We apply the Hamiltonian algorithm combined with ab initio molecular orbital calculation to the optimization of molecular structure. The 6000 iterative calculations at Hartree-Fock 6-31G** levels shows that the HCN structure can be obtained even starting from the optimized structure of the HNC molecule, which cannot be achieved by conventional optimization methods, such as the Newton-Raphson method. The initial kinetic energies of less than 0.05 hartree and greater than 0.5 hartree fail in the optimization. The incorporation of a mixing term in the momentum space can accelerate the optimization. (C) 2004 Elsevier B.V. All rights reserved.