10.5 Visualizing and Plotting Orbitals, Densities, and Other Volumetric Data 10.5.1 Introduction 10.5.3 Visualization of Natural Transition Orbitals

10.5.2 Visualizing Orbitals Using MolDen and MacMolPlt

(July 14, 2022)

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_FORMAT

MOLDEN_FORMAT
       Requests a MolDen-formatted input file containing information from a Q-Chem job.
TYPE:
       LOGICAL
DEFAULT:
       FALSE
OPTIONS:
       TRUE Append MolDen input file at the end of the Q-Chem output file.
RECOMMENDATION:
       None.

MolDen-formatted files can also be read by MacMolPlt, another freely-available visualization program. ¹¹⁹ Bode B. M., Gordon M. S.
J. Mol. Graphics Mod.
(1998), 16, pp. 133. Link ¹² Albrecht A. C.
J. Chem. Phys.
(1961), 34, pp. 1476. 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.

Example 10.8 Generating a MolDen file for molecular orbital visualization.

$molecule
   0 1
   O
   H  1  0.95
   H  1  0.95  2  104.5
$end

$rem
   METHOD           hf
   BASIS            cc-pvtz
   PRINT_ORBITALS   true (default is to print 5 virtual orbitals)
   MOLDEN_FORMAT    true
$end

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.

Example 10.9 Generating a MolDen file to step through a geometry optimization.

$molecule
   0  1
   O
   H  1  0.95
   H  1  0.95  2  104.5
$end

$rem
   JOBTYPE         opt
   METHOD          hf
   BASIS           6-31G*
   MOLDEN_FORMAT   true
$end

Search Results

10.5.2 Visualizing Orbitals Using MolDen and MacMolPlt