Journal of Molecular Structure 688 (2004) 79–86 www.elsevier.com/locate/molstruc Structures and vibrational spectra of indole carboxylic acids. Part I. Indole-2-carboxylic acid Barbara Morzyk-Ociepaa, Danuta Michalskab,*, Adam Pietraszkoc a Institute of Chemistry and Environmental Protection, Pedagogical University, Al. Armii Krajowej 13/15, 42-200 Cze˛stochowa, Poland b Institute of Inorganic Chemistry, Wrocław University of Technology, ul. Smoluchowskiego 23, 50-370 Wroclaw, Poland c Institute of Low Temperature and Structural Research, Polish Academy of Science, ul. Okólna 2, 50-950 Wroclaw, Poland Received 30 July 2003; accepted 24 September 2003 Abstract The crystal and molecular structures of indole-2-carboxylic acid (ICA) have been determined using single crystal X-ray diffraction, infrared spectroscopy and theoretical methods. The crystals are orthorhombic, space group Pna21, with a ¼ 30:144ð6Þ Å, b ¼ 6:466ð1Þ Å, c ¼ 3:819ð1Þ Å, V ¼ 744:4ð3Þ Å3 and z ¼ 2: The structure analysis revealed that two chains of ICA molecules form a planar ribbon, held together by intermolecular O – H· · ·O and N– H· · ·O hydrogen bonds. Both the O – H and N – H groups act as the donors, while the O atom of the carboxylic group is the acceptor of two hydrogen bonds. The carboxylic groups of ICA molecules in two chains are oriented perpendicularly to each other, which leads to formation of the zig-zag pattern of intermolecular hydrogen bond. Interestingly, the molecular layers, separated by about 3.819 Å in a stack, form a herringbone-like arrangement with the adjacent stacks. Theoretical studies of the four possible conformers of ICA monomer have been performed with ab initio (HF and MP2) and density functional (B3LYP) methods. The calculated bond lengths and angles of the most stable structure are in good agreement with the corresponding experimental results. The infrared spectrum of ICA in the solid state well supports the results from X-ray analysis. q 2003 Elsevier B.V. All rights reserved. Keywords: Indole-2-carboxylic acid; Crystal; Molecular structure; Hydrogen bond; Ab initio; Density functional calculations; Infrared spectra 1. Introduction The increasing interest in indole-2-carboxylic acid (ICA) and its derivatives is mainly due to their various biological activities: anticonvulsant effects [1,2]; antihypertensive ; antiarrhytmic  and antifungal [5,6] properties. Indole-2carboxylic acid hydrochloride is an active antagonist with high affinity for the N-methyl-D -aspartate (NMDA) receptor glycine-binding sites . ICA has been applied for evaluation of the effect of glycine site antagonist on memory and motor dysfunction following brain injury . The crystal structure of 3-bromobenzoyloctahydro-1Hindole-2-carboxylic acid has been reported . Molecular cocrystals of ICA with 2-aminopyrimidine ; 5-nitroquinoline ; 3,5-dinitrobenzoic acid ; 2-aminothiazoles ; 4,4-dipyridyl ; 2-amino-5-chlorobenzooxazole  and sulfamethazine  have been prepared and * Corresponding author. Tel.: þ 48-71-203759; fax: þ 8-71-224330. E-mail address: email@example.com (D. Michalska). 0022-2860/$ - see front matter q 2003 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2003.09.027 studied by X-ray diffraction techniques. However, no single crystal X-ray diffraction analysis has been performed for indole-2-carboxylic acid, as yet. In this work, we report for the first time, the crystal and molecular structure of the title molecule. The ab initio (HF and MP2) as well as density functional (DFT) methods have been applied to calculate the energy and geometrical parameters of four possible conformers of ICA. The results from X-ray analysis are supported by the infrared spectra. 2. Experimental 2.1. Preparation of crystals of indole-2-carboxylic acid Crystals of ICA were prepared as follows: to a suspension of 1 mmol (0.161 g) of ICA (Lancaster) in ethanol (50 cm3) was added 1 mmol (0.075 g) of KCl dissolved in H2O (10 cm3). The mixture was heated to 80 B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 Table 1 Crystal data and structure refinement for indole-2-carboxylic acid (ICA) Empirical formula Formula weight Temperature (K) Crystal system Space group Unit cell dimensions (Å) Volume (Å3) Z (molecule/cell) Density calculated (Mg m23) Crystal size (mm) Absorption coefficient (mm21) Fð000Þ Theta range for data collection (8) Reflections collected/unique Independent reflections Data/restraints/parameters Goodness-of-fit on F 2 Final R indices ½I . 2sigmaðIÞ R indices (all data) C9H7NO2 161.15 293(2) Orthorhombic Pna21 a ¼ 30:144ð6Þ b ¼ 6:466ð1Þ c ¼ 3:819ð1Þ 744.4(3) 4 1.438 0.28 £ 0.21 £ 0.19 0.103 336 4.62–26.0 6272/1392 ½RðintÞ ¼ 0:0644 1392 1392/1/138 0.899 R1 ¼ 0:0414; wR2 ¼ 0:0635 R1 ¼ 0:0743; wR2 ¼ 0:0741 240 K until ICA dissolved completely. After a week, yellow-crystals of ICA were formed. 2.2. X-ray analysis The X-ray diffraction data were collected using an automatic X-ray four-circle EXCALIBUR single crystal diffractometer with CCD area detectors. Graphite monochromated Mo Ka radiation (l ¼ 0:071073 nm) was generated at 50 kV and 25 mA. A single image for 18 rotation around the v-axis was obtained during 30 s and the full set of X-ray diffraction was collected in the u angle over the range from 4.62 to 26.08. The intensities of the reflections were recorded in 900 frames (each frame consisting of 512 £ 512 pixels with 2 £ 2 pixels binning). The lattice parameters were calculated from refinement of positions of all measured reflections. The data were corrected for Lorentz and polarization effects. No absorption correction was applied. The structure was solved by direct methods (program SHELXS-97  and refined by the full-matrix least-squares method based on F 2 using SHELXL-97 . All non-hydrogen atoms were refined anisotropically by unit-weighted full-matrix least-square methods. Hydrogen atoms were included from the difference Fourier Dr maps and refined with isotropic thermal parameters. Several cycles of refinement reduced the R value to 0.041 and wR2 to 0.063 for 1392 independent reflections. The crystal data together with the refinement details are given in Table 1. 2.3. Infrared measurements The FT-infrared spectrum of solid ICA in the region 4000– 400 cm21 was measured on a Nicolet-Nexus spectrometer using the KBr pellets. 2.4. Theoretical methods Calculations were performed by the HF and MP2 methods and B3LYP functional [19,20]. Two basis sets were employed: 6-311þ þ G(df,p), in HF method, and 6311þ þ G(d,p) [21,22] in B3LYP and MP2 methods. All calculations were carried out with the Gaussian 98 package . 3. Results and discussion 3.1. Theoretical studies on the conformers of indole-2carboxylic acid Full optimization of geometry has been performed for four possible ICA conformers, which differ in the relative orientation of atoms in the carboxylic group, as shown in Fig. 1. Structure I (in which the OH group is in the anti- Fig. 1. Relative differences in energy ðDEÞ between four conformers of ICA. The minimum energy values (in kcal mol21) are as follows: 2344665.1 (HF); 2346734.3 (B3LYP) and 2345776.4 (MP2). B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 81 Table 2 The selected bond lengths (Å) and bond angles (8), with e.s.d.s. in parentheses, determined for ICA by X-ray diffraction and the corresponding theoretical parameters, calculated for conformer I by the HF, B3LYP and MP2 methods Exp. Fig. 2. Overall view of indole-2-carboxylic acid (ICA) with atom labeling. position to the N –H group) is the most stable, as revealed by calculations at the HF, MP2 and DFT(B3LYP) levels of theory. Conformer II is slightly higher in energy, by about 1.1 –1.4 kcal mol21. In this isomer, the COOH group has rotated (by 1808), in comparison to I. Remaining conformers, III and IV are higher in energy, by about 5 kcal mol21. Subsequent calculations of vibrational frequencies have revealed that both I and II are stable, in the gas phase. 3.2. Description of the structure The overall view of ICA molecule with atom labeling is shown in Fig. 2. The single crystal X-ray diffraction study indicates the presence of conformer I in crystal. Selected bond lengths and angles are listed in Table 2, along with the corresponding theoretical values calculated by the HF, MP2 and B3LYP methods. It should be noted that the calculations have been performed for an isolated ICA molecule, in the gas phase, but agreement between the theoretical and experimental results is quite good. Some deviations from the experimentally observed values can be attributed to hydrogen bonds in the solid state. As follows from Table 2, the C0 – O1 bond length of 1.227(1) Å is slightly longer than the theoretical values, and this is caused by intermolecular hydrogen bonding in crystal. It should be emphasized that the calculated bond angles show very good agreement with experimental data. For example, the B3LYP-predicted angles: O1 –C0 – O2 (122.98) and O2 – C0 – C1 (113.18) agree well with experimental, 121.6(1) and 112.5(1)8, respectively. Several bond angles, e.g. N1 –C1 – C2 (109.48) are almost reproduced by the B3LYP calculation, as shown in Table 2. The biggest deviation between the calculated and experimental bond angle is noted for the C0 –O2 – H11 group. This is attributed to intermolecular hydrogen bonding in the crystal of ICA, which leads to an increase (opening) of the C0 – O2 – H11 angle, by about 108, in comparison with the theoretical value of the isolated monomer. O(1) –C(0) O(2) –C(0) O(2) –H(11) C(0)–C(1) C(1)–C(2) C(1)–N(1) C(2)–C(3) C(2)–H(1) C(3)–C(8) C(3)–C(4) C(4)–C(5) C(4)–H(4) C(5)–C(6) C(5)–H(5) C(6)–C(7) C(6)–H(6) C(7)–C(8) C(7)–H(7) C(8)–N(1) N(1) –H(2) O(1) –C(0)–O(2) O(1) –C(0)–C(1) O(2) –C(0)–C(1) C(0)–O(2) –H(11) C(0)–C(1) –N(1) N(1) –C(1)–C(2) C(1)–C(2) –C(3) C(1)–C(2) –H(1) C(2)–C(3) –C(8) C(2)–C(3) –C(4) C(3)–C(4) –C(5) C(3)–C(4) –H(4) C(4)–C(5) –C(6) C(4)–C(5) –H(5) C(5)–C(6) –C(7) C(5)–C(6) –H(6) C(6)–C(7) –C(8) C(6)–C(7) –H(7) C(7)–C(8) –C(3) C(7)–C(8) –N(1) C(8)–N(1) –C(1) C(1)–N(1) –H(2) 1.227(1) 1.326(1) 0.951(11) 1.439(1) 1.369(1) 1.384(1) 1.416(2) 0.932(9) 1.403(1) 1.409(2) 1.357(2) 0.974(8) 1.404(2) 0.964(8) 1.372(2) 1.026(11) 1.390(2) 1.045(10) 1.383(1) 0.968(11) 121.6(1) 125.9(1) 112.5(1) 116.0(6) 121.8(1) 109.4(1) 107.6(1) 125.3(6) 106.9(1) 134.2(1) 118.7(1) 117.0(5) 121.4(1) 121.2(5) 121.5(1) 117.7(6) 117.2(1) 122.6(6) 122.2(1) 129.6(1) 107.9(1) 122.9(7) HF 1.187 1.332 0.945 1.467 1.352 1.371 1.432 1.070 1.400 1.401 1.368 1.076 1.409 1.075 1.368 1.075 1.398 1.075 1.359 0.992 123.1 123.5 113.4 108.9 119.0 110.1 106.5 125.8 106.7 133.8 118.9 120.4 120.8 120.1 121.7 119.0 117.4 121.2 121.8 130.2 108.7 126.0 B3LYP 1.214 1.354 0.968 1.459 1.378 1.384 1.427 1.078 1.426 1.408 1.383 1.084 1.413 1.084 1.385 1.084 1.400 1.084 1.371 1.008 122.9 124.0 113.1 106.9 118.6 109.4 106.9 125.3 107.0 134.0 118.9 120.4 121.1 119.8 121.6 119.2 117.4 121.2 122.0 130.6 109.2 123.1 MP2 1.218 1.352 0.969 1.464 1.390 1.376 1.427 1.082 1.430 1.414 1.389 1.087 1.418 1.087 1.391 1.087 1.404 1.087 1.373 1.012 123.7 123.7 112.6 105.9 118.3 109.6 106.5 125.3 107.1 134.0 118.7 120.4 121.4 119.6 121.4 119.3 117.2 121.2 122.3 130.3 109.4 123.1 According to the X-ray results, the conjugated sixmembered and five-membered rings of indole part are nearly coplanar, for example, the C2 – C3 –C8 – C7 torsional angle is 179.0(1)8, and N1 –C1 – C2 – C3 torsional angle is nearly zero (0.1(1)8). The carboxylic group of ICA shows only a small distortion from the molecular plane: the dihedral angle between the best least-squares planes formed by the indole ring atoms (C1, C2, C3, C4, C5, C6, C7, C8 and N1) plane I, and the carboxylic group atoms (C0, O1 and O2) plane II, is 2.98(0.13)8. Comparison of the X-ray data of ICA (this work) and those of the parent indole  indicates that the presence of 82 B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 Table 3 Hydrogen bonds distances (Å) and angles (8) in ICA D –H· · ·A D –H H· · ·A D· · ·A /D–H· · ·A O(2) –H(11)· · ·O(1)i N(1) –H(2)· · ·O(1)ii 0.951(11) 0.969(11) 1.749(11) 2.172(11) 2.659(1) 3.118(1) 159.2(10) 165.3(10) Symmetry transformations used to generate equivalent atoms: (i) 2x þ 3=2; y þ 1=2; z þ 1=2; (ii) 2x þ 3=2; y 2 1=2; z 2 1=2: the carboxylic group affects the bond lengths and angles in the conjugated rings. For example, in ICA, the N1 –C1 and N1 – C8 bond lengths are longer (1.384(1) and 1.383(1) Å, respectively) than in indole (1.370 Å). On the other hand, both the C3 – C4 and C4 – C5 bonds in ICA (1.409(2) and 1.357(2) Å, respectively) are shorter than the corresponding bands in indole molecule (1.425 and 1.382 Å). It should also be noted that in ICA, the C3 – C8 bond length (1.403(1) Å) is elongated, in comparison to indole (1.382 Å) . Hydrogen bond lengths and bond angles of ICA are shown in Table 3. Fig. 3 illustrates the H-bond pattern in the crystal. The planar ribbon consists of two chains of molecules held together by intermolecular hydrogen bonds. It should be emphasized that the pattern of the intermolecular hydrogen bonding is different than that observed in typical cyclic carboxylic acid dimers. It is seen that the carboxylic group of the ICA molecule in one chain is facing almost perpendicularly to the direction of the carboxylic group in the other chain. This is caused by the fact that ICA contains two hydrogen-bond donor sites, the carboxylic O2 –H and indole N1 –H groups which point toward an approximately orthogonal directions. Both the O2 – H11 and N1 – H2 groups act as donor sites, while the O1 atom acts as the acceptor site for two hydrogen bonds, as shown in Table 3 and in Fig. 3. Of the two hydrogen bonds, O2 – H11· · ·(O1)i (i: 2x þ 3=2; y þ 1=2; z þ 1=2) and N1 – H2· · ·(O1)ii (ii: 2x þ 3=2; y 2 1=2; z 2 1=2) with the D· · ·A distances of 2.659 and 3.118 Å, and /D –H· · ·A angles of 159.2 and 165.38, respectively, the former is of a moderate strength, while the latter (N –H· · ·O) is much weaker. Interestingly, these hydrogen bonds form the nine-membered rings, which share the common C0 –O1 bond. This leads to a zig-zag structure of the H-bonded rings. Fig. 4 shows the packing arrangement of the molecules in the unit cell, viewed down c-axis. The ribbons containing the nine-membered hydrogen bonded zigzag rings are running along the b-axis. Fig. 5 shows the projection of the crystal structure on the 011 plane. It is interesting that the parallel layers consisting of molecular ribbons in one stack (column) are in a skew orientation with respect to the layers in the adjacent stacks. It should be noted that the carboxylic oxygen atoms in one layer are positioned above (or below) the oxygen atoms in the neighboring layers. Such an arrangement increases repulsion between the lone electron pairs of the oxygen atoms in the parallel layers, which decreases p – p stacking interaction between the aromatic rings in the neighboring layers. Consequently, these effects increase the distance between the parallel layers, to 3.819 Å. Fig. 3. The hydrogen bonding pattern in ICA (H-bonds are indicated by dashed lines). B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 83 Fig. 4. The arrangement of the ICA molecules in the unit cell, viewed down c-axis. Fig. 6 shows the projection of ICA crystal down the aaxis. It is seen that the planar layers form a herringbone-like arrangement between the adjacent stack. The torsion angle between the two adjacent stacks (determined as the angle between the normals to planes defined by indole rings of ICA molecules, in adjacent stacks) is equal to 49.58. This is a measure of the twist of ICA molecules in one stack with respect to those in an adjacent stack. It should be mentioned that very recently, a similar packing arrangement has been reported for 1,2,4,5-tetrazines . 3.3. Infrared spectrum The infrared spectrum of indole-2-carboxylic acid in the solid state (KBr pellets) is shown in Fig. 7. Recently, Tine et al.  studied the infrared spectrum of ICA, assuming that the two molecules form cyclic dimer associated by two O – H· · ·O hydrogen bonds, typical of carboxylic acid dimers, while the N – H group of ICA is not involved in hydrogen bonding. As we have shown in this work, the structure assumed by those authors was incorrect, since both the O –H and N – H groups of ICA (oriented in nearly orthogonal directions) act as the donors of hydrogen bonds. The strong band in the IR spectrum of ICA, at 3350 cm21, can be assigned to nðN – HÞ stretching vibration of the molecules associated by intermolecular N – H· · ·O hydrogen bond. In addition, a small satellite band is observed at 3453 cm21. Most probably, the latter band arises from the non-associated, end N –H groups of the ICA chains in the crystal. A strong and very broad band occurring between 3200 and 2000 cm21 is due to the nðO – HÞ stretching mode of the OH group involved in intermolecular O –H· · ·O hydrogen bond. Significant lowering and broadening of the nðO – HÞ band indicates that the O – H· · ·O hydrogen bond is stronger than N –H· · ·O hydrogen bond, which is confirmed by the X-ray data of ICA. The very strong band at 1707 cm21 is assigned to the nðCyOÞ stretching vibration. The frequency of this vibration is slightly lower than the frequency of the non-associated carboxylic CyO group in 9,10-dihydro-9-oxo-10-acridineacetic acid (1737 cm21) . This supports the conclusion that in the crystal of ICA, the CyO group participates in intermolecular hydrogen bonding. It should also be noted, that the CyO bond arising from the cyclic dimer of acetic acid was observed at 1681.5 cm21, in the gaseous state . In the IR spectrum of ICA, the strongest band appearing at 1194 cm21 can be assigned to the nðC – OÞ stretching vibration in the carboxylic group. Thus, the large difference between the frequencies of nðCyOÞ and nðC – OÞ stretching vibrations of the carboxylic group excludes the possibility of the existence of deprotonated B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 Fig. 5. Projection of the crystal structure of ICA on the 011 plane. 84 B. Morzyk-Ociepa et al. / Journal of Molecular Structure 688 (2004) 79–86 85 Fig. 6. Projection of the crystal structure of ICA along the a-axis. Fig. 7. The infrared spectrum of indole-2-carboxylic acid. ICA in crystal. In should be noted that in the IR spectrum of sodium indole-2-carboxylate (in solid state), two strong bands at 1562 and 1409 cm21 were assigned to asymmetric na ðCOO2 Þ and symmetric ns ðCOO2 Þ stretching vibrations, respectively . The presented assignment of the characteristic vibrations of ICA in the IR spectrum provides additional evidence for the structure and hydrogen bonding determined by the X-ray method. 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