Dispersion-Corrected Density Functional Theory Study of the Noncovalent Complexes Formed with Imidazo[1,2-a]pyrazines Adsorbed onto Silver Clusters

Imidazo[1,2-a]pyrazines are cyclic amidine-type compounds composed of α-amino acid residues. A full structural identification of these molecules constitutes an analytical challenge, especially when imidazo[1,2-a]pyrazines are obtained from physical processes (e.g., sublimation and pyrolysis of amino acids). A valuable source of molecular information can be obtained from absorption spectroscopies and related techniques encompassing the use of metallic substrates. The aim of this study is to provide new knowledge and insights into the noncovalent intermolecular interactions between imidazo[1,2-a]pyrazines and two Ag _n (n = 4 and 20) clusters using density functional theory (DFT) methods. Semiempirical DFT dispersion (DFT-D) corrections were addressed using Grimme's dispersion (GD2) and Austin-Petersson-Frisch (APF) functionals in conjunction with the 6-31+G(d,p) + LANL2DZ mixed basis set. These DFT-D methods describe strong interactions; besides, in all cases, the APF dispersion (APF-D) energies of interaction appear to be consistently overestimated. In comparison with B3LYP calculations, the mean values for the difference in the energies of interaction calculated are 2.25 (GD2) and 6.24 (APF-D) kcal mol^-1 for Ag₄-molecules, and 2.30 (GD2) and 8.53 (APF-D) kcal mol^-1 for Ag₂₀-molecules. The effect of applying GD2 and APF-D corrections to the noncovalent complexes is nuanced in the intermolecular distances calculated, mainly in the Ag···N(amidine) bonding, which appears to play the most important role for the adsorptive process. Selective enhancement and considerable red shifts for Raman vibrations suggest strong interactions, whereas a charge redistribution involving the metallic substrate and the absorbate leads to a significant rearrangement of frontier molecular orbitals mainly in the Ag₂₀-molecule complexes. Finally, time-dependent DFT calculations were carried out to access the orbital contributions to each of the transitions observed in the absorption spectrum. The corresponding UV-vis spectra involve transitions in the visible region at around 400 and 550 nm for the Ag₄-molecule and the Ag₂₀-molecule complexes, respectively.

Imidazo[1,2-a]pyrazine-3,6-diones derived from alpha-amino acids: a theoretical mechanistic study of their formation via pyrolysis and silica-catalyzed process

Imidazo[1,2-a]pyrazine-3,6-diones are unusual compounds composed of three alpha-amino acid fragments. These bicyclic amidines (BCAs) form under high temperatures or with the use of strong dehydrating reagents. We gave insight into the mechanisms of BCA formation via gas-phase pyrolytic and silica-catalyzed reactions of glycine (Gly) and alpha-aminoisobutyric acid (AIB) with related diketopiperazines (DKPs), using quantum chemical calculations. The entire process requires four steps: (1) O-acylation of DKP with free or silica-bonded amino acid, (2) acyl transfer from the oxygen to the nitrogen atom, (3) intramolecular condensation of the N-acyl DKP into a cyclol, and (4) elimination of water. To study step (1) at silica surface (modeled by H7Si8O12-OH cluster), we employed two-level ONIOM calculations (AM1:UFF, B3LYP/3-21G:UFF and B3LYP/6-31G(d):UFF); all gas-phase reactions were studied at the AM1, B3LYP/3-21G and B3LYP/6-31G(d) levels. The catalytic effect of silica was observed for both Gly and AIB: the activation energy in the O-acylation at the surface was lower by more than 9 kcal mol(-1) as compared to the gas-phase process. Contrary to the exothermic O-acylation, the gas-phase transfer reaction (step 2) was exothermic in both cases, but more favorable for Gly. The cyclocondensation of N-acylated DKPs into BCAs (steps 3 and 4) is endothermic for Gly and exothermic for AIB.

Coelenterazine (marine bioluminescent substrate): a source of inspiration for the discovery of novel antioxidants

Coelenterazine and derivatives were initially considered in the scientific community for their (bio)luminescent properties. Now, another interest of such hetero-bicycles has been pointed out by the discovery of remarkable antioxidative properties, and an unique mode of action as a "cascade": the mother-compound (imidazolopyrazinone) is transformed by ROS into a daughter-compound (2-amino-pyrazine) also endowed with antioxidative properties. This review illustrates the therapeutic potential of synthetic imidazolopyrazinones (coelenterazine analogues): chemical reactivity assays with singulet oxygen, radical anion superoxide, peroxynitrite, and radicals formed during lipid and LDL peroxidation, cellular tests of protection against oxidative stress using keratinocyte, hepatocyte, neuronal and erythrocyte cells, and finally in vivo evaluation in a hamster model of ischemia-reperfusion, are fully described.

Theoretical prediction of gas-phase infrared spectra of imidazo[1,2-a]pyrazinediones and imidazo[1,2-a]imidazo[1,2-d]pyrazinediones derived from glycine

Imidazo[1,2-a]pyrazine-3,6-diones and imidazo[1,2-a]imidazo[1,2-d]pyrazine-3,8-diones can be produced by pyrolysis of simple amino acids. While such bicyclic and tricyclic amidines were detected and characterized by IR spectroscopy for some alpha-substituted amino acids, the parent systems composed of glycine fragments are unknown up to now. IR spectra for five amidines derived from glycine were calculated by using different semi-empirical (PM3, AM1, MNDO and MINDO/3), HF, and hybrid DFT (B3LYP, B3P86 and B3PW91) methods in conjunction with 6-31G(d) basis set (for HF and DFT). Vibration frequencies in the experimental IR spectra were predicted based upon the B3LYP data, by correcting the calculated wavenumbers by a scaling factor of 0.959. The behavior of most characteristic bands (nu(CX), nu(NH), etc.) and their shifts with respect to such bands in the spectra of alanine and alpha-aminoisobutyric acid derivatives studied before, are discussed. Performance of the semi-empirical methods was tested, bearing in mind possible future needs for IR spectra predictions for larger molecular systems of similar chemical nature; the use of MINDO/3 and MNDO is recommended. A basis set effect on the B3LYP fundamental vibration frequencies for hexahydroimidazo[1,2-a]pyrazine-3,6-dione was studied by varying Pople basis sets from minimal STO-3G to 6-311++G(d, p). No significant improvements were found beyond the 6-31G(d) basis set, which thus can be recommended to predict IR spectra for the amidines and similar molecules.

Calculated gas-phase infrared spectra of imidazo[1,2-a]pyrazinediones derived from alanine

IR spectra of bicyclic and tricyclic amidine derivatives of alanine (2,5,8-trimethylhexahydroimidazo[1,2-a]pyrazine-3,6-dione, 2,5,8-trimethyltetrahydroimidazo[1,2-a]pyrazine-3,6-dione and 2,5,7,10-tetramethylhexahydroimidazo[1,2-a]imidazo[1,2-d]pyrazine-3,8-dione) were computed by the HF, B3LYP, B3P86 and B3PW91 methods in conjunction with the 6-31G(d) basis set. The IR spectra calculated are in a good agreement with the observed FTIR spectra. The correlation between the calculated and experimental vibration frequencies is characterized by the coefficients of 0.9997 for all three DFT methods; for HF it is about 0.9992. The calculated absolute band intensities satisfactory match the observed relative intensities. Optimal uniform scaling factors calculated for this series of compounds are 0.8967, 0.9598, 0.9544 and 0.9555 for HF, B3LYP, B3P86 and B3PW91, respectively. Taking into account small variations of the scaling factors for the derivatives of different amino acids, for future IR spectral predictions for unknown compounds of this class, one can recommend scaling factors of 0.897, 0.959, 0.954 and 0.955 for HF, B3LYP, B3P86 and B3PW91, respectively.

Calculated gas-phase infrared spectra of 2,2,5,5,8,8-hexamethylhexahydroimidazo [1,2-a]-pyrazine-3,6-dione: relative performance of Hartree-Fock and hybrid density functional theory methods

Geometric parameters and IR spectra of 2,2,5,5,8,8-hexamethylhexahydroimidazo[1,2-a]pyrazine-3,6-dione were computed by the HF, B3LYP, B3P86 and B3PW91 methods with the 6-31G(d) basis set. All the computation methods produce a boat conformation of the six-membered ring with the orientation opposite to the one experimentally observed, that is obviously due to incapability of such calculations to take into account mutual influence of the molecules in a crystal package. Quality of predicting the interatomic distances observed experimentally decreases in the series HF, B3LYP, B3PW91 and B3P86; for bond angles, in the series B3LYP, P3PW91, B3P86 and HF. At the same time, the IR spectra computed are in a good agreement with the observed FTIR spectrum. The correlation between the calculated and experimental vibration frequencies is characterized by the coefficients higher than 0.9999 for all three DFT methods; for HF it is slightly lower than 0.9995. The calculated absolute band intensities satisfactory match the observed relative intensities as well. Optimal uniform scaling factors calculated are 0.8973, 0.9593, 0.9540 and 0.9552 for HF, B3LYP, B3P86 and B3PW91, respectively.

Synthesis of substituted imidazopyrazines as ligands for the human somatostatin receptor subtype 5

A new preparation of trisubstituted imidazopyrazines and dihydroimidazopyrazines via parallel synthesis using aminoacids and bromoketones resulted in the discovery of non-peptidic sst5 selective agonists.

New imidazo(1,2-a)pyrazine derivatives with bronchodilatory and cyclic nucleotide phosphodiesterase inhibitory activities

New imidazo[1,2-a]pyrazine derivatives have been synthesized either by direct cyclization from pyrazines or by electrophilic substitutions. The presence of electron donating groups on position 8 greatly enhances the reactivity of the heterocycle towards such reactions on position 3 of the heterocycle. The activities of these derivatives in trachealis muscle relaxation and in inhibiting cyclic nucleotide phosphodiesterase (PDE) isoenzyme types III and IV have been assessed. All compounds demonstrated significantly higher relaxant potency than theophylline. All the derivatives were moderately potent in inhibiting the type IV isoenzyme of PDE but only those with a cyano group on position 2 were potent in inhibiting the type III isoenzyme.