Viewing an NBO analysis

Sign on to unix and have this web page open in a Microsoft window on the screen at the same time
cd ~nbwt3/work/listen
Use the standard unix program more to look at the file:

more mechsch2321nbo.log

This is the Gaussian output file for an NBO analysis of methyl thiirane at the RHF/3-21G* level. The model was discussed earlier in the course: see Notes while viewing the model of CH3CHSCH2 and the rotatable model . This NBO analysis produced the NBO plots , presented as a separate web document
More is the safest way to look at what is in text files in unix, because it cannot damage the file. The only commands to more that you need to know for this exercise are:

this lets you enter some text (at the bottom of the window), followed by pressing Enter. More then attempts to scroll to find the next occurrence of the text. Remember that upper and lower case are different in unix: you have to search for exactly what is present in the file, but it need not be a whole word

When you have finished with the following investigation, remember to exit from unix by entering exit
Use / to scan for NBO

You should find the Gaussian command line. This asks for a single-point rhf/3-21g* reading the initial guess and the geometry from a checkpoint file (where a previous geometry optimisation run had stored them). The keyword

You should see the SCF Done report, with the SCF energy in Hartrees. Towards the bottom of the screen is a list of the energies of the delocalised MOs, first the 20 occupied ones, then the empty, virtual ones

This should get you to the beginning of the output from the NBO module
From here on, you can find the following items by using space bar or enter or b to scroll down or up

The first table is the NAOs showing their occupancy and energies in this molecule

The Rydberg orbitals are there to account for the more extended bits of the basis functions used, including polarisation functions
The labels are the familiar natural orbital labels, 2s, 2p_x etc. used in teaching
Scroll down to the sulfur atom. You will see that despite using a d-type polarisation function in the 3-21G* basis set, there is very little occupation of the 3d orbitals

(Occupancy) Bond orbital/ Coefficients/ Hybrids

Use Enter to scroll gently (if necessary) until you have all of the entry for NBO number 2 on the screen

The first number, 1.96848, is the population: this is almost a two-electron bond
( 52.11%) and ( 47.89%) are the relative amounts of the NHOs on carbon and sulfur respectively used. This shows the polarisation of the bond (towards carbon)
The next numbers, 0.7218 and 0.6921, are the corresponding LCAO coefficients of NHOs (coefficient squared times 100 is the percentage, as in the stage 1 MO course!)
Both carbon and sulfur use NHOs which are mainly made from p orbitals: e.g. the sulfur NHO has 89.36% p character
The sulfur NHO has 0.96% d character. This is an answer to the common undergraduate question 'how much are d orbitals involved for a main group element?'
Scroll down until you can see NBOs 19 and 20

NBO 19 is an sp mixture which is 80.52% s. It sticks out in the plane of the ring
NBO 20 is pure p, sticking above and below the plane of the ring
Scroll down to find NBO 50

The NHOs used are the same as for the bonding orbital
The coefficients, 0.6921 and -0.7218, are now of opposite signs, so as to produce the antibonding node, and they are the other way round, so that the polarisation is in the opposite sense

Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis

The column headed E(2) is the stabilisation gained by donation from the donor NBO to the acceptor NBO
The biggest item in this column, 11.19 kcal mol^-1, is for NBO 2 (the C-S s bond) donating to NBO 53 (the other C-S s^* antibonding orbital)