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The effects of introducing electron-donating (NH2, OCH3, CH3) and electron-withdrawing (NO2, CF3, CN, F) groups to N,N-dimethylbenzylamine-2-selenol are studied to determine the effect of the selenium electron density on the efficiency of the reduction of hydrogen peroxide. Introducing substituents in the meta and para positions decreases or increases the energy barrier of the reaction in the expected way, due to changes in the electronic environment of the reacting selenium center. Ortho substituents are found to have a greater effect on the electronic environment of the selenium center, which is mitigated by changing the steric environment. Insight into the origins of the substituent effects is obtained through quantum theory of atoms in molecules (QTAIM) and electrostatic potential analysis. [ABSTRACT FROM AUTHOR]

The reaction mechanism for the reduction of hydrogen peroxide by N,N-dimethylbenzylamine diselenide, its selenol analogue, and the charged analogues of the diselenide and selenol are elucidated using reliable electronic structure techniques. It is found that the reaction using the diselenide has a large Gibbs energy barrier of 173.5 kJ/mol. The cationic diselenide, with both amines protonated, shows a lower barrier of 103.5 kJ/mol. Both diselenide species show significant Se−Se bond lengthening upon oxidation. An unusual two-step mechanism is found for the selenol with barriers of 136.3 and 141.9 kJ/mol, respectively, showing that it is unlikely that the selenol is the active form. The zwitterion, selenolate, and protonated amine analogues of the selenol show one-step reactions with energy barriers of 82.7, 92.7, and 102.3 kJ/mol, respectively. The zwitterion of the selenol shows the most favorable reaction energies, which is in good agreement with proposed mechanisms for this reaction. [ABSTRACT FROM AUTHOR]

The direct oxidation of ebselen and several derivatives by hydrogen peroxide is investigated using the B3LYP/6-31G(d,p) method to elucidate the effects of substituents on GPx-like activity. While previous studies have attributed the differences in GPx activity of substituted ebselen compounds to the electronic nature of the substituents, the influence of functional groups is poorly understood. The effects of various solvents are incorporated by employing the CPCM method. It is shown that a substituent in the ortho position to the selenium atom sterically hinders attack of a nucleophile at selenium and thus increases the barrier to reaction. The observed increase in GPx-like activity of an ebselen derivative with an ortho substituent is explained by the fact that the steric hindrance prevents thiol exchange reactions. [ABSTRACT FROM AUTHOR]

Density functional theory calculations at the B3LYP/6-311G(3df,3pd)//B3LYP/6-31G(d,p) level have been performed to elucidate the mechanism and reaction energetics for the reduction of hydrogen peroxide by ebselen, ebselen diselenide, ebselen selenol, and their sulfur analogues. The effects of solvation have been included with the CPCM model, and in the case of the selenol anion reaction, diffuse functions were used on heavy atoms for the geometry optimizations and thermochemical calculations. The topology of the electron density in each system was investigated using the quantum theory of atoms in molecules, and a detailed interpretation of the electronic charge and population data as well as the atomic energies is presented. Reaction free energy barriers for the oxidation of ebselen, ebselen diselenide, and ebselen selenol are 36.8, 38.4, and 32.5 kcal/mol, respectively, in good qualitative agreement with experiment. It is demonstrated that the oxidized selenium atom is significantly destabilized in all cases and that the exothermicity of the reactions is attributed to the peroxide oxygen atoms via reduction. The lower barrier to oxidation exhibited by the selenol is largely due to entropic effects in the reactant complex. [ABSTRACT FROM AUTHOR]

Theoretical calculations have been performed on three model reactions representing the reduction of hydrogen peroxide by ebselen, ebselen selenol, and ebselen diselenide. The reaction surfaces have been investigated at the B3PW91/6-311G(2df,p) level, and single-point energies were calculated using the 6-311G(3df,3pd) basis set. Solvent effects were included implicitly with the conductor-like polarizable continuum model and in one case with explicit inclusion of three water molecules. Mechanistic information is gained from investigating the critical points using the quantum theory of atoms in molecules. The barriers for the reduction of hydrogen peroxide with the ebselen, ebselen selenol, and ebselen diselenide models are 56.7, 53.4, and 35.3 kcal/mol, respectively, suggesting that ebselen diselenide may be the most active antioxidant in the ebselen GPx redox pathway. Results are also compared to that of the sulfur analogues of the model compounds. [ABSTRACT FROM AUTHOR]

A mechanism involving a six-membered cyclic transition state where the hydrogen of the hydroxyl group interacts with the oxygen of the carbonyl group has been proposed previously to describe the thermolysis of many -hydroxyl compounds. In this paper, the proposed mechanism is studied for a series of -hydroxyl aldehydes. Rate constants and activation energies are reported as well as a study of the influence of tunneling on the reaction rates. The electron density at the ring critical points, population analyses by the theory of atoms in molecules (AIM) and the natural bond orbital (NBO) method, as well as atomic energy analyses are used to gain insight into this interesting mechanism and into the effects of substituents. [ABSTRACT FROM AUTHOR]

A systematic comparison of the optimized geometries of five organotin compounds, ClnSn(CH3)4-n, n0−4, with the available gas-phase electron diffraction results is reported. All optimizations were carried out with the B3LYP density functional method. Comparison of 10 basis sets and three effective core potentials leads to the conclusion that the combination of the SDB-aug-cc-pVTZ basis set and the LANL2 effective core potential for tin, together with the 6-31G(d,p) basis set for the other atoms, is recommended for the prediction of the geometries of organotin compounds. [ABSTRACT FROM AUTHOR]

Density functional theory is usedto study a series of model ironporphyrins in the gas phase. In the first part of this study, threerange-separated hybrid density functionals developed by Chai and Head-Gordonwere assessed; ωB97, ωB97X, and ωB97XD. The effectsof including full Hartree–Fock exchange at long-range and dispersioncorrections are reported with respect to the geometries and bindingenergies of oxygen to the iron porphyrin systems. The functionalsall correctly predict the quintet ground state for the deoxy-ironporphyrins, where typically hybrid functionals fail and predict atriplet ground state. Including dispersion in ωB97XD is shownto give the best results for the O2binding energy andgeometrical parameters. The second part of the study employs ωB97XDto study iron porphine systems with different amino acids in the axialposition. Geometrical parameters are reported and compared to experimentaldata, where available. Binding energies of the systems with oxygenare also reported and discussed. [ABSTRACT FROM AUTHOR]

Enthalpies and entropies of dimerization have been determined as functions of concentration for dibutyltin dipropoxide, dibutyltin dibutoxide, and dibutyltin diisopropoxide in toluene-d8and cyclohexane-d12solutions from the variation in 119Sn NMR chemical shifts with temperature. The values of ΔHand ΔSobtained in toluene-d8for dibutyltin dibutoxide were −69.5 ± 3.0 kJ mol−1and −197 ± 10 J mol−1K−1, respectively, and for dibutyltin diisopropoxide −67.1 ± 1.4 kJ mol−1and −244 ± 9 J mol−1K−1, respectively. Enthalpies and entropies of activation for this process for dibutyltin diisopropoxide have been derived by simulation of the temperature-dependent broadening of the 119Sn NMR spectra. The free energy of activation for dimerization was 33 kJ mol−1. The same thermodynamic parameters for a greater range of dibutyltin dialkoxides were derived theoretically by using MP2 single-point calculations on B3LYP-optimized geometries using the LANL2DZdp basis set with diffuse and polarization functions and its effective core potential for tin and 6-311G(2d,p)//6-31G(d,p) for other atoms. Quite good agreement with the experimental results was achieved with this level of theory. The present study confirms that steric effects dictate the degree of dimerization for dibutyltin dialkoxides, with monomers becoming favored at room temperature when the alkoxide groups are changed from primary to secondary. [ABSTRACT FROM AUTHOR]

5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant. [ABSTRACT FROM AUTHOR]

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known π-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described:  (i) interactions between atoms in the bases and atoms belonging to the backbone (base−backbone) and (ii) interactions among atoms within the backbone itself (backbone−backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen−hydrogen bonding, and several other weak closed-shell X−Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5−3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title. [ABSTRACT FROM AUTHOR]

The displacement of the iron(II) atom from the porphyrin plane in iron(II) porphyrin complexes is investigated with respect to the spin state of iron(II) employing density functional theory. In this study the quantum theory of atoms in molecules (QTAIM) is used to show that the atomic volume of iron is smaller in the quintet state of imidazolium ligated iron(II) porphyrin than in the triplet state. This is consistent with what has been found for free atoms and contradicts the original interpretation of structural studies with X-rays, which assumed that the out-of-plane displacement of iron from the porphyrin ring in the quintet state is due to the increased spatial size of the high-spin iron atom. The bonding environment of the iron atom is analyzed with respect to the electron density (ρ) at the bond critical points (BCPs). It is found that in the quintet state, relative to the triplet state, there is a stronger bonding interaction between iron and the nitrogen atoms of the porphyrin despite a longer bond length. It has previously been suggested that the weakening of these bonds is the cause of the out-of-plane displacement of iron. Since this is not the case, this implies that the magnitude of the bonding interaction between the iron atom and the axial ligand has a more significant role in the domed structure of the quintet state. [ABSTRACT FROM AUTHOR]

Guanine quadruplexes have received a lot of attention due to their possible role as therapeutic agents. Specifically, it is the ability of these quadruplex structures to inhibit telomerase, an enzyme found to be highly active in a large percentage of tumor cells and thought to confer immortality upon these cells. However, although a great deal of research has focused on enhancing the formation of these structures and their anticancer activity, many questions remain about the quadruplex structures themselves. The current study probes the nature of these quadruplex structures at the atomic level. Individual atomic energies have been computed for the quadruplex structure and compared to the atomic energies of the unfolded telomere to determine the energetic consequences of quadruplex formation. The results suggest several interesting trends, most notably that the guanine quartets exhibit an alternating pattern of stabilization and destabilization and these regions actually overlap in the intact quadruplex. In addition, the TTA loop segments are largely stabilized, whereas the atoms in the sugar−phosphate backbone exhibit mostly minor changes going from the unfolded to folded state. Inclusion of additional sodium cations in the central core of the quadruplex has a minimal effect on the atomic energies except for the atoms that are closest to the cations, which are largely stabilized in the presence of these ions. [ABSTRACT FROM AUTHOR]

The structures of 19 α-helical alanine-based peptides, 13 amino acids in length, have been fully optimized using density functional theory and analyzed by means of the quantum theory of atoms in molecules. Two types of N−H···O bonds and one type of C−H···O bond have been identified. The value of the electron density at hydrogen bond critical points corresponding to N−H···O interactions is higher than that of C−H···O interactions. The effect of amino acid substitution at the central position of the peptide on the hydrogen bond network of the α-helix has been assessed. The strength of the hydrogen bond network, measured as the summation of the electron density over the hydrogen bond critical points, may be used to explain experimental relative helix propensities of amino acids in cases where solvation and entropic effects cannot. [ABSTRACT FROM AUTHOR]