Protein has many roles in your body. It helps repair and build your body's tissues, allows metabolic reactions to take place and coordinates bodily functions. In addition to providing your body with a structural framework, proteins also maintain proper pH and fluid balance.
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Carboxylic acids boil at considerably higher temperatures than do alcohols, ketones, or aldehydes of similar molecular weights. This is because they form stable hydrogen-bonded dimers.
Carboxylic acid dimers are useful model systems for understanding the interplay of hydrogen bonding, hydrophobic effects, and entropy in self-association and assembly.
Through extensive sampling with a classical force field and careful free energy analysis, it is demonstrated that both hydrogen bonding and hydrophobic interactions are indeed important for dimerization of carboxylic acids (except formic acid).
The dimers are only weakly ordered, and the degree of ordering increases with stronger hydrophobic interactions between longer alkyl chains. Comparison of calculated and experimental dimerization constants reveals a systematic tendency for excessive self-aggregation in current classical force fields.
Qualitative and quantitative information on the thermodynamics of hydrogen bonding and hydrophobic interactions derived from these simulations is in excellent agreement with existing results from experiment and theory. These results provide a verification from first principles of previous estimations based on two statistical mechanical hydrophobic theories.
We also revisit and clarify the fundamental statistical thermodynamics formalism for calculating absolute binding constants, external entropy, and solvation entropy changes upon association from detailed free energy simulations. This analysis is believed to be useful for a wide range of applications including computational studies of protein-ligand and protein-protein binding.
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