PubMed Health⌕ Search

Biomedical subjects

S P Cramer

Publications and source records attributed to S P Cramer.

At least 19 recordsLinked to original sources
PubMed2004

X-ray absorption spectroscopy study of the LixFePO4 cathode during cycling using a novel electrochemical in situ reaction cell.

The extraction and insertion of lithium in LiFePO4 has been investigated in practical Li-ion intercalation electrodes for Li-ion batteries using Fe K-edge X-ray absorption spectroscopy (XAS). A versatile electrochemical in situ reaction cell was utilized, specifically designed for long-term X-ray experiments on battery electrodes during the lithium-extraction/insertion process in electrode materials for Li-ion batteries. The electrode contained about 7.7 mg of LiFePO4 on a 20 microm-thick Al foil. In order to determine the charge compensation mechanism and structural perturbations occurring in the system during cycling, in situ X-ray absorption fine-structure spectroscopy (XAFS) measurements were conducted on the cell at a moderate rate using typical Li-ion battery operating voltages (3.0-4.1 V versus Li/Li+). XAS studies of the LiFePO4 electrode measured at the initial state (LiFePO4) showed iron to be in the Fe(II) state corresponding to the initial state (0.0 mAh) of the battery, whereas in the delithiated state (FePO4) iron was found to be in the Fe(III) state corresponding to the final charged state (3 mAh) of the battery. The X-ray absorption near-edge structure (XANES) region of the XAS spectra revealed a high-spin configuration for the two states [Fe(II), d6 and Fe(III), d5]. The XAFS data analysis confirmed that the olivine structure of the LiFePO4 and FePO4 is retained by the electrodes, which is in agreement with the X-ray diffraction observations on these compounds. The XAFS data that were collected continuously during cycling revealed details about the response of the cathode to Li insertion and extraction. These measurements on the LiFePO4 cathode show that the material retains good structural short-range order leading to superior cycling.

Electric Power Supplies↗
PubMed2003

Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy.

We have reexamined the Ni EXAFS of oxidized, inactive (as-isolated) and H(2) reduced Desulfovibrio gigas hydrogenase. Better spatial resolution was achieved by analyzing the data over a 50% wider k-range than was previously available. A lower k(min) was obtained using the FEFF code for phase shifts and amplitudes. A higher k(max) was obtained by removing an interfering Cu signal from the raw spectra using multiple energy fluorescence detection. The larger k-range allowed us to better resolve the Ni-S bond lengths and to define more accurately the Ni-O and Ni-Fe bond lengths. We find that as-isolated, hydrogenase has two Ni-S bonds at approximately 2.2 A, but also 1-2 Ni-S bonds in the 2.35+/-0.05 A range. A Ni-O interaction is evident at 1.91 A. The as-isolated Ni-Fe distance cannot be unambiguously determined. Upon H(2) reduction, two short Ni-S bonds persist at approximately 2.2 A, but the remaining Ni-S bonds lengthen to 2.47+/-0.05 A. Good simulations are obtained with a Ni-Fe distance at 2.52 A, in agreement with crystal structures of the reduced enzyme. Although not evident in the crystal structures, an improvement in the fit is obtained by inclusion of one Ni-O interaction at 2.03 A. Implications of these distances for the spin-state of H(2) reduced H(2)ase are discussed.

Absorption↗
PubMed2001

Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation.

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S(3) --> [S(4)] --> S(0) transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kbeta X-ray emission spectroscopy (Kbeta XES) to this problem for the first time. The Kbeta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S(2) --> S(3) transition, in contrast to the S(0) --> S(1) and S(1) --> S(2) transitions, does not involve a Mn-centered oxidation. On the basis of new structural data from the S(3)-state, manganese mu-oxo bridge radical formation is proposed for the S(2) --> S(3) transition, and three possible mechanisms for the O-O bond formation are presented.

Electron Spin Resonance Spectroscopy↗
PubMed2001

Mn K-edge XANES and Kbeta XES studies of two Mn-oxo binuclear complexes: investigation of three different oxidation states relevant to the oxygen-evolving complex of photosystem II.

Two structurally homologous Mn compounds in different oxidation states were studied to investigate the relative influence of oxidation state and ligand environment on Mn K-edge X-ray absorption near-edge structure (XANES) and Mn Kbeta X-ray emission spectroscopy (Kbeta XES). The two manganese compounds are the di-mu-oxo compound [L'2Mn(III)O2Mn(IV)L'2](ClO4)3, where L' is 1,10-phenanthroline (Cooper, S. R.; Calvin, M. J. Am. Chem. Soc. 1977, 99, 6623-6630) and the linear mono-mu-oxo compound [LMn(III)OMn(III)L](ClO4)2, where L- is the monoanionic N,N-bis(2-pyridylmethyl)-N'-salicylidene-1,2-diaminoethane ligand (Horner, O.; Anxolabéhère-Mallart, E.; Charlot, M. F.; Tchertanov, L.; Guilhem, J.; Mattioli, T. A.; Boussac, A.; Girerd, J.-J. Inorg. Chem. 1999, 38, 1222-1232). Preparative bulk electrolysis in acetonitrile was used to obtain higher oxidation states of the compounds: the Mn(IV)Mn(IV) species for the di-mu-oxo compound and the Mn(III)Mn(IV) and Mn(IV)Mn(IV) species for the mono-mu-oxo compound. IR, UV/vis, EPR, and EXAFS spectra were used to determine the purity and integrity of the various sample solutions. The Mn K-edge XANES spectra shift to higher energy upon oxidation when the ligand environment remains similar. However, shifts in energy are also observed when only the ligand environment is altered. This is achieved by comparing the di-mu-oxo and linear mono-mu-oxo Mn-Mn moieties in equivalent oxidation states, which represent major structural changes. The magnitude of an energy shift due to major changes in ligand environment can be as large as that of an oxidation-state change. Therefore, care must be exercised when correlating the Mn K-edge energies to manganese oxidation states without taking into account the nature of the ligand environment and the overall structure of the compound. In contrast to Mn K-edge XANES, Kbeta XES spectra show less dependence on ligand environment. The Kbeta1,3 peak energies are comparable for the di-mu-oxo and mono-mu-oxo compounds in equivalent oxidation states. The energy shifts observed due to oxidation are also similar for the two different compounds. The study of the different behavior of the XANES pre-edge and main-edge features in conjunction with Kbeta XES provides significant information about the oxidation state and character of the ligand environment of manganese atoms.

Electrochemistry↗
PubMed2001

A quantitative description of the ground-state wave function of Cu(A) by X-ray absorption spectroscopy: comparison to plastocyanin and relevance to electron transfer.

To evaluate the importance of the electronic structure of Cu(A) to its electron-transfer (ET) function, a quantitative description of the ground-state wave function of the mixed-valence (MV) binuclear Cu(A) center engineered into Pseudomonas aeruginosa azurin has been developed, using a combination of S K-edge and Cu L-edge X-ray absorption spectroscopies (XAS). Parallel descriptions have been developed for a binuclear thiolate-bridged MV reference model complex ([(L(i)(PrdacoS)Cu)(2)](+)) and a homovalent (II,II) analogue ([L(i)(Pr2tacnS)Cu)(2)](2+), where L(i)(PrdacoS) and L(i)(Pr2tacnS) are macrocyclic ligands with attached thiolates that bridge the Cu ions. Previous studies have qualitatively defined the ground-state wave function of Cu(A) in terms of ligand field effects on the orbital orientation and the presence of a metal--metal bond. The studies presented here provide further evidence for a direct Cu--Cu interaction and, importantly, experimentally quantify the covalency of the ground-state wave function. The experimental results are further supported by DFT calculations. The nature of the ground-state wave function of Cu(A) is compared to that of the well-defined blue copper site in plastocyanin, and the importance of this wave function to the lower reorganization energy and ET function of Cu(A) is discussed. This wave function incorporates anisotropic covalency into the intra- and intermolecular ET pathways in cytochrome c oxidase. Thus, the high covalency of the Cys--Cu bond allows a path through this ligand to become competitive with a shorter His path in the intramolecular ET from Cu(A) to heme a and is particularly important for activating the intermolecular ET path from heme c to Cu(A).

Azurin↗
PubMed2001

High-resolution X-ray spectroscopy of rare events: a different look at local structure and chemistry.

The combination of large-acceptance high-resolution X-ray optics with bright synchrotron sources permits quantitative analysis of rare events such as X-ray fluorescence from very dilute systems, weak fluorescence transitions or X-ray Raman scattering. Transition-metal Kbeta fluorescence contains information about spin and oxidation state; examples of the characterization of the Mn oxidation states in the oxygen-evolving complex of photosystem II and Mn-consuming spores from the marine bacillus SG- are presented. Weaker features of the Kbeta spectrum resulting from valence-level and 'interatomic' ligand to metal transitions contain detailed information on the ligand- atom type, distance and orientation. Applications of this spectral region to characterize the local structure of model compounds are presented. X-ray Raman scattering (XRS) is an extremely rare event, but also represents a unique technique to obtain bulk-sensitive low-energy (<600 eV) X-ray absorption fine structure (XAFS) spectra using hard (approximately 10 keV) X-rays. A photon is inelastically scattered, losing part of its energy to promote an electron into an unoccupied level. In many cases, the cross section is proportional to that of the corresponding absorption process yielding the same X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) features. XRS finds application for systems that defy XAFS analysis at low energies, e.g. liquids or highly concentrated complex systems, reactive compounds and samples under extreme conditions (pressure, temperature). Recent results are discussed.

Bacillus↗
PubMed2000

X-ray Raman spectroscopy of carbon in asphaltene: light element characterization with bulk sensitivity.

X-ray Raman spectra of the carbon K-edge have been recorded using 6.461 keV radiation for a petroleum asphaltene. By comparison with coronene, graphite, and paraffin standards, the asphaltene spectrum is seen to be composed of contributions from saturated and aromatic carbon species. The information contained in the carbon K-edge was extracted with bulk (approximately 1 mm) sensitivity, because the Raman method used hard X-rays. This helps alleviate concerns about surface artifacts that frequently occur with soft X-ray spectroscopy of light elements. X-ray Raman spectroscopy shows great potential for characterization of light elements in fuels, catalysts, and other complex materials under chemically relevant conditions.

Carbon↗
PubMed1997

High-resolution X-ray fluorescence and excitation spectroscopy of metalloproteins.

A spectrograph has been developed with sufficient efficiency to make high-resolution fluorescence experiments on metalloproteins possible. The resolution of this spectrometer can reach 0.45 eV at 7.1 keV emission energy. The focus images of this multiple curved-crystal array spectrometer are presented. The chemical sensitivity of Kbeta emission spectra can be used to identify chemical states, and the spin-polarized near-edge structure provides a new measure of the spin density. The high-resolution fluorescence metalloprotein studies should become routine with third-generation synchrotron facilities, and the strength of both site and spin selectivity should complement the structural information from other spectroscopies.

Journal Article↗
PubMed1994

Spinach carbonic anhydrase: investigation of the zinc-binding ligands by site-directed mutagenesis, elemental analysis, and EXAFS.

The enzyme carbonic anhydrase has been well characterized in mammalian systems, but the structural properties of the plant isozymes remain elusive. To investigate the nature of the zinc-binding site in spinach carbonic anhydrase, we targeted potential zinc ligands for mutagenesis and examined the resulting enzymes for catalytic activity and stoichiometric zinc binding. In addition, we examined the wild-type protein using extended X-ray absorption fine structure analysis. Our results suggest that spinach carbonic anhydrase utilizes a Cys-His-Cys-H2O ligand scheme to bind the zinc ion at the active site.

Amino Acid Sequence↗
PubMed1993

X-ray absorption spectroscopy of oriented cytochrome oxidase.

The polarized X-ray absorption spectra of the copper, iron and zinc sites of mitochondrial cytochrome oxidase in oriented membrane multilayers have been examined. The copper X-ray absorption edge spectra indicate the presence of a tetragonal copper, which we assign as CuB, oriented with the long axis approximately orthogonal to the membrane normal. We have also detected the presence of a relatively long (2.6 A) Cu-S or Cu-Cl interaction, which we assign to a copper-thioether (probably Met210) coordination at the CuA site, with the bond oriented along the membrane normal. The coordination of the zinc, the iron and the CuB heme a3 binuclear site are discussed.

Animals↗
PubMed1992

Nitrogen chemical structure in DNA and related molecules by X-ray absorption spectroscopy.

The electronic environment of nitrogen in nucleic acid bases, nucleotides, polynucleotides and DNA has been studied, for the first time using X-Ray Absorption Near-Edge Spectroscopy (XANES). Generally, the spectra of these complex molecules consist of low energy bands corresponding to 1s-->pi* transitions and high energy bands corresponding to 1s-->sigma* transition, as illustrated using several nitrogen model compounds. The 1s-->pi* transitions show particular sensitivity to the chemical environment of the nitrogen. Oxygen substitution on ring carbon atoms generally results in a significant blue shift of the lowest 1s-->pi* bands while halogen substitution results in a small blue shift. These observations illustrate the significance of the disturbance of the aromatic ring system produced by exocyclic carbonyl groups. Direct substitution on the nitrogen frequently results in significant spectral perturbations. Differences between the spectra of the polynucleotides and the sums of spectra of the individual nucleotides point to the effects of hydrogen-bonding in complementary double-helix structures. The XANES spectrum of a DNA sample with a known ratio of the polynucleotides is equivalent to the weighted sum of the spectra of individual polynucleotides, indicating that the difference in base stacking interactions produces negligible spectral effects. The variability of nitrogen K-edge spectra in these samples and in protein may be useful for chemically specific imaging using X-ray microscopes.

Animals↗
PubMed1991

Identification and characterization of zinc binding sites in protein kinase C.

Metal ion coordination in the regulatory domain of protein kinase C (PKC) is suggested by the conservation of six cysteines and two histidines in two homologous regions found therein. By monitoring x-ray fluorescence from a purified sample of rat PKC beta I overexpressed in insect cells, direct evidence has been obtained that PKC beta I tightly binds four zinc ions (Zn2+) per molecule. Extended x-ray absorption fine structure (EXAFS) data are best fit by an average Zn2+ coordination of one nitrogen and three sulfur atoms. Of the plausible Zn2+ coordination models, only those featuring nonbridged Zn2+ sites accommodate the EXAFS data and all of the conserved potential ligands.

Absorptiometry, Photon↗
PubMed1989

Structure of the active site of sulfite oxidase. X-ray absorption spectroscopy of the Mo(IV), Mo(V), and Mo(VI) oxidation states.

The active site of sulfite oxidase has been investigated by X-ray absorption spectroscopy at the molybdenum K-edge at 4 K. We have investigated all three accessible molybdenum oxidation states, Mo(IV), Mo(V), and Mo(VI), allowing comparison with the Mo(V) electron paramagnetic resonance data for the first time. Quantitative analysis of the extended X-ray absorption fine structure indicates that the Mo(VI) oxidation state possesses two terminal oxo (Mo = O) and approximately three thiolate-like (Mo-S-) ligands and is unaffected by changes in pH and chloride concentration. The Mo(IV) and Mo(V) oxidation states, however, each have a single oxo ligand plus one Mo-O- (or Mo-N less than) bond, most probably Mo--OH, and two to three thiolate-like ligands. Both reduced forms appear to gain a single chloride ligand under conditions of low pH and high chloride concentration.

Animals↗
PubMed1989

X-ray-absorption and electron-paramagnetic-resonance spectroscopic studies of the environment of molybdenum in high-pH and low-pH forms of Escherichia coli nitrate reductase.

Previous e.p.r. work [George, Bray, Morpeth & Boxer (1985) Biochem. J. 227, 925-931] has provided evidence for a pH- and anion-dependent transition in the structure of the Mo(V) centre of Escherichia coli nitrate reductase, with the low-pH form bearing both an anion and probably a hydroxy-group ligand. Initial e.x.a.f.s. measurements [Cramer, Solomonson, Adams & Mortenson (1984) J. Am. Chem. Soc. 106, 1467-1471] demonstrated the presence of sulphur (or chloride) ligands in the Mo(IV) and Mo(VI) oxidation states, as well as a variable number of terminal oxo (Mo = O) groups. To synthesize the e.p.r. and e.x.a.f.s. results better, we have conducted new e.p.r. experiments and complementary e.x.a.f.s. measurements under redox and buffer conditions designed to give homogeneous molybdenum species. In contrast with results on other molybdoenzymes, attempts to substitute the enzyme with 17O by dissolving in isotopically enriched water revealed only very weak hyperfine coupling to 17O. The significance of this finding is discussed. Experiments with different buffers indicated that buffer ions (e.g. Hepes) could replace the Cl- ligand in the low-pH Mo(V) enzyme form, with only a small change in e.p.r. parameters. E.x.a.f.s. studies of the oxidized and the fully reduced enzyme were consistent with the e.p.r. work in indicating a pH- and anion-dependent change in structure. However, in certain cases non-stoichiometric numbers of Mo = O interactions were determined, complicating the interpretation of the e.x.a.f.s. Uniquely for a molybdenum cofactor enzyme, a substantial proportion of the molecules in a number of enzyme samples appeared to contain no oxo groups. No evidence was found in our samples for the distant 'heavy' ligand atom reported in the previous e.x.a.f.s. study. The nature of the high-pH-low-pH transition is briefly discussed.

Chlorides↗
PubMed1989

The manganese site of the photosynthetic water-splitting enzyme.

As the originator of the oxygen in our atmosphere, the photosynthetic water-splitting enzyme of chloroplasts is vital for aerobic life on the earth. It has a manganese cluster at its active site, but it is poorly understood at the molecular level. Polarized synchrotron radiation was used to examine the x-ray absorption of manganese in oriented chloroplasts. The manganese site, in the "resting" (S1) state, is an asymmetric cluster, which probably contains four manganese atoms, with interatomic separations of 2.7 and 3.3 angstroms; the vector formed by the 3.3-angstrom manganese pair is oriented perpendicular to the membrane plane. Comparisons with model compounds suggest that the cluster contains bridging oxide or hydroxide ligands connecting the manganese atoms, perhaps with carboxylate bridges connecting the 3.3-angstrom manganese pair.

Chloroplasts↗
PubMed1988

Spectroscopic properties of the hydroxylase of methane monooxygenase.

The hydroxylase component of methane monooxygenase (EC 1.14.13.25), which catalyzes the oxidation of methane to methanol, has been studied by visible, electron spin resonance and X-ray spectroscopies. The enzyme appears to possess a mu-oxo- or mu-hydroxo-bridged binuclear iron site, with no sulfur ligands to the cluster. Each Fe has 4-6 oxygen (or nitrogen) ligands, at an average distance of 1.92 +/- 0.03 A. The Fe-Fe distance is 3.05 +/- 0.05 A. Essentially all of the irons are in the Fe3+ state as the enzyme is prepared, but reduction with N-methylphenazonium methosulfate generates ESR-detectable states that appear to emanate from mixed-valence binuclear sites. One of these, with gav near 1.85, displays typical Curie law microwave saturation behavior, but the other, gav near 1.73, has a very potent method of spin-relaxation. Together they account for approximately 0.6 spins per molecule.

Binding Sites↗
PubMed1986

Structural aspects of the copper sites in cytochrome c oxidase. An X-ray absorption spectroscopic investigation of the resting-state enzyme.

Copper K-edge X-ray absorption spectroscopy (XAS) has been used to investigate the structural details of the coordination environment of the copper sites in eight resting-state samples of beef heart cytochrome c oxidase prepared by different methods. The unusual position and structure of the resting-state copper edge spectrum can be adequately explained by the presence of sulfur-containing ligands, with a significant amount of S----Cu(II) charge transfer (i.e., a covalent site). Quantitative curve-fitting analysis of the copper extended X-ray absorption fine structure (EXAFS) data indicates similar average first coordination spheres for all resting-state samples, regardless of preparation method. The average coordination sphere (per 2 coppers) mainly consists of 6 +/- 1 nitrogens or oxygens at an average Cu-(N,O) distance of 1.99 +/- 0.03 A and 2 +/- 1 sulfurs at an average Cu-S distance of 2.28 +/- 0.02 A. Quantitative curve-fitting analysis of the outer shell of the copper EXAFS indicates the presence of a Cu...Fe interaction at a distance of 3.00 +/- 0.03 A. Proposed structures of the two copper sites based on these and other spectroscopic results are presented, and differences between our results and those of other published copper XAS studies [Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465-498] are discussed.

Animals↗