Substituent-Controlled Tailoring of Chalcogen-Bonded Supramolecular Nanoribbons in the Solid State

Article abstract of DOI:10.1021/acs.cgd.0c01318

In this work, we design and synthesize supramolecular 2,5-substituted chalcogenazolo[5,4-β]pyridine (CGP) synthons arranging in supramolecular ribbons at the solid state. A careful choice of the combination of substituents at the 2- and 5-positions on the

Full text of DOI:10.1021/acs.cgd.0c01318

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Article
Substituent-Controlled Tailoring of Chalcogen-Bonded
Supramolecular Nanoribbons in the Solid State
Nicolas Biot, Deborah Romito, and Davide Bonifazi*
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ABSTRACT: In this work, we design and synthesize supramolecular 2,5-substituted chalcogenazolo[5,4-β]pyridine (CGP)
synthons arranging in supramolecular ribbons at the solid state. A careful choice of the combination of substituents at the 2- and 5-
positions on the CGP scaffold is outlined to accomplish supramolecular materials by means of multiple hybrid interactions,
comprising both chalcogen and hydrogen bonds. Depending on the steric and electronic properties of the substituents, different
solid-state arrangements have been achieved. Among the different moieties on the 5-position, an oxazole unit has been incorporated
on the Se- and Te-congeners by Pd-catalyzed cross-coupling reaction and a supramolecular ribbon-like organization was consistently
obtained at the solid state.
developments in catalysis23−28 and sensing,25,29 EB inter-
INTRODUCTION
■
actions have been mainly exploited in crystal engineering,30,31
In recent years, crystal engineering has soared interest in the
providing a distinctive series of persistent recognition
scientific community, given its valuable implications in the
motifs.32−35 The structure of the most part of these
rational design of functional materials.1−5 Several studies have
chalcogen-bonding synthons builds on a heterocyclic scaffold,
focused on the use of supramolecular bonds, selectively
in which the chalcogen bond donors and acceptors are
involving recognition motifs to generate stable and predictable
proximal to each other,36−38 thus effectively developing
multidimensional networks in the solid state.6−10 Among the
several noncovalent interactions, hydrogen bonds embody the
macrocyclic39−41 and wire-like42,43 supramolecular architec-
main interaction occurring in biological systems,11,12 as well as
tures. Previous work done in our group with 2-substituted
benzo-1,3-chalcogenazoles described the formation of poly-
being used for many applications in chemistry and materials
meric structures achieved through single EB interactions.44,45
When using the chalcogenazolo[5,4-β]pyridine (CGP) mod-
ule, frontal double chalcogen bonds are obtained in the solid
state with high recognition fidelity when the Te chalcogen is
used.46 Notably, changing the derivatization in the 2-position
of the CGP ring has allowed the complexity of the molecular
assembly to be expanded, engineering organic solids through
science.13−16 However, over the past decades, there has been a
flourishing interest for a class of exotic noncovalent
interactions, namely, Secondary Bonding Interactions
(SBIs),17 as attractive alternatives to the ubiquitous hydrogen
bond in crystal engineering. SBIs’ nature relies on electrostatic
(explained in terms of σ-holes)18 and van der Waals
contributions, as well as on orbital mixing described as
n2(Y)→σ*(E-X) donation (X-E···Y), which involves non-
bonding electrons of the electron-donating atom Y and the
Received: September 25, 2020
Revised: November 18, 2020
empty antibonding σX−E located on the E atom.19 When the
*
central polarizable E atom belongs to Group VI of the periodic
table, the term chalcogen bonding (EB, known also as ChB) is
used to describe the interaction between a positively polarized
chalcogen atom and a Lewis base.20−22 Despite recent
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Figure 1. Representation of the design of 2- and 5-substituted CGP scaffold with the recognition modes expected by modulating the repulsive
interactions (e.g., steric or electrostatic) between the 2- and the 5-substituents (i.e., green and orange): frontal EB dimers (A), head-to-tail ribbon-
(B) and wire-like (C) organizations.
the co-crystallization of heteromolecular supramolecular
polymers, held by concurring chalcogen- and halogen-bonding
interactions.47 Building on these results, in this work, we
pursue the idea of expanding the functionalization space of the
CGP module in the 5-position. This would allow face-to-face
dimer association to be disrupted and originate new
recognition modes in the solid state (see Figure 1).
thiophenyl (Th), and CF3 moieties for the 2-position. To
describe the different combinations of substituents in the 2-
and 5-positions, the molecules are labeled as Y-E-R, where Y
stands for the substituent in the 5-position (schematized as an
orange sphere, Figure 1), E is the chalcogen atom of interest,
and R is the moiety in the 2-position (schematized as a green
sphere, Figure 1), respectively.
In our molecular engineering plan, the CGP modules
bearing the CF3 moiety in the 2-position and the bulkiest (Me)
and electronegative (Cl) groups in the 5-position (e.g., Me-Te-
CF3 and Cl-E-CF3) are expected to assemble in a head-to-tail
fashion. Similarly, oxazole-bearing Ox-E-CF3 is expected to
arrange head-to-tail in ribbon-like architectures, with the
oxazole ring further strengthening the association through
weak H-bonding interactions. On the other hand, when a
sizable group is added in the 2-position, the formation of wire-
like assemblies is expected (e.g., Cl-Te-R and I-Te-Ph). Given
that repulsive forces originating from the close proximity of the
substituents in the self-assembled structure could arise from
either steric or electrostatic contributions, electrostatic surface
potential (ESP) maps were computed to further understand
the contribution of the electrostatic component (see
Supporting Information (SI), Table S1 for the calculated
VS,max values).
Design of 2- and 5-Substituted CGP Derivatives. We
conjectured that, depending on the electronic and steric
properties of the substituents in the 2- and 5-positions, one
could disrupt the typical doubly chalcogen-bonded recognition
of a CGP-based derivative (recognition mode A, Figure 1) and
force the module to associate in a different fashion. For
instance, if the substituent in the 5-position (orange) sterically
clashes with that in the 2-position (green) in the frontal
arrangement, one could envisage that a head-to-tail recognition
mode is favored (e.g., B and C modes displayed in Figure 1).
In this arrangement, an EB is established between the N atom
of the chalcogenazole ring (Nc) and the chalcogen atom of a
neighboring CGP moiety. If no homo-repulsions are present
between the substituents in the 2-position (green), a
noncovalent ribbon-like organization, held together by a
combination of frontal hydrogen- and chalcogen-bonding
interactions, is expected to develop (mode B, Figure 1).
Finally, if all substituents would undergo homo- and hetero-
repulsions in the frontal arrangements, then the only possibility
would be for the motif to assemble into nonplanar chalcogen-
bonded wire-like assemblies (mode C, Figure 1), as previously
observed by us.45 Aiming at developing synthetically accessible
modules with high recognition fidelity, we have focused on the
preparation of Te-containing derivatives. Cl, I, and Me groups
were chosen as substituents for the 5-position, whereas phenyl,
RESULTS AND DISCUSSION
■
Synthesis. The synthesis started with the selective
bromination of the commercially available amines 1Me and
1Cl using N-bromo succinimide (NBS) in MeCN, which
provided compounds 2Me and 2Cl, respectively, in good and
excellent yields. Brominated amines 2Me and 2Cl were treated
with 1 equiv of n-BuLi, followed by the addition of 1 equiv of
B
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a
Scheme 1. Synthetic Pathway to 2,5-Functionalized CGP Derivatives
a
Reagents and conditions: (a) NBS, MeCN, r.t., 5 min; (b) 1. n-BuLi, THF, 0 °C, 10 min; 2. i-PrBu2MgLi·LiCl, 0 °C, 1 h; 3. E0, r.t., overnight; 4.
Se: K3Fe(CN)6, H2O, r.t., 10 min; Te: NH4Cl, H2O, air, r.t., 2 h; (c) 1. NaBH4, MeOH, THF, r.t., 1 h; 2. MeI, r.t., 1.5 h; (d) 1. (CF3CO)2O,
CH2Cl2, pyridine, 0 °C to r.t., overnight; 2. POCl3, DIPEA, 1,4-dioxane, reflux, overnight; (e) acyl chloride, CH2Cl2, pyridine, 0 °C to r.t.,
overnight; (f) POCl3, DIPEA, 1,4-dioxane, reflux, overnight; (g) AcCl, NaI, MeCN, 80 °C, MW, 12 h; (h) oxazol-2-ylzinc(II) chloride,
[Pd(PPh3)4] 10 mol %, THF, reflux, 2 h.
trialkyl magnesate (freshly prepared by mixing i-PrMgCl with 2
equiv of n-BuLi).48 Subsequent addition of the relevant freshly
grounded elemental chalcogen powder to the reaction mixture
led to the corresponding bischalcogenides 3X‑E in significantly
improved yields (28−55%) when compared to synthetic
protocols previously implemented by our group.46 The
synthesis of derivatives 4X‑E was completed by the reductive
cleavage of the dichalcogenide bond using NaBH4 and MeOH
in THF, followed by addition of MeI. To insert the CF3 moiety
in the 2-position, a one-pot amidation/dehydrative cyclization
reaction was performed on 4X‑E using Tf2O in a 1:1 mixture of
CH2Cl2 and pyridine, followed by the addition of POCl3 in a
1:1 DIPEA/dioxane solution under refluxing conditions to give
X-E-CF3. In parallel, Te-bearing amine 4Cl‑Te was converted
into amides 5Cl‑R upon reaction with the relevant acyl chloride
which, followed by cyclization in the presence of POCl3 in
DIPEA and dioxane, afforded Cl-Te-R in excellent yields.
Given the proved chemical compatibility of the CGP moiety
with Pd-catalyzed cross-coupling conditions, a Negishi cross-
coupling reaction was attemped to prepare Ox-Te-Ph starting
from chloro-derivative Cl-Te-Ph.49 Nevertheless, no con-
version was observed.
Thus, we moved our attention to the iodo-bearing congeners
as electrophilic substrates. As a result, cyclized products
bearing chlorine in the 5-position, i.e., Cl-E-CF3 and Cl-Te-
Ph, were transformed into iodo-containing I-E-CF3 and I-Te-
Ph using NaI in the presence of AcCl in MeCN at 80 °C under
microwave irradiation.50 Finally, reaction between the
iodinated derivatives and oxazol-2-ylzinc(II) chloride using
[Pd(PPh3)4] in THF at reflux afforded targeted molecules Ox-
E-R in good yields (Scheme 1). All compounds were fully
1
characterized by H, 19F, and 13C NMR spectroscopy, IR, mp,
and HR-mass spectrometry (see SI).
Solid-State Self-Assembly. The association properties of
the 2,5-functionalized CGP derivatives in the solid state were
probed by X-ray analysis of single crystals, generally obtained
C
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Figure 2. X-ray structures and their respective ESP maps of (a) Me-Te-CF3, (c) Cl-Se-CF3, and (e) Cl-Te-CF3; π−π stacking arrangements of (b)
Me-Te-CF3, (d) Cl-Se-CF3, and (f) Cl-Te-CF3. Space group: P21/m. Crystallization solvent: CHCl3.
by slow evaporation of a CHCl3 solution. Governed by
fluorophilic domains established by the CF3 moiety in the 2-
position, crystals of Me-Te-CF3 and Cl-E-CF3 are isomorphs,
despite bearing either a Me or Cl atom in the 5-position, either
Se or Te atoms. Te-congeners Me-Te-CF3 (Figure 2a) and Cl-
Te-CF3 (Figure 2e) develop in a ribbon-like arrangement, in
which each molecule is involved in frontal interactions
Moving to the crystal structure of iodo-derivative I-Te-CF3,
a different molecular packing could be observed. Interestingly,
doubly chalcogen-bonded, distorted noncovalent dimers are
observed (dN ···Te = 3.217 Å). Given the low electronegativity
p
and high polarizability of the I atom, the solid-state
arrangement suggests the presence of a weaker repulsion
between the CF3 and I atoms, compared to that between CF3
and Cl (Figure 3a). Moreover, each dimer associates through
comprising a chalcogen bond (dN ···Te = 3.423 and 3.406 Å
c
for Me-Te-CF3 and Cl-Te-CF3, respectively) and a hydrogen
bond, with the latter established between the pyridyl H and N
double hydrogen bonds involving the Nc atom (dN ···Te = 3.486
c
Å), hence generating a kinked ribbon at the solid state (Figure
3b). π−π stacking interactions are also observed (dπ−π = 3.824
Å with an offset of 2.585 Å), with each column interconnected
by multiple halogen bonds (dI···I = 3.482 Å). In this
arrangement, each I atom acts simultaneously as both
halogen-bonding acceptor and donor (Figure 3c).
atoms (dN ···C = 3.420 and 3.385 Å, respectively, for Me-Te-
p
CF3 and Cl-Te-CF3) of two neighboring molecules. Surpris-
ingly, the Se-based congener, Cl-Se-CF3, arranges in an
analogue ribbon-like orientation (Figure 2c), though held
together only by hydrogen-bonding interactions (dN ···C
=
p
As previously observed for compound Cl-Se-CF3, also I-Se-
CF3 crystallizes through the formation of ribbon-like structures
with no detectable chalcogen-nitrogen contacts. In these
crystals, the monomers organize through hydrogen-bonding
3.351 Å). Additional π−π stacking interactions, governing the
columnar stacking arrangement in a head-to-tail fashion, are
also observed (dπ−π = 3.529, 3.464, and 3.484 Å; Figure 2b,d,f
respectively), with the longest distance reported for Me-Te-
CF3. Considering the ESP map of the two different moieties in
the 5-position (i.e., depicting the Me group mostly positive and
Cl atom mostly negative), one can easily conjecture that the
formation of assembly A for Me-Te-CF3 is hampered by steric
repulsion in the case of CF3 and Me, whereas, in Cl-Te-CF3,
CF3 and Cl repel each other through a strong electrostatic
component.
interaction (dN ···C = 3.418 Å), which are considerably longer
p
than those observed for Cl-Se-CF3 (Figure 3d). Notably, I-Se-
CF3 forms columns through π−π stacking interactions
(estimated dπ−π = 3.489 Å), having the CF3 moieties
segregated in fluorinated domains (dF···F = 2.573 and 2.933
Å; Figure 3e). The functionalization of the 2-position with the
thiophenyl unit for Cl-Te-Th and the phenyl ring for Cl-Te-
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Figure 3. X-ray structures and their ESP maps of (a) I-Te-CF3 and (d) I-Se-CF3; (b) kinked ribbon of I-Te-CF3; columnar orientations of (c) I-
Te-CF3 and (e) I-Se-CF3 (the halogen-bonding and F···F contacts are also displayed). Space groups: C2/c for I-Te-CF3, Cmca for I-Se-CF3.
Crystallization solvent: CHCl3.
Ph and I-Te-Ph leads to the growth of wire-like supra-
molecular structures, held together by single EB between the
Nc atom and the Te atom of each neighboring molecule.
Notably, the asymmetric unit of compound Cl-Te-Th includes
two molecules, building a wire-like supramolecular assembly
through single EB interactions involving the tellurazole N atom
Building on these observations, one can notice that wire-like
structures are consistently attained over ribbon and dimeric
arrangements with 5-functionalized CGP modules bearing a
phenyl moiety in the 2-position. Remarkably, a shortening of
the Nc···Te distance can be observed when passing from
phenyl-substituted Cl-Te-Ph and I-Te-Ph to Cl-Te-Th.
Aiming at validating the occurrence of recognition motifs
with multiple intermolecular interactions in the solid state,
several crystallization attempts for oxazole derivatives Ox-Te-
Ph and Ox-E-CF3 have been performed. However, only the
CF3-containing compounds provided single crystals suitable
for X-ray diffraction analysis. Notably, Te-congener Ox-Te-
CF3 develops HB/EB ribbons in the solid state. These
structures differentiate from those described so far because the
O atom of the oxazole and the N atom of the pyridyl moiety
both engage in two hydrogen bonds with the H atoms in
positions 6 and 7 of a neighboring molecule (dO···C = 3.211 Å
and dN···C = 3.423 Å, respectively). A frontal chalcogen bond is
also established between the Nc and Te atoms of two adjacent
(dN ···Te = 3.385 Å; Figure 4a). A similar solid-state
c
organization, as that obtained for Cl-Te-Th, was observed
for Cl-Te-Ph. In this case, both Te σ-holes are involved in EB
interactions (Figure 4b). Specifically, the σ-hole(α) engages
with the tellurazole Nc atom, developing the wire-like
arrangement (dN ···Te = 3.464 Å; Figure 4d), whereas the σ-
c
hole(β) bridges the neighboring supramolecular wires through
the interaction with the Np atom (dN ···Te = 3.431 Å).
p
Furthermore, the molecules are held together through π−π
stacking interactions in a quasi-parallel fashion (estimated dπ−π
= 3.460 Å), with halogen−halogen interactions connecting the
columnar architectures (dCl···Cl = 3.244 Å; Figure 4c). In the
case of iodo-derivative I-Te-Ph, the asymmetric unit contains
two molecules, each interacting with a nearby module through
molecules (dN ···Te = 3.355 Å; Figure 5a). Considering that the
c
length of this EB is shorter (dN ···Te = 3.355 Å) than those
c
single EB with the Nc atom (dN ···Te = 3.464 and 3.582 Å). The
c
found in the crystal structures of Me-Te-CF3 and Cl-Te-CF3
resulting wire-like organization is further strengthened by weak
hydrogen contacts established between the Np atom and one of
(dN ···Te = 3.423 and 3.406 Å, respectively), it is suggested that
c
two HB interactions synergistically strengthen the association
between the two molecular modules. Supplementary π−π
stacking interactions can be discerned in the molecular packing
(dπ−π = 3.392 Å; Figure 5b), with each molecular module
arranged in an antiparallel fashion. An analogue supra-
molecular organization is observed for Se-based congener
Ox-Se-CF3, having the O atom involved in a hydrogen bond,
the H atoms of the phenyl ring (dN ···C = 3.237 and 3.321 Å;
p
Figure 4e). In contrast to chlorinated analogue Cl-Te-Ph, π−π
stacking interactions govern the formation of columnar
arrangements in a quasi-parallel head-to-tail fashion (estimated
dπ−π = 3.542 Å), with I···π interactions (σ*-π, dC···I = 3.505 Å)
bridging the columns (Figure 4f).
E
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Figure 4. X-ray structures and their ESP maps of (a) Cl-Te-Th and (b) Cl-Te-Ph, chalcogen bonds are highlighted; wire-like supramolecular
architectures of (d) Cl-Te-Ph and (e) I-Te-Ph; stick representation of columnar arrangements of (c) Cl-Te-Ph and (f) I-Te-Ph, with π−π stacking
and halogen-bonding interactions highlighted. H atoms are omitted for clarity. Space groups: Pbac for I-Te-Ph, P21/c for Cl-Te-Th and Cl-Te-Ph.
Crystallization solvent: CHCl3.
as well as the Np atom, with the H atoms in 6- and 7-positions
of the facing molecular neighbor (dO···C = 3.201 Å, dN ···C
3.418 Å). This governs the arrangement of the synthons in
ribbons at the solid state (Figure 5c). Similarly to Cl-Se-CF3
and I-Se-CF3, no chalcogen bond could be observed for Ox-
Se-CF3, given that the Se···N distance was longer than the sum
molecules Ox-Te-CF3 and Ox-Se-CF3 have been prepared,
with the latter used as reference compound to study the role of
the chosen chalcogen atom in the new recognition systems. As
expected, the choice of a small moiety as CF3 in the 2-position,
combined with Me, Cl, and oxazole substituents in the 5-
position, governed the formation of supramolecular head-to-
tail HB/EB ribbons. Replacing Cl with an I atom in the 5-
position in Te-congener I-Te-CF3 led to the formation of
distorted EB dimers, arranged into a kinked ribbon in the solid
state. Furthermore, derivatives bearing sterically demanding
phenyl and thiophenyl groups showed the typical wiring
organization. These results could open the road toward the
engineering of a large variety of materials marked by tunable
molecular arrangements, as well as depicting heteromolecular
recognition systems involving HB and EB interactions. The
encoding of concomitant weak interactions at the solid state
could allow the design of multiresponsive materials for
applications in optoelectronics and sensing.
=
p
of their van der Waals radii (dN ···Se = 3.514 Å > 3.45 Å). In
c
addition, the crystal packing develops through antiparallel π−π
stacking (dπ−π = 3.369 Å; Figure 5d).
CONCLUSIONS
■
In this paper, we have expanded the recognition space of the
CGP moiety in the solid state. By combining the substituents
in positions 2 (phenyl, thiophenyl, and CF3 moieties) and 5
(Me group, Cl and I atoms), a large variety of supramolecular
assemblies in the solid state could be obtained by modulating
the substituents’ steric and electronic properties. Aiming at
developing a recognition pattern based on multiple HB and
simultaneous single EB interactions, oxazolyl-bearing CGP
F
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Figure 5. X-ray structures and their ESP maps of (a) Ox-Te-CF3 and (c) Ox-Se-CF3; stick representation of the π−π stacking of (b) Ox-Te-CF3
and (d) Ox-Se-CF3. H atoms are omitted for clarity. Space groups: Pnma for Ox-Te-CF3, P21/c for Ox-Se-CF3. Crystallization solvents: EtOH for
Ox-Te-CF3, C6H6 for Ox-Se-CF3.
Notes
ASSOCIATED CONTENT
■
The authors declare no competing financial interest.
sı
* Supporting Information
The Supporting Information is available free of charge at
https://pubs.acs.org/doi/10.1021/acs.cgd.0c01318.
ACKNOWLEDGMENTS
■
D.B. gratefully acknowledges Cardiff University, the University
of Vienna, and the EU through the MSCA-RISE funding
scheme (project INFUSION) for the financial support. The
authors also acknowledge the use of the Advanced Computing
(ARCCA) at Cardiff University, and associated support
services for the theoretical calculations.
Synthetic protocols and spectroscopic data for all
molecules, computational studies, X-ray data (PDF)
Accession Codes
CCDC 1954271, 1954273−1954278, and 2015556−2015558
contain the supplementary crystallographic data for this paper.
These data can be obtained free of charge via www.ccdc.ca-
m.ac.uk/data_request/cif, or by emailing data_request@ccdc.
cam.ac.uk, or by contacting The Cambridge Crystallographic
Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax:
+44 1223 336033.
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AUTHOR INFORMATION
■
Corresponding Author
Davide Bonifazi − Institute of Organic Chemistry, University
of Vienna, 1090 Vienna, Austria; orcid.org/0000-0001-
5717-0121; Email: davide.bonifazi@univie.ac.at
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information towards self-organization and complex matter. Rep.
Prog. Phys. 2004, 67, 249.
Authors
Nicolas Biot − School of Chemistry, Cardiff University, CF10
3AT Cardiff, United Kingdom
Deborah Romito − Institute of Organic Chemistry, University
of Vienna, 1090 Vienna, Austria
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Complete contact information is available at:
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