Synthesis, X-ray crystal structures, and computational studies of 1,1′-bridged 4,4′-diaryl-2,2′-bibenzimidazoles: Building blocks for supramolecular structures

Article abstract of DOI:10.1039/b820502g

A series of C-shaped, 1,1′-alkyl-bridged 4,4′-diaryl-2, 2′-bibenzimidazoles has been synthesized. The crystal structures of these compounds have been determined and packing diagrams demonstrate that these molecules either form linear intercalated molecula

Full text of DOI:10.1039/b820502g

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PAPER
www.rsc.org/obc | Organic & Biomolecular Chemistry
Synthesis, X-ray crystal structures, and computational studies of
1,1¢-bridged 4,4¢-diaryl-2,2¢-bibenzimidazoles: building blocks
for supramolecular structures†
Derik K. Frantz, Ashley A. Sullivan, Yoshizumi Yasui,‡ Anthony Linden, Kim K. Baldridge* and Jay S. Siegel*
Received 18th November 2008, Accepted 9th February 2009
First published as an Advance Article on the web 30th March 2009
DOI: 10.1039/b820502g
A series of C-shaped, 1,1¢-alkyl-bridged 4,4¢-diaryl-2,2¢-bibenzimidazoles has been synthesized. The
crystal structures of these compounds have been determined and packing diagrams demonstrate that
these molecules either form linear intercalated molecular chains or include solvent molecules in the
solid state. Crystal structures are compared to computational structures determined using density
functional theory, with the BMK/DZV(2d,p) method. The C-shaped or tweezer-like geometry enables
them to act as building blocks for supramolecular architectures.
(and tweezers) have garnered much attention due to their abil-
Introduction
ity to complex substates via noncovalent interactions. Seminal
Synthetic access to supramolecular building blocks with discrete
work in this field includes examples in which chemical pincers
molecular geometries1 enables the design of molecular machines2
and devices.3 To achieve this goal, such systems regularly
incorporate multidentate ligands and metal complexes, which
often exhibit additional useful coordination, photophysical, and
electrochemical properties.4 Bipyridine (bpy)5 and phenanthroline
(phen)6 derivatives play a dominant role in this field, owing to
their ready availability. A consequence of the use of bpy and
phen is the construction of molecular geometries with multiples
of 60◦ between bonding vectors (Fig. 1). In contrast, a 6,5 ring
fusion presents a 90◦ relationship between positions 2 and 4, and
coupling of the 2-positions results in a dimer with a 0◦ (syn) or
180◦ (anti) relationship between 4,4¢ vectors. Heterocycles like 4,4¢-
disubstituted-2,2¢-bibenzimidazole (BBI) represent such a class of
ligands and can be easily prepared.7
are connected by one bond to rotatable spacers8 or flexible,
heteroaromatic scaffolds.9 Other examples incorporate aromatic
pincers that are connected to spacers by two bonds at their ortho
positions.10 N,N¢-Bridged derivatives of 4,4¢-diaryl-BBI resemble
molecular tweezers comprising dibenz[c,h]acridine, which were
synthesized and investigated by Zimmerman and coworkers.9
The distance between C(2) and C(12) of dibenz[c,h]acridine
˚
is 7.2 A, allowing the tweezers to complex many aromatic
substrates.9b The distance between pincers connected to the
4- and 4¢-positions of a BBI-based spacer could vary, depending
on the length and type of the group bridging the 1- and
˚
1¢-positions. This distance would be expected to be ~8 A in a
flat BBI spacer, which is within the range expected to complex
aromatic substrates.
The parent BBI complexes transition metals in a variety of
binding modes11 and states of deprotonation, formally neutral,12–14
monoanionic,15 and dianionic states.16–18 Often used as a bridging
ligand, BBI can participate in mono-, di-, tri-, and tetram-
etallic complexes.11 BBI derivatives have appeared recently in
general supramolecular applications,19 as well as in the formation
of a molecular switch20 and in photophysical energy transfer
complexes.21 The N–H groups at the 1,1¢-positions act as hydrogen
bond donors to carboxylate anions, and several BBI–carboxylate
complexes have been developed.22 Hydrogen bonding has also
been observed between the 1,1¢-positions of BBI and a metal
nitrile complex.23 Therefore, BBI building blocks embody func-
tional and geometrical features of importance for supramolecular
architectures.
Fig.
1
Structural comparison of 4,4¢-disubstituted BBI and
6,6¢-disubstituted bpy.
In the present work we show that N,N¢-bridged derivatives of
4,4¢-disubstituted-BBI form a versatile class of organic molecular
clips with tunable pitch and tweezer geometry. Molecular clips
Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse
190, CH-8057, Zurich, Switzerland. E-mail: jss@oci.uzh.ch; Fax: +41
(0)44 635 6888; Tel: +41 (0)44 635 4281
† Electronic supplementary information (ESI) available: Experimental
information. CCDC reference numbers 710114–710119. For ESI and
crystallographic data in CIF or other electronic format see DOI:
10.1039/b820502g
Synthesis24
We have recently reported the synthesis of Boc-protected 4,4¢-
diaryl-BBI derivatives7 of type 1 via Negishi25 cross-coupling
reactions. These fluorescent compounds exist primarily in the anti
(Z-shaped) conformation.26
‡ Current address: WPI Advanced Institute for Materials Research,
Tohoku University, Japan.
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alkyl dihalide or by coupling aryl groups to a bridged dihalide
(Scheme 1). It was found that the first approach yielded good
results and the second approach was unsuccessful, likely because
poor solubility of the bridged dibromides 5 hindered their ability to
partake in coupling reactions. Synthesis of 3a–f was accomplished
by treating 2a and 2b with alkyl dihalides in the presence of Cs2CO3
and NaI in THF (Scheme 2).
Connecting the 1,1¢-positions with small bridges forces the BBI
structure to adopt a C-shaped conformation suitable for a variety
of more complex structures (Fig. 2). Examples of such structures
are tetrahedral complexes of BBI derivatives with two small
monodentate ligands (A), one bidentate ligand (B), or another BBI
derivative (C). Macrocyclic ligands (D) and molecular rectangles
(E) could also be generated from BBI-based building blocks.
Additional supramolecular utility arises from the distance between
˚
the 4,4¢-aryl groups (~8 A), which nears the ideal van der Waals
distance for inclusion of an aryl group by a tweezer system.
Scheme 1 The two attempted synthetic routes to bridged BBI 3.
Fig. 2 Examples of higher order structures that could include the
1,1¢-bridged 4,4-diaryl-BBI structural motif.
Bridging of the 1,1¢-positions could be accomplished by several
means: 1) alkyl bridges could serve as strong, covalently bonded
tethers that would completely impede rotation about the inter-
annular 2,2¢-C–C bond;27 2) hydrogen-bonded bridges20,21 at the
1,1¢-positions could induce a structural change in BBI, leading
to the syn conformer; 3) inorganic bridges could be generated by
introduction of bulky metal complexes28 that selectively bind to
the exo binding sites.
Scheme 2 Synthesis of 1,1¢-bridged 4,4¢-diaryl-BBI.
Focusing on method 1, six bridged BBI derivatives (3a–f), which
differ in the type and length of their bridge and the conformational
preferences of their 4,4¢-aryl substituents, were targeted for
synthesis and structural study (X-ray and DFT computations29).
Bridges were limited to o-xylylene (3a–b), trimethylene (3c–d),
and dimethylene (3e–f) and aryl substituents at the 4,4¢-positions
were limited to 4-methoxyphenyl (3a,c,e) and 4-methoxy-2,6-
dimethylphenyl groups (3b,d,f).30 The length of the bridge was
expected to control the torsion angle about the 2,2¢-C–C bond, as
larger bridges were expected to lead to more twisted – and more
flexible – ground-state structures. The two types of 4,4¢-aryl sub-
stituents differ in their conformational preference against the BBI
framework; the 4-methoxyphenyl groups prefer skewed-close-to-
conjugated geometries and have relatively free rotation profiles,31
whereas the 4-methoxy-2,6-dimethylphenyl groups, which bear
sterically bulky flanking methyl groups, prefer a skewed-close-to-
orthogonal conformation and have a hindered rotational profile.
The synthesis of a generic, bridged BBI 3 can be accomplished
by either deprotecting 1 and treating BBI derivative 2 with an
The generation of 3a–f by alkylation of 2a–b in THF often re-
quires long reaction times. Recently, we discovered that the dibro-
mides 5a–c could be prepared from 4,4¢-dibromo-6,6¢-dimethyl-
BBI7 (4) by analogous alkylation using K2CO3 in DMF at shorter
reaction times and with good yields (Scheme 3). Preliminary
investigation of the DMF conditions for the formation of 3 from
2 is promising. Further work to elaborate these results is ongoing.
Structure
Structural parameters of relevance to this study include the torsion
angles about the a- (purple and blue) and f-axes (green) and the
distance between the centroids of the 4- and 4¢-aryl groups (Fig. 3).
The aBBI torsion angle is defined as the dihedral angle between the
two planar bibenzimidazole moieties.32 The abridge torsion angle is
defined as the twist about the 2,2¢ C–C axis of the first carbon
atom on each side of the bridge. The aaryl torsion angle is defined
as the twist about the 2,2¢ C–C axis of the centroids of the 4- and
4¢-aryl groups. The f torsion angle is defined as the dihedral angle
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Fig. 4 Trend in aBBI torsion vs. bridge length (left); trend in f torsion vs.
ortho-aryl substitution (right) – computational data of C2 structures.
Scheme 3 Synthesis of bridged dibromides 5a–c.
In the case of the trimethylene bridge, a Cs isomer was consid-
ered and found to be of comparable energy to the C2 conformer. In
all other cases, the C2 form was predicted to dominate. The twisted,
C2-symmetry-optimized structures were calculated to have lower
energies than their respective Cs structures by 1.4 kcal/mol (3c)
and 2.4 kcal/mol (3d). The 7-membered rings in 3c and 3d, which
arise from bridging the 1,1¢-positions with a 3-atom bridge, can
adopt an envelope or a twisted conformation, leading to Cs- or C2-
symmetric structures, respectively. By definition, the optimized Cs-
symmetric structures must have a torsion angles equal to zero. A
further structural ramification of the Cs conformer is to effectively
“shorten” the aryl-centroid distance by ca. 1.5 A. No significant
effect on f was seen in the Cs conformers compared to the C2
conformers.
Crystals of 3a–f, suitable for X-ray crystallographic analysis,
were obtained from several solvent systems. 3a, 3c, and 3d crystal-
lized from either a solvent-layered or slowly evaporating mixture
of CH2Cl2 and hexane. Compound 3b crystallized from a slowly
evaporating mixture of CH2Cl2 and acetone. The poorly soluble 3e
crystallized upon cooling a hot solution in DMF. Layering ether
above an NMR sample in CDCl3 yielded crystals of 3f upon slow
Fig. 3 Diagram of measurements used in the discussion of the structural
properties of bridged BBI.
between the planes of the rings at the 4- and 4¢-positions and the
planes of the benzimidazole moieties connected to them.33
Structural data for 3a–f was collected from X-ray crystallo-
graphic and computational studies (Table 1).34 Computational
BMK/DZV(2d,p) structures of 3a–f were determined in symme-
tries C2 and/or Cs. Frequency analysis confirmed each structure
to be a minimum on the potential energy surface. These structures
are taken as ideal structures for the molecule in isolation. Two
general trends can be seen among the C2-symmetric structures: 1)
bridge length correlates to a torsion angle; 2) ortho-substitution
on the 4-aryl group increases f (Fig. 4).
˚
Table 1 Selected geometric parameters of 1,1¢-bridged-BBI compounds 3a–f, as determined from the crystal structures and BMK/DZV(2d,p)
calculations. Experimental values from crystal structures are given in plain text; calculated values are in italics together with their molecular symmetry
aBBI torsion (◦)
abridge torsion (◦)
aaryl torsion (◦)
f torsion (◦)
4,4¢-aryl distance (A)
˚
3a
3a (C2)
3b
3b (C2)
3c
3c (Cs)
3c (C2)
3d
3d (Cs)
3d (C2)
3ea (A)
3ea (B)
3e (C2)
3f
38.8(1)
57.9c
58.4(1)c
55.1c
22.8(1)
0
58.1(1)
64.6
64.2(1)
63.8
19.7(2)
0
47.3
12.1(1)
0
47.5
18.2(1)
17.3(1)
16.7
32.2(2)
66.8
65.1(2)
60.5
23.3(2)
0
43.5
13.0(1)
0
43.1
2.6(2)
12.5(2)
10.2
27.7(3), 37.8(3)
32.4
71.6(1), 81.7(1)
65.3
36.4(1), 44.9(1)
25.1
32.7
8.586(2)
9.88
9.782(3)
9.52
8.382(4)
7.71
9.20
7.655(3)
7.51
9.01
8.595(4)
9.145(3)
8.99
40.3
16.6(1)
0
41.4
15.6(1)
15.1(1)
10.5
5.5(1)
13.1
55.5(2)
70.2(1), 71.0(1)
65.4
65.7
48.7(1)b
30.3(1)b
28.8
14.1(2)
17.5
62.9(2)
5.1(4)
15.3
67.1(2), 68.4(2)
66.0
—
8.193(7)
8.93
—
3f (C2)
5a
64.4(7)d
a Compound 3e crystallized with two symmetry-independent molecules (A and B) in the unit cell. b The molecules have crystallographic C2-symmetry,
giving equal values of f for both aryl groups. c The literature value of 63.9◦ for aBBI in the crystal structure of 1,1¢:3,3¢-o-xylylene-dibridged BBI is slightly
higher than this range.35 d The aaryl torsion angle of 5a involved the pendant bromine atoms instead of ring centroids.
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mixing of the solvents. Dibromide 5a crystallized from a slowly
evaporating CH2Cl2–ethyl acetate solvent mixture.
calculated values. Its f torsion angles are higher than the calculated
values, which is likely due to crystal packing in accommodating
the solvent molecule. In contrast to 3b, the experimental structure
of 3a deviates significantly from its optimized gas-phase structure.
The packing in linear molecular arrays, which stack tightly and
extend in alternating, opposite directions, leads to a reduction of
the aBBI and aaryl torsion angles. The experimental structure of 3a
exhibits aBBI and aaryl torsion angles that are more than 19◦ and
34◦ lower than the calculated values, respectively. This increase
in planarity also causes the 4,4¢-aryl distance to be shorter in
the crystal structure than in the optimized gas-phase structure
In addition to the calculated structures, the a torsion angles
of the molecular structures of o-xylylene-bridged compounds 3a
and 3b (Fig. 5) can be compared to the molecular structure
of bridged dibromide 5a. The a torsion angles in 5a, which
has crystallograpically-imposed twofold symmetry, are similar to
those found in the calculated structures of 3a and 3b.
˚
by nearly 1.3 A. The disparity between the abridge and the other
a torsion angles primarily arises from non-planarity of the 1,1¢-
nitrogen atom centers, which show some sp3 character.
The p-interactions between the neighboring aromatic groups
within the tongue-and-groove arrangement is not ideal nor
symmetric; the aryl planes form a ca. 14◦ or 26◦ angle with the
plane of the neighboring xylyl ring along the stack. The former
˚
being close to parallel and having a 3.7 A plane-to-centroid
distance is indicative of a face-to-face center-to-edge geometry.
The distances between the centroid-to-centroid distances of the
Fig. 5 (left) Experimental structure36 of 3a. (right) Experimental struc-
ture of 3b, with the molecule of acetone removed for clarity.
˚
˚
xylylene and neighboring aryl rings are 4.36 A and 4.74 A,
respectively. In contrast, the angle between aryl rings of adjacent
stacks is prescribed by the unit cell symmetry to be parallel, the
The crystal structure of 3a exhibits tongue-in-groove stacking
(Fig. 6) with the xylylene moiety of one molecule filling the cavity
between the 4- and 4¢-aryl groups of a neighboring molecule. In
contrast, the crystal structure of 3b is an acetone solvate with
the molecule of acetone situated beside the 4,4¢ aryl groups. Each
molecule–solvent complex is a discrete entity within the lattice.
This difference shows up in the molecular geometry as compared
to the computational ideal. The experimental structure of 3b
exhibits aBBI, abridge, and aaryl torsion angles that are similar to the
˚
distance centroid-to-plane being ca. 3.6 A, essentially an ideal
face-to-face, center-to-edge geometry. Overall, it would seem that
molecules of 3a “bind” their neighbor in the crystal and clamp
down to optimize the interactions.
The crystal structures of 3c and 3d contain solvent molecules
(CH2Cl2) in the cavities between their 4- and 4¢-aryl arms (Fig. 7).
There is one molecule of CH2Cl2 per molecule of 3c and two
molecules of CH2Cl2 per molecule of 3d in their respective
crystal structures. The included solvent molecule(s) may cause
the experimental structure of 3c and 3d to have larger f torsion
angles than their computational structures. The molecules in
both crystal structures exhibit a torsion angles that are smaller
than their optimized C2 structures. The a torsion angles and
Fig. 7 (top left) Experimental structure of 3c, containing one molecule of
CH2Cl2 in its cavity. (top right) Experimental structure of 3d, containing
two molecules of CH2Cl2. (bottom left) 1,1¢-Trimethylene-bridged-BBI
moiety of 3c, showing some puckering of the central atom of the bridge.
(bottom right) Same view of 3d, showing significant puckering of the
central atom of the bridge.
Fig. 6 (right) Packing of 3a, showing linear, tongue-in-groove stacking.
(left) Face-to-face packing of molecules of 3a (hydrogen atoms removed
for clarity).
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the 4,4¢-aryl distance in the experimental structure of 3c indicate
a structure that lies roughly halfway between the Cs and C2
optimized structures. The solid state molecular geometry of 3d also
appears to lie between the computational Cs and C2 structures, but
resembles the optimized Cs structure more closely. Its a torsion
angles are small and its 4,4¢-aryl distance is much closer to that of
the optimized Cs structure than that of the optimized C2 structure.
The dimethylene-bridged compounds, 3e and 3f (Fig. 8), partic-
ipate in tongue-in-groove stacking (Fig. 9) similar to that observed
in the crystal structure of 3a. Unlike the crystal structure of 3a,
neighboring molecules of 3e and 3f lie in alternating planes. Com-
pound 3e crystallized with two symmetry-independent molecules
(A and B) in the unit cell, each with crystallographic C2 symmetry.
In the tongue-in-groove stacking, the arms of a molecule (A)
grips the head of a molecule (B), and this continues to give
an ABAB pattern. The computational structure of 3e shows an
abridge torsion angle that is higher than both the aBBI and the aaryl
torsion angles, due to slight non-planarity of the 1,1¢-nitrogen
atom centers. This trend is observed to a lesser extent in the
experimental structure, both in molecule (A) and in molecule (B).
The experimental structure of molecule (A) deviates to some extent
from the calculated structure in the aaryl torsion angle and the
4,4¢-aryl distance, which are correlated. The f torsion angle is
much higher in the experimental structure of molecule (A) than
in its computational structure or the experimental structure of
molecule (B). This increase in torsion angle is caused by the
inclusion of part of molecule (B). Compound 3f also participates in
tongue-in-groove stacking, but all of the molecules are symmetry-
dependent. Values of the aBBI and aaryl torsion angles, are somewhat
lower in the experimental structure than in the computational
structure. The torsion angle37 between the BBI moieties of
neighboring molecules is 83◦ for 3e and 57◦ for 3f.
Conclusions
In this investigation, 1,1¢-bridged derivatives of 4,4¢-diaryl-BBI
were synthesized and their crystal structures examined and
compared to BMK/DZV(2d,p) calculated structures. Bridged
dibromides 5a–c were also prepared, and the crystal structure
of 5a was obtained. The crystal structures and DFT structures
of 3a–f usually closely agree, except when crystal packing causes
significant changes in molecular structure. The most noticeable
example of such a structural change was observed for 3a. These
BBI derivatives, which resemble clips, show a propensity to include
other molecules between their 4,4¢-aryl arms. Compounds 3a, 3e
and 3f crystallize with aromatic systems of neighboring molecules
within this cavity. Compounds 3b, 3c and 3d crystallize as solvates
and the molecules of solvent are located between the aryl groups in
3c and 3d. With an understanding of the structures of compounds
3a–3f, future work on the supramolecular applications of these
systems can be investigated.
Experimental24
Computational methods
The conformational analyses of the molecular systems described in
this study, including structural parameters, orbital arrangements,
and properties, were carried out using the Gaussian9838 and
GAMESS39 software packages. The density functional method
using the BMK functional,40 was used together with Dunning’s
double-polarized basis set DZ(2d,p).41 Full geometry optimiza-
tions were performed and uniquely characterized via second
derivatives (Hessian) analysis to determine the number of imag-
inary frequencies (0 = minima; 1 = transition state). Molecular
orbital contour plots, used as an aid in the analysis of results, were
generated and depicted using the program QMView.42
Fig. 8 Experimental structures of 3e (left) and 3f (right).
Acknowledgements
We thank the Swiss National Science Foundation for support
of this work. We acknowledge Severin Schneebeli for some
preliminary computational studies on 3e and 3f. YY would like to
thank the Legerlotz Fund of the Organic Chemistry Institute of
the University of Zurich.
References and notes
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and 3f (bottom).
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24 At the request of the editor, synthetic and crystal structure experimental
details have been moved to the ESI†.
25 E. Negishi, ‘Overview of the Negishi Protocol with Zn, Al, Zr,
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26 The molecular structure of 1,1¢-bis(tert-butoxycarbonyl)-4,4¢-dibromo-
6,6¢-dimethyl-BBI shows an anti conformation.
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28 Refs. 11–18.
29 Optimized structures for 1,1¢-bridged biindoles using early low-level
calculations have been reported in ref. 27a.
30 For information about the synthesis of 1,1¢-bridged BBI and 1,1¢;3,3¢-
dibridged 2,2¢-bibenzimidazolium salts, see ref. 27b and R. P. Thummel,
V. Goulle and B. Chen, J. Org. Chem., 1989, 54, 3057.
31 Although it is true that the 4-MeOC6H5-group does not exhibit true
“free” rotation (DG‡rot = 0), the rotational barrier could be expected to
be quite low, allowing for fast rotation at room temperature.
32 The aBBI measurements were calculated as the dihedral angle between
planes of best fit for all nine atoms of each bibenzimidazole moiety
system.
33 The f torsion angles were measured as the dihedral angle between
two planes: (1) the calculated plane of the six atoms in the ring
directly attached to the BBI moiety at the 4- and 4¢-positions; (2) the
calculated plane of the nine-atom benzimidazole moiety to which the
aryl substituent is attached.
15 (a) M. P. Gamasa, E. Garcia, J. Gimeno and C. Ballesteros,
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34 Throughout this work, molecular structures that have been computed
by DFT calculations will be referred to as ‘computational structures’
and molecular structures that have been determined by X-ray crystal-
lography will be referred to as ‘experimental structures’.
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18 For BBI complexes with metals of groups 9, 10 and 11, see: (a) D.
Carmona, J. Ferrer, A. Mendoza, F. J. Lahoz, L. A. Oro, F. Viguri and
J. Reyes, Organometallics, 1995, 14, 2066; (b) R. Uso´n and J. Gimeno,
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36 The atomic displacement ellipsoids are shown at 30% probability.
37 Average planes were calculated from the carbon and nitrogen atoms
comprising the bibenzimidazole moieties in neighboring molecules. The
mentioned angle refers to the angle between these two planes.
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2352 | Org. Biomol. Chem., 2009, 7, 2347–2352
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