Structures and vibrational spectra of indole carboxylic acids. Part I. Indole-2-carboxylic acid

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, β = 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.

Self-assembly controlled at the level of individual functional groups

Molecular self-assembly is driven by intermolecular interactions between the functional groups on the component molecules. Small changes in molecular structure can make large differences in extended structure, and understanding this connection will lead to predictive power and control of the self-assembly process. Scanning tunneling microscopy is used to study self-assembly in two-dimensional clusters and monolayers, and the experimental approach is to study "families" of molecules where one or more functional groups is varied in a methodical way. Studied families include indole carboxylic acids, isatin derivatives (which have the indole backbone), quinaldic acid, thioethers, and fluorenone derivatives. In these systems, a variety of intermolecular interactions drive the assembly of the molecular monolayer, including hydrogen bonds, van der Waals forces, zwitterionic interactions, surface interactions, and halogen interactions.

Structural Study of Model Rhodium(I) Carbonylation Catalysts Activated by Indole-2-/Indoline-2-Carboxylate Bidentate Ligands and Kinetics of Iodomethane Oxidative Addition

The rigid-backbone bidentate ligands Indoline-2-carboxylic acid (IndoliH) and Indole-2-carboxylic acid (IndolH) were evaluated for rhodium(I). IndoliH formed [Rh(Indoli)(CO)(PPh3)] (A2), while IndolH yielded the novel dinuclear [Rh1(Indol’)(CO)(PPh3)Rh2(CO)(PPh3)2] (B2) complex (Indol’ = Indol2−), which were characterized by SCXRD. In B2, the Rh1(I) fragment [Rh1(Indol’)(CO)(PPh3)] (bidentate N,O-Indol) exhibits a square-planar geometry, while Rh2(I) shows a ‘Vaska’-type trans-[O-Rh2(PPh3)2(CO)] configuration (bridging the carboxylate ‘oxo’ O atom of Indol2−). The oxidative addition of MeI to A2 and B2 via time-resolved FT-IR, NMR, and UV/Vis analyses indicated only Rh(III)-alkyl species (A3/B3) as products (no migratory insertion). Variable temperature kinetics confirmed an associative mechanism for A2 via an equilibrium-based pathway (ΔH≠ = (21 ± 1) kJ mol−1; ΔS≠ = (−209 ± 4) J K−1mol−1), with a smaller contribution from a reverse reductive elimination/solvent pathway. The dinuclear complex B2 showed the oxidative addition of MeI only at Rh1(I), which formed a Rh(III)-alkyl, but cleaved the bridged Rh2(I) site, yielding trans-[RhI(PPh3)2(I)(CO)] (5B) as a secondary product. A significantly smaller negative activation entropy [ΔH≠ = (73.0 ± 1.2) kJ mol−1; ΔS≠ = (−21 ± 4) J K−1mol−1] via a more complex/potential interchange mechanism (the contribution of ΔS≠ to the Gibbs free energy of activation, ΔG≠, only ±10%) was inferred, contrary to the entropy-driven oxidative addition of MeI to A2 (the contribution of ΔS≠ to ΔG≠ ± 75%).

Spectroscopic, electronic structure, molecular docking, and molecular dynamics simulation study of 7-Trifluoromethyl-1H-indole-2-carboxylic acid as an aromatase inhibitor

The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.

Ethyl 1H-indole-2-carboxyl-ate

Our work in the area of synthesis of tris indole compounds as a potential chelator led to the synthesis and crystallization of ethyl 1H-indole-2-carboxyl-ate, C11H11NO2, an indole that was synthesized by the thionyl chloride reaction of 1H-indole-2-carb-oxy-lic acid, followed by dissolution in ethanol. The mol-ecular packing exhibits a herringbone pattern with the zigzag running along the b-axis direction; the compound crystallizes as a hydrogen-bonded dimer resulting from O⋯H-N hydrogen bonds, between the indole N-H group and the keto oxygen atom, which build centrosymmetric R 2 2(10) ring motifs in the crystal.

Methyl 1-methyl-1H-indole-3-carboxylate

The title indole derivative, C11H11NO2, was synthesized from 1-methyl-1H-indole-3-carboxylic acid and methanol. The molecule is planar as it is situated on a mirror plane present in the space group Pbcm. In the crystal, molecules form three kinds of intermolecular C—H...O hydrogen bonds, resulting in a sheet structure in the ab plane. Parallel sheets interact by C—H...π stacking, stabilizing the crystal packing.

(R)-(-)-2-Pyrrolidinemethanol: A combined experimental and DFT vibrational analysis of monomers, dimers and hydrogen bonding

Experimental IR and solution phase spectra of (R)-(-)-2-Pyrrolidinemethanol showing evidence of hydrogen bonding have been interpreted by computing vibrational modes of monomers and dimers with the molecular species due to intra- and inter-molecular hydrogen bonding, at B3LYP/6-311+G(d,p) level density functional theoretical calculations. Computed vibrational frequencies of Boltzmann population-weighted dimers for stretching and bending of O-H and N-H modes associated with the inter-molecular N-H⋯O and O-H⋯O hydrogen bonding are in good agreement with the measured IR absorption, Raman and solution-phase IR values near 3289 cm(-1), 3450 cm(-1) and 1400-1300 cm(-1). Further, the H⋯O length is shorter in O-H⋯O than in N-H⋯O by ∼10% suggesting that O-H⋯O is a stronger bond. While the solution-phase IR spectral features suggest strong inter-molecular associations, it is short of demonstrating which type of bonding is dominant factor. We conclude that the measured IR, Raman and solution-phase IR spectral features indicate the presence of both types of hydrogen bonds.

Impact of structural differences in carcinopreventive agents indole-3-carbinol and 3,3'-diindolylmethane on biological activity. An X-ray, ¹H-¹⁴N NQDR, ¹³C CP/MAS NMR, and periodic hybrid DFT study

Three experimental techniques (1)H-(14)N NQDR, (13)C CP/MAS NMR and X-ray and Density Functional Theory (GGA/BLYP with PBC) and Hirshfeld surfaces were applied for the structure-activity oriented studies of two phyto-antioxidants and anticarcinogens: indole-3-carbinol, I3C, and 3,3'-diindolylmethane, DIM, (its bioactive metabolite). One set of (14)N NQR frequencies for DIM (2.310, 2.200 and 0.110 MHz at 295K) and I3C (2.315, 1.985 and 0.330 MHz at 160K) was recorded. The multiplicity of NQR lines recorded at RT revealed high symmetry (chemical and physical equivalence) of both methyl indazole rings of DIM. Carbonyl (13)C CSA tensor components were calculated from the (13)C CP/MAS solid state NMR spectrum of I3C recorded under fast and slow spinning. At room temperature the crystal structure of I3C is orthorhombic: space group Pca21, Z=4, a=5.78922(16), b=15.6434(7) and c=8.4405(2)Å. The I3C molecules are aggregated into ribbons stacked along [001]. The oxygen atomsare disorderedbetween the two sites of different occupancy factors. It implies that the crystal is built of about 70% trans and 30% gauche conformers, and apart from the weak OH⋯O hydrogen bonds (O⋯O=3.106Å) the formation of alternative O'H⋯O bonds (O'⋯O=2.785Å) is possible within the 1D ribbons. The adjacent ribbons are further stabilised by O'H⋯O bonds (O'⋯O=2.951Å). The analysis of spectra and intermolecular interactions pattern by experimental techniques was supported by solid (periodic) DFT calculations. The knowledge of the topology and competition of the interactions in crystalline state shed some light on the preferred conformations of CH2OH in I3C and steric hindrance of methyl indole rings in DIM. A comparison of the local environment in gas phase and solid permitted drawing some conclusions on the nature of the interactions required for effective processes of recognition and binding of a given anticarcinogen to the protein or nucleic acid.

Conformational stability and thermal pathways of relaxation in triclosan (antibacterial/excipient/contaminant) in solid-state: combined spectroscopic ((1)H NMR) and computational (periodic DFT) study

The mechanism of molecular dynamics in the antibacterial/antifungal agent, triclosan (5-chloro-2-(2',4'-dichlorophenoxy)-phenol), in solid state was studied by (1)H NMR spectroscopy and periodic density functional theory (DFT) calculations. Temperature dependencies of the proton spin-lattice relaxation time (T1) in the ranges 86-293 and 90-250 K (at 15 and 24.667 MHz, respectively) and the second moment (M2) of the (1)H NMR resonant line in the range 103-300 K were measured. Two minima in the temperature dependence of T1 revealed a classical Arrhenius governed activation processes. The low temperature shallow minimum T1(T) of 71 s at 115 K, 15 MHz, which shifts with frequency, was assigned to classical hindered jumps of hydroxyl group around OC axis and with respect to a 5-chloro-2-phenol ring. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the experimental points is 9.68 kJ/mol. The pointed high temperature minimum T1(T) of 59 s at 190 K, 15 MHz, which also shifts with frequency, was assigned to the small angle librations by Θlib= ± 9° between two positions of equilibrium differing in energy by 7.42 kJ/mol. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the experimental points is 31.1 kJ/mol. Both motions result in a negligible reduction in the (1)H NMR line second moment, thus the second moment delivers an irrelevant description of the molecular motions in triclosan.

Spectroscopic (FT-IR, FT-Raman, and UV-visible) and quantum chemical studies on molecular geometry, Frontier molecular orbitals, NBO, NLO and thermodynamic properties of 1-acetylindole

Quantum chemical calculations of ground state energy, geometrical structure and vibrational wavenumbers of 1-acetylindole were carried out using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational wavenumbers were calculated and a good correlation between experimental and scaled calculated wavenumbers has been accomplished. Electric dipole moment, polarizability and first static hyperpolarizability values of 1-acetylindole have been calculated at the same level of theory and basis set. The results show that the 1-acetylindole molecule possesses nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-Visible spectrum of the molecule was recorded in the region 200-500nm and the electronic properties like HOMO and LUMO energies and composition were obtained using TD-DFT method. The calculated energies and oscillator strengths are in good correspondence with the experimental data. The thermodynamic properties of the compound under investigation were calculated at different temperatures.

Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization

Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state ¹³C NMR), we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation.

Photophysics of indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C): heavy atom effect

In this study the effect of carboxylic group substitution in the 2 and 5 position of indole ring on the photophysics of the parent indole chromophore has been studied. The photophysical parameters crucial in triplet state decay mechanism of aqueous indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C) have been determined applying our previously proposed methodology based on the heavy atom effect and fluorescence and phosphorescence decay kinetics [Kowalska-Baron et al., 2012]. The determined time-resolved phosphorescence spectra of I2C and I5C are red-shifted as compared to that of the parent indole. This red-shift was especially evident in the case of I2C and may indicate the possibility of hydrogen bonded complex formation incorporating carbonyl CO, the NH group of I2C and, possibly, surrounding water molecules. The possibility of the excited state charge transfer process and the subsequent electronic charge redistribution in such a hydrogen bonded complex may also be postulated. The resulting stabilization of the I2C triplet state is manifested by its relatively long phosphorescence lifetime in aqueous solution (912 μs). The relatively short phosphorescence lifetime of I5C (56 μs) may be the consequence of more effective ground-state quenching of I5 C triplet state. This hypothesis may be strengthened by the significantly larger value of the determined rate constant of I5C triplet state quenching by its ground-state (4.4 × 10(8)M(-1)s(-1)) as compared to that for indole (6.8 × 10(7)M(-1)s(-1)) and I2C (2.3 × 10(7)M(-1)s(-1)). The determined bimolecular rate constant for triplet state quenching by iodide [Formula: see text] is equal to 1 × 10(4)M(-1)s(-1); 6 × 10(3)M(-1)s(-1) and 2.7 × 10(4)M(-1)s(-1) for indole, I2 C and I5 C, respectively. In order to obtain a better insight into iodide quenching of I2C and I5C triplet states in aqueous solution, the temperature dependence of the bimolecular rate constants for iodide quenching of the triplet states has been expressed in Arrhenius form. The linearity of the obtained Arrhenius plots clearly indicated the existence of one temperature-dependent non-radiative process for the de-excitation of I2C and I5C triplet state in the presence of iodide. This process may be attributed to the solute-quenching by iodide and, most probably, proceeds via reversibly formed exciplex. The activation energies obtained from linear Arrhenius plots (1.89 kcal/mol for I5 C; 2.55 kcal/mol for I2 C) are smaller as compared to that for diffusion controlled reactions in aqueous solution (about 4 kcal/mol), which may indicate the great importance of the electrostatic interactions between solute and iodide ions in lowering the energy barrier needed for the formation of the triplet-quencher complex. Based on the theoretical predictions (at the DFT(CAM-B3LYP)/6-31+G(d,p) level of theory) and careful analysis of the obtained FTIR spectra it may be concluded that in the solid state I2 C and I5 C molecules form associates by intermolecular NH · · · OC and OH · · · OC hydrogen bonding interactions, whereas the existence of intramolecular NH · · · OC interactions in the solid state of I2C and I5C is highly unlikely.

Formyl- and acetylindols: vibrational spectroscopy of an expectably pharmacologically active compound family

In the present paper, indole and its seven derivatives were compared, namely 3-formylindole, 1-methyl-3-formylindole, 1-ethyl-3-formylindole, 3-acetylindole, 1-methyl-3-acetylindole, 1-ethyl-3-acetylindole and 1,3-diacetylindole. The substitution of indole in position 3 with aldehydes and with alkyl groups cause only minor changes in the molecular geometry, however, substantially larger alterations are found in the charge distribution and in the vibrational force constants. The appearance of the aldehyde groups increased the degree of association as it was observable on the shape of infrared NH stretching band and its shifts. The alkyl substitution shifts the aldehyde carbonyl stretch band frequencies to somewhat higher values. The effect of the second acetyl group in position 1 is not comparable with those of the 1-alkyl groups. The latter effect is observable in the molecular geometry, however, it is more pronounced in the changes of the net charge distribution, the vibrational force constants and the infrared spectra.

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.

A short hydrogen bond investigation by polarized Raman spectra of Co2+ and Zn2+ salts of pyromellitic acid

Cobalt and zinc salts of 1,2,4,5-benzenetetracarboxylic acid (pyromellitic acid), [C(6)H(2)(COO)(4)H(4)], have been synthesized and investigate by polarized Raman spectroscopy. These compounds present short intramolecular hydrogen bonds (SHB) between adjacent carboxyl groups. Raman spectra indicate the presence of this interaction in both salts. Three specific vibrational of SHB modes have been investigated: O-H-O symmetric [nu(sym)(OHO)] and asymmetric [nu(asym)(OHO)] stretching modes and O-H stretching mode [nu(O-H)], which they were observed around 300, 850 and 2500 cm(-1), respectively. In crystallographic point of view, the cobalt salt presents a symmetric SHB while the zinc salt presents an asymmetric SHB. In cobalt salt all three vibrational modes of O-H-O groups in polarized Raman spectra occur in A(g) orientation although in zinc salts two of them are observed in A(g) orientation and one in B(g). Spectra analysis indicate that nu(sym)(OHO) mode is observed as A(g) to cobalt salt and B(g) to zinc salt. This mode occurs in a crowded spectral region and its identification was made by deconvolution techniques. Comparing spectra of the two salts, it is observed a small difference in relative intensity and wavenumber shift of nu(sym)(OHO) (deviance of 43 cm(-1)) and nu(OH) (deviance of 21 cm(-1)) modes due probably to differences in O...O distance between salts and in orientation of pyromellitate anion in unit cell. The nu(asym)(OHO) mode does not present significant wavenumber shift due difference in SHB. The nu(OH) band presents a great potential for hydrogen bond studies due to the fact that in its vibrational region (around 2500 cm(-1)) it is not observed other vibrational modes of these compounds.