In a recent paper [D. Babikov, J. Chem. Phys. 121, 7577 (2004)], quantum optimal control theory was applied to analyze the accuracy of quantum gatesin a quantum computer based on molecular vibrational eigenstates. The effects of the anharmonicity parameter of the molecule, the target time of the pulse, and the penalty function on the accuracy of the qubit transformations were investigated. We demonstrate that the effects of all the molecular and laser-pulse parameters can be explained utilizing the analytical pulse area theorem, which originates from the standard two-level model. Moreover, by analyzing the difference between the optimal control theory results and those obtained using the pulse area theorem, it is shown that extremely high quantum gate fidelity can be achieved for a qubit system based on vibrational eigenstates.