Keywords in the Jaguar Input File That Specify Physical Properties
- Overview
- Examples
The keywords that specify physical properties of atoms are listed and defined in Table 1. Values for these keywords can appear in restart files.
The formal keyword is useful for solvation jobs (because the van der Waals radii are adjusted according to the chemical structure found by Jaguar) and for generating an improved initial guess for transition-metal-containing systems (along with the multip keyword). See Initial Guess Orbitals for Molecules Containing Transition Metals for more information on using this improved initial guess method.
The esp keyword can be used to freeze the charge on an atom to a particular value while fitting charges to other atoms, leave an atom out of charge fitting, or fit a charge to a dummy atom. If the esp column entry for an atom is set to a real number, the atomic charge for that atom is held fixed to that number during charge fitting. If the esp column entry for an atom is set to "n" or "no" (or 0), the atom is not included in charge fitting. If the esp column entry for a dummy atom is "y" or "yes", it is included in the charge fit.
Several warnings apply to the use of the esp column. First, the esp settings must not be inconsistent with the symmetry used for the rest of the job. Second, you should be careful not to overconstrain the charge fitting job. Third, if you are including any dummy atoms in the charge fitting, it may be advisable to perform the charge fitting in a separate job (based on the restart file) for which the charge fitting grid has been altered to include points around the dummy atoms by including a grid column in the atomic section, with "y" or "yes" entries for the dummy atoms, as described below.
The van der Waals surface used for charge fitting is constructed using DREIDING [108] van der Waals radii for hydrogen and for carbon through argon, and universal force field [105] van der Waals radii for all other elements. These radii are listed in Table 2, and can be changed using the vdw keyword.
The van der Waals radii for PBF solvation calculations are listed in Table 3, and can be changed using the vdw2 keyword. The radii for the elements H, C, N, O, F, P, Cl, Br, and I can be adjusted by Jaguar in some functional groups. See The PBF Radii File for Jaguar Calculations for more information on how Jaguar uses these radii in solvation calculations.
1.150 |
|
1.181 |
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1.226 |
1.373 |
|
2.042 |
1.900 |
1.600 |
1.600 |
1.682 |
1.621 |
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1.491 |
1.510 |
|
2.249 |
2.147 |
2.074 |
1.900 |
1.974 |
1.934 |
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1.906 |
1.700 |
1.647 |
1.587 |
1.572 |
1.511 |
1.480 |
1.456 |
1.436 |
1.417 |
1.748 |
1.381 |
2.192 |
2.140 |
2.115 |
2.103 |
2.095 |
2.071 |
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2.057 |
1.821 |
1.673 |
1.562 |
1.583 |
1.526 |
1.499 |
1.481 |
1.464 |
1.450 |
1.574 |
1.424 |
2.232 |
2.196 |
2.210 |
2.235 |
2.250 |
2.202 |
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2.259 |
1.851 |
1.761 |
1.570 |
1.585 |
1.534 |
1.477 |
1.560 |
1.420 |
1.377 |
1.647 |
1.353 |
2.174 |
2.148 |
2.185 |
|
|
|
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The van der Waals and intrinsic Coulomb radii for SM6 calculations are listed in Table 4. These values cannot be changed.
1.20 |
|
1.40 |
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1.82 |
2.00 |
|
2.00 |
1.70 |
1.55 |
1.52 |
1.47 |
1.54 |
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2.27 |
1.73 |
|
2.00 |
2.10 |
1.80 |
1.80 |
1.75 |
1.88 |
|||||||||||||||||||||||||||||||||||||||||||||
2.75 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
1.63 |
1.40 |
1.39 |
1.87 |
2.00 |
1.85 |
1.90 |
1.80 |
2.02 |
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2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
1.63 |
1.72 |
1.58 |
2.93 |
2.17 |
2.00 |
2.06 |
1.98 |
2.16 |
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2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
2.00 |
1.74 |
1.66 |
1.55 |
1.96 |
2.02 |
2.00 |
2.00 |
2.00 |
2.00 |
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The covalent radii used to determine which atoms are bonded are given in Table 5. Two atoms are considered to be bonded if the distance between them is less than covfac times the sum of their covalent radii, where covfac is a gen section keyword with a default value of 1.2. The radii can be changed using the cov keyword. See Covalent Bonding Keyword in the Jaguar Input File for more information on how Jaguar uses and presents covalent radii and bonding information.
0.32 |
|
0.93 |
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1.23 |
0.90 |
|
0.82 |
0.77 |
0.75 |
0.73 |
0.72 |
0.71 |
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1.54 |
1.36 |
|
1.18 |
1.11 |
1.06 |
1.02 |
0.99 |
0.98 |
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2.03 |
1.74 |
1.44 |
1.32 |
1.22 |
1.18 |
1.17 |
1.17 |
1.16 |
1.15 |
1.17 |
1.25 |
1.26 |
1.22 |
1.20 |
1.16 |
1.14 |
1.12 |
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2.16 |
1.91 |
1.62 |
1.45 |
1.34 |
1.30 |
1.27 |
1.25 |
1.25 |
1.28 |
1.34 |
1.48 |
1.44 |
1.41 |
1.40 |
1.36 |
1.33 |
1.31 |
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2.35 |
1.98 |
1.69 |
1.44 |
1.34 |
1.30 |
1.28 |
1.26 |
1.27 |
1.30 |
1.34 |
1.49 |
1.48 |
1.47 |
1.46 |
|
|
|
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Single Point Energy Examples
Example: B3LYP-D3/LACV3P single point energy for transition metal complex FeC8S4O4. User-defined charge and multiplicity of the total molecule. Use of the &atomic section to set charge and multiplicity of individual atoms
&gen dftname=b3lyp-d3 basis=lacv3p iuhf=1 molchg=-2 multip=5 & &zmat Fe1 4.2790000000 1.6230000000 0.9160000000 S2 5.1260000000 0.2170000000 -0.8060000000 S3 3.9930000000 -0.1270000000 2.5250000000 S4 5.4270000000 3.5210000000 1.8230000000 S5 2.2710000000 2.7920000000 0.3720000000 O6 1.0340000000 5.8730000000 1.7610000000 O7 3.9540000000 6.5300000000 3.2050000000 O8 5.2370000000 -3.4260000000 -0.9770000000 O9 4.2860000000 -3.6930000000 2.1560000000 C10 4.0070000000 4.4170000000 1.8550000000 C11 2.7590000000 4.1370000000 1.2760000000 C12 2.1290000000 5.3630000000 1.8060000000 C13 3.4980000000 5.6900000000 2.4770000000 C14 4.9190000000 -1.1840000000 0.1370000000 C15 4.4790000000 -1.3210000000 1.4470000000 C16 4.5460000000 -2.8020000000 1.3920000000 C17 4.9880000000 -2.6590000000 -0.0770000000 & &atomic atom formal multip Fe1 +2 5 S2 -1 1 S3 -1 1 S4 -1 1 S5 -1 1 &
$SCHRODINGER/jaguar run -jobname=ene_atomdef_0001 ene-atomdef-0001.in
Calculation of Molecular Properties Examples
Example: Moessbauer spectrum calculation of FeCl5(H2O)2- with B3LYP
&gen mossbauer=1 dftname=b3lyp basis=cc-pvdz multip=6 molchg=-2 nops=1 vshift=0.0 & &zmat Fe1 5.3897000000 2.9179000000 3.3439000000 Cl2 7.0882000000 1.4535000000 4.1314000000 Cl3 3.7609000000 1.4064000000 4.1734000000 Cl4 3.6737000000 4.5069000000 2.9302000000 Cl5 7.0474000000 4.4650000000 2.7828000000 Cl6 5.3231000000 2.0080000000 1.2007000000 O7 5.4927000000 3.7637000000 5.3506000000 H8 5.3019000000 3.2697000000 6.1216000000 H9 4.9612000000 4.5148000000 5.4634000000 & &atomic atom formal multip Fe1 +3 6 Cl2 -1 1 Cl3 -1 1 Cl4 -1 1 Cl5 -1 1 Cl6 -1 1 atom basis Fe1 partridge-1 &
$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0001 prop-moessbauer-0001.in
Example: Moessbauer spectrum calculation of FeCl5(H2O)2- with B3LYP. Use of a non-default value for moss_nuc_quadrupole of 0.18
&gen mossbauer=1 moss_nuc_quadrupole=0.18 dftname=b3lyp basis=cc-pvdz multip=6 molchg=-2 nops=1 vshift=0.0 & &zmat Fe1 5.3897000000 2.9179000000 3.3439000000 Cl2 7.0882000000 1.4535000000 4.1314000000 Cl3 3.7609000000 1.4064000000 4.1734000000 Cl4 3.6737000000 4.5069000000 2.9302000000 Cl5 7.0474000000 4.4650000000 2.7828000000 Cl6 5.3231000000 2.0080000000 1.2007000000 O7 5.4927000000 3.7637000000 5.3506000000 H8 5.3019000000 3.2697000000 6.1216000000 H9 4.9612000000 4.5148000000 5.4634000000 & &atomic atom formal multip Fe1 +3 6 Cl2 -1 1 Cl3 -1 1 Cl4 -1 1 Cl5 -1 1 Cl6 -1 1 atom basis Fe1 partridge-1 &
$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0002 prop-moessbauer-0002.in