# Blog Archives

## Basis Set Superposition Error (BSSE). A short intro

Molecular Orbitals (MOs) are linear combinations of Atomic Orbitals (AOs), which in turn are linear combinations of other functions called ‘basis functions’. A basis, or more accurately a basis set, is a collection of functions which obey a set of rules (such as being orthogonal to each other and possibly being normalized) with which all AOs are constructed, and although these are centered on each atomic nucleus, the canonical way in which they are combined yield delocalized MOs; in other words, an MO can occupy a large space spanning several atoms at once. We don’t mind this expansion across a molecule, but what about between two molecules? Calculating the interaction energy between two or more molecular fragments leads to an artificial extra–stabilization term that stems from the fact that electrons in molecule 1 can occupy AO’s (or the basis functions which form them) centered on atoms from molecule 2.

Fundamentally, the interaction energy of any A—B dimer, Eint, is calculated as the energy difference between the dimer and the separately calculated energies for each component (Equation 1).

Eint = EAB – EA – EB (1)

However the calculation of Eint by this method is highly sensitive to the choice of basis set due to the Basis Set Superposition Error (BSSE) described in the first paragraph. The BSSE is particularly troublesome when small basis sets are used, due to the poor description of dispersion interactions but treating this error by just choosing a larger basis set is seldom useful for systems of considerable sizes. The Counterpoise method is a nifty correction to equation 1, in which EA and EB are calculated with the basis set of A and B respectively, i.e., only in EAB a larger basis set (that of A and B simultaneously) is used. The Counterpoise method calculates each component with the AB basis set (Equation 2)

EintCP = EABAB – EAAB– EBAB (2)

where the superscript AB means the whole basis set is used. This is accomplished by using ‘ghost‘ atoms with no nuclei and no electrons but empty basis set functions centered on them.

In Gaussian, BSSE is calculated with the Counterpoise method developed by Boys and Simon. It requires the keyword Counterpoise=N where N is the number of fragments to be considered (for an A—B system, N=2). Each atom in the coordinates list must be specified to which fragment pertains; additionally, the charge and multiplicity for each fragment and the whole supermolecular ensemble must be specified. Follow the example of this hydrogen fluoride dimer.

```%chk=HF2.chk
#P opt wB97XD/6-31G(d,p) Counterpoise=2

HF dimer

0,1 0,1 0,1
H(Fragment=1) 0.00 0.00 0.00
F(Fragment=1) 0.00 0.00 0.70
H(Fragment=2) 0.00 0.00 1.00
F(Fragment=2) 0.00 0.00 1.70```

For closed shell fragments the first line is straightforward but one must pay attention that the first pair of numbers in the charge multiplicity line correspond to the whole ensemble, whereas the folowing pairs correspond to each fragment in consecutive order. Fragments do not need to be specified contiguously, i.e., you don’t need to define all atoms for fragment 1 and after those the atoms for fragment 2, etc. They could be mixed and the program still assigns them correctly. Just as an example I typed wB97XD but any other method, DFT or ab initio, may be used; only semiempirical methods do not admit a BSSE calculation because they don’t make use of a basis set in the first place!

The output provides the corrected energy (in atomic units) for the whole system, as well as the BSSE correction (which added to the previous term yields the un-corrected energy of the system). Gaussian16 also provides these values in kcal/mol as ‘Complexation energies’ first raw (uncorrected) and then the corrected energy.

BSSE is always present and cannot be entirely eliminated because of the use of finite basis sets but it can be correctly dealt with if the Counterpoise method is included.

## Some .fchk files wont open in GaussView5.0 (Update)

A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.

```CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Orbital Energies
Line Number 1234```

Although the method described in the previous post works just fine, the following update is a better approach. Due to a change of spelling between G03 and G09 (which has been corrected for G09 but not available for GV versions prior to 5.0.9) one must change “independent” for “independant

To make the change directly from the terminal the following command is needed:

`sed -i 's/independent/independant/g' file.fchk`

Alternatively you can redirect the output to a new file

`sed -e 's/independent/independant/g' file.fchk > newfile.fchk`

if you want to keep the old version and work with a new one.

Of course this edition can be performed manually with any text editor available (for example if you work in Windows) but solutions from the terminal always seem easier and a lot more fun to me.

Thanks to Dr. Fernando Cortés for sharing his insight into this issue.

## If a .fchk file wont open in GaussView5.0

I’ve found the following error regarding the opening of .fchk files in GaussView5.0.

```CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Orbital Energies
Line Number 1234```

The error is prevented to a first approximation (i.e. it at least will allow GV to open and visualize the file but other issues may arise) by opening the file and modifying the number of basis functions to equal the number of independent functions (which is lower)

```FILE HEADER
FOpt RM062X 6-311++G(d,p)
Number of atoms I 75
Info1-9 I N= 9
163 163 0 0 0 110
2 18 -502
Charge I 0
Multiplicity I 1
Number of electrons I 314
Number of alpha electrons I 157
Number of beta electrons I 157
Number of basis functions I 1199
Number of independent functions I 1199
Number of point charges in /Mol/ I 0
Number of translation vectors I 0
Atomic numbers I N= 75
... ...
... ...```

Once both numbers match you can open the file normally and work with it. My guess is this will continue to happen with highly polarized basis sets but I need to run some tests.