Binding Of Molecular Oxygen Research Articles

Coordination Variations within Binuclear Copper Dioxygen-Derived (Hydro)Peroxo and Superoxo Species; Influences upon Thermodynamic and Electronic Properties.

Copper ion is a versatile and ubiquitous facilitator of redox chemical and biochemical processes. These include the binding of molecular oxygen to copper(I) complexes where it undergoes stepwise reduction-protonation. A detailed understanding of thermodynamic relationships between such reduced/protonated states is key to elucidate the fundamentals of the chemical/biochemical processes involved. The dicopper(I) complex [CuI2(BPMPO-)]1+ {BPMPOH = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} undergoes cryogenic dioxygen addition; further manipulations in 2-methyltetrahydrofuran generate dicopper(II) peroxo [CuII2(BPMPO-)(O22-)]1+, hydroperoxo [CuII2(BPMPO-)(-OOH)]2+, and superoxo [CuII2(BPMPO-)(O2•-)]2+ species, characterized by UV-vis, resonance Raman and electron paramagnetic resonance (EPR) spectroscopies, and cold spray ionization mass spectrometry. An unexpected EPR spectrum for [CuII2(BPMPO-)(O2•-)]2+ is explained by the analysis of its exchange-coupled three-spin frustrated system and DFT calculations. A redox equilibrium, [CuII2(BPMPO-)(O22-)]1+ ⇄ [CuII2(BPMPO-)(O2•-)]2+, is established utilizing Me8Fc+/Cr(η6-C6H6)2, allowing for [CuII2(BPMPO-)(O2•-)]2+/[CuII2(BPMPO-)(O22-)]1+ reduction potential calculation, E°' = -0.44 ± 0.01 V vs Fc+/0, also confirmed by cryoelectrochemical measurements (E°' = -0.40 ± 0.01 V). 2,6-Lutidinium triflate addition to [CuII2(BPMPO-)(O22-)]1+ produces [CuII2(BPMPO-)(-OOH)]2+; using a phosphazene base, an acid-base equilibrium was achieved, pKa = 22.3 ± 0.7 for [CuII2(BPMPO-)(-OOH)]2+. The BDFEOO-H = 80.3 ± 1.2 kcal/mol, as calculated for [CuII2(BPMPO-)(-OOH)]2+; this is further substantiated by H atom abstraction from O-H substrates by [CuII2(BPMPO-)(O2•-)]2+ forming [CuII2(BPMPO-)(-OOH)]2+. In comparison to known analogues, the thermodynamic and spectroscopic properties of [CuII2(BPMPO-)] O2-derived adducts can be accounted for based on chelate ring size variations built into the BPMPO- framework and the resulting enhanced CuII-ion Lewis acidity.

Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome.

Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•- is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide-FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thaliana cryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2-FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.

An alkane monooxygenase (AlkB) family in which all electron transfer partners are covalently bound to the oxygen-activating hydroxylase

Alkane monooxygenase (AlkB) is a non-heme diiron enzyme that catalyzes the hydroxylation of alkanes. It is commonly found in alkanotrophic organisms that can live on alkanes as their sole source of carbon and energy. Activation of AlkB occurs via two-electron reduction of its diferric active site, which facilitates the binding, activation, and cleavage of molecular oxygen for insertion into an inert CH bond. Electrons are typically supplied by NADH via a rubredoxin reductase (AlkT) to a rubredoxin (AlkG) to AlkB, although alternative electron transfer partners have been observed. Here we report a family of AlkBs in which both electron transfer partners (a ferredoxin and a ferredoxin reductase) appear as an N-terminal gene fusion to the hydroxylase (ferr_ferrR_AlkB). This enzyme catalyzes the hydroxylation of medium chain alkanes (C6-C14), with a preference for C10-C12. It requires only NADH for activity. It is present in a number of bacteria that are known to be human pathogens. A survey of the genome neighborhoods in which is it found suggest it may be involved in alkane metabolism, perhaps facilitating growth of pathogens in non-host environments.

Hydration modulates oxygen channel residues for oxygenation of cysteine dioxygenase: Perspectives from molecular dynamics simulations

Cysteine dioxygenase (CDO) regulates the concentration of l-cysteine substrate by its oxidation in the body to prevent different diseases, including neurodegenerative and autoimmune diseases. CDO catalyzes the oxidation of thiol group of l-cysteine to l-cysteine sulfinic acid using molecular oxygen. In this study, molecular dynamics simulations were applied to ligand-free CDO, cysteine-bound CDO, and oxygen-bound CDO-cysteine complex which were primarily subjected to the evaluation of their structural and dynamical properties. The simulation data provided significant information not only on the conformational changes of the enzyme after its ligation but also on the co-ligation by sequential binding of l-cysteine and molecular oxygen. It was found that the ligation and co-ligation perturbed the active site region as well as the overall protein dynamics which were analyzed in terms of root mean square deviation, root mean square fluctuation and dynamic cross correlation matrices as well as principal component analysis. Furthermore, oxygen transport pathways were successfully explored by taking various tunnel clusters into account and one of those clusters was given preference based on the throughput value. The bottleneck formed by different amino acid residues was examined to figure out their role in the oxygenation process of the enzyme. The residues forming the tunnel's bottleneck and their dynamics mediated by water molecules were further investigated using radial distribution functions which gave insights into the hydration behavior of these residues. The findings based on the hydration behavior in turn served to explore the water-mediated dynamics of these residues in the modulation of the pathway, including tunnel gating for the oxygen entry and diffusion to the active site, which is essential for the CDO's catalytic function.

Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein.

Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacterized role in reactive oxygen species generation, apparently at the level of the electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) and/or its redox partner electron-transfer flavoprotein (ETF). These enzymes comprise a key pathway through which electrons are sequentially shuttled from several dehydrogenases to the respiratory chain. The exact mechanisms of superoxide production have not been fully established, but a crucial starting point would be the binding of molecular oxygen within one of the protein complexes. The present investigation offers a comprehensive computational approach for the determination of binding modes and characteristic binding times of small molecules inside proteins, which is then used to reveal several O2 binding sites near the flavin adenine dinucleotide cofactor of the ETF enzyme. The binding sites are further characterized to extract the necessary parameters for further studies of possible electron transfer between flavin and O2 leading to radical pair formation and possible superoxide production.

Chromism of phosphomolybdate-dye moiety: A material for molecular nitrogen and oxygen binding

Abstract Chromism from phosphomolybdate – malachite green dye moiety through hydrogen bonding interaction with water molecules is reported. Interestingly, the substance with bound di-nitrogen or di-oxygen together with water molecules also exhibits color change. N2 or O2 binding vis-a-vis chromism is a new insight.

Molecular and Dissociative Adsorption of Oxygen on Au-Pd Bimetallic Clusters: Role of Composition and Spin State of the Cluster.

Utilization of molecular oxygen as an oxidizing agent in industrially important reactions is the ultimate goal to design environmentally benign processes under ambient conditions. However, the high thermal stability and a large O–O dissociation barrier in O2 molecule pose a great challenge toward its successful application in the oxidative chemistry. To achieve this goal, different catalysts based on monometallic and bimetallic clusters have been developed over the years to promote binding and dissociation of molecular oxygen. The successful design of efficient metal cluster catalysis needs an in-depth knowledge of synergistic effects between different metal atoms and intrinsic catalytic mechanisms for O2 adsorption and dissociation. Here, we present a systematic theoretical investigation of reaction pathways for O2 adsorption and dissociation on Au8, Pd8, and Au8–nPdn (n = 1–7) nanoclusters in different spin states. The density functional calculations point out that the O2 dissociation barriers can be significantly reduced with the help of certain bimetallic clusters along specific spin channels. Our results particularly indicate that Au5Pd3 and Au1Pd7 show very large O2 binding energies of 1.76 and 1.69 eV, respectively. The enhanced O2 binding subsequently leads to low activation barriers of 0.98 and 1.19 eV along the doublet and quartet spin channels, respectively, without the involvement of any spin flip-over for O2 dissociation. Furthermore, the computed O2 dissociation barriers are significantly low as compared to the already reported barriers (1.95–3.65 eV) on monometallic and bimetallic Au–Ag clusters. The results provide key mechanistic insights into the interaction and dissociation of molecular oxygen with Au–Pd clusters, which can prove informative for the design of efficient catalysts for oxidative chemistry involving molecular oxygen as a reactant.

Cobalt-Chelated Polyamine Brushes on Solid Microspheres for Rapid Binding and Chemical Storage of Molecular Oxygen

Methylated poly(vinyl amine) brushes generated on PS-DVB microspheres were demonstrated as excellent macroligands, forming hydrophilic Co(II) chelates capable of reversible molecular oxygen binding. The oxygenation is extremely fast when counteranions of cobalt are replaced with hydroxyl ions. The experiments carried out using oxygen sensor, FT-IR, TGA techniques, and gas volumetric measurements showed that the polymer complexes with either 4/1 or 2/1 [amine]/[Co] ratios form 1:1 molecular oxygen adducts which are stable up to 110–120 °C. In order to impart the chain extension effect, poly(vinyl amine-stat-DADMAC) brushes were also generated on the microspheres by using DADMAC as additional comonomer. Fast oxygenation, high oxygen binding capacity (ca. 80 mL/g), and long-term stability of the oxygen adducts make the polymeric complex superior to current systems. The cobalt complex system presented can be considered as a high capacity solid matrix for dissociation and chemical storage of the molecular oxyg...

Structure of formylglycine-generating enzyme in complex with copper and a substrate reveals an acidic pocket for binding and activation of molecular oxygen.

The formylglycine generating enzyme (FGE) catalyzes oxidative conversion of specific peptidyl-cysteine residues to formylglycine. FGE mediates O2-activation and hydrogen-atom abstraction in an active site that contains Cu(i) coordinated to two cysteine residues. Similar coordination geometries are common among copper-sensing transcription factors and copper-chaperone but are unprecedented among copper-dependent oxidases. To examine the mechanism of this unusual catalyst we determined the 1.04 Å structure of FGE from Thermomonospora curvata in complex with copper and a cysteine-containing peptide substrate. This structure unveils a network of four crystallographic waters and two active site residues that form a highly acidic O2-binding pocket juxtaposed to the trigonal planar tris-cysteine coordinated Cu(i) center. Comparison with structures of FGE in complex with Ag(i) and Cd(ii) combined with evidence from NMR spectroscopy and kinetic observations highlight several structural changes that are induced by substrate binding and prime the enzyme for O2-binding and subsequent activation.

Spin crossover dynamics studies on the thermally activated molecular oxygen binding mechanism on a model copper complex.

The theoretical description of the primary dioxygen (O2) binding and activation step in many copper or iron enzymes, suffers from the intrinsically electronic non-adiabaticity of the spin flip events of the triplet dioxygen molecule (3O2), mediated by spin-orbit couplings. In this work, we presented the early-stage ultrafast spin flip dynamics of O2 binding for a simplified monocopper complex, involving the coupled singlet and triplet electronic states. The on-the-fly trajectory surface hopping (TSH) simulations have identified the dynamical effects that may influence the mode of O2 coordination (end-on vs. side-on), and the electronic structures can be viewed as complexes of molecular O2 with Cu(i) or as Cu(ii)-superoxide compounds. In addition, significant spin flip events are obversed within the sub-picosecond regime. We hope this work may provide complimentary insights on the traditional interpretation of O2 binding on copper complexes and subsequent catalytic reaction mechanisms.

Study of Intermediates in Iridium–(Phosphoramidite,Olefin)-Catalyzed Enantioselective Allylic Substitution

Experimental mechanistic studies of iridium-catalyzed, enantioselective allylic substitution enabled by (phosphoramidite,olefin) ligands are reported. (η2-Allylic alcohol)iridium(I) and (η3-allyl)iridium(III) complexes were synthesized and characterized by NMR spectroscopy as well as X-ray crystallography. The substrate complexes are catalytically and kinetically competent to be intermediates in allylic substitutions of branched, racemic allylic alcohols with various nucleophiles. In addition, we have identified an off-cycle pathway involving reversible binding of molecular oxygen to iridium, which contributes to the air tolerance of the catalyst system.

Theoretical study of the interaction between molecular oxygen and tetraaza macrocyclic manganese complexes.

Theoretical chemistry calculations using theDensity Functional Theory(DFT) were carried outto understand the interaction between oxygen (O2) and MnN4 type manganese-based complexes during the formation of MnN4-O2 adducts. In order to understand how this interaction is affected by different macrocyclic ligands, O2 was bonded to manganese-porphyrin (MnP), manganese-octamethylporphyrin (MnOMP), manganese-tetraaza[14]annulene (MnTAA), manganese-dibenzo [b,i] [1, 4, 8, 11]-tetraaza [14] annulene (MnDBTAA), manganese-2,3,9,10-tetramethyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(tim)Mn](2+)), and manganese-2,3,9,10-tetraphenyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(ph-tim)Mn](2+)). Thebinding and activation of the oxygen molecule was facilitated by an increasing trend in theO-O bond lengths and a decreasing one in the O-O vibrational frequency, with preference for the O2side-on interaction among MnN4 macrocycles. The catalytic activities of the MnN4 complexes toward the O2binding process increased in the followingorder: [(ph-tim)Mn](2+) < MnP < MnOMP < MnDBTAA < MnTAA < [(tim)Mn](2+). Therefore, it was concluded that the [(tim)Mn](2+)complex was the most active for the binding and activation of molecular oxygen.

Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation.

A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.

Identifying the Catalytic Active Sites in Heteroatom‐Doped Graphene for the Oxygen Reduction Reaction

AbstractDensity functional theory (DFT) calculations can be used to help elucidate the structures of active sites on the surface of fuel cell cathode catalysts, which are exceptionally difficult to identify by experimental techniques. The cathode catalysts were modeled in nitrogen‐, boron‐, sulfur‐, and phosphorus‐doped graphene basal planes. Dually‐doped graphene structures combining nitrogen with phosphorus or sulfur are also studied. Potential energy profiles were obtained, and the energies and activation barriers of molecular oxygen binding to the doped graphene model structures were estimated in order to identify potentially active sites for the oxygen reduction reaction in fuel cells. Among the investigated doped graphene structures, the active sites for molecular oxygen chemisorption are identified in graphene doped with either two nitrogen, or two phosphorus, or one sulfur and one phosphorus atoms. Further, the analysis of atomic spin densities and charges in the model structures enables the correlation of the catalytic activity with electron density distribution.

Redox-Dependent Dynamics in Heme-Bound Bacterial Iron Response Regulator (Irr) Protein.

The iron response regulator (Irr) protein from Bradyrhizobium japonicum mediates iron-dependent regulation of heme biosynthesis. Irr degrades in response to heme availability through a process that involves the binding of heme to Cys-29 in the heme regulatory motif (HRM) in the presence of molecular oxygen. In this work, we assessed the dynamics of one-electron reduction of heme-bound Irr by monitoring the formation of transient intermediates by pulse radiolysis. Hydrated electrons generated by pulse radiolysis reduced heme iron-bound Irr, facilitating the binding of molecular oxygen to the heme iron in Irr through an initial intermediate with an absorption maximum at 420 nm. This initial intermediate was converted to a secondary intermediate with an absorption maximum at 425 nm, with a first-order rate constant of 1.0 × 10(4) s(-1). The Cys-29 → Ala (C29A) mutant of Irr, on the other hand, did not undergo the secondary phase, implying that ligand exchange of Cys-29 for another ligand takes place during the process. Spectral changes during the reduction of the heme-bound Irr revealed that binding of CO to ferrous heme consisted of two phases with kon values of 1.3 × 10(5) and 2.5 × 10(4) M(-1) s(-1), a finding consistent with the presence of two distinct hemes in Irr. In aerobic solutions, by contrast, oxidation of the ferrous heme to the ferric form was found to be a two-phase process. The C29A mutant was similarly oxidized, but this occurred as a single-phase process. We speculate that a reactive oxygen species essential for degradation of the protein is generated during the oxidation process.

Influence of mutations at the proximal histidine position on the Fe-O2 bond in hemoglobin from density functional theory.

Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.

Unusual oxygen affinity of linear polyvinyl amine–cobalt complexes with hydroxyl counter ions: an efficient way of separation and chemical storage of molecular oxygen

Methylated poly(vinyl amine) and its copolymer with diallyldimethylammonium chloride (DADMAC) were prepared by polymerization of N-vinyl formamide (NVF) or copolymerization with DADMAC. Acid hydrolysis of the polymers and subsequent methylation yielded corresponding polyamines. Co(II) complexes of the polyamines were demonstrated to be reasonably fast in molecular oxygen binding, when counter anions of cobalt are exchanged with hydroxyl ions. The oxygenation tests performed with oxygen sensor, FT-IR, and gas-volumetric methods revealed that complexes either with 4/1 or with 2/1 [amine]/[Co] ratios give 1:1 molecular oxygen adducts. Fast oxygenation (c.a. 2–4 min), high storage capacity, and smooth oxygen releasing within 70–120 °C are typical characteristics of the oxygenation–deoxygenation. The system seems to be useful for harvesting and chemical storage of air oxygen.

Detecting O2 binding sites in protein cavities.

Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in 1H, 15N, and 13C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.

Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe-tetracarbene superoxo complex.

The dioxygen reactivity of a cyclic iron(ii) tetra-NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(iii) whereas in the latter case an oxide bridged Fe(iii) dimer is formed. In acetone, an Fe(iii)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(iii)-O-Fe(iii) dimer is formed from the Fe(iii) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(ii) complex in both solvents is a reversible process. For the regeneration of the initial Fe(ii) complex both organic and inorganic reducing agents can be used.

Reversible binding of molecular oxygen to catecholate and o-amidophenolate complexes of SbV: energy approach

The theoretical study of the reactivity of catecholate and o-amidophenolate complexes of SbV in the reversible binding of molecular oxygen was performed. The evaluation of the strength of intramolecular interactions in pre-reaction complexes provides the assessment of the strength of oxygen binding in the coordination sphere of Sb. The initial complexes, their transition states, and final spiroendoperoxide complexes were modeled. The calculated activation energies of the reaction and ionization can serve as the energy criteria providing the explanation and prediction of interactions of these complexes with molecular oxygen.