A gradient-corrected density functional study of indole self-association through N–H hydrogen bonding (original) (raw)
Chemical Physics, 2004
Density functional theory (DFT) has gained much popularity over the last decades, due to its computational efficiency as compared to other correlated electronic structure methods. It is generally found that the accuracy of DFT rivals that of MP2 for conventional hydrogenbonded systems . However, probably the most significant deficiency of current density functionals is their inability to correctly account for the dispersion interaction . The reason for this is that both local density approximation (LDA) and generalized gradient approximation (GGA) functionals, and consequently also hybrid functionals (in which a fraction of the exact Hartree-Fock exchange energy is mixed into the exchange functional) are essentially local and therefore do not directly account for the electron density on a second, remote atom (as explained in more detail in ). This implies that state-of-the-art DFT is not suitable for systems containing dispersion-dominated interactions. Thus, current DFT functionals cannot be employed to describe the interaction of the rare-gas dimers: DFT yields He 2 interaction energies ranging from 1 to 120 K, depending on the particular density functional employed, whereas the exact result is 11 K [4]. Other dispersion-rich interactions include base-stacking interactions, water molecules interacting with aromatic rings; and indeed, all interactions involving p electron clouds.
The effect of small substituents on the properties of indole. An ab initio 6-31G* study
Journal of Molecular Structure: THEOCHEM, 1998
The effect of small substituents (the isoelectronic series F, OH, NH 2 , CH 3 ) in position 5 and 6 of indole on its electronic distribution has been examined using molecular electrostatic potential (MEP) maps and NMR properties. To clarify the nature of the effects observed the NO 2 , COO − and O − substituents have also been considered. The geometries of each conformer have been optimised at the HF/6-31G* level. The anti conformers are slightly more stable (by about 0.5 kcal/mol) than the syn conformers for 5,OH and 5 or 6,CH 3 -indole, while for 6,OH-indole the two forms are almost equal in energy. The 6-31G* Mulliken charges are stronger than those produced by the STO-3G minimal basis set computed on the 6-31G* geometry, as expected. The Merz-Kollman (MK) charges, derived from the best-fit to both the ab-initio 6-31G* and STO-3G MEP around the molecule, differ one from the other slightly less than the corresponding net Mulliken populations and re-equilibrate the strong charge displacement between the ring N and C 3 , observed in the 6-31G* Mulliken charges. By comparing the MEP produced, the Gasteiger-Hückel charges are of about the same quality as the Pullman charges, even though they are somewhat worse than the MK charges, whose MEP is hardly distinguishable from the ab initio one; they are, however, decidedly better than the Gasteiger-Marsili charges, as expected, because the latter are devised for non conjugated p systems. The methyl group has no effect on the MEP outside of the condensed ring plane. The F and OH lone pairs produce a noticeable negative potential, enhancing the polarity of the N proton. The p density is increased by the presence of the NH 2 group which, however, reduces the positive potential at the proton linked to the ring N. The chemical shift at the N proton turns out to be correlated to its MK charge. The bond length change with respect to indole is very limited (0.01 Å at most, and on average below 0.005 Å ). The pyrrole ring has a more localised charge distribution than the benzene ring. ᭧
Physical Chemistry Chemical Physics, 2010
High-resolution electronic spectra of indole (C 8 H 7 N) and their detailed analysis are reported. Thirteen low-lying vibronic bands-from the electronic origin transition at 35 231.4 cm À1 up to 1000 cm À1 above-are recorded with rotational resolution. Besides inertial parameters and inertial defects these spectra yield detailed information, for each individual band, on the transition-dipole-moment orientations in the molecular inertial frame as well as on the reorientation of that inertial frame upon electronic excitation. The natural lifetimes of the individual vibronic states have also been determined. Strongly varying orientations of the transition-dipole-moments, unexpected positive inertial defects, and decreasing lifetimes, which are only partly related to increased excitation energy, are observed. These results are clear indications of the interaction of the two lowest electronically excited singlet states ( 1 L b and 1 L a ). Our experimental findings are strongly supported by, and in excellent agreement with, the theoretical description of the interaction of the two electronic states described in the preceding paper. These results provide clear evidence for strong vibronic coupling of the two electronic states 1 L b and 1 L a and for the energetic location of the 1 L a -state more than 1000 cm À1 above the 1 L b vibrationless state. w Electronic supplementary information (ESI) available: The rovibronic spectra of the vibronic bands at 480, 539, 718, 720, 737, 909, 910 and 968 cm À1 above the electronic origin at 35 231.4 cm À1 . See
Physical Chemistry Chemical Physics, 2010
The properties of the three lowest singlet electronic states (ground, 1 L b , and 1 L a states) of indole (C 8 H 7 N) have been calculated with second-order approximate coupled-cluster theory (CC2) within the resolution-of-the-identity approximation. Refined electronic energies at the CC2 optimized structures and transition dipole moments were calculated using a density functional theory multi-reference configuration-interaction (DFT/MRCI) approach. Structures, energies, and dipole moments are reported for all three states and compared to experimental values. From the optimized structures and calculated transition dipole moments, we predict that pure 1 L b bands will have positive signs for both the axis reorientation angle y T and the angle y of the transition dipole moment with respect to the inertial a axis. For 1 L a bands the signs of both angles will be reversed. Vibronically coupled bands can exhibit opposite signs for y and y T . The absorption and emission spectra of indole are calculated based on the Franck-Condon Herzberg-Teller approximation using numerical transition dipole moment derivatives at the DFT/MRCI level of theory. Implications for the experimentally observed vibronic spectra are discussed. Predictions are made for rotationally resolved spectra of various rovibronic bands. A conical intersection, connecting the 1 L b and 1 L a states, which can be accessed to varying extents via different Herzberg-Teller active modes is found approximately 2000 cm À1 above the 1 L b minimum. w Electronic supplementary information (ESI) available: The Cartesian coordinates (in Å ) for all optimized structures of indole at the CC2 level with the cc-pVTZ basis set, the Molden files, containing the vibrational spectrum for all optimized structures and the Gaussian log file containing the optimization of the structure of the conical intersection at the (10,9)-CASSCF level of theory with the 6-311G(d,p) basis set. See y It should be pointed out that for molecules without at least C 2v symmetry the notations '' 1 L a '' and '' 1 L b '' are not based on symmetry arguments and in fact in the C s case, as for indole, they belong to states with the same symmetry. These labels are merely a historic and convenient naming convention 11 to specify the lowest excited electronic states.
Substituent Effects and Vibrational Coupling in Indole-2,3-diones: An IR , NMR and Theoretical Study
Heterocyclic Communications, 2001
The IR C=0 stretching vibrational wave numbers, 'H, IJ C and l5 N NMR chemical shifts are reported for 5-and 6-substituted indole-2,3-diones and correlated with Hammett substituent constants and semiempirical AMI data. As an alternative to the previous assignment of the C=0 stretching vibrational wave numbers the two v(C=0) absorption bands can also be interpreted as the symmetric and asymmetric stretching vibrational modes in the mechanically coupled cyclic α-dicarbonyl system. The use of 2D NMR techniques enabled to make correct assignments of the l3 C NMR chemical shifts, which are substantially different from those reported earlier.
Electronic structure and conformational properties of 1H-indole-3-acetic acid
Journal of Molecular Modeling, 2011
The conformational space of 1H-Indole-3-Acetic Acid (IAA) was scanned using molecular dynamics at semiempirical level, and complemented with functional density calculations at B3LYP/6-31G** level, 14 conformers of lowest energy were obtained. Electronic distributions were analyzed at a higher calculation level, thus improving the basis set (B3LYP/6-311++G**). A topological study based on Bader's theory (AIM: atoms in molecules) and natural bond orbital (NBO) framework performed with the aim to analyze the stability and reactivity of the conformers allowed the understanding of electronic aspects relevant in the study of the antioxidant properties of IAA. Intramolecular hydrogen bonds were found and were characterized as blue-shifting hydrogen bonding interactions. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and analyzed in the light of AIM and NBO results, thus showing subtle but essential features related not only to reactivity but also with intramolecular weak interactions, charge delocalization and structure stabilization. Keywords Atoms in molecules (AIM theory). Density functional theory. 1H-indole-3-acetic acid (IAA). Maps of electrostatic potential. Natural bond orbital analysis. Topological properties Electronic supplementary material The online version of this article
Vibronic analysis of indole and 1H-indole-d6
The Journal of Physical Chemistry, 1993
The excitation spectra of indole and indole-2,3,4,5,6,7-d6 have been obtained with jet-cooled one-color resonant two-photon ionization (1 C R2PI) time-of-flight mass spectrometry (TOFMS). The deuterated indole spectra have been vibronically analyzed in the region 0; to 0; + 904 cm-I using the single vibronic level fluorescence (SVLF) results of Bickel et al.5 as a guide for the deuterated species and an ab initio ground-state vibrational calculation of both species. This calculation was obtained by using Gaussian 90, from which the excited-state frequencies of the deuterated species have been estimated from the known excited-state normal protonated values. Comparison of both excited-state vibronic spectra has shown an essentially 1:l porrespondence between all of the bands, suggesting that there is no significant band in the indole spectrum in this interval which can uniquely be assigned as belonging to a system other than the l L b-'A' transition. Vibronic Analysis of Indole
Open Chemistry, 2017
(5-Methoxy-1H-indol-1-yl)(5-methoxy-1H-indol-2-yl)methanone (MIMIM) is a bis-indolic derivative that can be used as a precursor to a variety of melatonin receptor ligands. In this work, the energetic and spectroscopic profiles of MIMIM were studied by a combined DFT and experimental approach. The IR, Raman, UV-Vis, 1 H NMR and 13 C NMR spectra were calculated by PBEPBE and B3LYP methods, and compared with experimental ones. Results showed good agreement between theoretical and experimental values. Mulliken population and natural bond orbital analysis were also performed by time-dependent DFT approach to evaluate the electronic properties of the title molecule.
Journal of Molecular Structure, 2016
The present communication deals with the eco-friendly synthesis, spectral properties and X-ray crystal structure of an indole derivative-Ethyl 2'-amino-3'-cyano-6'-methyl-5-nitro-2-oxospiro [indoline-3,4'-pyran]-5'-carboxylate. The title compound was synthesized in 87% yield. The crystal structure of the molecule is stabilized by intermolecular NeH … N, NeH … O and CeH … p interactions. The molecule is organized in the crystal lattice forming sheet like structure. To interpret the experimental data, ab initio computations of the vibrational frequencies were carried out using the Gaussian 09 program followed by the full optimizations done using Density Functional Theory (DFT) at B3LYP/6-31+G(d,p) level. The combined use of experiments and computations allowed a firm assignment of the majority of observed bands for the compound. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap were presented. The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs) and density of states (DOS). From the optimized geometry of the molecule, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title compound have been calculated in the ground state theoretically. The theoretical results showed good agreement with the experimental values. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compound.