10.5.2 Visualizing Orbitals Using MolDen and MacMolPlt

Upon request, Q-Chem will generate an input file for MolDen, a freely-available molecular visualization program.^{G. Schaftenaar and J. H. Noordik (2000), 13} MolDen can be used to view ball-and-stick molecular models (including stepwise visualization of a geometry optimization), molecular orbitals, vibrational normal modes, and vibrational spectra. MolDen also contains a powerful Z-matrix editor. In conjunction with Q-Chem, orbital visualization via MolDen is currently supported for $s$, $p$, and $d$ functions (pure or Cartesian), as well as pure $f$ functions. Upon setting MOLDEN_FORMAT to TRUE, Q-Chem will append a MolDen-formatted input file to the end of the Q-Chem log file. As some versions of MolDen have difficulty parsing the Q-Chem log file itself, we recommend that the user cut and paste the MolDen-formatted part of the Q-Chem log file into a separate file to be read by MolDen.

MolDen-formatted files can also be read by MacMolPlt, another freely-available visualization program. ¹²⁹ Bode B. M., Gordon M. S.
J. Mol. Graphics Mod.
(1998), 16, pp. 133. Link ¹² Alam B., Morrison A. F., Herbert J. M.
J. Phys. Chem. C
(2020), 124, pp. 24653. Link MacMolPlt generates orbital iso-contour surfaces much more rapidly than MolDen, however, within MacMolPlt these surfaces are only available for Cartesian Gaussian basis functions, i.e., PURECART = 2222, which may not be the default.

For geometry optimizations and vibrational frequency calculations, one need only set MOLDEN_FORMAT to TRUE, and the relevant geometry or normal mode information will automatically appear in the MolDen section of the Q-Chem log file.