Discovery of a New Polymorph of 5-Methoxy-1H-Indole-2-Carboxylic Acid: Characterization by X-ray Diffraction, Infrared Spectroscopy, and DFT Calculations.

This study presents a new 5-methoxy-1H-indole-2-carboxylic acid (MI2CA) polymorph investigated by single-crystal X-ray diffraction, infrared spectroscopy, and density functional theory (ωB97X-D) calculations employing two basis sets (6-31++G(d,p) and aug-cc-pVTZ). The compound crystallizes in the monoclinic system, space group P21/c (a = 4.0305(2) Å, b = 13.0346(6) Å, c = 17.2042(9) Å, ß = 91.871(5)°, Z = 4). In the crystalline structure, the formation of cyclic dimers via double hydrogen bonds O-H⋯O between MI2CA molecules was observed. Interactions between the NH groups of the indole rings and the adjacent methoxy groups, as well as C-H⋯O contacts, significantly influence the spatial arrangement of molecules. The results from DFT calculations, including dimeric and trimeric structures, agree well with the experimental structural and spectroscopic data. Analysis of the infrared spectra confirms the conclusions drawn from X-ray diffraction studies and reveals differences between the IR spectra of the newly obtained polymorph and that reported earlier in the literature. This comprehensive study sheds some light on the MI2CA polymorphism and is important for a potential pharmacological applications of this compound.

X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers.

3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, ß=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.

Vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes part VIII. 5-methoxyindole-2-carboxylic acid and its Zn(II) complex.

The complex of 5-methoxyindole-2-carboxylic acid with Zn(II) has been synthesized and characterized by the infrared and Raman spectroscopic methods. Moreover, the infrared and Raman spectra of 5-methoxyindole-2-carboxylic acid (5-MeOI2CAH) and the infrared spectrum of deuterated derivative of 5-metoxyindole-2-carboxylic acid (5-MeOI2CA-d2) are recorded in the solid phase. The theoretical wavenumbers, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(df,p) basis set for 5-MeOI2CAH and 5-MeOI2CA-d2 and with the 6-311++G(df,p)/LanL2DZ basis sets for the theoretical model of [Zn(5-MeOI2CA)(2)(H(2)O)(2)](n). The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution for 5-MeOI2CAH, 5-MeOI2CA-d2 and [Zn(5-MeOI2CA)(2)(H(2)O)(2)](n). The results from natural bond orbitals (NBO) analyses for indole-2-carboxylic acid (I2CAH) and 5-MeOI2CAH are discussed.

Vibrational spectra of 1-methylthymine: matrix isolation, solid state and theoretical studies.

The infrared spectra of 1-methylthymine (1-MeT) in argon and nitrogen cryogenic matrices are presented, for the first time. The molecular structure, conformations, vibrational frequencies, infrared intensities and Raman scattering activities of 1-MeT have been calculated by the DFT(B3LYP), MP2 and HF methods using the D95V** basis set. The theoretically predicted intensity pattern of the IR and Raman bands has proved to be of great help in assigning the experimental spectra. Rigorous normal coordinate analysis has been performed, at each level of theory. The unequivocal and complete vibrational assignment for 1-MeT has been made on the basis of the calculated potential energy distribution (PED). Comparison of the experimental matrix isolation spectra with the theoretical results has revealed that the B3LYP method is superior to both the MP2 and HF methods in predicting the frequencies of uracil derivatives. The MP2 method consistently underestimates the frequencies of the out-of-plane gamma(C=O) and gamma(C-H) bending modes, while the HF method yields the reverse order of the frequencies of two nu(C=O) stretching vibrations. Investigation of the frequency shift of several bands, on passing from matrix isolation to solid state spectra, has provided information on the strength of intermolecular hydrogen bonding in the crystal of 1-MeT. Several ambiguities in the earlier assignments of the vibrational spectra of polycrystalline 1-MeT have been clarified.

Vibrational spectra of 1-methyluracilate complex with silver(I) and theoretical studies of the 1-MeU anion.

The FT-Raman and FT-infrared spectra of (1-methyluracilato)silver, [Ag(C(5)H(5)N(2)O(2))] in the solid state have been studied. The complex is a polymer in which one silver ion is linearly bonded to two 1-MeU ligands through the deprotonated N(3) sites and another silver ion is tetrahedrally coordinated to the four 1-MeU ligands through the O2 and O4 carbonyl oxygen atoms. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the N(3)-deprotonated 1-methyluracilate anion have been calculated using density functional (B3LYP) and ab initio (HF and MP2) methods with the 6-31G(d,p) and 6-31++G(df,pd) basis sets. The calculated potential energy distribution (PED) for the 1-MeU anion has proved to be of great help in assigning the spectra of the title complex. It can be concluded that the two strong Raman bands at 1263 and 796 cm(-1) are diagnostic for the N3-deprotonation of the 1-methyluracilate ring and complexation with silver ion. The linear N-Ag-N stretching vibrations are assigned to the bands at 448 and 362 cm(-1) (IR) and 453, 362 cm(-1) (Raman). The Ag-O stretching vibrations are assigned to the bands in the range of 280-250 cm(-1).