A gradient-corrected density functional study of indole self-association through N–H hydrogen bonding (original) (raw)
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Journal of Molecular Structure, 2000
Fourier transform infrared spectra of indole in carbon tetrachloride solutions were recorded. The spectroscopic data indicate that even at relatively low concentrations, the solute forms molecularly associated pairs through N-H·· ·p hydrogen bonding. Both NIR data and AM1 calculations show that, in comparison with the monomeric n(N-H) mode, the anharmonicity of the n(N-H···p) mode decreases, and that of the dimeric n(N-H) mode slightly increases. The anharmonicity constants for these modes are calculated on the basis of the NIR data, and the changes of the n(N-H) potential upon N-H·· ·p hydrogen bonding are quantitatively studied. The orientational dynamics of monomeric and associated indole species are studied within the framework of the time correlation function formalism. The period of essentially free rotation in the condensed phase reduces from 2.3 ps for the monomeric indole to 0.4 ps for the proton-donor molecule within the dimer. ᭧
Research Journal of Pharmaceutical, Biological and Chemical Sciences
Molecular geometry, vibrational frequencies, energy gaps, net charges, dipole moments and heats of indole formation at the ground state have been calculated by using the Molecular Mechanics, PM3, ab initio/HF and DFT/B3LYP methods. The optimized geometrical parameters are in good agreement with experimental values. Comparison of the obtained fundamental vibrational frequencies of Indole result by DFT/B3LYP (6-311G++(d,p)) method, are in a close agreement with the experimental data. Ab initio/HF with 6-31G basis set was used to investigate the effects of a variety of substituents (methyl, cyanide and dimethylamino) on the electronic properties of Indole derivatives.
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.
Journal of Molecular Modeling, 2011
Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A exploratory study of the conformational space of dimeric species was performed. Our analysis showed that dimeric forms predicted theoretically contribute distinctively to the assignments of experimental results. These structures are defined by the orientation of the acetyl moieties with respect to the plane of indole ring. The dimers are formed by two symmetrical IAA monomers (one of them with the acetyl moiety upward oriented, Re-face, and the other isomer having the acetyl moiety downward oriented, Si-face) in tail-to-tail way. The X-ray geometry and FTIR vibrational frequencies were compared with the results of DFT calculations. A conformational equilibrium involving the non-equivalent IAA dimers: CCT-CCT,
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