Theoretical Study of the Trapping of the OOH Radical by Coenzyme Q

Endogenous chemicals guard health through inhibiting ferroptotic cell death

Ferroptosis is a new form of regulated cell death caused by iron-dependent accumulation of lethal polyunsaturated phospholipids peroxidation. It has received considerable attention owing to its putative involvement in a wide range of pathophysiological processes such as organ injury, cardiac ischemia/reperfusion, degenerative disease and its prevalence in plants, invertebrates, yeasts, bacteria, and archaea. To counter ferroptosis, living organisms have evolved a myriad of intrinsic efficient defense systems, such as cyst(e)ine-glutathione-glutathione peroxidase 4 system (cyst(e)ine-GPX4 system), guanosine triphosphate cyclohydrolase 1/tetrahydrobiopterin (BH4) system (GCH1/BH4 system), ferroptosis suppressor protein 1/coenzyme Q10 system (FSP1/CoQ10 system), and so forth. Among these, GPX4 serves as the only enzymatic protection system through the reduction of lipid hydroperoxides, while other defense systems ultimately rely on small compounds to scavenge lipid radicals and prevent ferroptotic cell death. In this article, we systematically summarize the chemical biology of lipid radical trapping process by endogenous chemicals, such as coenzyme Q10 (CoQ10), BH4, hydropersulfides, vitamin K, vitamin E, 7-dehydrocholesterol, with the aim of guiding the discovery of novel ferroptosis inhibitors.

Dissociations of free radicals to generate protons, electrophiles or nucleophiles: role in DNA strand breaks

The concept behind the research described in this article was that of marrying the 'soft' methods of radical generation with the effectiveness and flexibility of nucleophile/electrophile synthetic procedures. Classic studies with pulse radiolysis and laser flash photolysis had shown that free radicals could be more acidic than their closed shell counterparts. QM computations harmonised with this and helped to define which radical centres and which structural types were most effective. Radicals based on the sulfonic acid moiety and on the Meldrum's acid moiety (2,2-dimethyl-1,3-dioxane-4,6-dione) were found to be extreme examples in the superacid class. The ethyne unit could be used as a very effective spacer between the radical centre and the site of proton donation. The key factor in promoting acidity was understood to be the thermodynamic stabilisation of the conjugate anion-radicals released on deprotonation. Solvation played a key part in promoting this and theoretical microhydration studies provided notable support. A corollary was that heterolytic dissociations of free radicals to yield either electrophiles or nucleophiles were also enhanced relative to non-radical models. The most effective radical types for spontaneous releases of both these types of reagents were identified. Ethyne units were again effective as spacers. The enhancement of release of phosphate anions by adjacent radical centres was an important special case. Reactive oxygen species and also diradicals from endiyne antibiotics generate C4'-deoxyribose radicals from nucleotides. Radicals of these types spontaneously release phosphate and triphosphate and this is a contributor to DNA and RNA strand breaks.

Targeted Antioxidants in Exercise-Induced Mitochondrial Oxidative Stress: Emphasis on DNA Damage

Exercise simultaneously incites beneficial (e.g., signal) and harming (e.g., damage to macromolecules) effects, likely through the generation of reactive oxygen and nitrogen species (RONS) and downstream changes to redox homeostasis. Given the link between nuclear DNA damage and human longevity/pathology, research attempting to modulate DNA damage and restore redox homeostasis through non-selective pleiotropic antioxidants has yielded mixed results. Furthermore, until recently the role of oxidative modifications to mitochondrial DNA (mtDNA) in the context of exercising humans has largely been ignored. The development of antioxidant compounds which specifically target the mitochondria has unveiled a number of exciting avenues of exploration which allow for more precise discernment of the pathways involved with the generation of RONS and mitochondrial oxidative stress. Thus, the primary function of this review, and indeed its novel feature, is to highlight the potential roles of mitochondria-targeted antioxidants on perturbations to mitochondrial oxidative stress and the implications for exercise, with special focus on mtDNA damage. A brief synopsis of the current literature addressing the sources of mitochondrial superoxide and hydrogen peroxide, and available mitochondria-targeted antioxidants is also discussed.

Microhydration and the Enhanced Acidity of Free Radicals

Recent theoretical research employing a continuum solvent model predicted that radical centers would enhance the acidity (RED-shift) of certain proton-donor molecules. Microhydration studies employing a DFT method are reported here with the aim of establishing the effect of the solvent micro-structure on the acidity of radicals with and without RED-shifts. Microhydration cluster structures were obtained for carboxyl, carboxy-ethynyl, carboxy-methyl, and hydroperoxyl radicals. The numbers of water molecules needed to induce spontaneous ionization were determined. The hydration clusters formed primarily round the CO₂ units of the carboxylate-containing radicals. Only 4 or 5 water molecules were needed to induce ionization of carboxyl and carboxy-ethynyl radicals, thus corroborating their large RED-shifts.

Density functional study of S(N) 2 substitution reactions for CH(3) Cl + CX(1) X(2•-) (X(1) X(2) = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II)

A systematic investigation on the S(N) 2 displacement reactions of nine carbene radical anions toward the substrate CH(3) Cl has been theoretically carried out using the popular density functional theory functional BHandHLYP level with different basis sets 6-31+G (d, p)/relativistic effective core potential (RECP), 6-311++G (d, p)/RECP, and aug-cc-pVTZ/RECP. The studied models are CX(1) X(2•-) + CH(3) Cl → X(2) X(1) CH(3) C(•) + Cl(-) , with CX(1) X(2•-) = CH(2) (•-) , CHF(•-) , CHCl(•-) , CHBr(•-) , CHI(•-) , CF(2) (•-) , CCl(2) (•-) , CBr(2) (•-) , and CI(2) (•-) . The main results are proposed as follows: (a) Based on natural bond orbital (NBO), proton affinity (PA), and ionization energy (IE) analysis, reactant CH(2) (•-) should be a strongest base among the anion-containing species (CX(1) X(2•-) ) and so more favorable nucleophile. (b) Regardless of frontside attacking pathway or backside one, the S(N) 2 reaction starts at an identical precomplex whose formation with no barrier. (c) The back-S(N) 2 pathway is much more preferred than the front-S(N) 2 one in terms of the energy gaps [ΔE cent≠(front)-ΔE cent≠(back)], steric demand, NBO population analysis. Thus, the back-S(N) 2 reaction was discussed in detail. On the one hand, based on the energy barriers (ΔE cent≠ and ΔE ovr≠) analysis, we have strongly affirmed that the stabilization of back attacking transition states (b-TSs) presents increase in the order: b-TS-CI(2) < b-TS-CBr(2) < b-TS-CCl(2) < b-TS-CHI < b-TS-CHBr < b-TS-CHCl < b-TS-CF(2) < b-TS-CHF < b-TS-CH(2) . On the other hand, depended on discussions of the correlations of ΔE ovr≠ with influence factors (PA, IE, bond order, and ΔE def≠), we have explored how and to what extent they affect the reactions. Moreover, we have predicted that the less size of substitution (α-atom) required for the gas-phase reaction with α-nucleophile is related to the α-effect and estimated that the reaction with the stronger PA nucleophile, holding the lighter substituted atom, corresponds to the greater exothermicity given out from reactants to products.

Detailed Investigation of the OH Radical Quenching by Natural Antioxidant Caffeic Acid Studied by Quantum Mechanical Models

The effectiveness of naturally occurring antioxidant caffeic acid in the inactivation of the very damaging hydroxyl radical has been theoretically investigated by means of hybrid density functional theory. Three possible pathways by which caffeic acid may inactivate free radicals were analyzed: hydrogen abstraction from all available hydrogen atoms, hydroxyl radical addition to all carbon atoms in the molecule, and single electron transfer. The reaction paths were traced independently, and the respective thermal rate constants were calculated using variational transition-state theory including the contribution of tunneling. The more reactive sites in caffeic acid are the C4OH phenolic group and the C4 carbon atom, for the hydrogen abstraction and radical addition, respectively. The single electron transfer process seems to be thermodynamically unfavored, in both polar and nonpolar media. Both hydrogen abstraction and radical addition are very feasible, with a slight preference for the latter, with a rate constant of 7.29 × 10(10) M(-1) s(-1) at 300 K. Tunnel effects are found to be quite unimportant in both cases. Results indicate caffeic acid as a potent natural antioxidant in trapping and scavenging hydroxyl radicals.

Scales of oxidation potentials, pK(a), and BDE of various hydroquinones and catechols in DMSO

The one-electron oxidation potentials [E(ox)(NHE)(H(2)Q)], pK(a) (pK(a1) and pK(a2)) values, and bond dissociation energies (BDE(1) and BDE(2)) of 118 important p- and o-dihydroquinones in DMSO were systematically predicted for the first time by using DFT method and the PCM cluster continuum model. The calculated results agree well with the available experimental determinations. The study shows that all the five thermodynamic parameters correlate well with the Hammett substituent parameters σ(p) (for p-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.66Σσ(p) + 0.54, pK(a1) = -5.69Σσ(p) + 16.54, pK(a2) = -5.19Σσ(p) + 23.91, BDE(1) = 3.43Σσ(p) + 82.29, BDE(2) = 4.64Σσ(p) + 67.70 and for o-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.85Σσ(p) + 0.46, pK(a1) = -5.53Σσ(p) + 13.28, pK(a2) = -5.24Σσ(p) + 26.70, BDE(1) = 3.54Σσ(p) + 82.08, BDE(2) = 3.82Σσ(p) + 75.93), which hints that we can get these thermodynamic parameters as long as the structure of the hydroquinones were known. The comparisons of the calculated five thermodynamic parameters between p-hydroquinones and o-hydroquinones and the number of the phenyl ring effects on these thermodynamic parameters were also studied. At last, intramolecular hydrogen bond energies in hydroquinones at neutral, radical cation, radical, anion different state were systematically calculated and analyzed. Combined with the papers published in our group before, we will have a systematic thermodynamic picture of the transfer details between different kinds of quinones and corresponding hydroquinones, which strongly promote the fast development of the understanding and applications of quinones.

The inactivation of lipid peroxide radical by quercetin. A theoretical insight

The effectiveness of naturally occurring antioxidant quercetin in the inactivation of the damaging lipid peroxide radical was investigated by means of hybrid density functional based approach, using the direct dynamics method, where the thermal rate constants were calculated using variational transition-state theory with multidimensional tunneling. H-atom abstraction in quercetin by CH(3)OO peroxide occurs preferentially at the 4'OH phenolic site, from both kinetic and thermodynamic points of view. In principle, the narrowness of the obtained adiabatic potential-energy profile makes the occurrence of a significant tunnelling contribution possible. In fact, this contribution enhances the value of the computed rate constant at 300 K from 1.94 x 10(1) to 9.63 x 10(3) M(-1) s(-1) indicating that quercetin is a potent natural antioxidant in trapping and scavenging free radicals.

Effects of quinones on free-radical processes of oxidation and fragmentation of hydroxyl-containing organic compounds

The coenzymes Q and Vitamin K(3), as well as their synthetic analogues, have been found to inhibit free-radical processes of fragmentation of hydroxyl-containing organic compounds and oxidation of the latter by molecular oxygen. It has been established that the observed effects are due to the ability of quinones to oxidize the alpha-hydroxyl-containing carbon-centered radicals formed from the starting compounds.

Concurrent Cyclopropanation by Carbenes and Carbanions? A Density Functional Theory Study on the Reaction Pathways

The mechanisms for the addition reactions of phenylhalocarbenes and phenyldihalomethide carbanions with acrylonitrile (ACN) and trimethylethylene (TME) have been investigated using an ab initio BH and HLYP/6-31G (d, p) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (THF). These model calculations show that for the addition of phenylhalocarbenes, a TME species may readily undergo addition reactions with carbenes while ACN has a high-energy barrier to overcome. It was also found that phenyldihalomethide carbanions do not readily add to the electron-rich TME. The cyclopropane yields only appear to occur via addition of PhCBr to TME. However, the cyclopropanation proceeds not only via slow addition of phenylhalocarbenes to ACN but also forms through the stepwise reaction of phenyldihalomethide carbanions with ACN. Our calculation results are in good agreement with experimental observations (Moss, R.A.; Tian, J.-Z. J. Am. Chem. Soc. 2005, 127, 8960) that indicate that the cyclopropanation of phenylhalocarbenes and phenyldihalomethide carbanions with ACN are concurrent in THF.

Tunneling in Green Tea: Understanding the Antioxidant Activity of Catechol-Containing Compounds. A Variational Transition-State Theory Study

The catechol functionality present in the catechins is responsible for the protective effects exerted by green tea against a wide range of human diseases. High-level electronic structure calculations and canonical variational transition-state theory including multidimensional tunneling corrections have allowed us to understand the key factors of the antioxidant effectiveness of the catechol group. This catechol group forms two hydrogen bonds with the two oxygen atoms of the lipid peroxyl radical, leading to a very compact reactant complex. This fact produces an extremely narrow adiabatic potential-energy profile corresponding to the hydrogen abstraction by the peroxyl radical, which makes it possible for a huge tunneling contribution to take place. So, quantum-mechanical tunneling highly increases the corresponding rate constant value, in such a way that catechins become able to trap the lipid peroxyl radicals in a dominant competition with the very damaging free-radical chain-lipid peroxidation reaction.

On the Gas Phase Hydrogen Bond Complexes between Formic Acid and Hydroperoxyl Radical. A Theoretical Study

We present a systematic study on the gas-phase hydrogen-bonded complexes formed between formic acid and hydroperoxyl radical, which has been carried out by using B3LYP and CCSD(T) theoretical approaches in connection with the 6-311+G(2df,2p) basis set. For all complexes we have employed the AIM theory by Bader and the NBO partition scheme by Weinhold to analyze the bonding features. We have found 17 stationary points, and 11 of them present a cyclic structure. Their computed stabilities vary from 0.3 to 11.3 kcal/mol, depending on several factors, such as involvement in the hydrogen bond interaction, the geometrical constraints, and the possible concurrence of further effects such as resonance-assisted hydrogen bonds or inductive effects. In addition, three stationary points correspond to transition structures involving a double proton-transfer process whose features are also analyzed.

Trapping of the OH radical by alpha-tocopherol: a theoretical study

The antioxidant activity of alpha-tocopherol against the damaging hydroxyl radical was analyzed theoretically by hybrid density functional theory, following the direct dynamics method, where the thermal rate constants were calculated using variational transition-state theory with multidimensional tunneling. We found that the OH radical is only slightly or not at all selective, attacking by different mechanisms at several positions of the alpha-tocopherol molecule, giving competitive reactions. The most favorable pathways are the hydrogen abstraction reaction from the phenolic hydrogen and the electrophilic addition onto the aromatic ring. We propose a final rate constant, the sum of the competitive hydrogen abstraction and addition reactions, > or =2.7 x 10(8) M(-1) s(-1) at 298 K, where the hydrogen abstraction reaction represents only 20% of the total OH radical reaction. This result indicates that, molecule by molecule, in an apolar environment, alpha-tocopherol is less effective than coenzyme Q (which presents a rate constant of 6.2 x 10(10) M(-1) s(-1) at 298 K) as a scavenger of OH radicals. It was also found that both mechanisms are not direct but pass through intermediates in the entry channel, with little or no influence on the dynamics of the reactions. The hydrogen abstraction reaction also presents another intermediate in the exit channel, which may have a significant role in preventing the pro-oxidant effects of alpha-tocopherol, although less important than with free radicals other than OH.

Synthesis of Cyclic Peroxides by Chemo- and Regioselective Peroxidation of Dienes with Co(II)/O2/Et3SiH

In the competitive peroxidation of mixtures of two alkenes with Co(II)/O(2)/Et(3)SiH, it was found that the relative reactivities of the alkene substrates are influenced by three major factors:. (1) relative stability of the intermediate carbon-centered radical formed by the reaction of the alkene with HCo(III) complex, (2) steric effects around the C=C double bond, and (3) electronic factors associated with the C=C double bond. Consistent with results from simple alkenes, the chemo- and regioselective peroxidation of dienes was also realized. Depending on the diene structure, the product included not only the expected acyclic unsaturated triethylsilyl peroxides but also 1,2-dioxolane and 1,2-dioxane derivatives via intramolecular cyclization of the unsaturated peroxy radical intermediates.