Crystal Structures of Bis(pyridinecarboxamido) - American Chemical

CRYSTAL GROWTH & DESIGN

Amide-to-Amide Hydrogen Bonds in the Presence of a Pyridine Functionality: Crystal Structures of Bis(pyridinecarboxamido)alkanes

2006 VOL. 6, NO. 1 202-208

Madhushree Sarkar and Kumar Biradha* Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India ReceiVed June 27, 2005

ABSTRACT: Crystal structures of bis(4-pyridinecarboxamido)alkane and bis(3-pyridinecarboxamido)alkane derivatives were determined and analyzed in terms of hydrogen bond networks. Seven crystal structures out of the eight structures studied exhibited amide-to-amide hydrogen bonds. Out of these seven, five form the anticipated β-sheet network whereas two structures form a doubly interpenetrated (4,4)-network. In only one structure does the pyridyl group interfere in the amide-to-amide hydrogen bond, leading to the formation of an N-H‚‚‚N hydrogen bond network. The analyses and rationalization of these structures and also related derivatives in the Cambridge Structural Database suggested that amide-to-amide hydrogen bond formation depends on the interplanar angle between amide and pyridine groups. Introduction Recent times have witnessed a gigantic rise in crystal engineering studies;1 in spite of the number of crystallographically characterized structures, it is still rare to find among them sets of homologous series. Furthermore, the isostructurality of such homologous series is not an obvious fact, as there are clearcut differences in the aggregation, size, and solvation of the molecules. The crystal packing is the result of the optimization of various possible intermolecular interactions between the molecules. Identification of supramolecular synthons between various functional groups simplifies the understanding and prediction of crystal structures to some extent.2 Therefore, the crystal structure prediction is a straightforward exercise, if the given molecule has a smaller number of functional groups which are self-complementary to form predictable robust synthons. As the number of functional groups on a molecule increases, the interference between supramolecular synthons becomes a major concern and an understanding of this phenomenon is an essential aspect for the predetermined packing of the molecules in crystals. For example, the carboxylic acid functional group forms the dimeric synthon I in the absence of any other strongly hydrogen bonding functional groups.3 However, the presence of a pyridine moiety disrupts the formation of synthon I and forms synthon II (Chart 1).4 In this contribution, we wish to present the crystal structures of homologous series of bis(pyridinecarboxamido)alkanes, 2 and 3, and compare these structures with the crystal structures of homologous series of 1 which were already reported.5 Pyridine moieties in 2 and 3 can form N-H‚‚‚N hydrogen bonds with amide N-H groups, thereby disrupting the amide-to-amide hydrogen bond, or they may be involved in two types of C-H‚ ‚‚N hydrogen-bonded synthons (III and IV) when the amideto-amide hydrogen bond is intact. The crystal structures of the phenyl analogues 1, except 1a, contain a β-sheet network, except 1a, which packs further through aromatic π-π and edge-toface interactions. The network exhibited by the structure of 1a can be described as a 2D sheet containing (4,4)-topology. Recently we and others have shown the importance of some of these molecules (2 and 3) in the construction of coordination * To whom correspondence should be addressed. Fax: +91-3222282252. Tel: +91-3222-283346. E-mail: [email protected].

Chart 1

polymers containing hydrogen bonds.6 The focus of our study in the present contribution will be on the following aspects. (1) the homologous series of 1-3 being isostructural; (2) determining when the pyridine moiety interferes in amide-to-amide hydrogen bonds; (3) β-sheet formation via amide-to-amide hydrogen bonds in 1-3; (4) C-H‚‚‚N hydrogen bond synthons III and IV; (5) relation between the geometry of the molecules and hydrogen bond formation; (6) use of the Cambridge structural database to rationalize the observed results. Results and Discussion The compounds 2 and 3 have been prepared by reacting the corresponding diamines with isonicotinic acid and nicotinic acid, respectively. Crystal structures of the compounds 2a-d and 3b-e were determined by single-crystal X-ray diffraction. Our efforts to crystallize 2e and 3a were unsuccessful. Pertinent crystallographic details were given in Table 1. The crystal structures of these analogues exhibit three structural types: a β-sheet,7 a doubly interpenetrated (4,4)-network,8 and an N-H‚ ‚‚N-mediated herringbone network.9 In all the cases the asymmetric units contain half of the molecule as they sit on an inversion center and the alkyl chains exhibit a staggered conformation. In 2a, the hydrogen bonds between amide functionalities were disturbed by the pyridyl groups and form a herringbone network via N-H‚‚‚N hydrogen bonds. Crystal structures of 2c,d and 3c-e exhibit β-sheet networks, while compounds 2b and 3b form a doubly interpenetrated (4,4)-

10.1021/cg050292l CCC: $33.50 © 2006 American Chemical Society Published on Web 09/09/2005

Bis(pyridinecarboxamido)alkanes

Crystal Growth & Design, Vol. 6, No. 1, 2006 203

Table 1. Crystallographic Data and Structure Refinement Parameters for Compounds 2a-d and 3b-e formula mol wt T (K) syst space group a (Å) b (Å) c (Å) R (deg) β (deg) γ (deg) V (Å3) Z Dcalcd (Mg/m3) R1 (I > 2σ(I)) wR2 (on F2; all data)

2a

2b

2c

2d

3b

3c

3d

3e

C14H14N4O2 270.29 293(2) monoclinic P21/n 4.2660(9) 15.070(3) 10.262(2) 90 100.73(3) 90 648.2(2) 2 1.385 0.0423 0.1169

C16H18N4O2 298.34 293(2) monoclinic C2/c 26.519(5) 5.637(1) 10.084(2) 90 101.36(3) 90 1477.9(5) 4 1.341 0.0459 0.1501

C18H22N4O2 326.40 293(2) monoclinic P21/c 5.102(1) 5.279(1) 30.784(6) 90 91.04(3) 90 829.0(3) 2 1.308 0.0408 0.1170


C16H18N4O2 298.34 293(2) monoclinic C2/c 29.146(6) 5.4240(11) 9.852(2) 90 99.29(3) 90 1537.1(5) 4 1.289 0.0451 0.1340



C18H14N4O2 318.33 293(2) triclinic P1h 5.194(1) 6.926(1) 11.034(2) 94.82(3) 102.00(3) 107.64(3) 365.4(2) 1 1.447 0.0350 0.1014

Chart 2. Representations of (a) a β-Sheet Network and (b) a (4,4)-Network

Table 2. Hydrogen Bond Parameters in the Crystal Structures of 2a-d and 3b-e compd

typea

H‚‚‚A (Å)

D‚‚‚O (Å)

D-H‚‚‚A (deg)

2a

N(2)-H(2N)‚‚‚N(1)a C(5)-H(5)‚‚‚O(1)b

2.15 2.62

2.982(3) 3.485(3)

155 155

2b

N(12)-H(12)‚‚‚O(15)c C(12)-H(12A)‚‚‚N(11)d

2.12 2.58

2.945(3) 3.461(4)

161 159

2c

N(2)-H(2)‚‚‚O(6)e C(5)-H(5)‚‚‚N(1)f

2.16 2.60

2.987(3) 3.476(4)

162 156

2d

N(12)-H(12)‚‚‚O(15)g C(12)-H(12A)‚‚‚N(11)h

2.17 2.59

2.999(2) 3.456(3)

162 156

3b

N(12)-H(12)‚‚‚O(10)i C(12)-H(12A)‚‚‚N(11)j

2.07 2.64

2.897(2) 3.534(4)

161 162

3c

N(20)-H(20)‚‚‚O(15)k C(12)-H(12)‚‚‚N(10)l

2.18 2.67

3.001(5) 3.536(7)

159 156

3d

N(20)-H(20)‚‚‚O(10)m C(12)-H(12)‚‚‚N(10)n

2.19 2.67

3.010(3) 3.537(4)

160 155

3e

N(12)-H(12)‚‚‚O(16)o C(12)-H(12A)‚‚‚N(11)p

2.20 2.68

3.014(2) 3.518(3)

158 150

a Symmetry operators: (a) -1/ + x, 5/ - y, 1/ + z. (b) 1/ - x, 1/ + 2 2 2 2 2 y, 1/2 - z. (c) x, -y, -1/2 + z. (d) 1/2 - x, 1/2 + y, 1/2 - z. (e) -1 + x, y, 1 1 1 1 z. (f) -1 - x, - /2 + y, /2 - z. (g) -1 + x, y, z. (h) -x, /2 + y, /2 - z. (i) x, -y, 1/2 + z. (j) 1/2 - x, -1/2 + y, 1/2 - z. (k) x, 1 + y, z. (l) 2 - x, 1/ + y, 1/ - z. (m) x, 1 + y, z. (n) -1 - x, 1/ + y, 1/ - z. (o) 1 + x, y, 2 2 2 2 z. (p) -x, 1 - y, 1 - z.

network (Chart 2). The parameters of hydrogen bonds that are discussed in the text are given in Table 2. Compound 2a does not exhibit an amide-to-amide hydrogen bond in its crystal structure, as the N-H group of the amide engages in N-H‚‚‚N hydrogen bond formation with the pyridyl moiety.10 The network formed can be described as a herringbone network, (4,4)-topology, via N-H‚‚‚N hydrogen bonds (Figure 1). The N-H‚‚‚N network observed here is isostructural with

Figure 1. Crystal structure of 2a: herringbone network via N-H‚‚‚N hydrogen bonds (blue dots) and network of C-H‚‚‚O hydrogen bonds (red dots).

the C-H‚‚‚N network which was observed in the structurally related di-Schiff base ligand of 1,2-ethylenediamine and 4-acetylpyridine.11 Further, the amide O atom in this structure forms a C-H‚‚‚O hydrogen bond with phenyl C-H and forms another (4,4)-topological network via C-H‚‚‚O hydrogen bonds (Figure 1). The disruption of the amide-to-amide hydrogen bond in this structure prompted us to look at the crystal structures of higher analogues of 2 and 3. Here it is noteworthy that the crystal structure of 1a contains an amide-to-amide hydrogen bond but the β-sheet network does not. The crystallization of compound 3a was attempted in several solvents without success. In contrast, the crystal structures of compounds both 2b and 3b contains amide-to-amide hydrogen bonds (N-H‚‚‚O) but not a N-H‚‚‚N hydrogen bond network. Both of the crystal structures are isostructural and do not contain a β-sheet network. The network observed here can be classified as a (4,4)-network when the molecules are considered as points and hydrogen bonds are considered as lines joining those points (Figure 2a). The geometry of the each loop of the network is rectangular with dimensions of 9 × 7.4 Å. Furthermore, the networks observed here are doubly interpenetrated in a parallel fashion (Figure 2b). The double interpenetration occurs through methyl-methyl interactions of alkyl chains which are perpendicular to each other. The angles between alkyl chains in 2b and 3b are 96

204 Crystal Growth & Design, Vol. 6, No. 1, 2006

Sarkar and Biradha

Figure 2. Crystal structures of 2b and 3b: (a) (4,4)-network via N-H‚‚‚O hydrogen bonds in 3b; (b) double interpenetration of networks (pyridyl moieties were not shown for the sake of clarity); (c) side view of the network in 2b; (d) side view of the network in 3b.

Figure 3. 2D layers via C-H‚‚‚N hydrogen bond synthon III: (a) 2b; (b) 3b.

and 105°, respectively. A similar network was exhibited by the ethylene analogue of 1 (1a), but they are non-interpenetrated. In both of the structures, the pyridyl groups point above and below the doubly interpenetrated layers and engage in the formation of the C-H‚‚‚N hydrogen bond synthon III. The layer of 3b has more thickness than that of 2b (14.56 vs 13.26 Å) (Figure 3). Although 2b and 3b have different pyridyl groups, the C-H‚‚‚N hydrogen bond synthons that links the doubly interpenetrated layers are identical. Five compounds, 2c,d and 3c-e, exhibited a β-sheet network in their crystal structures. Except for 3e, all of the remaining four compounds, and also their phenyl analogues, crystallized in the P21/c space group. Further, the unit cell lengths are similar for a and b axes: approximately 5 Å. The structures of 2c,d can be termed as isostructural, as they have striking similarities.

The N-H‚‚‚O hydrogen bonds which propagate the β-sheet run along the a axis for both of the structures (Figure 4). In these structures, the a axis length indicates the repeat distance of the molecules that are involved in β-sheet formation. The pyridyl groups of 2c,d engage in C-H‚‚‚N hydrogen bonds via synthon III and form a layer which is perpendicular to the β-sheet network (Figure 5). In fact, these two structures are isostructural with the phenyl analogues (1b-d), with the exception that the aromatic C-H‚‚‚π interactions observed in 1 are replaced by C-H‚‚‚N interactions. Unlike 2c and 2d, the 3-pyridyl analogues 3c6c and 3d form N-H‚‚‚O hydrogen bonds of β-sheets along the b axis (Figure 6). Further, the β-sheets join together via the C-H‚‚‚N hydrogen-bonded synthon III to form an infinite 2D layer containing N-H‚‚‚O hydrogen bonds and C-H‚‚‚N hydrogen

Bis(pyridinecarboxamido)alkanes


Figure 4. Crystal structures of 2c and 2d, showing the β-sheet networks observed in (a) 2c and (b) 2d.

Figure 5. 2D layers via C-H‚‚‚N synthon III exhibited by crystal structures of (a) 2c and (b) 2d.

bonds. These layers pack along the a axis via π-π and methylmethyl interactions. The compound 3e crystallizes in the space group P1h, whereas its phenyl analogue 1e has two polymorphic forms with the space groups P21/c (monoclinic) and Pbca (orthorhombic).5e,f The monoclinic form exhibits a β-sheet network, while the orthorhombic form exhibits a (4,4)-network similar to the pattern in Chart 2b. However, the crystal structure of 3e exhibits a β-sheet network along the a axis, but the structure observed here is not isostructural with any of the structures of 1e (Figure 7). The β-sheets join together via the C-H‚‚‚N hydrogen bond synthon IV along the c axis. These layers pack along the b axis via aromatic π-π interactions. Geometry of the Molecules versus Hydrogen Bond Formation. Efforts have been made to understand the occurrence

of amide-to-amide hydrogen bonds in the presence of pyridine by analyzing the geometries of the molecules 1-3. From these analyses of the structures it is apparent that the amide-to-amide hydrogen bond occurs only when the interplanar angles (θ) between amide and pyridine planes are greater than or equal to 20°. The structures of 1 have a θ range of 19-30° and accordingly all form amide-to-amide hydrogen bonds (Table 3). Similarly, the structures of 2b-d and 3b-e exhibit a θ range of 20-30° and form amide-to-amide hydrogen bonds, whereas in 2a the θ value is 12° and the structure does not form amideto-amide hydrogen bonds. To verify the observed preference of θ value further, the Cambridge Structural Database was searched for the fragments 4 and 5, with only amides with a trans geometry being considered. The 2-pyridyl derivative was

206 Crystal Growth & Design, Vol. 6, No. 1, 2006

Sarkar and Biradha

Figure 6. Crystal structures of 3c and 3d: β-sheet network exhibited by (a) 3c and (b) 3d. 2D layers containing the β-sheet network and C-H‚‚‚N hydrogen synthon III in the crystal structures of (c) 3c and (d) 3d.

Figure 7. 2D layer containing the β-sheet network and C-H‚‚‚N hydrogen bond synthon IV in the crystal structure of 3e.

not considered, as it has a strong preference for forming the N-H‚‚‚N hydrogen bond multicentered synthon V.

Table 3. Interplanar Angles (θ, deg) between Amide and Aryl Planes in 1-3

1 2 3

In version 5.26 of the database, only five structures for fragment 4 were found with the refcodes ACANOH, BAXNIY, DOBBIF, ESEPUN (2a), and ETENUM (Chart 3).12 The

a

b

c

d

e

19 11.9

30.0 29.4 20.7

29.3 29.5 26.4

29.2 29.3 26.8

29, 24 29.4

structures of ACANOH and DOBBIF have the amide-to-amide hydrogen bonds despite the presence of pyridine and other strong hydrogen acceptors and donors; further, they have θ values greater than 20° (23 and 33°). The compound ETENUM has a θ value of 24.6° but does not exhibit an amide-to-amide hydrogen bond, as the amide N-H group forms a multicentered hydrogen bond with PdO. In contrast, BAXNIY has an amide-

Bis(pyridinecarboxamido)alkanes Chart 3.

Chart 4.

Chemical Drawings of the Structures Containing Fragment 4

Chemical Drawings of the Structures Containing Fragment 5 and the Interplanar Angles (θ)

to-amide hydrogen bond but the θ value is less than 20° (14°). The reason for this could be that the aryl ring, which is attached to the N of amide, is perpendicular to the amide plane. Fragment 5 was found in 13 structures which have the refcodes ENIXOO, FILHUD, FUDZOT, FUWNIU, HIFWUO, HIFXAV, JEPMAS, MBNICT, MURWUR, PYDCXA10, RETBOH, TEJFIX (3c), and YEDKEX (Chart 4). Out of these 13, 8 structures from amide-to-amide hydrogen bonds, and interestingly all eight of these structures have a θ value of greater than 20°. The remaining five structures (ENIXOO, HIFWUO, HIFXAV, MURWUR, YEDKEX) do not form amide-to-amide hydrogen bonds and contain θ values of less than 20°. These structures clearly indicate that amide-to-amide hydrogen bond formation occurs only if the θ value is greater than or equal to 20°.


Conclusion The results presented here reveals that the crystal structures of homologous series of 2 and 3 are not completely isostructural and there exist subtle differences. These analogues exhibited three types of structural features, namely (1) a β-sheet via N-H‚ ‚‚O hydrogen bonds, (2) a (4,4)-network via N-H‚‚‚O hydrogen bonds, and (3) a herringbone network via N-H‚‚‚N hydrogen bonds. The results obtained here indicate that the pyridyl group does not interfere in amide-to-amide hydrogen bonds, provided the interplanar angle θ is greater than or equal to 20° and participates in two types of C-H‚‚‚N hydrogen bond synthons. The interplay between the β-sheet and (4,4)-network is not well understood from the molecular geometries of 1-3. However, from the packing point of view it can be said that the β-sheet is favored only when the interactions between the spacers are good enough. Accordingly, the higher alkyl spacers (n-hexyl and n-octyl) and phenyl formed the β-sheet network, whereas spacers such as ethyl and n-butyl formed the (4,4)-networks. Experimental Section Synthesis of N,N′-Bis(4-pyridinecarboxamide)-1,2-ethane (2a). 1,2-Diaminoethane (1.0 mL, 0.016 mol) was added to a 50 mL pyridine solution of isonicotinic acid (4.0 g, 0.032 mol), and the solution was stirred for 15 min. To this solution was added triphenyl phosphite (9.0 mL, 0.032 mol), and the mixture was refluxed for 6 h. The volume of solution was reduced to 5.0 mL by distilling out the pyridine, and a white precipitate was obtained from the solution. The solid was filtered and washed with ethanol. Yield: 70%. Mp: 278-280 °C. Anal. Calcd for C14H14N4O2: C, 62.22; H, 5.19; N, 20.74. Found: C, 62.29; H, 4.72; N, 20.60. Synthesis of Compounds 2b-e and 3a-e. A procedure similar to that above was adopted for the synthesis of 2b-e and 3a-e by using corresponding diamines and pyridinecarboxylic acids. 2b. Yield: 66%. Mp: 230-232 °C. Anal. Calcd for C16H20N4O2: C, 64.42; H, 6.04; N, 18.79. Found: C, 65.01; H, 5.98; N, 18.91. 2c. Yield: 70%. Mp: 178-180 °C. Anal. Calcd for C18H24N4O2: C, 66.25; H, 6.75; N, 17.18. Found: C, 65.56; H, 6.61; N, 16.61. 2d. Yield: 65%. Mp: 165-166 °C. Anal. Calcd for C20H28N4O2: C, 67.79; H, 7.34; N, 15.81. Found: C, 68.5; H, 7.59; N, 15.68. 2e. Yield: 90%. Mp: >300 °C. Anal. Calcd for C18H14N4O2: C, 67.9; H, 4.4; N, 17.6. Found: C, 66.93; H, 3.85; N, 16.51. 3a. Yield: 56%. Mp: 216-220 °C. Anal. Calcd for C14H14N4O2: C, 62.22; H, 5.19; N, 20.74. Found: C, 62.56; H, 5.22; N, 20.88. 3b. Yield: 50%. Mp: 199-204 °C. Anal. Calcd for C16H20N4O2: C, 64.42; H, 6.04; N, 18.79. Found: C, 64.39; H, 5.90; N, 18.41. 3c. Yield: 60%. Mp: 155-156 °C. Anal. Calcd for C18H24N4O2: C, 66.25; H, 6.75; N, 17.18. Found: C, 66.20; H, 6.78; N, 17.19. 3d. Yield: 50%. Mp: 150-154 °C. Anal. Calcd for C20H28N4O2: C, 67.79; H, 7.34; N, 15.81. Found: C, 68.02; H, 7.17; N, 15.67. 3e: Yield: 80%. Mp: >300 °C. Anal. Calcd for C18H14N4O2: C, 67.9; H, 4.4; N, 17.6. Found: C, 67.61; H, 3.96; N, 16.76. Database Searches. The structural data of the compounds discussed in the paper were obtained through systematic searches of the Cambridge Structural Database (version 5.26, 325 709 hits). The fragments 4 and 5 were searched using Conquest version 1.7. Only the structures containing R factors

Crystal Structures of Bis(pyridinecarboxamido) - American Chemical

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