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The results of the first (with the use of both experimental and theoretical methods) on pyrazine-2-amidoxime ( PAOX) were shown and discussed. FT-IR spectra were recorded in different concentrations of the PAOX in apolar solvent to check the possibility of the inter- or hydrogen-bond formation. All possible tautomers-rotamers of PAOX were then theoretically considered at the DFT(B3LYP)/6-311+G** level in vacuo. For selected isomers, calculations were also performed at higher levels of theory {B3LYP/6-311+G(3df,2p) and G3B3}. Based on the results of DFT calculations, the most stable isomers were found, and their total free energies and infrared spectra were calculated. The energy variation plots for the N8C7N9O10 and N1C2C7N9 dihedral angles were also computed to find two energy barriers, one for E/ Z around the C7N9 double bond and the other one for rotation of the pyrazinyl ring around the C2C7 single bond. The results show that the stability of the PAOX isomers strongly depend on their configuration and orientation of the substituents. The possibilities of inter- and hydrogen bonds were also experimentally and theoretically checked. Finally, a potential of mean force was determined in CHCl3 for a dimer of PAOX with hexamethylphosphoramide. Both, experimental and theoretical results are in agreement. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Quantum-chemical calculations {G2 and/or B3LYP/6-311+G(d,p)} were performed in the gas phase for neutral and ionized hydroxyazines (2- and 4-hydroxy derivatives of pyridine and pyrimidine). For each derivative, all possible tautomeric conversions were considered and all possible prototropic tautomers (OH, NH, and CH) analyzed. Rotational isomerism of the OH group was also taken into account. An interesting change of the relative stabilities takes place when proceeding from the neutral to ionized forms. Positive ionization favors the NH tautomers, and negative ionization the CH ones, except 2-hydroxypyrimidine for which the NH tautomer predominates for both ionized forms. A good relation exists between prototropy and electron delocalization solely for the neutral NH and CH tautomers. The OH forms are separated from the subfamily of the NH and CH tautomers due to significant differences between the stabilities of the tautomeric oxo and hydroxy groups. Intramolecular interactions affect both the geometric and energetic parameters, but the relative stabilities in higher degree. When compared to series of aminoazines, the total geometric effects of the exo O and NH groups are similar for neutral azines. [ABSTRACT FROM AUTHOR]

Highlights: [•] Good relation exists between prototropy and electron delocalization for the neutral isomers. [•] Aromaticity is one of the main factors that dictates the tautomeric preferences for 2-aminopyrimidine. [•] Ionization increases the stability of the imine NH isomers in higher degree in water solution. [•] The non-aromatic imine CH isomer may be neglected at each oxidation state. [•] The IP and EA values change in water solution by ca. 2eV. [ABSTRACT FROM AUTHOR]

Highlights: [•] Structural and energetic parameters are achieved for 37 isomers of neutral and redox adenine. [•] Good relation between prototropy and electron delocalization exists for neutral adenine. [•] One-electron oxidation has slight effect on the general HOMED/ΔG relation. [•] Except reduced adenine, aromaticity is the main factor that dictates the tautomeric preferences. [•] The reduced NHNH and NHCH subfamilies are separated in the HOMED vs ΔG plot. [ABSTRACT FROM AUTHOR]

Abstract: The HF, MP2, and DFT structures of neutral (N6) and monoprotonated (N6H+) hexazine, nitrogen analogues of benzene, were discussed. For neutral N6, the extended geometry-based HOMED (harmonic oscillator model of electron delocalization) index, being a measure of π-electron delocalization, is close to that of benzene. Protonation of one N atom in planar N6 has no important effect on the HOMED value. Contrary to benzene, planar N6H+ does not lose its aromatic character. π-Electrons of the ring are not engaged in the formation of the NH bond. The proton affinity (PA) of N6 seems to be considerably lower than that of benzene (by ca. 16kcalmol−1 at the G2 level), indicating great Nirs repulsion and electron-withdrawing effects of the N-aza groups (ca. 12kcalmol−1 for each N atom). [ABSTRACT FROM AUTHOR]

Complete tautomeric equilibria and π-electron delocalization were studied at the B3LYP/6-311+G** level for neutral purine (P) and its charged radicals (P+• and P-•). All possible nine tautomers (four NH and five CH forms) and all possible 36 tautomeric equilibria (six NiH → NkH, twenty NH → CH, and ten CiH → CkH conversions) were considered. The greatest variations of the tautomeric equilibrium constants (as pKT) were observed for the NH → CH conversions when proceeding from neutral to reduced purine (P + e → P-•). These variations completely change the tautomeric preferences. One-electron oxidation (P - e → P+•) has considerably smaller effect on the pKT values and does not change the tautomeric preferences. π-Electron delocalization depends on the position of the moving proton and on the type of the electron transfer. For individual tautomers, some linear relations between the relative stabilities and the HOMA (harmonic oscillator model of aromaticity) indices occur for neutral and oxidized purine. For reduced purine, a scatter plot is found. Copyright © 2010 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Two types of bimolecular adducts were studied for the substrate and inhibitor of lactate dehydrogenase (LDH), one type of adducts between ionic species, α-keto-carboxylates (pyruvate and oxamate) and the guanidinium cation, and the other type of adducts between neutral species, α-ketocarboxylic (pyruvic and oxamic) acids and guanidine. Calculations were performed in the gas phase and aqueous solution using the MP2 and PCM methods and the 6-31++G** basis set. Application of the DFT(B3LYP) and PCM methods led to similar results. A change of the adducts' preference was observed when proceeding from the gas phase to aqueous solution. This change is in good agreement with the acidity–basicity scales in both phases. Formation constant (KHB) for adduct between neutral species is greater for pyruvic than for oxamic acid in the gas phase, whereas a reverse situation takes place in aqueous solution, where the KHB value for adduct between ionic species is smaller for pyruvate than for oxamate. The water molecules favor interactions of more polar oxamate with the guanidinium cation. Stronger interaction with this cation, a model of the arginine fragment of the LDH pocket, suggests that oxamate (inhibitor of LDH) has stronger binding properties in aqueous solution than pyruvate (substrate of LDH). Copyright © 2008 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: The DFT calculations using B3PW91 hybrid functional and 6-311++G** basis set were performed for the two most stable isomers of cytisine (1a and 1b). The conformation 1a differs from 1b by the orientation (equatorial and axial, respectively) of the hydrogen atom at the piperidine nitrogen atom. In terms of the Gibbs free energy, the conformation 1a is less stable than 1b by 0.25kcalmol−1, only. The isomers are separated by 3.6kcalmol−1—an activation energy barrier, which is higher in energy than the vibrational modes inverting one isomer into another. Presence of such a barrier explains the existence of the two isomers (equatorial and axial) observed previously in apolar solvents. [Copyright &y& Elsevier]

Infrared and Raman spectra were recorded for solid cytisine—an agonist of nicotinic acetylcholine receptors (nAChRs), and analysed with help of the semiempirical (AM1) and ab initio {DFT(B3PW91)/6-311++G**} calculations performed for monomeric and associated structures (dimer, trimer and tetramer). Among two stable conformers of cytisine (1a and 1b) identified in solution, only one (1a) is present in the solid state, where it is stabilized by intermolecular H-bonds (&z.lbond2;C&z.dbnd6;O⋯HN&z.rbond2;). Two different environments for the associated molecules give two different spectral properties. Two component bands can be distinguished for the piperidine ν(NH) and γ(NH) as well as for the pyridine ν(CH), ν(C&z.dbnd6;O) and ν(CC) contours. [Copyright &y& Elsevier]