First Principles Computational Biochemistry with deMon2k

The growth of computational power, provided by new hardware technologies and the development of better theoretical methods and algorithms, allows more than ever an improvement in the reliability of computational predictions in medical sciences, along with a better understanding of the underlying molecular mechanisms. However, one limitation of computational chemistry approaches in the field of biological systems is the complexity of the molecules and the environment in which such molecules are to be studied. Important issues such as the determination of molecular properties which depend on the electronic structure face a considerable challenge when all-electron methodologies are required in the investigation. The most rigorous and sophisticated electronic structure methodologies, like density functional theory (DFT), are usually overwhelmed by the molecular size of most pharmacological targets. However, important implementations were recently achieved by the developers group of the computational chemistry code deMon2k. Knowing that the computation of electrostatic interaction integrals is an important bottleneck in all-electron calculations three new implementations have been worked out in order to eliminate such bottleneck. These implementations allow deMon2k now to explore biological and pharmacological systems in the framework of all-electron DFT methodologies.

Keywords: Asymptotic expansions, born-oppenheimer molecular dynamics, copper coordination, density functional theory, electron repulsion integrals, nuclear magnetic resonance, prion protein.