Mechanism and kinetics of the oxidative damage to ergosterol induced by peroxyl radicals in lipid media: a theoretical quantum chemistry study

In this work, we have studied the mechanisms and kinetics of the initial damage to ergosterol induced by ^?OOH and ^?OOCH₃ peroxyl radicals in a lipid media, using quantum chemistry and computational kinetics methods. The initial damage to ergosterol induced by these radicals occurs predominantly through the hydrogen transfer mechanism (HT) from the allylic position C14 of ergosterol. For the reaction of ergosterol with ^?OOH, the HT‐9 pathway represents ~90.8% of the overall rate constant, while in the case of ^?OOCH₃, the HT‐14 pathway represents more than ~97.2% of the overall rate constant. The calculated overall reaction rates for the initial damage to ergosterol caused by the ^?OOH and ^?OOCH₃ are 2.05 × 10⁶ and 6.26 × 10⁴ M^?1 s^?1, respectively, indicating that the oxidative damage to ergosterol initiated by these radicals, and probably other alkyl‐peroxyl radicals, could be significantly dangerous to their integrity. Taking into account the calculated values of the overall rate coefficients, we can conclude that ergosterol is more susceptible to damage produced by peroxyl radicals than cholesterol and fatty acids. This suggests that fungal cells might be more sensitive to these radicals than animal cells, coinciding with the fact that one of the targets in combating fungi is precisely ergosterol. Finally, theoretical calculations confirm the antioxidant potential of ergosterol and could help explaining the nutraceutical activity of edible and medicinal mushrooms. Copyright © 2015 John Wiley & Sons, Ltd.     

Theoretical study on the oxidative damage to cholesterol induced by peroxyl radicals

The density functional and the transition state theories were used to estimate detailed thermochemical and kinetic data for the oxidative damage to cholesterol induced by peroxyl radicals (ROO^?) in lipid media. Two mechanisms of reactions were considered, the hydrogen transfer and the radical adduct formation, and it was found that hydrogen transfer is the only important route in this case, particularly at allylic sites. 7α products are predicted to represent more than 90% of the total initial damage, albeit 7β products are expected to be found in small but not negligible proportion. The chlorination degree was found to play an important role in the extent of the oxidative damage to cholesterol inflicted by the ROO^? family. The estimated rate constants are 2.74 × 10⁵, 1.32 × 10⁵, 3.09 × 10², 6.07 × 10¹, and 8.75 × 10^?1 M^?1 s^?1 for the reactions with ^?OOCHCl₂, ^?OOCCl₃, ^?OOCH₂Cl, ^?OOH, and ^?OOCH₃, respectively. These values indicate that only chlorinated peroxyl radicals represent a significant hazard to the chemical integrity of cholesterol. Copyright © 2015 John Wiley & Sons, Ltd.     

EPR studies of free-radical reactions of carboxyfullerenes

Carboxyfullerene is a class of water-soluble buckminsterfullerene with three malonic acids. Electron paramagnetic resonance (EPR) experiments are performed to examine the capacity of carboxyfullerenes to scavenge reactive oxygen species, methyl radicals and peroxyl radicals. Three types of reactions are reported: (1) reactions of^⋅OH and^⋅O ₂ ⁻ with carboxyfullerenes with 5,5-dimethyl-1-pyrroline N-oxide as the trapping agent, (2) reaction of^⋅CH₃ with scavenging agents, and (3) reactions of lipid alkyl/peroxyl radicals with carboxyfullerenes. The study enables one to evaluate the efficacy of carboxyfullerene as a free-radical scavenger and an antioxidatant.     

Effect Of Calcium Ions On The Irradiation Induced Inactivation Of Cellulase

Abstract

The activity of cellulase irradiated at various temperatures was examined as a function of irradiation dose. The effect of calcium ions in radiation inactivation of cellulase at irradiation temperature of 30°C was studied by using calcium sulfate. The calcium ions have a protective ability against radiation caused inactivation of cellulase by scavenging species such as OH^? formed by irradiation of cellulase aqueous solution, in which the effective concentration range of the calcium ions was ～ 10^?3 M. The calcium ions do not act for the heat inactivation of the enzyme and the enzyme hydrolysis of filter paper or chaff as an activator because the calcium ions do not associate with the enzyme to form a calcium ion-enzyme complex.     

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ～1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation–O_NMA radial distribution function decreases whereas the Cl^?─H_NMA radial distribution function increases with ion concentration. On the other hand, the cation–O_water and Cl^?─H_water radial distribution function shows very negligible change with respect to ion concentration. We have also calculated NMA–water and water–water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O_NMA─H_water is comparatively slower than the H_NMA─O_water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.     

Submillimeter wave spectrum and molecular constants of N2O

The submillimeter wave spectrum of the N₂O molecule has been investigated within the 375–565 GHz frequency range with a sensitivity better than 10^?8 cm^?1. The measured frequencies include 161 lines with intensities γ ? 10^?6 cm^?1 belonging to 22 spectroscopically different species of the molecule (specifically, the ground and some excited vibrational states of the five most abundant isotopic species of the molecule in natural abundance) with a statisticall and systematic error of the order of magnitude 10^?8. Rotational and two centrifugal stretching constants could be determined for each spectroscopic species. For each isotopic species observed, we have made a general analysis of the spectrum in different vibrational states bearing in mind resonance effects. The total number of the rotational and rovibrational constants obtained exceeds 40.     

Infrared spectra and rotational isomerism of ethylenediammonium ion in aqueous solution

The infrared spectra of ethylenediamine hydrochloride, sulfate and their N-deuterium derivatives in water or heavy water were studied at various pH or pD and at various concentrations. The frequencies of the CH₂ deformation vibration bands in the region 1500-1250 dm^?1 were found to be sensitive to the conformation of the ethlenediamine molecule and mono- and diammonium ions. The behaviors of these bands indicate that in aqueous solution the ethylenediamine molecule takes the gauche form, the ethylenemonoamine monoammonium ion takes mostly the gauche form and the ethylenediammonium ion takes both the trans and gauche forms.     

Effect of electron scavengers on the gamma radiolysis of H2S-Ch3Br systems

Abstract

The mechanism of mixed dimer negative ion formation in the gamma radiolysis of the gaseous system hydrogen sulphide-methyl bromide has been investigated using carbon tetrachloride and chloroform as the electron scavengers. The concentration of methane was measured gas-chromatographically. The measurements were performed at different total pressures.

ΔG(CH4)-1 is a linear function of [CH³Br][H2S]2/[Sc] (where Sc═CCl4 or CHCl3). On the basis of the above dependencies the mechanism of the formation of the (CH³Br-H³S)? ion was confirmed and the rate constant was calculated to be k=K-ka-kc/ka = 6.5 ×l0^?49 cm⁹ molecule ^?3s^?1     

Vibrational Spectroscopic Studies of Molecules with Biochemical Interest: The Cysteine Zwitterion

Abstract

The L-cysteine zwitterions in the orthorhombic crystal structure and in aqueous solution, including the deuterated isotopologues HSCD₂CH(NH₃ ⁺)COO^?, DSCH₂CH(ND₃ ⁺)COO^?, and DSCD₂CH(ND₃ ⁺)COO^?, have been studied by mid-infrared, far-infrared, and Raman spectroscopy. Density functional theory (DFT) calculations were performed for an equilibrium molecular geometry of the cysteine zwitterion to obtain vibrational frequencies of fundamental modes, infrared (IR) and Raman intensities, and the depolarization ratio of the Raman bands and combined with normal coordinate force field analyses. The force field obtained for dissolved (in H₂O and D₂O) cysteine, based on the 4 × 36 experimental fundamental modes of the four isotopologues, was successfully transferred to the two conformers in the solid state. The experimentally observed multiple bands (generally doublets) of L-cysteine and its deuterated isotopologues in the solid state were interpreted based on the coexistence of two conformers in the unit cell. The calculated frequencies were used for full assignments of the fundamental IR and Raman vibrational transitions, including an attempt to interpret all low-frequency vibrations (below 400 cm^?1) of the zwitterion also in the solid state. In particular, the hydrogen bonding effects on conformation, bond lengths, and force constants were studied, including those of the distorted NH₃ ⁺ amino group. The –S-H and -S-D stretching vibrations were found to be local modes, not sensitive to deuterium substitution of the -CH₂ and -NH₃ ⁺ groups in the molecule or to the H(D)-S-C-C torsional angle. The two major -S-H or -S-D stretching bands observed in the solid state correspond to different S-H/D bond lengths and resulted in the force constants K _SH = 3.618 N·cm^?1 and 3.657 N·cm^?1 for the SH^… S and SH^… O hydrogen-bonded interactions. A remarkable result was that the S(H)^… O interaction was weaker than the S(H)^… S interaction in the solid state and even weaker in aqueous solution, K _SH = 3.715 N·cm^?1, possibly due to intramolecular interactions between the thiol and amino groups. A general correlation between the S-H/D bond length and vibrational frequency was developed, allowing the bond length to be estimated for sulfhydryl groups in, for example, proteins. The C-S stretching modes were fitted with different C-S stretching force constants, K _CS = 3.213 and 2.713 N·cm^?1, consistent with the different CS bond lengths for the two solid-state conformers.     

Are HBO− and BOH− electronically stable?

The binding of an excess electron to HBO and BOH was studied at the coupled cluster level of theory with single, double and non-iterative triple excitations and with extended basis sets to accommodate the loosely bound excess electron. The bent BOH molecule, with a dipole moment of 2.803 D, binds an electron by 39cm^?1, whereas the linear HBO tautomer possesses a similar dipole moment (2.796 D) yet binds the electron by less than 1 cm^?1. It is therefore likely that HBO^? is not stable when rotational energies are included whereas BOH^? is for low rotational quantum numbers.     

Two salts and the salt cocrystal of ciprofloxacin with thiobarbituric and barbituric acids: The structure and properties

Ciprofloxacin (CfH, C₁₇H₁₈FN₃O₃) crystallizes with 2‐thiobarbituric (H₂tba) and barbituric acid (H₂ba) in the aqueous solution to yield salt CfH₂(Htba)·3H₂O ( 1 ), salt cocrystal CfH₂(Hba)(H₂ba)·3H₂O ( 2 ), and salt CfH₂(Hba)·H₂O ( 3 ). The compounds are structurally characterized by the X‐ray single‐crystal diffraction. The numerous intermolecular hydrogen bonds N–H?O and O–H?O formed by water molecules, Htba^?/Hba^? and CfH₂⁺ ions, and H₂ba molecules stabilize the crystal structures of 1 to 3 . Hydrogen bonds form a 2D plane network in the salts of 1 and 3 and a 3D network in the salt cocrystal of 2 . There are different π‐π interactions in 1 to 3 . The compounds have been characterized by powder X‐ray diffraction, thermogravimetry/differential scanning calorimetry, and Fourier transform infrared spectroscopy. The compounds dehydration ends at 130°C to 150°C, and their oxidative decomposition is observed in the range of 250°C to 275°C.     

The role of guaiacyl moiety in free radical scavenging by 3,5-dihydroxy-4-methoxybenzyl alcohol: thermodynamics of 3H+/3e− mechanisms

ABSTRACT

Participation of guaiacyl moiety of 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA) in inactivation of free radicals was investigated using the DFT method. The thermodynamics of triple (3H⁺/3e^?) free radical scavenging mechanisms was investigated. The Gibbs free energies of reactions of inactivation of selected 10 free radicals indicate DHMBA as a potent scavenger. Obtained results allow us to suggest that the contribution of guaiacyl moiety to antioxidant activity of phenolic compounds should be taken into account, what has been scarcely considered until now.     

Effect of substituents and conjugated chain length on the UV spectra of α,ω‐di‐substituted phenyl polyenes

A series of α,ω‐di‐substituted phenyl polyenes, p‐X–Ph(CH = CH)_nPh–p‐Y (n = 1, 2, or 3) were synthesized, and their ultraviolet (UV) absorption maximum wavelength were determined. The correlation between molecular structure and the maximum wavelength energy (wavenumber/cm^?1) was carried out. The results show that the maximum wavelength energy of the title compounds is mainly affected by both substituent excited‐state parameters and maximum wavelength energy of the parent molecule. However, the two influence factors are not independent, and the action of substituent is governed by the parent molecular absorption energy. In the case of the compounds containing NO₂ or NH₂ groups, the influence of interaction of polarity parameters on the maximum wavelength energy must also be considered. In addition, the exploration was also made for the quantifying correlation of UV absorption maximum wavelength energy with the conjugated polarizability potential CPP replacing the parent molecular absorption energy. And the results indicate that the equation with CPP parameters is more accurate and convenient. Copyright © 2013 John Wiley & Sons, Ltd.     

Solvent effects on guanidinium‐anion interactions and the problem of guanidinium Y‐aromaticity

We have calculated the complexes formed by guanidine/guanidinium and HCl/Cl^?, HNO₃/NO₃^? and H₂SO₄/HSO₄^? both in the gas and aqueous Polarizable Continuum Model (PCM) phase to understand the effect that solvation has on their interaction energies. In the gas phase, the cation–anion complexes are much more stable than the rest; however, when PCM‐water is considered, this energetic difference is not as large due to the extra stabilization that the ions suffer when in aqueous solution. All the complexes were analyzed in terms of their AIM and NBO properties. In all cases, water solvation seems to “dampen” those properties observed in the gas phase. The values of Nucleus Independent Chemical Shift (NICS)(1) and NICS(2) indicate a huge influence of the proximity of the carbon atom for short distances; thus, the 3D NICS values on the van der Waal isosurfaces have been used to evaluate the possible Y‐aromaticity of the guanidinium system. The isosurface in this system is more similar to cyclohexane than to benzene as indication of poor aromaticity. Copyright © 2013 John Wiley & Sons, Ltd.     

Vertically aligned α-MnO<Subscript>2</Subscript> nanosheets on carbon nanotubes as cathodic materials for aqueous rechargeable magnesium ion battery

In this work, vertically aligned α-MnO₂ nanosheets on carbon nanotubes are synthesized simply by a solution process and the electrochemical performance as host materials of magnesium ion is tested in aqueous solution. Cyclic voltammetry analysis confirms the enhanced electrochemical activity of carbon nanotube-supported samples. Moreover, carbon nanotubes skeleton could reduce the charge transfer resistant of the cathode materials, which is confirmed by electrochemical impedance spectroscopy. Furthermore, when tested as magnesium ion batteries cathodic electrode, the α-MnO₂/carbon nanotube sample registers a prominent discharge capacity of 144.6 mAh g^?1 at current density of 0.5 A g^?1, which is higher than the discharge capacity of α-MnO₂ (87.5 mAh g^?1) due to the synergistic effect of insertion/deinsertion reaction and physical adsorption/desorption process. After the 1000th cycle, a remarkable discharge capacity of 48.3 mAh g^?1 is collected for α-MnO₂/carbon nanotube at current density of 10 A g^?1, which is 85% of the original. It is found that the carbon skeleton not only improved the capacity but also enhanced the cycling performance of the α-MnO₂ electrode significantly. Therefore, α-MnO₂/carbon nanotube is a very promising candidate for further application in environmentally benign magnesium ion batteries.     

Does gold cluster promote or scavenge radicals? A controversy at DFT

Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au₃ cluster on RO^? vs its impacts on RO–H bond dissociation enthalpy, at B3LYP/ LACVP+* level (R═H, methyl, ethyl, n‐propyl, i‐propyl, n‐butyl, t‐butyl, and phenyl). In the presence of Au₃ cluster, bond dissociation enthalpy of O–H bond and the spin density at the RO^? oxygen are reduced dramatically. These are clear evidences for both the Au₃ facilitation of the RO–H bond breakage and its scavenging of RO^? radical. Since O–Au anchoring bond is responsible for the interaction of Au₃ cluster and ROH (or RO^?), its nature was interpreted by means of the quantum theory of atoms in molecules and the natural bond orbital. The results indicate that O–Au bond is stronger and has more covalent character in RO^?–Au₃ than in ROH–Au₃. The interaction of Au₃ cluster with RO^? is 1.5 to 3 times more than that with ROH. As a result, gold cluster scavenging property appears more prominent than its free radical initiation activity.     

A high level computational study of the CH4/CF4 dimer: how does it compare with the CH4/CH4 and CF4/CF4 dimers?

The interaction within the methane–methane (CH₄/CH₄), perfluoromethane–perfluoromethane (CF₄/CF₄) methane–perfluoromethane dimers (CH₄/CF₄) was calculated using the Hartree–Fock (HF) method, multiple orders of Møller–Plesset perturbation theory [MP2, MP3, MP4(DQ), MP4(SDQ), MP4(SDTQ)], and coupled cluster theory [CCSD, CCSD(T)], as well as the PW91, B97D, and M06-2X density functional theory (DFT) functionals. The basis sets of Dunning and coworkers (aug-cc-pVxZ, x?=?D, T, Q), Krishnan and coworkers [6-311++G(d,p), 6-311++G(2d,2p)], and Tsuzuki and coworkers [aug(df, pd)-6-311G(d,p)] were used. Basis set superposition error (BSSE) was corrected via the counterpoise method in all cases. Interaction energies obtained with the MP2 method do not fit with the experimental finding that the methane–perfluoromethane system phase separates at 94.5?K. It was not until the CCSD(T) method was considered that the interaction energy of the methane–perfluoromethane dimer (?0.69?kcal?mol^?1) was found to be intermediate between the methane (?0.51?kcal?mol^?1) and perfluoromethane (?0.78?kcal?mol^?1) dimers. This suggests that a perfluoromethane molecule interacts preferentially with another perfluoromethane (by about 0.09?kcal?mol^?1) than with a methane molecule. At temperatures much lower than the CH₄/CF₄ critical solution temperature of 94.5?K, this energy difference becomes significant and leads perfluoromethane molecules to associate with themselves, forming a phase separation. The DFT functionals yielded erratic results for the three dimers. Further development of DFT is needed in order to model dispersion interactions in hydrocarbon/perfluorocarbon systems.     

Combined XPS and SIMS study of amino acid overlayers

Factors influencing the SIMS fragmentation patterns are studied for three simple amino acids-glycine, α-alanine, and serine-deposited onto Ag substrates from aqueous solution. Secondary ion emissions are measured for 1 keV Ar⁺ ions incident at 70° from sample normal as a function of substrate preparation and solution concentration. Studies by XPS and X-ray induced AES prior to SIMS analysis show that the amino acids adsorb in a film on the Ag surface and that the film thickness increases with solution concentration. In addition, considerable amounts of amino acid can be deposited on the surface from a water film retained during extraction from a concentrated solution. On acid etched samples, positive ion fragments of mass AgM, Ag(M ? 45), Ag, M + 1, and M ? 45 are observed, where M is the molecular, weight of the parent amino acid. With the exception of the (M + 1)⁺ fragment, these peak intensities behaved similarly for the different surface concentrations. When the adsorbed film grows too thick, the positive molecular ion emissions drop considerably; this substantiates the need for proximity between the Ag substrate and the amino acid molecule.     

Photocatalytic properties of zinc oxide nanorods grown by different methods

A comparison of photocatalytic properties of ZnO nanostructures fabricated by different methods was carried out. The photocatalytic properties of as grown and Ar-ion-treated ZnO materials were tested using photocatalytic degradation of an aqueous solution of methyl orange dye serving as a model water contaminant. The reaction rate constants of methyl orange photodegradation for untreated ZnO nanorods grown by the method of gas-transport reactions and hydrothermal method were equal to 5.3 × 10^?5 and 3.7 × 10^?4 s^?1, respectively, whereas for the case of the Ar-ion-treated samples they reached 1.85 × 10^?4 and 5.9 × 10^?4 s^?1, respectively. Based on the analysis of the photoluminescence spectra, it is assumed that the difference in photocatalytic activity is connected with different type of defects predominant on the surfaces of ZnO nanorods grown by the hydrothermal and gas-transport reactions methods. The experimental results show that ZnO nanostructures grown by the hydrothermal method would be promising for producing efficient catalysts.