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Received 19 Oct 2016 | Accepted 3 Jan 2017 | Published 21 Feb 2017 DOI: 10.1038/ncomms14522 OPEN

NO3 anions can act as Lewis acid


in the solid state
Antonio Bauza1, Antonio Frontera1 & Tiddo J. Mooibroek2,3

Identifying electron donating and accepting moieties is crucial to understanding molecular


aggregation, which is of pivotal signicance to biology. Anions such as NO3 are typical
electron donors. However, computations predict that the charge distribution of NO3 is
anisotropic and minimal on nitrogen. Here we show that when the nitrates charge is suf-
ciently dampened by resonating over a larger area, a Lewis acidic site emerges on nitrogen
that can interact favourably with electron rich partners. Surveys of the Cambridge Structural
Database and Protein Data Bank reveal geometric preferences of some oxygen and sulfur
containing entities around a nitrate anion that are consistent with this p-hole bonding
geometry. Computations reveal donoracceptor orbital interactions that conrm the coun-
terintuitive Lewis pacidity of nitrate.

1 Department of Chemistry, Universitat de les Illes Balears, Carretera de Valldemossa km 7.5, 07122 Palma, Baleares, Spain. 2 Faculteit der

Natuurwetenschappen, Wiskunde en Informatica, van t Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands. 3 School of Chemistry, Faculty of Science, University of Bristol, Cantocks Close, Bristol BS8 1TS, UK. Correspondence and
requests for materials should be addressed to A.F. (email: toni.frontera@uib.es) or to T.J.M. (email: t.j.mooibroek@uva.nl).

NATURE COMMUNICATIONS | 8:14522 | DOI: 10.1038/ncomms14522 | www.nature.com/naturecommunications 1


ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14522

range of weak to strong hydrogen bonding18. An atoms-

M
olecular recognition phenomena are of pivotal signi-
cance in biology and dene the eld of supramole- in-molecules (AIM) analysis19 revealed a single-bond critical
cular chemistry14. Well-known intermolecular forces point between the nitrate N-atom and N/Cl of the interacting
include hydrogen and halogen bonding. Both have recently been partner (see Supplementary Figs 1 and 2).
contextualized as instances of s-hole bonding57. A s-hole can
be seen as a region of electropositive potential on a molecule that
Database analyses. Encouraged by these computational predic-
is roughly located on the unpopulated s* antibonding orbital of a
tions we wondered if there might be any experimental evidence
covalent bond. Typical examples of such s-holes can be found
for p-hole bonding with NO3 within the crystal structures
along the OH/CBr vectors in phenol or bromobenzene8. In
deposited in the CSD20 and the Brookhaven PDB21. More
analogy, a p-hole can be seen as a region of electropositive
in particular we were interested in ascertaining any possible
potential on a molecule that is roughly located on an unpopulated
directional behaviour22 of this interaction. We limited our
p* antibonding orbital of a p bond, for example, on carbonyls or
inquiries to uncoordinated nitrate anions to simplify our
p-acidic aromatics like hexauorobenzene811.
analysis. Also, if uncoordinated nitrate can act as Lewis acid, it
It is known that p-holes in nitro-compounds such as
is likely that coordinated nitrate will do so as well (and likely even
nitrobenzene (Fig. 1a) can be directional in the solid state8,12.
more so). Initial data sets were retrieved by limiting the
The magnitude of such p-holes can be enhanced when the  O N    El.R. distance to 5 (El.R. electron rich atom).
3
negative charge is diluted over a larger area, for example, if the
The data are thus conned within a sphere with 5 radius but
O-atoms interact with water or NaCl (Fig. 1b,c). We wondered to
willdue to symmetrybe represented as contained within a 5
what extend this rationale applies to nitrate anions and if perhaps
high and 10 wide hemisphere. The interacting entities
this anion might function as a p-hole to enable so-called
considered here are H2O, O X (X any atom for the CSD
(pseudo)anti-electrostatic interactions13,14. This seems counteri-
data and only C for the PDB data) and S (CSD)/SC (PDB).
ntuitive, yet the charge distribution in naked NO3 is anisotropic
Further details of the methods employed can be found in the
and reminiscent of a p-hole (Fig. 1d)15. Dampening the charge
Methods section.
with water further exposes the p-hole (Fig. 1e), and the potential
Shown in Fig. 3 are the distributions in three dimensional space
even becomes positive at 25 kcal mol  1 in charge-neutral
of O-atoms in H2O (left of panel), O X/C (middle of panel) and
[LiNO3  2H2O] (Fig. 1f). We found that such an exposed
of S-atoms (right of panel) around a nitrate anion as found within
p-hole on NO3 can form complexes with electron rich
the CSD (top of panel) and the PDB (bottom of panel). These
partners with calculated energies of up to 31.6 kcal mol  1.
distributions are remarkably similar in both databases. Water
Statistical evaluations of the Cambridge Structural Database
molecules seem to cluster near the O-atoms and are relatively
(CSD) and the Protein Data Bank (PDB) indeed reveal some
in-plane with NO3 , suggesting that hydrogen bonding dom-
geometric preferences consistent with this p-hole bonding
inates. On the other hand sp2hybridized O-atoms and S-atoms
geometry. Several examples lifted from these databases are
tend to cluster perpendicular to the NO3 plane, above/below the
highlighted, where the Lewis acidity of NO3 seems evident.
nitrates N-atom. This clustering is consistent with a p-hole
bonding geometry. Four dimensional (4D) density plots
(Supplementary Fig. 3) further conrm these trends and
Results
directionality plots clearly indicate that NO3 p-hole bonding is
Computational models. To further evaluate a possible p-hole on
about as directional as NH    paryl hydrogen bonding
NO3 computationally, we designed trisurea based receptors that
(Supplementary Fig. 4)8,2225. Also, signicant amounts of data
fully surround a nitrate anion with hydrogen bond donors
directly above/below N (1321%) consist of overlapping van der
(Fig. 2a, related [2 2] macrocycles are known)16,17. This might
Waals shells (Supplementary Fig. 5).
mimic nitrate anions in crystal structures, which are typically
enclosed by several (charge assisted) hydrogen bonds and/or
charge compensated by coordination to a metal ion. In the Concrete examples. Finally, we selected several examples of
anionic complexes 2 (Fig. 2b), the p-hole region represents a crystal structures displaying short  O3N    El.R. distances and
relative electron depletion and is positive at 25 kcal mol  1 in geometries consistent with a p-hole interaction (El.R. electron
the anionic species 2c. rich atom). Shown in Fig. 4 (top) are charge-neutral selections of
Next, we computed some complexes of 2 with electron the small salts EVIKEA26, ORUHOZ27 and BIDHAX28 lifted
rich partners and found that complexes [2c    NCCH3]  from the CSD. In all these instances the  O3N    El.R. distances
and [2c    Cl]2 gave interaction energies of  7.7 and are within the sum of the van der Waals radii of the elements
 31.6 kcal mol  1, respectively (see Supplementary Note 1 and involved and the nitrate anion is concurrently entrenched in a
Supplementary Tables 1 and 3, for details). These values are in the hydrogen bonding pocket (not shown).

+18
+25 +46

112 75 +27

a b c d e f
Figure 1 | Some molecular electrostatic potential maps (MEPs) of nitrobenzene and nitrate. Nitrobenzene (a) interacting with water (b) and NaCl
(c) and NO3 (d) interacting with three water molecules (e) or one Li and two water molecules (f). Geometries were optimized with DFT/BLYP/6-31G*
and MEPs and energetic values (in kcal mol  1) generated at the MP2/6-311 G** level of theory. The colour codes of the MEPs represent more negative
(red) to more positive (blue) potentials in between: 36 and 24 (a,b); 0 and 48 (c);  155 and  122 (d);  102 and  75 (e);  48 and 27 (f).

2 NATURE COMMUNICATIONS | 8:14522 | DOI: 10.1038/ncomms14522 | www.nature.com/naturecommunications


NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14522 ARTICLE

a R
R R
R
b
2a 2b 2c
2a, R = H
N 2b, R = F
O NH H HN O
2c, R = CN 20 5 +25
NH O O HN
R N R
NH O HN
R H H R
N N
R R
O
R R

Figure 2 | Nitrate complexes with trisurea macrocycles. (a) Schematic drawing of 2. (b) MEPs of 2a, 2b and 2c. Geometries were optimized with DFT/
BLYP/6-31G* and MEPs and energetic values (in kcal mol  1) generated at the B3LYP/6-31G* level of theory. The colour codes of the MEPs represent more
negative (red) to more positive (blue) potentials in between:  80 and  18 (2a);  72 and  1 (2b);  80 and 35 (2c).

O3N...OH2 CIFs = 2,649 O3N...O=X O3N...S


CIFs = 5,787 CIFs = 732
5 5 5
CSD N = 10,526 N = 26,364 N = 2,139
4 4 4

3 3 3
Z axis

2 2 2

1 1 1
0 4 5 0 4 5 0 4 5
5 4
3 2 2 3 5 4
3 2 2 3 5 4
3 2 2 3
1 1 1
1 0 1 0 1 0 1 0 1 0 1 0
1 2 xis 1 2 xis 1 2 x is
Xa
xis
2 3 4
3 Ya Xa
xis
2 3 4
3 Ya Xa
xis
2 3 4
3 Ya
4 5 4 5 4 5
5 5 5

O3N...OH2 PDBs = 1,437 O3N...O=C PDBs = 1,560 O3N...SC PDBs = 120


5 5 5
PDB N = 24,218 N = 20,058 N = 840
4 4 4

3 3 3
Z axis

2 2 2

1 1 1
0 4 5 0 4 5 0 4 5
5 4
3 2 2 3 5 4
3 2 2 3 5 4
3 2 2 3
1 1 1
1 0 1 0 1 0 1 0 1 0 1 0
1 2 xis 1 2 xis 1 2 x is
Xa
xis
2 3 4
3 Ya Xa
xis
2 3 4
3 Ya Xa
xis
2 3 4
3 Ya
4 5 4 5 4 5
5 5 5

Figure 3 | Database analyses. Distribution of the O- or S-atoms (belonging to water (left of panel), OX/OC (middle of panel) or S/SC (right of panel)
entities) around an uncoordinated nitrate anion as found within the CSD (top of panel) and PDB (bottom of panel) and contained by the parameter
nitrateN    O/Sr5 . X any atom.

EVIKEA ORUHOZ BIDHAX

3.161

43 kcal mol1 Ag(I)


3.325
3.376

62 kcal mol1 97 kcal mol1

Gly-51 (A)
Chain A

2.70 Arg-54
3EZH
2.81
Arg-54 H2O-36
85 kcal mol1

Chain B Gly-51 (B)

Figure 4 | Examples of crystal structures exhibiting nitrate p-hole interactions. Top of panel: three structures found in the CSD. Bottom of panel:
example lifted from the PDB with a zoom-in of the nitrate ligands binding pocket (residues r4 displayed). All these selected fragments were computed
at the BP86-D3/def2TZVP level of theory leading to the indicated energies (dominated by charge compensation). Colour code: carbon grey,
hydrogen white, nitrogen blue, oxygen red, sulfur yellow, chloride green, bromide brown and silver light grey. See Supplementary Table 3 for
Cartesian coordinates of selected (and computed) fragments.

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ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14522

Protein structure 3EZH (ref. 29; Fig. 4, bottom) consists of two {0,c,0} f
isostructural chains (A and B) that are stuck together surrounding O1
a central nitrate ligand. The NO3 anion is H-bonded to two c
b e Y
arginine residues (Arg-54) with N    N distances of about {0,0,0} {I,m,n} Z
3 . In addition, the carbonyl O-atoms of two glycine residues N
(Gly-51) appear to interact with the nitrate ligands p-hole. a
d X
Indeed, the interatomic N    O distances (2.70 and 2.81 ) are 2O O3 {0,0,0}
well within the van der Waals benchmark for N O (3.07 ). {x,y,0}
The AIM analyses of these four examples revealed a clear bond Figure 5 | Query used for PDB and CSD search. Relevant interatomic
critical point between the nitrates N-atom and the interacting distances (e.g. af) and triatomic angles (e.g. O1-N-O3) were retrieved from
electron donor for both EVIKEA and 3EZH (Supplementary the databases in order to construct a model of the central NO3 anion and
Fig. 6). A natural bond orbital analysis (with a focus on to obtain the Cartesian coordinates (l,m,n) of the interacting atom (large
second order perturbation)30 for each example revealed electron red sphere) as is detailed in the methods section. The XYZ axis on the right
donation from a lone pair of electrons (LP) into an unoccupied is meant as a guide to the eye, centered on {0,0,0} and with the Y axis in
orbital of the nitrate anion (for example, 0.35 kcal mol  1 for the line with N-O1.
LP(C O)-p*(NO3 ) in 3EZH, see Supplementary Note 2 for
details). This conrms that the NO3 anion can act as a Lewis
acid in these examples.

Discussion
The above computations, database analyses and examples clearly
point out that a genuine p-hole might persist on a nitrate anion
and that NO3 may thus act as a Lewis acid to form formally
(pseudo)anti-electrostatic interactions in the solid state. One
naturally wonders what other anions might be capable of
displaying such behaviour (using other atoms than hydrogen).
It occurred to us that nitrate actually has a rather unique set of
properties that set it apart from other common anions in this Figure 6 | Nitrate model and the volumes used to access directionality.
respect: NO3 is fairly polarized and further polarizable, not so The central nitrate model was constructed with Autodesk Inventor
charge-dense and nitrate is at, rendering the p-hole sterically Professional 2016 using the average distances/angles as observed in a
accessible (see Supplementary Note 3 for a discussion of possible database and with literature van der Waals radii. The gray bodies illustrate
candidates). As nitrate anions are very common in chemistry and the cylindrically trimmed hemispheres at r 1, 2, 3, 4, and 5 used to
biology, we anticipate that our nding may serve as a (retro- assess directionality.
spective) guide to interpret chemical data where nitrate anions are
the tip of a tetrahedron (see Fig. 5) so that Cartesian Coordinates {X, Y, Z} of all the
involved; for example, orthonitrate formation31,32, cases where atoms could be derived as follows: the N-atom was taken as the centre {0, 0, 0}, O1
NO3 anions may be a structural determinant (as in 3EZH), or in as {0, c, 0}, O3 as {x, y, 0} and the interacting atom at {l, m, n}. Distances af were
transport phenomena involving this ubiquitous anion33,34. measured, from which y, x, m, l and n can be derived using equations (15),
respectively.

Methods a2 c2  b2
y 1
Computations. The energies of all complexes included in this study were 2c
computed at the BP86-D3/def2-TZVP level of theory. The calculations have been
performed by using the programme TURBOMOLE version 7.0 (ref. 35). For the p
x a2  y2 2
calculations we have used the BP86 functional with the latest available correction
for dispersion (D3)36. The optimization of the molecular geometries has been
performed imposing the C3v symmetry point group. The Baders Atoms in c2 e2  d 2
molecules theory has been used to study the interactions discussed herein by m
2c 3
means of the AIMall calculation package37. X-value

Queries used to retrieve data from the CSD and PDB. The CSD (version 5.37 a2 e2  f 2  2my
(November 2015 including two updates) was inspected using ConQuest (version l
2x 4
1.18) on the 3rd of April 2016. The PDB was inspected with the online Query Y-value
Sketcher of Relibase version 3.2.1 on the 2nd of March 2016. For the CSD search, a
subset of data was rst created containing uncoordinated nitrate anions (9,439 p
crystallographic information les). All searches of the CSD were limited to high n e2  m2  l2
quality structure (Rr0.1) and powder structures and structures containing errors 5
Z-value
were omitted. The NO bonds were set to any type. All covalent bond distances
and selected triatomic angles were collected to reconstruct the average models Thus, the distance between the interacting atom and the plane dened by
(one for the PDB data and one for the CSD data) used for accessing directionality O1NO3 is n, that is, the Z-value. With this and the N    interacting atom
(see below). The interatomic distance between the interacting atom (O in O C or distance (e) the parallel displacement parameter (r) could be derived according to
OH2; S in S, SC or SCC; or F, Cl, Br, I, At, O, S, Se, Te, N, P or As in El.R. (electron equation (6):
rich) and the nitrates N-atom (e, highlighted in red in Fig. 5) was set as r5 so p
that the data was conned within a 10 diameter sphere centred on N. In the PDB r e2  n2 6
study the NO3 central unit was marked as a ligand and the interacting atom(s) were
marked as part of a protein, or in the case of water the interacting O was specied With this procedure the sign of n (that is, the Z-axis) is always positive, meaning
as water. that data in one half of the sphere were reected to the other half of the sphere to
obtain the data within a 5 high and 10 wide hemisphere. To obtain all {X, Y, Z}
coordinates of the average models, it was assumed that O2 was coplanar with
Deriving XYZ coordinates and r. The interatomic distances between the inter- O1NO3. The averages of relevant distances and angles were then used together
acting atom and O1 and O3, as well as the O1O3 distance were also collected with the rules of sine and cosine to obtain the {X, Y, Z} coordinates. The relative
(set to r8 in the PDB search and left unspecied for the CSD search). The standard deviations of the parameters used were typically below 5%. A numerical
triangle formed by O1NO3 was chosen as the base, and the interacting atom as overview of the data retrieved is shown in Supplementary Table 2.

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NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14522 ARTICLE

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6 NATURE COMMUNICATIONS | 8:14522 | DOI: 10.1038/ncomms14522 | www.nature.com/naturecommunications

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