ARTICLE

pubs.acs.org/JPCA

Are There Atomic Orbitals in a Molecule?

I. Mayer,* I. Bak
o, and A. Stirling
Chemical Research Center, Hungarian Academy of Sciences, H-1525 Budapest, P.O. Box 17, Hungary

ABSTRACT: Effective atomic orbitals (AOs) have been calcu-

lated by the method of the “fuzzy atoms” analysis by using the
numerical molecular orbitals (MOs) obtained from plane-wave
DFT calculation, i.e., without introducing any atom-centered
functions. The results show that in the case of nonhypervalent
atoms there are as many effective AOs with non-negligible
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occupation numbers, as many orbitals are in the classical

minimal basis set of the given atom. This means that, for nonhypervalent systems, it is possible to present the MOs as sums of
effective atomic orbitals that resemble very much the atomic minimal basis orbitals of the individual atoms (or their hybrids). For
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hypervalent atoms some additional orbitals basically of d-type are also of some importance; they are necessary to describe the back-
donation to these positive atoms. It appears that the d-type orbitals play a similar role also for strongly positive carbon atoms. The
method employed here is also useful to decide whether the use of polarization functions of a given type is a matter of conceptual
importance or has only a numerical effect.

1. INTRODUCTION
A qualitative discussion of the electronic structure of a
molecule is traditionally done in terms of molecular orbitals
(MOs) formed as a linear combination of the atomic orbitals
(AOs) of the constituting atoms (the LCAO principle). The first
quantum chemical calculations used directly the orbitals occu-
pied in the free atoms, but it became evident very soon that the
atomic orbitals undergo deformations (e.g., orbital shrinking and
polarization) during the bond formation. Later on, the original
minimal basis set calculations have been replaced by those using
extended basis sets—mostly of Gaussian orbitals—but most
chemists continue thinking in terms of minimal basis atomic
orbitals, or their hybrids, at least if nonhypervalent systems are
concerned.
One of us has showed that this picture chemists are using
can actually be justified by performing a special a posteriori
“Hilbert-space” analysis of the wave functions:1
3 usually one
can construct as many orthogonal linear combinations of the
basis orbitals centered on the given atom and having a non-
negligible contribution to the molecular wave function, as
is the number of orbitals in the respective classical minimal basis
set. These orbitals can be said to form an effective minimal basis.
Depending on the system, the effective minimal basis either
consists of orbitals of nearly pure s, p, etc. character or represents
some hybrids of them. To obtain these results, one has to
perform a localization procedure for each atom separately, by
using the Magnasco
Perico localization criterion,4 in which the
net Mulliken populations on the selected atom, corresponding
to the localized orbitals, are requested to be maximal or, at
least, stationary. Similar results were obtained also in the “fuzzy
atom” analysis,5 when the localization criterion was selected as
to make stationary the net atomic population6 in a three-
dimensional (3D) “fuzzy” atomic domain. (The “fuzzy atoms”
analysis divides the 3D physical space into atomic regions,
but the regions assigned to the individual atoms have no sharp
boundaries and exhibit a continuous transition from one to
another.)
Although the populations on the “fuzzy atoms” do not directly
correspond to those on the individual atomic basis functions, the
results could heavily be influenced by the employment of the
atom-centered basis sets. One might argue that such basis sets
inherently bias the localization procedures toward the formation
of atomic-type orbitals. In other words, “one is very much
tempted to think that the LCAO approach somehow 'induces’
rather than 'describes' the 'chemistry'.”7 It is, therefore, an
important conceptual question whether the existence of effective
minimal basis sets featuring s, p, d-type orbitals or their hybrids
is a “law of nature” or an artifact of the computation. To address
this issue, we have performed the respective analysis of
wave functions obtained in plane wave calculations, without
introducing any atom-centered basis sets in the course of the
calculations.
2. THEORY
The formalism of defining effective AOs in the “fuzzy atoms”
framework has been developed in the recent paper,5 so here we
repeat only the most important points. (At the abstract theore-
tical level it makes no difference whether the MOs considered
were calculated by using an atom-centered basis or a plane-wave
basis.)
In the “fuzzy atoms” analysis one introduces a set of non-
negative atomic weight functions wA(rB) for each atom A and
Special Issue: Richard F. W. Bader Festschrift
Received: April 20, 2011
Revised: June 6, 2011
Published: June 23, 2011

r 2011 American Chemical Society 12733 dx.doi.org/10.1021/jp2036923 | J. Phys. Chem. A 2011, 115, 12733–12737
The Journal of Physical Chemistry A
r of the 3D space, satisfying the requirement:
every point B
∑A wA ðrBÞ ¼ 1 ð1Þ
everywhere. These weight functions are requested to be ∼1
“inside” the atom (near the nucleus) and vanish gradually with
the distance from the nucleus. In the present work we have used
the simple Becke weight functions.8 (For a detailed discussion
see the Appendix in ref 6.) It is a polynomial function, having
the property that each wA(rB) is exactly equal one at the “own”
nucleus and is zero at the other nuclei.
In accord with the definition (1) of the weight functions, any
orbital ψ(rB) can be presented as a sum of the components
ψðrBÞ ¼ ∑A wA ðrBÞ ψðrBÞ ð2Þ
which may be attributed to the different atoms A. Then the
integral
Z localized MOs.
M ¼ wA 2 ðrBÞjψðrBÞj2 dv ð3Þ
defines the weight of the intraatomic part of ψ(rB), assuming that
it is normalized to unity.
Now, starting from the set of the occupied canonic MOs
ψj(rB), and subjecting them to a proper unitary transformation,
one can find the set of localized orbitals
occ
ji ðrBÞ ¼ ∑ Uji ψj ðrBÞ
j¼1
ð4Þ
which have maximal, or at least stationary, weights of their
intraatomic parts wA(rB) ji(rB). It is easy to see that matrix U
should diagonalize matrix Q with the elements
Z tentials. The molecules have been placed in a cubic box with an

Q ij ¼ wA 2 ðrBÞ ψi ðrBÞ ψj ðrBÞ dv ð5Þ
(The canonic orbitals are assumed orthonormalized, Æψi|ψjæ = δij.)
That means
U† Q U ¼ diagfMi g ð6Þ
The diagonal values Mi may be called “degrees of localization” (they
measure the extent to which the molecular orbital ji is localized on
the given atom) or simply “occupation numbers” (see below). By
virtue of the unitary character of the transformation (4), and the
definition of the quantities Mi as eigenvalues, the renormalized
functions
1 MOs have been normalized in the same manner.)
jAi ðrBÞ ¼ pffiffiffiffiffi wA ðrBÞ ji ðrBÞ ð7Þ
Mi
form an orthonormalized set of effective atomic orbitals. The sum of
the corresponding eigenvalues Mi gives the net atomic population
for each spin of the atom A, as defined in ref 6. The net atomic
population is, of course, invariant of the unitary transformation, but
the transformation influences how many orbitals give a consider-
able contribution to it.
By using the decomposition (1), the first-order density matrix
for spin σ, ρσ(rB,rB0 ), can obviously be presented as the sum of
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components as
r 0Þ ¼
ρσ ðrB, B ∑ ρσAB ðrB, Br 0 Þ
A, B
¼ ∑ wA ðrBÞρσ ðrB, Br 0 ÞwBðrB0 Þ ð8Þ
A, B
It is easy to show that the functions jAi (rB) are the eigenvectors of
the intraatomic part ρσAA(rB, B r 0 ), and thus represent a rather
straightforward generalization of McWeeny’s classical “natural
hybrid orbitals”,9 with the occupation numbers being equal to Mi
for each spin. (The analogous relation for the analysis performed
in the Hilbert space of the atomic basis orbitals has been
discussed in ref 3.)
The procedure described above may also be considered as
L€owdin’s canonic orthogonalization of the intraatomic compo-
nents wA(rB) ψi(rB) of the MOs. This also means that the present
orthogonalization scheme is the only one leading to an orthogonal
set of effective AOs, defined as intraatomic parts of the
3. METHOD OF CALCULATIONS
The plane-wave calculations of the valence electron-structure
have been performed by using the known CPMD code10 within
the Kohn
Sham DFT formalism,11 employing the BLYP
exchange
correlation functional12 and replacing the core elec-
trons with an effective potential. The electronic orbitals were
expanded in a plane-wave basis set up to a kinetic energy cutoff of
70 Ry. Test calculations with a higher cutoff (150 Ry) have
shown no qualitative differences in the derived effective orbitals
and their occupancies.The interaction between the valence and
core electrons has been accounted for using norm-conserving
pseudopotentials generated with the Troullier
Martins
scheme.13 The Kleinman
Bylander construction14 has been
applied to the evaluation of the nonlocal part of the pseudopo-
edge length of 15.0 Å. Their structures have been fully optimized,
and the corresponding Kohn
Sham orbitals have been calcu-
lated on a grid in the Gaussian “cube file” format. The orbitals
represented in this way have been the subject of the subsequent
wave function analysis. When we have processed the “cube files”
of molecular orbitals, we have essentially performed an analysis of
the numerical solutions of the Kohn
Sham equations, and it is
only a matter of technical relevance that the orbitals originate
from a plane wave calculation.
The Becke weight functions wA(rB) have been calculated in
every grid point of the cube file by using the routine of the
program described in ref 6. The numerical integrations have been
performed simply by performing summations over the grid
points, attributing equal weights to every point. (The individual
The “Hilbert-space analysis”1,3 shown in Figure 10 has been
performed by a version of the program EFF-AO.15
4. SAMPLE CALCULATIONS
We have performed several calculations of different molecules
and ions. Tables 1
5 display the occupation numbers (eigenvalues
Mi) obtained for the different atoms in several molecules and ions.
It can be seen that for every atom there are as many “strongly
occupied” effective AOs (having considerable Mi values) as
the number of classical valence orbitals on that atom—one for
dx.doi.org/10.1021/jp2036923 |J. Phys. Chem. A 2011, 115, 12733–12737
The Journal of Physical Chemistry A ARTICLE

Table 1. Largest Occupation Numbers (Degrees of Table 4. Largest Occupation Numbers (Degrees of
Localization) Mi for Different Atoms in the Molecules CO, Localization) Mi for the Heavy Atoms in the Alanine Molecule
H2O, SF6, C2H2, C2H4, and C2H6
orbital C1 C2 C3 O1 O2 N
CO H2O SF6 C2H2 C2H4 C2H6 1 0.54 0.50 0.51 0.89 0.89 0.81
orbital C O O H S F H C H C H 2 0.42 0.39 0.46 0.61 0.69 0.67
3 0.40 0.35 0.36 0.53 0.53 0.48
1 0.97 0.98 0.94 0.39 0.39 0.98 0.58 0.33 0.56 0.38 0.53 0.34 4 0.34 0.32 0.27 0.24 0.37 0.39
2 0.33 0.67 0.82 0.04 0.20 0.91 0.41 0.01 0.40 0.01 0.39 0.01 5 0.008 0.025 0.11 0.01 0.01 0.008
3 0.22 0.67 0.46 0.02 0.20 0.91 0.41 0.40 0.38 6 0.014 0.09
4 0.22 0.48 0.43 0.20 0.67 0.34 0.36 0.34 7 0.04
5 0.004 0.007 0.06 0.02 0.01 0.01 0.01 8 0.02
6 0.004 0.007 0.06 0.02 0.01 0.01 0.01
7 0.03
8 0.03 Table 5. Largest Occupation Numbers (Degrees of
9 0.03 Localization) Mi for Different Atoms in the Ions OH
, NO3
,
ClO4
, and SO42

OH
NO3
ClO4
SO42

Table 2. Largest Occupation Numbers (Degrees of
Localization) Mi for Different Atoms in the Dimethyl Ether orbital O H N O Cl O S O
and Dimethyl Sulfide Molecules
1 0.98 0.37 0.62 0.98 0.79 0.91 0.62 0.96
dimethyl ether dimethyl sulfide 2 0.89 0.05 0.52 0.82 0.59 0.65 0.40 0.75
3 0.89 0.05 0.43 0.68 0.59 0.65 0.40 0.75
orbital C O H1 H2,3 C S H1 H2,3 4 0.51 0.01 0.43 0.34 0.59 0.25 0.40 0.42
1 0.56 0.92 0.32 0.37 0.53 0.97 0.33 0.37 5 0.05 0.006 0.23 0.002 0.14 0.02
2 0.44 0.83 0.008 0.006 0.40 0.91 0.006 0.008 6 0.05 0.23 0.14
3 0.41 0.58 0.38 0.61 7 0.04 0.23 0.14
4 0.25 0.48 0.24 0.50 8 0.04 0.19 0.12
5 0.02 0.01 0.007 0.004 9 0.02 0.19 0.12
10 0.01 0.07 0.04

Table 3. Largest Occupation Numbers (Degrees of

Localization) Mi for Different Atoms in the Acetone and
Thioacetone Molecules

acetone thioacetone

orbital C1,3 C2 O H1 H2,3 C1,3 C2 S H1 H2,3

Figure 1. Strongly occupied oxygen orbitals in the CO molecule.
1 0.53 0.50 0.98 0.37 0.36 0.54 0.51 0.99 0.36 0.36
2 0.41 0.36 0.84 0.008 0.008 0.40 0.35 0.92 0.008 0.009
3 0.39 0.30 0.60 0.39 0.27 0.64
4 0.35 0.29 0.49 0.33 0.25 0.52
5 0.005 0.035 0.011 0.005 0.01 0.003
6 0.025 0.007
Figure 2. Strongly occupied oxygen orbitals in the water molecule.

H, four for C, N, O, S, etc. (We note again that in the present plane
wave calculations the core electrons have been compressed to the
effective potentials.) The Mi values are close to 1 for lone pair
orbitals and scatter around 1/2 for the bonding ones. The “weakly
occupied” AOs have significantly lower, in most cases negligible, Mi
values.† Hypervalent atoms represent intermediate cases; they have
also some small but non-negligible Mi values, in full analogy to that
already observed in the framework of the Hilbert-space analysis.1
These orbitals are necessary to describe the “back-donation” to the
positive hypervalent atoms. (An analogical effect is observed,
although to a lesser extent, for the (obviously positive) central
carbon atom of the acetone molecule and the carboxylic carbon in
alanine.)
12735
Figures 1
9 show the shapes of the effective AOs for some
of the molecules considered. It can be seen that the “strongly
occupied” orbitals in all systems resemble the conventional s and
p atomic orbitals, or their hybrids, with the limitation that the
orbitals of a given atom do not significantly extend to the spatial
domains of the other atoms. (This implies significant deviations
from the conventional orbital shapes if not too large orbital cutoff
values are used on the figures.) The “weakly occupied” orbitals,
where they are not negligible at all, have basically the shapes
resembling conventional d-orbitals. That sheds some new light to
the importance of using them as “polarization functions” in the
SCF calculations. Inspecting these orbitals, we should recall once
again that the calculations have been performed by using plane
dx.doi.org/10.1021/jp2036923 |J. Phys. Chem. A 2011, 115, 12733–12737
The Journal of Physical Chemistry A
Figure 3. Strongly occupied hydrogen orbital (above) and the first
weakly occupied hydrogen orbital (below) in the water molecule.
Figure 4. Strongly occupied orbitals of the central carbon atom in the
acetone molecule.
Figure 5. First two weakly occupied orbitals of the central carbon atom
in the acetone molecule.
Figure 6. Strongly occupied orbitals of the sulfur atom in the SF6 molecule.
wave basis, and no atom-centered functions were employed in
the calculations. (The role of d-orbitals could be further clarified
by performing also an explicit decomposition of the “strongly
occupied” effective AOs into pure s, p, d, etc. components.)
The oxygen orbitals of the CO molecule show a classical
example of the sp hybridization. The first, lone pair, atomic
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Figure 7. Weakly occupied orbitals of the sulfur atom in the SF6
molecule.
Figure 8. Strongly occupied orbitals of the nitrogen atom in the
NO3
ion.
Figure 9. Weakly occupied orbitals of the nitrogen atom in the
NO3
ion.
orbital is more s-like, while the second, bonding, orbital is more
p-like. This ordering can easily be explained by the energy order
of the s and p atomic orbitals. Then follow two orthogonal
p-orbitals, as expected.
The situation for the occupied oxygen orbitals of the water
molecule (Figure 2) is quite similar to that in the CO, except that
the bonding sp-like orbital has not the second but the fourth
largest occupation number. On this figure it appears more
spectacularly that the AOs are sharply “cut” where the domain
of another atom is started.
Of course, the π-type molecular orbital in the water is not
strictly confined to the spatial domain of oxygen atom; however, it
has only a very small tail in the hydrogen domain, leading to a
small (ca. 0.04) occupation number of the hydrogen’s first p-type
orbital, shown in Figure 3.
The strongly occupied orbitals on the central carbon atom of
the acetone molecule (Figure 4) are similar to those of the
oxygen orbitals considered previously. The most peculiar feature
is the basically s-type hybrid having the largest occupation
number because of the characteristic hollow on the side directed
to the oxygen atom. This is not an artifact of the inverse Fourier-
transform or other numerical effects: an analogous hollow on the
oxygen side can be observed on the respective Hartree
Fock
orbital obtained in a Hilbert-space analysis1,3 of a cc-pVTZ basis
set calculation, shown in Figure 10.
Very interesting are the weakly (but not quite negligibly)
occupied orbitals of that carbon atom (Figure 5): they have well-
expressed d-orbital character. This result questions the common
belief that back-donation to d-type orbitals has an importance
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The Journal of Physical Chemistry A ARTICLE

’ ADDITIONAL NOTE
†
In the case of water molecule and of the OH
ion, there are only
four valence molecular orbitals, so there are no “weakly occu-
pied” AOs on the oxygen atoms. The same holds for the carbon
in methane molecule.

’ REFERENCES
Figure 10. First strongly occupied valence orbital of the central carbon
atom in the acetone molecule, calculated by the Hilbert-space analysis
from the results of a cc-pVTZ Hartree
Fock calculation.
only started from the third row of the periodic system (silicon,
etc.) as there are no free atomic orbitals of 2d-type. This result
also indicates that plane wave calculations with the present type
of analysis can serve, in general, to decide independently whether
orbitals of the given type are of conceptual importance for
systems in question.
The sulfur orbitals shown on Figures 6 and 7 corroborate our
picture about the behavior of hypervalent atoms. The most
occupied orbitals represent an sp-type set (with the significant
cuts where the domains of the fluorine orbitals start) while a set
of d-type orbitals (four of them are shown) has smaller, but in no
way negligible, occupation numbers, permitting a classical back-
donation to the positive sulfur.
Figures 8 and 9 show the nitrogen effective AOs in the
NO3
ion. The formally pentavalent nitrogen shows all the
characteristics of a hypervalent atom: there is an sp set of strongly
occupied orbitals, whereas the weakly (but not quite negligibly)
occupied orbitals are basically of d-character, although a diffuse
π-type p-orbital also appears there.
Finally we mention that quite analogous calculations could
also be performed by using Bader’s topological definition of the
atoms in molecules16 instead of “fuzzy atoms”; the respective
equations have been derived already in ref 2.
(1) Mayer, I. Chem. Phys. Lett. 1995, 242, 499.
(2) Mayer, I. Can. J. Chem. 1996, 74, 939.
(3) Mayer, I. J. Phys. Chem. 1996, 100, 6249.
(4) Magnasco, V.; Perico, A. J. Chem. Phys. 1967, 47, 971.
(5) Mayer, I.; Salvador, P. J. Chem. Phys. 2009, 130, 234106.
(6) Mayer, I.; Salvador, P. Chem. Phys. Lett. 2004, 383, 368.
(7) Salvador, P. personal communication to I.M., 2011.
(8) Becke, A. D. J. Chem. Phys. 1988, 88, 2547.
(9) McWeeny, R. Rev. Mod. Phys. 1960, 32, 335.
(10) CPMD, version 3.11.1, http://www.cpmd.org; IBM Corp.:
Armonk, NY, 1990
2006; MPI f€ur Festk€orperforschung Stuttgart:
Stuttgart, 1997
2001.
(11) Kohn, W.; Sham, L. J. Phys. Rev. A 1965, 140, 1133.
(12) Becke, A. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R.
Phys. Rev. B 1988, 37, 785.
(13) Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993.
(14) Kleinman, L.; Bylander, D. M. Phys. Rev. Lett. 1982, 48, 1425.
(15) Mayer, I. Program EFF-AO, Budapest, 2008. May be down-
loaded from the site http://occam.chemres.hu/programs.
(16) Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Oxford
University Press: Oxford, U.K., 1990.

5. CONCLUSIONS
Effective atomic orbitals have been calculated by the method of
the “fuzzy atoms” analysis by using the numerical molecular
orbitals obtained from plane-wave DFT calculation, i.e., without
introducing any atom-centered functions. The results show that
in the case of nonhypervalent atoms there are as many effective
AOs with non-negligible occupation numbers as there are orbitals
in the classical minimal basis set of the given atom. This means
that, for nonhypervalent systems, it is possible to present the MOs
as sums of effective atomic orbitals that resemble very much the
atomic minimal basis orbitals of the individual atoms (or their
hybrids). For hypervalent atoms some additional orbitals basically
of d-type are also of some importance; they are necessary to
describe the back-donation to these positive atoms. It appears that
the d-type orbitals play a similar role also for strongly positive
carbon atoms. The method employed here is also useful to decide
whether the use of polarization functions of a given type is a
matter of conceptual importance or has only a numerical effect.

’ ACKNOWLEDGMENT
We acknowledge the partial financial support of the Hungarian
Scientific Research Fund (grant OTKA 71816).
12737 dx.doi.org/10.1021/jp2036923 |J. Phys. Chem. A 2011, 115, 12733–12737