118 results on '"Jeffrey Harmer"'
Search Results
2. Mapping the Pathway to Organocopper(II) Complexes Relevant to Atom Transfer Radical Polymerization
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Jeffrey Harmer, Paul V. Bernhardt, and Miguel A. Gonzálvez
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010405 organic chemistry ,Ligand ,Atom-transfer radical-polymerization ,010402 general chemistry ,01 natural sciences ,Spectral line ,0104 chemical sciences ,law.invention ,Inorganic Chemistry ,Crystallography ,chemistry.chemical_compound ,chemistry ,law ,Density functional theory ,Amine gas treating ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Acetonitrile ,Hyperfine structure - Abstract
The rare organocopper(II) complex [Cu(Metren)(CHCN)] (Metren = tris(2-(dimethylamino)ethyl)amine) has emerged as an important model of potential byproducts in copper-catalyzed atom transfer radical polymerization. This complex has been generated by controlled potential electrolysis of [Cu(Metren)(NCMe)] in the presence of BrCHCN. Time-resolved UV-vis and continuous wave and pulse electron paramagnetic resonance (EPR) spectra identified [Cu(Metren)Br] as an intermediate. Hyperfine sublevel correlation and electron nuclear double resonance spectroscopy of samples at different timepoints reveal signals that are assigned to a C-bound cyanomethylate ligand, with distinct N and H hyperfine coupling constants in comparison with the corresponding N-bound acetonitrile and bromido complexes. The experimental EPR data are supported by density functional theory calculations to understand how the geometries of the species involved produce distinct spectroscopic signatures, and a clear picture of how this unusual organocopper(II) complex is formed has emerged.
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- 2021
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3. Understanding the Mechanistic Requirements for Efficient and Stereoselective Alkene Epoxidation by a Cytochrome P450 Enzyme
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Paul V. Bernhardt, Joshua S. Harbort, Alicia M. Kirk, Stephen Bell, M.N. Podgorski, Elizabeth H. Krenske, Luke R. Churchman, Rebecca R. Chao, Jeffrey Harmer, John B. Bruning, T. Coleman, and James J. De Voss
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chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Alkene ,Stereochemistry ,Reactive intermediate ,Epoxide ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Hydroxylation ,chemistry.chemical_compound ,Catalytic cycle ,Stereoselectivity ,Chemoselectivity - Abstract
The cytochrome P450 (CYP) family of heme monooxygenase enzymes commonly catalyzes enantioselective hydroxylation and epoxidation reactions. Epoxidation reactions have been hypothesized to proceed via multiple mechanisms involving different reactive intermediates. Here, we use activity, spectroscopic, structural, and molecular dynamics data to investigate the activity and stereoselectivity of 4-vinylbenzoic acid epoxidation by the bacterial enzyme CYP199A4 from Rhodopseudomonas palustris HaA2. The epoxidation of 4-vinylbenzoic acid by CYP199A4 proceeded with high enantioselectivity, giving the (S)-epoxide in 99% ee at an activity of 220 nmol nmol-CYP–1 min–1. Optical and EPR spectroscopy, redox potential measurements, and the crystal structure of 4-vinylbenzoic acid-bound CYP199A4 indicated the partial retention of an aqua ligand at the heme center in the presence of the substrate, providing a justification of the lower activity (∼20%) compared to the oxidative demethylation of 4-methoxybenzoic acid. Mutagenesis at the conserved acid–alcohol pair (D251/T252), which perturbs the generation of the reactive oxygen intermediates, was employed to investigate their role in epoxidation reactions. The T252A mutant increased the rate of turnover of the catalytic cycle, but an elevation in hydrogen peroxide generation via uncoupling resulted in a similar rate of epoxide formation. The activity of epoxidation significantly reduced with the D251N mutant. The chemoselectivity and stereoselectivity of the epoxidation reaction were maintained in the turnovers by these mutants. Overall, there was little evidence that other intermediates, aside from the archetypal reactive ferryl porphyrin cation radical, Compound I, contributed significantly to the epoxidation reaction. The observation of the high selectivity for the (S)-enantiomer was rationalized by molecular dynamics simulations. When the arrangement of the alkene and the active intermediate approached an ideal transition state structure for epoxidation, one face of the alkene was more often exposed to the iron oxo unit.
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- 2021
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4. A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA
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Jacqueline R. Morey, Michael Isselstein, Thorben Cordes, Christopher A. McDevitt, Jeffrey Harmer, James C. Paton, Stephanie L. Neville, Katherine Ganio, Evelyne Deplazes, Alina E. Motygullina, Bostjan Kobe, Victoria G. Pederick, Nikolaos Eleftheriadis, Zhenyao Luo, Aimee Tan, and Molecular Biophysics
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Protein Conformation ,Protein domain ,Virulence ,chemistry.chemical_element ,ATP-binding cassette transporter ,Zinc ,Molecular Dynamics Simulation ,Microbiology ,Host-Microbe Biology ,03 medical and health sciences ,Protein structure ,Bacterial Proteins ,Protein Domains ,Virology ,Binding site ,030304 developmental biology ,0303 health sciences ,Binding Sites ,biology ,Chemistry ,030302 biochemistry & molecular biology ,Solute-binding protein ,biology.organism_classification ,QR1-502 ,respiratory tract diseases ,Transport protein ,Streptococcus pneumoniae ,Biochemistry ,ATP-Binding Cassette Transporters ,ABC transporter ,Bacteria ,0605 Microbiology ,Research Article - Abstract
Zinc is an essential nutrient for the virulence of bacterial pathogens such as Streptococcus pneumoniae. Many Gram-positive bacteria use a two-domain lipoprotein for zinc acquisition, but how this class of metal-recruiting proteins acquire zinc and interact with the uptake machinery has remained poorly defined., Zinc is an essential element in all domains of life. Nonetheless, how prokaryotes achieve selective acquisition of zinc from the extracellular environment remains poorly understood. Here, we elucidate a novel mechanism for zinc-binding in AdcA, a solute-binding protein of Streptococcus pneumoniae. Crystal structure analyses reveal the two-domain organization of the protein and show that only the N-terminal domain (AdcAN) is necessary for zinc import. Zinc binding induces only minor changes in the global protein conformation of AdcA and stabilizes a highly mobile loop within the AdcAN domain. This loop region, which is conserved in zinc-specific solute-binding proteins, facilitates closure of the AdcAN binding site and is crucial for zinc acquisition. Collectively, these findings elucidate the structural and functional basis of selective zinc uptake in prokaryotes.
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- 2021
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5. Amyloid β chaperone — lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme
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Justin Ng Tze Yang, Jeffrey Harmer, Ralf Kather, Konstantin Pervushin, Bhuvaneswari Kannaian, Mu Yuguang, Margaret Phillips, and School of Biological Sciences
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0301 basic medicine ,Protein Conformation ,Bilirubin ,Heme ,Molecular Dynamics Simulation ,Ligands ,Ferric Compounds ,Biochemistry ,Prostaglandin-D synthase ,Electron-Paramagnetic-Resonance ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Biochemical Techniques & Resources ,Alzheimer Disease ,Structural Biology ,Chemical Biology ,L-PGDS ,Extracellular ,Humans ,Benzothiazoles ,Molecular Biology ,Research Articles ,Fluorescent Dyes ,Peroxidase ,Amyloid beta-Peptides ,biology ,Ligand binding assay ,Electron Spin Resonance Spectroscopy ,Biological sciences [Science] ,Transporter ,Cell Biology ,Lipocalins ,Site-Directed Mutagenesis ,Intramolecular Oxidoreductases ,030104 developmental biology ,chemistry ,Chaperone (protein) ,biology.protein ,amyloid β ,peroxidases ,Hydrophobic and Hydrophilic Interactions ,030217 neurology & neurosurgery ,Molecular Chaperones ,Protein Binding - Abstract
The extracellular transporter, lipocalin-type prostaglandin D synthase (L-PGDS) binds to heme and heme metabolites with high affinity. It has been reported that L-PGDS protects neuronal cells against apoptosis induced by exposure to hydrogen peroxide. Our study demonstrates that when human WT L-PGDS is in complex with heme, it exhibits a strong peroxidase activity thus behaving as a pseudo-peroxidase. Electron paramagnetic resonance studies confirm that heme in the L-PGDS-heme complex is hexacoordinated with high-spin Fe(III). NMR titration of heme in L-PGDS points to hydrophobic interaction between heme and several residues within the β-barrel cavity of L-PGDS. In addition to the transporter function, L-PGDS is a key amyloid β chaperone in human cerebrospinal fluid. The presence of high levels of bilirubin and its derivatives, implicated in Alzheimer's disease, by binding to L-PGDS may reduce its chaperone activity. Nevertheless, our ThT binding assay establishes that heme and heme metabolites do not significantly alter the neuroprotective chaperone function of L-PGDS. Guided by NMR data we reconstructed the heme L-PGDS complex using extensive molecular dynamics simulations providing a platform for mechanistic interpretation of the catalytic and transporting functions and their modulation by secondary ligands like Aβ peptides and heme metabolites. Ministry of Education (MOE) Published version The research for this paper was supported by the MOE-Tier 2 grant M4020231. J.R.H. acknowledges support from the ARC (FT120100421).
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- 2020
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6. Mechanochemically Synthesised Flexible Electrodes Based on Bimetallic Metal–Organic Framework Glasses for the Oxygen Evolution Reaction
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Zhonghua Zhu, Zhiliang Wang, Jingwei Hou, Jeffrey Harmer, Sebastian Beyer, Wupeng Wang, Dominique R. T. Appadoo, Andraž Krajnc, Ana Guilherme Buzanich, Lianzhou Wang, Vicki Chen, Simon Smart, Linzhou Zhuang, Zhiheng Li, Rijia Lin, Gregor Mali, Thomas D. Bennett, Xuemei Li, and Mengran Li
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chemistry.chemical_classification ,Materials science ,010405 organic chemistry ,Oxygen evolution ,chemistry.chemical_element ,General Medicine ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Coordination complex ,chemistry.chemical_compound ,Chemical engineering ,chemistry ,Mechanochemistry ,Imidazolate ,Metal-organic framework ,Bimetallic strip ,Cobalt ,Zeolitic imidazolate framework - Abstract
The melting behaviour of metal-organic frameworks (MOFs) has aroused significant research interest in the areas of materials science, condensed matter physics and chemical engineering. This work first introduces a novel method to fabricate a bimetallic MOF glass, through melt-quenching of the cobalt-based zeolitic imidazolate framework (ZIF) [ZIF-62(Co)] with an adsorbed ferric coordination complex. The high-temperature chemically reactive ZIF-62(Co) liquid facilitates the formation of coordinative bonds between Fe and imidazolate ligands, incorporating Fe nodes into the framework after quenching. The resultant Co-Fe bimetallic MOF glass therefore shows a significantly enhanced oxygen evolution reaction performance. The novel bimetallic MOF glass, when combined with the facile and scalable mechanochemical synthesis technique for both discrete powders and surface coatings on flexible substrates, enables significant opportunities for catalytic device assembly.
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- 2021
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7. TOAC spin-labeled peptides tailored for DNP-NMR studies in lipid membrane environments
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Frances Separovic, Shiying Zhu, Marc-Antoine Sani, Louise J. Brown, Ehsan Kachooei, and Jeffrey Harmer
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Circular dichroism ,Antimicrobial peptides ,Biophysics ,Phospholipid ,Peptide ,010402 general chemistry ,01 natural sciences ,Micelle ,law.invention ,Cyclic N-Oxides ,03 medical and health sciences ,chemistry.chemical_compound ,law ,Electron paramagnetic resonance ,Lipid bilayer ,Phospholipids ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Spin–lattice relaxation ,Articles ,0104 chemical sciences ,chemistry ,Spin Labels ,Peptides - Abstract
The benefit of combining in-cell solid-state dynamic nuclear polarization (DNP) NMR and cryogenic temperatures is providing sufficient signal/noise and preservation of bacterial integrity via cryoprotection to enable in situ biophysical studies of antimicrobial peptides. The radical source required for DNP was delivered into cells by adding a nitroxide-tagged peptide based on the antimicrobial peptide maculatin 1.1 (Mac1). In this study, the structure, localization, and signal enhancement properties of a single (T-MacW) and double (T-T-MacW) TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid) spin-labeled Mac1 analogs were determined within micelles or lipid vesicles. The solution NMR and circular dichroism results showed that the spin-labeled peptides adopted helical structures in contact with micelles. The peptides behaved as an isolated radical source in the presence of multilamellar vesicles, and the electron paramagnetic resonance (EPR) electron-electron distance for the doubly spin-labeled peptide was ∼1 nm. The strongest paramagnetic relaxation enhancement (PRE) was observed for the lipid NMR signals near the glycerol-carbonyl backbone and was stronger for the doubly spin-labeled peptide. Molecular dynamics simulation of the T-T-MacW radical source in phospholipid bilayers supported the EPR and PRE observations while providing further structural insights. Overall, the T-T-MacW peptide achieved better (13)C and (15)N signal NMR enhancements and (1)H spin-lattice T(1) relaxation than T-MacW.
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- 2020
8. Trivalent copper stabilised by acetylacetone dithiocarbazate Schiff base ligands: structural, spectroscopic and electrochemical properties
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Jeffrey Harmer, Nicole V. Silajew, Paul V. Bernhardt, Graeme R. Hanson, and Jessica K. Bilyj
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chemistry.chemical_classification ,Schiff base ,Ketone ,010405 organic chemistry ,Dimer ,Acetylacetone ,Pyrazoline ,010402 general chemistry ,01 natural sciences ,Redox ,0104 chemical sciences ,Coordination complex ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Polymer chemistry ,Moiety - Abstract
The copper coordination chemistry of N2S2 Schiff base ligands derived from acetylacetone and S-methyl or S-benzyl dithiocarbazate (H3acacsR, R = Me, Bn) reveals a rich variety of products depending on the reaction conditions. The free ligands spontaneously cyclise to their pyrazoline isomers but ring-open upon complexation with CuII. In the absence of oxygen, the ligands form CuIIN2S2 complexes ([CuII(HacacsR)]) that have been characterised electrochemically, spectroscopically and structurally. Intermediates in the complexation reaction are observed with time-resolved UV-Vis spectroscopy. Upon exposure to air, a number of different complexes are formed. Facile oxidation of [CuII(HacacsR)] to the trivalent analogue [CuIII(acacsR)] occurs in air. This compound is the precursor to two further oxidation reactions; one to the ketone [CuII(acacsRO)] where a carbonyl group has been installed at the apical C atom of the acetylacetone moiety and another to afford the novel dinuclear complex [(CuIII(acacsR))2]. The presence of excess base (Et3N) favours formation of the dimer.
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- 2019
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9. Biophysical Techniques for Distinguishing Ligand Binding Modes in Cytochrome P450 Monooxygenases
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Stephen Bell, Luet-Lok Wong, M.N. Podgorski, Jeanette E. Stok, Paul V. Bernhardt, Jeffrey Harmer, Jake A. Yorke, Joshua S. Harbort, T. Coleman, John B. Bruning, and James J. De Voss
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Models, Molecular ,Stereochemistry ,Heme ,010402 general chemistry ,Ligands ,01 natural sciences ,Biochemistry ,Benzoates ,Mixed Function Oxygenases ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Cytochrome P-450 Enzyme System ,030304 developmental biology ,Benzoic acid ,0303 health sciences ,Binding Sites ,biology ,Active site ,Cytochrome P450 ,Monooxygenase ,Ligand (biochemistry) ,0104 chemical sciences ,Kinetics ,Rhodopseudomonas ,chemistry ,Catalytic cycle ,biology.protein ,Protein Binding - Abstract
The cytochrome P450 superfamily of heme monooxygenases catalyzes important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 enzyme (Uniprot entry Q2IUO2), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investigate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a ≥95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)benzoic acid induced different type II ultraviolet-visible (UV-vis) spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 nm vs 422 nm) along with a larger overall absorbance change and other differences in the α-, β-, and δ-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl compounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse electron paramagnetic resonance data in frozen solution revealed that the substrates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation among binding modes, spectroscopic properties, and the observed biochemical activity.
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- 2020
10. Efficient biosynthesis of heterodimeric C3-aryl pyrroloindoline alkaloids
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Dongqing Zhu, Jeffrey Harmer, Mingjia Yu, Mei Zheng, Yanan Zhang, Xudong Qu, Xinying Jia, Haidong Peng, Chenghai Sun, Mehdi Mobli, Wenya Tian, Shi-Lu Chen, and Zixin Deng
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0301 basic medicine ,Indole test ,Multidisciplinary ,Stereochemistry ,Science ,Aryl ,General Physics and Astronomy ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Chemical synthesis ,General Biochemistry, Genetics and Molecular Biology ,0104 chemical sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Cascade reaction ,Biosynthesis ,Biocatalysis ,Intramolecular force ,Molecule ,lcsh:Q ,lcsh:Science - Abstract
Many natural products contain the hexahydropyrrolo[2, 3-b]indole (HPI) framework. HPI containing chemicals exhibit various biological activities and distinguishable structural arrangement. This structural complexity renders chemical synthesis very challenging. Here, through investigating the biosynthesis of a naturally occurring C3-aryl HPI, naseseazine C (NAS-C), we identify a P450 enzyme (NascB) and reveal that NascB catalyzes a radical cascade reaction to form intramolecular and intermolecular carbon–carbon bonds with both regio- and stereo-specificity. Surprisingly, the limited freedom is allowed in specificity to generate four types of C3-aryl HPI scaffolds, and two of them were not previously observed. By incorporating NascB into an engineered strain of E. coli, we develop a whole-cell biocatalysis system for efficient production of NAS-C and 30 NAS analogs. Interestingly, we find that some of these analogs exhibit potent neuroprotective properties. Thus, our biocatalytic methodology offers an efficient and simple route to generate difficult HPI framework containing chemicals.
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- 2018
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11. Heteroatom-Interchanged Isomers of Lissoclinamide 5: Copper(II) Complexation, Halide Binding, and Biological Activity
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Dianne Watters, Andrei I. Savchenko, Glen M. Boyle, Peter Comba, Craig M. Williams, Sida Xie, Elizabeth H. Krenske, Lawrence R. Gahan, Peter G. Parsons, Natasa Broit, Michelle J. Bauer, Rebecca L. Grange, Jeffrey Harmer, Paul V. Bernhardt, and Marion Kerscher
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chemistry.chemical_classification ,Denticity ,010405 organic chemistry ,Organic Chemistry ,Heteroatom ,Halide ,Cavitand ,Oxazoline ,010402 general chemistry ,01 natural sciences ,Cyclic peptide ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Amide ,Polymer chemistry ,Physical and Theoretical Chemistry ,Thiazole - Abstract
Cyclic peptides, especially those produced by marine cyanobacteria symbionts, are considered to play an important ecological role in host defence. Chemists have long compared the cyclic peptide cavitand architecture with that of macrocyclic ligands, and proposed that they mediate metal-ion transport. The study presented herein investigated the metal chelation of non-natural heteroatom-interchanged (HI) isomers of lissoclinamide 5, by using MS, EPR, and DFT calculations. The latter identified three possible structures for the Cu complex with natural lissoclinamide 5, with the most likely determined to be that with the metal ion bound through the nitrogen donors of the thiazoles and one deprotonated amide. For HI-lissoclinamide 5 the calculations suggest that the Cu ion is bound in a bidentate manner by the oxazoline nitrogen atom and one deprotonated amide nitrogen atom, with the S donor of the thiazole not involved in coordination. Along with evidence of copper binding these systems also bound halide ions. Evaluation of the anti-cancer properties demonstrated that the biological activity of HI-lissoclinamide 5 against T24 bladder cells was eleven-fold lower as compared to natural lissoclinamide 5. Addition of a Cu salt had no effect on the activity of lissoclinamide 5. Overall, this comprehensive study of the HI concept has demonstrated that small changes propagate dramatic effects in complexation, halide binding, and biological activity.
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- 2018
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12. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron–Electron Resonance Spectroscopy
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Francesco Mercuri, Nicola Hoskins, Ruihong Qiao, Janet E. Lovett, Luet Lok Wong, Eachan O. D. Johnson, James S. O. McCullagh, Alice M. Bowen, Weihong Zhou, Stephen Bell, Christiane R. Timmel, Jeffrey Harmer, University of St Andrews. Biomedical Sciences Research Complex, and University of St Andrews. School of Physics and Astronomy
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0301 basic medicine ,P-450 ,Stereochemistry ,chemistry.chemical_element ,Molecular Dynamics ,Biochemistry ,Oxygen ,Catalysis ,law.invention ,03 medical and health sciences ,Colloid and Surface Chemistry ,Cytochrome ,law ,QD ,Spectroscopy ,Electron paramagnetic resonance ,R2C ,Ferredoxin ,biology ,Chemistry ,Cytochrome P450 ,DAS ,General Chemistry ,respiratory system ,Monooxygenase ,QD Chemistry ,Resonance (chemistry) ,enzymes and coenzymes (carbohydrates) ,030104 developmental biology ,biology.protein ,NAD+ kinase ,BDC - Abstract
This research was supported by the Engineering & Physical Sciences Research Council (EPSRC) and the Biotechnology & Biological Sciences Research Council (BBSRC), UK (EP/D048559). AMB and EOJD were supported by graduate studentships from the BBSRC (BB/F01709X/1) and NJH and JEL were supported by graduate studentships from the EPSRC, and JEL after her DPhil by EP/D048559. AMB gratefully acknowledges her current fellowship support from the Royal Society and EPSRC for a Dorothy Hodgkin Fellowship (DH160004). JRH acknowledges support from the ARC (FT120100421) and the Centre for Advanced Imaging, The University of Queensland. Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C–H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe2S2] cluster-binding loop and the α3 helix, and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe2S2] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity. Postprint
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- 2018
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13. The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions
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Mihwa Lee, Farzana Darain, Ulrike Kappler, Megan J. Maher, Jeffrey Harmer, Paul V. Bernhardt, Aaron P. McGrath, Palraj Kalimuthu, Linda Kielmann, Ju-Chun Hsiao, and Kimberley Meyers
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0301 basic medicine ,Half-reaction ,Arginine ,Cytochrome ,Stereochemistry ,Sulfite Dehydrogenase ,Mutation, Missense ,Biophysics ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Electron Transport ,03 medical and health sciences ,Bacterial Proteins ,Oxidoreductase ,Catalytic Domain ,Sulfite dehydrogenase ,Sulfite oxidase deficiency ,Molybdenum ,chemistry.chemical_classification ,biology ,Chemistry ,Active site ,Cell Biology ,0104 chemical sciences ,Kinetics ,030104 developmental biology ,Amino Acid Substitution ,Catalytic cycle ,biology.protein ,Oxidation-Reduction ,Sinorhizobium meliloti - Abstract
A central conserved arginine, first identified as a clinical mutation leading to sulfite oxidase deficiency, is essential for catalytic competency of sulfite oxidizing molybdoenzymes, but the molecular basis for its effects on turnover and substrate affinity have not been fully elucidated. We have used a bacterial sulfite dehydrogenase, SorT, which lacks an internal heme group, but transfers electrons to an external, electron accepting cytochrome, SorU, to investigate the molecular functions of this arginine residue (Arg78). Assay of the SorT Mo centre catalytic competency in the absence of SorU showed that substitutions in the central arginine (R78Q, R78K and R78M mutations) only moderately altered SorT catalytic properties, except for R78M which caused significant reduction in SorT activity. The substitutions also altered the Mo-centre redox potentials (MoVI/V potential lowered by ca. 60-80mV). However, all Arg78 mutations significantly impaired the ability of SorT to transfer electrons to SorU, where activities were reduced 17 to 46-fold compared to SorTWT, precluding determination of kinetic parameters. This was accompanied by the observation of conformational changes in both the introduced Gln and Lys residues in the crystal structure of the enzymes. Taking into account data collected by others on related SOE mutations we propose that the formation and maintenance of an electron transfer complex between the Mo centre and electron accepting heme groups is the main function of the central arginine, and that the reduced turnover and increases in KMsulfite are caused by the inefficient operation of the oxidative half reaction of the catalytic cycle in enzymes carrying these mutations.
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- 2018
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14. High Resolution Crystal Structures of the Acetohydroxyacid Synthase‐Pyruvate Complex Provide New Insights into Its Catalytic Mechanism
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Mario D. Garcia, Jeffrey Harmer, James A. Fraser, Christopher J. Noble, Craig M. Williams, Luke W. Guddat, and Thierry G. A. Lonhienne
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0301 basic medicine ,chemistry.chemical_classification ,Flavin adenine dinucleotide ,biology ,010405 organic chemistry ,Stereochemistry ,Active site ,Substrate (chemistry) ,General Chemistry ,01 natural sciences ,Cofactor ,0104 chemical sciences ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Enzyme ,chemistry ,Biosynthesis ,biology.protein ,Transferase - Abstract
Acetohydroxyacid synthase (AHAS) is the first enzyme in the biosynthesis pathway of the branched-chain amino acids, catalyzing the condensation of pyruvate with another molecule of pyruvate or with 2-ketobutyrate, to produce 2-acetolactate or 2-acetohydroxybutyrate, respectively. The catalytic subunit of the dimeric enzyme has thiamin diphosphate (ThDP), a divalent metal ion, flavin adenine dinucleotide (FAD), and two molecules of oxygen (O-2(I) and O-2(II)) as cofactors. Here, crystal structures of Saccharomyces cerevisiae AHAS in complex with pyruvate provide novel insights into the mechanistic features of this enzyme including: i) The precise position taken by pyruvate molecules as they enter the active site (i.e. prior to catalysis occurring) with conformations suitable for the transfer of electrons to/from O-2(I) and FAD; ii) The formation of ternary donor-acceptor-O-2(I) complexes and iii) The location of O-2(II) relative to the substrate showing that it plays a critical role in the organization of substrate for catalysis. These structural data, accompanied by electron paramagnetic resonance evidence that a radical is produced during AHAS catalysis, lead to the proposal that FAD and O-2 are involved in an indirect one-electron redox cycle. In this mechanism, the spatial configurations of O-2 and FAD in the active site can allow electrons to be exchanged with the substrates and catalytic intermediates to satisfy and control the overall AHAS catalyzed reaction.
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- 2017
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15. (L)2 C2 P2 : Dicarbondiphosphide Stabilized by N-Heterocyclic Carbenes or Cyclic Diamido Carbenes
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Xiaodan Chen, Zhongshu Li, Jeffrey Harmer, Zoltán Benkõ, Diego M. Andrada, Cheng-Yong Su, Yaqi Li, Hansjoerg Grutzmacher, and Gernot Frenking
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010405 organic chemistry ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Medicinal chemistry ,Catalysis ,0104 chemical sciences ,chemistry ,Yield (chemistry) ,Electrophile ,Organic chemistry ,Molecule ,Carbon - Abstract
Carbon phosphides, Cn Pm , may have highly promising electronic, optical, and mechanical properties, but they are experimentally almost unexplored materials. Phosphaheteroallenes stabilized by N-heterocyclic carbenes undergo a one-electron reduction to yield compounds of the type (L)2 C2 P2 with diverse structures. The use of imidazolylidenes as ligands L give complexes with a central four-membered ring C2 P2 , while more electrophilic cyclic diamidocarbenes (DAC) give a compound with an acyclic π-conjugated CP-PC unit. Cyclic C2 P2 compounds are best described as non-Kekule molecules that are stabilized by coordination to the NHC ligands NHC→(C2 P2 )←NHC. These species can be easily oxidized to give stable radical cations [(NHC)2 C2 P2 ]+. . The remarkably stable molecules with an acylic C2 P2 core are best described with electron-sharing bonds (DAC)=C=P-P=C=(DAC).
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- 2017
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16. Non-Oxido-Vanadium(IV) Metalloradical Complexes with Bidentate 1,2-Dithienylethene Ligands: Observation of Reversible Cyclization of the Ligand Scaffold in Solution
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Matthias Vogt, Enno Lork, Simon Grabowsky, Dirk Schlüter, Florian Kleemiss, Jeffrey Harmer, Malte Fugel, and Kunihisa Sugimoto
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ligand design ,Denticity ,Vanadium ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Catalysis ,reversible ligand cyclization ,law.invention ,Photochromism ,law ,dithienylethene ,Electron paramagnetic resonance ,Molecular switch ,Atropisomer ,Full Paper ,010405 organic chemistry ,Ligand ,Chemistry ,Organic Chemistry ,General Chemistry ,Full Papers ,0104 chemical sciences ,Crystallography ,Coordination Chemistry ,Axial chirality ,cooperative effects ,vanadium ,axial chirality ,EPR spectroscopy - Abstract
Derivatives of 1,2‐dithienylethene (DTE) have superb photochromic properties due to an efficient reversible photocyclization reaction of their hexatriene structure and, thus, have application potential in materials for optoelectronics and (multi‐responsive) molecular switches. Transition‐metal complexes bearing switchable DTE motifs commonly incorporate their coordination site rather distant from the hexatriene system. In this work the redox active ligand 1,2‐bis(2,5‐dimethylthiophen‐3‐yl)ethane‐1,2‐dione is described, which reacts with [V(TMEDA)2Cl2] to give a rare non‐oxido vanadium(IV) species 3(M,M/P,P). This blue complex has two bidentate en‐diolato ligands which chelate the VIV center and give rise to two five‐membered metallacycles with the adjacent hexatriene DTE backbone bearing axial chirality. Upon irradiation with UVA light or prolonged heating in solution, the blue compound 3(M,M/P,P) converts into the purple atropisomer 4(para,M/para,P). Both complexes were isolated and structurally characterized by single‐crystal X‐ray diffraction analysis (using lab source and synchrotron radiation). The antiparallel configuration (M or P helicity) present in both 3(M,M/P,P) and 4(para,M/para,P) is a prerequisite for (reversible) 6π cyclization reactions. A CW EPR spectroscopic study reveals the metalloradical character for 3(M,M/P,P) and 4(para,M/para,P) and indicates dynamic reversible cyclization of the DTE backbone in complex 3(M,M/P,P) at ambient temperature in solution., A rare species: In this work, the redox active ligand 1,2‐bis(2,5‐dimethylthiophen‐3‐yl)ethane‐1,2‐dione is described. Chelation of a vanadium metal center gives rise to an en‐diolate motif in two five‐membered VIV metallacycles with hexatriene DTE backbones bearing axial chirality. Two non‐oxido VIV atropisomeric complexes with metalloradical character were isolated. Their dynamic behavior (reversible cyclization) in solution was studied in a CW EPR spectroscopic study.
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- 2019
17. The oxidation-reduction and electrocatalytic properties of CO dehydrogenase from Oligotropha carboxidovorans
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Paul V. Bernhardt, Palraj Kalimuthu, Russ Hille, Jeffrey Harmer, Dimitri Niks, Stephanie Dingwall, and Mélanie Petitgenet
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0301 basic medicine ,Stereochemistry ,Biophysics ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Redox ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,Multienzyme Complexes ,Redox titration ,Catalytic Domain ,Metalloproteins ,Xanthine oxidase ,Oligotropha carboxidovorans ,chemistry.chemical_classification ,Molybdenum ,030102 biochemistry & molecular biology ,biology ,Electron Spin Resonance Spectroscopy ,Active site ,Cell Biology ,Cobalt ,Electron acceptor ,biology.organism_classification ,Aldehyde Oxidoreductases ,Bradyrhizobiaceae ,0104 chemical sciences ,Quinone ,chemistry ,Enzyme ,biology.protein ,Flavin-Adenine Dinucleotide ,Voltammetry ,Biochemistry and Cell Biology ,Cyclic voltammetry ,Redox potential ,Physical Chemistry (incl. Structural) - Abstract
CO dehydrogenase (CODH) from the Gram-negative bacterium Oligotropha carboxidovorans is a complex metalloenzyme from the xanthine oxidase family of molybdenum-containing enzymes, bearing a unique binuclear Mo-S-Cu active site in addition to two [2Fe-2S] clusters (FeSI and FeSII) and one equivalent of FAD. CODH catalyzes the oxidation of CO to CO2 with the concomitant introduction of reducing equivalents into the quinone pool, thus enabling the organism to utilize CO as sole source of both carbon and energy. Using a variety of EPR monitored redox titrations and spectroelectrochemistry, we report the redox potentials of CO dehydrogenase at pH 7.2 namely MoVI/V, MoV/IV, FeSI2+/+, FeSII2+/+, FAD/FADH and FADH/FADH−. These potentials are systematically higher than the corresponding potentials seen for other members of the xanthine oxidase family of Mo enzymes, and are in line with CODH utilising the higher potential quinone pool as an electron acceptor instead of pyridine nucleotides. CODH is also active when immobilised on a modified Au working electrode as demonstrated by cyclic voltammetry in the presence of CO.
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- 2019
18. Phosphanyl Cyanophosphide Salts: Versatile PCN Building Blocks
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Zhongshu Li, Jaap E. Borger, Fabian Müller, Cheng-Yong Su, Jeffrey Harmer, and Hansjörg Grützmacher
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010405 organic chemistry ,Phosphorus ,chemistry.chemical_element ,Phosphor ,General Chemistry ,010402 general chemistry ,Alkali metal ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Heterocumulene ,Transition metal ,chemistry ,Reagent ,Polymer chemistry - Abstract
The facile preparation of alkali salts of phosphanyl cyanophosphides [NHP-PCN]- (NHP=N-heterocyclic phosphenium) is reported. Their formation is achieved by isoelectronic replacement of O for [N]- in the phosphaketenes NHP-PCO using alkaline hexamethyldisilazide M[N(SiMe3)2] (M=Na, K) as reagent. The new anionic entities are versatile PCN building blocks which allow the formation of a diversity of new cyanophosphine derivates including the first example of a PCNB hetero-cumulene and a PCN-ligated transition metal complex.
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- 2019
19. Elucidating the mechanism of the Ley–Griffith (TPAP) alcohol oxidation
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Peter W. Moore, Jeffrey Harmer, George A. Koutsantonis, Manuel Martínez, Craig M. Williams, Lindsay T. Byrne, Joshua S. Harbort, Paul V. Bernhardt, Timothy J. Zerk, and Sharon Chow
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010405 organic chemistry ,Diphenylmethanol ,Induction period ,Alcohol ,Context (language use) ,General Chemistry ,010402 general chemistry ,Rate-determining step ,01 natural sciences ,0104 chemical sciences ,Catalysis ,chemistry.chemical_compound ,Tetrapropylammonium perruthenate ,chemistry ,Alcohol oxidation ,Organic chemistry - Abstract
The Ley–Griffith reaction is utilized extensively in the selective oxidation of alcohols to aldehydes or ketones. The central catalyst is commercially available tetra-n-propylammonium perruthenate (TPAP, n-Pr4N[RuO4]) which is used in combination with the co-oxidant N-methylmorpholine N-oxide (NMO). Although this reaction has been employed for more than 30 years, the mechanism remains unknown. Herein we report a comprehensive study of the oxidation of diphenylmethanol using the Ley–Griffith reagents to show that the rate determining step involves a single alcohol molecule, which is oxidised by a single perruthenate anion; NMO does not appear in rate law. A key finding of this study is that when pure n-Pr4N[RuO4] is employed in anhydrous solvent, alcohol oxidation initially proceeds very slowly. After this induction period, water produced by alcohol oxidation leads to partial formation of insoluble RuO2, which dramatically accelerates catalysis via a heterogeneous process. This is particularly relevant in a synthetic context where catalyst degradation is usually problematic. In this case a small amount of n-Pr4N[RuO4] must decompose to RuO2 to facilitate catalysis.
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- 2017
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20. AIM-1: An Antibiotic-Degrading Metallohydrolase That Displays Mechanistic Flexibility
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Nataša Mitić, Gerhard Schenk, David L. Ollis, Jeffrey Harmer, Marcelo Monteiro Pedroso, Luke W. Guddat, David L. Tierney, Waleed Helweh, Christopher Selleck, Whitney R. Craig, and James A. Larrabee
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0301 basic medicine ,Stereochemistry ,medicine.drug_class ,Antibiotics ,Human pathogen ,Computational biology ,010402 general chemistry ,01 natural sciences ,beta-Lactamases ,Catalysis ,Metallo β lactamase ,Substrate Specificity ,03 medical and health sciences ,Antibiotic resistance ,medicine ,Aurora Kinase B ,Humans ,Nitrocefin ,Flexibility (engineering) ,Chemistry ,Organic Chemistry ,General Chemistry ,Anti-Bacterial Agents ,Cephalosporins ,0104 chemical sciences ,Kinetics ,030104 developmental biology ,Substrate specificity ,Mobile genetic elements - Abstract
Antibiotic resistance has emerged as a major threat to global health care. This is largely due to the fact that many pathogens have developed strategies to acquire resistance to antibiotics. Metallo-β-lactamases (MBL) have evolved to inactivate most of the commonly used β-lactam antibiotics. AIM-1 is one of only a few MBLs from the B3 subgroup that is encoded on a mobile genetic element in a major human pathogen. Here, its mechanism of action was characterised with a combination of spectroscopic and kinetic techniques and compared to that of other MBLs. Unlike other MBLs it appears that AIM-1 has two avenues available for the turnover of the substrate nitrocefin, distinguished by the identity of the rate-limiting step. This observation may be relevant with respect to inhibitor design for this group of enzymes as it demonstrates that at least some MBLs are very flexible in terms of interactions with substrates and possibly inhibitors.
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- 2016
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21. Controlling Au Photodeposition on Large ZnO Nanoparticles
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Jeffrey Harmer, Eric R. Waclawik, Esa Jaatinen, Matthew P. Shortell, Joseph F. S. Fernando, and Christopher J. Noble
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Permittivity ,Materials science ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,Photoexcitation ,chemistry.chemical_compound ,Electron transfer ,chemistry ,Oleylamine ,Transmission electron microscopy ,Photocatalysis ,General Materials Science ,Solvent effects ,0210 nano-technology ,Deposition (law) - Abstract
This study investigated how to control the rate of photoreduction of metastable AuCl2(-) at the solid-solution interface of large ZnO nanoparticles (NPs) (50-100 nm size). Band-gap photoexcitation of electronic charge in ZnO by 370 nm UV light yielded Au NP deposition and the formation of ZnO-Au NP hybrids. Au NP growth was observed to be nonepitaxial, and the patterns of Au photodeposition onto ZnO NPs observed by high-resolution transmission electron microscopy were consistent with reduction of AuCl2(-) at ZnO facet edges and corner sites. Au NP photodeposition was effective in the presence of labile oleylamine ligands attached to the ZnO surface; however, when a strong-binding dodecanethiol ligand coated the surface, photodeposition was quenched. Rates of interfacial electron transfer at the ZnO-solution interface were adjusted by changing the solvent, and these rates were observed to strongly depend on the solvent's permittivity (ε) and viscosity. From measurements of electron transfer from ZnO to the organic dye toluidine blue at the ZnO-solution interface, it was confirmed that low ε solvent mixtures (ε ≈ 9.5) possessed markedly higher rates of photocatalytic interfacial electron transfer (∼3.2 × 10(4) electrons·particle(-1)·s(-1)) compared to solvent mixtures with high ε (ε = 29.9, ∼1.9 × 10(4) electrons·particle(-1)·s(-1)). Dissolved oxygen content in the solvent and the exposure time of ZnO to band-gap, near-UV photoexcitation were also identified as factors that strongly affected Au photodeposition behavior. Production of Au clusters was favored under conditions that caused electron accumulation in the ZnO-Au NP hybrid. Under conditions where electron discharge was rapid (such as in low ε solvents), AuCl2(-) precursor ions photoreduced at ZnO surfaces in less than 5 s, leading to deposition of several small, isolated ∼6 nm Au NP on the ZnO host instead.
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- 2016
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22. Active site architecture reveals coordination sphere flexibility and specificity determinants in a group of closely related molybdoenzymes
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Palraj Kalimuthu, Daniel Ellis, Paul V. Bernhardt, Martin L. Kirk, Zhenyao Luo, Bernd Clement, Bostjan Kobe, Jeffrey Harmer, Qifeng Zhong, Ulrike Kappler, K.C. Khadanand, Michel A. Struwe, Jing Yang, and Alastair G. McEwan
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0301 basic medicine ,Rs, Rhodobacter sphaeroides ,BV, benzyl viologen ,EPR, electron paramagnetic resonance ,Protein Conformation ,DMSO, dimethyl sulfoxide ,Ligands ,Biochemistry ,Substrate Specificity ,chemistry.chemical_compound ,molybdenum ,enzyme kinetics ,BSO, biotin sulfoxide ,Catalytic Domain ,lpH, low pH ,MetSO, methionine sulfoxide ,Sm, Shewanella massilia ,chemistry.chemical_classification ,MPTSO, methyl p-tolyl sulfoxide ,TorA, TorA TMAO reductase ,biology ,TMAO, trimethylamine N-oxide ,Chemistry ,BisC, biotin sulfoxide reductases ,CV, cyclic voltammetry ,Enzyme structure ,enzyme structure ,Amino acid ,PGD, pyranopterin guanine dinucleotide ,Methionine sulfoxide reductase ,MV, methyl viologen ,Oxidoreductases ,Oxidation-Reduction ,Research Article ,Stereochemistry ,racMetSO, racemic methionine sulfoxide ,Ec, Escherichia coli ,Nitrate reductase ,Catalysis ,methionine sulfoxide ,GC, glassy carbon ,03 medical and health sciences ,HiMtsZ, methionine sulfoxide reductase from Haemophilus influenzae ,Bacterial Proteins ,Hi, Haemophilus influenzae ,Metalloproteins ,Rc, Rhodobacter capsulatus ,Amino Acid Sequence ,Enzyme kinetics ,enzyme specificity ,Molecular Biology ,DorA, DorA DMSO reductase ,Sequence Homology, Amino Acid ,030102 biochemistry & molecular biology ,ZORA, zero-order regular approximation ,Ligand ,Methionine sulfoxide ,Active site ,Cell Biology ,Haemophilus influenzae ,electron paramagnetic resonance (EPR) ,Kinetics ,030104 developmental biology ,electrochemistry ,biology.protein ,NHE, normal hydrogen electrode ,NarGH, NarGH dissimilatory nitrate reductase - Abstract
MtsZ is a molybdenum-containing methionine sulfoxide reductase that supports virulence in the human respiratory pathogen Haemophilus influenzae (Hi). HiMtsZ belongs to a group of structurally and spectroscopically uncharacterized S-/N-oxide reductases, all of which are found in bacterial pathogens. Here, we have solved the crystal structure of HiMtsZ, which reveals that the HiMtsZ substrate-binding site encompasses a previously unrecognized part that accommodates the methionine sulfoxide side chain via interaction with His182 and Arg166. Charge and amino acid composition of this side chain-binding region vary and, as indicated by electrochemical, kinetic, and docking studies, could explain the diverse substrate specificity seen in closely related enzymes of this type. The HiMtsZ Mo active site has an underlying structural flexibility, where dissociation of the central Ser187 ligand affected catalysis at low pH. Unexpectedly, the two main HiMtsZ electron paramagnetic resonance (EPR) species resembled not only a related dimethyl sulfoxide reductase but also a structurally unrelated nitrate reductase that possesses an Asp-Mo ligand. This suggests that contrary to current views, the geometry of the Mo center and its primary ligands, rather than the specific amino acid environment, is the main determinant of the EPR properties of mononuclear Mo enzymes. The flexibility in the electronic structure of the Mo centers is also apparent in two of three HiMtsZ EPR-active Mo(V) species being catalytically incompetent off-pathway forms that could not be fully oxidized.
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- 2021
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23. Copper Complexes of Benzoylacetone Bis-Thiosemicarbazones: Metal and Ligand Based Redox Reactivity
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Paul V. Bernhardt, Jeffrey Harmer, and Jessica K. Bilyj
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chemistry.chemical_classification ,Ketone ,Chemistry ,Ligand ,Substituent ,General Chemistry ,Redox ,law.invention ,Coordination complex ,chemistry.chemical_compound ,Deprotonation ,law ,Polymer chemistry ,Reactivity (chemistry) ,Electron paramagnetic resonance - Abstract
Bis-thiosemicarbazones derived from the β-diketone benzoylacetone (H3banR, R=Me, Et, Ph) are potentially tetradentate N2S2 ligands whose coordination chemistry with copper is reported. In the absence of oxygen and in the presence of base they form anionic CuII complexes of the fully deprotonated ligands [CuII(banR)]–. Upon exposure to atmospheric oxygen they undergo a complex series of reactions leading to two types of products; one a ligand oxidised ketone complex [CuII(banRO)] and the other an unprecedented dimeric di-CuIII complex [(CuIII(banR))2] depending on the R substituent. Time-resolved UV-vis spectroscopy, cyclic voltammetry, spectroelectrochemistry, and electron paramagnetic resonance (EPR) spectroscopy have been used to identify intermediates on the way to stable products formed under both anaerobic and aerobic conditions. It is found that both ligand-centred and Cu-centred oxidation reactions are occurring in parallel leading to this unusually complicated mixture of products.
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- 2021
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24. Cross-linking, DEER-spectroscopy and molecular dynamics confirm the inward facing state of P-glycoprotein in a lipid membrane
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Ian D. Kerr, Jeffrey Harmer, Deborah A. Briggs, Richard Callaghan, Megan L. O'Mara, and Alex R. Carey Hulyer
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Protein Conformation ,Molecular Dynamics Simulation ,Membrane Lipids ,Mice ,03 medical and health sciences ,Molecular dynamics ,Structural Biology ,Animals ,Humans ,Nucleotide ,ATP Binding Cassette Transporter, Subfamily B, Member 1 ,Binding site ,Lipid bilayer ,030304 developmental biology ,P-glycoprotein ,chemistry.chemical_classification ,0303 health sciences ,Binding Sites ,biology ,Nucleotides ,Hydrolysis ,Cell Membrane ,030302 biochemistry & molecular biology ,Electron Spin Resonance Spectroscopy ,Ligand (biochemistry) ,Transmembrane domain ,chemistry ,biology.protein ,Biophysics ,Cysteine - Abstract
The drug efflux pump P-glycoprotein (P-gp) displays a complex transport mechanism involving multiple drug binding sites and two centres for nucleotide hydrolysis. Elucidating the molecular mechanism of transport remains elusive and the availability of P-gp structures in distinct natural and ligand trapped conformations will accelerate our understanding. The present investigation sought to provide biochemical data to validate specific features of these structures; with particular focus on the transmembrane domain that provides the transport conduit. Hence our focus was on transmembrane helices six and twelve (TM6/TM12), which are believed to participate in drug binding, as they line the central transport conduit and provide a direct link to the catalytic centres. A series of P-gp mutants were generated with a single cysteine in both TM6 and TM12 to facilitate measurement of inter-helical distances using cross-linking and DEER strategies. Experimental results were compared to published structures per se and those refined by MD simulations. This analysis revealed that the refined inward-facing murine structure (4M1M) of P-gp provides a good representation of the proximity, topography and relative motions of TM6 and TM12 in reconstituted human P-gp.
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- 2020
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25. Metastable phosphorus neutral monoradical: a key intermediate in the bicyclic cage formation
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Zhongshu Li, Alexander Hinz, Jeffrey Harmer, and Xiaodan Chen
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Bicyclic molecule ,010405 organic chemistry ,Concerted reaction ,Phosphorus ,Substrate (chemistry) ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Cycloaddition ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Metastability ,Cage ,Carbene - Abstract
A key intermediate in the formation of a bicyclic cage formed between a biradical (LCP)2 (L = carbene) and an unsaturated substrate via a [2 + 2] cycloaddition reaction has been isolated and fully characterized including by X-ray diffraction analysis. The isolation of this intermediate proves that this cycloaddition reaction proceeds stepwise which is preferred over a concerted mechanism.
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- 2019
26. Optimizing the transformation of HYSCORE data using the maximum entropy algorithm
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Jeffrey Harmer, Alina E. Motygullina, and Mehdi Mobli
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Nuclear and High Energy Physics ,Pulsed EPR ,Principle of maximum entropy ,Biophysics ,Nonuniform sampling ,Large range ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Biochemistry ,Nmr data ,Spectral line ,030218 nuclear medicine & medical imaging ,0104 chemical sciences ,03 medical and health sciences ,0302 clinical medicine ,Data Noise ,Entropy (information theory) ,Algorithm ,Mathematics - Abstract
Non-uniform sampling (NUS) in combination with the Maximum Entropy (MaxEnt) algorithm as applied to multi-dimensional NMR data has been thoroughly investigated and the NUS approach shown to provide significant sensitivity improvements as compared to methods using uniformly sampled (US) data and the discrete Fourier transform (DFT). Hyperfine sublevel correlation (HYSCORE) is a standard pulse EPR experiment that can potentially benefit greatly from this approach, but the data present unique challenges as compared to NMR. HYSCORE data typically exhibit a very large range of peak intensities, signals are in the form of irregularly shaped ridges with variable intensities, and time traces are generally truncated to save measurement time. MaxEnt has the advantageous properties that it does not require US data, dampens weak signals (noise) and does not suffer from windowing artifacts due to truncation of the time traces. Critical to the success of the MaxEnt algorithm is the choice of the two input parameters aim and def which describe the data noise and contribution of entropy in the optimization, respectively. In this paper we expand our preliminary study on the application of MaxEnt to the reconstruction of HYSCORE spectra to include a detailed analysis on sensitivity to detect weak peaks, investigate the non-linearity of the transformation and ascertain if it can be characterized by the introduction of synthetic peaks, and define a general range for the choice of aim and def. Furthermore, the ability of the MaxEnt method to remove windowing artefacts in uniformly sampled truncated HYSCORE data is described.
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- 2019
27. Isolation and Characterization of a Bismuth(II) Radical
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Simon Granville, Jeffrey Harmer, Matthias Lein, Christopher M. Fitchett, Ryan J. Schwamm, and Martyn P. Coles
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Chemistry ,Magnesium ,Inorganic chemistry ,chemistry.chemical_element ,General Medicine ,General Chemistry ,Chloride ,Catalysis ,law.invention ,Bismuth ,Crystallography ,Paramagnetism ,Main group element ,Unpaired electron ,law ,Oxidation state ,medicine ,Electron paramagnetic resonance ,medicine.drug - Abstract
More than 80 years after Paneth's report of dimethyl bismuth, the first monomeric Bi(II) radical that is stable in the solid state has been isolated and characterized. Reduction of the diamidobismuth(III) chloride Bi(NON(Ar))Cl (NON(Ar)=[O(SiMe2NAr)2](2-); Ar=2,6-iPr2C6H3) with magnesium affords the Bi(II) radical ˙Bi(NON(Ar)). X-ray crystallographic measurements are consistent with a two-coordinate bismuth in the +2 oxidation state with no short intermolecular contacts, and solid-state SQUID magnetic measurements indicate a paramagnetic compound with a single unpaired electron. EPR and density functional calculations show a metal-centered radical with >90% spin density in a p-type orbital on bismuth.
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- 2015
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28. L 3 C 3 P 3 : Tricarbontriphosphide Tricyclic Radicals and Cations Stabilized by Cyclic (alkyl)(amino)carbenes
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Guy Bertrand, Yuanfeng Hou, Zhongshu Li, Yaqi Li, Hansjörg Grützmacher, Cheng-Yong Su, Alexander Hinz, Jeffrey Harmer, Department of Chemistry, UCSD-CNRS Joint Research Chemistry Laboratory (UMI 3555), University of California [San Diego] (UC San Diego), and University of California-University of California-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
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Radical ,Conjugated system ,[CHIM.INOR]Chemical Sciences/Inorganic chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Medicinal chemistry ,Catalysis ,law.invention ,chemistry.chemical_compound ,law ,[CHIM.COOR]Chemical Sciences/Coordination chemistry ,Electron paramagnetic resonance ,Alkyl ,ComputingMilieux_MISCELLANEOUS ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,Cationic polymerization ,General Chemistry ,[CHIM.CATA]Chemical Sciences/Catalysis ,3. Good health ,0104 chemical sciences ,Carbene ,Tricyclic - Abstract
Alkynes usually oligomerize to give rings with a conjugated π-electron system. In contrast, phosphaalkynes, R-C≡P, frequently give compounds with polycyclic structures, which are thermodynamically more stable than the corresponding π-conjugated isomers. The syntheses of the first CP tricyclic compounds are reported with either radical or cationic ground states stabilized by cyclic (alkyl)(amino)carbenes (CAACs). These compounds may be considered as examples of tricarbontriphosphide coordinated by carbenes and are likely formed via trimerization of the corresponding mono-radicals CAAC-CP. The mechanism for the formation of these tricarbontriphosphide radicals has been rationalized by a combination of experiments and DFT calculations.
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- 2018
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29. Exploiting orientation-selective DEER : determining molecular structure in systems containing Cu(II) centres
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Michael W. Jones, Alice M. Bowen, Jonathan R. Dilworth, Christiane R. Timmel, Thembanikosi G. Gaule, Jeffrey Harmer, Michael J. McPherson, Janet E. Lovett, The Royal Society, University of St Andrews. School of Physics and Astronomy, and University of St Andrews. Biomedical Sciences Research Complex
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Models, Molecular ,Porphyrins ,Molecular model ,Dimer ,General Physics and Astronomy ,Nanotechnology ,02 engineering and technology ,Molecular Dynamics Simulation ,Physics and Astronomy(all) ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,Molecular dynamics ,Coordination Complexes ,Molecule ,Physical and Theoretical Chemistry ,Conformational isomerism ,QC ,Molecular Structure ,Electron Spin Resonance Spectroscopy ,DAS ,021001 nanoscience & nanotechnology ,Resonance (chemistry) ,Porphyrin ,0104 chemical sciences ,Crystallography ,QC Physics ,chemistry ,ddc:540 ,Density functional theory ,Amine Oxidase (Copper-Containing) ,0210 nano-technology ,Copper - Abstract
We gratefully acknowledge financial support from the EPSRC, BBSRC and Royal Society. JRH thanks the ARC (FT120100421) for financial support. JEL and AMB would like to thank University College, Oxford for financial support. JEL would also like to thank The Royal Society for a University Research Fellowship. TGG and AMB were supported by a BBSRC studentships. Orientation-selective DEER (Double Electron-Electron Resonance) measurements were conducted on a series of rigid and flexible molecules containing Cu(ii) ions. A system with two rigidly held Cu(ii) ions was afforded by the protein homo-dimer of copper amine oxidase from Arthrobacter globiformis. This system provided experimental DEER data between two Cu(ii) ions with a well-defined distance and relative orientation to assess the accuracy of the methodology. Evaluation of orientation-selective DEER (os DEER) on systems with limited flexibility was probed using a series of porphyrin-based Cu(ii)-nitroxide and Cu(ii)-Cu(ii) model systems of well-defined lengths synthesized for this project. Density functional theory was employed to generate molecular models of the conformers for each porphyrin-based Cu(ii) dimer studied. Excellent agreement was found between DEER traces simulated using these computed conformers and the experimental data. The performance of different parameterised structural models in simulating the experimental DEER data was also investigated. The results of this analysis demonstrate the degree to which the DEER data define the relative orientation of the two Cu(ii) ions and highlight the need to choose a parameterised model that captures the essential features of the flexibility (rotational freedom) of the system being studied. Publisher PDF
- Published
- 2017
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30. Neural response after a single ECT session during retrieval of emotional self-referent words in depression: a randomized, sham-controlled fMRI study
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Olaf B. Paulson, Julian Macoveanu, M.M. Støttrup, Anders Jørgensen, Jeffrey Harmer, Martin Balslev Jørgensen, Hans Mørch Jensen, Caroline V Ott, Lars Vedel Kessing, Hartwig R. Siebner, and Kamilla W. Miskowiak
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Male ,medicine.medical_treatment ,Emotions ,Self-referent memory ,Neuropsychological Tests ,Audiology ,Regular Research Articles ,law.invention ,Depressive Disorder, Treatment-Resistant ,0302 clinical medicine ,Electroconvulsive therapy ,Randomized controlled trial ,law ,emotional bias ,Medicine ,Pharmacology (medical) ,Electroconvulsive Therapy ,Language ,Brain Mapping ,medicine.diagnostic_test ,Depression ,fMRI ,Brain ,Emotional bias ,Magnetic Resonance Imaging ,Antidepressive Agents ,self-referent memory ,Psychiatry and Mental health ,FMRI ,depression ,Major depressive disorder ,Female ,Clinical psychology ,Adult ,medicine.medical_specialty ,03 medical and health sciences ,Double-Blind Method ,Memory ,Humans ,Pharmacology ,Depressive Disorder, Major ,business.industry ,ECT ,Magnetic resonance imaging ,medicine.disease ,Self Concept ,030227 psychiatry ,Mood ,FMRIB Software Library ,business ,Functional magnetic resonance imaging ,Neurocognitive ,030217 neurology & neurosurgery - Abstract
Background Negative neurocognitive bias is a core feature of depression that is reversed by antidepressant drug treatment. However, it is unclear whether modulation of neurocognitive bias is a common mechanism of distinct biological treatments. This randomized controlled functional magnetic resonance imaging study explored the effects of a single electroconvulsive therapy session on self-referent emotional processing. Methods Twenty-nine patients with treatment-resistant major depressive disorder were randomized to one active or sham electroconvulsive therapy session at the beginning of their electroconvulsive therapy course in a double-blind, between-groups design. The following day, patients were given a self-referential emotional word categorization test and a free recall test. This was followed by an incidental word recognition task during whole-brain functional magnetic resonance imaging at 3T. Mood was assessed at baseline, on the functional magnetic resonance imaging day, and after 6 electroconvulsive therapy sessions. Data were complete and analyzed for 25 patients (electroconvulsive therapy: n = 14, sham: n = 11). The functional magnetic resonance imaging data were analyzed using the FMRIB Software Library randomize algorithm, and the Threshold-Free Cluster Enhancement method was used to identify significant clusters (corrected at P < .05). Results A single electroconvulsive therapy session had no effect on hippocampal activity during retrieval of emotional words. However, electroconvulsive therapy reduced the retrieval-specific neural response for positive words in the left frontopolar cortex. This effect occurred in the absence of differences between groups in behavioral performance or mood symptoms. Conclusions The observed effect of electroconvulsive therapy on prefrontal response may reflect early facilitation of memory for positive self-referent information, which could contribute to improvements in depressive symptoms including feelings of self-worth with repeated treatments.
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- 2017
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31. Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community
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David L. Tierney, Waleed Helweh, Philip Hugenholtz, Whitney R. Craig, Marcelo Monteiro Pedroso, James A. Larrabee, Christopher Selleck, Jeffrey Harmer, Gerhard Schenk, Charmaine Enculescu, Nataša Mitić, and Gene W. Tyson
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0301 basic medicine ,Models, Molecular ,Modern medicine ,medicine.drug_class ,030106 microbiology ,Antibiotics ,Population ,Biophysics ,Permafrost ,Sequence Homology ,Human pathogen ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,beta-Lactamases ,Microbiology ,Substrate Specificity ,Biomaterials ,03 medical and health sciences ,Antibiotic resistance ,Bacterial Proteins ,medicine ,Humans ,Microbiome ,Amino Acid Sequence ,education ,Genetics ,chemistry.chemical_classification ,education.field_of_study ,biology ,Metals and Alloys ,Active site ,0104 chemical sciences ,Anti-Bacterial Agents ,Enzyme ,Phenotype ,chemistry ,Chemistry (miscellaneous) ,Metals ,biology.protein ,Metagenome - Abstract
Antibiotic resistance is a major global health problem, one that threatens to derail the benefits garnered from arguably the greatest success of modern medicine, the discovery of antibiotics. Among the most potent agents contributing to antibiotic resistance are metallo-β-lactamases (MBLs). The discovery of MBL-like enzymes in microorganisms that are not in contact with the human population is of particular concern as these proteins already have the in-built capacity to inactivate antibiotics, even though they may not need MBL activity for their survival. Here, we demonstrate that a microbiome from a remote and frozen environment in Alaska harbours at least one highly efficient MBL, LRA-8. LRA-8 is homologous to the B3 subgroup of MBLs and has a substrate profile and catalytic properties similar to well-known members of this enzyme family, which are expressed by major human pathogens. LRA-8 is predominantly a penicillinase, but is also active towards carbapenems, but not cephalosporins. Spectroscopic studies indicate that LRA-8 has an active site structure similar to that of other MBLs (in particular B3 subgroup representative AIM-1), and a combination of steady-state and pre-steady-state kinetic data demonstrate that the enzyme is likely to employ a metal ion-bridging hydroxide to initiate catalysis. The rate-limiting step is the decay of a chromophoric, tetrahedral intermediate, as is observed in various other MBLs. Thus, studying the properties of such “pristine” MBL-like proteins may provide insight into the structural plasticity of this family of enzymes that may facilitate functional promiscuity, while important insight into the evolution of MBLs may also be gained.
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- 2017
32. Reaction mechanism of the metallohydrolase CpsB from Streptococcus pneumoniae, a promising target for novel antimicrobial agents
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Nataša Mitić, Lawrence R. Gahan, Jeffrey Harmer, Alistair J. Standish, James A. Larrabee, Christopher Selleck, Gerhard Schenk, David L. Tierney, Marcelo Monteiro Pedroso, and Jessica K. Bilyj
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0301 basic medicine ,Circular dichroism ,Stereochemistry ,Metal ions in aqueous solution ,Calorimetry ,010402 general chemistry ,Crystallography, X-Ray ,01 natural sciences ,Inorganic Chemistry ,03 medical and health sciences ,Anti-Infective Agents ,Bacterial Proteins ,Catalytic Domain ,Hydrolase ,Nitrocefin ,Binding site ,Manganese ,Binding Sites ,biology ,Chemistry ,Circular Dichroism ,Hydrolysis ,Electron Spin Resonance Spectroscopy ,Substrate (chemistry) ,Active site ,Isothermal titration calorimetry ,Cobalt ,0104 chemical sciences ,Cephalosporins ,Kinetics ,030104 developmental biology ,Streptococcus pneumoniae ,biology.protein ,Biocatalysis ,Protein Tyrosine Phosphatases - Abstract
CpsB is a metal ion-dependent hydrolase involved in the biosynthesis of capsular polysaccharides in bacterial organisms. The enzyme has been proposed as a promising target for novel chemotherapeutics to combat antibiotic resistance. The crystal structure of CpsB indicated the presence of as many as three closely spaced metal ions, modelled as Mn2+, in the active site. While the preferred metal ion composition in vivo is obscure Mn2+ and Co2+ have been demonstrated to be most effective in reconstituting activity. Using isothermal titration calorimetry (ITC) we have demonstrated that, in contrast to the crystal structure, only two Mn2+ or Co2+ ions bind to a monomer of CpsB. This observation is in agreement with magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) data that indicate the presence of two weakly ferromagnetically coupled Co2+ ions in the active site of catalytically active CpsB. While CpsB is known to be a phosphoesterase we have also been able to demonstrate that this enzyme is efficient in hydrolyzing the β-lactam substrate nitrocefin. Steady-state and stopped-flow kinetics measurements further indicated that phosphoesters and nitrocefin undergo catalysis in a conserved manner with a metal ion-bridging hydroxide acting as a nucleophile. Thus, the combined physicochemical studies demonstrate that CpsB is a novel member of the dinuclear metallohydrolase family.
- Published
- 2017
33. EPR analysis of cyanide complexes of wild-type human neuroglobin and mutants in comparison to horse heart myoglobin
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Jeffrey Harmer, Florin Trandafir, Luc Moens, Sylvia Dewilde, and Sabine Van Doorslaer
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Models, Molecular ,Cyanide ,Biophysics ,Neuroglobin ,Nerve Tissue Proteins ,Biochemistry ,law.invention ,chemistry.chemical_compound ,Nuclear magnetic resonance ,law ,medicine ,Animals ,Humans ,Point Mutation ,Horses ,Electron paramagnetic resonance ,Biology ,Hyperfine structure ,Electron nuclear double resonance ,Cyanides ,Myoglobin ,Physics ,Organic Chemistry ,Electron Spin Resonance Spectroscopy ,Heart ,Carbon-13 NMR ,Globins ,Chemistry ,Crystallography ,chemistry ,Ferric ,Mutant Proteins ,medicine.drug - Abstract
Electron paramagnetic resonance (EPR) data reveal large differences between the ferric (C-13-)cyanide complexes of wild-type human neuroglobin (NGB) and its H64Q and F28L point mutants and the cyanide complexes of mammalian myo- and haemoglobin. The point mutations, which involve residues comprising the distal haem pocket in NGB, induce smaller, but still significant changes, related to changes in the stabilization of the cyanide ligand. Furthermore, for the first time, the full C-13 hyperfine tensor of the cyanide carbon of cyanide-ligated horse heart myoglobin (hhMb) was determined using Davies ENDOR (electron nuclear double resonance). Disagreement of these experimental data with earlier predictions based on C-13 NMR data and a theoretical model reveal significant flaws in the model assumptions. The same ENDOR procedure allowed also partial determination of the corresponding C-13 hyperfine tensor of cyanide-ligated NGB and H64QNGB. These C-13 parameters differ significantly from those of cyanide-ligated hhMb and challenge our current theoretical understanding of how the haem environment influences the magnetic parameters obtained by EPR and NMR in cyanide-ligated haem proteins. (C) 2014 Elsevier B.V. All rights reserved.
- Published
- 2014
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34. Stable GaX2, InX2 and TlX2 radicals
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Nicholas Phillips, Michael J. Kelly, Simon Aldridge, Cameron Jones, Krishna Hassomal Birjkumar, Jeffrey Harmer, Deepak Dange, Andrew D. Schwarz, Christina Y. Tang, Nikolas Kaltsoyannis, Philip Mountford, Rémi Tirfoin, and Andrey V. Protchenko
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General Chemical Engineering ,Radical ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,Medicinal chemistry ,Ion ,chemistry.chemical_compound ,Monomer ,Main group element ,chemistry ,Group (periodic table) ,Thallium ,Gallium ,Indium - Abstract
The chemistry of the Group 13 metals is dominated by the +1 and +3 oxidation states, and simple monomeric M(II) species are typically short-lived, highly reactive species. Here we report the first thermally robust monomeric MX2 radicals of gallium, indium and thallium. By making use of sterically demanding boryl substituents, compounds of the type M(II)(boryl)2 (M = Ga, In, Tl) can be synthesized. These decompose above 130 °C and are amenable to structural characterization in the solid state by X-ray crystallography. Electron paramagnetic resonance and computational studies reveal a dominant metal-centred character for all three radicals (>70% spin density at the metal). M(II) species have been invoked as key short-lived intermediates in well-known electron-transfer processes; consistently, the chemical behaviour of these novel isolated species reveals facile one-electron shuttling processes at the metal centre.
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- 2014
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35. Back Cover: Phosphanyl Cyanophosphide Salts: Versatile PCN Building Blocks (Angew. Chem. Int. Ed. 33/2019)
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Zhongshu Li, Hansjörg Grützmacher, Fabian Müller, Jaap E. Borger, Jeffrey Harmer, and Cheng-Yong Su
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Heterocumulene ,chemistry ,Phosphorus ,INT ,Polymer chemistry ,chemistry.chemical_element ,Cover (algebra) ,General Chemistry ,Catalysis - Published
- 2019
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36. Non-uniform sampling in EPR – optimizing data acquisition for HYSCORE spectroscopy
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Mehdi Mobli, Jeffrey Harmer, Yasvir A. Tesiram, Ian M. Brereton, and K. K. Nakka
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Chemistry ,Pulsed EPR ,Nonuniform sampling ,Analytical chemistry ,General Physics and Astronomy ,Sampling (statistics) ,law.invention ,Computational physics ,Data acquisition ,law ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Spectroscopy ,Hyperfine structure ,Order of magnitude - Abstract
Non-uniform sampling combined with maximum entropy reconstruction is a powerful technique used in multi-dimensional NMR spectroscopy to reduce sample measurement time. We adapted this technique to the pulse EPR experiment hyperfine sublevel correlation (HYSCORE) and show that experimental times can be shortened by approximately an order of magnitude as compared to conventional linear sampling with negligible loss of information.
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- 2014
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37. Sodium phosphaethynolate, Na(OCP), as a 'P' transfer reagent for the synthesis of N-heterocyclic carbene supported P3and PAsP radicals
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Aaron M. Tondreau, Jeffrey Harmer, Zoltán Benkő, and Hansjörg Grützmacher
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Electron transfer ,chemistry.chemical_compound ,chemistry ,Phosphinidene ,Reagent ,Radical ,Inorganic chemistry ,General Chemistry ,DABCO ,Carbene ,Medicinal chemistry ,Cycloaddition ,Adduct - Abstract
Sodium phosphaethynolate, Na(OCP), reacts as a P− transfer reagent with the imidazolium salt [DippNHC–H][Cl] [DippNHC = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene] to give the parent phosphinidene–carbene adduct, DippNHCPH, with the loss of CO. In a less atom economic reaction, the cage compound, P7(TMS)3 (TMS = SiMe3) reacts likewise with the imidazolium salt to yield DippNHCPH thereby giving two entry points into parent phosphinidene-based chemistry. From the building block DippNHCPH, the carbene-supported P3 cation [(DippNHC)2(μ-P3)][Cl] was rationally synthesized using half an equivalent of PCl3 in the presence of DABCO (1,4-diazabicyclo[2.2.2]octane). The corresponding arsenic analogue, [(DippNHC)2(μ-PAsP)][Cl], was synthesized in the same manner using AsCl3. The reduction of both [(DippNHC)2(μ-P3)][Cl] and [(DippNHC)2(μ-PAsP)][Cl] into their corresponding neutral radical species was achieved simply by reducing the compounds with an excess of magnesium. This allowed the electronic structures of the compounds to be investigated using a combination of NMR and EPR spectroscopy, X-ray crystallography, and computational studies. The findings of the investigation into (DippNHC)2(μ-P3) and (DippNHC)2(μ-PAsP) reveal the central pnictogen atom in both cases as the main carrier of the spin density (∼60%), and that they are best described as the P3 or PAsP analogues of the elusive allyl radical dianion. The phosphorus radical was also able to undergo a cycloaddition with an activated acetylene, followed by an electron transfer to give the ion pair [(DippNHC)2(μ-P3)][P3(C(COOMe))2].
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- 2014
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38. Double Electron-Electron Resonance traces recorded on the CYP199A2-HaPux complex and the distances found to correspond these measurements
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Eachan Johnson, Francesco Mercuri, Nicola Hoskins, Ruihong Qiao, James McCullagh, Janet Lovett, Stephen Bell, Weihong Zhou, Christiane Timmel, Luet Lok Wong, Jeffrey Harmer, Alice Bowen, Eachan Johnson, Francesco Mercuri, Nicola Hoskins, Ruihong Qiao, James McCullagh, Janet Lovett, Stephen Bell, Weihong Zhou, Christiane Timmel, Luet Lok Wong, Jeffrey Harmer, and Alice Bowen
- Published
- 2018
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39. Development of a Metal-Ion-Mediated Base Pair for Electron Transfer in DNA
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Christian Wellner, Patrick Carl, Hans-Achim Wagenknecht, Timo Augenstein, Wolfgang Schmucker, Thomas Ehrenschwender, Jeffrey Harmer, and Frank Breher
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Base pair ,Metal ions in aqueous solution ,Electrons ,Photochemistry ,Catalysis ,law.invention ,Electron Transport ,Metal ,Electron transfer ,chemistry.chemical_compound ,law ,Electron paramagnetic resonance ,Base Pairing ,Ligand ,Organic Chemistry ,Electron Spin Resonance Spectroscopy ,Nucleosides ,DNA ,General Chemistry ,Fluorescence ,chemistry ,Metals ,visual_art ,Hydroxyquinolines ,visual_art.visual_art_medium ,Copper - Abstract
A new C-nucleoside structurally based on the hydroxyquinoline ligand was synthesized that is able to form stable pairs in DNA in both the absence and the presence of metal ions. The interactions between the metal centers in adjacent CuII-mediated base pairs in DNA were probed by electron paramagnetic resonance (EPR) spectroscopy. The metal-metal distance falls into the range of previously reported values. Fluorescence studies with a donor-DNA-acceptor system indicate that photoinduced charge-transfer processes across these metal-ion-mediated base pairs in DNA occur more efficiently than over natural base pairs. Ace of base: DNA duplex stability can be significantly increased by coordinating CuII ions to hydroxyquinoline base pairs (metal-mediated base pairing; see scheme). Fluorescence studies with a donor-DNA-acceptor system indicate that photoinduced charge-transfer processes across these metal-ion-mediated base pairs in DNA occur more efficiently than over natural base pairs.
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- 2013
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40. CW and Pulse EPR of Cytochrome P450 to Determine Structure and Function
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Jeanette E. Stok, Jeffrey Harmer, Stephen Bell, James J. De Voss, and Joshua S. Harbort
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0301 basic medicine ,Materials science ,030102 biochemistry & molecular biology ,biology ,Pulsed EPR ,Active site ,010402 general chemistry ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,law.invention ,03 medical and health sciences ,Paramagnetism ,Catalytic cycle ,Oxidation state ,law ,biology.protein ,Continuous wave ,Sample preparation ,Electron paramagnetic resonance - Abstract
Cytochromes P450 (P450s) are a diverse class of biological monooxygenases found in a wide variety of organisms, known for their chemical versatility and reaction specificity. While an array of chemical techniques are available to study P450s, continuous wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies provide unique insight into the structure and function of the protein by probing various paramagnetic states. In this review we will demonstrate how EPR techniques are used to reveal information about the arrangement and conformation of P450 electron-transport protein complexes, characterise the active site oxidation state and the interactions with substrates and inhibitors. In addition, when combined with sample preparation using cryoreduction and freeze-quench techniques, EPR can be used to characterise short-lived intermediates formed during the catalytic cycle.
- Published
- 2017
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41. Hyperfine Spectroscopy - ENDOR
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Jeffrey Harmer
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Coupling ,Materials science ,Resonance ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Rf excitation ,Measure (mathematics) ,Spectral line ,0104 chemical sciences ,Paramagnetism ,Atomic physics ,0210 nano-technology ,Spectroscopy ,Hyperfine structure - Abstract
Electron-nuclear double resonance (ENDOR) is a widely used technique to measure the nuclear frequencies of paramagnetic centers in solution, single crystals, and disordered systems such as powders and frozen solutions. This article starts with a theoretical overview of the energy levels and corresponding ENDOR spectra of low-and high-spin systems in the strong and weak coupling regimes. Advantages of high-field ENDOR are considered. The basis of CW ENDOR and triple CW ENDOR is then explained. The important concepts behind pulse ENDOR techniques are then introduced, starting with 1D Davies and 1D Mims ENDOR, triple, and followed by two-dimensional techniques that aim to increase the information content extractable from the data. Methods to determine the sign of the hyperfne coupling are described, as well as the advantages of stochastic RF excitation, nonlinear acquisition schemes, and echo train detection sequences that are designed to increase experiment stability and sensitivity.
- Published
- 2016
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42. Stereochemical control of the redox potential of tetracoordinate rhodium complexes
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Hansjörg Grützmacher, Cécile Laporte, Jeffrey Harmer, Jens Geier, Arthur Schweiger, and Frank Breher
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chemistry ,Tetracoordinate ,Computational chemistry ,chemistry.chemical_element ,General Chemistry ,Photochemistry ,Electrochemistry ,Redox ,Catalysis ,Non-innocent ligand ,Rhodium - Abstract
An apitite for reduction: The diastereoisomers of the tetrachelating ligand 1,3-bis[(5H-dibenzo[a,d]cyclohepten-5-yl)phenylphosphanyl propane, bis(troppPh)propane, can be used to control the redox potentials of 16-electron rhodium(1) complexes. Whereas the R,S-isomer of the ligand enforces a more planar complex which is difficult to reduce, the R,R(S,S)-isomer favors a tetrahedrally distorted structure which is easily reduced to give a stable rhodium(0) complex (see structure, Rh silver, P yellow, C black, H white).
- Published
- 2016
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43. Photoisomerization of a fullerene dimer
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and Arzhang Ardavan, John J. L. Morton, Kyriakos Porfyrakis, Jinying Zhang, Li Xiao, Jeffrey Harmer, G. Andrew D. Briggs, and Mark R. Sambrook
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Fullerene ,Photoisomerization ,Stereochemistry ,Dimer ,Relaxation (NMR) ,Zero field splitting ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,law.invention ,Crystallography ,chemistry.chemical_compound ,General Energy ,chemistry ,law ,Endohedral fullerene ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Cis–trans isomerism - Abstract
A photo-switchable fullerene dimer and its analogous nitrogen endohedral species have been synthesized and characterized. Irradiation by ultraviolet and visible light has been used to switch between the trans and cis isomers of both the C60- and N@C60- based dimers. Environmental perturbations experienced by the encapsulated nitrogen atom upon switching between the two isomers in degassed carbon disulfide has been determined by pulse electron paramagnetic resonance. Both T1 and T2 electron spin relaxation times of the two isomers of the endohedral fullerene containing dimer revealed a biexponential decay. Although the zero field splitting parameter Deff for both isomers in solution was similar, around 13.0 MHz, the molecular rotation correlation time τC of the trans and cis isomers was calculated to be 37.2 ± 1.6 and 34.8 ± 2.7 ps, respectively. © 2008 American Chemical Society.
- Published
- 2016
44. Mechanistic insights into stereoselective catalysis-the effects of counterions in a CuII-bissulfoximine-catalyzed Diels-Alder reaction
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Marc Martin, Jeffrey Harmer, Georg Gescheidt, Cornelia G. Palivan, Helmut Bertagnolli, Tsvetanka Stanoeva, Martin P. Feth, Carsten Bolm, Arthur Schweiger, and George Mitrikas
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Electron nuclear double resonance ,Extended X-ray absorption fine structure ,Chemistry ,Ligand ,Organic Chemistry ,Enantioselective synthesis ,General Chemistry ,Photochemistry ,Catalysis ,law.invention ,law ,Stereoselectivity ,Electron paramagnetic resonance ,Hyperfine structure ,Diels–Alder reaction - Abstract
The initial steps of an enantioselective Diels-Alder reaction catalyzed by a CuII-bissulfoximine complex were followed by EXAFS (EXAFS=extended X-ray absorption fine structure), EPR (EPR=electron paramagnetic resonance) spectroscopy (CW-EPR, FID-detected EPR, pulse ENDOR, HYSCORE; CW=continuous wave; ENDOR=electron nuclear double resonance; HYSCORE=hyperfine sublevel correlation; FID=free induction decay), and UV-visible spectroscopy. The complexes formed between the parent CuX2 (X=Cl-, Br-, TfO-, SbF6-) salts, the chiral bissulfoximine ligand (S,S)-1, and N-(1-oxoprop-2-en-1-yl)oxazolidin-2-one (2) as the substrate in CH2Cl2 were investigated in frozen and fluid solution. In all cases, penta- or hexacoordinated CuII centers were established. The complexes with counterions indicating high stereoselectivity (TfO- and SbF6-) reveal one unique species in which substrate 2 binds to pseudoequatorial positions (via O atoms), shifting the counterions to axial locations. On the other hand, those lacking stereoselectivity (X=Cl- and Br-) form two species in which the parent halogen anions remain at equatorial positions preventing the formation of geometries compatible with those found for X=TfO- and SbF6-.
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- 2016
45. Characterization of the MCRred2 form of methyl-coenzyme M reductase: a pulse EPR and ENDOR study
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Felix Mahlert, Cinzia Finazzo, Bernhard Jaun, Sabine Van Doorslaer, Jeffrey Harmer, Rudolf K. Thauer, Arthur Schweiger, and Evert C. Duin
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Nitrogen ,Coenzyme B ,Inorganic chemistry ,Coenzyme M ,Crystallography, X-Ray ,Biochemistry ,Cofactor ,law.invention ,Inorganic Chemistry ,chemistry.chemical_compound ,law ,Pyrroles ,Electron paramagnetic resonance ,Spectroscopy ,Hyperfine structure ,biology ,Chemistry ,Pulsed EPR ,Electron Spin Resonance Spectroscopy ,Substrate (chemistry) ,Isoenzymes ,Crystallography ,Phosphothreonine ,biology.protein ,Oxidoreductases ,Algorithms ,hormones, hormone substitutes, and hormone antagonists - Abstract
JBIC Journal of Biological Inorganic Chemistry, 8 (5), ISSN:0949-8257, ISSN:1432-1327
- Published
- 2016
46. Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron-electron resonance
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Maxie M. Roessler, Jeffrey Harmer, Alan J. Robinson, Judy Hirst, Martin S. King, and Fraser A. Armstrong
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Models, Molecular ,Chemistry & allied sciences ,Analytical chemistry ,Flavin mononucleotide ,Flavin group ,law.invention ,Electron Transport ,chemistry.chemical_compound ,Electron transfer ,Bacterial Proteins ,law ,Animals ,Electron paramagnetic resonance ,Multidisciplinary ,Electron Transport Complex I ,biology ,Molecular Structure ,Pulsed EPR ,Thermus thermophilus ,Electron Spin Resonance Spectroscopy ,Biological Sciences ,biology.organism_classification ,Electron transport chain ,Protein Structure, Tertiary ,Crystallography ,chemistry ,Energy Transfer ,Cattle ,Inorganic chemistry - Abstract
In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from Bos taurus have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on B. taurus complex I with the structure of the hydrophilic domain of Thermus thermophilus complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed.
- Published
- 2016
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47. Tropad: a new ligand for the synthesis of water-stable paramagnetic [16+1]-electron rhodium and iridium complexes
- Author
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Frank Breher, Jeffrey Harmer, Hansjörg Grützmacher, Gilles Frison, Carsten Böhler, Arthur Schweiger, and Lorenz Liesum
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Pulsed EPR ,Ligand ,Organic Chemistry ,chemistry.chemical_element ,General Chemistry ,Photochemistry ,Electrochemistry ,Catalysis ,law.invention ,Rhodium ,Crystallography ,chemistry ,law ,Moiety ,Iridium ,Electron paramagnetic resonance ,Hyperfine structure - Abstract
The new tetradentate ligand 1,4-bis(5 H-dibenzo[a,d]cyclohepten-5-yl)-1,4-diazabuta-1,3-diene ((H)tropdad) allows the syntheses of the 16-electron cationic rhodium complexes [M((H)tropdad)](O(3)SCF(3)) (M=Rh, Ir). The structure of the rhodium complex was determined by X-ray analysis and points to a description of these as [M(+1)((H)tropdad)(0)] with short Cd-N bonds (av 1.285 A) and a long C-C bond (1.46 A) in the diazabutadiene (dad) moiety, that is the M-->dad charge-transfer is negligible. Both [Rh((H)tropdad)](+) and [Ir((H)tropdad)](+) are reduced at very low potentials (E(1) (1/2)= -0.56 V and E(1) (1/2)=-0.35 V, respectively) which allowed the quantitative synthesis of the neutral paramagnetic complexes [M((H)tropdad)](0) (M=Rh, Ir) by reacting the cationic precursor complexes simply with zinc powder. The [M((H)tropdad)](0) complexes are stable against protic reagents in organic solvents. Continuous wave and pulse EPR spectroscopy was used to characterize the paramagnetic species and the hyperfine coupling constants were determined: [Rh((H)tropdad)](0): A(iso)((14)N)=11.9 MHz, A(iso)((1)H)=14.3 MHz, A(iso)((103)Rh)= -5.3 MHz; [Ir((H)tropdad)](0): A(iso)((14)N)=11.9 MHz, A(iso)((1)H)=14.3 MHz. In combination with DFT calculations, the experimentally determined g and hyperfine matrices could be orientated within the molecular frame and the dominant spin density contributions were determined. These results clearly show that the complexes [M((H)tropdad)](0) are best described as [M(+1)((H)tropdad)(.-)] with a [16+1] electron configuration.
- Published
- 2016
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48. Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase
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Stefan Mayr, Markus Reiher, Rudolf K. Thauer, Sieglinde Ebner, Bernhard Jaun, Jeffrey Harmer, Meike Goenrich, and Dariush Hinderberger
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Coenzyme B ,Stereochemistry ,Chemistry & allied sciences ,Catalytic cycle ,Factor F-430 ,chemistry.chemical_element ,Photochemistry ,Biochemistry ,Catalysis ,Cofactor ,Substrate Specificity ,law.invention ,Inorganic Chemistry ,chemistry.chemical_compound ,Thioether ,Nickel ,law ,Nickel enzyme ,Electron paramagnetic resonance ,Mesna ,Binding Sites ,biology ,Methyl-coenzyme M reductase ,Electron Spin Resonance Spectroscopy ,Active site ,Substrate (chemistry) ,Enzyme Activation ,Models, Chemical ,chemistry ,Isotope Labeling ,MCR ,biology.protein ,Oxidoreductases ,Oxidation-Reduction - Abstract
JBIC Journal of Biological Inorganic Chemistry, 13 (8), ISSN:0949-8257, ISSN:1432-1327
- Published
- 2016
49. A nickel-alkyl bond in an inactivated state of the enzyme catalyzing methane formation
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Bernhard Jaun, Jeffrey Harmer, Meike Goenrich, Rafal Piskorski, Rudolf K. Thauer, Dariush Hinderberger, and Arthur Schweiger
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chemistry.chemical_classification ,Methanogenesis ,Electron Spin Resonance Spectroscopy ,chemistry.chemical_element ,Bioinorganic chemistry ,General Chemistry ,General Medicine ,Medicinal chemistry ,Methane ,Catalysis ,law.invention ,Methyl coenzyme M ,Nickel ,chemistry.chemical_compound ,Enzyme ,chemistry ,Alkanesulfonic Acids ,law ,Organic chemistry ,Electron paramagnetic resonance ,Oxidoreductases ,Alkyl - Abstract
(Chemical Equation Presented) The spin reveals all: Electron paramagnetic resonance spectroscopy reveals the formation of a nickel-alkyl bond in the active site of methyl-coenzyme M reductase (MCR), the key enzyme of methanogenesis, when active MCRred1 reacts with the irreversible inhibitor 3-bromopropane sulfonate to form the MCRBPS species. © 2006 Wiley-VCH Verlag GmbH and Co. KGaA.
- Published
- 2016
50. Characterisation of the paramagnetic [2Fe-2S]+ centre in palustrisredoxin-B (PuxB) from Rhodopseudomonas palustris CGA009: g-matrix determination and spin coupling analysis
- Author
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Alice M. Bowen, Joseph A. B. Abdalla, Jeffrey Harmer, Luet Lok Wong, Stephen Bell, and Christiane R. Timmel
- Subjects
Models, Molecular ,Magnetic moment ,Chemistry ,Protein Conformation ,Iron ,Magnetic Phenomena ,Electron Spin Resonance Spectroscopy ,General Physics and Astronomy ,Electron ,Crystallography, X-Ray ,Spin probe ,Paramagnetism ,Dipole ,Rhodopseudomonas ,Coupled cluster ,Ferredoxins ,Density functional theory ,Physical and Theoretical Chemistry ,Atomic physics ,Hyperfine structure ,Sulfur - Abstract
Palustrisredoxin-B (PuxB) from Rhodopseudomonas palustris (CGA009) is a [2Fe-2S] ferredoxin which is able to accept electrons from NADH via the flavin-dependent palustrisredoxin reductase (PuR); these electrons can then be transferred to the P450 enzyme (CYP199A2). This work reports on the paramagnetic state of the [2Fe-2S](+) cluster in PuxB, both alone and in the PuR-PuxB complex. Aided by the X-ray crystal structure of PuxB, the protons nearest to the reduced [2Fe-2S](+) cluster were used as magnetic probes to quantify the g-matrix orientation and anisotropic magnetic moment of the paramagnetic centre. (1)H hyperfine couplings were measured with W-band Davies ENDOR and X-band HYSCORE spectroscopy and fitted to a model in which (1)H dipolar couplings were calculated assuming point magnetic moments located at the Fe ions, and bridging and coordinating cysteine sulfur atoms. The absolute sign of a (1)H hyperfine coupling was measured using a variable mixing time ENDOR experiment to confirm the assignment of the Fe(3+) and Fe(2+) ions. For the anti-ferromagnetically coupled cluster the magnetic moment is described in terms of spin projection factors, and our analysis yields values of K(exp)(A) = +2.33 to +1.85 (ferric site), and K(exp)(B) = -1.33 to -0.85 (ferrous site). These values are discussed in terms of the delocalisation of the spin density and hence the limitations of applying a local site spin coupling model to calculate the spin projection factors in a complex with considerable overlap of the α- and β-spin magnetic oribitals. The accurate description of the g-matrix orientation and magnetic moment of this [2Fe-2S](+) cluster enable it to be utilised as a paramagnetic spin probe, for example, to measure electron-electron distances. In the pdb reference frame of PuxB (code ) the g(∥) axis vector is g(∥) = [-0.6524 ± 0.0248, -0.6269 ± 0.0115, 0.4259 ± 0.0405], with the principal g-values of g(⊥) = 1.9328 ± 0.0003, g(∥) = 2.0233 ± 0.0003.
- Published
- 2016
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