A Gaussian-3 theoretical study of the alkylthio radicals and their anions: structures, thermochemistry, and electron affinities

The optimized geometries, electron affinities, and dissociation energies of the alkylthio radicals have been determined with the higher level of the Gaussian-3(G3) theory. The geometries are fully optimized and discussed. The reliable adiabatic electron affinities with ZPVE correction have been predicted to be 1.860 eV for the methylthio radical, 1.960 eV for the ethylthio radical, 1.980 and 2.074 eV for the two isomers (n-C₃H₇S and i-C₃H₇S) of the propylthio radical, 1.991, 2.133 and 2.013 eV for the three isomers (n-C₄H₉S, t-C₄H₉S, and i-C₄H₉S) of the butylthio radical, and 1.999, 2.147, 2.164, and 2.059 eV for the four isomers (n-C₅H₁₁S, b-C₅H₁₁S, c-C₅H₁₁S, and d-C₅H₁₁S) of the pentylthio radical, respectively. These corrected EA_ad values for the alkylthio radicals are in good agreement with available experiments, and the average absolute error of the G3 method is 0.041 eV. The dissociation energies of S atom from neutral C_nH_2n+1S (n?=?1–5) and S^- from corresponding anions C_nH_2n+1S^- species have also been estimated respectively to examine their relative stabilities.     

A quantum chemical investigation of structures,vibrational spectra and electron affinities of the radicals of quinone model compounds

In the present study, the first quantum chemical calculations of structures and vibrational spectra of radicals of 1,4-naphthoquinone and 2-methoxy-1,4-benzoquinone that account for electron correlation are presented. In the case of 1,4-naphthoquinone a good agreement between calculated vibrational frequencies and ¹⁸O-shifts of the 1,4-naphthoquinone radical (protonated radical anion) with experimental data of a species detected after irradiation of vitamin K₁ in solution is found. Our calculations, thus, support the previous assignment. In the case of 2-methoxy-1,4-benzoquinone we have localized the stable conformations with respect to the orientation of the methoxy group and we have determine the harmonic force fields for these structures. Our calculation suggest that, while the frequencies of the two conformers are similar, the ¹⁸O-shift of the most intensive absorptions in the spectral region between 1400 and 1700 cm^–1 of the two conformers differ significantly and might serve as a tool to distinguish between the two conformers. The applied DFT method is shown to predict electron affinities which are systematically underestimated by 10%.     

Density functional studies on the electron affinities of DNA and RNA bases

Influence of basis sets on electron affinities (EAs) of DNA and RNA bases has been investigated using density functional method (B3LYP functional) with different basis sets (6-31G, TZVP and 6-311+ + G**). Effect of some PBE functionals namely, PBEOP, PBELYP and PBEVWN, on EA values of the nucleobases was studied using basis set which predicted the most reliable values with B3LYP functional. Observation of the trends in the values of EA and dipole moment of the molecules enable us to identify the features of a basis set that shows the presence of dipole-bound state of some of the nucleobases. The vertical electron affinities with B3LYP and PBEOP functionals are close to the experimental values. The adiabatic electron affinities of uracil and thymine were found to be positive for basis set with diffuse functions using B3LYP functional. Adenine does not have a stable covalently bound anion at all levels of basis sets and functionals. The sign of adiabatic electron affinity value of cytosine is inconsistent with that of experimental value but in agreement with previous theoretical results. For guanine the adiabatic electron affinity value with 6-311+ + G** basis set was found to be very high as comparison with other two basis sets confirming the formation of mixed covalent-dipole character.     

Free radicals generated during oxidation of green tea polyphenols: Electron paramagnetic resonance spectroscopy combined with density functional theory calculations

Electron paramagnetic resonance spectroscopy and density functional theory calculations have been used to investigate the redox properties of the green tea polyphenols (GTPs) (?)-epigallocatechin gallate (EGCG), (?)-epigallocatechin (EGC), and (?)-epicatechin gallate (ECG). Aqueous extracts of green tea and these individual phenols were autoxidized at alkaline pH and oxidized by superoxide anion (O₂^?) radicals in dimethyl sulfoxide. Several new aspects of the free radical chemistry of GTPs were revealed. EGCG can be oxidized on both the B and the D ring. The B ring was the main oxidation site during autoxidation, but the D ring was the preferred site for O₂^? oxidation. Oxidation of the D ring was followed by structural degradation, leading to generation of a radical identical to that of oxidized gallic acid. Alkaline autoxidation of green tea extracts produced four radicals that were related to products of the oxidation of EGCG, EGC, ECG, and gallic acid, whereas the spectra from O₂^? oxidation could be explained solely by radicals generated from EGCG. Assignments of hyperfine coupling constants were made by DFT calculations, allowing the identities of the radicals observed to be confirmed.     

Crystal structures and thermotropic properties of alkyl alpha-D-glucopyranosides and their hydrates

Thermotropic properties and crystal structures of alkyl alpha-D-glucopyranosides and their hydrates were estimated by X-ray, DSC and thermogravimetric measurements (TGA). Monohydrates rapidly lose their crystal water several degrees below the melting point of the anhydrous glucopyranosides. The melting points of the monohydrates measured in DSC pressure cells (chain length longer than seven) are lower, and the clearing points higher than those of the anhydrous glucosides. Layer distances of smectic and crystalline phases of anhydrous compounds were established. Melting points, densities and layer distances of the crystalline anhydrous glucopyranosides display strong even-odd effects. The strong decrease of these effects in the case of the monohydrates can be elucidated by the results of X-ray crystal structure analysis.     

Estimation of the hydrophobic effect based on the density functional theory

Using the fundamental measure treatment of the density functional theory, we have developed a method to calculate the solvation of hydrophobic solutes. The method allows one to calculate the density profile and the solvation energy for hydrophobic molecules. An additional benefit of the method is the possibility to calculate interaction forces and the mean force potential between hydrophobic nanoparticles. On the basis of the method, the solvation energies for spherical solutes of different sizes from one angstrom up to several nanometers were calculated.     

Studies on the functional morphology of rat ocular vessels with scanning electron microscopy

Tests are still lacking about the suitability of scanning electron microscopy (SEM) of vascular resin casts to show different functional states of peripheral blood vessels. With the aid of a vitalmicroscopic device, we tried to elaborate a vascular casting method using the model of the albino rat iris vasculature. Functional variations of the vasculature were induced by local application of epinephrine to one eye using the untreated fellow eye as a control. It was found that if our modification of Araldite plastic is injected via a systemic access and without preceding rinsing with fixatives or salt solutions there is a good correlation between the vessel diameters seen in SEM of resin casts and the vessel diameters found in the vitalmicroscopic observations. Thus, this method appears also suitable for studying the effect of vasoactive substances.     

The hands and feet of Archaeolemur: metrical affinities and their functional significance

Recent expeditions to Madagascar have recovered abundant skeletal remains of Archaeolemur, one of the so-called "monkey lemurs" known from Holocene deposits scattered across the island. These new skeletons are sufficiently complete to permit reassembly of entire hands and feet--postcranial elements crucial to drawing inferences about substrate preferences and positional behavior. Univariate and multivariate analysis of intrinsic hand and foot proportions, phalangeal indices, relative pollex and hallux lengths, phalangeal curvature, and distal phalangeal shape reveal a highly derived and unique morphology for an extinct strepsirrhine that diverges dramatically from that of living lemurs and converges in some respects on that of Old World monkeys (e.g., mandrills, but not baboons or geladas). The hands and feet of Archaeolemur are relatively short (extremely so relative to body size); the carpus and tarsus are both "long" relative to total hand and foot lengths, respectively; phalangeal indices of both the hands and feet are low; both pollex and hallux are reduced; the apical tufts of the distal phalanges are very broad; and the proximal phalanges are slightly curved (but more so than in baboons). Overall grasping capabilities may have been compromised to some extent, and dexterous handling of small objects seems improbable. Deliberate and noncursorial quadrupedalism was most likely practiced on both the ground and in the trees. A flexible locomotor repertoire in conjunction with a eurytopic trophic adaptation allowed Archaeolemur to inhabit much of Madagascar and may explain why it was one of the latest surviving subfossil lemurs.     

On the functional significance of electron density protein structure alignments

Electron density protein alignments are analyzed in terms of their underlying similarity measure, the density overlap. These alignments are conceptually unrelated to biochemical structural elements and, therefore, are appropriate in structure-only similarity studies. The analysis is focused on the low sequence similarity subset of protein domains. A remarkable association is found between simple, density overlap measures and the expert designed Structural Classification of Proteins (SCOP) for which functional and evolutive analogies prevail. The association found validates the functional significance of electron density alignments.     

The study of the electronic structures and properties of pure and transition metal-doped silicon nanoclusters: a density functional theory approach

This report presents the study of ab initio electronic structure and properties of pure and transition metal (TM = Ti, Zr and Hf)-doped silicon clusters, TM@Si(n), by using density functional theory with a polarised basis set (LanL2DZ) within the spin-polarised generalised gradient approximation for different values of n varying from 8 to 20. As the first step of the study, different optimised geometries of pure and doped clusters are calculated. These optimised clusters are then used to calculate different structural and physical parameters of the clusters, like binding energy, Highest Occupied Molecular Orbital – Lowest Unoccupied Molecular Orbital (HOMO–LUMO) gap, charge transfer, etc. In order to check the stability of the clusters, the second-order difference in the energy of the optimised structures is calculated. To study the optical behaviour of the clusters, infrared and Raman spectra are also calculated. Further calculations are also done on cation and anion clusters of both pure and doped nanoclusters to obtain their ionisation potential, electron affinity and chemical potential. An effort has been made to correlate the variation of different calculated parameters with the size of the clusters to explain the real existence and stabilities of different TM-doped clusters.     

Studies on the activity of phospholipase D with alkyl phosphorylcholines

The activity of phospholipase D from the Savoy cabbage on alkyl phosphorylcholines containing alkyl groups of C14 to C22 was examined. Apparent Km and maximal velocity values in the presence of diethyl ester were 3.6-8.3 mM and 0.14-0.29 mumol/(min.mg protein), respectively. The maximal velocities for alkyl phosphorylcholine homologues were lower than the value for pig phosphatidylcholines, but higher than those for lysophosphatidylcholines and synthetic phosphatidylcholine with saturated acyl chains. Results suggest that solubilities of the substrates in the organic solvent play an important role in activity observed with phospholipase D.     

Studies on molecular structure and tautomerism of a vitamin B<Subscript>6</Subscript> analog with density functional theory

This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.     

A density functional theory study of the decomposition mechanism of nitroglycerin

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO₂ (a product obtained following the abstraction of three H atoms from NG by NO₂) include O–NO₂ cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO₂ concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O–NO₂ cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO₂ concentration. However, when a threshold NO₂ concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.     

Theoretical study on the adsorption of phenol on activated carbon using density functional theory

Density functional theory (DFT) calculations performed at the PBE/DZP level using the DFT-D2 method were utilized to investigate the adsorption of phenol on pristine activated carbon (AC) and on activated carbon functionalized with OH, CHO, or COOH groups. Over the pristine AC, the phenol molecule undergoes weak physical adsorption due to van der Waals interactions between the aromatic part of the phenol and the basal planes of the AC. Among the three functional groups used to functionalize the AC, the carboxylic group was found to interact most strongly with the hydroxyl group of phenol. These results suggest that functionalized AC-COOH has great potential for use in environmental applications as an adsorbent of phenol molecules in aqueous phases.     

A density functional theory study on the hydrogen bonding interactions between luteolin and ethanol

Ethanol is one of the most commonly used solvents to extract flavonoids from propolis. Hydrogen bonding interactions play an important role in the properties of liquid system. The main objective of the work is to study the hydrogen bonding interactions between flavonoid and ethanol. Luteolin is a very common flavonoid that has been found in different geographical and botanical propolis. In this work, it was selected as the representative flavonoid to do detailed research. The study was performed from a theoretical perspective using density functional theory (DFT) method. After careful optimization, there exist nine optimized geometries for the luteolin ? CH₃CH₂OH complex. The binding distance of X ? H···O, and the bond length, vibrational frequency, and electron density changes of X ? H all indicate the formation of the hydrogen bond in the optimized geometries. In the optimized geometries, it is found that: (1) except for the H2’, H5’, and H6’, CH₃CH₂OH has formed hydrogen bonds with all the hydrogen and oxygen atoms in luteolin. The hydrogen atoms in the hydroxyl groups of luteolin form the strongest hydrogen bonds with CH₃CH₂OH; (2) all of the hydrogen bonds are closed-shell interactions; (3) the strongest hydrogen bond is the O3’ ? H3’···O in structure A, while the weakest one is the C3 ? H3···O in structure E; (4) the hydrogen bonds of O3’ ? H3’···O, O ? H···O4, O ? H···O3’ and O ? H···O7 are medium strength and covalent dominant in nature. While the other hydrogen bonds are weak strength and possess a dominant character of the electrostatic interactions in nature.     

A density functional theory study on the interactions between dibenzothiophene and tetrafluoroborate-based ionic liquids

The interactions between dibenzothiophene (DBT) and N-butyl-N-methylimidazolium tetrafluoroborate ([BMIM][BF₄]), N-butyl-N-methylmorpholinium tetrafluoroborate ([Bmmorpholinium][BF₄]), N-butyl-N-methylpiperdinium tetrafluoroborate ([BMPiper][BF₄]), N-butyl-N-methylpyrrolidinium tetrafluoroborate ([BMPyrro][BF₄]), and N-butylpyridinium tetrafluoroborate ([BPY][BF₄]) were investigated using density functional theory approach. Geometric, electron, and topological properties were analyzed using natural bond orbital, atoms in molecules theory, and noncovalent interaction methods in order to understand intermolecular interactions between DBT and ionic liquids. The result shows that hydrogen bond and van der Waals interactions are widespread in all the ionic liquids-DBT systems. Ion-π interactions between DBT and cation or anion are also observed, while π⁺-π interactions are only found in the [BMIM][BF₄]-DBT and [BPY][BF₄]-DBT systems. The order of interaction energy is [BPY][BF4]-DBT > [BMIM][BF₄]-DBT >> [BMPiper][BF₄]-DBT > [BMPyrro][BF₄]-DBT > [BMmorpholinum][BF₄]-DBT. The energies between DBT and the two ionic liquids containing aromatic cations are significantly higher.