Optimal control theory is applied to a molecular vibrational system in light of its possible application to quantum computing (QC). We present the numerical results of an ammonia molecular vibrational model system with two modes: a bending mode and an asymmetric stretching mode. We demonstrate logic gates fundamental to QC algorithms, namely Hadamard and controlled-NOT gates. Our results show that averages of population transfers at each gate are above 93% high fidelity. A mode that has a double-well structured potential is found to have many transfer pathways, which facilitates obtaining optimal laser pulses. (c) 2005 Elsevier B.V. All rights reserved.