Chapter 15 - Dynamics of Biomolecules From First Principles

Abstract

Abstract The biomolecular systems in general are characterized by specificity and complexity, both in structure and chemical reactivity. In this work, we review the origins of complexity and the computational techniques used to study the biomolecules. First-principles biosimulations have become an essential tool in the study of atoms and molecules and, increasingly, in modeling complex systems as those in biology. With the advent of density functional theory and gradient-corrected exchange-correlation functionals, the ability to obtain accurate enough solutions to the electronic Schrodinger equation for systems containing thousands of atoms has revolutionized biophysics and biochemistry. As an example of the first-principles biosimulations, we discuss the results of the extensive Born–Oppenheimer molecular dynamics study of the amino acid l -alanine zwitterion in aqueous solution. The whole system, that is, the l -alanine zwitterion and amino acid hydration shell consisting of 50 water molecules, has been treated fully quantum mechanically. Within the scope of this work, we determine the structure and properties of the hydration shell around alanine and describe the zwitterion dynamics and its structural stability in a polar water environment. The work presented here is an example of how quantum mechanical techniques can be successfully applied to biologically relevant problems in rather large and complex systems.