Vibrational and Electronic Circular Dichroism Spectra

VCD, ECD, jaguar spectroscopy

VCD and ECD spectra can be used to determine the chirality of a molecule, by comparing the predicted spectrum with the experimental spectrum. The circular dichroism (CD) spectrum of a molecule is the mirror image of the CD spectrum of its enantiomer, so the assignment of a spectrum to a particular enantiomer is usually straightforward. Jaguar writes the VCD and ECD spectral data to files called jobname_vcd.spm and jobname_ecd.spm which can be read into the Spectrum Plot panel in Maestro to generate a simulated spectrum.

Because different conformers have significantly different CD spectra, it is important to compute a conformationally averaged spectrum when the molecule of interest has conformers with similar energies. You can use MacroModel to perform the conformational search (using the OPLS4 or OPLS_2005 force field), then refine the geometries with Jaguar, and eliminate redundant or high-lying conformers with MacroModel.

This procedure is automated in the Jaguar Spectroscopy Workflow, which also calculates the Boltzmann weights used to average the spectrum (see spectroscopy.py Command Help). Averaged spectra are written out for both VCD and ECD spectra to the jobname/vcd or jobname/ecd folder. For VCD, the files are jobname_avg_vcd.spm and jobname_avg_vcd.csv, where the former has just the peak data, and the latter has the plot points (wavenumber, intensity) of a broadened spectrum and the mirror-image spectrum normalized to a maximum intensity of 1.0. The average spectrum of the enantiomer is written to the file ent_jobname_avg_vcd.spm. For ECD, a spectrum generated using the velocity form of the dipole operator is written by default, with the name jobname_avg_ecd_velocity.spm. If desired, one can also generate the length form, jobname_avg_ecd_length_od.spm, by including "ecd_write_len=1" in the Keywords text box. Plot points are written to jobname_avg_ecd.csv, with columns for wavenumber, length intensity (if length form was requested), and velocity intensity.

The velocity form for the dipole operator for ECD calculations is preferred, as it is gauge-invariant. The length form is gauge-dependent, and not recommended for reliability.

To aid in the matching of experimental and theoretical spectra, you can use the spectrum_align utility, which is described in spectrum_align: Align Predicted and Experimental Circular Dichroism Spectra.

To open the Jaguar Spectroscopy Panel, click the Tasks button and browse to Quantum Mechanics → Spectroscopy Workflows.

To open the Spectrum Plot Panel, choose click the Tasks button and browse to Quantum Mechanics → Plot Spectra.