Frequency-Related Keywords in the Jaguar Input File
- Overview
- Examples
For jobs that include a calculation of vibrational frequencies, various frequency-related properties can also be computed by setting the appropriate keywords. Most of these keywords, which are listed in Table 1, correspond to GUI options described in Vibrational Frequencies and Related Properties from Jaguar Calculations. Only the values listed in the table are allowed.
The thermochemical properties are listed in cal/mol K and kcal/mol by default. Use the output option eunit=2 for output in J/mol K and kJ/mol.
When the calculation of vibrational frequencies is requested with ifreq=1 for Hartree-Fock or DFT calculations, intensities for the IR-active vibrational modes are automatically calculated (irder is set to 1 automatically). For any other level of theory, you must explicitly set irder=1, and the derivatives must be calculated numerically by setting nmder=2. The calculation of IR intensities involves the calculation of the dipole moment derivatives. Raman activities and intensities can be calculated by setting iraman=1. They involve the calculation of polarizability derivatives. The Raman intensity is computed [115] from the Raman activities by including frequency-dependent factors (set with laser_freq) and Boltzmann weighting of excited vibrational states (at a temperature set by room_temperature). The output from intensity calculations includes a spectrum file, jobname_vib.spm for IR spectra and jobname_raman_vib.spm for Raman spectra. These files can be read into the Spectrum Plot Panel in Maestro to generate a simulated spectrum.
If you only want to calculate dipole moment derivatives using the Hartree-Fock method but don’t want to do the frequency calculation that is normally required to get them, you must set up a special path section (see The path Section of the Jaguar Input File) with the appropriate sequence of executables to run.
The path section to use is:
&path pre onee hfig probe grid rwr scf ira rwr irb &
You must also set irder=1, isymm=0, and ifreq=1. The ifreq setting is necessary to force tight accuracy in the SCF, but no frequency calculation is actually performed.
To compute partial frequencies for a fragment, you must first define the fragments in an atomic section, then make the setting freqfrag=fragno in the gen section for the frequency calculation. These settings are in addition to any other frequency-related settings.
To calculate the vibrational circular dichroism (VCD) spectrum [269, 270], set ivcd=1. VCD spectra can be used to determine the chirality of a molecule, by comparing the predicted spectrum with the experimental spectrum. The VCD spectrum of a molecule is the mirror image of the VCD spectrum of its enantiomer, so the assignment of a spectrum to a particular enantiomer is usually straightforward. Jaguar writes the VCD spectral data to a file called jobname_vcd.spm, which can be read into the Spectrum Plot Panel in Maestro to generate a simulated spectrum.
Because different conformers have significantly different VCD spectra, it is important to compute a conformationally averaged spectrum when the molecule of interest has two or more conformers with similar energies. The procedure involves using MacroModel to perform the conformational search, refining the resultant geometries with Jaguar, and eliminating redundant or high-lying conformers with MacroModel, then calculating the Boltzmann factors and generating an averaged spectrum. This procedure is automated in the VCD Workflow, which you can run with a Python script, spectroscopy.py. See Vibrational and Electronic Circular Dichroism Spectra for more information.
|
Keyword |
Value |
Description |
|
0 |
Do not calculate frequencies (second derivatives) |
|
|
|
1 |
Calculate frequencies from second derivatives of energy (sets irder=1 for HF and DFT wave functions). |
|
|
−1 |
Calculate frequencies from most recent Hessian (from end of optimization or from initial Hessian if initial Hessian was never updated) |
|
0 |
Do not compute dipole derivatives or IR intensities |
|
|
|
1 |
Compute derivatives of dipole moment and IR intensities (see text for details) |
|
0 |
Do not compute Raman intensities |
|
|
|
1 |
Compute Raman intensities. Sets iacc=1 automatically. |
|
9398.5 |
Laser frequency for Raman intensities, in cm−1. |
|
|
300.0 |
Room temperature, in kelvin. This is used for the Boltzmann weighting of vibrational modes in Raman intensities. |
|
|
0 |
Do not calculate vibrational circular dichroism spectra. |
|
|
|
1 |
Calculate vibrational circular dichroism spectra (sets ifreq=1 and nmr=1). |
|
35 |
Maximum number of CPHF iterations |
|
|
5×10−5 |
CPHF convergence threshold |
|
|
0 |
Print normal modes in cartesian coordinates without mass-weighting |
|
|
|
1 |
Print normal modes in mass-weighted cartesian coordinates |
|
0 |
Do not scale frequencies using Pulay’s Modified Scaled Quantum Mechanical Force Fields (SQM) method |
|
|
|
1 |
Scale frequencies using Pulay’s SQM method, and use scaled frequencies for thermochemical calculations (only allowed for B3LYP calculations with the 6‑31G* basis set) |
|
0 |
Do not automatically scale frequencies. |
|
|
|
1 |
Automatically scale frequencies using a tabulated set of scale factors for various combinations of method and basis set (see Table 1). If factors are not available for the method and basis set, frequencies are not scaled. |
|
>0 |
Scale vibrational frequencies by this factor (default is 1.0), and use scaled frequencies for thermochemical calculations. |
|
|
0 |
Do not calculate and print out thermochemical properties. |
|
|
|
1 |
Calculate and print out thermochemical properties if ifreq ≠ 0. |
|
|
2 |
Calculate and print out thermochemical properties, and also print out contributions to these properties from individual frequencies, if ifreq ≠ 0. |
|
0.0 |
Threshold in cm−1 for inclusion of frequencies in zero-point energy calculations and thermochemical analysis. Frequencies below this threshold are discarded in the analysis. Suggested value is 10.0. freqcut takes precedence over quasi_harmonic_thresh, so frequencies below freqcut are discarded and will not be set to quasi_harmonic_thresh. |
|
|
100.0 |
Threshold in cm−1 for frequencies to which the quasi-harmonic approximation [284] is applied. Any frequency that is below this threshold and above freqcut is set to the threshold value. |
|
|
1.0 |
Pressure for thermochemical calculations from frequencies, in atm. |
|
|
0.0 |
Pressure step size (difference between consecutive pressures) for thermochemical calculations, in atm. Cannot be set to a nondefault value if press_mult has a nondefault value. |
|
|
1.0 |
Pressure step factor (ratio between consecutive pressures) for thermochemical calculations, in atm. Cannot be set to a nondefault value if press_step has a nondefault value. |
|
|
1 |
Number of pressures at which thermochemical properties are computed. You must set either press_step or press_mult to a nondefault value (but not both). |
|
|
298.15 |
Initial temperature for thermochemical calculations, in K. |
|
|
10.0 |
Temperature step size (difference between consecutive temperatures) for thermochemical calculations, in K. |
|
|
1 |
Number of temperatures at which thermochemical properties are computed. |
Vibrational Frequency Examples
Example: B3LYP-D3/6-31G** calculation of the vibrational circular dichroism (VCD) spectrum of 1-fluoroethanol
&gen ivcd=1 basis=6-31G** dftname=B3LYP-D3 & &zmat C1 -2.7565700000000 -0.2960450000000 2.0069770000000 C2 -1.4423850000000 0.4354780000000 2.1427720000000 H3 -3.3549210000000 -0.1183190000000 2.9039730000000 H4 -2.5784630000000 -1.3681900000000 1.8986410000000 H5 -3.3045710000000 0.0697680000000 1.1352730000000 H6 -0.7846110000000 0.2738960000000 1.2736930000000 O7 -1.7034970000000 1.7834170000000 2.3484260000000 F8 -0.7457830000000 -0.0824410000000 3.2401850000000 H9 -0.8567960000000 2.2431540000000 2.4317590000000 &
$SCHRODINGER/jaguar run -jobname=freq_vcd_0001 freq-vcd-0001.in
Geometry Optimization Examples
Example: B3LYP-D3/6-31G** geometry optimization of water followed by a calculation of the harmonic vibrational frequencies. Print additional useful information to the output file
&gen basis=6-31G** dftname=B3LYP-D3 igeopt=1 ifreq=1 ! gaussian function list for basis set ip1=2 ! memory, disk, and i/o information ip5=2 ! detailed timing information ip6=2 ! gaussian function list for derivatives of basis functions ip8=2 ! bond lengths and angles (3,4,5 adds all possible bonds, angles, torsions) ip11=2 ! connectivity table ip12=2 ! overlap matrix ip18=2 ! one-electron Hamiltonian ip19=2 ! all keyword setting including internal ones ip24=2 ! multiple moments in atomic units ip25=2 ! geometries in bohr as well as angstroms ip26=2 ! diagonal force constants in internal coords (3,4 is all force constants) ip192=2 & &zmat O1 0.0000000000 0.0000000000 -0.0667079824 H2 0.0000000000 0.7594973815 0.5293520449 H3 0.0000000000 -0.7594973815 0.5293520449 &
$SCHRODINGER/jaguar run -jobname=opt_prop_freq_moreprint_0001 opt_prop-freq_moreprint-0001.in
Workflow Examples
Example: Calculate the electronic circular dichroism (ECD) spectrum of (1S)-1-aminoethanol via the spectroscopy.py workflow script. Run conformational search and retain conformations within 5 kcal/mol of the lowest energy, according to the force field. The final ECD spectrum is a Boltzmann average over the ECD spectra of the final set of conformers
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
i_m_Molecular_charge
i_m_Spin_multiplicity
i_m_ct_format
:::
Structure1
0
1
2
m_atom[11] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
i_m_color
i_m_atomic_number
s_m_color_rgb
s_m_atom_name
i_m_minimize_atom_index
:::
1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080 "C1" 1
2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0 "C2" 2
3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF "" 3
4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF "" 4
5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF "" 5
6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF "" 6
7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF "N7" 7
8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F "O8" 8
9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF "" 9
10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF "" 10
11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF "" 11
:::
}
m_bond[10] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
5 2 6 1
6 2 7 1
7 2 8 1
8 7 10 1
9 7 11 1
10 8 9 1
:::
}
}
${SCHRODINGER}/jaguar run spectroscopy.py -jobname=wflow_spectroscopy_ecd_0001 -ecd -forcefield OPLS4 -conf_search_method mixed -conf_search_steps 200 -mm_energy_window 5.0 -outconfs 100 -max_atom_dev 0.5 -qm_energy_window 5.0 -solvent None -k=dftname=b3lyp-d3 '-k=basis=lacvp**' -k=iacc=1 wflow-spectroscopy_ecd-0001.mae
Example: Calculate the vibrational circular dichroism spectrum of (1S)-1-aminoethanol via the spectroscopy.py workflow script. Run conformational search and retain conformations within 5 kcal/mol of the lowest energy, according to the force field. The final VCD spectrum is a Boltzmann average over the VCD spectra of the final set of conformers
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
i_m_Molecular_charge
i_m_Spin_multiplicity
i_m_ct_format
:::
Structure1
0
1
2
m_atom[11] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
i_m_color
i_m_atomic_number
s_m_color_rgb
s_m_atom_name
i_m_minimize_atom_index
:::
1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080 "C1" 1
2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0 "C2" 2
3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF "" 3
4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF "" 4
5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF "" 5
6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF "" 6
7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF "N7" 7
8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F "O8" 8
9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF "" 9
10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF "" 10
11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF "" 11
:::
}
m_bond[10] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
5 2 6 1
6 2 7 1
7 2 8 1
8 7 10 1
9 7 11 1
10 8 9 1
:::
}
}
$SCHRODINGER/jaguar run spectroscopy.py -jobname=wflow_spectroscopy_vcd_0001 -vcd -forcefield OPLS4 -conf_search_method mixed -conf_search_steps 200 -mm_energy_window 5.0 -outconfs 100 -max_atom_dev 0.5 -qm_energy_window 5.0 -solvent None -k=dftname=b3lyp-d3 '-k=basis=lacvp**' -k=iacc=1 wflow-spectroscopy_vcd-0001.mae