of the dissipative entropy into contributions from different parts of the system promises to improve the understanding of the role of conformational changes in biochemical reactions.
authors.affiliation: Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.
authors.forename: Mazen
authors.initials: M
authors.lastname: Ahmad
authors.affiliation: Center for Bioinformatics, Saarland University , 66123 Saarbrücken, Germany.
authors.forename: Volkhard
authors.initials: V
authors.lastname: Helms
authors.affiliation: Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
authors.affiliation: Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics , Campus E1 4, 66123 Saarbrücken, Germany.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Kalinina
mesh_terms: D005563:Formic Acid Esters / Q000737:chemistry*; D006139:Guaiacol / Q000737:chemistry*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D005563:Formic Acid Esters; C025468:methyl formate; D006139:Guaiacol