Matrix-Isolation FT−IR Studies and Theoretical Calculations of Hydrogen-Bonded Complexes of Molecules Modeling Adenine Tautomers. 1. H-Bonding of Benzimidazoles with H₂O in Ar Matrices

Abstract

This work opens a series of studies on the water complexes of adenines. We use a similar approach as used in our earlier studies of cytosine−water complexes (i.e., first we investigate the IR spectral manifestations of hydrogen−bonding at selected interaction sites of the stable amino N9H tautomeric form of adenine by studying simpler model molecules which have only a single or a very few selected hydrogen-bond interaction sites typical for adenine). The present study concerns the first two of such model molecules, benzimidazole and 1-CH3−benzimidazole. IR vibrational spectra of matrix-isolated benzimidazole, 1-CH3−benzimidazole, and their complexes with water are analyzed and assigned by comparing the experimental spectra with the IR frequencies and intensities computed with the use of ab initio and density functional theory (DFT) methods. When the DFT/B3LYP/6-31++G** monomer frequencies are scaled with three different scaling factors, the mean differences between the experimental and calculated frequencies are only 10 and 8 cm-1 for benzimidazole and 1-CH3−benzimidazole, respectively. The calculated, MP2/6-31++G**//RHF/6-31++G** (MP2 denotes the second-order Møller−Plesset Perturbation Theory, RHF denotes the restricted Hartree-Fock method, and notation MP2//RHF denotes that the molecular geometries were optimized at the RHF level and then used to calculate total energies using the MP2 method), H-bond interaction energies, with the basis set superposition error accounted for, are −22.6, −21.2, and −22.0 kJ/mol for the benzimidazole N1−H···OH2 and N3···H−OH complexes and the 1-CH3−benzimidazole N3···H−OH complex, respectively. The DFT/B3LYP/6-31++G** method yields similar H-bond interaction energies. The frequency shifts of the vibrational modes directly involved in the H-bond interactions are better predicted by the DFT method than by the RHF method. For other vibrational modes not directly involved in the H-bonds, the two methods provide a similar level of accuracy in predicting the shifts of the fundamental modes caused by H-bonding interactions. In this work we also establish correlations between experimental and theoretical characteristics of the N−H···OH2 H-bonding in water complexes of benzimidazole and 1-CH3−benzimidazole, and these correlations will be used in future elucidation of FT−IR spectra of water complexes of adenine.

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

“…17 These reported IR spectra have also comparable band features to IR spectra of BZI in the gaslike state (spectrum E in both Figures). 25 Polarized IR and Raman spectra of polycrystalline BZI and polarized Raman spectra of a large single crystal of BZI were reported in our earlier study. 17 The high-resolution polarized Raman spectra from a single crystal of BZI has been used to identify some of the poorly resolved or weakly represented fundamentals from the Raman spectrum of polycrystalline BZI in the 100-1700 cm -1 range ( Figure 1S).…”

Adenine−Hydrogen Peroxide System: DFT and MP2 Investigation

“…This energy range is easily released from the packing forces, in addition to the Complexes (1, 3, and 5) larger dipolar moments and the possibility of other additional hydrogen bonds from the neighboring complexes, yielding structure 1 as the experimental one. This had physiological relevance in DNA damage, because in nucleic acids the N 1 , N 9 , and H 7 sites are involved in the N-glycosidic linkage or Watson-Crick base pair, leaving only the N 7 and H 6 sites accessible for additional linkages. The study of the binding energy in the intermolecular complexes was affected by the so-called BSSE.…”

Vibrational spectra, X‐ray and molecular structure of 1H‐ and 3H‐imidazo[4,5‐b]pyridine and their methyl derivatives: DFT quantum chemical calculations

“…They show pharmaceutical activity, 1 -7 such as lowering of blood sugar level, inhibition of phosphodiesterase-5, 8 as well as casein kinase-2 and -5. 9 They exhibit also fungicidal, 10 anti-hypertensive, 11 anti-diabetic 12 and sedative 13 activities. Spectroscopic properties of BI 14 -16 and its derivatives 17 -19 have been studied previously.…”