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)


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.

#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.

About joaquinbarroso

Computational and theoretical chemist in his early forties, in love with life, science, baseball, and literature. Science literacy makes us responsible citizens, it is therefore a scientific duty to talk, write, and engage with the general public; as Feynman said, if you find science boring, your learning from the wrong teacher. "Make like a molecule and react!"

Posted on December 8, 2020, in Computational Chemistry, Gaussian, Theoretical Chemistry, White papers and tagged , , , , , , , , , , , , , , , , , . Bookmark the permalink. 7 Comments.

  1. Thank you Dr for always edifying the novice into this wondery field. Best regards, Tendongmo Hilaire

    On Tue, Dec 8, 2020, 15:56 Dr. Joaquin Barroso’s Blog wrote:

    > joaquinbarroso posted: ” 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 ” >

  2. Please Dr having difficulties with TDDFT calculations using Gaussian 9version D. Kindly need your help if possible 🙏

  3. Hi. Thanks a lot for this post. It is very useful. I have two questions.
    – If I already optimize my system, do I have to still use the ‘opt’ keyword when doing counterpoise correction, or can it be omitted?
    – If the counterpoise calculation does not finish in the allowed job time, can I try to restart the calculation or would this be useless?


    • If the system is already optimized, assuming this system is composed of two fragments, then you don’t need to optimize it again, just perform de BSSE Counterpoise correction separately. BSSE calculations cannot be restarted, you need to start them again.

  4. Your posts have been providing much guidance to newbies like me, thank you!

    A question on counterpoise calculation, please?
    I have two fragments and clearly indicate the fragments with keyword counterpoise=2 in the input file (Gaussian 09).

    I did get the counterpoise corrected energy from the output file. However, my output file does not show the sum of monomer and the complexation energy. I intend to obtain the interaction energy between the two fragment (single point calculation) so I suppose I need to use the counterpoise corrected energy substrate with the sum of monomer?

    Thank you in advance and wish you have a pleasant day!

  5. Awesome blog. I am new to using fragments, and was wondering if all species in a single fragment need to be bound/ uninterrupted. For example, if I have a cluster taken from a MOF of three metal centers with high spin. I want to treat those as 3 individual fragments. Can I put all the neutral, closed-shell linker molecules in a single fragment, even though they are separated by the metal centers?

  1. Pingback: Percentage of Molecular Orbital Composition – G09,G16 | Dr. Joaquin Barroso's Blog

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