The lmp2 Section of the Jaguar Input File
- Overview
- Examples
The lmp2 section has two uses. The first use is for specifying electron pairs that are to be correlated, while all other electron pairs are treated at the Hartree-Fock level. This is known as a “local” LMP2 calculation. The second use, in the case where all valence electron pairs are being correlated, is to specify delocalizations for particular pairs. These two uses are mutually exclusive, and are controlled by the setting of the idelocv keyword. A local LMP2 calculation is requested by setting idelocv=1, while a delocalized LMP2 calculation is requested by setting idelocv=2.
The lmp2 section should contain a line for each atom pair describing atoms to be treated at the LMP2 level. Each line describing an LMP2 pair should begin with two atom numbers or labels, which specify the two atoms in the pair. A lone pair is indicated by specifying the same atom number or label twice. All bond pairs between two specified atoms are included. Pairs can be listed in any order. On each line, any atom numbers or names following the first two indicate atoms over which the LMP2 pair is to be delocalized.
The following example is for a local LMP2 calculation in which the bond pair between atoms 6 and 9, and the bond pair between atoms 9 and 10, are treated at the LMP2 level, while all other electron pairs are treated at the Hartree-Fock level.
&gen mp2=3 idelocv=1 & &lmp2 6 9 9 10 &
The following example is for a delocalized LMP2 calculation in which all valence electron pairs are treated by LMP2, and in addition, the bond pair between atoms C2 and C3 is delocalized over atoms C1 and C4, and the lone pair on N3 is delocalized over all four carbon atoms.
&gen mp2=3 idelocv=2 & &lmp2 C2 C3 C1 C4 N3 N3 C1 C2 C3 C4 &
A common situation in which extra delocalization is desirable is in the treatment of molecules containing aromatic rings. To automate the specification of the appropriate delocalizations, you may use the ireson keyword instead of an lmp2 section (you do not need to set the idelocv keyword either, as it will be set internally). When you use the ireson keyword, the molecular structure is analyzed and aromatic rings detected, and the appropriate delocalizations are defined automatically. It is safe to use the ireson keyword even when there are no aromatic rings in the structure, but if you are going to compare energies for different molecules, be sure to use the same ireson setting. You can see whether any aromatic rings have been found, and what delocalizations will be used, by looking at the Jaguar output file, where you will see a table like the following:
atom1 atom2 delocalization atoms -------- -------- ----------------------------------- C1 C2 C3 C18 C13 C6 C2 C3 C1 C18 C13 C6 C3 C18 C1 C2 C13 C6 C18 C13 C1 C2 C3 C6 C13 C6 C1 C2 C3 C18 C6 C1 C2 C3 C18 C13
A similar table is printed when you specify the delocalizations in an lmp2 section.
For QST-guided transition-state searches with LMP2 wave functions, LMP2 delocalization will automatically be performed over neighboring atoms for any bonds present in one structure and not in another, unless the input file contains the gen section keyword setting idelocv=0.
For Jaguar to properly detect aromatic rings, it needs to determine the connectivity and bond orders between atoms to create an appropriate Lewis structure. When you run Jaguar from Maestro, the connectivity and bond orders that you see for the structure in the Workspace are used, because Maestro ensures that the Jaguar input file contains a MAEFILE directive pointing to the Maestro structure file for the job. If you do not provide a MAEFILE directive, then Jaguar tries to assign connectivity and create a Lewis structure. However, for reliable detection of aromatic rings, we recommend that you use Maestro to create the Jaguar input, because you can use Maestro’s Build tools to ensure that the connectivity and bond orders for the structure are appropriate. If you run from the command line, we recommend that you still use a Maestro file to define connectivity by including a MAEFILE directive in your Jaguar input file.
Single Point Energy Examples
Example: Local MP2/cc-pvtz single point energy for water using default Jaguar settings
&gen mp2=3 basis=cc-pvtz isymm=0 & &zmat S -1.65300 -0.13190 0.12570 C -0.38310 -1.32590 0.09810 C 0.86170 -0.75050 0.16170 N 0.82690 0.64390 0.23240 C -0.41850 1.11420 0.22410 N -0.74130 2.45540 0.28570 H 1.81950 -1.25060 0.16230 H -0.62770 -2.37480 0.03720 C 0.09720 3.63730 0.36450 H -1.73360 2.63760 0.27430 H -0.50780 4.54420 0.37780 H 0.70430 3.61010 1.27040 H 0.76920 3.67970 -0.49370 &
$SCHRODINGER/jaguar run -jobname=ene_lmp2_0001 ene-lmp2-0001.in
Example: Local MP2/cc-pvtz single point energy. Bond pairs of aromatic ring allowed to delocalize over the ring using ireson=2
&gen mp2=3 ireson=2 basis=cc-pvtz isymm=0 & &zmat S -1.65300 -0.13190 0.12570 C -0.38310 -1.32590 0.09810 C 0.86170 -0.75050 0.16170 N 0.82690 0.64390 0.23240 C -0.41850 1.11420 0.22410 N -0.74130 2.45540 0.28570 H 1.81950 -1.25060 0.16230 H -0.62770 -2.37480 0.03720 C 0.09720 3.63730 0.36450 H -1.73360 2.63760 0.27430 H -0.50780 4.54420 0.37780 H 0.70430 3.61010 1.27040 H 0.76920 3.67970 -0.49370 &
$SCHRODINGER/jaguar run -jobname=ene_lmp2_0002 ene-lmp2-0002.in