  Computational chemistry at the atomic level has largely branched into two
major fields, one based on quantum mechanics and the other on molecular
mechanics using classical force fields. Because of high computational costs,
quantum mechanical methods have been typically relegated to the study of small
systems. Classical force field methods can describe systems with millions of
atoms, but suffer from well known problems. For example, these methods have
problems describing the rich coordination chemistry of transition metals or
physical phenomena such as charge transfer. The requirement of specific
parametrization also limits their applicability. There is clearly a need to
develop new computational methods based on quantum mechanics to study large and
heterogeneous systems. Quantum based methods are typically limited by the
calculation of two-electron integrals and diagonalization of large matrices.
Our initial work focused on the development of fast techniques for the
calculation of two-electron integrals. In this publication the diagonalization
problem is addressed and results from molecular dynamics simulations of alanine
decamer in gas-phase using a new fast pseudo-diagonalization method are
presented. The Hamiltonian is based on the standard Extended Hueckel approach,
supplemented with a term to correct electrostatic interactions. Besides
presenting results from the new algorithm, this publication also lays the
requirements for a new quantum mechanical method and introduces the extended
Hueckel method as a viable base to be developed in the future.
