How Well Can New-Generation Density Functionals Describe the Energetics of Bond-Dissociation Reactions Producing Radicals?

Improved photocatalytic hydrogen evolution driven by chloro(terpyridine)platinum(ii) derivatives tethered to a single pendant viologen acceptor

Chloro(terpyridine)platinum(ii) derivatives tethered to a single pendant viologen acceptor exhibit drastically improved turnover number in the photocatalytic H₂ evolution reaction from water.

Computational-aided design of melatonin analogues with outstanding multifunctional antioxidant capacity

The IIcD melatonin-analogue was identified as the most promising multifunctional antioxidant from a set of 19, and better for that purpose than the parent molecule and Trolox.

Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study

The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter-molecular non-covalent interactions.

Assessing the Protective Activity of a Recently Discovered Phenolic Compound against Oxidative Stress Using Computational Chemistry

The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times and 4 orders of magnitude better than Trolox for that purpose in lipid and aqueous media, respectively. It was also found to react faster with HOO(•) than other known antioxidants such as resveratrol and ascorbic acid. DHMBA is also predicted to be able to sequester Cu(II) ions, consequently inhibiting the OS induced by Cu(II)-ascorbate mixtures and downgrading the (•)OH production via the Haber-Weiss reaction. However, it is proposed that DHMBA is more efficient as a primary antioxidant (free radical scavenger), than as a secondary antioxidant (metal ion chelator). In addition, it was found that DHMBA can be efficiently regenerated in aqueous solution, at physiological pH. Such regeneration is expected to contribute to increase the antioxidant protection exerted by DHMBA. These results suggest that probably synthetic routes for this compound should be pursued, because albeit its abundance in nature is rather low, its antioxidant activity is exceptional.

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training data for any of the functionals, in particular 164 main-group energetic data in 7 databases, 39 bond lengths, 38 vibrational frequencies, and 9 multiplicity-changing electronic transition energies. These tests include a variety of new challenges for complex systems, including large-molecule atomization energies, organic isomerization energies, interaction energies in uracil trimers, and bond distances in crowded molecules (in particular, cyclophanes). The M08-HX functional performs slightly better than M08-SO and M06-2X on average, significantly better than M05-2X, and much better than B3LYP for a combination of main-group thermochemistry, kinetics, noncovalent interactions, and electronic spectroscopy. More important than the slight improvement in accuracy afforded by M08-HX is the conformation that the optimization procedure works well for data outside the training set. Problems for which the accuracy is especially improved by the new M08-HX functional include large-molecule atomization energies, noncovalent interaction energies, conformational energies in aromatic peptides, barrier heights, multiplicity-changing excitation energies, and bond lengths in crowded molecules.

Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry

We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S-S bond cleavages with some minor C-S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S-S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C-S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S-S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S-S bond (SH2). The activation energy for this process is substantially lower by ∼9-10 kcal mol-1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C-S or S-S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.

Adrenaline and noradrenaline: protectors against oxidative stress or molecular targets?

Density functional theory was used to investigate the potential role of neurotransmitters adrenaline and noradrenaline regarding oxidative stress. It is predicted that they can be efficient as free radical scavengers both in lipid and aqueous media, with the main reaction mechanism being the hydrogen transfer and the sequential proton loss electron transfer, respectively. Despite the polarity of the environment, adrenaline and noradrenaline react with (•)OOH faster than Trolox, which suggests that they are better peroxyl radical scavengers than the reference compound. Both catecholamines are also proposed to be capable of efficiently inhibiting the oxidative stress induced by copper(II)-ascorbate mixtures, and the (•)OH production via Haber-Weiss reaction, albeit the effects on the later are only partial. They exert such beneficial effects by sequestering Cu(II) ions. In summary, these catecholamines can be capable of reducing oxidative stress, by scavenging free radicals and by sequestering metal ions. However, at the same time they might lose their functions in the process due to the associated structural modifications. Consequently, adrenaline and noradrenaline can be considered as both protectors and molecular targets of oxidative stress. Fortunately, under the proper conditions, both catecholamines can be regenerated to their original form so their functions are restored.

Synthesis and properties of the strained alkene perfluorobicyclo[2.2.0]hex-1(4)-ene

The title fluoroalkene has been generated by dehalogenation of dibromide and diiodide precursors and trapped in situ. retro-Diels-Alder reaction of its adduct with N-benzylpyrrole has made the alkene available in high yield and purity. In sharp contrast to its extremely labile hydrocarbon counterpart, the fluoroalkene is very stable yet highly reactive. Its characterization includes its electron affinity, photoelectron spectrum, and the previously reported structure determination by electron diffraction.

A tricarboxylated PtCl(terpyridine) derivative exhibiting pH-dependent photocatalytic activity for H2 evolution from water

A ‘negatively charged’ PtCl(terpyridine) derivative was found to be the first example of a Pt(ii)-based molecular photocatalyst capable of driving H₂ evolution coupled with a PCET process at the ligand geometry.

Site reactivity in the free radicals induced damage to leucine residues: a theoretical study

The reactions of leucine with free radicals are kinetically controlled and are faster in hydrophilic than in hydrophobic media.

Photoelectron spectroscopy and theoretical studies of anion–π interactions: binding strength and anion specificity

Direct experimental measurements of non-covalent interactions between various anions and a π-electron-deficient cavity show significant binding strength and anion specificity.

A computational study on Lewis acid-catalyzed diastereoselective acyclic radical allylation reactions with unusual selectivity dependence on temperature and epimer precursor

In stereoselective radical reactions, it is accepted that the configuration of the radical precursor has no impact on the levels of stereoinduction, as a prochiral radical intermediate is planar, with two identical faces, independently of its origin. However, Sibi and Rheault (J. Am. Chem. Soc. 2000, 122, 8873-8879) remarkably obtained different selectivities in the trapping of radicals originated from two epimeric bromides, catalyzed by chelating Lewis acids. The selectivity rationalization was made on the basis of different conformational properties of each epimer. However, in this paper we show that the two epimers have similar conformational properties, which implies that the literature proposal is unable to explain the experimental results. We propose an alternative mechanism, in which the final selectivity is dependent on different reaction rates for radical formation from each epimer. By introducing a different perspective of the reaction mechanism, our model also allows the rationalization of different chemical yields obtained from each epimer, a result not rationalized by the previous model. Adaptation to other radical systems, under different reaction conditions, is also possible.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Lipoic acid and dihydrolipoic acid. A comprehensive theoretical study of their antioxidant activity supported by available experimental kinetic data

The free radical scavenging activity of lipoic acid (LA) and dihydrolipoic acid (DHLA) has been studied in nonpolar and aqueous solutions, using the density functional theory and several oxygen centered radicals. It was found that lipoic acid is capable of scavenging only very reactive radicals, while the dehydrogenated form is an excellent scavenger via a hydrogen transfer mechanism. The environment plays an important role in the free radical scavenging activity of DHLA because in water it is deprotonated, and this enhances its activity. In particular, the reaction rate constant of DHLA in water with an HOO(•) radical is close to the diffusion limit. This has been explained on the basis of the strong H-bonding interactions found in the transition state, which involve the carboxylate moiety, and it might have implications for other biological systems in which this group is present.

Palladium hydride promoted stereoselective isomerization of unactivated di(exo)methylenes to endocyclic dienes

The exomethylenes of 2,6-disubstituted bicyclo[3.3.1]nonan-9-ones 2 are readily isomerized over a palladium catalyst under an atmosphere of hydrogen to predominantly form the isomer 3 with C2 symmetry with very little formation of the analogous product with C(s) symmetry. A hydrogen source is essential to effect the rearrangement.

The chemistry of bowtiene (tricyclo[5.3.0.02,6]decapentaene): a computational study

Reactions of bowtiene (tricyclo[5.3.0.02,6]decapentaene, cyclobuta[1,2:3,4]dicyclopentene, bicyclopentadienylene, a tricyclic analogue of [10]annulene), in the sphere of unimolecular decomposition and dimerization were studied computationally to gauge its stability and reactivity, which are relevant to its feasability as a synthetic goal. The intuitively likeliest rearrangement mode to give species of lower energy begins with rearrangement to the 1,5-dehydronaphthalene diradical; this was calculated to have a barrier of approximately 220 kJ mol−1, too high for reaction at room temperature. Nevertheless, the energetics of rearrangement of the 1,5-diradical to the monocyclic 1,6-didehydro[10]annulene, a species of interest regarding its relationship to bowtiene and the diradical, were studied. The energy of bowtiene was compared with that of several other tricyclic 10π C10H6cyclic polyenes.

Ellagic acid: an unusually versatile protector against oxidative stress

Several aspects related to the antioxidant activity of ellagic acid were investigated using the density functional theory. It was found that this compound is unusually versatile for protecting against the toxic effects caused by oxidative stress. Ellagic acid, in aqueous solution at physiological pH, is able of deactivating a wide variety of free radicals, which is a desirable capability since in biological systems, these species are diverse. Under such conditions, the ellagic acid anion is proposed as the key species for its protective effects. It is predicted to be efficiently and continuously regenerated after scavenging two free radicals per cycle. This is an advantageous and unusual behavior that contributes to increase its antioxidant activity at low concentrations. In addition, the ellagic acid metabolites are also capable of efficiently scavenging a wide variety of free radicals. Accordingly, it is proposed that the ellagic acid efficiency for that purpose is not reduced after being metabolized. On the contrary, it provides continuous protection against oxidative stress through a free radical scavenging cascade. This is an uncommon and beneficial behavior, which makes ellagic acid particularly valuable to that purpose. After deprotonation, ellagic acid is also capable of chelating copper, in a concentration dependent way, decreasing the free radical production. In summary, ellagic acid is proposed to be an efficient multiple-function protector against oxidative stress.

Intramolecular Diels-Alder reactions of cycloalkenones: stereoselectivity, Lewis acid acceleration, and halogen substituent effects

The intramolecular Diels-Alder reactions of cycloalkenones and terminal dienes occur with high endo stereoselectivity, both thermally and under Lewis-acidic conditions. Through computations, we show that steric repulsion and tether conformation govern the selectivity of the reaction, and incorporation of either BF3 or α-halogenation increases the rate of cycloaddition. With a longer tether, isomerization from a terminal diene to the more stable internal diene results in a more facile cycloaddition.

Ab initio calculations on the 1O2 quenching mechanism by trans-resveratrol

Computational exploration of possible reaction mechanisms of trans-resveratrol with singlet molecular oxygen shows benzaldehydes as the most probable products.

Antioxidant activity of fraxetin and its regeneration in aqueous media. A density functional theory study

Fraxetin is an excellent and versatile antioxidant in aqueous media. In addition it regenerates, scavenging two radical equivalents per cycle.