Observations of tetrel bonding between sp3-carbon and THF

Article abstract of DOI:10.1039/d0sc01559h

We report the direct observation of tetrel bonding interactions between sp³-carbons of the supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas and crystalline phase. The intermolecular contact is establishedvias-holes and is driven mainly by electrostatic forces. The complex manifests distinct binding geometries when captured in the crystalline phase and in the gas phase. We elucidate these binding trends using complementary gas phase quantum chemical calculations and find a total binding energy of -11.2 kcal mol^-1for the adduct. Our observations pave the way for novel strategies to engineer sp³-C centred non-covalent bonding schemes for supramolecular chemistry.

Full text of DOI:10.1039/d0sc01559h

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S. R. Domingos, A. P. Davis and T. J. Mooibroek, Chem. Sci., 2020, DOI: 10.1039/D0SC01559H.
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Observations of tetrel bonding between sp3–carbon and
THF
V. L. Heywood,[b] T. P. J. Alford,[b] J. J. Roeleveld,[a] S. J. Lekanne Deprez,[a] A. Verhoofstad,[a] J.
I. van der Vlugt,[a,c] S. R. Domingos,[d] M. Schnell,[d, e] A. P. Davis[b] and T. J. Mooibroek*[a]
[a] J. J. Roeleveld, S. J. Lekanne Deprez, A. Verhoofstad, Dr. J. I. van der Vlugt, Dr. T. J. Mooibroek
van ‘t Hoff Institute for Molecular Sciences
Universiteit van Amsterdam
Science Park 904, 1098 XH Amsterdam, The Netherlands
E-mail: t.j.mooibroek@uva.nl
[b] V. L. Heywood, T. P. J. Alford, Prof. Dr. A. P. Davis
School of Chemistry
University of Bristol
Cantock’s Close, Bristol, BS8 1TS, United Kingdom
[c] Dr. J. I. van der Vlugt
Institute of Chemistry
Carl von Ossietzky University Oldenburg
Carl von Ossietzky-Straße 9-11, D-26211 Oldenburg, Germany
[d] Dr. S. R. Domingos, Prof. Dr. M. Schnell
Deutsches Elektronen-Synchrotron (DESY)
Notkestraße 85, 22607 Hamburg, Germany
[e] Prof. Dr. M. Schnell
Institut für Physikalische Chemie
Christian-Albrechts-Universität zu Kiel
Max-Eyth-Str.1, 24118 Kiel, Germany
Supporting information for this article is given via a link at the end of the document.
Keywords
sp3-C tetrel bonding interactions • supramolecular chemistry • crystallography • rotational
spectroscopy • DFT calculations and analysis
Abstract

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We report the direct observation of tetrel bonding interactions between sp3-carbons of the
supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas
and crystalline phase. The intermolecular contact is established via σ–holes and is driven mainly
by electrostatic forces. The complex manifests distinct binding geometries when captured in the
crystalline phase and in the gas phase. We elucidate these binding trends using complementary
quantum chemistry calculations and find a total binding energy of –11.2 kcal∙mol-1 for the adduct.
Our observations pave the way for novel strategies to engineer sp3-C centred non-covalent
bonding schemes for supramolecular chemistry.

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Introduction
Non-covalent interactions are key forces that drive phenomena such as host-guest chemistry,
2
molecular aggregation, crystallization and protein folding.1,
In recent years, important
intermolecular interactions like hydrogen and halogen bonding1, 3-7 have been contextualized as
σ-hole interactions.8-10 A σ-hole can be seen as a Lewis acidic site along the vector of a covalent
bond, the location of which coincides with the σ* orbital of that bond. The extreme outcome of a
σ-hole interaction can be the breaking and/or making of a σ bond, such as in the formation of [I3]–
from molecular I2 and I–.11, 12 A similar rationale can be applied to so-called ‘π-hole interactions’
involving electron deficient aromatic rings,13, 14 or polarized double bonds with related covalent
bond-forming chemistry such as in aldol-type reactions. In principle, σ- and π-hole interactions
should be available with all the non-metallic elements of the periodic table. This includes carbon;15-
17 an element of central importance to life and ubiquitous presence in synthetic chemistry.
One might thus wonder to what extend carbon can be exploited as locus of Lewis acidity to
establish ‘tetrel-bonding interactions’ (in analogy to halogen- and chalcogen-bonds).18 Such
interactions are well-known for sp2-hybridized C-atoms in carbonyls19-26 and have recently been
reported for the sp-hybridized C-atoms of (coordinated) acetonitrile,27 carbon monoxide28 and
carbon dioxide.29-32 Non-covalent interactions with sp3-hybridized carbon atoms are implicated in
the advent of canonical SN2 nucleophilic displacement reactions12, 33-35 and can persist with methyl
groups in crystal structures.36-38
However, a supramolecular synthon to predictably generate directional tetrel-bonding interactions
centred on sp3-C has not yet been experimentally disclosed. We envisaged that 1,1,2,2-
tetracyanocyclopropane (TCCP) derivatives could fulfil this role.39, 40 These rings are synthetically
viable and contain a sterically accessible electrophilic site located roughly on the two sp3 C-atoms
in the (NC)2C–C(CN)2 fragment. This is exemplified by the molecular electrostatic potential (MEP)
map of 3,3-dimethyl-TCCP (1) shown in Figure 1. The calculated σ-hole potential of +44 kcal·mol-1
lies in-between the σ-holes of water (+55 kcal·mol-1) and ammonia (+35 kcal·mol-1), which are
prototypical σ-hole (i.e. hydrogen bond) donors. The Lewis acidic site of 1 should thus be able to
bind with an electron-rich partner such as the lone pair electron cloud on tetrahydrofuran (THF,
estimated at –40 kcal·mol-1).39-41 Here we report on the verification of this hypothesis by
synthesizing 1 and showing that –as anticipated– 1 binds to THF via intermolecular sp3-C···O
interactions, both in the crystalline state and in the gas phase.

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Figure 1. Molecular Electrostatic Potential maps (MEP) of water, ammonia, 3,3-dimethyl-TCCP (1) and tetrahydrofuran
(THF) calculated at the DFT/B3LYP-D3/def2-TZVP level of theory. The MEP is colour coded from electropositive (blue)
to electronegative (red), and the indicated potentials are in kcal·mol-1.
Results and Discussion
Cyclopropane 1 was readily prepared in a one-pot cascade reaction from acetone, malononitrile
and molecular bromine (Scheme 1). Presumably, cyclization to 1 proceeds from an intermediate
formed by the nucleophilic attack of in situ generated [BrC(CN)2]– on the Knoevenagel
condensation product of acetone and malononitrile.42 The yield of our procedure (83%) is higher
than those reported before42-48 (max. 72%).47 All literature procedures with a yield in excess of
50%42, 43, 45-48 (maximum 72%)47 use a two-step approach starting from an activated malononitrile
derivative42, 43, 45-47 and/or use electrochemical synthesis.47, 48
Scheme 1. One-pot cascade synthesis of 1.
Single crystals suitable for X-ray diffraction measurements (see ESI for details) were obtained by
slow evaporation of a solution of 1 in THF. The molecular model of [1···THF] resulting from the
diffraction study is shown in Figure 2a. All the intramolecular distances and angles within this

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structure can be considered as normal (not shown).49 The plane running through the O- and C-
atoms of the THF molecule is roughly coplanar with the cyclopropane ring plane in 1 (plane – plane
= 8.2°). Interestingly, the oxygen atom of the THF molecule is directed towards C1/C3/C4 of the
cyclopropane ring in 1, with very short intermolecular distances, in particular sp3-C1···O1 of 3.007
Å (C3/C4 ···O1 = 3.1 Å, not shown). This is 0.213 Å within the van der Waals radii of O (1.52 Å)
and C (1.70 Å) and thus consistent with a bonding interaction.12, 27, 39, 40, 50 Further stacking of
[1···THF] in the crystal is aided by weak N1/N2···C1/C3/C4 interactions (max. 0.067 Å van der
Waals overlap, see Figure S3).§
Figure 2. Left: single crystal X-ray diffraction structure of [1···THF] with heavy atoms represented as thermal ellipsoids
drawn at 50% probability and hydrogen atoms drawn as spheres with 0.15 Å radius (the unit cell was expanded along
a two-fold symmetry axis running through C2 and O1). Right: Capped sticks representation of the energy minimum (ΔE
= –11.2 kcal·mol-1) of [1···THF] found by DFT (B3LYP-D3(BJ)/def2-TZVP) and consistent with gas phase microwave
spectroscopy data. carbon = grey, nitrogen = blue, oxygen = red and hydrogen = white.
A DFT optimization at the B3LYP51, 52-D3(BJ)53/def2-TZVP54, 55 level of theory of the atomic
coordinates found in the crystal structure converged at a nearly identical structure (see Figure
S5). The interaction energy (ΔE) was computed to be –10.1 kcal/mol. This is much larger than
interactions of dimethyl ether halogen bonded to I–C6F5 (–5.6 kcal/mol) or hydrogen bonded to
water (–6.7 kcal/mol) at this same level of theory.37, 56 Interestingly, the [1···THF] structure shown
in Figure 2b was found to be 1.1 kcal/mol more stable, representing the true energetic minimum
with ΔE = –11.2 kcal/mol (see also Figure S6). The structure is similar to the crystal structure but
with the THF oriented almost perpendicular to the cyclopropane plane, with plane – plane = 83.8°.
The distances between the THF-O and the two sp3 (NC)2C–C(CN)2 atoms display up to 0.297 Å
van der Waals overlap, which is 0.084 Å more than observed in the crystal structure. This

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difference likely originates from the lack of any other interactions in the idealized gas phase
computation versus various other potential weak interactions within the crystal of [1···THF].
Rotational spectroscopy is the technique to experimentally discriminate between the two relative
orientations of [1···THF] (Figure 2) that are so close in energy in the gas phase calculations (1.1
kcal/mol). Thus, we conducted chirped pulse Fourier transform microwave (CP-FTMW)
spectroscopy57, 58 to assign the geometry of [1···THF] in the gas phase (see ESI for details). Shown
in Table 1 are spectroscopic parameters extracted from this experiment together with predicted
values based on DFT calculations of [1···THF] with ‘coplanar’ or ‘perpendicular’ THF orientations.
The experimental rotational constants (in particular B and C) provide a conclusive assignment of
the [1···THF] complex in the ‘perpendicular’ orientation, which is also the DFT-energetic minimum
(right-hand side of Figure 2).
Table 1. Rotational constants A, B, C, quartic centrifugal distortion constant DJ, and dipole moment components μi, for
[1···THF] obtained from high resolution rotational spectroscopy and compared to values predicted with DFT.[a]
DFT[c]
Experiment[b]
coplan
ar
perpendicul
ar
A / MHz
B / MHz
632.927(43) 633.88
635.59
341.81
342.56932(9 326.09
3)
C / MHz
316.7863(10 325.50
)
317.89
DJ / kHz
|μa| / D
|μb| / D
|μc| / D
N[d]
0.0135(35)
observed
not observed
not observed
46
-
2.6
0.0
0.0
-
-
2.6
0.0
0.0
-
σ / kHz[e]
22.1
-
-
ΔΔE
-
+1.1
0
(kcal/mol)[
c]

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[a] For the purpose of structure determination of the [1···THF] adduct in the gas phase, the hyperfine structure observed
in the rotational spectrum has not been fitted entirely and only centre frequencies are used for the reported fit. As such
the quadrupole coupling constants for the four nitrogen nuclei are not reported at this moment. This second layer of
analysis of the spectrum goes beyond the scope of this work and will be reported later in a separate manuscript. [b]
The errors for the measured values are standard errors. The experimental frequency accuracy is 25 kHz. [c] The
predicted rotational constants were obtained from DFT calculation at the B3LYP-D3(BJ)/def2-TZVP level of theory.
‘Coplanar’ and ‘perpendicular’ refer to the orientation of the THF ring relative to the cyclopropane ring in 1 (see also
Figure 1); [d] number of lines included in the fit. [e] standard deviation of the fit.
To date we were unable to quantify tetrel bonding interactions with 1 in solution, but we did
observe a very large and unusual solvent dependency of the 1H and 13C NMR resonances of 1
(detailed in Figure S7 and Table S4). For example, the methyl protons of 1, which are  to CN,
span a range of 1.39 p.p.m. passing from benzene through toluene, acetonitrile, methanol and
chloroform, to acetone. In comparison, the ethoxy methyl protons in ethyl acetate and diethyl
ether vary by just 0.34 and 0.12 p.p.m., despite being closer to functional groups. These results
seem to suggest strong and geometrically specific interactions between 1 and most solvent
molecules. Based on these preliminary observations we anticipate that future studies will
demonstrate tetrel bonding interactions with tetracyanocyclopropane derivatives in solution.
To gain more insight into the physical origins of the [1···THF] adduct, the ‘perpendicular’ structure
59-61
was subjected to a Morokuma-Ziegler inspired energy decomposition,37,
an ‘atoms-in-
molecules’62, and a non-covalent interaction analysis.63 The energy decomposition analysis
revealed that the interaction is mainly electrostatic in origin (52.7%) followed by dispersion
(30.7%) and orbital interactions (16.8%). Interestingly, orbital mixing occurred between the HOMO
of THF and the LUMO of 1 (–3.86 kcal·mol-1 stabilization) and between the HOMO-1 of THF and
the HOMO of 1 (–4.80 kcal·mol-1 stabilization, see Figure S8 for details). The ‘atoms-in-molecules’
analysis of [1···THF] shown in Figure 3a reveals several bond critical points (bcp’s) between the
N-atoms of 1 and several CH hydrogens of THF, indicating very weak hydrogen bonding
interactions (ρ ≈ 0.005 a.u.). The densest bcp of ρ = 0.0115 a.u. is present between the THF O-
atom and one of the sp3 (NC)2C–C(CN)2 atoms (highlighted in yellow).§§ In line with these results,
the NCI plot shown in Figure 3b clearly reveals that there are two sp3–C···O interactions that are
mainly electrostatic in origin (blue), and that the C–H···N interactions are mainly dispersive
(yellow/green).

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Figure 3. Geometry optimized structures (B3LYP-D3/def2-TZVP) and ‘atoms-in-molecules’ analysis of [1···THF] (a, see
also Figure 2) and [1···cyclopentane] (c, obtained after in silico OCH2 mutation and optimization). The bond densities
of the intermolecular bond critical points are represented by small red spheres (ρ in a.u. x 100). b) and d) show a non-
covalent interactions (NCI) analysis using NCIPLOT. Isolevel = 0.3 and regions in blue are mainly electrostatic
interactions, in green are van der Waals dispersive forces and repulsions are in red.
For comparison purposes, a cyclopentane adduct was calculated after in silico OCH2 mutation
and geometry optimization of structure [1···THF]. This resulted in the structurally similar
[1···cyclopentane] adduct shown in Figure 3c (see also Figure S9). The ‘atoms-in-molecules’
analysis of this adduct reveals only two C–H···C≡N bcp’s (ρ ≈ 0.0055 a.u.). The adduct is also
much less stable with ΔE = –4.0 kcal/mol, which is mainly driven by dispersion (59.4%) followed
by electrostatic interactions (22.2%). The NCI analysis of this adduct depicted in Figure 3d clearly
shows that this adduct is only held by dispersive C–H···N interactions (green).
Summary and concluding remarks
In summary, it was shown that 1 can form [1···THF] complexes in the crystalline state and in the
gas phase with a calculated interaction energy of up to –11.2 kcal/mol. These complexes are held

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together by strong polar interactions between the de facto Lewis acidic site in between the sp3-
hybridized C-atoms of 1 and the Lewis basic THF-O. These results demonstrate that tetrel-
bonding interactions with sp3-carbon centres can indeed be used to engineer supramolecular
complexes, thus paving the way for their exploration in other molecular disciplines, e. g.
supramolecular chemistry, crystal engineering and medicine.
Conflicts of interest
The authors declare no conflict of interest.
Acknowledgements
TJM thanks NWO (VIDI project 723.015.006) and the EPSRC (EP/I028501/1) for funding. MS
acknowledges financial support by the Deutsche Forschungsgemeinschaft in the context of the
priority program SPP1807 (SCHN1280/4-2).
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Chemical Science
Page 12 of 12
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DOI: 10.1039/D0SC01559H
Supramolecular adducts were generated using sp3-C centred tetrel bonding interactions, both in
the crystalline state and in the gas phase. Calculations using density functional theory revealed
interaction energies up to –11.2 kcal·mol-1 and showed that these adducts are held together
mainly by electrostatics.