Binding of Reactive Oxygen Species at FeS Cubane Clusters

Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron?sulfur proteins are particularly oxygen‐sensitive and their inorganic cofactors frequently undergo ROS‐induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe₄S₄] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O₂ to singlet O₂ is required for binding to valence‐saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H₂O₂ as attacking agents. The thermodynamic picture of ROS binding to iron?sulfur clusters established here can serve as a starting point for studying reactivity‐modulating effects of the cluster‐embedding protein environment on ROS‐induced decomposition of iron?sulfur proteins.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Characterization of Mononuclear Non‐heme Iron(III)‐Superoxo Complex with a Five‐Azole Ligand Set

Reaction of O₂ with a high‐spin mononuclear iron(II) complex supported by a five‐azole donor set yields the corresponding mononuclear non‐heme iron(III)–superoxo species, which was characterized by UV/Vis spectroscopy and resonance Raman spectroscopy. ¹H NMR analysis reveals diamagnetic nature of the superoxo complex arising from antiferromagnetic coupling between the spins on the low‐spin iron(III) and superoxide. This superoxo species reacts with H‐atom donating reagents to give a low‐spin iron(III)–hydroperoxo species showing characteristic UV/Vis, resonance Raman, and EPR spectra.     

On the Role of the Electronic Structure of the Heteronuclear Oxide Cluster [Ga2Mg2O5].+ in the Thermal Activation of Methane and Ethane: An Unusual Doping Effect

The reactivity of the heteronuclear oxide cluster [Ga₂Mg₂O₅]^.+, bearing an unpaired electron at a bridging oxygen atom (O_b^.?), towards methane and ethane has been studied using Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS). Hydrogen‐atom transfer (HAT) from both methane and ethane to the cluster ion is identified experimentally. The reaction mechanisms of these reactions are elucidated by state‐of‐the‐art quantum chemical calculations. The roles of spin density and charge distributions in HAT processes, as revealed by theory, not only deepen our mechanistic understanding of C? H bond activation but also provide important guidance for the rational design of catalysts by pointing to the particular role of doping effects.     

Protein environmental effects on iron‐sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

The structural properties and reactivity of iron‐sulfur proteins are greatly affected by interactions between the prosthetic groups and the surrounding amino acid residues. Thus, quantum chemical investigations of the structure and properties of protein‐bound iron‐sulfur clusters can be severely limited by truncation of computational models. The aim of this study was to identify, a priori, significant interactions that must be included in a quantum chemical model. Using the [2Fe‐2S] accessory cluster of the FeFe‐hydrogenase as a demonstrative example with rich electronic structural features, the electrostatic and covalent effects of the surrounding side chains, charged groups, and backbone moieties were systematically mapped through density functional theoretical calculations. Electron affinities, spin density differences, and delocalization indexes from the quantum theory of atoms in molecules were used to evaluate the importance of each interaction. Case studies for hydrogen bonding and charged side‐chain interactions were used to develop selection rules regarding the significance of a given protein environmental effect. A set of general rules is proposed for constructing quantum chemical models for iron‐sulfur active sites that capture all significant interactions from the protein environment. This methodology was applied to our previously used models in galactose oxidase and the 6Fe‐cluster of FeFe‐hydrogenase. © 2016 Wiley Periodicals, Inc.     

Inactivation of [Fe?Fe]‐hydrogenase by O2. Thermodynamics and frontier molecular orbitals analyses

The oxidation of H‐cluster in gas phase, and in aqueous enzyme phase, has been investigated by means of quantum mechanics (QM) and combined quantum mechanics–molecular mechanics (QM/MM). Several potential reaction pathways (in the above‐mentioned chemical environments) have been studied, wherein only the aqueous enzyme phase has been found to lead to an inhibited hydroxylated cluster. Specifically, the inhibitory process occurs at the distal iron (Fe_d) of the catalytic H‐cluster (which isalso the atom involved in H₂ synthesis). The processes involved in the H‐cluster oxidative pathways are O₂ binding, e^? transfer, protonation, and H₂O removal. We found that oxygen binding is nonspontaneous in gas phase, and spontaneous for aqueous enzyme phase where both Fe atoms have oxidation state II; however, it is spontaneous for the partially oxidized and reduced clusters in both phases. Hence, in the protein environment the hydroxylated H‐cluster is obtained by means of completely exergonic reaction pathway starting with proton transfer. A unifying endeavor has been carried out for the purpose of understanding the thermodynamic results vis‐à‐vis several other performed electronic structural methods, such as frontier molecular orbitals (FMO), natural bond orbital partial charges (NBO), and H‐cluster geometrical analysis. An interesting result of the FMO examination (for gas phase) is that an e^? is transferred to LUMO_α rather than to SOMO_β, which is unexpected because SOMO_β usually resides in a lower energy rather than LUMO_α for open‐shell clusters. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin

Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B₁ and B₂ states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B₁ and B₂ states correspond to Fe…CO (with carbon atom closer to iron center of heme) and Fe…OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B₁ and B₂ is 13.1 cm^-1, which is in good agreement with experimental value of 11.5 cm^-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.     

Vibrational study on the cobalt binding mode of Carnosine

The Co(II)-l-Carnosine (Carnos) system was investigated at different pH and metal/ligand molar ratios by Raman and IR spectroscopy. Raman spectra present some marker bands yielding information on the ability of the Co(II)/Carnos system to bind molecular oxygen and to identify the metal co-ordination site of the imidazole ring (N_π or N_τ atom) of Carnos.The existence of different oxygenated species is greatly affected by pH and the structure of the predominant complexes depends on the available nitrogen atoms. Under basic conditions, binuclear complexes binding molecular oxygen are the predominant species and two forms (monobridged and dibridged) were identified by the Raman νO-O band (750-850 cm⁻¹).Decreasing pH to 7, the species present in the system are less able to bind oxygen. Hydrogen peroxide and a Co(III) chelate not binding O₂, were formed with a significant conversion of peroxo into superoxo complexes. A slight excess of Carnos does not enhance metal chelation.In slightly acidic conditions, the formation of H₂O₂ and superoxo species is more enhanced than at pH 7 and another Co(III) chelate is probably formed.     

A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants

The core histones, H2A, H2B, H3 and H4, undergo post‐translational modifications (PTMs) including lysine acetylation, methylation and ubiquitylation, arginine methylation and serine phosphorylation. Lysine residues may be mono‐, di‐ and trimethylated, the latter resulting in an addition of mass to the protein that differs from acetylation by only 0.03639 Da, but that can be distinguished either on high‐performance mass spectrometers with sufficient mass accuracy and mass resolution or via retention times. Here we describe the use of chemical derivatization to quantify methylated and acetylated histone isoforms by forming deuteroacetylated histone derivatives prior to tryptic digestion and bottom‐up liquid chromatography‐mass spectrometric analysis. The deuteroacetylation of unmodified or mono‐methylated lysine residues produces a chemically identical set of tryptic peptides when comparing the unmodified and modified versions of a protein, making it possible to directly quantify lysine acetylation. In this work, the deuteroacetylation technique is used to examine a single histone H3 peptide with methyl and acetyl modifications at different lysine residues and to quantify the relative abundance of each modification in different deacetylase and methylase knockout yeast strains. This application demonstrates the use of the deuteroacetylation technique to characterize modification ‘cross‐talk’ by correlating different PTMs on the same histone tail. Copyright © 2013 John Wiley & Sons, Ltd.     

Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Singlet Oxygen Formation during the Charging Process of an Aprotic Lithium–Oxygen Battery

Aprotic lithium–oxygen (Li–O₂) batteries have attracted considerable attention in recent years owing to their outstanding theoretical energy density. A major challenge is their poor reversibility caused by degradation reactions, which mainly occur during battery charge and are still poorly understood. Herein, we show that singlet oxygen (¹Δ_g) is formed upon Li₂O₂ oxidation at potentials above 3.5 V. Singlet oxygen was detected through a reaction with a spin trap to form a stable radical that was observed by time‐ and voltage‐resolved in operando EPR spectroscopy in a purpose‐built spectroelectrochemical cell. According to our estimate, a lower limit of approximately 0.5 % of the evolved oxygen is singlet oxygen. The occurrence of highly reactive singlet oxygen might be the long‐overlooked missing link in the understanding of the electrolyte degradation and carbon corrosion reactions that occur during the charging of Li–O₂ cells.     

The Decisive Role of Spin States and Spin Coupling in Dictating Selective O2 Adsorption in Chromium(II) Metal–Organic Frameworks**

The coordinatively unsaturated chromium(II)-based Cr₃[(Cr₄Cl)₃(BTT)₈]₂ (Cr−BTT; BTT³⁻=1,3,5-benzenetristetrazolate) metal–organic framework (MOF) has been shown to exhibit exceptional selectivity towards adsorption of O₂ over N₂/H₂. Using periodic density functional theory (DFT) calculations, we attempted to decipher the origin of this puzzling selectivity. By computing and analyzing the magnetic exchange coupling, binding energies, the partial density of states (pDOS), and adsorption isotherms for the pristine and gas-bound MOFs [(Cr₄(X)₄Cl)₃(BTT)₈]³⁻ (X=O₂, N₂, and H₂), we unequivocally established the role of spin states and spin coupling in controlling the gas selectivity. The computed geometries and gas adsorption isotherms are consistent with the earlier experiments. The binding of O₂ to the MOF follows an electron-transfer mechanism resulting in a Cr^III superoxo species (O₂^.−) with a very strong antiferromagnetic coupling between the two centers, whereas N₂/H₂ are found to weakly interact with the metal center and hence only slightly perturb the associated coupling constants. Although the gas-bound and unbound MOFs have an S=0 ground state (GS), the nature of spin the configurations and the associated magnetic exchanges are dramatically different. The binding energy and the number of oxygen molecules that can favorably bind to the Cr center were found to vary with respect to the spin state, with a significant energy margin (47.6 kJ mol⁻¹). This study offers a hitherto unknown strategy of using spin state/spin couplings to control gas adsorption selectivity in MOFs.     

Poly(L‐lysine)‐Induced Aggregation of Single‐Strand Oligo‐DNA‐Modified Gold Nanoparticles

Single‐strand oligo‐DNA‐modified Au nanoparticles (AuNPs) undergo aggregation in the presence of poly(L ‐lysine) (PLL), which is attributed to the interactions between the oligo‐DNA and PLL. These interactions between the oligo‐DNA and PLL were identified to be electrostatic when the lysine residues of PLL were positively charged and to be hydrogen bonding when the residues were deprotonated. The aggregation was promoted with an increase in the pH value at a pH level lower than the pK_a value of PLL (pK_a≈10.0) due to the gradual deprotonation of the lysine residues and thus suppressed electrostatic interactions between the positively charged lysine residues of PLL and the negatively charged backbone phosphate groups of the oligo‐DNA. At pH levels higher than the pK_a value of PLL, the aggregation was identified to be dominated by the hydrogen bonds between the bases of the oligo‐DNA and the deprotonated lysine residues of PLL. This study prompts the possibility that the spectral, and thus color, change of AuNPs upon aggregation can be used as a probe to follow the interactions between oligo‐DNA and polypeptides.     

Strong Interplay between the Electron Spin Lifetime in Chemically Synthesized Graphene Multilayers and Surface‐Bound Oxygen

The electron spin lifetime in an assembly of chemically synthesized graphene sheets was found to be extremely sensitive to oxygen. Introducing small concentrations of physisorbed O₂ onto the graphene surface reduced the exceptionally long 140 ns electron spin lifetime by an order of magnitude. This effect was completely reversible: Removing the O₂ by using a dynamic vacuum restored the spin lifetime. The presence of covalently bound oxygen also decreased the electron spin lifetime in graphene, although to a far lesser extent compared to physisorbed O₂. The conduction electrons in graphene were found to play a significant role by counter‐balancing the spin depolarization caused by oxygen molecules. Our results highlight the importance of chemical environment control and device packing in practical graphene‐based spintronic applications.     

C?H Bond Activation by Metal–Superoxo Species: What Drives High Reactivity?

Metal–superoxo species are ubiquitous in metalloenzymes and bioinorganic chemistry and are known for their high reactivity and their ability to activate inert C? H bonds. The comparative oxidative abilities of M–O₂^.? species (M=Cr^III, Mn^III, Fe^III, and Cu^II) towards C? H bond activation reaction are presented. These superoxo species generated by oxygen activation are found to be aggressive oxidants compared to their high‐valent metal–oxo counterparts generated by O???O bond cleavage. Our calculations illustrate the superior oxidative abilities of Fe^III– and Mn^III–superoxo species compared to the others and suggest that the reactivity may be correlated to the magnetic exchange parameter.     

C?H Bond Activation by Metal–Superoxo Species: What Drives High Reactivity?

Metal–superoxo species are ubiquitous in metalloenzymes and bioinorganic chemistry and are known for their high reactivity and their ability to activate inert C H bonds. The comparative oxidative abilities of M–O₂^.− species (M=Cr^III, Mn^III, Fe^III, and Cu^II) towards C H bond activation reaction are presented. These superoxo species generated by oxygen activation are found to be aggressive oxidants compared to their high‐valent metal–oxo counterparts generated by O⋅⋅⋅O bond cleavage. Our calculations illustrate the superior oxidative abilities of Fe^III– and Mn^III–superoxo species compared to the others and suggest that the reactivity may be correlated to the magnetic exchange parameter.     

Skin Bond Electron Relaxation Dynamics of Germanium Manipulated by Interactions with H2, O2, H2O,H2O2, HF,and Au

Although germanium performs amazingly well at sites surrounding hetero‐coordinated impurities and under‐coordinated defects or skins with unusual properties, having important impact on electronic and optical devices, understanding the behavior of the local bonds and electrons at such sites remains a great challenge. Here we show that a combination of density functional theory calculations, zone‐resolved X‐ray photoelectron spectroscopy, and bond order length strength correlation mechanism has enabled us to clarify the physical origin of the Ge 3d core‐level shift for the under‐coordinated (111) and (100) skin with and without hetero‐coordinated H₂, O₂, H₂O, H₂O₂, HF impurities. The Ge 3d level shifts from 27.579 (for an isolated atom) by 1.381 to 28.960 eV upon bulk formation. Atomic under‐coordination shifts the binding energy further to 29.823 eV for the (001) and to 29.713 eV for the (111) monolayer skin. Addition of O₂, HF, H₂O, H₂O₂ and Au impurities results in quantum entrapment by different amounts, but H adsorption leads to polarization.     

Manganese,Iron, Cobalt,and Nickel Oxo‐, Peroxo‐, and Superoxoclusters: A Density Functional Theory Study

The 3d‐transition‐metal dioxo‐, peroxo‐, and superoxoclusters with the general composition MO₂, M(O₂), and MOO (M=Mn, Fe, Co, and Ni) were studied by DFT by the B1LYP functional. The dioxides in their ground states represent the global minima for the M+O₂ system. Both ground‐state dioxides and the lowest‐energy peroxides are in their (d‐only) highest spin states. The ⁶A₁ state of Co(O₂) exceeds the d‐only spin‐multiplicity value (quartet), being nearly isoenergetic with the ⁴A₁ state of Co(O₂). The energy gain on transforming the peroxides to the corresponding dioxides decreases in the order Mn(O₂)>Fe(O₂)>Co(O₂)>Ni(O₂) and varies in the range 0.27–1.8 eV. The dissociation energy to M+O₂ for all studied peroxides is less than 1 eV being the lowest (0.47 eV) for Mn(O₂). The Mn and Fe peroxides need less than 0.3 eV to rupture one of the MO bonds to form the corresponding superoxide. Mn and Fe superoxides are less stable than the corresponding peroxides; the superoxide of Co is more stable than its peroxide, while Ni superoxide is unstable—its energy is above the limit of dissociation to Ni+O₂. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides, in which the terminal oxygen atom is more nucleophilic than the M‐bonded oxygen atom. This result differs from the expectations based on charge‐distribution analysis.