Elucidating the intermolecular hydrogen bonding interaction of proline with amides—quantum chemical calculations

Structural Chemistry - The hydrogen-bonded complexes formed between proline and amides have been investigated completely by the use of computational methods such as Atoms In Molecules (AIM),...     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Quantum chemical investigation on the influence of amino substitution on proton affinity of oxazolidin-2-one

The scenarios of preferred protonation sites and the absolute gas-phase proton affinities of C5- and N4-amino derivatives of oxazolidinone (OXA) molecules possessing two oxygen and two nitrogen atoms, are studied to investigate the effect of substitution of amino group on geometry, electronic structure, and proton affinities of these molecules. The natural bond orbital analysis is invoked to obtain the second-order delocalization energies, occupations of lone pairs, charge distribution, and bond orders to rationalize the obtained results. Our findings reveal a strong nucleophilicity of O1 site in C5-amino and N4-amino-substituted OXA isomers just as in un-substituted OXA. The substituent nitrogen in N4-amino-substituted OXA has comparable electrophilicity to O1 site while lesser than acyl oxygen and higher than nitrogen of OXA ring in C5-amino-substituted OXA. The PA values of C5- and N4-amino-substituted OXA isomers span in the range 172.06–205.77 kcal mol^?1 (at CBS-Q). The PA values for the potential sites increase in the range 1.96–27.08 kcal mol^?1 as a result of the amino substitution at C5 and N4 in orientation (b) while exceptionally they decrease by 0.57–2.95 kcal mol^?1 as a result of the amino substitution at N4 in orientation (a). The results for the order of PA values of potential sites have been supported by molecular electrostatic potential maps. Our findings indicate that the factors such as geometrical rearrangements, variations in atomic charge densities and electron delocalization, effect of substituent, intramolecular hydrogen bonding, and electronic changes direct the relative stabilities and proton affinities of N, C5-substituted amino OXA isomers.     

Insight into the acidic behavior of oxazolidin-2-one,its thione and selone analogs through computational techniques

Deprotonation thermochemistry of Oxazolidin-2-one (OXA), Oxazolidine-2-thione (OXA-S), and Oxazolidine-2-selone (OXA-Se) has been studied in order to find the most acidic site and relative acidities of these heterocyclics at various sites. The deprotonation enthalpies at MP2/6-311++G**//MP2/6-31+G* and B3LYP/6-31+G* levels, while the free energies for deprotonation process and pKa values at B3LYP/6-31+G* level both in gas and aqueous phase (using PCM continuum model) of the anions of the three heterocyclics have been computed at 298 K. Calculated aqueous phase pKa values of OXA vary by ~6–7 units from the experimental aqueous phase pKa values of OXA and its derivatives. The deprotonation at the nitrogen is favored in OXA over the carbon atoms in contrast to the OXA-S and OXA-Se where in the deprotonation at the carbon attached to the nitrogen is most preferred. Deprotonation at this carbon induces an important C–O bond rupture in OXA-S and OXA-Se promoting an energetically favored ring-opening process. The finding offers a rare case when C–H acidity is able to dominate over the N–H acidity. In order to explain the relative stabilities, relative acidities and deprotonation enthalpies various characteristics of these molecules as well as their anions such as molecular electrostatic potential surface (MEP), frontier molecular orbital (FMO) features, chemical hardness, softness have been governed. The three dimensional MEP maps and HOMO–LUMO orbitals encompassing these molecules yield a reliable relative stability and reactivity (in terms of acidity) map displaying the most probable regions for deprotonation. The differential distribution of the electrostatic potential over the neutral and anionic species of OXA, OXA-S, and OXA-Se molecules is authentically reflected by HOMO–LUMO orbitals and NBO charge distribution analysis. The lone pair occupancies, second order delocalization energies for orbital interactions and the distribution of atomic charges over the entire molecular framework as obtained from natural bond orbital (NBO) analysis are found to faithfully replicate the predictions from the MEP maps and HOMO–LUMO band gaps in respect of explaining the relative stabilities and acidities in most of the cases. Good linear correlations have been obtained between HOMO–LUMO gap and pKa values in the aqueous phase for OXA and OXA-S molecules.     

Theoretical studies on the conformations of selenamides

Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe-NH₂ to estimate the Se-N rotational barriers and N-inversion barriers. Two conformers have been found withsyn andanti arrangement of the NH₂ hydrogens with respect to Se-H bond. The N inversion barriers in selenamide are 1.65, 2.47, 1.93 kcal/mol and the Se-N rotational barriers are 6.58, 6.56 and 6.12 kcal/mol respectively at HF/6-31+G*, MP2/6-31+G* and B3LYP/6-31+G* levels respectively. The n_N →Σ *_Se-H negative hyperconjugation is found to be responsible for the higher rotational barriers.     

Interactions of some peptides with sodium acetate and magnesium acetate in aqueous solutions at 298.15 K: A volumetric approach

The apparent molar volumes, V of diglycine, triglycine and glycyl-l-leucine have been determined in water and in aqueous sodium acetate (0.5, 1.0, 2.0, and 4.0 m_B) and magnesium acetate (0.5, 1.0, 1.5, and 2.0 m_B) solutions at 298.15 K by the measurement of densities using vibrating-tube digital densimeter. The partial molar volumes, V_2,m⁰ obtained from V have been used to calculate the partial molar volumes of transfer, Δ_trV_2,m⁰ for these peptides from water to aqueous solutions of sodium acetate (SA) and magnesium acetate (MA) solutions. The hydration numbers, n_H and volumetric interaction coefficients have also been calculated. The Δ_trV_2,m⁰ data suggest that ion-charged/or peptide group interactions of peptides are stronger with MA in comparison to SA.     

Intra and intermolecular hydrogen bonding in formohydroxamic acid

The presence of hydrogen bonding interactions in several tautomeric forms of formohydroxamic acid (FHA) and 1:1 association among the tautomeric forms and water‐coordinated tautomeric forms of FHA is explored theoretically. Out of the seven equilibrium structures, four tautomeric forms have been selected for aggregation with single water molecule and dimer formation. Fifteen aggregates of FHA with H₂O have been optimized at MP2/AUG‐cc‐PVDZ level and analyzed for intramolecular and intermolecular H‐bond interactions. Twenty‐seven dimers of the four tautomeric forms have been obtained at MP2/6‐31+G* level. The stabilization energies associated with dimerization and adduct formation with water are the result of H‐bond interactions and range from very weak to medium. The atomic charges and NBO analysis indicate that the electrostatic and the charge transfer are the important components favoring H‐bond formation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The saturated five‐membered heterocyclic molecules as organic hydride donors: a computational study

Several five‐membered heterocyclic molecules were studied theoretically as organic hydride donors. The density functional theory and ab initio methods are employed to study the direct one‐step or multistep sequence suggested for the hydride transfer from the selected molecules: H atom/electron, electron/proton/electron or electron/H atom. Out of the three multistep mechanisms, electron/H atom seems to be a probable pathway in the presence of suitable catalyst/photoreaction that can cause ionization. In the lack of such catalyst/photoreaction, the direct hydride transfer seems to be most probable with the presence of suitable hydride acceptor. A detailed mechanism of the hydride transfer from the five‐membered heterocylic compounds is important in understanding chemical and biological reactions and required for scientifically designing and synthesizing new desired five‐membered heterocyclic compounds as organic hydride donor. Copyright © 2014 John Wiley & Sons, Ltd.     

Understanding hydrogen bonding of hydroxamic acids with some amino acid side chain model molecules

The hydrogen-bonding abilities of a few amino acid side chains have been studied through aggregation of methylamine, methanol, and acetic acid (as model molecules) with formo- and thioformo- hydroxamic acids using ab initio calculations. Forty six aggregates representing all possible H-bond interactions between these amino acid side chain groups and two most stable keto and enol tautomeric forms of both hydroxamic acids have been optimized. Although participation of conventional H-bond donors and acceptors leads to significant stabilization energies, yet C–H···O, C–H···N, S–H···O, and S–H···N etc. unconventional H-bonds also contribute to stabilize interactions in many aggregates. Strength of H-bonds of the molecules with formo- and thioformo- hydroxamic acid studied follows the order acetic acid > methylamine > methanol. A comparative study of atomic charges and orbital interactions employing NBO analysis has been carried out to explore the role of bond polarizations, charge transfer, and electron delocalizations as contributors to stabilization energy.     

Comparison of hydrogen- and halogen-bonding interactions in the complexes of the substituted carbonyl compounds with hypohalous acids and monohaloamines

Structural Chemistry - An ab initio study of the complexes formed by hypohalous acids and monohaloamines (designated as HAX where A = O or NH and X = Cl, Br, or I) with RCHO (R = H, CH3, OCH3, and...