Establishing Amide ... Amide reliability and synthon transferability in the supramolecular assembly of metal-containing one-dimensional architectures

Article abstract of DOI:10.1021/ic801992t

On the basis of a combination of new structural data (eleven single-crystal structure determinations are presented) and information from the Cambridge Structural Database, it has been shown that self-complementary hydrogen-bond based amide ... amide dimer

Full text of DOI:10.1021/ic801992t

Inorg. Chem. 2009, 48, 4052-4061
Establishing Amide· · · Amide Reliability and Synthon Transferability in
the Supramolecular Assembly of Metal-Containing One-Dimensional
Architectures
Christer B. Aakero¨y,* Benjamin M. T. Scott, Michelle M. Smith, Joaquin F. Urbina, and John Desper
Department of Chemistry, Kansas State UniVersity, CBC Hall, Manhattan, Kansas 66506
Received October 17, 2008
On the basis of a combination of new structural data (eleven single-crystal structure determinations are presented)
and information from the Cambridge Structural Database, it has been shown that self-complementary hydrogen-
bond based amide · · · amide dimers can be relied upon as effective supramolecular synthons for the assembly and
organization of acac- and paddle-wheel complexes of a variety of metal(II) ions. The targeted molecular recognition
event and intended extended one-dimensional motif appear with a supramolecular yield of 78% (a total of 28
structures were examined). Despite the fact that the hydrogen bonds that give rise to the R22(8) motif can be
disrupted by both carboxylate- and acac-ligands, as well as by solvent molecules, they remain remarkably resilient
and therefore represent useful synthetic tools in inorganic crystal engineering.
Introduction
structural interference that solvent molecules and counterions
offer. Furthermore, even though the metal ions themselves
are frequently a source of desirable properties (e.g., mag-
netism,3 catalysis4), or structure-driving capability (e.g., as
nodes in three-dimensional porous networks5), many transi-
tion-metal ions are capable of displaying a range of
coordination numbers/geometries which often ruins attempts
at “controlled” assembly. Consequently, a major challenge
The construction of metal-containing supramolecular
architectures has proceeded primarily through ligand-metal
interactions producing “coordination polymers”,1 or via a
combination of metal-ligand and non-covalent ligand-ligand
interactions.2 The former approach has led to the publication
of over 4000 papers in the last five-year period, and this
field continues to expand unabated.1 Strategies that employ
coordinate-covalent bonds coupled with the deliberate use
of directional hydrogen bonds, on the other hand, have not
received anywhere near the same attention. Nevertheless,
materials that are constructed with inherently weaker bonds
may display better solubility and greater structural flexibility
when compared to their coordination-polymer counterparts
because of the relative elasticity of non-covalent interactions.
However, any synthetic protocol that relies on hydrogen
bonds is also likely to be less reliable because of the potential
(2) (a) Aakero¨y, C. B.; Schultheiss, N.; Desper, J. Dalton. Trans. 2006,
1627. (b) Aakero¨y, C. B.; Schultheiss, N.; Desper, J. CrystEngComm
2006, 9, 421. (c) Aakero¨y, C. B.; Schultheiss, N.; Desper, J. Inorg.
Chem. 2005, 44, 4983. (d) Aakero¨y, C. B.; Desper, J.; Mart´ınez, J. V.
CrystEngComm 2004, 6, 413. (e) Aakero¨y, C. B.; Beatty, A. M.;
Lorimer, K. R. J. Chem. Soc., Dalton Trans. 2000, 3869. (f) Aakero¨y,
C. B.; Beatty, A. M.; Leinen, D. S.; Lorimer, K. R. Chem. Commun.
2000, 935. (g) Burchell, T. J.; Eisler, D. J.; Puddephatt, R. J. Inorg.
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J.-M.; Wegelius, E.; Rissanen, K. Eur. J. Inorg. Chem. 2001, 1515.
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M. W. New J. Chem. 2008, 32, 99. (o) Burchell, T. J.; Eisler, D. J.;
Puddephatt, R. J. Chem. Commun. 2004, 944. (p) Yue, N. L. S.; Eisler,
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M.; Kyritsakas, N. New. J. Chem. 2006, 30, 71. (r) Natale, D.;
Mareque-Rivas, C. Chem. Commun. 2008, 425. (s) Mart´ınez-Vargas,
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* To whom correspondence should be addressed. E-mail: aakeroy@
ksu.edu.
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Des. 2005, 5, 901. (c) Matsuda, R.; Kitaura, R.; Kitigawa, S.; Kubota,
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4052 Inorganic Chemistry, Vol. 48, No. 9, 2009
10.1021/ic801992t CCC: $40.75  2009 American Chemical Society
Published on Web 04/02/2009

Amide· · · Amide Hydrogen-Bonded Dimer
Scheme 1. Equatorially “Blocked” (a) acac Complex and (b)
“paddle-wheel” Complex with Axial Sites (Arrows) Available for
Coordination by Two Additional Ligands
in crystal engineering is presented by the lack of reliable
and versatile synthetic methods for preparing coordination
networks with specific topologies and dimensionalities.
The assembly and spatial organization of a series of
coordination complexes could, in principle, be accomplished
using a bifunctional ligand, where one end of the ligand binds
to a metal ion, whereas the second moiety is capable of
forming a structure-directing interaction with a neighboring
ligand through a well-defined and preconceived supramo-
lecular synthon.6 Ideally, the metal-ligand and ligand-ligand
interactions should be insensitive to the relative positioning
of the two binding sites on the ligand, and the shape/size of
the coordination complex should not affect the desired
molecular-recognition events. The nature of the resulting
extended network (e.g., dimensionality, topology, and met-
rics) could then be varied/controlled in a systematic manner
through simple covalent modifications of the ligand.
The goal of this study is to establish the robustness of a
supramolecular synthetic strategy based upon a ligand compris-
ing an N-heterocycle (for binding to the metal ion) and an amide
(for providing intermolecular amide · · ·amide synthons).
To determine the ability of such ligands to achieve the
desired metal-containing extended structural motif in the
absence of potentially disruptive counterions, we decided to
target a set of neutral coordination complexes, Scheme 1.
In addition, by using chelating ligands we also restrict the
number of possible geometries that each metal ion can adopt,
thereby simplifying the assembly process further.
Scheme 2. Representation of the Targeted Supramolecular 1-D Chain
Constructed via Both Metal Coordination (Shown As a Circle), and
Amide· · ·Amide Hydrogen-Bonding
The supramolecular target in each case presented in this
study is first of all an infinite one-dimensional (1-D) chain,
Scheme 2. Therefore, each metal complex is required to have
exactly two available binding sites that can be occupied by
N-heterocycle/amide ligands.
Bidentate acetylacetonate (acac) and acetate “paddle-
wheel” complexes are particularly useful in this context as
they both produce neutral complexes (with M2+ metal ions)
that present two open binding sites oriented in a trans-
geometry, Scheme 1.7
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Isonicotinamide8 and benzimidazol-1-yl benzamides9 have
previously been used successfully to create infinite 1-D
chains with Ag(I), and the former has also been employed
extensively with more complex ions.10 However, there have
been no systematic studies of the relative effectiveness of a
series of N-heterocycle/amide ligands to connect neutral
coordination complexes into infinite 1-D chains. We now
present the structural outcome of reactions between six
different N-heterocycle/amide ligands, Scheme 3, and a series
of acac and paddle-wheel based complexes. This will allow
us to establish whether or not the assembly process is
sensitive to how the N-heterocycle/amide ligand is con-
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Inorganic Chemistry, Vol. 48, No. 9, 2009 4053

Aakero¨y et al.
Scheme 3. Bifunctional Ligands: 4-[(2-Methylbenzimidazol-1-yl)methyl]-benzamide 1, 4-[(5,6-Dimethylbenzimidazol-1-yl)methyl]-benzamide 2,
4-[2-Phenylimidazol-1-yl)methyl]-benzamide 3, 3-[2-Phenylimidazol-1-yl)methyl]-benzamide 4, 4-[Pyrazol-1-yl)methyl]-benzamide 5,
3-[Pyrazol-1-yl)methyl]-benzamide 6
formed were separated using a separatory funnel, and the THF layer
structed and, therefore, if the synthetic process itself is likely
to be versatile and transferable to other targets.
was dried over anhydrous MgSO4. The MgSO4 was filtered off,
and the solvent removed under vacuum to give a yellow solid (5.26
g, 96%); Mp: 128-130 °C. 1H NMR (δH; 400 MHz, CDCl3): 5.30
(s, 2H), 6.98 (d, 1H, J ) 4 Hz), 7.16 (d, 2H, J ) 8 Hz), 7.24 (d,
1H, J ) 4 Hz), 7.40-7.41 (m, 3H), 7.47-7.49 (m, 2H), 7.65 (d,
Experimental Section
Materials and Measurements. All chemicals were purchased
from Aldrich and used without further purification. Melting points
were determined on a Fisher-Johns melting point apparatus and
were uncorrected. 1H NMR spectra were recorded on a Varian Unity
plus 400 MHz spectrometer (NMR solvent detailed in experimen-
tal). Synthesis and characterization of 1,11 2,9 5, and 612 have been
reported elsewhere.
2H, J ) 8 Hz); IR (KBr): 2231 cm-1
.
Synthesis of 4-[(2-Phenylimidazol-1-yl)methyl]benzamide,
3. 4-[(2-Phenylimidazol-1-yl)methyl]-benzonitrile (5.2 g, 20.08
mmol) was dissolved in DMSO (30 mL) with heat and stirring
in a 250 mL three-necked flask under a N2 atmosphere. The
reaction flask was then cooled in an ice-water bath, and
anhydrous K2CO3 (0.80 g, 5.77mmol) was added to the reaction
mixture. A 30 wt % H2O2 solution (60 mL) was added dropwise
into the reaction mixture, and a white solid formed almost
immediately. The reaction was then allowed to warm to room
temperature with continued stirring for 1 h while covered in
aluminum foil. Distilled water (50 mL) was added to the reaction
mixture. A white solid was obtained upon vacuum filtration,
which was washed with two small portions of distilled water
and dried (5.06 g, 90%); Mp: 75-80 °C. 1H NMR (δH; 400 MHz,
CDCl3): 5.28 (s, 2H), 5.83 (bs, 1H), 6.33 (bs, 1H), 6.99 (d, 1H,
J ) 4 Hz), 7.14 (d, 2H, J ) 8 Hz), 7.22 (d, 1H, J ) 4 Hz),
7.38-7.40 (m, 3H), 7.49-7.52 (m, 2H), 7.80 (d, 2H, J ) 4 Hz);
13C NMR: (δC; 400 MHz, CDCl3): 49.99, 121.23, 126.54, 128.15,
128.65, 128.68, 129.06, 129.09, 130.09, 133.04, 140.94, 148.29,
Synthesis.13 Synthesis of 4-[(2-Phenylimidazol-1-yl)methyl]ben-
zonitrile. 2-Phenylimidazole (3.061 g, 21mmol) was dissolved in
dry THF (THF, 40 mL) with stirring in a 250 mL round-bottomed
flask. To the colorless solution was added NaOH (8.4 g, 210mmol)
resulting in an orange solution, which was stirred for 2 h at room
temperature under an N2 atmosphere. To this mixture was added a
solution of dry THF (60 mL) containing R-bromo-p-tolunitrile (4.12
g, 21.03mmol). Stirring was continued for 24 h under an N2
atmosphere, after which distilled water (20 mL) was added to
dissolve remaining NaOH pellets and the NaBr. The two layers
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2004, 6, 413. (b) Bera, J. K.; Vo, T.-T.; Walton, R. A.; Dunbar, K. R.
Polyhedra 2003, 22, 3009. (c) Aakero¨y, C. B.; Beatty, A.; Desper, J.;
O′Shea, M.; Valdes-Martinez, J. Dalton Trans. 2003, 3956. (d) Zhang,
J.-P.; Lin, Y.-Y.; Huang, X.-C.; Chen, X.-M. J. Am. Chem. Soc. 2005,
127, 5495. (di) Zhang, J.-P.; Lin, Y.-Y.; Huang, X.-C.; Chen, X.-M.
J. Am. Chem. Soc. 2005, 127, 5495. (e) Kozlevcar, B.; Leban, I.; Turel,
I.; Segedin, P.; Petric, M.; Pohleven, F.; White, A. J. P.; Williams,
D. J.; Sieler, J. Polyhedra 1999, 18, 755. (f) Tsintsadze, G. V.;
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1992, 46, 29. (i) Antsyshkina, A. S.; Koksharova, T. V.; Sadikov,
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Khim. 2006, 51, 972. (j) Kozlevcar, B.; Lah, N.; Leban, I.; Turel, I.;
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2044.
(13) The synthetic methods typically lead to very small amounts of products
(the first crystals of suitable size are harvested), and their uniform
morphology and color, sharp melting points indicate a structurally
homogenous product. The amounts obtained were not enough to allow
us to perform X-ray powder diffraction analysis, but for several
compounds we determined the unit cell on multiple crystals and they
were consistent with the structures reported herein.
168.74; IR (KBr): 3293, 3179, 1649 cm-1
.
Synthesis of 3-[(2-Phenylimidazol-1-yl)methyl]benzonitrile.
2-Phenylimidazole (3.016 g, 20.9 mmol) was dissolved in dry THF
(50 mL) with stirring in a 250 mL round-bottomed flask. To the
colorless solution was added NaOH (8.36 g, 209mmol), and the
mixture was stirred for 2 h at room temperature under an N2
atmosphere. To this mixture was added a solution of dry THF (60
mL) containing R-bromo-m-tolunitrile (4.10 g, 20.91mmol). Stirring
was continued for 24 h under a N2 atmosphere, after which distilled
water (10 mL) was added to dissolve the NaOH pellets and NaBr.
The two layers formed were separated using a separatory funnel,
and the THF layer was dried over anhydrous MgSO4. The MgSO4
was filtered off, and the solvent removed under vacuum to give a
yellow oil. Purification by column chromatography (hexanes/ethyl
1
acetate 10:1f4:1) yielded an orange oil (3.52 g, 65%). H NMR
(δH; 400 MHz, CDCl3): 5.18 (s, 2H), 6.92 (1H, d, J ) 4 Hz), 7.13
(1H, d, J ) 4 Hz), 7.19 (1H, d, J ) 8 Hz), 7.24 (1H, s), 7.30 (3H,
4054 Inorganic Chemistry, Vol. 48, No. 9, 2009

Amide· · · Amide Hydrogen-Bonded Dimer
m), 7.38 (1H, t, J ) 8 Hz), 7.39-7.42 (2H, m), 7.48 (1H, d, J )
stand under ambient conditions. Green prisms, 5a, suitable for X-ray
diffraction were formed after a few days. Mp 132-135 °C.
[4-(Pyrazol-1-yl)methylbenzamide]bis-(dibenzoylmetha-
nato)nickel(II), 5b. 5 (0.02 g, 0.099mmol) and bis-(dibenzoyl-
methanato)nickel(II) (0.024 g, 0.0498mmol) were added to a vial
and dissolved with heat in ethanol and allowed to stand under
ambient conditions. Yellow blocks, 5b, suitable for X-ray diffraction
were formed after a few days. Mp 152-155 °C.
Tetrakis(µ-2-fluorobenzoato-O,O′)-bis(4-(pyrazol-1-yl)meth-
ylbenzamide)-dicopper(II), 5c. 5 (0.015 g, 0.075 mmol) and
copper 2-fluorobenzoate (0.0147 g, 0.043 mmol) were added to a
beaker and dissolved in acetonitrile. A few drops of acetic acid
were added to make the solution transparent, and the solution was
allowed to stand under ambient conditions. Aqua-blue prisms, 5c,
suitable for X-ray diffraction were formed after a few days. Mp
208-211 °C.
Tetrakis(µ-acetato-O,O′)-bis(4-(pyrazol-1-yl)methylbenzamide)-
dicopper(II), 5d. 5 (0.015 g, 0.075 mmol) and copper acetate
(0.0082 mg, 0.045 mmol) were added to a beaker and dissolved in
acetonitrile. A few drops of acetic acid were added to make the
solution transparent, and the solution was allowed to stand under
ambient conditions. Green prisms, 5d, suitable for X-ray diffraction
were formed after a few days. Mp 149-151 °C.
8 Hz); IR (KBr): 2224.10 cm-1
.
Synthesis of 3-[(2-Phenylimidazol)methyl]benzamide, 4. 3-[(2-
Phenylimidazol-1-yl)methyl]-benzonitrile (3.52 g, 13.6mmol)
was dissolved in DMSO (20 mL) with heat and stirring in a
250 mL three-necked flask under a N2 atmosphere. The reaction
flask was then cooled in an ice-water bath, and anhydrous
K2CO3 (0.57 g, 4.1mmol) was added to the reaction mixture.
Thirty wt % H2O2 solution (40 mL) was added dropwise into
the reaction mixture, and a white solid formed almost im-
mediately. The reaction was then allowed to warm to room
temperature with continued stirring for 1 h while covered in
aluminum foil. Distilled water (50 mL) was added to the reaction
mixture. A solid was obtained upon vacuum filtration, which
was washed with two small portions of distilled water and dried.
Recrystallization from ethanol gave a white solid (3.34 g, 88%);
Mp: 170-174 °C. 1H NMR (δH; 400 MHz, CDCl3): 5.27 (s,
2H), 5.81 (bs, 1H), 6.25 (bs, 1H), 6.98 (d, 1H, J ) 4 Hz), 7.19
(s, 1H), 7.21 (s, 1H), 7.39-7.41 (m, 3H), 7.43 (t, 1H, J ) 4
Hz), 7.51-7.58 (m, 2H), 7.59 (s, 1H), 7.74 (d, 1H, J ) 8 Hz);13C
NMR: (δC; 200 MHz, CDCl3): 50.03, 121.13, 125.75, 126.79,
128.64, 128.73, 128.97, 129.24, 129.35, 129.99, 130.31, 134.10,
137.65, 168.62; IR (KBr): 3324, 3180, 1675 cm-1
.
[3-(Pyrazol-1-yl)methylbenzamide]bis(hexafluoroacetylace-
tonato)copper(II), 6a. 6 (0.025 g, 0.124mmol) and bis-(hexafluo-
roacetylacetonato)copper(II) (0.030 g, 0.0545mmol) were added to
a vial and dissolved with heat in chloroform and allowed to stand
under ambient conditions. Green prisms, 6a, suitable for X-ray
diffraction were formed after a few days. Mp 137-140 °C.
Tetrakis(µ-acetato-O,O′)-bis(3-(pyrazol-1-yl)methylbenzamide)-
dicopper(II), 6b. 6 (0.015 g, 0.082 mmol) and copper acetate
(0.0082 g, 0.045 mmol) were added to a beaker and dissolved in
acetonitrile. A few drops of acetic acid were added to make the
solution transparent, and the solution was allowed to stand under
ambient conditions. Green blocks, 6b, suitable for X-ray diffraction
were formed after a few days. Mp 188-190 °C.
[4-(2-Methylbenzimidazol-1-yl)methylbenzamide]bis-(diben-
zoylmethanato)cobalt(II) THF, 1a. 1 (0.040 g, 0.153 mmol) was
dissolved in dry THF with heat in a small vial and cooled to room
temperature. To this was added a solution of bis-(dibenzoylmetha-
nato)cobalt(II) (0.039 g, 0.076 mmol) in dry acetonitrile with the
resulting solution covered and allowed to stand under ambient
conditions. Orange plates, 1a, suitable for X-ray diffraction appeared
after 4 days. Mp >300 °C.
[4-(2-Methylbenzimidazol-1-yl)methylbenzamide]bis-(diben-
zoylmethanato)nickel(II) THF, 1b. 1 (0.040 g, 0.153mmol) was
dissolved in dry THF with heat in a small vial and cooled to
room temperature. To this solution was added bis-(dibenzoyl-
methanato)nickel(II) (0.039 g, 0.076mmol) dissolved in dry
acetonitrile. The resulting solution was covered and allowed to
stand under ambient conditions. Green plates, 1b suitable for
X-ray diffraction were obtained after 2 weeks. Mp 283-287 °C
(decomp.).
[4-(5,6-Dimethylbenzimidazol-1-yl)methylbenzamide]bis-
(hexafluoroacetylacetonato)copper(II), 2a. 2 (0.02 g, 0.0628mmol)
and bis-(hexafluoroacetylacetonato)copper(II) (0.01 g, 0.0209mmol)
were added to a vial and dissolved with heat in a methanol/
acetonitrile mix and allowed to stand under ambient conditions.
Green prisms, 2a, suitable for X-ray diffraction were obtained after
a few days. Mp 155-157 °C.
Tetrakis(µ-2-fluorobenzoato-O,O′)-bis(4-(2-phenylimidazol-
1-yl)methylbenzamide)-dicopper(II), 3a. 3 (0.015 g, 0.054 mmol)
and Cu(II) 2-fluorobenzoate (0.01 g, 0.018mmol) were added
to a beaker and dissolved in acetonitrile. Green prisms, 3a,
suitable for X-ray diffraction were formed after a few days. Mp:
154-157 °C.
X-ray Crystallography. Crystallographic data for all compounds
are presented in Table 1.
Results and Discussion
Hydrogen bond geometries for 1a, 1b, 2a, 3a, 4a, 5a-5d,
and 6a, 6b are listed in Table 2.
Compounds 1a (with Co(II)) and 1b (with Ni(II)) are
isostructural. Both contain two dibenzoylmethanato (dbm)
ligands coordinated to a M(II) ion with the remaining axial
coordination sites on the metal ion occupied by two 4-[(2-
methylbenzimidazol-1-yl)methyl]-benzamide ligands, Co-N,
2.175(2) and (Ni-N, 2.114(4) Å, respectively, resulting in
octahedral metal complexes. Neighboring ions are linked by
amide · · · amide hydrogen-bonded dimers involving the syn-
hydrogen atom and carbonyl oxygen atom (1a: N-H · · ·O,
2.954(4) Å), 1b; (N-H· · ·O, 2.922(6) Å) to generate infinite
l-D chains, Figure 1.
Additionally, the anti-hydrogen atom of the amide moiety
interacts with an oxygen atom of a THF molecule (1a:
(N-H· · ·O, 2.932(7) Å; 1b: (N-H· · ·O, 2.975(8) Å). In both
structures the intrachain M-M distances is 21 Å.
The crystal structure of 2a is constructed from two
hexafluoroacetylacetonato (hfacac) ligands occupying the
equatorial sites of the copper(II) ion and the axial sites
coordinated by two 4-[(5,6-dimethylbenzimidazol-1-yl)-
Tetrakis(µ-2-fluorobenzoato-O,O′)-bis(3-(2-phenylimidazol-
1-yl)methylbenzamide)-dicopper(II), 4a. 4 (0.015 g, 0.054 mmol)
and Cu(II) 2-fluorobenzoate (0.01 g, 0.018mmol) were added to a
beaker and dissolved in acetonitrile. Green prisms, 4a, suitable for
X-ray diffraction were formed after 1 h. Mp: 144-146 °C.
[4-(Pyrazol-1-yl)methylbenzamide]bis-(hexafluoroacetylaceto-
nato)copper(II), 5a. 5 (0.025 g, 0.124mmol) and bis-(hexafluo-
roacetylacetonato)copper(II) (0.03 g, 0.0545mmol) were added
to a vial and dissolved with heat in chloroform and allowed to
Inorganic Chemistry, Vol. 48, No. 9, 2009 4055

Aakero¨y et al.
4056 Inorganic Chemistry, Vol. 48, No. 9, 2009

Amide· · · Amide Hydrogen-Bonded Dimer
Table 2. Hydrogen Bond Geometries for 1a, 1b, 2a, 3a, 4a, 5a-5d, and 6a, 6b
compound
D-H· · ·A
D-H/Å
H · · ·A/Å
D · · ·A/Å
<(DHA)/deg
symmetry transformations
1a
N(27)-H(27A)· · ·O(27)#2
N(27)-H(27B)· · ·O(1A)#3
N(27)-H(27A)· · ·O(27)#2
N(27)-H(27B)· · ·O(1A)#3
N(37)-H(37B)· · ·N(1S)
N(37)-H(37A)· · ·O(37)#2
N(47)-H(47A)· · ·O(24)#1
N(47)-H(47B)· · ·O(12)#2
N(87)-H(87A)· · ·O(41)#3
N(47)-H(47A)· · ·O(14)
N(47)-H(47B)· · ·O(12)#2
N(37)-H(37B)· · ·N(1S)
N(37)-H(37A)· · ·O(37)#2
N(31)-H(31A)· · ·O(31)#2
N(27)-H(27A)· · ·O(27)#2
N(27)-H(27B)· · ·O(48)#3
N(17)-H(17A)· · ·O(31)#2
N(17)-H(17B)· · ·N(1S)
N(27)-H(27A)· · ·O(27)#2
N(27)-H(27B)· · ·O(31)#3
0.87
0.87
0.87
0.87
0.74(9)
0.86(9)
0.87(2)
0.82(2)
0.88
0.82(2)
0.85(2)
0.88
2.09
2.11
2.06
2.17
2.41(9)
2.04(9)
2.21(2)
2.27(2)
2.27
2.61(2)
2.38(2)
2.19
2.954(4)
2.932(7)
2.922(6)
2.975(8)
3.121(9)
2.896(8)
2.9963(19)
3.0105(18)
2.943(2)
3.2986(19)
3.1466(18)
3.011(7)
2.879(5)
2.852(5)
2.859(3)
3.098(3)
3.086(3)
3.045(4)
2.9359(18)
3.1634(18)
171.4
156.8
171.9
153.9
163(9)
172(8)
150.5(18)
150(2)
133.4
143.2(19)
150.0(19)
154.3
#2 -x+2,-y,-z
#3 -x+2,-y+1,-z
#2 -x+2,-y,-z
#3 -x+2,-y+1,-z
#1 -x+1,-y+1,-z+1
#2 -x+2,-y,-z
#1 -x+1,-y+1,-z+1
#2 x-1,y,z
1b
2a
5a
5b
6a
#3 x,y+1,z
#2 x,-y+3/2,z-1/2
3a
#2 -x+2,-y+1,-z+1
0.88
0.95(5)
0.88
2.02
1.91(5)
1.99
164.4
169(4)
168.8
4a
5c
#2 -x,-y,-z
#2 -x+1,-y,-z+1
#3 -x+1/2,y-1/2,-z+1/2
#2 -x+1,-y+1,-z+1
0.88
2.43
132.9
5d
6b
0.87(4)
0.80(4)
0.78(2)
0.81(2)
2.24(4)
2.26(4)
2.16(2)
2.47(2)
164(3)
167(4)
172(2)
144(2)
#2 -x,-y+2,-z+1
#3 -x+1,-y+1,-z+1
methyl]benzamide ligands, (Cu-N, 1.995(5) Å) resulting in
an octahedral geometry. The complex is assembled into 1-D
chains through amide · · ·amide dimers via N-H· · ·O hydro-
gen bonds (3.121(9) Å) Figure 2. The anti-amide proton
forms a hydrogen bond to a MeCN solvent molecule.
Copper(II) ions within chains are approximately 22 Å apart.
The crystal structure of 3a consists of two 4-[2-phenylimi-
dazol-1-yl)methyl]-benzamide ligands coordinated via the
imidazole nitrogen atoms to the axial positions of a copper(II)
2-fluorobenzoate “paddle wheel” unit, Cu-N, 2.162(3) Å,
Figure 3.
The metal complex becomes part of an infinite 1-D chain
as a result of self-complementary homomeric amide · · ·amide
dimers, N-H · · · O, 2.879(5) Å. Additionally, the anti-
hydrogen atom of the amide moiety interacts with an
acetonitrile molecule via a N-H· · ·N hydrogen bond (3.011(7)
Å). The Cu-Cu distance within the “paddle wheel” is
2.6881(9) Å.
Figure 1. Supramolecular 1-D chain in the structure of 1a. The Co(II)
ions (dark blue) are located in the plane between two chelating dbm ligands
(oxygen atoms in red) and coordinated in the axial positions through the
nitrogen atoms (light blue) of two benzimidazole ligands. Solvent molecules
removed for clarity, and hydrogen bonds shown as blue dotted lines.
Figure 2. 1-D chain in the crystal structure of 2a. The Cu(II) ions (orange)
are located in the plane between two chelating hfacac ligands (oxygen atoms
in red, fluorine atoms in yellow) and coordinated in the axial positions
through the nitrogen atoms (light blue) of two benzimidazole ligands.
Hydrogen bonds shown as blue dotted lines.
Inorganic Chemistry, Vol. 48, No. 9, 2009 4057

Aakero¨y et al.
Figure 3. 1-D chain in the crystal structure of 3a. Each paddlewheel unit comprises two Cu(II) ions (orange) and four benzoate ligands (oxygen atoms in
red, fluorine atoms in yellow). The axial positions are occupied by imidazole ligands with coordination through the nitrogen atoms (light blue). Hydrogen
bonds shown as blue dotted lines.
Figure 4. 1-D “wavy” chain in the crystal structure of 4a. Each paddlewheel unit comprises two Cu(II) ions (orange) and four benzoate ligands (oxygen
atoms in red, fluorine atoms in yellow). The axial positions are occupied by imidazole ligands with coordination through the nitrogen atoms (light blue).
Hydrogen bonds shown as blue dotted lines.
The crystal structure of 4a contains two 3-[2-phenylimi-
dazol-1-yl)methyl]-benzamide ligands coordinated to the
axial positions of the copper(II) 2-fluorobenzoate “paddle
wheel” unit (Cu-N, 2.154(3) Å). 1-D chains are produced
through self-complementary amide · · · amide dimers via
N-H · · · O hydrogen bonds, 2.879(5) Å, Figure. 4. The
Cu-Cu distance within the “paddle wheel” is 2.6936(8) Å.
The complex ion in 5c comprises two 4-[(pyrazol-1-
yl)methyl]benzamide ligands coordinated to the axial sites
of a copper(II) 2-fluorobenzoate “paddle wheel” unit, Cu-N,
2.165(2) Å, Figure 5.
The ions are subsequently assembled into 1-D chains
through amide · · · amide dimers via N-H · · · O hydrogen
bonds, 2.859(3) Å. The anti-hydrogen atom of the amide
moiety interacts with a 2-fluorobenzoate oxygen atom via a
N-H· · ·O hydrogen bond, 3.098(3) Å. The Cu-Cu distance
within the “paddle wheel” unit is 2.6480(5) Å.
via an N-H· · ·O hydrogen bond, 3.1634(18) Å. The Cu-Cu
ions within the “paddle wheel” unit are 2.6596(3) Å apart.
The coordination complex, 5b, contains two different
nickel(II) centers in the unit cell. In one complex, two
4-[(pyrazol-1-yl)methyl]benzamide ligands occupy the
axial positions via coordination through the pyrazole
nitrogen atoms (Ni-N 2.006(12) Å). However, this time
the amide does not engage in a self-complementary dimer
but instead forms an O-H · · · O hydrogen bond (2.733 Å)
to an ethanol molecule that is coordinated to the second
nickel ion (the second Ni(II) complex has two ethanol
molecules in the axial positions and no pyrazole). The
syn-hydrogen atom of the amide forms a N-H · · · O
hydrogen bond (2.943(2) Å) to an acac oxygen atom,
Figure 7. The overall primary motif is a 1-D chain (but
not assembled in the intended manner) with intrachain
Ni-Ni distances of approximately 10.5 Å.
The coordination complex, 6b, consists of two 3-[(pyrazol-
1-yl)methyl]benzamide ligands coordinating to the axial
positions of a copper(II) acetate “paddle wheel” unit via the
pyrazole nitrogen, Cu-N, 2.1908(12) Å, Figure 6. Adjacent
complex ions are organized into 1-D chains through
amide · · · amide dimers via N-H · · · O hydrogen bonds,
N · · · O 2.9359(18) Å. Additionally, the anti-hydrogen atom
of the amide moiety interacts with an acetate oxygen atom
The complex ion in the crystal structure of 5d contains
two 4-[(pyrazol-1-yl)methyl]benzamide ligands coordinated
to the free axial sites of a copper(II) acetate “paddle wheel”
unit, Cu-N, 2.191(2) Å. This time the intended 1-D chain
is disrupted by the presence of an acetonitrile molecule which
binds to an amide moiety via a N-H · · · N hydrogen bond,
3.045(4) Å, and also because the syn-hydrogen atom is
interacting with an acetate oxygen atom via an N-H · · ·O
4058 Inorganic Chemistry, Vol. 48, No. 9, 2009

Amide· · · Amide Hydrogen-Bonded Dimer
Figure 5. 1-D chain in the crystal structure of 5c. Each paddlewheel unit comprises two Cu(II) ions (orange) and four benzoate ligands (oxygen atoms in
red, fluorine atoms in yellow). The axial positions are occupied by pyrazole ligands with coordination through the nitrogen atoms (light blue). Hydrogen
bonds shown as blue dotted lines.
Figure 6. 1-D chain in the crystal structure of 6b. Each paddlewheel unit comprises two Cu(II) ions (orange) and four acetate ligands (oxygen atoms in red).
The axial positions are occupied by pyrazole ligands with coordination through the nitrogen atoms (light blue). Hydrogen bonds shown as blue dotted lines.
Figure 7. Interaction between the two unique Ni(II) complexes in the crystal structure of 5b. Ni(II) ions (green) are located in the plane between two
chelating acac ligands (oxygen atoms in red) and coordinated in the axial positions through (a) the nitrogen atoms (light blue) of two pyrazole ligands and
(b) through the oxygen atoms of two ethanol molecules Hydrogen bonds shown as blue dotted lines.
hydrogen bond, 3.086(3) Å, Figure 8. The Cu-Cu distance
within the “paddle wheel” unit is 2.6282(5) Å.
2.0320(13) Å and Cu-O, 2.2297(12) Å, and Cu-N,
2.0040(13) Å and Cu-O, 1.9725(12) Å, respectively. In each
compound the result is a discrete metallacyclic species with
Cu-Cu distances of approximately 10.3 Å and 9 Å, re-
spectively, Figure. 9. In addition, both syn and anti amide
hydrogen atoms form hydrogen bonds to oxygen atoms of
two hfacac ligands (N-H · · · O, 2.9963(19) and 3.0105(18)
The complex ion in the crystal structures of both 5a and
6a display unexpected coordination geometries, since the
central ions are coordinated to two acac-type ligands in a
cis arrangement, with the remaining two sites occupied by a
pyrazole nitrogen donor, and an amide oxygen donor, Cu-N,
Inorganic Chemistry, Vol. 48, No. 9, 2009 4059

Aakero¨y et al.
Figure 8. Primary non-covalent interactions in the crystal structure of 5d. Each paddlewheel unit comprises two Cu(II) ions (orange) and four acetate
ligands (oxygen atoms in red). The axial positions are occupied by pyrazole ligands with coordination through the nitrogen atoms (light blue). Hydrogen
bonds shown as blue dotted lines.
Figure 9. Metallacycles in the crystal structures of 5a (left), and 6a (right). Each Cu(II) ion (orange) is coordinated to two chelating hfacac ligands (oxygen
atoms in red, fluorine atoms in yellow) in a cis geometry. The remaining two positions are occupied by pyrazole ligands with coordination through the
nitrogen atoms (light blue).
Table 3. acac- and “Paddle-Wheel” Coordination Complexes of
Å, and (N-H · · · O, 3.2986(19) and 3.1466(18) Å, respec-
tively.
The slight difference in ring size between the metallacycle
in 5a and 6a is a result of the geometry of the bridging
ligand; it is 4-[(pyrazol-1-yl)methyl]benzamide ligands in 5a
whereas it is the 3-isomer in 6a.
Isonicotinamide and Nicotinamide from CSD Searcha
desired
metal
coordination
amide· · ·amide
dimer yielding
1D chain
metal complex
Isonicotinamide+Co(DBM)2+CHCl3
(HAJPOY)10a
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
×
ꢀ
ꢀ
×
×
×
ꢀ
ꢀ
ꢀ
×
×
Isonicotinamide+Ni(DBM)2+PhBr
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
×
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
(HAJPUE)10a
Isonicotinamide+Co(DBM)2+DMF
(HAJQAL)10a
Discussion
Isonicotinamide+Ni(DBM)2+CHCl3+THF
(HAJQEP)10a
The use of chelating acac or bridging carboxylate ligands
(for generating “paddle wheel” structures) offers an effective
method for controlling the coordination chemistry of a variety
of first-row transition metals. In nine of the eleven (82%)
structures obtained, the desired coordination geometry was
obtained, with only 5a and 6a failing to produce the intended
central metal-containing building block. The subsequent
supramolecular synthetic goal, an infinite 1-D chain con-
structed from amide · · ·amide hydrogen-bond based synthons,
was achieved in seven of the remaining nine structures
(78%). The high supramolecular yield (i.e., the frequency
with which a desired supramolecular motif appears) obtained
in this study was supported by existing structural data from
the Cambridge Structural Database (CSD).14 Combining the
11 crystal structures presented herein with the 17 crystal
structures containing isonicotinamide and nicotinamide,
Table 3, (a search of imidazole and pyrazole amide ligands
yielded no hits) gives a supramolecular yield of 86% for the
Isonicotinamide+Rh(OAc)2+(CH3)2O
(BEDHEY)10b
Isonicotinamide+Cu(OAc)2+MeCN
(EMAWAQ)10c
Isonicotinamide+Cu(OAc)2
(TALKEX)10d
Nicotinamide+Rh(OAc)2+(CH3)2O
(BEDHIC)10b
Nicotinamide+Cu(OAc)2
(BENQEQ)10e
Nicotinamide+Cu(OAc)2
(BENQAM)10e
Nicotinamide+Cu(OAc)2+H2O
(BEXNOH01)10f
Nicotinamide+Zn(OAc)2+H2O
(TAYFIJ)10g
Nicotinamide+Cu(OPr)2
(VORWUV)10h
Nicotinamide+Cu(OVal)2
(GETQEC)10i
Nicotinamide+Cu(OHep)2
(CAYHIT01)10j
Nicotinamide+Cu(OHep)2
(CAYHIT)10j
Nicotinamide+Cu(ONon)2
(CAYHUF)10j
(14) Cambridge Structural Database, version 5.29, January 2008.
a CSD codes in bold in parentheses.
4060 Inorganic Chemistry, Vol. 48, No. 9, 2009

Amide· · · Amide Hydrogen-Bonded Dimer
desired coordination chemistry and geometry with a 76%
supramolecular yield observed for the formation of an infinite
1-D chain.
amide· · ·amide synthon. For the same reason that hydrogen-
bond based supramolecular synthesis is more likely to be
successful in the absence of potentially competing counter-
ions, it is also useful to try to avoid solvent molecules such
as H2O, MeOH, and EtOH. In the structures presented in
this study, the desired 1-D motif appeared even in the
presence of solvents such as chloroform, acetonitrile, DMF,
bromobenzene, acetone and THF
It is interesting to note that the effectiveness of the amide
moiety to successfully organize adjacent complex ions into
infinite chains through amide · · ·amide synthons, approaches
the degree of control that can be achieved over the coordina-
tion chemistry despite the fact that the former interactions
are significantly weaker than most coordinate-covalent bonds.
In the three cases (out of a total of 28 cases) where the
desired coordination chemistry was not attained (5a, 6a and
BENQAM), the amide binds directly to the metal ion via
its CdO moiety. It is at this point unclear why both 5a and
6a contain a metallacyclic structure. The presence of the
hfacac ligand in itself does not, based upon existing data
and upon structure 2a, make the Cu(II) predisposed to
binding two chelating ligand in a cis-manner (which is a
prerequisite for a cyclic structure in this context). Further-
more, a particular geometry of the supramolecular ligand is
also not, in itself, a noticeable driving force for a cyclic
structure. Again, 4-[(5,6-dimethylbenzimidazol-1-yl)meth-
yl]benzamide, which is the supramolecular ligand in 2a,
could readily form a cyclic dinuclear motif but instead it
opts for a 1-D chain.
The amide · · · amide interaction is disrupted in three cases
(5c, TALKEX, and CAYHIT) because an oxygen atom
from an acetate ligand (as part of the “paddle-wheel”
complex) competes successfully for the attention of the syn-
amide hydrogen atom, which also prevents the formation of
a 1-D chain. The fact that the homomeric amide · · · amide
R22(8) motif remains intact 75% of the time even in the
presence of ligand-based hydrogen-bond acceptors, serves
to underscore its importance as a supramolecular synthetic
tool.11,12 The presence of solvent molecules within the lattice
is another potential source of supramolecular strife as many
such compounds are very capable hydrogen-bond donors/
acceptors. In three cases, 5b, (ethanol as a ligand), BEX-
NOH1, and TAYFIJ (both with non-coordinating H2O),
an included solvent molecule manages to disrupt the
Conclusions
Self-complementary hydrogen-bond based amide · · ·amide
dimers are shown to be robust supramolecular synthons for
the assembly and organization of acac- and paddle-wheel
complex ions involving a variety of metals. The desired
molecular recognition event, and intended extended motif
appears with a supramolecular yield of 78% (a total of 28
structures were examined). Despite the fact that the hydrogen
bonds that give rise to the R22(8) motif can be disrupted by
both carboxylate- and acac-ligands, as well as by solvent
molecules, they remain remarkable resilient and should
therefore be useful as a synthetic tool in a wide range of
inorganic crystal engineering efforts. The versatility of the
strategy is underscored by the fact that four different
N-heterocyclic moieties (imidazole, benzimidazole, pyridine,
and pyrazole) have been incorporated into ligands with
different geometries, yet the coordinating ability and the
supramolecular effectiveness of these bifunctional, structure-
directing, compounds have remained consistent.
Acknowledgment. Acknowledgment is made to the
Donors of the American Chemical Society Petroleum
Research Fund for support (or partial support) of this research
(#46011-AC1) and to the NSF (CBET 0609318).
Supporting Information Available: X-ray crystallographic files
are available for complexes 1a, 1b, 2a, 3a, 4a, 5a-5d and 6a, 6b.
This material is available free of charge via the Internet at
http://pubs.acs.org.
IC801992T
Inorganic Chemistry, Vol. 48, No. 9, 2009 4061