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X-ray diffraction and vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes
Vibrational Spectroscopy 49 (2009) 68–79
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X-ray diffraction and vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes Part VII. Indole-2-carboxylic acid and catena-poly[[diaquazinc(II)]-bis (m2-indole-2-carboxylato-O:O0 )] Barbara Morzyk-Ociepa * Institute of Chemistry and Environmental Protection, Jan Długosz University, Armii Krajowej 13/15 Avenue, 42-200 Cze˛stochowa, Poland
A R T I C L E I N F O
A B S T R A C T
Article history: Received 29 November 2007 Received in revised form 25 April 2008 Accepted 28 April 2008 Available online 8 May 2008
The catena-poly[[diaquazinc(II)]-bis(m2-indole-2-carboxylato-O:O0 )], [Zn(I2CA)2(H2O)2]n has been synthesized and characterized by X-ray diffraction analysis and the infrared and Raman spectroscopic methods. The co-ordination of the indole-2-carboxylate anion to Zn(II) results in the formation of the [Zn(I2CA)2(H2O)2]n, in which the Zn(II) cations lie on inversion centres in space group P21/c, with water ligands in the apical sites of octahedral geometry. Moreover, the infrared and Raman spectra of indole-2carboxylic acid (I2CA) and the infrared spectrum of deuterated derivative of indole-2-carbocylic acid (I2CA-d2) are recorded in the solid phase. The theoretical wavenumbers, infrared intensities and Raman scattering activities were calculated by density functional B3LYP and mPW1PW91 methods with the 6311++G(d,p) basis set for I2CA and I2CA-d2 and with the 6-311++G(d,p)/LanL2DZ basis sets for the theoretical model of Zn(I2CA)2(H2O)2]n. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution for all molecules. ß 2008 Elsevier B.V. All rights reserved.
Keywords: Zinc complex Indole-2-carboxylic acid Crystal Molecular structure Hydrogen bond FT-IR and FT-Raman spectra Density functional theory
1. Introduction The indole-2-carboxylic acid (I2CA) moiety is present in a great number of molecules with a broad spectrum of pharmacological activity, anticonvulsant, antihypertensive, antiarrhytmic and antifungal properties [1–7]. It has been found that the biological activities of the therapeutic agents are considerably increased when they are bonded into metal complex molecules. For example, such effects have been observed for Zn(II) and Cu(II) chelates with indomethacin (which is a derivative of indole-3-acetic acid). These complexes of indomethacin are superior to uncomplexed indomethacin for treatment of a range of conditions and most importantly induce considerably lower incidences of gastrointestinal damage [8–13]. To gain deeper insight into the factors controlling the metal complex biological activity, it is first necessary to know the binding properties of the biological ligands to the metal ions as well as the geometrical structures and spectroscopic data of the complexes.
* Tel.: +48 34 366 5322; fax: +48 34 366 5322. E-mail address: [email protected]. 0924-2031/$ – see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.vibspec.2008.04.014
Tine et al. [14] performed the subtracted-infrared (SUBSTR-IR) spectra of mixtures of indolecarboxylic acids and lanthanide. Authors conclude that indolecarboxylates can form in DMSO associations with Ln(III) ions, including bidentate and monodentate complexes [14]. The molecular structures of Co(II), Ni(II) and Cu(II) with indole-2-carboxylic acid and 4-substituted hydrazinethiocarbamide were proposed by molar conductance, electronic, IR, 1H NMR, mass spectra as well as thermogravimetric (TG) by Achmed [15]. The structural studies of Sn(IV) with indole2-carboxylic acid and chlorobenzyl were performed by Han-Dong et al. [16]. Moreover, Viossat et al. [17–19] performed structural studies of Mn(II) and Zn(II) complexes with indole-2-carboxylic acid and 2,9-dimethyl-1,10-phenanthroline or imidazole, with differ by solvate molecule (dimethylacetemide, dimethylformamide and dimethyl sulfoxide) in the crystal structure and the authors shortly discussed the infrared spectra of these complexes. In this work, we continue the studies on the synthesis and vibrational spectra of indolecarboxylic acids and their metal complexes [20–25]. In this paper, the [Zn(I2CA)2(H2O)2]n is examined using single crystal X-ray diffraction analysis. Moreover, the infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and infrared spectrum of I2CA-d2 are discussed.
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2. Experimental 2.1. Preparation of the crystals of [Zn(I2CA)2(H2O)2]n Crystals of [Zn(I2CA)2(H2O)2]n were prepared as follows. To a suspension of 0.16 g of indole-2-carboxylic acid (Lancaster) in ethanol (50 cm3) the 0.14 g of ZnCl22H2O and 2 cm3 1 M NaOH were added. The mixtures were heated to 318 K for about 1 h. The obtained solutions were filtered and left for crystallization. After a week translucent crystals of [Zn(I2CA)2(H2O)2]n were formed. The deuterated derivative I2CA-d2 was prepared by repeated crystallization from C2H5OD. 2.2. X-ray diffraction analysis The X-ray diffraction data were collected at 290(2) K, using an XCALIBURTM 3 CCD diffractometer with graphite-monochromated Mo Ka radiation (l = 0.71073 A˚). The structure was solved by direct methods using the SHELXS-97 program [26] and refined by full-matrix least-squares on F2 with SHELXL-97 [26]. The hydrogen atoms bonded to C and N atoms were introduced at calculated positions as riding atoms, with C–H and N–H distances of 0.93 and 0.86 A˚, respectively, while the O-bound H atoms were located from difference maps. The O–H distances were restrained with a DFIX command in SHELXL-97 [26]. For all H atoms, Uiso (H) values were constrained to be 1.2 Ueq (C, N) or 1.5 Ueq (O). Complete crystallographic data have been deposited at the Cambridge Crystallographic Data Centre and allocated under deposition number CCDC 668995. The crystal data together with the refinement details are given in Table 1. 2.3. Spectroscopic measurements The infrared spectra of solid I2CA, I2CA-d2 and [Zn(I2CA)2 (H2O)2]n in the region 4000–400 cm1 were measured at 2 cm1 resolution on a Nicolet-Nexus spectrometer using the KBr pellet technique. The far infrared spectra in the frequency range 700– 50 cm1 were measured at 2 cm1 resolution on a PerkinElmer 2000 FT-IR spectrometer. Samples were prepared as Nujol mulls placed between polyethylene windows.
Table 1 Crystal data and structure refinement for [Zn(I2CA)2(H2O)2]n Empirical formula Formula weight Temperature (K) Crystal system Space group
C18H16ZnN2O6 421.71 290(2) Monoclinic P21/c
Unit cell dimensions (A˚, 8)
a = 17.8339 (14) b = 6.4682 (5) c = 7.4305 (6) b = 90.795 (8) 857.05 (12) 2 1.634 0.12 0.09 0.01 1.473 Analytical [27] 432 3.9 to 25.4 4505 1534 1534/3/133 0.98 R1 = 0.069, wR2 = 0.159 0.72, 0.66 <0.001
Volume (A˚ 3) Z (molecule/cell) Density calculated (Mg m3) Crystal size (mm) Absorption coefficient (mm1) Absorption correction F(0 0 0) Theta range for data collection(8) Reflections collected Independent reflections Data/restraints/parameters Goodness-of-fit on F2 Final R indices [I > 2sigma(I)] Drmax and Drmin (e A˚3) D/smax
69
The FT-Raman spectrum of solid I2CA was recorded on a Nicolet Magna 860 spectrometer at 2 cm1 resolution and with an exciting laser operating at 1064 nm. The Raman spectrum of solid [Zn(I2CA)2(H2O)2]n was recorded on a Nicolet Almega dispersive Raman spectrometer at 2 cm1 resolution with an exciting laser operating at 780 nm. 2.4. Theoretical methods The theoretical studies have been performed using the threeparameter density functional method, B3LYP [28,29] and oneparameter hybrid method, mPW1PW91, introduced by Adamo and Barone [30] with the LanL2DZ [31] basis set for zinc atoms and the 6-311++G(d,p) [32,33] basis set for the remaining atoms of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n. In Part I [20] we have determined the crystal structure of I2CA and we have performed theoretical studies of the four possible conformers of I2CA, which differed in the relative orientation of atoms in the carboxylic group. Conformer I (shown in Scheme 1) in which the OH group is in the anti-position the NH group was the most stable, as revealed the ab initio (HF and MP2) and density functional (B3LYP) calculations. Moreover, the single crystal X-ray diffraction study indicated the presence of conformer I in crystal. It should be noted that the calculations have been performed for an isolated I2CA molecule, but agreement between the theoretical and experimental bond lengths and bond angles was good [20]. Therefore, the harmonic wavenumbers, infrared intensities and Raman scattering activities were calculated for conformer I of I2CA and I2CA-d2. For [Zn(I2CA)2(H2O)2]n the theoretical model was limited to bidentate I2CA representing the ligand bonded to two zinc ions via two oxygen atoms of carboxylic group. Prior to normal mode calculations, the optimization of molecular geometry was carried out starting from structural parameters determined by the X-ray method for [Zn(I2CA)2(H2O)2]n. Selected bond lengths and angles are listed in Table 2, along with the corresponding theoretical values calculated for theoretical model of [Zn(I2CA)2(H2O)2]n by the B3LYP and mPW1PW91 methods. The biggest deviation between the calculated and experimental values are noted for the C–O–Zn bond angles, as the result of the limitation of the theoretical model. Basing on the optimized structure for the theoretical model of [Zn(I2CA)2(H2O)2]n, the normal vibration wavenumbers, IR intensities and Raman activities were calculated. The deficiencies of the computed harmonic force field of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n were corrected by selective scale factors. The wavenumbers calculated by the B3LYP and mPW1PW91 methods were scaled, similarly as in our earlier studies [22–25].
Scheme 1. The atom numbering for I2CA.
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Table 2 Comparison of experimental and theoretical bond lengths (A˚) and angles (8) for theoretical model of [Zn(I2CA)2(H2O)2]n calculated by the mPW1PW91 and B3LYP methods with 6-311++G(d,p)/LanL2DZ basis sets
C(5)–C(6) C(6)–C(7) C(7)–C(8) C(3)–C(8) C(3)–C(4) C(2)–C(3) C(1)–C(2) N(1)–C(1) C(1)–C(0) C(0)–O(2) C(0)–O(1) O(2)–Zn O(1)–Zn C(5)–C(6)–C(7) C(6)–C(7)–C(8) C(7)–C(8)–C(3) C(8)–C(3)–C(4) C(8)–C(3)–C(2) C(3)–C(2)–C(1) C(2)–C(1)–N(1) C(2)–C(1)–C(0) C(1)–C(0)–O(2) C(1)–C(0)–O(1) C(0)–O(2)–Zn C(0)–O(1)–Zn
Experimental
mPW1PW91
B3LYP
1.393 (15) 1.356 (12) 1.382 (10) 1.426 (10) 1.409 (10) 1.406 (9) 1.340 (9) 1.392 (8) 1.441 (9) 1.265 (8) 1.299 (8) 2.070 (5) 2.135 (5) 122.0 (9) 119.1 (10) 120.1 (8) 119.3 (8) 105.5 (6) 109.8 (7) 107.9 (6) 129.5 (7) 118.8 (6) 119.7 (6) 131.4 (4) 129.5 (4)
1.401 1.426 1.370 1.430 1.435 1.377 1.440 1.345 1.443 1.279 1.281 1.945 1.948 123.07 116.50 122.03 119.88 107.60 107.14 108.35 127.90 118.33 117.83 141.63 139.10
1.402 1.436 1.371 1.433 1.441 1.381 1.449 1.346 1.459 1.280 1.281 1.983 1.985 122.86 116.59 122.18 119.70 107.72 107.19 108.27 128.07 117.68 117.37 142.51 140.05
The normal co-ordinate analyses for the theoretical models of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n have been carried out, including the calculation of the potential energy distribution (PED) terms for each normal mode, according to the procedures described in ref. [34] (BALGA program). The non-redundant set of internal co-ordinates has been derived, as recommended by Fogarasi and Pulay [35–37].
The computations were carried out with the Gaussian 03 programs [38]. 3. Results and discussion 3.1. Description of the structure of [Zn(I2CA)2(H2O)2]n The overall view and labelling of the atoms in the title [Zn(I2CA)2(H2O)2]n is displayed in Fig. 1. In contrast to recently reported complexes of indole-3-carboxylic acid with Zn(II) ([Zn(I3CA)2(H2O)]n) [23], indole-3-propionic acid with Zn(II) ([Zn(I3PA)2(H2O)]n) [24], indole-2-carboxylic acid with Zn(II) ([Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2(CN)]DMF, and [Zn(I2CA)2 (CN)]DMSO, where CN, 2,9-dimethyl-1,10-phenanthroline; DMA, dimethylacetamide; DMF, dimethylformamide; DMSO, dimethyl sulfoxide) [18], in the title [Zn(I2CA)2(H2O)2]n each anionic ligands act as bidentate bridging. It should be noted that in three [Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2 (CN)]DMF and [Zn(I2CA)2(CN)]DMSO complexes, the Zn(II) ion is five-coordinated by two I2CA anionic ligands one of which is monodentate, and the other is bidentate chelating and one bidentate chelating NC [18]. In [Zn(I3CA)2(H2O)]n each zinc centre is also fivecoordinated by the bidentate chelating I3CA anionic ligand, one oxygen atom bidentate bridging I3CA anionic ligand, one oxygen atom bidentate bridging I3CA anionic ligand from an adjacent [Zn(I3CA)2(H2O)] unit and water molecule [23]. Moreover, in [Zn(I3PA)2(H2O)]n each zinc centre is six-coordinated by two oxygen atoms of the bidentate chelating I3PA anionic ligand, two oxygen atoms tridentate chelating–bridging I3PA anionic ligand, one oxygen atom tridentate chelating–bridging I3PA anionic ligand from an adjacent [Zn(I3PA)2(H2O)] unit and water molecule [24]. As can be seen in Figs. 1 and 2, in [Zn(I2CA)2(H2O)2]n the Zn(II) cation is located on an inversion centre of the octahedral geometry.
Fig. 1. ORTEP III drawing of [Zn(I2CA)2(H2O)2]n with 30% probability displacement ellipsoids and the numbering system.
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Fig. 2. Part of the crystal structure of [Zn(I2CA)2(H2O)2]n showing the six-coordination geometry around Zn(II) as well as the strong hydrogen bonds (dashed line): N(1)– H(1A) O(3), O(3)–H(3B) O(1) and O(3)–H(3A) O(1). The symmetry codes are given in Table 4.
The co-ordination sphere consists of water oxygen atoms [O(3) and O(3)#1; symmetry code: #1 (x, 1 y, 1 z)] and indole-2carboxylate oxygen atoms [O(1) and O(1)#1, O(2) and O(2)#1; symmetry code: #1 (x, 1 y, 1 z)] of four anions. Moreover, each anion links two Zn(II) centres by means of indole-2carboxylote units. The Zn–O(2) bond is shorter than Zn–O(3) and Zn–O(1) (Table 3). In the co-ordination octahedron, the basal angles O–Zn(1)–O are in the range from 86.5(2) to 93.5(2)8, so that the octahedral geometry is small distorted from ideal. It should be noted that in [Zn(I3CA)2(H2O)]n, the Zn–O bond distances for the bidentate bridging I3CA anionic ligand are 1.978 (4) and 1.983 (3) A˚ and these are shorter than those found for the bidentate chelating I3CA anionic ligand (1.977 (4) and 2.519 (4) A˚) [23]. In [Zn(I3PA)2(H2O)]n, the Zn–O bond distances for the tridentate chelating–bridging I3PA anionic ligand are 2.001 (4), 2.070 (4) and 2.342 (4) A˚ and these are shorter than those found for the bidentate chelating I3PA anionic ligand (2.015 (4) and 2.418 (4) A˚) [24]. Moreover, in [Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2(CN)]DMF and [Zn(I2CA)2(CN)]DMSO complexes, the Zn–O bond distances are
Table 3 The selected bond lengths (A˚) and bond angles (8), with e.s.d.s. in parentheses, determined for [Zn(I2CA)2(H2O)2]n by X-ray diffraction Metal surrounding Interatomic distances Zn–O(1) Zn–O(2) Zn–O(3) Interatomic angles O(1)–Zn–O(2) O(1)–Zn–O(3) O(2)–Zn–O(3)
2.136 (5) 2.070 (5) 2.123 (5)
92.91 (19) 93.25 (19) 93.5 (2)
Zn–O(1)#1 Zn–O(2)#1 Zn–O(3)#1
O(1)–Zn–O(2)#1 O(1)–Zn–O(3)#1 O(2)–Zn–O(3)#1
2.136 (5) 2.070 (5) 2.123 (5)
87.09 (19) 86.76 (19) 86.5 (2)
Symmetry transformations used to generate equivalent atoms: #1: x, 1 y, 1 z.
much larger for the bidentate chelating I2CA anionic ligand (in the range from 2.114 (3) to 3.314 (3) A˚) than these found for the monodentate I2CA anionic ligand (in the range from 1.931 (2) to 1.940 (2) A˚) [18]. I should remember that in the complex of Zn(II) with crotonate, the Z–O bond distances of the bridging ligand are 1.935 (3) A˚ for the conformation syn-anti and these are similar to the corresponding bond lengths of the bridging ligands for the conformation syn–syn (in the range from 1.920 (4) to 1.948 (4) A˚) [39]. It is interesting to compared the geometry of [Zn(I2CA)2 (H2O)2]n with the recently recorded crystal structure of the polymeric complex of Zn(II) with acetylenedicarboxylic acid ([Zn(C4O4)(H2O)2]n) [40]. The crystal structure is composed of zinc ions co-ordinated octahedrally by four oxygen atoms stemming from four different acetylenedicarboxylate anions with the Zn–O bond distances 2.151 (3) and 2.094 (3) A˚ (these bond distances are approximately 0.02 A˚ shorter than those found in [Zn(I2CA)2(H2O)2]n) and two water molecules in trans positions with the Zn–O bond distances 2.067 (3) A˚ (these bond distances are approximately 0.06 A˚ shorter than those found in [Zn(I2CA)2 (H2O)2]n). The observed Zn–O(3) and Zn–O(3)#1 (symmetry code: #1: x, 1 y, 1 z) bond distances of the title complex are very similar to the corresponding bond lengths in the {[Zn(L)2(H2O)2]2H2O}n (where L,3-cyano-4-dicyanomethylene5-oxo-4,5-dihydro-1H-pyrrol-2-olate anion) in which the water ligands lie in the apical sites of octahedral geometry with the Zn–O distances 2.1344 (14) A˚ [41]. The structure of [Zn(I2CA)2(H2O)2]n is also stabilized by hydrogen-bonding interactions (Table 4 and Fig. 2). There is the strong interaction between a water oxygen atom and a amide hydrogen atom of a neighboring chain [N(1)– H(1A) O(3)#1 = 2.29(9) A˚; symmetry code: #1 x, 1 y, 1 z]. There are also the strong O(3)–H(3B) O(1)#2 and O(3)– H(3A) O(1)#3 interactions (symmetry codes: #2: x, 3/2 y, 1/2 + z; #3: x, 1/2 + y, 3/2 z) between carboxyl oxygen atoms
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Fig. 3. The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and the infrared spectrum of deuterated derivative I2CA-d2 in the frequency range 3700–600 cm1.
and a water hydrogen atoms of neighboring chains (O(3)– H(3B) O(1)#2 = 1.93(9) A˚ and O(3)–H(3A) O(1)#3 = 2.01(9) A˚). A˚). In contrast to the strong hydrogen bonds, there is the weak C– H p interaction. The carbon atom C(2) acts as hydrogen bond donor, via H(2) to the five-membered ring of atoms N(1)–C(8) (centroid Cg 1) of the unit at (x, 3/2 y, 1/2 + z).
Table 4 Hydrogen bonds distances (A˚) and angles (8) in [Zn(I2CA)2(H2O)2]n D–H A
D–H
HA
DA
N(1)–H(1A) O(3) #1 O(3)–H(3B) O(1) #2 O(3)–H(3A) O(1) #3 C(2)–H(2) Cg1 #4
0.86 (8) 0.82 (9) 0.82 (8) 0.93
2.29 (9) 1.93 (9) 2.01 (9) 2.93
3.113 2.729 2.804 3.425
159 (9) 166 (11) 163 (8) 115
Cg1 denotes the centroid of the five-membered ring of atoms N(1)–C(8). Symmetry transformations used to generate equivalent atoms: #1: x, 1 y, 1 z; #2: x, 3/ 2 y, 1/2 + z; #3: x, 1/2 + y, 3/2 z; #4: x, 3/2 y, 1/2 + z.
3.2. Vibrational spectra of I2CA, [Zn(I2CA)2(H2O)2]n and infrared spectrum of I2CA-d2 The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and the infrared spectrum of I2CA-d2 in the range from 3700 to 700 cm1 are presented in Fig. 3. In Fig. 4 the infrared and Raman spectra of title complex and free ligand are shown in the range from 700 to 50 cm1. Moreover, in Fig. 4 the infrared spectrum of I2CA-d2 is presented in the range from 700 to 400 cm1. In Tables 5 and 6, the experimental bond positions of I2CA and I2CA-d2 are compared with the theoretical wavenumbers, IR intensities, and Raman scattering activities calculated for conformer I of I2CA and I2CA-d2 (which is presented in Scheme 1). The results have been obtained by the B3LYP density functional method with 6-311++G(d,p) basis set. In Table 7, the experimental bond positions of [Zn(I2CA)2 (H2O)2]n are compared with the theoretical wavenumbers, IR intensities, and Raman scattering activities calculated for theoretical model of [Zn(I2CA)2(H2O)2]n. The results have been obtained
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wavenumbers by using the scale factor of 0.93 at 3509 cm1 for I2CA and at 2553 cm1 for I2CA-d2, respectively. The theoretical nO–H/nO–D isotopic ratio is about 1.37 for both DFT methods. In the infrared and Raman spectra of I2CA, I failed to localize the stretching O2H mode, but in the infrared spectrum of I2CA-d2 the medium band at 2311 cm1 can be assigned to the stretching O2D modes. In opposition to the O2H and O2D stretching vibrations, the O2H and O2D in-plane and out-of-plane bending vibrations are not predicted to be a ‘‘pure’’ vibrations and contributed to other modes, for the both DFT methods, as can be seen in Tables 1 and 2 of Supplementary material. The theoretical dO–H/dO–D isotopic ratios are 1286 cm1/998 cm1 = 1.29 and 1280 cm1/990 cm1 = 1.29 by mPW1PW91 and B3LYP calculations, respectively. In the infrared and Raman spectra of I2CA the bands at 1304 and 1302 cm1 can be assigned to the dO2H mode. It should be noted that the band at 1304 cm1 in the infrared spectrum of I2CA disappears in the infrared spectrum of I2CA-d2 and in the infrared and Raman spectra of [Zn(I2CA)2(H2O)2]n, where oxygen atom O2 of the carboxylic group of I2CA is deprotonated. In the infrared spectrum of I2CA-d2 are appearance two bands at 1031 and 1010 cm1, which can be assigned to the dO2D mode. The experimental dO–H/dO–D isotopic ratios are 1304 cm1 / 1031 cm1 = 1.26 and 1304 cm1 /1010 cm1 = 1.29, respectively. The O2H out-of-plane bending mode is calculated at 613 and 524 cm1 with predominant contribution at 524 cm1 for I2CA by B3LYP calculations. For I2CA-d2 the O2D out-of-plane vibration is predicted theoretically at 629 and 391 cm1, with predominant contribution at 391 cm1 by B3LYP calculations. The theoretical gO–H/gO–D isotopic ratio is about 1.34 for both DFT methods. The strong bands at 820 in the infrared and Raman spectra of I2CA can be assigned to the gO–H mode. Unfortunately, the band at 820 cm1 not disappear in the infrared spectrum of I2CA-d2, but disappears in the vibrational spectra of [Zn(I2CA)2(H2O)2]n, which confirms assignment of the band at 820 cm1 to the gO2H mode. Moreover, in the infrared spectrum of I2CA-d2 is observed new band at 687 cm1, which can be assigned to the gO2D mode. The experimental gO–H/gO–D isotopic ratio, 1.19 is in bad agreement with theoretical gO–H/gO–D isotopic ratios.
Fig. 4. The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n in the frequency range 700–50 cm1 and the infrared spectrum of I2CA-d2 in the frequency range 700–400 cm1.
by the B3LYP density functional method with 6-311++G(d,p)/ LanL2DZ basis sets. It should be noted that comparison of the experimental and the theoretical wavenumbers, IR intensities and Raman scattering activities and the PED analysis at the mPW1PW91 and B3LYP methods for conformer I of I2CA, I2CA-d2 and theoretical model of [Zn(I2CA)2(H2O)2]n are available in Supplementary material (Tables 1–3). The bands due to the OH or NH vibrations of I2CA are influenced by the existing hydrogen bonds [20]. The theoretical calculations were performed for isolated molecule without intermolecular interactions. Therefore, the infrared spectrum of I2CA-d2 and also the infrared and Raman spectra of the title complex were helpful in assigning the N–HO and O–HO group vibrations of I2CA. 3.2.1. The OH vibrations of I2CA and the OD vibrations of I2CA-d2 As is seen in Tables 5 and 6, the O2H and O2D stretching vibrations have been calculated from the B3LYP harmonic
3.2.2. The NH vibrations of I2CA and [Zn(I2CA)2(H2O)2]n and the ND vibrations of I2CA-d2 The very strong band at 3350 cm1 (IR) and the medium at 3352 cm1 (R) of I2CA and the strong at 3363 cm1 (IR) of [Zn(I2CA)2(H2O)2]n can be attributed to the N–H stretching vibration. Unfortunately, in the infrared spectrum of I2CA-d2 the band of the nNH mode not disappear fully, but in the infrared spectrum of I2CA-d2 is observed new medium band at 2492 cm1 which can be assigned to the N1D stretching vibration. The experimental isotopic ratio nN–H/nN–D is 1.34. The theoretical N1H stretching modes are predicted from the B3LYP harmonic wavenumbers by using the scale factor of 0.93 at 3395 and 3336 cm1 for I2CA and [Zn(I2CA)2(H2O)2]n, respectively and the theoretical N1D stretching mode at 2492 cm1 for I2CA-d2. The theoretical nN–H/nN–D isotopic ratio is about 1.36 for both DFT methods. According to the PED the in-plane N1H bending mode in I2CA contributes to two modes at calculated wavenumbers 1417 and 1200 cm1, with predominant contribution at 1200 cm1 (39%) by B3LYP calculations. The theoretical results for I2CA-d2 show that the dN1D mode is calculated at 947 and 768 cm1 with predominant contribution at 947 cm1 (42%) by B3LYP calculations. The theoretical dN–H/dN–D isotopic ratios are 1.26 and 1.27 by mPW1PW91 and B3LYP calculations, respectively. In the infrared spectrum of I2CA-d2, the dN1D mode can be assigned the new
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74
Table 5 Comparison of the experimental (FT-IR and FT-Raman band positions of the I2CA) and the theoretical wavenumbers (n, cm1), IR integrated intensities (Ath, km mol1) and Raman scattering activities (Bth, A˚4 amu1) calculated for conformer I of I2CA Experimental FT-IR
Calculated B3LYP/6-311++G(d,p) FT-Raman
na
Ath
Bth
PED (%)
3509
134
157
nO2H (100)
3395 3125
107 0
72 77
nN1H (100) nC2H (99)
3453w 3350vs
3352m 3135m
3086w
3095m
3065
16
319
nC5H (39), nC6H (35), nC4H (13), nC7H (13)
3052s
3066s 3054s 3028w 1725w
3056 3046 3039
22 2 0
63 139 28
nC7H (36), nC4H (29), nC5H (18), nC6H (17) nC4H (38), nC7H (36), nC6H (16), nC5H (10) nC5H (33), nC6H (32), nC4H (20), nC7H (15)
1707vs 1622m 1579w 1519s 1500m 1438s 1417s 1367w 1346s
1644s 1625m 1580w 1532s 1507w 1445vs 1414m 1367w 1347m 1337m 1302s 1237m 1192s
1729 1624 1580 1538 1499 1438 1417 1383 1342 1320 1280 1227 1135b 1200 1158 1118 1093 1009 962 960 929
633 10 9 116 2 15 40 78 60 68 2 9 397 73 88 5 47 0 0 5 2
363 78 25 274 12 119 38 13 7 109 75 15 90 2 13 16 1 60 0 26 0
nC0O1 (54), nC0O2 (26) nC7C8 (21), nC4C5 (16), nC3C4 (13), nC6C7 (10) nC3C8 (15), nC5C6 (14), nC6C7 (10) nC1C2 (36), nC1C0 (11) dC5H (22), nC4C5 (13), nC6C7 (11) dC7H (21), dC4H (18), nC3C8 (14) nC1N1 (36), dN1H (13) dC6H (11) dC5H (19) dO2H (14), nC3C8 (11), nC2C3 (11) dO2H (21), nN1C8 (18), nC2C3 (11) dC4H (22), dC7H (18), nC7C8 (13), nC2C3 (11) dO2H (22), nC0O2 (16), dC2H (14) dN1H (39), dC2H (15) dC6H (23), dC5H (22), dC7H (11), dO2H (10) nC4C5 (17), dC5H (16), nC6C7 (14), dC4H (12), d6R (11), dC6H (10) dC2H (29), nC0O2 (21), nN1C8 (20) nC5C6 (47), nC6C7 (12), nC4C5 (12) gC5H (45), gC6H (34), gC4H (21) d5R (47), nC3C8 (19), nC0O2 (10) gC4H (37), gC6H (34), gC7H (29)
887 844 822 524b 801 768 744 680b 734 613 608 569 545b 566 473
1 8 14 142 1 35 76 28 19 0 2 30 14 4 28
6 1 1 2 18 0 0 16 0 1 13 0 4 0 0
429 366 342
3 2 5
1 1 5
t6R (90) dCOOrock (26), d6R (26) nC1C0 (25), dCOOsciss (23), d5R (12)
263 247
0 0
0 0
(6R (67), gC1C0 (28) t6R (59), t5R (30)
139
3
0
dC1C0 (64), dCOOrock (22)
88 82
2 0
2 0
gC1C0 (35), (6R (21), t5R (19), gCOOtwist (17) gCOOtwist (72), gC1C0 (12)
1304m 1238s 1194vs 1153s 1122w 1115m
1154w 1120s 1014s
969w 934w 926w 899w 848 w 820s
969vs
897w 869vw 847w 820s
769s 743s 736s 728s 614m 578m 567m 556w 518m,br 452w 428m 391w 378m 281m
609s 578w
367s 281w
260w
259w
205m 150w 128w 100w 74w
203w
555w
432w
d6R (59) gC2H (29), gC7H (26), gC5H (16), gC4H (15) gC2H (55), gC7H (18), gC4H (15) gO2H (77) nC3C8 (30), nC7C8 (13), nC3C4 (13) gCOOwag (48), t6R (21), t5R (12) t6R (35), gCOOwag (18), t5R(16), gC5H (10) dCOOsciss (35), d6R (16), nC0O2 (13), d5R (10) gC6H (23), gC5H (19), gC7H (18) t5R (78), gO2H (16) d5R (45), d6R (28), nC7C8 (11), nC3C4 (11) d6R (55), dCOOsciss (20) dCOOrock (33), dC1C0 (23), d6R (22) t6R (75), t5R (25) gN1H (95)
131m
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak; v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching NH and OH by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers.
band at 958 cm1. Unfortunately, I failed to localize the dN1H mode in the infrared and Raman spectra of I2CA. Also, in the infrared and Raman spectra of [Zn(I2CA)2(H2O)2]n is very true assigned band of the dN1H vibration. Both DFT calculations show
that in the complex the dN1H mode has not predominant contribution. The calculations show that the out-of-plane N1H and N1D bending modes not contribute to other modes for I2CA,
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
75
Table 6 Comparison of the experimental (FT-IR band positions of the I2CA-d2) and the theoretical wavenumbers (n, cm1) and IR integrated intensities (Ath, km mol1) calculated for conformer I of I2CA-d2 Experimental
Calculated B3LYP/6-311++G(d,p)
FT-IR
na
Ath
PED (%)
3453w 3350mc 3134m
3125 3065
0 16
nC2H (99) nC5H (39), nC6H (35), nC4H (13), nC7H (13)
3051m
3056 3046 3039
22 2 0
nC7H (36), nC4H (29), nC5H (18), nC6H (17) nC4H (38), nC7H (36), nC6H (16), nC5H (10) nC5H (33), nC6H (32), nC4H (20), nC7H (15)
2492m 2311m 1700s 1619m 1577w 1520s 1484s 1429s 1401m 1363w 1345m 1336s 1326s 1253s 1235s 1195sc 1152m 1136w 1120m
2492b 2553 1719 1622 1572 1535 1487 1436 1398 1367 1333 1306
69 86 626 11 4 126 17 18 118 6 27 152
nN1D (98) nO2D (100) nC0O1 (58), nC0O2 (27) nC7C8 (20), nC4C5 (16), nC3C4 (14), nC6C7 (12) nC5C6 (18), nC3C8 (16) nC1C2 (39), nC1C0 (10) dC5H (22), nC6C7 (14), nC3C4 (11) dC7H (21), dC4H (18), nC3C8 (14), nC4C5 (14) nC1N1 (46), nC1C0 (11) nC5C6 (14), dC6H (11) nN1C8 (16), dC5H (15), dC7H (15), dC6H (13) nC2C3 (17), nC3C8 (15), nC4C5 (13), nC8N1 (12)
1227 1221 1150 1127 1118
39 237 23 13 5
1011
1
dC4H (22), nC4C3 (14), dC7H (12) nN1C1 (15), nC2C3 (11), nC0O1 (11), dC6H (28), dC5H (21), dC7H (18) dC2H (58) nC4C5 (16), dC5H (16), nC6C7 (14), dC4H (12), d6R (12), dC6H (10) nC5C6 (44), nC6C7 (11), nC4C5 (11), dC7H (11)
990 963 947 940 929
126 0 17 8 2
871 843 822
1 6 13
d6R (43), nC2C3 (12) gC2H (27), gC7H (27), gC5H (17), gC4H (16) gC2H (57), gC7H (17)
768 765 743 734 391 b 629 606 594 562 558 523 433 356 361 337 260 244 137 87 82
0 19 73 18 45 18 2 0 0 32 28 23 40 2 6 0 0 3 2 0
nC3C8 (23), dN1D (16), nC3C4 (11) gCOOwag (44), t6R (26), t5R (11) t6R (30), gCOOwag (20), t5R (15), gC5H (11) gC6H (22), gC5H (18), gC7H (17), gC2H (11) gO2D (85) d6R (28), dO2D (17), dCOOsciss (15), nC1C0 (11) d5R (44), d6R (29), nC7C8 (11), nC3C4 (11) t5R (82) d6R (76), tR5 (24) d6R (32), dCOOsciss (23), dCOOrock (10) dCOOrock (26), dC1C0 (18), d6R (14) t6R (70), t5R (23) gN1D (100) d6R (26), dCOOrock (23) dCOOsciss (24), nC1C0 (23), d5R (12) d6R (64), gC1C0 (19) t6R (58), t5R (39) dC1C0 (64), dCOOrock (22) gC1C0 (36), (6R (21), t5R (18), gCOOtwist (17) gCOOtwist (76), gC1C0 (12)
1031m 1010m 986w 958m 941m 926w 913w 891w 848w 820mc 791w 768s 744s 728s 687m 608w 591w 573m 541m 429m
dO2D (45), nC0O2 (37) gC5H (45), gC6H (34), gC4H (21) dN1D (42), d6R (11), d5R (43), dO2D (15), nC3C8 (14) gC4H (37), gC6H (34), gC7H (29)
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak; v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching ND and OD by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers. c See text.
[Zn(I2CA)2(H2O)2]n and I2CA-d2 and these are predicted at 473, 607 and 356 cm1, respectively by B3LYP calculations. The theoretical gN–H/gN–D isotopic ratios are 1.32 and 1.33 by mPW1PW91 and B3LYP calculations, respectively. In the infrared
spectrum of I2CA the medium band at 518 cm1 disappears in the infrared spectrum of I2CA-d2, therefore, this band can be assigned to the gN1H mode. In the infrared spectrum of [Zn(I2CA)2(H2O)2]n is very true assigned band for gN1H mode, because board
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
76
Table 7 Comparison of the experimental (FT-IR and Raman band positions of the [Zn(I2CA)2(H2O)2]n) and the theoretical wavenumbers (n, cm1), IR integrated intensities (Ath, km mol1) and Raman scattering activities (Bth, A˚4 amu1) calculated for the theoretical model of [Zn(I2CA)2(H2O)2]n Experimental FT-IR
Calculated B3LYP/6-311++G(d,p)/LanL2DZ Raman
na
Ath
Bth
3336
140
72
PED (%)
3445w 3363s
nN1H (100)
3241w 3131w
3144w
3121 3081
13 64
29 871
nC2H (99) nC5H (78), nC4H (15)
3057w
3052w 3008w
3072 3068 3060
37 4 12
289 84 156
nC7H (83), nC6H (11) nC4H (78), nC5H (14) nC6H (80), nC7H (11)
1619wc 1574m
1577
1619m 1575w
c
192
1282
b
238 279
5 10
nC7C8 (47) nasCOO (73) nC2C3 (21), nC3C4 (16), nC5C6 (10)
1542s,br
1550m 1534w
1405 1560
1494w 1445m 1427m 1418m 1406m 1386w 1372w 1335m 1291m 1233w 1221w
1496w 1442m
1391m 1358w 1341m 1294m 1235w 1225w
1492 1469 1421 1418 1255b 1367
179 84 211 125 180 61
14 212 18 107 15 83
nC1N1 (30), dN1H (25), nC4C5 (30), dC5H (23), dC6H (16) nC3C8 (15), nC2C3 (14), nasCOO (14) nC5C6 (19), dC5H (12) nsCOO (33), nC1C0 (12) dC4H (23), nC5H (20), nC6H (16)
1345 1298
30 501
478 62
nC1C2 (23), nC1N1 (19), dR5 (11) nC7H (22)
1204
33
13
1153w
1151w
1174 1160
106 1
24 368
dC6H (28), dC5H (27), nC5C6 (16) nC8N1 (28), dC4H (15), dR6 (10)
1118w 1105w
1118w
1120 1089
121 63
14 278
dC2H (39), nsCOO (21), nC1C2 (11) nC4C5 (26)
1004w
1004vs
993 b 1008
127 1
75 1
nC6C7 (35), nC5C6 (32), dC7H (11) gC5H (56), gC6H (44)
974w 930w 895w 858w 833w
974s 896w 864w 830w
985 934 895 878 869
1 22 3 5 21
3 37 1 37 2
gC4H (45), gC6H (23), gC7H (19), gC5H (13) dR5 (37), nC3C8 (14), nC1C2 (13) gC2H (49), gC7H (35), gC4H (11) dR6 (59) gC2H (42), gC7H (35), gC4H (11)
805w 770m
808 757 b
40 10
39 16
nC3C8 (33), dCOOsciss (13) gCOOwag (65), gC1C0 (13)
735 b 774 685
1 47 11
2 2 5
607 594 578 563 547
78 13 19 54 7
2 29 11 6 116
457
14
3
396 384
35 9
11 60
dR6 (27), nZnO1 (17), dCOOrock (10) dCOOsciss (20), nZnO2 (19), nC1C0 (10)
372 273 263 225 214
6 26 34 16 17
11 8 5 12 21
tR6 (63), tR5 (26) tR6 (35), nZnO2 (17), gC1C0 (15), dZnO2 (11) tR6 (21), nZnO1 (15) tR6 (42), tR5 (20), nZnO1 (15) nZnO2 (29), nZnO1 (14), dR6 (10),
143s
150 133
1 5
1 29
dC1C0 (32), gZnO2 (18), gZnO1 (17), dCOOrock (14) dZnO2 (37), dZnO1 (28), tR5 (10)
118vs
126
1
178
72 68
5 0
2 52
794m
1421m
750m 735s 670w 628w,br 613w 588w 575w 556w 485w c 438m
613w 593vw 566vw 547vw 489vwc 435vw
392w 384vw 324vw 289m 263vw 248vw 216w 180m
335vw 303vw 267vw 239vw
154w
dC2H (24), dN1H (23)
dCOOsciss (31), dR5 (11) gC5H (23), gC6H (21), gC4H (18), tR6 (15) tR5 (51), tR6 (27) gN1H (100) dR5 (43), dCOOrock (16), nC3C4 (14) tR5 (61), gC1C0 (12) dR6 (20), dCOOrock (18), dR6 (13), dC1C0 (11) dR6 (49) tR6 (71)
122w
106w 96w
dZnO1 (25), dZnO2 (22), nZnO1 (11), gCOOtwist (10) gC1C0 (27), tR6 (13), dZnO1 (12) gZnO1 (33), gZnO2 (32), dZnO2 (12), dZnO1 (12)
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
77
Table 7 (Continued ) Experimental FT-IR 77w 68w
Calculated B3LYP/6-311++G(d,p)/LanL2DZ Raman
na
Ath 50 34
1 0
Bth 26 6
PED (%)
gZnO2 (38), gZnO1 (17), dC1C0 (12), gC1C0 (12) gCOOtwist (70), gZnO1 (14)
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak, v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching NH by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers. c See text.
absorption between 700–500 cm1 of the librational lattice modes of the co-ordinated water molecules, this makes impossible. 3.2.3. The C O and C–O group vibrations of I2CA and I2CA-d2 and the [Zn(COO)] group vibrations of [Zn(I2CA)2(H2O)2]n According to the B3LYP calculations, the wavenumber of the nC0O1 mode is calculated at 1729 cm1 for I2CA with contribution 54%. For I2CA-d2 the nC0O1 mode is calculated at 1719 and 1221 cm1 with predominant contribution 58% at 1719 cm1 by B3LYP calculations. In the crystal structure of I2CA both the O2H and N1H groups act as donor sites, while the O1 atom acts as the acceptor site for two hydrogen bonds [20]. Therefore, the C0O1 groups within the dimmer interact and produce so-called factor group splitting. Its magnitude can be evaluated easily by subtracting nC O (IR) from nC O (Raman) [42]. The wavenumbers of the nC0O1 mode are 1707 and 1644 cm1 in the infrared and Raman spectra of I2CA, respectively, and thus the value 63 cm1 is comparable with this for b,b’-dichloropivalic acid (62 cm1) [42]. The band for the nC0O1 mode is observed for I2CAd2 at 1700 cm1 in the infrared spectrum. The nC0O1 mode for I2CA and I2CA-d2 is coupled with nC0O2 mode for the both DFT methods. According to the both DFT calculations the nC0O2 mode has not predominant contribution for I2CA and I2CA-d2. The nC0O2 mode at 1135 cm1 with contribution 16% is coupled with the dO2H mode with contribution 22% for I2CA. This theoretical wavenumber at 1135 cm1 are assigned bands at 1194 and 1192 cm1 in the infrared and Raman spectra of I2CA, respectively. The band at 1194 cm1 in the infrared spectrum of I2CA not disappear in the infrared spectrum of I2CA-d2 but both bands at 1194 and 1192 cm1 in the vibrational spectra of I2CA disappear in the vibrational spectra of [Zn(I2CA)2(H2O)2]n. This shows that these bands can be assigned to nC0O2 vibration of I2CA. According to the both DFT calculations the nasCOO mode of [Zn(I2CA)2(H2O)2]n is lower than the nC0O1 mode of I2CA and the nsCOO mode of [Zn(I2CA)2(H2O)2]n is higher than the nC0O2 mode of I2CA. The nasCOO mode of the bidentate bridging I2CA anionic ligand of the [Zn(I2CA)2(H2O)2]n is calculated at 1405 and 1421 cm1 by B3LYP calculations. The mode at 1405 cm1 is pure mode as evidenced from 73% of PED. The nsCOO mode of the [Zn(I2CA)2(H2O)2]n is calculated at 1255 and 1120 cm1 with predominant contribution 33% at 1255 cm1. New strong band at 1542 cm1 in the infrared spectrum and new medium band at 1550 cm1 in the Raman spectrum and new medium band at 1406 cm1 in the infrared spectrum corresponds to the nasCOO and nsCOO modes, respectively for [Zn(I2CA)2(H2O)2]n. The discrepancies between the theoretical and the experimental wavenumbers for the nasCOO and nsCOO modes are probably partly caused by the limits of the applied computational model for [Zn(I2CA)2(H2O)2]n. However, it should be emphasized that the separations between the nasCOO and nsCOO are 154 and 150 cm1 by mPW1PW91 and B3LYP calculations, respectively and 136 cm1 by experimental data. It should be noted that in diamminetetrakis(m-indole-3-carboxylato-O,O’)dicopper(II)
([Cu2(I3CA)4(NH3)2]) [22], [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2 (H2O)]n [24], the separations between the experimental nasCOO and nsCOO are 149 and 122 cm1 in the bidentate bridging indole3-carboxylate anions and 142 cm1 in the tridentate chelating– bridging indole-3-propionate anion. Moreover, in the infrared spectrum of di[(m2-acetato)(2-acetylpyridine4N-ethylthiosemicarbazonato)zinc] the band at 1575 and 1418 cm1 were assigned to nasCOO and nsCOO in the bidentate bridging acetate anion, respectively [43]. In [Zn(2-pyrrolecarboxylato)2(H2O)] the separation between the experimental nasCOO and nsCOO is 120 cm1 in the bidentate bridging 2-pyrrolecarboxylate anion [44]. The dCOOsciss, dCOOrock, gCOOwag and gCOOtwist in-plane and out-of-plane bending vibrations, respectively are not predicted to be a ‘‘pure’’ vibrations and contributed to other modes, for the both DFT methods, as can be seen in Tables 1–3 of Supplementary material. However, the strong band at 736 cm1 in the Raman spectrum of I2CA and the medium band at 750 cm1 in the infrared spectrum of [Zn(I2CA)2(H2O)2]n can be assigned to the dCOOsciss mode. In the infrared spectra of I2CA and I2CA-d2 the medium bands at 567 and 541 cm1, respectively can be assigned to the dCOOrock mode. For [Zn(I2CA)2(H2O)2]n the dCOOrock mode has not predominant contribution by the both DFT calculations. In the infrared spectra of I2CA and I2CA-d2 the strong bands at 769 cm1 and 768 cm1, respectively can be assigned to the gCOOwag mode. The gCOOwag mode for [Zn(I2CA)2(H2O)2]n can be assigned to the medium band at 770 cm1 in the Raman spectrum. In the infrared spectra of the investigated molecules the bands below 100 cm1 can be assigned to the gCOOtwist mode. The zinc ion forms four Zn–O bonds with I2CA anions, as shown in Fig. 1. According to the calculated PED by the both DFT calculations, the nZnO1 and nZnO2 stretching vibrations are strongly mixed between themselves and overlap with other modes as can be seen in Table 7. As results from the X-ray, the Zn–O bond distances are longer for [Zn(I3CA)2(H2O)]n (in the range from 1.977 (4) to 2.519 (4) A˚) [23] than these found in [Zn(I3PA)2(H2O)]n (in the range from 2.001 (4) to 2.418 (4) A˚) [24]. Therefore, the Zn–O stretching vibrations in [Zn(I3CA)2(H2O)]n were observed at lower wavenumber (at 470 (IR) and 467 cm1 (R)) [23] than in [Zn(I3PA)2(H2O)]n (at 504 (IR) and 518 cm1 (IR)) [24]. The Zn– O bond distances for the bidentate bridging anionic ligand of [Zn(I2CA)2(H2O)2]n (2.070(5) and 2.136(5) A˚) are shorter than these found in [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24]. This implies that the Zn–O stretching vibration of [Zn(I2CA)2 (H2O)2]n should be observed at higher wavenumber than that of [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24]. However, in [Zn(I2CA)2(H2O)2]n each I2CA anionic ligand act as bidentate bridging, but in [Zn(I3CA)2(H2O)]n one I3CA anionic ligand act as bidentate bridging, and the other as bidentate chelating [23]. In [Zn(I3PA)2(H2O)]n one I3PA anionic ligand is tridentate chelating– bridging, and the other is bidentate chelating. Therefore, it is interesting to compared the Zn–O bond distances for the bidentate bridging I2CA anionic ligand in [Zn(I2CA)2(H2O)2]n with these recorded for the bidentate bridging I3CA anionic ligand in [Zn(I3CA)2(H2O)]n [23]. The Zn–O bond distances for the bidentate
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B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
bridging I2CA anionic ligand of [Zn(I2CA)2(H2O)2]n are longer than these found in the bidentate bridging I3CA anionic ligand of [Zn(I3CA)2(H2O)]n [23]. Therefore, the corresponding the Zn–O stretching vibration in [Zn(I2CA)2(H2O)2]n should be observed at lower wavenumber than in [Zn(I3CA)2(H2O)]n. However, in the infrared spectrum of [Zn(I2CA)2(H2O)2]n appear new band at 485 cm1. The band is not observed in the infrared spectrum of I2CA. Therefore, this band was assigned to stretching Zn–O vibrations with oxygen atom of the carboxylic group of [Zn(I2CA)2(H2O)2]n. The lowering energy of the stretching Zn–O mode to 470 cm1 in the infrared spectrum of [Zn(I3CA)2(H2O)]n [23] is caused by the Zn–O bond distances of the bidentate chelating I3CA anionic ligand. 3.2.4. The CH vibrations of I2CA, I2CA-d2, [Zn(I2CA)2(H2O)2]n According to the calculated PED by the both DFT calculations, the C2H, C4H, C5H, C6H and C7H stretching vibrations can be assigned to bands at the wavenumber range from 3144 to 3008 cm1 in the vibrational spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n. The calculated PED has revealed that the C4H, C5H, C6H and C7H stretching modes are mixed between themselves for all investigated molecules as can be seen in Tables 5–7, except the C6H and C7H stretching modes of [Zn(I2CA)2(H2O)2]n calculated by mPW1PW91 method (Table 3 of Supplementary material). Moreover, for all investigated molecules the C2H stretching mode is not mix with other modes by the both DFT calculations. The CH in-plane bending vibrations in all investigated molecules are strongly coupled with other modes and contribute to several bands in the range from 1507 to 1004 cm1. As revealed by the PED, the several normal modes corresponding to the pure CH out-of-plane bending vibrations at 962, 929, 844, 822 and 734 cm1 for I2CA, and at 963, 929, 843, 822 and 734 cm1 for I2CA-d2 and at 1008, 985, 895 and 869 cm1 for [Zn(I2CA)2(H2O)2]n by B3LYP calculations. The detailed vibrational assignments of the dCH modes and of the pure and remaining the gCH modes are given in Tables 5–7. 3.2.5. The [Zn(H2O)] group vibrations of [Zn(I2CA)2(H2O)2]n In the infrared spectrum of [Zn(I2CA)2(H2O)2]n is shown a broad and complicated structure of the bands from 3600 to 2700 cm1. These bands correspond to the anti-symmetric and symmetric OH stretch and confirm the presence of water in the compound. The infrared spectrum exhibits characteristic band at 1619 cm1, which can be assigned to the OH in-plane bending mode. In the infrared spectrum of the title complex, the rocking HOH, wagging HOH modes is difficult to assigned separate bands. These bands are probably the effect of superposition of I2CA modes and rocking and wagging modes of co-ordinated water molecules, of very similar wavenumbers. Board absorption between 700 and 500 cm1 in the infrared spectrum of [Zn(I2CA)2(H2O)2]n is connected with the librational lattice modes of the co-ordinated water molecules. The ZnO stretching band with oxygen atoms of water molecules have been assigned at 364, 360 and 368 cm1 of solid [Zn(H2O)6]SO4H2O [45], [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24], respectively. Unfortunately, in the spectrum of [Zn(I2CA)2(H2O)2]n, I failed to localize the bands of the Zn–H2O stretching modes. 3.2.6. The overtones or combination modes The weak band at 2644 cm1 in the infrared spectrum of I2CA, the weak bands at 2568, 1296 and 1275 cm1 in the infrared spectrum of I2CA-d2 and the weak bands at 2939, 2911, 2778, 1280 and 1265 cm1 and the medium band at 2738 cm1 in the Raman spectrum of [Zn(I2CA)2(H2O)]n are not enumerated in the
Tables 5–7. These bands can be assigned to overtones or combination modes. 4. Conclusions In this work the novel [Zn(I2CA)2(H2O)2]n was investigated experimentally by the X-ray diffraction. Moreover, the vibrational spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n have been calculated by the mPW1PW91 and B3LYP calculations with the 6-311++G(d,p) basis set for I2CA and I2CA-d2 and with the 6-311++G(d,p)/LanL2DZ basis sets for [Zn(I2CA)2(H2O)2]n. The comparison of the vibrational spectra I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n calculated by mPW1PW91 and B3LYP suggests that the both DTF calculations produce similar results (which are available in tables of Supplementary material). The calculations for I2CA and I2CA-d2 were performed for the most stable conformer of I2CA. This conformer is not only a minimum energy conformer but also it corresponds to the experimentally found geometry [20]. For [Zn(I2CA)2(H2O)2]n the theoretical model was limited to bidentate I2CA representing the ligand bonded to two zinc ions via two oxygen atoms of carboxylic group. Because part of the ligand and complex are used for calculations, therefore, the obtained vibrational results must be carefully verified. In such situation, the theoretical reproductions of experimental data of all investigated molecules were very useful for reasonable bands attribution for these molecules. The frequency shift of several vibrational modes has been analyzed in going from theoretical calculations to the solid state spectra, for example NH and OH modes of I2CA and nasCOO and nsCOO modes of [Zn(I2CA)2(H2O)2]n. These effects are caused by the intermolecular hydrogen bonding in the solid state and the limitations of the theoretical models. The presented experimental and theoretical spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n and vibrational assignment can assist in the interpretation of the vibrational spectra of new I2CA agents. Acknowledgements I am grateful to Dr. Ewa Rozycka-Sokolowska from Jan Długosz University of Cze˛stochowa for the X-ray structure determinations. The Wrocław Centre for Networking and Supercomputing is acknowledged for generous computer time.
Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.vibspec.2008.04.014. References [1] A.C. Nichols, K.L. Yielding, Mol. Chem. Neuropathol. 19 (1993) 269. [2] M. Mugnaini, M. Antolini, M. Corsi, F.T. Vanamsterdam, J. Recept. Signal Transduct. Res. 18 (1998) 91. [3] S. Nagata, K. Takeyama, F. Fukuya, R. Nagai, K. Hosoki, K. Nishimura, T. Deguchi, T. Karasawa, Arzneimittel-Forschung/Drug Res. 45 (1995) 853. [4] M.I. Vlasova, N.A. Kogan, Y.Y. Lesiovskaya, L.V. Pastushenkov, Khimico-Farmatsevticheskii Zhurnal. 26 (1992) 23. [5] C. Kipp, A.R. Young, Photochem. Photobiol. 70 (1999) 191. [6] P. Kutschy, M. Dzurilla, M. Takasugi, A. Sabova, Coll. Czech. Chem. Commun. 64 (1999) 348. [7] B.M. Baron, R.J. Cregge, R.A. Farr, D. Friedrich, R.S. Gross, B.L. Harrison, D.A. Janowick, D. Matthews, T.C. McCloskey, S. Meikrantz, P.L. Nyce, R. Vaz, W.A. Metz, J. Med. Chem. 48 (2005) 995.
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79 [8] J.E. Weder, T.W. Hambley, B.J. Kennedy, P.A. Lay, D. MacLachlan, R. Bramley, C.D. Delfs, K.S. Murray, B. Moubaraki, B. Warwick, J.R. Biffin, H.L. Regtop, Inorg. Chem. 38 (1999) 1736. [9] Q. Zhou, T.W. Hambley, B.J. Kennedy, P.A. Lay, P. Turner, B. Warwick, J.R. Biffin, H.L. Regtop, Inorg. Chem. 39 (2000) 3742. [10] Y.R. Morgan, P. Turner, B.J. Kennedy, T.W. Hambley, P.A. Lay, J.R. Biffin, H.L. Regtop, B. Warwick, Inorg. Chim. Acta 324 (2001) 150. [11] J.E. Weder, T.W. Hambley, B.J. Kennedy, P.A. Lay, G.J. Foran, A.M. Rich, Inorg. Chem. 40 (2001) 1295. [12] Q. Zhou, T.W. Hambley, B.J. Kennedy, P.A. Lay, Inorg. Chem. 42 (2003) 8557. [13] C.T. Dillon, T.W. Hambley, B.J. Kennedy, P.A. Lay, Q. Zhou, N.M. Davies, J. Ray Biffin, H.L. Regtop, Chem. Res. Toxicol. 16 (2003) 28. [14] A. Tine, P. Guillaume, A. Massat, J.J. Aaron, Spectrochim. Acta A 54 (1998) 1451. [15] I.T. Achmed, Spectrochim. Acta A 63 (2006) 416. [16] Y. Han-Dong, W. Qi-Bao, X. Sheng-Cai, X. Wuji-Huaxne, Chin. J. Inorg. Chem. 20 (2004) 1477. [17] V. Viossat, P. Lemoine, E. Dayan, D. Nguyen-Huy, B. Viossat, Polyhedron 22 (2003) 1461. [18] V. Viossat, P. Lemoine, E. Dayan, D. Nguyen-Huy, B. Viossat, J. Mol. Struct. 741 (2005) 45. [19] P. Lemoine, V. Viossat, E. Dayan, D. Nguyen-Huy, B. Viossat, Inorg. Chim. Acta 359 (2006) 4274. [20] B. Morzyk-Ociepa, D. Michalska, A. Pietraszko, J. Mol. Struct. 688 (2004) 79. [21] B. Morzyk-Ociepa, D. Michalska, A. Pietraszko, J. Mol. Struct. 688 (2004) 87. [22] B. Morzyk-Ociepa, E. Rozycka-Sokolowska, J. Mol. Struct. 784 (2006) 69. [23] B. Morzyk-Ociepa, B. Marciniak, Vibr. Spectrosc. 43 (2007) 297. [24] B. Morzyk-Ociepa, E. Rozycka-Sokolowska, Vibr. Spectrosc. 43 (2007) 405. [25] B. Morzyk-Ociepa, Vibr. Spectrosc. 46 (2008) 115. [26] G.M. Sheldrick, SHELXS97 and SHELXL97, University of Go¨ttingen, Germany, 1997. [27] CrysAlis PRO, Oxford Diffraction, 2006. [28] A.D. Becke, J. Chem. Phys. 104 (1996) 1040. [29] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785. [30] C. Adamo, V. Barone, J. Chem. Phys. 108 (1998) 664.
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X-ray diffraction and vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes Part VII. Indole-2-carboxylic acid and catena-poly[[diaquazinc(II)]-bis (m2-indole-2-carboxylato-O:O0 )] Barbara Morzyk-Ociepa * Institute of Chemistry and Environmental Protection, Jan Długosz University, Armii Krajowej 13/15 Avenue, 42-200 Cze˛stochowa, Poland
A R T I C L E I N F O
A B S T R A C T
Article history: Received 29 November 2007 Received in revised form 25 April 2008 Accepted 28 April 2008 Available online 8 May 2008
The catena-poly[[diaquazinc(II)]-bis(m2-indole-2-carboxylato-O:O0 )], [Zn(I2CA)2(H2O)2]n has been synthesized and characterized by X-ray diffraction analysis and the infrared and Raman spectroscopic methods. The co-ordination of the indole-2-carboxylate anion to Zn(II) results in the formation of the [Zn(I2CA)2(H2O)2]n, in which the Zn(II) cations lie on inversion centres in space group P21/c, with water ligands in the apical sites of octahedral geometry. Moreover, the infrared and Raman spectra of indole-2carboxylic acid (I2CA) and the infrared spectrum of deuterated derivative of indole-2-carbocylic acid (I2CA-d2) are recorded in the solid phase. The theoretical wavenumbers, infrared intensities and Raman scattering activities were calculated by density functional B3LYP and mPW1PW91 methods with the 6311++G(d,p) basis set for I2CA and I2CA-d2 and with the 6-311++G(d,p)/LanL2DZ basis sets for the theoretical model of Zn(I2CA)2(H2O)2]n. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution for all molecules. ß 2008 Elsevier B.V. All rights reserved.
Keywords: Zinc complex Indole-2-carboxylic acid Crystal Molecular structure Hydrogen bond FT-IR and FT-Raman spectra Density functional theory
1. Introduction The indole-2-carboxylic acid (I2CA) moiety is present in a great number of molecules with a broad spectrum of pharmacological activity, anticonvulsant, antihypertensive, antiarrhytmic and antifungal properties [1–7]. It has been found that the biological activities of the therapeutic agents are considerably increased when they are bonded into metal complex molecules. For example, such effects have been observed for Zn(II) and Cu(II) chelates with indomethacin (which is a derivative of indole-3-acetic acid). These complexes of indomethacin are superior to uncomplexed indomethacin for treatment of a range of conditions and most importantly induce considerably lower incidences of gastrointestinal damage [8–13]. To gain deeper insight into the factors controlling the metal complex biological activity, it is first necessary to know the binding properties of the biological ligands to the metal ions as well as the geometrical structures and spectroscopic data of the complexes.
* Tel.: +48 34 366 5322; fax: +48 34 366 5322. E-mail address: [email protected]. 0924-2031/$ – see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.vibspec.2008.04.014
Tine et al. [14] performed the subtracted-infrared (SUBSTR-IR) spectra of mixtures of indolecarboxylic acids and lanthanide. Authors conclude that indolecarboxylates can form in DMSO associations with Ln(III) ions, including bidentate and monodentate complexes [14]. The molecular structures of Co(II), Ni(II) and Cu(II) with indole-2-carboxylic acid and 4-substituted hydrazinethiocarbamide were proposed by molar conductance, electronic, IR, 1H NMR, mass spectra as well as thermogravimetric (TG) by Achmed [15]. The structural studies of Sn(IV) with indole2-carboxylic acid and chlorobenzyl were performed by Han-Dong et al. [16]. Moreover, Viossat et al. [17–19] performed structural studies of Mn(II) and Zn(II) complexes with indole-2-carboxylic acid and 2,9-dimethyl-1,10-phenanthroline or imidazole, with differ by solvate molecule (dimethylacetemide, dimethylformamide and dimethyl sulfoxide) in the crystal structure and the authors shortly discussed the infrared spectra of these complexes. In this work, we continue the studies on the synthesis and vibrational spectra of indolecarboxylic acids and their metal complexes [20–25]. In this paper, the [Zn(I2CA)2(H2O)2]n is examined using single crystal X-ray diffraction analysis. Moreover, the infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and infrared spectrum of I2CA-d2 are discussed.
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
2. Experimental 2.1. Preparation of the crystals of [Zn(I2CA)2(H2O)2]n Crystals of [Zn(I2CA)2(H2O)2]n were prepared as follows. To a suspension of 0.16 g of indole-2-carboxylic acid (Lancaster) in ethanol (50 cm3) the 0.14 g of ZnCl22H2O and 2 cm3 1 M NaOH were added. The mixtures were heated to 318 K for about 1 h. The obtained solutions were filtered and left for crystallization. After a week translucent crystals of [Zn(I2CA)2(H2O)2]n were formed. The deuterated derivative I2CA-d2 was prepared by repeated crystallization from C2H5OD. 2.2. X-ray diffraction analysis The X-ray diffraction data were collected at 290(2) K, using an XCALIBURTM 3 CCD diffractometer with graphite-monochromated Mo Ka radiation (l = 0.71073 A˚). The structure was solved by direct methods using the SHELXS-97 program [26] and refined by full-matrix least-squares on F2 with SHELXL-97 [26]. The hydrogen atoms bonded to C and N atoms were introduced at calculated positions as riding atoms, with C–H and N–H distances of 0.93 and 0.86 A˚, respectively, while the O-bound H atoms were located from difference maps. The O–H distances were restrained with a DFIX command in SHELXL-97 [26]. For all H atoms, Uiso (H) values were constrained to be 1.2 Ueq (C, N) or 1.5 Ueq (O). Complete crystallographic data have been deposited at the Cambridge Crystallographic Data Centre and allocated under deposition number CCDC 668995. The crystal data together with the refinement details are given in Table 1. 2.3. Spectroscopic measurements The infrared spectra of solid I2CA, I2CA-d2 and [Zn(I2CA)2 (H2O)2]n in the region 4000–400 cm1 were measured at 2 cm1 resolution on a Nicolet-Nexus spectrometer using the KBr pellet technique. The far infrared spectra in the frequency range 700– 50 cm1 were measured at 2 cm1 resolution on a PerkinElmer 2000 FT-IR spectrometer. Samples were prepared as Nujol mulls placed between polyethylene windows.
Table 1 Crystal data and structure refinement for [Zn(I2CA)2(H2O)2]n Empirical formula Formula weight Temperature (K) Crystal system Space group
C18H16ZnN2O6 421.71 290(2) Monoclinic P21/c
Unit cell dimensions (A˚, 8)
a = 17.8339 (14) b = 6.4682 (5) c = 7.4305 (6) b = 90.795 (8) 857.05 (12) 2 1.634 0.12 0.09 0.01 1.473 Analytical [27] 432 3.9 to 25.4 4505 1534 1534/3/133 0.98 R1 = 0.069, wR2 = 0.159 0.72, 0.66 <0.001
Volume (A˚ 3) Z (molecule/cell) Density calculated (Mg m3) Crystal size (mm) Absorption coefficient (mm1) Absorption correction F(0 0 0) Theta range for data collection(8) Reflections collected Independent reflections Data/restraints/parameters Goodness-of-fit on F2 Final R indices [I > 2sigma(I)] Drmax and Drmin (e A˚3) D/smax
69
The FT-Raman spectrum of solid I2CA was recorded on a Nicolet Magna 860 spectrometer at 2 cm1 resolution and with an exciting laser operating at 1064 nm. The Raman spectrum of solid [Zn(I2CA)2(H2O)2]n was recorded on a Nicolet Almega dispersive Raman spectrometer at 2 cm1 resolution with an exciting laser operating at 780 nm. 2.4. Theoretical methods The theoretical studies have been performed using the threeparameter density functional method, B3LYP [28,29] and oneparameter hybrid method, mPW1PW91, introduced by Adamo and Barone [30] with the LanL2DZ [31] basis set for zinc atoms and the 6-311++G(d,p) [32,33] basis set for the remaining atoms of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n. In Part I [20] we have determined the crystal structure of I2CA and we have performed theoretical studies of the four possible conformers of I2CA, which differed in the relative orientation of atoms in the carboxylic group. Conformer I (shown in Scheme 1) in which the OH group is in the anti-position the NH group was the most stable, as revealed the ab initio (HF and MP2) and density functional (B3LYP) calculations. Moreover, the single crystal X-ray diffraction study indicated the presence of conformer I in crystal. It should be noted that the calculations have been performed for an isolated I2CA molecule, but agreement between the theoretical and experimental bond lengths and bond angles was good [20]. Therefore, the harmonic wavenumbers, infrared intensities and Raman scattering activities were calculated for conformer I of I2CA and I2CA-d2. For [Zn(I2CA)2(H2O)2]n the theoretical model was limited to bidentate I2CA representing the ligand bonded to two zinc ions via two oxygen atoms of carboxylic group. Prior to normal mode calculations, the optimization of molecular geometry was carried out starting from structural parameters determined by the X-ray method for [Zn(I2CA)2(H2O)2]n. Selected bond lengths and angles are listed in Table 2, along with the corresponding theoretical values calculated for theoretical model of [Zn(I2CA)2(H2O)2]n by the B3LYP and mPW1PW91 methods. The biggest deviation between the calculated and experimental values are noted for the C–O–Zn bond angles, as the result of the limitation of the theoretical model. Basing on the optimized structure for the theoretical model of [Zn(I2CA)2(H2O)2]n, the normal vibration wavenumbers, IR intensities and Raman activities were calculated. The deficiencies of the computed harmonic force field of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n were corrected by selective scale factors. The wavenumbers calculated by the B3LYP and mPW1PW91 methods were scaled, similarly as in our earlier studies [22–25].
Scheme 1. The atom numbering for I2CA.
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
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Table 2 Comparison of experimental and theoretical bond lengths (A˚) and angles (8) for theoretical model of [Zn(I2CA)2(H2O)2]n calculated by the mPW1PW91 and B3LYP methods with 6-311++G(d,p)/LanL2DZ basis sets
C(5)–C(6) C(6)–C(7) C(7)–C(8) C(3)–C(8) C(3)–C(4) C(2)–C(3) C(1)–C(2) N(1)–C(1) C(1)–C(0) C(0)–O(2) C(0)–O(1) O(2)–Zn O(1)–Zn C(5)–C(6)–C(7) C(6)–C(7)–C(8) C(7)–C(8)–C(3) C(8)–C(3)–C(4) C(8)–C(3)–C(2) C(3)–C(2)–C(1) C(2)–C(1)–N(1) C(2)–C(1)–C(0) C(1)–C(0)–O(2) C(1)–C(0)–O(1) C(0)–O(2)–Zn C(0)–O(1)–Zn
Experimental
mPW1PW91
B3LYP
1.393 (15) 1.356 (12) 1.382 (10) 1.426 (10) 1.409 (10) 1.406 (9) 1.340 (9) 1.392 (8) 1.441 (9) 1.265 (8) 1.299 (8) 2.070 (5) 2.135 (5) 122.0 (9) 119.1 (10) 120.1 (8) 119.3 (8) 105.5 (6) 109.8 (7) 107.9 (6) 129.5 (7) 118.8 (6) 119.7 (6) 131.4 (4) 129.5 (4)
1.401 1.426 1.370 1.430 1.435 1.377 1.440 1.345 1.443 1.279 1.281 1.945 1.948 123.07 116.50 122.03 119.88 107.60 107.14 108.35 127.90 118.33 117.83 141.63 139.10
1.402 1.436 1.371 1.433 1.441 1.381 1.449 1.346 1.459 1.280 1.281 1.983 1.985 122.86 116.59 122.18 119.70 107.72 107.19 108.27 128.07 117.68 117.37 142.51 140.05
The normal co-ordinate analyses for the theoretical models of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n have been carried out, including the calculation of the potential energy distribution (PED) terms for each normal mode, according to the procedures described in ref. [34] (BALGA program). The non-redundant set of internal co-ordinates has been derived, as recommended by Fogarasi and Pulay [35–37].
The computations were carried out with the Gaussian 03 programs [38]. 3. Results and discussion 3.1. Description of the structure of [Zn(I2CA)2(H2O)2]n The overall view and labelling of the atoms in the title [Zn(I2CA)2(H2O)2]n is displayed in Fig. 1. In contrast to recently reported complexes of indole-3-carboxylic acid with Zn(II) ([Zn(I3CA)2(H2O)]n) [23], indole-3-propionic acid with Zn(II) ([Zn(I3PA)2(H2O)]n) [24], indole-2-carboxylic acid with Zn(II) ([Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2(CN)]DMF, and [Zn(I2CA)2 (CN)]DMSO, where CN, 2,9-dimethyl-1,10-phenanthroline; DMA, dimethylacetamide; DMF, dimethylformamide; DMSO, dimethyl sulfoxide) [18], in the title [Zn(I2CA)2(H2O)2]n each anionic ligands act as bidentate bridging. It should be noted that in three [Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2 (CN)]DMF and [Zn(I2CA)2(CN)]DMSO complexes, the Zn(II) ion is five-coordinated by two I2CA anionic ligands one of which is monodentate, and the other is bidentate chelating and one bidentate chelating NC [18]. In [Zn(I3CA)2(H2O)]n each zinc centre is also fivecoordinated by the bidentate chelating I3CA anionic ligand, one oxygen atom bidentate bridging I3CA anionic ligand, one oxygen atom bidentate bridging I3CA anionic ligand from an adjacent [Zn(I3CA)2(H2O)] unit and water molecule [23]. Moreover, in [Zn(I3PA)2(H2O)]n each zinc centre is six-coordinated by two oxygen atoms of the bidentate chelating I3PA anionic ligand, two oxygen atoms tridentate chelating–bridging I3PA anionic ligand, one oxygen atom tridentate chelating–bridging I3PA anionic ligand from an adjacent [Zn(I3PA)2(H2O)] unit and water molecule [24]. As can be seen in Figs. 1 and 2, in [Zn(I2CA)2(H2O)2]n the Zn(II) cation is located on an inversion centre of the octahedral geometry.
Fig. 1. ORTEP III drawing of [Zn(I2CA)2(H2O)2]n with 30% probability displacement ellipsoids and the numbering system.
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Fig. 2. Part of the crystal structure of [Zn(I2CA)2(H2O)2]n showing the six-coordination geometry around Zn(II) as well as the strong hydrogen bonds (dashed line): N(1)– H(1A) O(3), O(3)–H(3B) O(1) and O(3)–H(3A) O(1). The symmetry codes are given in Table 4.
The co-ordination sphere consists of water oxygen atoms [O(3) and O(3)#1; symmetry code: #1 (x, 1 y, 1 z)] and indole-2carboxylate oxygen atoms [O(1) and O(1)#1, O(2) and O(2)#1; symmetry code: #1 (x, 1 y, 1 z)] of four anions. Moreover, each anion links two Zn(II) centres by means of indole-2carboxylote units. The Zn–O(2) bond is shorter than Zn–O(3) and Zn–O(1) (Table 3). In the co-ordination octahedron, the basal angles O–Zn(1)–O are in the range from 86.5(2) to 93.5(2)8, so that the octahedral geometry is small distorted from ideal. It should be noted that in [Zn(I3CA)2(H2O)]n, the Zn–O bond distances for the bidentate bridging I3CA anionic ligand are 1.978 (4) and 1.983 (3) A˚ and these are shorter than those found for the bidentate chelating I3CA anionic ligand (1.977 (4) and 2.519 (4) A˚) [23]. In [Zn(I3PA)2(H2O)]n, the Zn–O bond distances for the tridentate chelating–bridging I3PA anionic ligand are 2.001 (4), 2.070 (4) and 2.342 (4) A˚ and these are shorter than those found for the bidentate chelating I3PA anionic ligand (2.015 (4) and 2.418 (4) A˚) [24]. Moreover, in [Zn(I2CA)2(CN)]DMA, [Zn(I2CA)2(CN)]DMF and [Zn(I2CA)2(CN)]DMSO complexes, the Zn–O bond distances are
Table 3 The selected bond lengths (A˚) and bond angles (8), with e.s.d.s. in parentheses, determined for [Zn(I2CA)2(H2O)2]n by X-ray diffraction Metal surrounding Interatomic distances Zn–O(1) Zn–O(2) Zn–O(3) Interatomic angles O(1)–Zn–O(2) O(1)–Zn–O(3) O(2)–Zn–O(3)
2.136 (5) 2.070 (5) 2.123 (5)
92.91 (19) 93.25 (19) 93.5 (2)
Zn–O(1)#1 Zn–O(2)#1 Zn–O(3)#1
O(1)–Zn–O(2)#1 O(1)–Zn–O(3)#1 O(2)–Zn–O(3)#1
2.136 (5) 2.070 (5) 2.123 (5)
87.09 (19) 86.76 (19) 86.5 (2)
Symmetry transformations used to generate equivalent atoms: #1: x, 1 y, 1 z.
much larger for the bidentate chelating I2CA anionic ligand (in the range from 2.114 (3) to 3.314 (3) A˚) than these found for the monodentate I2CA anionic ligand (in the range from 1.931 (2) to 1.940 (2) A˚) [18]. I should remember that in the complex of Zn(II) with crotonate, the Z–O bond distances of the bridging ligand are 1.935 (3) A˚ for the conformation syn-anti and these are similar to the corresponding bond lengths of the bridging ligands for the conformation syn–syn (in the range from 1.920 (4) to 1.948 (4) A˚) [39]. It is interesting to compared the geometry of [Zn(I2CA)2 (H2O)2]n with the recently recorded crystal structure of the polymeric complex of Zn(II) with acetylenedicarboxylic acid ([Zn(C4O4)(H2O)2]n) [40]. The crystal structure is composed of zinc ions co-ordinated octahedrally by four oxygen atoms stemming from four different acetylenedicarboxylate anions with the Zn–O bond distances 2.151 (3) and 2.094 (3) A˚ (these bond distances are approximately 0.02 A˚ shorter than those found in [Zn(I2CA)2(H2O)2]n) and two water molecules in trans positions with the Zn–O bond distances 2.067 (3) A˚ (these bond distances are approximately 0.06 A˚ shorter than those found in [Zn(I2CA)2 (H2O)2]n). The observed Zn–O(3) and Zn–O(3)#1 (symmetry code: #1: x, 1 y, 1 z) bond distances of the title complex are very similar to the corresponding bond lengths in the {[Zn(L)2(H2O)2]2H2O}n (where L,3-cyano-4-dicyanomethylene5-oxo-4,5-dihydro-1H-pyrrol-2-olate anion) in which the water ligands lie in the apical sites of octahedral geometry with the Zn–O distances 2.1344 (14) A˚ [41]. The structure of [Zn(I2CA)2(H2O)2]n is also stabilized by hydrogen-bonding interactions (Table 4 and Fig. 2). There is the strong interaction between a water oxygen atom and a amide hydrogen atom of a neighboring chain [N(1)– H(1A) O(3)#1 = 2.29(9) A˚; symmetry code: #1 x, 1 y, 1 z]. There are also the strong O(3)–H(3B) O(1)#2 and O(3)– H(3A) O(1)#3 interactions (symmetry codes: #2: x, 3/2 y, 1/2 + z; #3: x, 1/2 + y, 3/2 z) between carboxyl oxygen atoms
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Fig. 3. The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and the infrared spectrum of deuterated derivative I2CA-d2 in the frequency range 3700–600 cm1.
and a water hydrogen atoms of neighboring chains (O(3)– H(3B) O(1)#2 = 1.93(9) A˚ and O(3)–H(3A) O(1)#3 = 2.01(9) A˚). A˚). In contrast to the strong hydrogen bonds, there is the weak C– H p interaction. The carbon atom C(2) acts as hydrogen bond donor, via H(2) to the five-membered ring of atoms N(1)–C(8) (centroid Cg 1) of the unit at (x, 3/2 y, 1/2 + z).
Table 4 Hydrogen bonds distances (A˚) and angles (8) in [Zn(I2CA)2(H2O)2]n D–H A
D–H
HA
DA
N(1)–H(1A) O(3) #1 O(3)–H(3B) O(1) #2 O(3)–H(3A) O(1) #3 C(2)–H(2) Cg1 #4
0.86 (8) 0.82 (9) 0.82 (8) 0.93
2.29 (9) 1.93 (9) 2.01 (9) 2.93
3.113 2.729 2.804 3.425
159 (9) 166 (11) 163 (8) 115
Cg1 denotes the centroid of the five-membered ring of atoms N(1)–C(8). Symmetry transformations used to generate equivalent atoms: #1: x, 1 y, 1 z; #2: x, 3/ 2 y, 1/2 + z; #3: x, 1/2 + y, 3/2 z; #4: x, 3/2 y, 1/2 + z.
3.2. Vibrational spectra of I2CA, [Zn(I2CA)2(H2O)2]n and infrared spectrum of I2CA-d2 The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n and the infrared spectrum of I2CA-d2 in the range from 3700 to 700 cm1 are presented in Fig. 3. In Fig. 4 the infrared and Raman spectra of title complex and free ligand are shown in the range from 700 to 50 cm1. Moreover, in Fig. 4 the infrared spectrum of I2CA-d2 is presented in the range from 700 to 400 cm1. In Tables 5 and 6, the experimental bond positions of I2CA and I2CA-d2 are compared with the theoretical wavenumbers, IR intensities, and Raman scattering activities calculated for conformer I of I2CA and I2CA-d2 (which is presented in Scheme 1). The results have been obtained by the B3LYP density functional method with 6-311++G(d,p) basis set. In Table 7, the experimental bond positions of [Zn(I2CA)2 (H2O)2]n are compared with the theoretical wavenumbers, IR intensities, and Raman scattering activities calculated for theoretical model of [Zn(I2CA)2(H2O)2]n. The results have been obtained
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wavenumbers by using the scale factor of 0.93 at 3509 cm1 for I2CA and at 2553 cm1 for I2CA-d2, respectively. The theoretical nO–H/nO–D isotopic ratio is about 1.37 for both DFT methods. In the infrared and Raman spectra of I2CA, I failed to localize the stretching O2H mode, but in the infrared spectrum of I2CA-d2 the medium band at 2311 cm1 can be assigned to the stretching O2D modes. In opposition to the O2H and O2D stretching vibrations, the O2H and O2D in-plane and out-of-plane bending vibrations are not predicted to be a ‘‘pure’’ vibrations and contributed to other modes, for the both DFT methods, as can be seen in Tables 1 and 2 of Supplementary material. The theoretical dO–H/dO–D isotopic ratios are 1286 cm1/998 cm1 = 1.29 and 1280 cm1/990 cm1 = 1.29 by mPW1PW91 and B3LYP calculations, respectively. In the infrared and Raman spectra of I2CA the bands at 1304 and 1302 cm1 can be assigned to the dO2H mode. It should be noted that the band at 1304 cm1 in the infrared spectrum of I2CA disappears in the infrared spectrum of I2CA-d2 and in the infrared and Raman spectra of [Zn(I2CA)2(H2O)2]n, where oxygen atom O2 of the carboxylic group of I2CA is deprotonated. In the infrared spectrum of I2CA-d2 are appearance two bands at 1031 and 1010 cm1, which can be assigned to the dO2D mode. The experimental dO–H/dO–D isotopic ratios are 1304 cm1 / 1031 cm1 = 1.26 and 1304 cm1 /1010 cm1 = 1.29, respectively. The O2H out-of-plane bending mode is calculated at 613 and 524 cm1 with predominant contribution at 524 cm1 for I2CA by B3LYP calculations. For I2CA-d2 the O2D out-of-plane vibration is predicted theoretically at 629 and 391 cm1, with predominant contribution at 391 cm1 by B3LYP calculations. The theoretical gO–H/gO–D isotopic ratio is about 1.34 for both DFT methods. The strong bands at 820 in the infrared and Raman spectra of I2CA can be assigned to the gO–H mode. Unfortunately, the band at 820 cm1 not disappear in the infrared spectrum of I2CA-d2, but disappears in the vibrational spectra of [Zn(I2CA)2(H2O)2]n, which confirms assignment of the band at 820 cm1 to the gO2H mode. Moreover, in the infrared spectrum of I2CA-d2 is observed new band at 687 cm1, which can be assigned to the gO2D mode. The experimental gO–H/gO–D isotopic ratio, 1.19 is in bad agreement with theoretical gO–H/gO–D isotopic ratios.
Fig. 4. The infrared and Raman spectra of I2CA and [Zn(I2CA)2(H2O)2]n in the frequency range 700–50 cm1 and the infrared spectrum of I2CA-d2 in the frequency range 700–400 cm1.
by the B3LYP density functional method with 6-311++G(d,p)/ LanL2DZ basis sets. It should be noted that comparison of the experimental and the theoretical wavenumbers, IR intensities and Raman scattering activities and the PED analysis at the mPW1PW91 and B3LYP methods for conformer I of I2CA, I2CA-d2 and theoretical model of [Zn(I2CA)2(H2O)2]n are available in Supplementary material (Tables 1–3). The bands due to the OH or NH vibrations of I2CA are influenced by the existing hydrogen bonds [20]. The theoretical calculations were performed for isolated molecule without intermolecular interactions. Therefore, the infrared spectrum of I2CA-d2 and also the infrared and Raman spectra of the title complex were helpful in assigning the N–HO and O–HO group vibrations of I2CA. 3.2.1. The OH vibrations of I2CA and the OD vibrations of I2CA-d2 As is seen in Tables 5 and 6, the O2H and O2D stretching vibrations have been calculated from the B3LYP harmonic
3.2.2. The NH vibrations of I2CA and [Zn(I2CA)2(H2O)2]n and the ND vibrations of I2CA-d2 The very strong band at 3350 cm1 (IR) and the medium at 3352 cm1 (R) of I2CA and the strong at 3363 cm1 (IR) of [Zn(I2CA)2(H2O)2]n can be attributed to the N–H stretching vibration. Unfortunately, in the infrared spectrum of I2CA-d2 the band of the nNH mode not disappear fully, but in the infrared spectrum of I2CA-d2 is observed new medium band at 2492 cm1 which can be assigned to the N1D stretching vibration. The experimental isotopic ratio nN–H/nN–D is 1.34. The theoretical N1H stretching modes are predicted from the B3LYP harmonic wavenumbers by using the scale factor of 0.93 at 3395 and 3336 cm1 for I2CA and [Zn(I2CA)2(H2O)2]n, respectively and the theoretical N1D stretching mode at 2492 cm1 for I2CA-d2. The theoretical nN–H/nN–D isotopic ratio is about 1.36 for both DFT methods. According to the PED the in-plane N1H bending mode in I2CA contributes to two modes at calculated wavenumbers 1417 and 1200 cm1, with predominant contribution at 1200 cm1 (39%) by B3LYP calculations. The theoretical results for I2CA-d2 show that the dN1D mode is calculated at 947 and 768 cm1 with predominant contribution at 947 cm1 (42%) by B3LYP calculations. The theoretical dN–H/dN–D isotopic ratios are 1.26 and 1.27 by mPW1PW91 and B3LYP calculations, respectively. In the infrared spectrum of I2CA-d2, the dN1D mode can be assigned the new
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Table 5 Comparison of the experimental (FT-IR and FT-Raman band positions of the I2CA) and the theoretical wavenumbers (n, cm1), IR integrated intensities (Ath, km mol1) and Raman scattering activities (Bth, A˚4 amu1) calculated for conformer I of I2CA Experimental FT-IR
Calculated B3LYP/6-311++G(d,p) FT-Raman
na
Ath
Bth
PED (%)
3509
134
157
nO2H (100)
3395 3125
107 0
72 77
nN1H (100) nC2H (99)
3453w 3350vs
3352m 3135m
3086w
3095m
3065
16
319
nC5H (39), nC6H (35), nC4H (13), nC7H (13)
3052s
3066s 3054s 3028w 1725w
3056 3046 3039
22 2 0
63 139 28
nC7H (36), nC4H (29), nC5H (18), nC6H (17) nC4H (38), nC7H (36), nC6H (16), nC5H (10) nC5H (33), nC6H (32), nC4H (20), nC7H (15)
1707vs 1622m 1579w 1519s 1500m 1438s 1417s 1367w 1346s
1644s 1625m 1580w 1532s 1507w 1445vs 1414m 1367w 1347m 1337m 1302s 1237m 1192s
1729 1624 1580 1538 1499 1438 1417 1383 1342 1320 1280 1227 1135b 1200 1158 1118 1093 1009 962 960 929
633 10 9 116 2 15 40 78 60 68 2 9 397 73 88 5 47 0 0 5 2
363 78 25 274 12 119 38 13 7 109 75 15 90 2 13 16 1 60 0 26 0
nC0O1 (54), nC0O2 (26) nC7C8 (21), nC4C5 (16), nC3C4 (13), nC6C7 (10) nC3C8 (15), nC5C6 (14), nC6C7 (10) nC1C2 (36), nC1C0 (11) dC5H (22), nC4C5 (13), nC6C7 (11) dC7H (21), dC4H (18), nC3C8 (14) nC1N1 (36), dN1H (13) dC6H (11) dC5H (19) dO2H (14), nC3C8 (11), nC2C3 (11) dO2H (21), nN1C8 (18), nC2C3 (11) dC4H (22), dC7H (18), nC7C8 (13), nC2C3 (11) dO2H (22), nC0O2 (16), dC2H (14) dN1H (39), dC2H (15) dC6H (23), dC5H (22), dC7H (11), dO2H (10) nC4C5 (17), dC5H (16), nC6C7 (14), dC4H (12), d6R (11), dC6H (10) dC2H (29), nC0O2 (21), nN1C8 (20) nC5C6 (47), nC6C7 (12), nC4C5 (12) gC5H (45), gC6H (34), gC4H (21) d5R (47), nC3C8 (19), nC0O2 (10) gC4H (37), gC6H (34), gC7H (29)
887 844 822 524b 801 768 744 680b 734 613 608 569 545b 566 473
1 8 14 142 1 35 76 28 19 0 2 30 14 4 28
6 1 1 2 18 0 0 16 0 1 13 0 4 0 0
429 366 342
3 2 5
1 1 5
t6R (90) dCOOrock (26), d6R (26) nC1C0 (25), dCOOsciss (23), d5R (12)
263 247
0 0
0 0
(6R (67), gC1C0 (28) t6R (59), t5R (30)
139
3
0
dC1C0 (64), dCOOrock (22)
88 82
2 0
2 0
gC1C0 (35), (6R (21), t5R (19), gCOOtwist (17) gCOOtwist (72), gC1C0 (12)
1304m 1238s 1194vs 1153s 1122w 1115m
1154w 1120s 1014s
969w 934w 926w 899w 848 w 820s
969vs
897w 869vw 847w 820s
769s 743s 736s 728s 614m 578m 567m 556w 518m,br 452w 428m 391w 378m 281m
609s 578w
367s 281w
260w
259w
205m 150w 128w 100w 74w
203w
555w
432w
d6R (59) gC2H (29), gC7H (26), gC5H (16), gC4H (15) gC2H (55), gC7H (18), gC4H (15) gO2H (77) nC3C8 (30), nC7C8 (13), nC3C4 (13) gCOOwag (48), t6R (21), t5R (12) t6R (35), gCOOwag (18), t5R(16), gC5H (10) dCOOsciss (35), d6R (16), nC0O2 (13), d5R (10) gC6H (23), gC5H (19), gC7H (18) t5R (78), gO2H (16) d5R (45), d6R (28), nC7C8 (11), nC3C4 (11) d6R (55), dCOOsciss (20) dCOOrock (33), dC1C0 (23), d6R (22) t6R (75), t5R (25) gN1H (95)
131m
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak; v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching NH and OH by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers.
band at 958 cm1. Unfortunately, I failed to localize the dN1H mode in the infrared and Raman spectra of I2CA. Also, in the infrared and Raman spectra of [Zn(I2CA)2(H2O)2]n is very true assigned band of the dN1H vibration. Both DFT calculations show
that in the complex the dN1H mode has not predominant contribution. The calculations show that the out-of-plane N1H and N1D bending modes not contribute to other modes for I2CA,
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Table 6 Comparison of the experimental (FT-IR band positions of the I2CA-d2) and the theoretical wavenumbers (n, cm1) and IR integrated intensities (Ath, km mol1) calculated for conformer I of I2CA-d2 Experimental
Calculated B3LYP/6-311++G(d,p)
FT-IR
na
Ath
PED (%)
3453w 3350mc 3134m
3125 3065
0 16
nC2H (99) nC5H (39), nC6H (35), nC4H (13), nC7H (13)
3051m
3056 3046 3039
22 2 0
nC7H (36), nC4H (29), nC5H (18), nC6H (17) nC4H (38), nC7H (36), nC6H (16), nC5H (10) nC5H (33), nC6H (32), nC4H (20), nC7H (15)
2492m 2311m 1700s 1619m 1577w 1520s 1484s 1429s 1401m 1363w 1345m 1336s 1326s 1253s 1235s 1195sc 1152m 1136w 1120m
2492b 2553 1719 1622 1572 1535 1487 1436 1398 1367 1333 1306
69 86 626 11 4 126 17 18 118 6 27 152
nN1D (98) nO2D (100) nC0O1 (58), nC0O2 (27) nC7C8 (20), nC4C5 (16), nC3C4 (14), nC6C7 (12) nC5C6 (18), nC3C8 (16) nC1C2 (39), nC1C0 (10) dC5H (22), nC6C7 (14), nC3C4 (11) dC7H (21), dC4H (18), nC3C8 (14), nC4C5 (14) nC1N1 (46), nC1C0 (11) nC5C6 (14), dC6H (11) nN1C8 (16), dC5H (15), dC7H (15), dC6H (13) nC2C3 (17), nC3C8 (15), nC4C5 (13), nC8N1 (12)
1227 1221 1150 1127 1118
39 237 23 13 5
1011
1
dC4H (22), nC4C3 (14), dC7H (12) nN1C1 (15), nC2C3 (11), nC0O1 (11), dC6H (28), dC5H (21), dC7H (18) dC2H (58) nC4C5 (16), dC5H (16), nC6C7 (14), dC4H (12), d6R (12), dC6H (10) nC5C6 (44), nC6C7 (11), nC4C5 (11), dC7H (11)
990 963 947 940 929
126 0 17 8 2
871 843 822
1 6 13
d6R (43), nC2C3 (12) gC2H (27), gC7H (27), gC5H (17), gC4H (16) gC2H (57), gC7H (17)
768 765 743 734 391 b 629 606 594 562 558 523 433 356 361 337 260 244 137 87 82
0 19 73 18 45 18 2 0 0 32 28 23 40 2 6 0 0 3 2 0
nC3C8 (23), dN1D (16), nC3C4 (11) gCOOwag (44), t6R (26), t5R (11) t6R (30), gCOOwag (20), t5R (15), gC5H (11) gC6H (22), gC5H (18), gC7H (17), gC2H (11) gO2D (85) d6R (28), dO2D (17), dCOOsciss (15), nC1C0 (11) d5R (44), d6R (29), nC7C8 (11), nC3C4 (11) t5R (82) d6R (76), tR5 (24) d6R (32), dCOOsciss (23), dCOOrock (10) dCOOrock (26), dC1C0 (18), d6R (14) t6R (70), t5R (23) gN1D (100) d6R (26), dCOOrock (23) dCOOsciss (24), nC1C0 (23), d5R (12) d6R (64), gC1C0 (19) t6R (58), t5R (39) dC1C0 (64), dCOOrock (22) gC1C0 (36), (6R (21), t5R (18), gCOOtwist (17) gCOOtwist (76), gC1C0 (12)
1031m 1010m 986w 958m 941m 926w 913w 891w 848w 820mc 791w 768s 744s 728s 687m 608w 591w 573m 541m 429m
dO2D (45), nC0O2 (37) gC5H (45), gC6H (34), gC4H (21) dN1D (42), d6R (11), d5R (43), dO2D (15), nC3C8 (14) gC4H (37), gC6H (34), gC7H (29)
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak; v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching ND and OD by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers. c See text.
[Zn(I2CA)2(H2O)2]n and I2CA-d2 and these are predicted at 473, 607 and 356 cm1, respectively by B3LYP calculations. The theoretical gN–H/gN–D isotopic ratios are 1.32 and 1.33 by mPW1PW91 and B3LYP calculations, respectively. In the infrared
spectrum of I2CA the medium band at 518 cm1 disappears in the infrared spectrum of I2CA-d2, therefore, this band can be assigned to the gN1H mode. In the infrared spectrum of [Zn(I2CA)2(H2O)2]n is very true assigned band for gN1H mode, because board
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
76
Table 7 Comparison of the experimental (FT-IR and Raman band positions of the [Zn(I2CA)2(H2O)2]n) and the theoretical wavenumbers (n, cm1), IR integrated intensities (Ath, km mol1) and Raman scattering activities (Bth, A˚4 amu1) calculated for the theoretical model of [Zn(I2CA)2(H2O)2]n Experimental FT-IR
Calculated B3LYP/6-311++G(d,p)/LanL2DZ Raman
na
Ath
Bth
3336
140
72
PED (%)
3445w 3363s
nN1H (100)
3241w 3131w
3144w
3121 3081
13 64
29 871
nC2H (99) nC5H (78), nC4H (15)
3057w
3052w 3008w
3072 3068 3060
37 4 12
289 84 156
nC7H (83), nC6H (11) nC4H (78), nC5H (14) nC6H (80), nC7H (11)
1619wc 1574m
1577
1619m 1575w
c
192
1282
b
238 279
5 10
nC7C8 (47) nasCOO (73) nC2C3 (21), nC3C4 (16), nC5C6 (10)
1542s,br
1550m 1534w
1405 1560
1494w 1445m 1427m 1418m 1406m 1386w 1372w 1335m 1291m 1233w 1221w
1496w 1442m
1391m 1358w 1341m 1294m 1235w 1225w
1492 1469 1421 1418 1255b 1367
179 84 211 125 180 61
14 212 18 107 15 83
nC1N1 (30), dN1H (25), nC4C5 (30), dC5H (23), dC6H (16) nC3C8 (15), nC2C3 (14), nasCOO (14) nC5C6 (19), dC5H (12) nsCOO (33), nC1C0 (12) dC4H (23), nC5H (20), nC6H (16)
1345 1298
30 501
478 62
nC1C2 (23), nC1N1 (19), dR5 (11) nC7H (22)
1204
33
13
1153w
1151w
1174 1160
106 1
24 368
dC6H (28), dC5H (27), nC5C6 (16) nC8N1 (28), dC4H (15), dR6 (10)
1118w 1105w
1118w
1120 1089
121 63
14 278
dC2H (39), nsCOO (21), nC1C2 (11) nC4C5 (26)
1004w
1004vs
993 b 1008
127 1
75 1
nC6C7 (35), nC5C6 (32), dC7H (11) gC5H (56), gC6H (44)
974w 930w 895w 858w 833w
974s 896w 864w 830w
985 934 895 878 869
1 22 3 5 21
3 37 1 37 2
gC4H (45), gC6H (23), gC7H (19), gC5H (13) dR5 (37), nC3C8 (14), nC1C2 (13) gC2H (49), gC7H (35), gC4H (11) dR6 (59) gC2H (42), gC7H (35), gC4H (11)
805w 770m
808 757 b
40 10
39 16
nC3C8 (33), dCOOsciss (13) gCOOwag (65), gC1C0 (13)
735 b 774 685
1 47 11
2 2 5
607 594 578 563 547
78 13 19 54 7
2 29 11 6 116
457
14
3
396 384
35 9
11 60
dR6 (27), nZnO1 (17), dCOOrock (10) dCOOsciss (20), nZnO2 (19), nC1C0 (10)
372 273 263 225 214
6 26 34 16 17
11 8 5 12 21
tR6 (63), tR5 (26) tR6 (35), nZnO2 (17), gC1C0 (15), dZnO2 (11) tR6 (21), nZnO1 (15) tR6 (42), tR5 (20), nZnO1 (15) nZnO2 (29), nZnO1 (14), dR6 (10),
143s
150 133
1 5
1 29
dC1C0 (32), gZnO2 (18), gZnO1 (17), dCOOrock (14) dZnO2 (37), dZnO1 (28), tR5 (10)
118vs
126
1
178
72 68
5 0
2 52
794m
1421m
750m 735s 670w 628w,br 613w 588w 575w 556w 485w c 438m
613w 593vw 566vw 547vw 489vwc 435vw
392w 384vw 324vw 289m 263vw 248vw 216w 180m
335vw 303vw 267vw 239vw
154w
dC2H (24), dN1H (23)
dCOOsciss (31), dR5 (11) gC5H (23), gC6H (21), gC4H (18), tR6 (15) tR5 (51), tR6 (27) gN1H (100) dR5 (43), dCOOrock (16), nC3C4 (14) tR5 (61), gC1C0 (12) dR6 (20), dCOOrock (18), dR6 (13), dC1C0 (11) dR6 (49) tR6 (71)
122w
106w 96w
dZnO1 (25), dZnO2 (22), nZnO1 (11), gCOOtwist (10) gC1C0 (27), tR6 (13), dZnO1 (12) gZnO1 (33), gZnO2 (32), dZnO2 (12), dZnO1 (12)
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
77
Table 7 (Continued ) Experimental FT-IR 77w 68w
Calculated B3LYP/6-311++G(d,p)/LanL2DZ Raman
na
Ath 50 34
1 0
Bth 26 6
PED (%)
gZnO2 (38), gZnO1 (17), dC1C0 (12), gC1C0 (12) gCOOtwist (70), gZnO1 (14)
Abbreviations: m, medium; s, strong; sh, shoulder; w, weak, v, very; n, stretching; d, in-plane bending; g, out-of-plane bending; t, torsion; sciss, scissoring; rock, rocking; wag, wagging; twist, twisting; 5R, five-membered indole ring; 6R, six-membered indole ring. a The calculated B3lyp wavenumbers were scaled: for stretching NH by 0.93, modes for stretching CH by 0.96 and the remaining modes by 0.98. b Reordered theoretical wavenumbers. c See text.
absorption between 700–500 cm1 of the librational lattice modes of the co-ordinated water molecules, this makes impossible. 3.2.3. The C O and C–O group vibrations of I2CA and I2CA-d2 and the [Zn(COO)] group vibrations of [Zn(I2CA)2(H2O)2]n According to the B3LYP calculations, the wavenumber of the nC0O1 mode is calculated at 1729 cm1 for I2CA with contribution 54%. For I2CA-d2 the nC0O1 mode is calculated at 1719 and 1221 cm1 with predominant contribution 58% at 1719 cm1 by B3LYP calculations. In the crystal structure of I2CA both the O2H and N1H groups act as donor sites, while the O1 atom acts as the acceptor site for two hydrogen bonds [20]. Therefore, the C0O1 groups within the dimmer interact and produce so-called factor group splitting. Its magnitude can be evaluated easily by subtracting nC O (IR) from nC O (Raman) [42]. The wavenumbers of the nC0O1 mode are 1707 and 1644 cm1 in the infrared and Raman spectra of I2CA, respectively, and thus the value 63 cm1 is comparable with this for b,b’-dichloropivalic acid (62 cm1) [42]. The band for the nC0O1 mode is observed for I2CAd2 at 1700 cm1 in the infrared spectrum. The nC0O1 mode for I2CA and I2CA-d2 is coupled with nC0O2 mode for the both DFT methods. According to the both DFT calculations the nC0O2 mode has not predominant contribution for I2CA and I2CA-d2. The nC0O2 mode at 1135 cm1 with contribution 16% is coupled with the dO2H mode with contribution 22% for I2CA. This theoretical wavenumber at 1135 cm1 are assigned bands at 1194 and 1192 cm1 in the infrared and Raman spectra of I2CA, respectively. The band at 1194 cm1 in the infrared spectrum of I2CA not disappear in the infrared spectrum of I2CA-d2 but both bands at 1194 and 1192 cm1 in the vibrational spectra of I2CA disappear in the vibrational spectra of [Zn(I2CA)2(H2O)2]n. This shows that these bands can be assigned to nC0O2 vibration of I2CA. According to the both DFT calculations the nasCOO mode of [Zn(I2CA)2(H2O)2]n is lower than the nC0O1 mode of I2CA and the nsCOO mode of [Zn(I2CA)2(H2O)2]n is higher than the nC0O2 mode of I2CA. The nasCOO mode of the bidentate bridging I2CA anionic ligand of the [Zn(I2CA)2(H2O)2]n is calculated at 1405 and 1421 cm1 by B3LYP calculations. The mode at 1405 cm1 is pure mode as evidenced from 73% of PED. The nsCOO mode of the [Zn(I2CA)2(H2O)2]n is calculated at 1255 and 1120 cm1 with predominant contribution 33% at 1255 cm1. New strong band at 1542 cm1 in the infrared spectrum and new medium band at 1550 cm1 in the Raman spectrum and new medium band at 1406 cm1 in the infrared spectrum corresponds to the nasCOO and nsCOO modes, respectively for [Zn(I2CA)2(H2O)2]n. The discrepancies between the theoretical and the experimental wavenumbers for the nasCOO and nsCOO modes are probably partly caused by the limits of the applied computational model for [Zn(I2CA)2(H2O)2]n. However, it should be emphasized that the separations between the nasCOO and nsCOO are 154 and 150 cm1 by mPW1PW91 and B3LYP calculations, respectively and 136 cm1 by experimental data. It should be noted that in diamminetetrakis(m-indole-3-carboxylato-O,O’)dicopper(II)
([Cu2(I3CA)4(NH3)2]) [22], [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2 (H2O)]n [24], the separations between the experimental nasCOO and nsCOO are 149 and 122 cm1 in the bidentate bridging indole3-carboxylate anions and 142 cm1 in the tridentate chelating– bridging indole-3-propionate anion. Moreover, in the infrared spectrum of di[(m2-acetato)(2-acetylpyridine4N-ethylthiosemicarbazonato)zinc] the band at 1575 and 1418 cm1 were assigned to nasCOO and nsCOO in the bidentate bridging acetate anion, respectively [43]. In [Zn(2-pyrrolecarboxylato)2(H2O)] the separation between the experimental nasCOO and nsCOO is 120 cm1 in the bidentate bridging 2-pyrrolecarboxylate anion [44]. The dCOOsciss, dCOOrock, gCOOwag and gCOOtwist in-plane and out-of-plane bending vibrations, respectively are not predicted to be a ‘‘pure’’ vibrations and contributed to other modes, for the both DFT methods, as can be seen in Tables 1–3 of Supplementary material. However, the strong band at 736 cm1 in the Raman spectrum of I2CA and the medium band at 750 cm1 in the infrared spectrum of [Zn(I2CA)2(H2O)2]n can be assigned to the dCOOsciss mode. In the infrared spectra of I2CA and I2CA-d2 the medium bands at 567 and 541 cm1, respectively can be assigned to the dCOOrock mode. For [Zn(I2CA)2(H2O)2]n the dCOOrock mode has not predominant contribution by the both DFT calculations. In the infrared spectra of I2CA and I2CA-d2 the strong bands at 769 cm1 and 768 cm1, respectively can be assigned to the gCOOwag mode. The gCOOwag mode for [Zn(I2CA)2(H2O)2]n can be assigned to the medium band at 770 cm1 in the Raman spectrum. In the infrared spectra of the investigated molecules the bands below 100 cm1 can be assigned to the gCOOtwist mode. The zinc ion forms four Zn–O bonds with I2CA anions, as shown in Fig. 1. According to the calculated PED by the both DFT calculations, the nZnO1 and nZnO2 stretching vibrations are strongly mixed between themselves and overlap with other modes as can be seen in Table 7. As results from the X-ray, the Zn–O bond distances are longer for [Zn(I3CA)2(H2O)]n (in the range from 1.977 (4) to 2.519 (4) A˚) [23] than these found in [Zn(I3PA)2(H2O)]n (in the range from 2.001 (4) to 2.418 (4) A˚) [24]. Therefore, the Zn–O stretching vibrations in [Zn(I3CA)2(H2O)]n were observed at lower wavenumber (at 470 (IR) and 467 cm1 (R)) [23] than in [Zn(I3PA)2(H2O)]n (at 504 (IR) and 518 cm1 (IR)) [24]. The Zn– O bond distances for the bidentate bridging anionic ligand of [Zn(I2CA)2(H2O)2]n (2.070(5) and 2.136(5) A˚) are shorter than these found in [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24]. This implies that the Zn–O stretching vibration of [Zn(I2CA)2 (H2O)2]n should be observed at higher wavenumber than that of [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24]. However, in [Zn(I2CA)2(H2O)2]n each I2CA anionic ligand act as bidentate bridging, but in [Zn(I3CA)2(H2O)]n one I3CA anionic ligand act as bidentate bridging, and the other as bidentate chelating [23]. In [Zn(I3PA)2(H2O)]n one I3PA anionic ligand is tridentate chelating– bridging, and the other is bidentate chelating. Therefore, it is interesting to compared the Zn–O bond distances for the bidentate bridging I2CA anionic ligand in [Zn(I2CA)2(H2O)2]n with these recorded for the bidentate bridging I3CA anionic ligand in [Zn(I3CA)2(H2O)]n [23]. The Zn–O bond distances for the bidentate
78
B. Morzyk-Ociepa / Vibrational Spectroscopy 49 (2009) 68–79
bridging I2CA anionic ligand of [Zn(I2CA)2(H2O)2]n are longer than these found in the bidentate bridging I3CA anionic ligand of [Zn(I3CA)2(H2O)]n [23]. Therefore, the corresponding the Zn–O stretching vibration in [Zn(I2CA)2(H2O)2]n should be observed at lower wavenumber than in [Zn(I3CA)2(H2O)]n. However, in the infrared spectrum of [Zn(I2CA)2(H2O)2]n appear new band at 485 cm1. The band is not observed in the infrared spectrum of I2CA. Therefore, this band was assigned to stretching Zn–O vibrations with oxygen atom of the carboxylic group of [Zn(I2CA)2(H2O)2]n. The lowering energy of the stretching Zn–O mode to 470 cm1 in the infrared spectrum of [Zn(I3CA)2(H2O)]n [23] is caused by the Zn–O bond distances of the bidentate chelating I3CA anionic ligand. 3.2.4. The CH vibrations of I2CA, I2CA-d2, [Zn(I2CA)2(H2O)2]n According to the calculated PED by the both DFT calculations, the C2H, C4H, C5H, C6H and C7H stretching vibrations can be assigned to bands at the wavenumber range from 3144 to 3008 cm1 in the vibrational spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n. The calculated PED has revealed that the C4H, C5H, C6H and C7H stretching modes are mixed between themselves for all investigated molecules as can be seen in Tables 5–7, except the C6H and C7H stretching modes of [Zn(I2CA)2(H2O)2]n calculated by mPW1PW91 method (Table 3 of Supplementary material). Moreover, for all investigated molecules the C2H stretching mode is not mix with other modes by the both DFT calculations. The CH in-plane bending vibrations in all investigated molecules are strongly coupled with other modes and contribute to several bands in the range from 1507 to 1004 cm1. As revealed by the PED, the several normal modes corresponding to the pure CH out-of-plane bending vibrations at 962, 929, 844, 822 and 734 cm1 for I2CA, and at 963, 929, 843, 822 and 734 cm1 for I2CA-d2 and at 1008, 985, 895 and 869 cm1 for [Zn(I2CA)2(H2O)2]n by B3LYP calculations. The detailed vibrational assignments of the dCH modes and of the pure and remaining the gCH modes are given in Tables 5–7. 3.2.5. The [Zn(H2O)] group vibrations of [Zn(I2CA)2(H2O)2]n In the infrared spectrum of [Zn(I2CA)2(H2O)2]n is shown a broad and complicated structure of the bands from 3600 to 2700 cm1. These bands correspond to the anti-symmetric and symmetric OH stretch and confirm the presence of water in the compound. The infrared spectrum exhibits characteristic band at 1619 cm1, which can be assigned to the OH in-plane bending mode. In the infrared spectrum of the title complex, the rocking HOH, wagging HOH modes is difficult to assigned separate bands. These bands are probably the effect of superposition of I2CA modes and rocking and wagging modes of co-ordinated water molecules, of very similar wavenumbers. Board absorption between 700 and 500 cm1 in the infrared spectrum of [Zn(I2CA)2(H2O)2]n is connected with the librational lattice modes of the co-ordinated water molecules. The ZnO stretching band with oxygen atoms of water molecules have been assigned at 364, 360 and 368 cm1 of solid [Zn(H2O)6]SO4H2O [45], [Zn(I3CA)2(H2O)]n [23] and [Zn(I3PA)2(H2O)]n [24], respectively. Unfortunately, in the spectrum of [Zn(I2CA)2(H2O)2]n, I failed to localize the bands of the Zn–H2O stretching modes. 3.2.6. The overtones or combination modes The weak band at 2644 cm1 in the infrared spectrum of I2CA, the weak bands at 2568, 1296 and 1275 cm1 in the infrared spectrum of I2CA-d2 and the weak bands at 2939, 2911, 2778, 1280 and 1265 cm1 and the medium band at 2738 cm1 in the Raman spectrum of [Zn(I2CA)2(H2O)]n are not enumerated in the
Tables 5–7. These bands can be assigned to overtones or combination modes. 4. Conclusions In this work the novel [Zn(I2CA)2(H2O)2]n was investigated experimentally by the X-ray diffraction. Moreover, the vibrational spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n have been calculated by the mPW1PW91 and B3LYP calculations with the 6-311++G(d,p) basis set for I2CA and I2CA-d2 and with the 6-311++G(d,p)/LanL2DZ basis sets for [Zn(I2CA)2(H2O)2]n. The comparison of the vibrational spectra I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n calculated by mPW1PW91 and B3LYP suggests that the both DTF calculations produce similar results (which are available in tables of Supplementary material). The calculations for I2CA and I2CA-d2 were performed for the most stable conformer of I2CA. This conformer is not only a minimum energy conformer but also it corresponds to the experimentally found geometry [20]. For [Zn(I2CA)2(H2O)2]n the theoretical model was limited to bidentate I2CA representing the ligand bonded to two zinc ions via two oxygen atoms of carboxylic group. Because part of the ligand and complex are used for calculations, therefore, the obtained vibrational results must be carefully verified. In such situation, the theoretical reproductions of experimental data of all investigated molecules were very useful for reasonable bands attribution for these molecules. The frequency shift of several vibrational modes has been analyzed in going from theoretical calculations to the solid state spectra, for example NH and OH modes of I2CA and nasCOO and nsCOO modes of [Zn(I2CA)2(H2O)2]n. These effects are caused by the intermolecular hydrogen bonding in the solid state and the limitations of the theoretical models. The presented experimental and theoretical spectra of I2CA, I2CA-d2 and [Zn(I2CA)2(H2O)2]n and vibrational assignment can assist in the interpretation of the vibrational spectra of new I2CA agents. Acknowledgements I am grateful to Dr. Ewa Rozycka-Sokolowska from Jan Długosz University of Cze˛stochowa for the X-ray structure determinations. The Wrocław Centre for Networking and Supercomputing is acknowledged for generous computer time.
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