Ergodic Algorithmic Model (<i>EAM</i>), with Water as Implicit Solvent, in Chemical, Biochemical, and Biological Processes

Abstract

For many years, we have devoted our research to the study of the thermodynamic properties of hydrophobic hydration processes in water, and we have proposed the Ergodic Algorithmic Model (EAM) for maintaining the thermodynamic properties of any hydrophobic hydration reaction at a constant pressure from the experimental determination of an equilibrium constant (or other potential functions) as a function of temperature. The model has been successfully validated by the statistical analysis of the information elements provided by the EAM model for about fifty compounds. The binding functions are convoluted functions, RlnKeq = {f(1/T)* g(T)} and RTlnKeq = {f(T)* g(lnT)}, where the primary linear functions f(1/T) and f(T) are modified and transformed into parabolic curves by the secondary functions g(T) and g(lnT), respectively. Convoluted functions are consistent with biphasic dual-structure partition function, {DS-PF} = {M-PF} ∙ {T-PF} ∙ {ζw}, composed by ({M-PF} (Density Entropy), {T-PF}) (Intensity Entropy), and {ζw} (implicit solvent). In the present paper, after recalling the essential aspects of the model, we outline the importance of considering the solvent as “implicit” in chemical and biochemical reactions. Moreover, we compare the information obtained by computer simulations using the models till now proposed with “explicit” solvent, showing the mess of information lost without considering the experimental approach of the EAM model.

Keywords

• hydrophobic hydration process
• Ergodic Algorithmic Model (<i>EAM</i>)
• Thermal Equivalent Dilution (TED)
• implicit solvent
• intensity entropy
• density entropy