ARTICLE pubs.acs.org/crystal
Crystal Engineering Studies with Monocarboxamidoalkanes Having C- or N-Terminal Pyridine and Their Coordination Complexes Gargi Mukherjee and Kumar Biradha* Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
bS Supporting Information ABSTRACT: Crystal structures of series of monopyridyl amides (14) are analyzed and compared with those of N, N0 -bis(pyridyl)alkanediamides (amides) and N,N0 -bis(pyridylcarboxamido)alkane (reverse amides). The amide analogues (1 and 2) are found to form amide-to-amide NH 3 3 3 O hydrogen bonds, whereas the reverse amide analogues (3 and 4) exhibit NH 3 3 3 N hydrogen bonds. Furthermore, complexation reactions of 14 have been carried out with various metal salts, and the hydrogen-bonding patterns in these crystal structures have been analyzed to compare with those observed in 14. The analyses and rationalization of these structures and related derivatives in the Cambridge Structural Database suggested that amide-to-amide recognition is mostly observed with halide metal salts.
’ INTRODUCTION The exploration and exploitation of various supramolecular synthons are of utmost importance in crystal engineering.1 The understanding of synthon interference in the crystal structures of molecules containing multiple functional groups is expected to help the prediction of crystal structures of complex molecules.2 The systematic study of the crystal structures of a class of analogous compounds is a well-recognized strategy employed in crystal engineering to achieve such understandings.3 We have previously explored the recognition patterns of N,N0 -bis(pyridyl)alkanediamides (amides) and N,N0 -bis(pyridylcarboxamido)alkanes (reverse amides), which have the same combination of functional groups at the molecular level and behave very differently at supramolecular level.4 In the case of amide analogues, it was shown that the pyridine group does not show any interference in amide-to-amide hydrogen bonds. In contrast, the pyridine group in reverse amide analogues does interfere in the amide-to-amide recognition pattern and forms NH 3 3 3 N(py) hydrogen bonds. From these studies, geometric criteria were evolved that the interplanar angle (θ) between the aryl (R) and the amide planes should be above 20° to form amide-toamide hydrogen bonds. In this contribution, our focus is on a similar class of compounds, monopyridyl amides (amides, 1 and 2, and reverse amides, 3 and 4) that contain one each of pyridine and amide functional groups. It is important to note here that bis amido pyridine derivatives have two H-donors and four H-acceptors, which are capable of forming four hydrogen bonds each (Chart 1), whereas monopyridyl amides (14, Chart 2) have one H-donor and two H-acceptors. The reduced number of hydrogen bonds in monopyridyl amides (14) is expected to reduce the complexities involved in bis amides, which are r 2011 American Chemical Society
observed to form a β-sheet and two-dimensional layers. It is interesting to note that in the case of bis-amido pyridines, the β-sheets observed in the organic compounds have been successfully transferred into the coordination networks.5 Furthermore, the amides and reverse amides were shown to form iso-structural coordination networks in particular when the spacers between the amido-pyridyl groups are larger.6 Accordingly, here, our studies are aimed at understanding the following aspects in comparison with those of bis-amides: 1 Does the pyridine interference or lack of it follow similar trends as those observed in bis-amides? 2 Does the formation of amide-to-amide hydrogen bonds depend on the interplanar angle (θ) between aryl and pyridine groups? 3 Do the mono-amides and reverse amides form the isostructural coordination complexes?
’ RESULTS AND DISCUSSION Compounds 14 were synthesized by employing two wellknown procedures of amide synthesis. The first method is the reaction of the hydrochloride salt of aliphatic amine with the hydrochloride salt of the corresponding acid chloride in the presence of pyridine.7 The second method is the coupling of acid chloride and the corresponding amine. The crystallization of the compounds 14 in various solvents resulted in single crystals suitable for X-ray diffraction. The crystal structure of 2a is Received: September 14, 2011 Revised: October 10, 2011 Published: October 11, 2011 5649
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reported earlier, and its coordinates were taken from the Cambridge Structural Database (CSD) for comparative analysis.8 We were not successful in synthesizing the compounds 1b and 2b. Furthermore, complexation reactions of 14 with various metal salts have been carried out with the goal of understanding the subtleties in transfer of molecular recognition information from organic materials to their coordination complexes and also to study the robustness of the hydrogen-bonding patterns in the presence of counteranions. However, crystals suitable for single crystal X-ray diffraction studies were obtained only in the case of 3a and 3b. Six coordination complexes (510) of 3a and 3b were synthesized by mixing the methanolic solution of the metal salt with the methanolic solution of the ligand. Crystalline complexes were obtained by slow evaporation of the solution at room temperature. The CSD Studies on molecules containing Chart 1. Hydrogen-Bonding Patterns: (a) Ribbon in Monoamides and (b) β-Sheet in Bis-amides
monoamido pyridines have been carried out for both organics and inorganic structures to compare with the results obtained here. The pertinent crystallographic details, geometrical parameters of strong hydrogen bonds involving amide functionality, and interplanar angles of compounds 14 and complexes 510 are given in Tables 15, respectively. Amide-to-Amide Hydrogen Bonds in 1a and 2a. Compound 1a crystallizes in the triclinic crystal system with space group, P1. The molecules are assembled via amide-to-amide hydrogen bonds, indicating no interference from the pyridine moiety (Figure 1). The hydrogen-bonding pattern of 1a is similar to the one observed in 2a. These two structures differ in secondary interactions: In 1a, the pyridineN is involved in hydrogen bonding with the methyl protons, while in 2a, it is hydrogen bonded to pyridine CH group. Interference of Pyridine in 3 and 4. Both 3a and 3b crystallize in the monoclinic, P21/n space group (Figure 2). The asymmetric unit of 3a contains two molecules each of 3a and water, while that of 3b has two molecules of 3b and one water. The inclusion of water in the crystal lattice in 3a and 3b is in agreement with our previous observation that among all four classes of compounds only 4-pyridyl derivatives of bis-amides (reverse) includes water. Compound 3a contains one water Table 2. Geometrical Parameters of Hydrogen Bonds in Compounds 1a, 2a, 3a, 3b, 4a, and 4b
Chart 2
compds
typea
H 3 3 3 A (Å)
D 3 3 3 A (Å)
DH 3 3 3 A (deg)
1a
NH 3 3 3 Oa NH 3 3 3 O NH 3 3 3 Ob
2.09
2.913(4)
160
2.06
2.899(4)
164
1.99
2.851(4)
175
NH 3 3 3 O NH 3 3 3 Nc NH 3 3 3 O NH 3 3 3 Nd
2.02
2.877(4)
176
2.08 2.04
2.930(1) 2.898(1)
170 174
2.12
2.979(3)
177
2.27
2.989(4)
141
2.14
3.004(4)
177
3a 3b 4a
NH 3 3 3 Ne NH 3 3 3 N
4b
Symmetry operators: (a) x, y, 1 + z; (b) 1 x, y, z; (c) 1/2 x, 1/2 + y, 3/2 z; (d) x, y, 1/2 + z; and (e) 1/2 + x, 1/2 y, 1/2 + z. a
Table 1. Crystallographic Parameters for Compounds 1a, 3a, 3b, 4a, and 4b compds
1a
3a
3b
4a
4b C8H10N2O
formula
C7H8N2O
C7H10N2O2
C16H20N4O3
C7H8N2O
mol. wt.
136.15
154.17
316.36
136.15
150.18
T (K) system
293(2) triclinic
293(2) monoclinic
293(2) monoclinic
293(2) monoclinic
293(2) monoclinic P21/n
space group
P1
P21/n
P21/n
C2/c
a (Å)
8.409(4)
11.936(2)
7.252(3)
15.070(9)
13.6085(2)
b (Å)
9.724(4)
9.768(2)
26.884(1)
7.742(4)
8.1708(9)
c (Å)
9.984(4)
14.267(3)
8.724(3)
12.065(7)
15.5985(2)
α (°)
75.782(2)
90.00
90.00
90.00
90.00
β (°)
72.520(1)
105.84(3)
94.642(1)
91.804(2)
110.465(1)
γ (°) V (Å3)
65.759(12) 703.0(5)
90.00 1600.2(6)
90.00 1695.4(11)
90.00 1407.0(1)
90.00 1625.0(3) 8
Z
4
8
4
8
D(mg/m3)
1.286
1.280
1.247
1.286
1.228
R1 [I > 2σ(I)]
0.0656
0.0673
0.0639
0.0527
0.0646
wR2 (on F2, all data)
0.1841
0.1983
0.1768
0.1414
0.1978
5650
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molecule per formula unit and does not exhibit an amide-toamide hydrogen bond in its crystal structure, as both the CdO and the NH groups of the amide are engaged in hydrogenbonding interactions with water. The water molecules join the amide molecules into 2D layers. These 2D layers are further packed via CH 3 3 3 N and CH 3 3 3 π interactions in an alternate fashion. The water exhibits identical 3-coordination with respect to hydrogen bonds in both of the structures. However, both of the structures differ significantly in their hydrogen-bonding patterns, probably due to the difference in number of water molecules present in the crystal lattice. The two symmetry independent molecules of 3b (A and B) have different set of interactions. Molecule A is hydrogen bonded to two water molecules and one amide NH group, whereas molecule B is hydrogen bonded to one water and one pyridyl group (Figure 2d). Thus, unlike 3a, the crystal structure of 3b contains NH 3 3 3 N hydrogen bonds along with NH 3 3 3 Ow and OwH 3 3 3 O interactions (w-water). Overall, 3a forms flat 2D layers, and 3b forms corrugated 2D layers via strong hydrogen bonds. These layers are further connected with adjacent layers via CH 3 3 3 O hydrogen bonds between amide carbonyl and pyridine CH groups. Compounds 4a and 4b crystallize in monoclinic C2/c and P21/n space groups, respectively. In both of the cases, the molecules are assembled via NH 3 3 3 N hydrogen bonds (Figure 3). These hydrogen-bonding patterns are reminiscent of those observed in 3-pyridyl analogues of bis-amides (reverse). The amide carbonyls are engaged in CH 3 3 3 O hydrogen bonds with pyridine CH from the neighboring 1D chains, leading to a 2D layer. The adjacent layers are packed opposite to one another via edge-to-edge and CH 3 3 3 π interactions in 4a and 4b, respectively. Hydrogen-Bonding Patterns in the Coordination Complexes of 3a and 3b. The reaction of 3a with AgNO3 in
methanol resulted in crystals of the complex [Ag(3a)2](NO3), 5 (Figure 4). In this complex, the asymmetric unit is constituted by one each of Ag(I), NO3, and two units of 3a. Two pyridine moieties are linearly coordinated to Ag atoms and two such units come closer via Ag 3 3 3 Ag interaction (Ag 3 3 3 Ag, 3.159 Å), giving rise to a dimeric aggregate. These dimeric aggregates are linked to each other through amide-to-amide hydrogen bonds forming a stair caselike 1D chain. Adjacent chains are linked through nitrate anions via CH 3 3 3 O hydrogen bonds with pyridine CH. Furthermore, face-to-face aromatic interactions between the pyridine moieties also involved in governing the 3D packing. It is interesting to note here that N-(4-pyridyl)benzamide (NPBA) exhibits similar coordination to Ag(I) in [Ag(NPBA)2](NO3).9 In this complex, one nitrate anion is coordinated to silver, and the dimers are assembled through NH 3 3 3 O interactions between the coordinated nitrate and the amide proton. In contrast to 5, no amide-to-amide contact is observed in this structure. Complex [Cu(3a)2(NO3)2], 6 (Figure 5), is obtained from 3a and copper nitrate in methanol. In 6, Cu(II) adopts the distorted octahedral geometry, but interestingly, here, the ligands are syn coordinated, generating a V-shaped geometry. These V-shaped Table 5. Geometrical Parameters of Hydrogen Bonds of Amide Functionality in Complexes (510) typea
complex
interplanar
2a
3a
3b
4a
2.03
2.876(7)
169
6
2.12 2.55
2.969(5) 3.203(3)
170 134
NH 3 3 NH 3 3
3 ONO2 d 3 OOCCH3
2.24
3.100(3)
172
7
1.96
2.807(3)
170
2.04
2.845(4)
155
1.92
2.736(4)
178
2.07
2.914(5)
168
2.94
3.768(3)
163
NH 3 3 NH 3 3
8
e 3 OOCCH2Cl
f 3 OOCCH3 NH 3 3 3 O NH 3 3 3 Ig
10
4b
DH 3 3 3 A (deg)
3 ONO2 b 3O c 3 ONO2
Table 3. Interplanar Angle between Amide and Pyridyl Plane 1a
D3 3 3A (Å)
NH 3 3 NH 3 3 NH 3 3
5
9 compd
a
H3 3 3A (Å)
Symmetry operators: (a) x, 1 y, z; (b) 1 x, y, z; (c) x, y, 1/2 + z; (d) x, 1 + y, z; (e) x, 1 + y, z; (f) x, 1/2 y, 1/2 + z; (g) x, 1 y, 1/2 + z. a
17.91, 39.09 22.11 5.93, 7.18 7.93, 9.61 9.21 9.42, 3.02
angle(θ°)
Table 4. Crystallographic Parameters of Complexes (510) compds
5
6
7
8
9
10
formula
C28H32Ag2N10O10
C14H16CuN6O8
C18H22N4O6Cu
C20H24N4O6Cl2Cu
C18H24N4O7Cd
C14H16N4O2I2Cd
mol. wt.
884.38
459.87
453.94
550.87
520.81
638.51
T (K) system
293(2) triclinic
293(2) monoclinic
293(2) triclinic
293(2) triclinic
293(2) monoclinic
293(2) monoclinic
space group
P1
C2/c
P1
P1
P21/c
C2/c
a (Å)
8.256(3)
9.1256(11)
7.6683(7)
8.403(3)
13.114(14)
10.2415(8)
b (Å)
10.458(3)
12.2367(15)
8.5377(8)
8.825(4)
20.024(2)
11.5816(9)
c (Å)
11.089(4)
17.072(2)
8.6050(8)
8.895(4)
8.487(9)
16.2866(12)
α (°)
94.642(1)
90.00
73.392(3)
89.555(11)
90.00
90.00
β (°)
104.619(8)
94.572(3)
71.199(3)
67.609(9)
97.524(3)
90.872(2)
γ (°) V (Å3)
111.931(8) 842.1(5)
90.00 1900.3(4)
83.191(3) 510.84(8)
78.394(11) 595.7(4)
90.00 2209.6(4)
90.00 1931.6(3)
Z
1
4
1
1
4
4
D(mg/m3)
1.744
1.607
1.476
1.536
1.566
2.196
R1 [I > 2σ(I)]
0.0589
0.0344
0.0424
0.0422
0.0364
0.0229
wR2 (on F2, all data)
0.0698
0.1205
0.1183
0.1518
0.1229
0.0637
5651
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Figure 1. Illustrations for the crystal structures of 1a and 2a: geometry of the ligand in (a) 1a and (b) 2a; 2D layer via NH 3 3 3 O and CH 3 3 3 N hydrogen bonds in (c) 1a and (d) 2a; packing of the adjacent layers (e) via alternate CH 3 3 3 N hydrogen bond and hydrophobic interaction and (f) via hydrophobic interactions.
units are assembled via NH 3 3 3 O hydrogen bonds between amide NH and O-atom of nitrate ions to form a 1D chain. Furthermore, the adjacent chains interact with each other via dipoledipole interactions between amide carbonyls (C 3 3 3 O distance, 3.297 Å) to form a 2D layer in bc-plane. The methyl groups of acetyl are not involved in CH 3 3 3 O interactions with the CO groups of acetyl (H 3 3 3 O, C 3 3 3 O, and CH 3 3 3 O: 3.208 Å, 3.530 Å, and 101°). We note here that a similar type of cis-coordination around Zn(II) was observed in Zn(NPBA)2(OAc)2.9 In the Zn(II) complex, π 3 3 3 π stacking interactions of pyridine rings also take part in the formation of 1D chain in addition to the aforementioned NH 3 3 3 O hydrogen bonds between amide NH and O-atom of anion. When the counteranion is changed from nitrate to acetate, 3a gives a crystalline complex, [Cu(3a)2 (OAc)2], 7 (Figure 6). Single crystal X-ray analysis reveals that the Cu(II) has a square planar geometry, but here, the two pyridyl ligands are coordinated trans to each other, while the two acetate anions occupy the other two positions in trans fashion. The amide protons are hydrogen bonded to one of the O-atom of acetate (NH 3 3 3 O), resulting in a 1D chain. Pyridyl groups are involved in face-to-face aromatic interaction and have a centroid to centroid distance of 3.322 Å. The amide carbonyls are engaged in CH 3 3 3 O hydrogen bonds with pyridine CH groups from the neighboring chains to form a 2D layer. Overall, these 2D layers are further assembled via hydrophobic interactions between the methyl groups of acetates from adjacent layer
(Figure 6e). The coordination around Cu(II) in 7 resembles that in trans-[Cu(NPBA)2(OAc)2], and in both of the cases, the 1D chains are bound via CH 3 3 3 O interactions between the amide keto and the pyridine ring protons.9 Complex [Cu(3b)2(ClCH2CO2)2], 8, exhibits a similar type of 1D chain as observed in complex 7 (Figure 6b). In this complex, the 1D chains are joined together via hydrophobic interactions between ethyl groups of 3b and CH 3 3 3 Cl interactions. No Cl 3 3 3 Cl interactions were observed (Figure 6d). Complexation of 3a with cadmium acetate under similar conditions to above reactions afforded complex [Cd(3a)2(OAc)2(H2O)], 9 (Figure 7). Cd(II) exhibits pentagonal bipyramid geometry as the equatorial plane contains two acetates and one water molecule, while the axial positions are coordinated by pyridine units. Each cluster is hydrogen bonded to five other clusters via eight noncovalent interactions: two amide-to-amide NH 3 3 3 O, two acetate to amide NH 3 3 3 O, and four acetate to water OH 3 3 3 O hydrogen bonds (Figure 7b). Joining the metal centers of the neighboring hydrogen bonded units reveals a 5-connected 3D network with 44.66-sqp topology (Figure 7c).10 The nodes exhibit a distorted square pyramidal geometry, with varied Cd 3 3 3 Cd distances of 14.907, 14.907, 9.405, 5.973, and 5.973 Å. The base of the pyramid is rather a rectangle than a square. We note here that the networks with five-connected nodes are very rare, and so far, only two usual varieties are known to exist. One of which is the bnn network that was observed in Mn[C(CN)3]2 L, where L=1,2-bis(4-pyridyl)ethane-N,N0 dioxide,10a whereas the second type is the one observed here, 5652
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Figure 2. Illustrations for the crystal structures of 3a and 3b: geometry of the ligands in (a) 3a and (b) 3b; 2D layer involving water molecules in (c) 3a and (d) 3b; packing of the adjacent layers through CH 3 3 3 N and CH 3 3 3 π interactions in (e) 3a and (f) 3b; 3D packing in (g) 3a and (h) 3b.
and recently, it was found to occur in the complex [Cu14I14(dabco)5(pyridine)]n.10b However, in that example, the networks were found to doubly interpenetrate to fill the channels. In the present case, the hexagonal channels of the network are occupied by the methyl groups. Recently, coordination polymers containing a new variety of five connected Archimedean 2D layer topology are reported.10f,g Because the nitrate and acetate anions are interfering into amide to amide hydrogen bonds, we thought to use metal halides, which are less prone to interfere in amide-to-amide recognition patterns. The crystalline complex of 3a was obtained with cadmium iodide as [Cd(3a)2I2], 10 (Figure 8). Cd(II) exhibits tetrahedral coordination geometry and is coordinated to two iodine and two pyridine units. Each discrete unit is hydrogen bonded to two neighboring units via NH 3 3 3 I hydrogen bond forming a 1D chain (Figure 8a). Furthermore, these units interact with each other through edge-to-edge aromatic interactions (closest CC distance, 3.536 Å) (Figure 8c). The 3D packing is governed by bifurcated iodide anions through weak NH 3 3 3 I and CH 3 3 3 I (3.065, 133.74, and 3.768 Å) interactions leading to a 3D structure. No amide-to-amide recognition is observed in this complex also.
CSD Studies. The CSD studies11 were performed to ratio-
nalize the results obtained here and to understand the following aspects. a. Probability of cis and trans Coordination of Nitrate and Acetate Anions. CSD (version 5.32) was searched for discrete coordination complexes containing ML2A2 or ML2A2S2 formulas with any transition metal (M), pyridine, or with 4-substituted pyridines (L), methanol, or water (S) and acetate or nitrate (A). For the ML 2 A 2 formula, after manual screening of large subsets, five complexes were found with nitrate and 11 complexes were found with acetate ions. The ligands found to exhibit cis geometry in three {NIPYZN [Zn(II)], TABBII [Zn(II)], ICUVEH [Pt(II)]} out of four nitrate complexes and in four {ZZZPKM01 [Zn(II)], MOHRAC [Zn(II)], FABFAR [Zn(II)], and LEVPAE [Zn(II)]} out of 11 acetate complexes. 9,12,13 Similarly, for the ML2A2S2 formula, it was found that there are total of 13 structures with nitrate and nine structures with acetate. Interestingly, all of these nitrate and acetate complexes were found to contain trans coordination of the ligands or anions around metals [Cu(II), Ni(II), Zn(II), Co(II), and Mn(II)].9,14,15 These results suggest that complex 6 is the first example of a complex containing cis-coordination of ligands and as well as nitrate anions having Cu(II) 5653
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Figure 3. Illustrations for the crystal structures of 4a and 4b: geometry of the ligand (a) 4a and (b) 4b; 2D layer via NH 3 3 3 N and CH 3 3 3 O hydrogen bonds in (c) 4a and (d) 4b; 3D packing (e) in 4a through edge-to-edge aromatic interactions and (f) in 4b through CH 3 3 3 π interactions.
Figure 4. Illustrations for the crystal structures of 5: (a) dimeric units assembled via amide-to-amide hydrogen bonds and (b) 3D packing through pyCH 3 3 3 O (nitrate) hydrogen bonds.
as the metal atom, as all of the related cis complexes are reported with Zn(II), except ICUVEH.11 We note here that CSD studies reveal that cis coordination is more common with Zn(II) (five out of five) but not with Cu(II) (zero out seven). b. Occurrence of Amide-to-Amide Hydrogen Bonds in Derivatives Containing Pyridine and Amide One Each. A CSD search was performed on the molecules having the fragments
IIV (Chart 3) with single amide functionality to analyze the interference of pyridine on amide-to-amide hydrogen bond in the published crystal structures of monoamido-pyridyl derivatives. Molecules having interfering groups and bulky substituents were not considered. The CSD contains five, three, three, and seven crystal structures for fragments IIV, respectively. All of the structures containing fragments I and II were found to form 5654
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Figure 5. Illustrations for the crystal structure of 6: (a) assembling of hydrogen-bonded chains via dipoledipole interactions between amide carbonyls and (b) 3D packing via CH 3 3 3 O hydrogen bonds.
Figure 6. Illustrations for the crystal structures of 7 and 8: tapelike 1D chain via NH 3 3 3 O(acetate) hydrogen bonds in (a) 7 and (b) 8; 2D layer (c) via CH 3 3 3 O hydrogen bonds in 7 and (d) via hydrophobic interactions between ethyl groups in 8; (e) 3D packing through hydrophobic interactions between the methyl groups of acetates in 7.
amide-to-amide hydrogen bonds.16,17 Furthermore, all of these compounds were found to exhibit interplanar angle (θ) of above 20° between amide and pyridine planes. For fragment III, two form amide-to-amide hydrogen bonds out of three structures and have θ values greater than 20°. FOVCUP forms NH 3 3 3 N hydrogen bonds and also has θ value (16.62°) of less than 20°.18 In contrast to the structures of fragments IIII, the crystal structures of IV prefer to assemble via NH 3 3 3 N hydrogen bonds (five out of seven) over amide-to-amide hydrogen bonds and also was found to have θ values less than 20°.19
From the CSD analyses, it clearly appears that for fragments I and II, whatever be the substituent on the amide NH, the interplanar angle (θ) is greater than 20°, and consequently, amide-to-amide contacts are favored in all of the structures, even in some cases in the presence of strong hydrogen-bonding groups also. However, this is not the case with the fragments III and IV. With the fragments III and IV, all of the molecules available in the literature have aromatic substituents on the amide NH, and depending on the θ values, the molecules exhibit NH 3 3 3 N hydrogen bonds (out of 10, six involve 5655
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Figure 7. Illustrations for the crystal structure of 9: (a) five-coordinated node formation; (b) top view of the sqp net; and (c) schematic representation of 3D 44.66-sqp topology.
Figure 8. Illustrations for the crystal structure of 10: (a) 1D chain via NH 3 3 3 I hydrogen bonds, (b) 2D layer via CH 3 3 3 O hydrogen bonds, and (c) 3D packing via NH 3 3 3 I and CH 3 3 3 O hydrogen bonds.
pyridine interference). These results are in agreement with our previous studies on bis-amide- and bis-pyridine-containing derivatives. c. Role of Anions in Amide-to-Amide Recognition. A CSD search on the fragments I IV coordinated to any transition metal was carried out to explore the role of anions in amide-toamide recognition. Similar constraints to the searches that are described in section a were applied. A total of eight and six crystal structures were found containing acetate and nitrates, respectively.9,20,21 Among the eight structures with acetates, only one entry, namely, MOHRIK (NH 3 3 3 O = 3.334 Å), exhibits amide-to-amide recognition, while in the remaining seven structures, amide proton hydrogen bonds to the noncoordinated O of acetate. Nitrate anions also were found to disrupt the amide-to-amide recognition in a similar fashion; six out of six contain
Chart 3. CSD Search on Organic Molecules Having Fragments IIV and Their Coordination Complexes
anion interference. However, in one of these six (DUQTOZ), amide-to-amide hydrogen bond as well as anion interference was found.21 In contrast, amide-to-amide hydrogen bond was found to be more prominent in the structures containing halide ions (three out of six). Two of the three structures (ALARAH and ALAQUA) do not form amide-to-amide hydrogen bonds due to the presence 5656
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Chart 4. Some Common Hydrogen-Bonding Patterns: (a) Anion Disrupting Amide-to-Amide Recognition, (b) Amide-to-Amide Recognition Even in the Presence of Interfering Anion, and (c) Amide-to-Amide Recognition in the Presence of Halides
of DMF in the crystal lattice.22 In HEBVIU, the amide group exclusively exhibits NH 3 3 3 Cl hydrogen bonding with amide NH, and similar hydrogen bonding was also found in ALARAH.22,23 Some of the common patterns observed in the above-described crystal structures are shown in Chart 4. The CSD analysis indicates that nitrate and acetate have more propensities to interfere in amide-to-amide recognition as compared to halide ions.
’ CONCLUSION The studies show that monoamides follow the same structural trend as observed previously in case of bis-amides. Here also, only the amide derivatives of monoamides exhibit amide-to-amide hydrogen bonding. The 3-pyridyl reverse amides derivatives are exclusively assembled via NH 3 3 3 N hydrogen bonding, whereas 4-pyridyl analogues exhibit the tendency to include water molecules in the crystal lattice. As of bis-amides, monoamides have also exhibited similar preference for angle (θ < 20°) to amide-toamide hydrogen bond. Only deviation occurs in 1a that has two molecules in the asymmetric unit and thus two θ values, one of which is greater than 20°. From the CSD data, it is observed that generally reverse amides prefer planar geometry as compared to their amide analogues, and in most of the cases, the θ value is less than 20° (36 out of 45). Also, the results observed here clearly indicate that amide-to-amide hydrogen bond formation occurs only if the θ value is greater than or equal to 20°. In the case of coordination complexes depending upon the metal atom and counteranions, 3a can adopt a variety of supramolecular structures. The amide-to-amide hydrogen bonding is not observed in 6, 7, 8, and 10 as the anions, that is, nitrate, acetate, or iodide are hydrogen bonding with amide functionality. However, in 5 and 9, the interference of anions is partial as one ligand participates in the amideto-amide hydrogen bond, while the other interacts with anions. ’ ASSOCIATED CONTENT
bS
Supporting Information. Experimental details, IR spectra, elemental analyses, and CSD tables. This material is available free of charge via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION Corresponding Author
*Tel: +91-3222-283346. Fax: +91-3222-282252. E-mail: kbiradha@ chem.iitkgp.ernet.in.
’ ACKNOWLEDGMENT We gratefully acknowledge the DST for the financial support and DST-FIST for the single-crystal X-ray facility. G.M. thanks CSIR for a research fellowship. ’ REFERENCES (1) (a) Desiraju, G. R. The Weak Hydrogen Bond: In Structural Chemistry and Biology; Oxford University Press: Oxford, 1999. (b) Zaworotko, M. J. Chem. Commun. 2001, 1. (2) (a) Desiraju, G. R. Crystal Engineering. The Design of Organic Solids; Elsevier: Amsterdam, 1989. (b) Desiraju, G. R. Angew. Chem., Int. Ed. 1995, 34, 2311. (c) Etter, M. C. Acc. Chem. Res. 1990, 23, 120. (3) (a) Nguyen, T. L.; Fowler, F. W.; Lauher, J. W. J. Am. Chem. Soc. 2001, 123, 11057. (b) Das, D.; Desiraju, G. R. Chem.-Asian J. 2006, 1, 231. (c) Bis, J. A.; Vishweshwar, P.; Middleton, R. A.; Zaworotko, M. J. Cryst. Growth Des. 2006, 6, 1048. (4) (a) Sarkar, M.; Biradha, K. Cryst. Growth Des. 2006, 6, 202. (b) Rajput, L.; Singha, S.; Biradha, K. Cryst. Growth Des. 2007, 7, 2788. (c) Mukherjee, G.; Biradha, K. Cryst. Growth Des. 2011, 11, 924. (d) Sarkar, M.; Biradha, K. Chem. Commun. 2005, 2229. (e) Biradha, K.; Rajput, L. Crystal Engineering with Molecules Containing Amide and Pyridine Functionalities. In Organic Crystal Engineering: Frontiers in Crystal Engineering; Tiekink, E. R. T., Vittal, J. J., Zaworotko, M. J., Eds.; John Wiley Publishers: Chichester, United Kingdom, 2010. (5) (a) Sarkar, M.; Biradha, K. Cryst. Growth Des. 2007, 7, 1319. (b) Rajput, L.; Biradha, K. New J. Chem. 2010, 34, 2415. (6) Biradha, K.; Rajput, L. CrystEngComm 2009, 11, 1220. (7) Lunn, G.; Sansone, E B. J. Org. Chem. 1986, 51, 513. (8) Srikrishnan, T.; Parthasarathy, R. Acta Crystallogr., Sect. -C 1990, C-46, 1723. (9) Noveron, J. C.; Lah, M. S.; Sesto, R. E. D.; Arif, A. M.; Miller, J. S.; Stang, P. J. J. Am. Chem. Soc. 2002, 124, 6613. (10) (a) Batten, S. R.; Neville, S. M.; Turner, D. R. Coordination Polymers: Design, Analysis and Application; RSC Publishing: Cambridge, 5657
dx.doi.org/10.1021/cg2012028 |Cryst. Growth Des. 2011, 11, 5649–5658
Crystal Growth & Design
ARTICLE
United Kingdom, 2009. (b) Hou, Q.; Yu, J.-H.; Xu, J.-N.; Yang, Q.-F.; Xu, J.-Q. CrystEngComm 2009, 11, 2452. (c) Deniz, M.; Pasan, J.; Fabelo, O.; Delgado, L. C.; Lloret, F.; Julve, M.; Perez., C. R. New J. Chem. 2010, 34, 2515. (d) Wang, Y.-T.; Tang, G.-M.; Wei, Y.-Q.; Qin, T.-X.; Li, T.-D.; He, C.; Ling, J.-B.; Long, X.-F.; Ng, S. W. Cryst. Growth Des. 2010, 10, 25. (e) Zhang, L.; Yao, Y.-L.; Che, Y.-X.; Zheng, J.-M. Cryst. Growth Des. 2010, 10, 528. (f) Sposato, L. K.; Nettleman, J. H.; Braverman, M. A.; Supkowski, R. M.; LaDuca, R. L. Cryst. Growth Des. 2010, 10, 335. (g) Blake, K. M.; Johnston, L. L; Nettleman, J. H.; Supkowski, R. M.; LaDuca, R. L. CrystEngComm. 2010, 12, 1927. (h) Aoyagi, M.; Biradha, K.; Fujita, M. Bull. Chem. Soc. Jpn. 2000, 73, 1369. (11) Allen, F. H. Acta Crystallogr. 2002, B58, 380–388. (12) (a) Cameron, A. F.; Taylor, D. W.; Nuttall, R. H. J. Chem. Soc. A 1971, 3402. (b) Li, G.; Song, Y.; Hou, H.; Li, L.; Fan, Y.; Zhu, Y.; Meng, X.; Mi, L. Inorg. Chem. 2003, 42, 913. (c) Tessier, C.; Rochon, F. D. Inorg. Chim. Acta 2001, 322, 37. (13) (a) Prakash, M. J.; Radhakrishnan, T. P. Inorg. Chem. 2006, 45, 9758. (b) Singh, B.; Long, J. R.; de Biani, F. F.; Gatteschi, D.; Stavropoulos, P. J. Am. Chem. Soc. 1997, 119, 7030. (c) Zhao, Q.; Yang, X.-J.; Jia, C.; Wu, B. Inorg. Chem. Commun. 2010, 13, 873. (14) (a) Cameron, A. F.; Taylor, D. W.; Nuttall, R. H. J. Chem. Soc., Dalton Trans. 1972, 422. (b) Kamenar, B.; Brundic, A. H.; Sikirica, M. Cryst.Struct.Commun. 1976, 5, 149. (c) Dakovic, M.; Popovic, Z. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2009, 65, m361. (d) Ge, C.-H.; Zhang, X.-D.; Guan, W.; Guo, F.; Liu, Q.-T. Chin. J. Chem. 2005, 23, 1001. (e) Li, X.-P.; Pan, M.; Zheng, S.-R.; Liu, Y.-R.; He, Q.-T.; Kang, B.-S.; Su, C.-Y. Cryst. Growth Des. 2007, 7, 2481. (f) Wang, Z.; Wilson, S. R.; Foxman, B. M.; Lin, W. Cryst. Eng. 1999, 2, 91. (g) Wang, F.; Wu, X.-Y.; Yu, R.-M.; Zhao, Z.-G.; Lu, C.-Z. J. Coord. Chem. 2009, 62, 3296. (15) (a) Drew, J.; Hursthouse, M. B.; Thornton, P. J. Chem. Soc., Dalton Trans. 1972, 1658. (b) Bailey, A.; Griffith, W. P.; Leung, D. W. C.; White, A. J. P.; Williams, D. J. Polyhedron 2004, 23, 2631. (16) (a) Little, R. G.; Morimoto, C. Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 1981, 37, 1637. (b) Gdaniec, M.; Jaskolski, M.; Kosturkiewicz, Z. Pol. J. Chem. 1979, 53, 2563. (c) Percival, D.; Storey, J. M. D.; Harrison, W. T. A. Acta Crystallogr., Sect. E 2007, 63, o1851. (17) (a) Kumar, D. K.; Jose, D. A.; Dastidar, P.; Das, A. Langmuir 2004, 20, 10413. (b) Fedorov, B. S.; Golovina, N. I.; Fadeev, M. A.; Strukov, G. V.; Kedrov, V. V.; Shilov, G. V.; Boiko, G. N.; Atovmyan, L. O. Izv. Akad. Nauk SSSR, Ser. Khim. (Russ.) (Russ. Chem. Bull.) 2001, 499. (18) McMahon, J.; Gallagher, J. F.; Andersonb, F. P.; Loughc, A. J. Acta Crystallogr., Sect. C 2009, C65, o345. (19) Donnelly, K.; Gallaghera, J. F.; Lough, A. J. Acta Crystallogr., Sect. C 2008, C64, o335. (20) (a) Moncol, J.; Mudra, M.; Lonnecke, P.; Hewitt, M.; Valko, M.; Morris, H.; Svorec, J.; Melnik, M.; Mazur, M.; Koman, M. Inorg. Chim. Acta 2007, 360, 3213. (b) Shi, C.-Y.; Ge, C.-H.; Gao, E.-J; Yin, H.-X.; Liu, Q.-T. Inorg. Chem. Commun. 2008, 11, 703. (c) Ge, C.-H; Zhang, X.-D; Guan, W; Liu, Q.-T. J. Chem. Cryst. 2006, 36, 459. (21) Shi, C.-Y.; Ge, C.-H.; Liu, Q.-T. Acta Crystallogr., Sect. E 2010, 66, m877. (22) Shi, C.-Y.; Gao, E.-J; Ma, S.; Wang, M.-L.; Liu, Q.-T. Bioorg. Med. Chem. Lett. 2010, 20, 7250. (23) Ge, C.-H; Kou, H.-Z; Ni, Z.-H; Jiang, Y.-B; Cui, A.-L. Inorg. Chim. Acta 2006, 359, 541.
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