Vibrational spectra of indole and assignments on the basis of ab initio force fields

Abstract

New high-resolution Fourier transform spectra for indole vapour and its Ndeuterated analogue and Fourier transform Raman spectra for solid indole are reported. Observed frequencies for normal modes are compared with those calculated from normal coordinate analyses carried out on the basi s of nb initio force fields. The latter were calculated using the 3-216 basis set and either the theoretical optimized geometry or that given by microwave spectroscopy. The force field obtained with the optimized geometry was shown to provide an excellent approach for calculating not only mode frequencies but also IR and Raman intensities. Except for the NH and CH stretching modes, only one scale factor for all the in-plane modes and another for all the out-of-plane modes are needed in order to bring closer the calculated and observed frequencies for indole and for eleven deuterated analogues. Assignments for each normal mode were obtained from potential energy distributions among internal coordinates. Those for normal modes corresponding, in particular, to bands observed also for the tryptophan residue are discussed in detail.

Normal Vibrational Mode Analysis and Assignment of Benzimidazole by ab Initio and Density Functional Calculations and Polarized Infrared and Raman Spectroscopy

“…On the other hand, computational results on fundamentals using DFT methods showed that these methods reproduce experimental vibrational frequencies with higher accuracy than do the HF and MP2 methods. [37][38][39][40][41][42][43][44] For example, results on predicting the fundamentals of 20 small molecules (e.g., benzene, ether, etc., whose vibrational spectra are exactly assigned) by Rauhut and Pulay 42 using BLYP and B3LYP functional methods derived uniform scaling factors of 0.995 and 0.963, respectively.…”

Modeling the heme vibrational spectrum: Normal‐mode analysis of nickel (II) etioporphyrin‐I from resonance raman, ft‐raman, and infrared spectra of multiple isotopomers

“…In ab initio force fields of molecules such as na~hthalene,~' indole, 53 and the nucleic acid bases, 14,54 stretch-stretch interaction terms extend to all bonds along the Telectron path. Examination of these ab initio force fields reveals that the algebraic signs of stretchstretch interaction terms alternate for conjugated bonds that are separated by even (+) and odd (-) numbers of intervening bonds.…”

Modeling vibrational spectra of indole in water

“…Calculation of the frequencies and intensites of the IR absorption spectrum of isolated indole (Table 3) showed that the strong experimental band at 387 cm -1 , which was interpreted earlier as in-plane vibration 14 [8,[10][11][12], was according to our calculation out-of-plane vibration 3 for deviation of the NH bond from the plane of the pyrrole ring. Vibration 14, the shape of which corresponded to a change of CCC bond angles, was weak although it also appeared …”

“…Therefore, changes of an identical nature and small magnitude in the frequencies of normal vibrations of indole are expected upon going from the isolated state to aqueous solution and the complex with water with the exception of out-of-plane vibrations ρ(NH), the frequency shifts of which can be very significant. Table 2 presents experimental frequencies of normal vibrations for indole in aqueous solution [7], the solid state [8,9], and the gas phase [8,10] together with results from ab initio [8,12] and semi-empirical [11] calculations in addition to results of our calculations for the aqueous solution (SCRF model) and isolated state. We used scaling factors 0.975 for vibrations 20-35 and 0.962 for vibrations 36-42 in order to account for anharmonism of the vibrations, the shape of which contains changes of CCH and CNH bond angles and CH and NH bond lengths.…”

“…Vibrational spectra of indole in various phase states (gas, liquid, solid) were studied earlier both experimentally and theoretically [7][8][9][10][11][12]. However, vibrational spectra of indole in the ranges 400-900 and 1200-1350 cm -1 have not been unambiguously interpreted for the isolated or condensed states.…”