ELECTRONIC-STRUCTURE-BASED MOLECULAR-DYNAMICS METHOD FOR LARGE BIOLOGICAL-SYSTEMS - APPLICATION TO THE 10-BASEPAIR POLY(DG)-CENTER-DOT-POLY(DC) DNA DOUBLE HELIX

Combining several recently developed theoretical techniques, we have d eveloped an electronic-structure-based method for performing molecular -dynamical simulations of large biological systems. The essence of the method can be summarized in three points: (i) There are two energy sc ales in the Hamiltonian and each is treated differently-the strong int ramolecular interactions are treated within approximate density-functi onal theory, whereas the weak intermolecular interactions (e.g., hydro gen bonds) are described within a simple theory that accounts for Coul omb, exchange, and hopping interactions between the weakly interacting fragments. (ii) A localized basis of atomic states is used, yielding sparse Hamiltonian and overlap matrices. (iii) The total energies and forces from the sparse Hamiltonian and overlap matrices are solved usi ng a linear scaling technique to avoid the N-3 scaling problem of stan dard electronic structure methods. As an initial benchmark and test ca se of the method, we performed calculations of a deoxyribonucleic acid (DNA) double-helix poly(dG). poly(dC) segment containing ten basepair s, with a total of 644 atoms. By a dynamical simulation, we obtained t he minimum-energy geometry and the electronic structure of this DNA de hydrated segment, as well as the full dynamical matrix corresponding t o the relaxed structure. The vibrational data and energy band gap obta ined compare qualitatively well with previous experimental data and ot her theoretical results.