Very strong chalcogen bonding: Is oxygen in molecules capable of forming
it? A First-Principles Perspective
Pradeep R. Varadwaj 1* Arpita
Varadwaj1,2, Helder M. Marques3
1 Department of Chemical System Engineering, School of
Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan
2 The National Institute of Advanced Industrial
Science and Technology (AIST), Tsukuba 305-8560, Japan
3 Molecular Sciences Institute, School of Chemistry,
University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein,
Johannesburg 2050, South Africa.
* Corresponding authors address: pradeep@t.okayama-u.ac.jp
Abstract
There are views prevalent in the noncovalent chemistry literature that
i) the O atom in molecules cannot form a chalcogen bond, and ii) if
formed, this bond is very weak. We have shown here that these views are
not necessarily true since the attractive energy between the oxygen atom
of some molecules and several electron-rich anionic bases examined in a
series of 34 ion-molecule complexes varied from the weak (ca –2.30 kcal
mol-1) to the ultra-strong (–90.10 kcal
mol-1). The [MP2 /aug-cc-pVTZ] binding energies
for several of these complexes were found to be comparable to or
significantly larger than that of the well-known hydrogen bond complex
[FH···F]– (~ 40 kcal
mol-1). The nature of the intermolecular interactions
was examined using the quantum theory of atoms in molecules,
second-order natural bond orbital and symmetric adaptive perturbation
theory energy decomposition analyses. It was found that many of these
interactions comprise mixed bonding character (ionic and covalent),
especially manifest in the moderate to strongly bound complexes. All
these can be explained by an n (lone-pair bonding orbital) → σ*
(anti-bonding orbital) donor-acceptor charge transfer delocalization.
This study, therefore, demonstrates that the covalently bound oxygen
atom in molecules can have a significant ability to act as an unusually
strong chalcogen bond donor.
- IntroductionChalconide (Ch) oxygen is generally regarded as the least polarizable
element in Group 16 of the periodic table.1,2Because of this, several studies have demonstrated that it does not
form a chalcogen bond.3-7 (A chalcogen bond is
formed when there is evidence of a positive site on the Ch atom in a
molecule that interacts attractively with a negative site on a Lewis
base in another molecule.8-15) The argument is that
the oxygen atom in molecules is often negative and therefore does not
feature a positive σ-hole on its electrostatic surface that can
attract the negative site on a base.3-15 (A
σ-hole16,17 is an electron density deficient region
on the surface of the atom Ch along the outer portion of the R–Ch
bond axis, where R is the remainder part of the
molecule.18) While this may indeed be so in many
cases (such as H2O and
H2CO),8,9 it should not always be
taken for granted.
We have recently shown that when the oxygen atom is covalently bonded
to an electron-withdrawing group X (X = F, Cl, Br) and –CN, the group
draws the electron density to the bonding region and generates a weak
to a moderately strong electron density deficient-region (σ-hole) on
the surface of the atom lying opposite to the bond.8,9 The interaction energy (also called the binding
energy) of putative 1:1 complexes formed by the O atom and the Lewis
bases was found to be small (< 3 kcal
mol-1).8,9 This has led to the
interpretation that the aforementioned complexes may be regarded as
being formed by van der Waals or weak interaction. These studies on
O-centered chalcogen bonding have been recognized by others, both
experimentally and theoretically.19,20 However, some
have claimed that these complexes may not involve true “chalcogen
bonding” since the intermolecular interactions in them are weakly
bound and “chalcogen bonding” should be regarded as an
“electrostatically driven” interaction – reminiscent of a debate
that is very common in the area of halogen
bonding.21,22 We counter this view by noting that
there is no hard and fast rule in which a “weakly bound” or “van
der Waals” complex cannot be regarded as truly “chalcogen bonded”.
The minimal criterion for the recognition of a “Type-II chalcogen
bond”11,23 is that there must be an attraction
between the electrophilic region on the Ch atom and a negative site,
and that the angle of approach of the electrophile should be such that
∠X⋯Ch–R = 140–180o.8-15We add further that the importance of weak interactions should not be
underestimated.24,25 They appear in many different
flavors,25-32 yet an understanding of their physical
and chemical behavior in chemical systems to date is not complete.
They are important factors, for example, not only in the theoretical
and experimental design of drug33,34 and polymer
network structures,35-37 but also for developments
in the fields of crystal engineering38 and molecular
recognition.24,39 The hydrogen bond between two
H2O molecules is also weak, and is never stronger than
about a twentieth the strength of the O–H covalent bond. Such bonds
are structure determining, and have profound significance in fields as
diverse as biology and materials science.40 The
energy of a van der Waals interaction is very weak, only about
1 kcal mol−1, comparable with the average kinetic
energy of a molecule in solution (approximately
0.4 kcal mol−1). It is significant only when many
of them are combined so they contribute to the overall structure of a
chemical system (as in interactions of complementary
surfaces).41,42 Accordingly, and based on their
energy of stability preferences, intermolecular interactions have been
classified as van der Waals (energy < 1 kcal
mol−1),43 weak (1–4 kcal
mol-1), 43,44 moderate (4 –15
kcal mol-1),45 strong (15–40 kcal
mol−1),44-46 very strong (40–60
kcal mol-1)47 and ultra-strong
(>> 60 kcal
mol-1).47-51 The first four have
been recognized in many systems, while the last two have been
identified in singly- and doubly charge-assisted composite systems,
respectively.48,51-53Whereas thousands of studies have been reported centering discussion
on the chemical physics and physical chemistry of halogen bonding and
chalcogen bonding interactions between molecules containing heavy atom
donors, the exploration of the chemistry of O-center chalcogen bonding
from a theoretical modeling perspective is very limited. To this end,
we report here an investigation of the structure, energy, electronic,
orbital, and topological properties of 34 ion-molecule complexes
formed by the attractive engagement between the positive sites
(positive σ-holes) on the O atoms of some O-containing molecules and a
series of anions. Analogous molecule-anion complexes, formed by
hydrogen- and halogen-bonds are well known and hundreds of structures
featuring these have been deposited in the Cambridge Structure
Database.54 Kumar and coworkers, for instance, have
examined the robustness of stable benzylic selenocynates for halide
ion recognition in the solid-state and in
solution.55 Their XRD analysis of various cocrystals
reveals that the NCSe···X– systems are driven by
structurally important Se···X⁻ (X = Cl, Br, I) chalcogen bonds.
Similar studies have been reported by ohers.56,57Similarly, Galmés and coworkers have recently performed a combined
Cambridge Structural Database and theoretical DFT study of charge
assisted chalcogen bonds involving sulfonium, selenonium, and
telluronium cations in which divalent chalcogen atoms typically have
up to two σ‐holes and form up to two chalcogen bonds; the same holds
for tetravalent chalcogens which adopt a seesaw
arrangement.58 Analogous studies have been reported
elsewhere.59 However, the complexes examined in this
study are uncommon; they are promoted by O-centered chalcogen bonding.
The results of the ab initio first-principles MP2
method60 show that the binding energy of many of
these complexes can be unusually high, comparable to or greater than
that of various halogen- and hydrogen-bonded systems already reported
in the noncovalent chemistry literature. In addition, we used the
results of symmetry adapted perturbation theory
(SAPT),61,62 the second-order perturbative estimates
of ’donor-acceptor’ (bond-antibond) interaction energies in the
natural bond orbital (NBO) basis,63 and the quantum
theory atoms in molecules (QTAIM)64 to show that the
intermolecular interactions responsible for the formation of the
ion-molecule complexes contain appreciable covalent character. Of
course, this adds to their inherent ionic character, which can well be
rationalized by the Coulomb’s law.
- Chemical model systems and computational details
The binary complexes of OX2 (X = F, Cl, Br, CN) with the
anions A– (A = F, Cl, Br, CN, Br3,
SCN, NCO, NO3) were fully energy minimized using MP2
(fc), in conjunction with the aug-cc-pVTZ basis set; the reliability of
this and other theoretical approaches to study noncovalent interactions
has been discussed elsewhere.8,9,65-67 The calculation
of the Hessian second derivative of the energy with respect to the fixed
nuclear coordinates of the atom was performed for all cases to ensure
that a true minimum was found; all eigenvalues were found to be
positive, and the structures reported here are not transition states.
All calculations were formed using Gaussian 09.68
The nature of electrostatic surface of each OX2 molecule
was examined using the popular molecular electrostatic surface potential
(MESP) approach.69 As has been done
elsewhere,8,69 the 0.001 a.u. isodensity envelopes of
these molecules were used on which to compute the potential. The local
maxima and minima of potential, often referred to asVS,max and VS,min ,
respectively, were used to identify the positive and negative regions,
respectively. It should be kept in mind that the sign ofVS,max and VS,min is not
always positive or always negative. The positive/negative sign
associated with these two properties depends on the nature of the
nucleophilicity/electrophilicity of a specific region on an atom or
fragment in a molecule. Nevertheless, when VS,max> 0 (or VS,max < 0) on
atom Ch along the outer extension of the R–Ch bond, it identifies a
positive (or a negative) σ-hole.17 Similarly, whenVS,min > 0 (orVS,min < 0) on a specific region, it
signifies an electrophilic (or nucleophilic) site. BothVS,max and VS,min were
calculated using Multiwfn,70 and the MESP plots were
generated using AIMAll71 with the wavefunctions
generated using the [MP2/aug-cc-pVTZ] geometries. The counterpoise
method of Boys and Bernardi was invoked to account for the effect of
Basis Set Superposition Error (BSSE) on energy.72
QTAIM calculations were performed with [MP2/aug-cc-pVTZ] – a theory
that relies on the zero-flux boundary condition to partition atomic
domains in real space.64,73,74 The typical topological
properties such as the gradient paths, bond paths, bond critical points
(bcps) of the charge density (ρ b), the Laplacian
of the charge density (∇2ρ b)
and the total energy density (H b) were evaluated.
In addition, the delocalization indices, δ , between various
atom-atom pairs were evaluated for each system to gain insight into the
covalent nature of the various bonding interactions
involved.75,76
We examined the nature of the charge transfer delocalization energiesE2 between ”filled” (donor) Lewis-type NBOs and
”empty” (acceptor) non-Lewis type NBOs in several complexes – all
within the second-order framework of NBO analysis (Eqt.
1).63 In Eqn. 1, qi is the
donor orbital occupancy, εi andεj are diagonal elements (orbital energies)
associated with each donor NBO (i ) and acceptor NBO (j ),
respectively, and F(i,j) is the off-diagonal NBO Fock matrix
element. These calculations were carried out within the Hartree–Fock
(HF) level theory using Gaussian 09’s NBO Version
3.1.63