Bioinorganic Chemistry Methods
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Questions and Answers

What is the primary goal of this chapter?

  • To focus on the principles of bioinorganic chemistry
  • To teach the principles behind each physical technique
  • To explore the applications of bioinorganic chemistry in industry
  • To provide a critical survey of physical methods in bioinorganic chemistry (correct)

    • What is a characteristic of metal ions that makes them suitable for study by physical techniques?

  • Their high electron densities (correct)
  • Their ability to form complexes
  • Their low molecular weight
  • Their high reactivity

    • Why is it important to understand the electronic states and magnetic properties of a transition-metal center in biology?

  • To determine its molecular structure
  • To determine its reactivity
  • To understand its role in biological processes (correct)
  • To determine its electronic properties and magnetic properties

    • What is a consequence of bioinorganic chemistry on physical methods?

    <p>It has improved the methodologies of physical methods</p> Signup and view all the answers

    What is the focus of the chapter regarding physical methods?

    <p>Their advantages and limitations in molecular structure determination and characterization of electronic structures</p> Signup and view all the answers

    Which physical techniques are mentioned as being rarely employed by the bioorganic chemist?

    <p>EXAFS, Mossbauer, resonance Raman, and electron-paramagnetic resonance spectroscopy</p> Signup and view all the answers

    What do the properties of a metal center affect?

    <p>The reactions that can occur at the site</p> Signup and view all the answers

    What is the basis for most spectroscopic techniques?

    <p>Electronic and magnetic phenomena</p> Signup and view all the answers

    What do all forms of spectroscopy have in common?

    <p>The irradiation of a sample with light of a given frequency or frequency range</p> Signup and view all the answers

    What does the frequency of light used in spectroscopy determine?

    <p>The time scale at which a chemical phenomenon can be probed</p> Signup and view all the answers

    What is analogous to the rate of a chemical reaction in the analogy of making a motion picture?

    <p>The speed of the rotating wheel</p> Signup and view all the answers

    What type of spectroscopy can resolve chemical changes occurring on the femtosecond time scale?

    <p>Electronic spectroscopy</p> Signup and view all the answers

    What is the typical time scale of 'H NMR spectroscopy?

    <p>Milliseconds</p> Signup and view all the answers

    What is the advantage of X-ray sources in determining molecular structure?

    <p>They have a wavelength on the same order of magnitude as interatomic distances</p> Signup and view all the answers

    What is required for X-ray diffraction?

    <p>A single crystal</p> Signup and view all the answers

    What is the precision of macromolecular structures determined by X-ray crystallography?

    <p>An order of magnitude less than small inorganic complexes</p> Signup and view all the answers

    What is a major limitation of protein crystals in diffracting X-rays?

    <p>Their high water content</p> Signup and view all the answers

    What is Bragg's law used to define?

    <p>The scattering angle between incident and diffracted X-ray beams</p> Signup and view all the answers

    What is the typical resolution of X-ray diffraction for protein crystals?

    <p>Slightly less than 2 A</p> Signup and view all the answers

    Why is it necessary to know the amino acid sequence when determining the structure of metalloproteins?

    <p>To assign electron density to specific amino acid residues</p> Signup and view all the answers

    What is the purpose of heavy atom derivatives in X-ray crystallography?

    <p>To determine the phase angles of measured reflections</p> Signup and view all the answers

    What is the name of the technique used to prepare heavy atom derivatives?

    <p>Isomorphous replacement</p> Signup and view all the answers

    What is the name of the complex shown in Figure 4.1 used for preparing heavy atom derivatives?

    <p>TAMM</p> Signup and view all the answers

    What is the significance of the structure of the nucleosome core particle?

    <p>It is a complex of eight polypeptide chains and 146 base pairs of DNA</p> Signup and view all the answers

    Why is X-ray diffraction used to study polycrystalline fibers of DNA?

    <p>To study the structure of nucleic acids</p> Signup and view all the answers

    What is the advantage of using area detectors and synchrotron radiation in X-ray diffraction?

    <p>They reduce the time required for data collection</p> Signup and view all the answers

    What is the main purpose of using electron-dense metal reagents in the study of DNA?

    <p>To provide phases for generating electron density maps</p> Signup and view all the answers

    What is the spacing between intercalated molecules at saturation, as depicted in Figure 4.3?

    <p>10.2 A</p> Signup and view all the answers

    What type of molecules are represented by the structures shown in Figure 4.3?

    <p>Organic intercalators</p> Signup and view all the answers

    What is the name of the protein data bank where atomic coordinates from X-ray diffraction work are deposited?

    <p>Brookhaven Protein Data Bank</p> Signup and view all the answers

    What is the primary application of X-ray absorption spectroscopy (XAS) in bioinorganic chemistry?

    <p>Determining the oxidation state of metal ions</p> Signup and view all the answers

    What type of radiation is used in X-ray absorption spectroscopy (XAS)?

    <p>Synchrotron radiation</p> Signup and view all the answers

    What is the term for the phenomenon where an intercalated molecule occupies every other interbase pair site at saturation?

    <p>Neighbor exclusion</p> Signup and view all the answers

    What is the name of the organic intercalator shown in Figure 4.3?

    <p>Ethidium bromide</p> Signup and view all the answers

    What is the purpose of X-ray diffraction studies on polycrystalline DNA fibers?

    <p>To study the binding of intercalators to DNA</p> Signup and view all the answers

    What is the name of the metallointercalator shown in Figure 4.3?

    <p>IPt(terpy) (HET)</p> Signup and view all the answers

    What is the primary advantage of Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy?

    <p>It can provide detailed information about metal-coordination geometries</p> Signup and view all the answers

    What is the typical temperature range used to minimize atomic thermal motion in EXAFS experiments?

    <p>Low temperatures (to 4.2 K)</p> Signup and view all the answers

    What is the purpose of performing control experiments in EXAFS studies?

    <p>To check if the high-intensity X-irradiation has altered the biological sample</p> Signup and view all the answers

    What is the name of the technique that involves the absorption of light by particles with a magnetic moment in a magnetic field?

    <p>Magnetic Resonance</p> Signup and view all the answers

    What is the typical frequency range used in Electron Paramagnetic Resonance (EPR) spectroscopy?

    <p>Microwave region</p> Signup and view all the answers

    What is the significance of the EXAFS study on rubredoxin?

    <p>It demonstrated that all four Fe-S(cysteine) distances in rubredoxin are equal to within 0.02 A</p> Signup and view all the answers

    What is the limitation of EXAFS spectroscopy in studying metallobiopolymers?

    <p>It can be difficult to fit unambiguously to a model structure for less symmetric sites</p> Signup and view all the answers

    What is the purpose of comparing EXAFS data with well-defined model compounds?

    <p>To help in fitting the data unambiguously to a model structure</p> Signup and view all the answers

    What is the name of the technique that involves the absorption of light by nuclei with a magnetic moment in a magnetic field?

    <p>Nuclear Magnetic Resonance (NMR) spectroscopy</p> Signup and view all the answers

    What is the advantage of using EXAFS spectroscopy in metalloprotein structural studies?

    <p>It provides detailed information about metal-coordination geometries</p> Signup and view all the answers

    What is a common characteristic of the metal ions studied by EPR spectroscopy?

    <p>They have unpaired electrons</p> Signup and view all the answers

    What is the advantage of using EPR spectroscopy to study iron-containing proteins?

    <p>It can detect high-spin ferric ions at concentrations as low as the pM range</p> Signup and view all the answers

    What is the purpose of freezing solutions in EPR spectroscopy?

    <p>To stop molecular tumbling and average out the anisotropy of the g-tensor</p> Signup and view all the answers

    What is the value of the free-electron g-value?

    <p>2.0023</p> Signup and view all the answers

    What is the shape of the geometry of copper(II) centers?

    <p>Tetragonal</p> Signup and view all the answers

    What is the significance of the Aiso value in EPR spectroscopy?

    <p>It is a measure of the hyperfine splitting parameter</p> Signup and view all the answers

    What is the typical application of EPR spectroscopy in bioinorganic chemistry?

    <p>To study metalloproteins containing Cu(II)</p> Signup and view all the answers

    What is the characteristic of the EPR signal of type-1 copper?

    <p>It has a small Aiso value</p> Signup and view all the answers

    What is the significance of the g-tensor in EPR spectroscopy?

    <p>It is a measure of the anisotropy of the EPR signal</p> Signup and view all the answers

    What is the advantage of using EPR spectroscopy to study biological samples?

    <p>It can be used to monitor biological samples at physiologically relevant temperatures</p> Signup and view all the answers

    What is the coordination environment of the copper in plastocyanin?

    <p>Two histidine nitrogen and one cysteine thiolate sulfur donors in a plane</p> Signup and view all the answers

    What type of EPR signal is characteristic of most cupric complexes?

    <p>Type 1 EPR signal with g-values characteristic of most cupric complexes</p> Signup and view all the answers

    What is the reason for the EPR silence of the third type of copper?

    <p>Both antiferromagnetic exchange coupling and rapid electron-spin relaxation</p> Signup and view all the answers

    What is the oxidation state of the iron in low- and high-spin forms?

    <p>Fe(II) and Fe(III)</p> Signup and view all the answers

    What is the purpose of ENDOR spectroscopy?

    <p>To resolve hyperfine splitting of the EPR lines that cannot be directly resolved</p> Signup and view all the answers

    What type of EPR signal is characteristic of Mn(I1) in bioinorganic chemistry?

    <p>A six-line hyperfine pattern</p> Signup and view all the answers

    What is the significance of the X-ray crystallographic determination of ascorbate oxidase?

    <p>It shows that the structural conclusions drawn from the spectroscopic studies are essentially correct</p> Signup and view all the answers

    What is the spatial arrangement of the four copper ions in ascorbate oxidase?

    <p>They are closely spaced together</p> Signup and view all the answers

    What is the purpose of EPR spectroscopy in studying iron in bioinorganic chemistry?

    <p>To readily distinguish between low- and high-spin forms of ferric ion</p> Signup and view all the answers

    What type of radical intermediate can be observed by EPR spectroscopy?

    <p>All of the above</p> Signup and view all the answers

    What is the purpose of ESEEM spectroscopy in the study of metal-ligand interactions?

    <p>To identify ligand hyperfine interactions</p> Signup and view all the answers

    What is the significance of superhyperfine interactions in EPR spectroscopy?

    <p>They provide information on the electron delocalization from the metal center</p> Signup and view all the answers

    What is the advantage of using Fourier-transform spectrometers in NMR spectroscopy?

    <p>They increase the applicability of NMR spectroscopy for macromolecular structural studies</p> Signup and view all the answers

    What is the significance of paramagnetic metal ions in NMR spectroscopy?

    <p>They produce shifted NMR signals that facilitate identification of amino-acid side-chain ligands</p> Signup and view all the answers

    Which nucleus has I = 1/2 and is useful for NMR studies?

    <p>203Tl</p> Signup and view all the answers

    What is the purpose of NMR spectroscopic studies of metal nuclei?

    <p>To provide yet another powerful dimension of NMR spectroscopy</p> Signup and view all the answers

    What is an advantage of NMR methods in kinetic studies?

    <p>High resolution and small line widths</p> Signup and view all the answers

    What is the advantage of using metal nuclei with I = 1/2 in NMR spectroscopy?

    <p>No quadrupolar line broadening occurs</p> Signup and view all the answers

    What type of nuclei are most naturally occurring metal isotopes?

    <p>Quadrupolar (I &gt; 1/2)</p> Signup and view all the answers

    What is the significance of EPR spectroscopy in the study of metal-ligand interactions?

    <p>It facilitates the identification of ligand hyperfine interactions</p> Signup and view all the answers

    What is a characteristic of the nuclei 'Cd, 'I3Cd, 203Tl, 'O'Tl, Ig5Pt, and '07Pb?

    <p>I = 1/2</p> Signup and view all the answers

    What is the purpose of detecting I4N and 15N nuclear superhyperfine interactions in EPR spectroscopy?

    <p>To estimate the extent of electron delocalization from the metal center</p> Signup and view all the answers

    What is the significance of the 2 x 10^3 sec^(-1) rate in NMR-based kinetic methods?

    <p>It is the maximum rate for observing line broadening</p> Signup and view all the answers

    What is the significance of deuteration in ESEEM spectroscopy?

    <p>It provides a clear confirmation of the spectral assignment</p> Signup and view all the answers

    What is the focus of NMR spectroscopic studies of metalloproteins?

    <p>To determine the structure of metalloproteins</p> Signup and view all the answers

    What is the significance of the 1 ppm difference in resonance positions?

    <p>It is the resolution limit for distinguishing signals</p> Signup and view all the answers

    In proteins like laccase and ascorbate oxidase, which type of copper is present?

    <p>All three types of copper</p> Signup and view all the answers

    What can be distinguished by EPR spectroscopy in ferric ions?

    <p>Both high- and low-spin forms</p> Signup and view all the answers

    What is the spatial arrangement of the four copper ions in ascorbate oxidase?

    <p>Close together, as shown in Figure 4.6</p> Signup and view all the answers

    Why is the third type of copper EPR silent?

    <p>Due to antiferromagnetic exchange coupling and/or rapid electron-spin relaxation</p> Signup and view all the answers

    What type of spectroscopy has been extensively used to study heme iron and iron-sulfur clusters?

    <p>EPR spectroscopy</p> Signup and view all the answers

    What is the significance of the X-ray crystallographic determination of ascorbate oxidase?

    <p>It confirmed the structural conclusions drawn from spectroscopic studies</p> Signup and view all the answers

    What is the primary application of electron-nuclear double resonance spectroscopy (ENDOR) in bioinorganic chemistry?

    <p>Study of 17O-labeled substrates with EPR active metal centers</p> Signup and view all the answers

    What can be estimated from the magnitude of superhyperfine coupling constants?

    <p>The extent of electron delocalization from the metal center</p> Signup and view all the answers

    What is the term for the technique that facilitates identification of ligand hyperfine interactions?

    <p>Electron-spin-echo envelope modulation (ESEEM) spectroscopy</p> Signup and view all the answers

    What is the application of NMR spectroscopy in bioinorganic chemistry?

    <p>Determination of the three-dimensional structure of biopolymers</p> Signup and view all the answers

    What is the significance of deuteration in ESEEM spectroscopy?

    <p>It confirms the spectral assignment</p> Signup and view all the answers

    What is the primary advantage of two- or higher dimensional NMR spectroscopy?

    <p>It facilitates macromolecular structural studies</p> Signup and view all the answers

    What is the application of EPR spectroscopy in bioinorganic chemistry?

    <p>All of the above</p> Signup and view all the answers

    What is the significance of ESEEM spectroscopy in bioinorganic chemistry?

    <p>It identifies ligand hyperfine interactions</p> Signup and view all the answers

    What is the application of ENDOR spectroscopy in bioinorganic chemistry?

    <p>Study of 17O-labeled substrates with EPR active metal centers</p> Signup and view all the answers

    What is the advantage of NMR spectroscopy in bioinorganic chemistry?

    <p>It facilitates kinetic studies of enzymatic reactions</p> Signup and view all the answers

    What is the significance of paramagnetic metal ions in NMR spectroscopy?

    <p>They can produce shifted NMR signals that facilitate identification of amino-acid side-chain ligands.</p> Signup and view all the answers

    Why are metal nuclei with I = 1/2 more useful in NMR spectroscopy?

    <p>They do not exhibit quadrupolar line broadening.</p> Signup and view all the answers

    What is the advantage of using NMR-based kinetic methods?

    <p>They can distinguish signals from species that are interconverting on a wide variety of time scales.</p> Signup and view all the answers

    What is the purpose of substituting diamagnetic metals with paramagnetic metals in metalloproteins?

    <p>To extract distance information from NMR line broadening.</p> Signup and view all the answers

    What is the significance of the isomer shift in Mossbauer spectroscopy?

    <p>It is a measure of the metal's spin state.</p> Signup and view all the answers

    Why are NMR signals from metal nuclei often not observable at achievable protein concentrations?

    <p>The metal nuclei have a low resonance frequency.</p> Signup and view all the answers

    What is the purpose of studying metal nuclei with NMR spectroscopy?

    <p>To study the metal's coordination geometry and ligand environment.</p> Signup and view all the answers

    What is the significance of line broadening in NMR spectroscopy?

    <p>It is a measure of the distance between the metal and nearby protons.</p> Signup and view all the answers

    What is the advantage of using Mossbauer spectroscopy to study 57Fe?

    <p>It provides information about the metal's oxidation state and spin state.</p> Signup and view all the answers

    What is the purpose of using NMR spectroscopy to study metalloproteins?

    <p>To identify amino-acid side-chain ligands and study their dynamics.</p> Signup and view all the answers

    What is the primary purpose of 57Fe Mossbauer spectroscopy in bioinorganic chemistry?

    <p>To estimate the rate of internal electron-transfer reactions</p> Signup and view all the answers

    What is the effect of protonation of the p-oxo bond on the quadrupole splitting (AEQ) in iron-oxo proteins?

    <p>It decreases the AEQ</p> Signup and view all the answers

    What is the typical frequency range used in Mossbauer spectroscopy?

    <p>Gamma-ray range</p> Signup and view all the answers

    What is the purpose of enriching metalloproteins with 57Fe in Mossbauer spectroscopy?

    <p>To increase the sensitivity of the technique</p> Signup and view all the answers

    What is the primary advantage of Mossbauer spectroscopy in the study of iron-containing metalloproteins?

    <p>It provides information on the magnetic properties of the metal</p> Signup and view all the answers

    What is the term for the shift in the Mossbauer spectrum due to the electric field surrounding the metal center?

    <p>Isomer shift</p> Signup and view all the answers

    What is the primary goal of assigning metal oxidation states in metalloenzymes?

    <p>To follow the reaction pathways in the enzyme</p> Signup and view all the answers

    What is the purpose of computer simulation of the Mossbauer spectrum?

    <p>To provide isomer-shift, quadrupole-splitting, and nuclear-electron magnetic hyperfine coupling parameters</p> Signup and view all the answers

    What is the advantage of using temperature-dependent spectral measurements in Mossbauer spectroscopy?

    <p>It provides information on the magnetic properties of the metal</p> Signup and view all the answers

    What is the advantage of using resonance Raman spectroscopy in metalloproteins?

    <p>It can enhance the vibrational frequencies of the ligands</p> Signup and view all the answers

    What is the primary limitation of using 57Fe Mossbauer spectroscopy in bioinorganic chemistry?

    <p>It requires enrichment of the metalloprotein with 57Fe</p> Signup and view all the answers

    What is the purpose of depleting a protein of one or more metal centers in spectroscopic studies?

    <p>To assign spectroscopic bands to specific metal centers</p> Signup and view all the answers

    What is the purpose of studying the quadrupole splitting (AEQ) in iron-oxo proteins?

    <p>To study the asymmetry of the electric field surrounding the metal center</p> Signup and view all the answers

    What is the primary application of X-ray photoelectron spectroscopy (XPS) in bioinorganic chemistry?

    <p>To measure the binding energies of core electrons</p> Signup and view all the answers

    What is the significance of near absorption edge XAS in bioinorganic chemistry?

    <p>It can assign oxidation states to metal centers</p> Signup and view all the answers

    Why is it challenging to assign spectroscopic bands to specific metal centers in polymetallic proteins?

    <p>Because the metal centers have similar spectroscopic properties</p> Signup and view all the answers

    What is the role of tunable lasers in resonance Raman spectroscopy?

    <p>To provide a wide range of visible and near-ultraviolet wavelengths</p> Signup and view all the answers

    What is the advantage of using XAS over other spectroscopic methods in bioinorganic chemistry?

    <p>It can assign oxidation states to metal centers</p> Signup and view all the answers

    What is the primary goal of using vibrational spectroscopy in metalloproteins?

    <p>To provide information on the coordinated ligands</p> Signup and view all the answers

    What is the significance of studying the coordination environment of metal centers in metalloenzymes?

    <p>To understand the role of the metal in the enzyme's function</p> Signup and view all the answers

    What is the purpose of measuring the magnetic susceptibility of metalloproteins?

    <p>To determine the number of unpaired electrons</p> Signup and view all the answers

    What is the advantage of using SQUID (superconducting quantum interference device) susceptometers in measuring magnetic properties of metalloproteins?

    <p>Higher sensitivity</p> Signup and view all the answers

    What is the phenomenon referred to as antiferromagnetic and ferromagnetic coupling in bioinorganic chemistry?

    <p>The interaction between magnetic centers connected by bridging ligands</p> Signup and view all the answers

    What is the significance of the magnetic exchange coupling parameter J in bioinorganic chemistry?

    <p>It determines the strength of antiferromagnetic or ferromagnetic coupling</p> Signup and view all the answers

    What is the purpose of measuring the redox potential of metalloproteins?

    <p>To understand the bioinorganic chemistry of redox-active species</p> Signup and view all the answers

    What is the classic approach to measuring the redox potential of metalloprotein cores?

    <p>Potentiometric titration with a redox agent of similar potential</p> Signup and view all the answers

    What is the significance of temperature-dependent studies in measuring the magnetic moment of metalloproteins?

    <p>It determines the occupancy of higher-lying states in the electron-spin manifold</p> Signup and view all the answers

    What is the advantage of using SQUID susceptometers in studying the magnetic properties of dimetallic centers?

    <p>Higher sensitivity</p> Signup and view all the answers

    What is the significance of the spin Hamiltonian in bioinorganic chemistry?

    <p>It describes the interaction between magnetic centers</p> Signup and view all the answers

    What is the purpose of studying the magnetic properties of metalloproteins?

    <p>To understand the bioinorganic chemistry of metalloproteins</p> Signup and view all the answers

    What is the advantage of using difference spectroscopy in vibrational spectroscopy?

    <p>To eliminate the solvent and protein matrix background signals</p> Signup and view all the answers

    What is the purpose of using isotopically substituted ligand derivatives in vibrational spectroscopy?

    <p>To identify the presence of a specific ligand</p> Signup and view all the answers

    What is the significance of the selection rules in circular dichroism (CD) spectroscopy?

    <p>They differ from those of absorption spectroscopy, allowing for the detection of electronic transitions</p> Signup and view all the answers

    What is the application of circular dichroism (CD) spectroscopy in bioinorganic chemistry?

    <p>To examine the secondary structure of biopolymers and nucleic acids</p> Signup and view all the answers

    What is the purpose of magnetic circular dichroism (MCD) spectroscopy?

    <p>To provide a fingerprint approach to identifying bound ligands</p> Signup and view all the answers

    What is the advantage of using MCD spectroscopy in bioinorganic chemistry?

    <p>It allows for the identification of bound ligands in certain well-defined cases</p> Signup and view all the answers

    What is the application of MCD spectroscopy in the study of metalloproteins?

    <p>To characterize paramagnetic metal centers</p> Signup and view all the answers

    What is the significance of the temperature- and field-dependence of an MCD spectrum?

    <p>It provides information about the magnetic spin states</p> Signup and view all the answers

    What is the advantage of using Co2+ substitution in MCD spectroscopy?

    <p>It allows for the study of metalloproteins with spectroscopically silent metal centers</p> Signup and view all the answers

    What is the application of MCD spectroscopy in the study of heme proteins?

    <p>To assign the presence of a specific ligand, such as a thiolate</p> Signup and view all the answers

    What is the purpose of using a mediator in facilitating electron transfer to the metal center?

    <p>To carry electrons to the protein center</p> Signup and view all the answers

    What is the advantage of using modified gold electrodes in bioelectrochemical methods?

    <p>To achieve direct electron transfer of redox-active proteins</p> Signup and view all the answers

    What is the role of 4,4'-bipyridyl in facilitating electron transfer at a gold electrode?

    <p>It acts as a promoter to facilitate rapid protein association and dissociation</p> Signup and view all the answers

    What is the application of bioelectrochemical methods in the field of biosensors?

    <p>To monitor cholesterol levels using electrodes with covalently attached ferrocene</p> Signup and view all the answers

    What is the advantage of using Electron Microprobe Analysis in bioinorganic chemistry?

    <p>It can achieve spatial resolution of 1 micrometer</p> Signup and view all the answers

    What is the significance of Proton-induced X-ray emission (PIXE) in bioinorganic chemistry?

    <p>It can detect elements of biological interest using a focused beam of protons</p> Signup and view all the answers

    Study Notes

    Electron Paramagnetic Resonance (EPR) Spectroscopy

    • EPR spectroscopy is a method suited for studying metalloproteins containing Cu(II), Co(II), Fe(II), Fe(III), Mn(II), Mn(III), and metal clusters like Fe20 and Fe4S4. • It is a sensitive method, capable of detecting high-spin ferric ions at concentrations as low as pM range. • EPR spectroscopy was used in the isolation and purification of iron-containing proteins, such as ferredoxins. • The method helps establish electronic structures and their dependence on metal coordination-sphere composition and geometry.

    Copper Bioinorganic Chemistry

    • Copper(II) is especially amenable to EPR investigation due to its single unpaired electron. • The 63Cu and 65Cu nuclei give rise to a characteristic four-line pattern due to electron-nuclear-spin hyperfine interactions, denoted by the parameter A. • The electronic spin-relaxation time is sufficiently long at room temperature, allowing spectra to be observed in fluid solution. • EPR spectra of frozen solutions can be investigated to stop molecular tumbling, which averages out the anisotropy of the g-tensor.

    Physical Methods in Bioinorganic Chemistry

    • The purpose of the chapter is to provide a critical survey of physical methods currently available to the bioinorganic chemist. • The chapter discusses how various physical methods have affected the development of bioinorganic chemistry and how bioinorganic chemistry has occasionally led to improved methodologies.

    Time Scales

    • To understand the nature of a transition-metal center in biology, it is often useful to obtain knowledge about its electronic states and magnetic properties. • The time scale of a spectroscopic technique is important, as it determines the rate of a chemical reaction that can be probed. • Table 4.1 summarizes the time scales for commonly used spectroscopic analysis techniques.

    X-ray Methods

    • X-rays have wavelengths similar to interatomic distances, making them useful for determining molecular structure. • Two fundamentally different sorts of X-ray methods are currently widely used: diffraction and absorption. • X-ray diffraction is useful for determining the structures of small molecules and macromolecules, including metal coordination geometries. • X-ray absorption spectroscopy (XAS) is useful for determining the oxidation state of the metal ion of interest and getting electronic structural information.

    X-ray Crystallography

    • X-ray crystallography offers the most powerful structural probe of macromolecular structure, including metal coordination geometries. • Resolution is limited in the best cases to slightly less than 2 Å, compared to less than 1 Å for most coordination complexes. • Protein crystals do not diffract X-rays as well as small molecule crystals do, largely due to their high water content, often - 50 percent, which is usually highly disordered.

    Heavy-Atom Derivatives

    • Derivatives with electron-dense atoms or groups must be prepared, usually by soaking crystals in solutions of heavy-metal complexes. • Examples of such reagents include tetrakis(acetoxymercuri)methane (TAMM) and di-iodobis(ethylenediamineplatinum(II)) (PIP). • These reagents are used in solving the structure of the nucleosome core particle, a complex of eight polypeptide chains and 146 base pairs of DNA.### Extended X-ray Absorption Fine Structure (EXAFS)

    • Modulation of X-ray absorption-energy spectrum by back-scattering from neighboring atoms produces EXAFS.
    • EXAFS provides details about metal-coordination geometries.
    • Noncrystalline solid and solution samples can be studied using EXAFS.
    • Geometric information derived from fitting EXAFS data to a model structure can be reliable to 0.01 A.

    Applications of EXAFS

    • One of the early triumphs of EXAFS spectroscopy was the study of the iron-sulfur protein rubredoxin.
    • EXAFS results for metallobiopolymers tend to be most accurate for symmetric sites with heavy elements (Z > 14) in the first coordination sphere.
    • Lower temperatures (to 4.2 K) may be required to minimize atomic thermal motion, which can alter protein-active-site structures.

    Magnetic Resonance Methods

    • Magnetic resonance occurs when a particle with a magnetic moment is placed in a magnetic field and transitions between states with different energies.
    • Depending on the particles, the method is called electron paramagnetic resonance (EPR) spectroscopy or nuclear magnetic resonance (NMR) spectroscopy.

    Electron Paramagnetic Resonance (EPR) Spectroscopy

    • EPR spectroscopy is used to study metal ions in bioinorganic chemistry.
    • EPR signals can be observed in metal ions, such as Cu(II), Mn(II), Fe(III), and Co(II), and in organic residues and substrates.
    • EPR spectroscopy can distinguish between different redox states and spin forms of metal ions.
    • Table 4.3 lists the EPR signatures for biologically interesting transition-metal centers.

    Copper Centers in Bioinorganic Chemistry

    • There are three types of copper EPR signals in bioinorganic chemistry.
    • The second type of copper EPR signal has g-values characteristic of most cupric complexes.
    • The third type of copper is EPR silent due to antiferromagnetic exchange coupling and/or rapid electron-spin relaxation.

    Iron Centers in Bioinorganic Chemistry

    • EPR spectroscopy can distinguish between Fe(I) and Fe(II) redox states and low- and high-spin forms of iron.
    • EPR spectra have been used to study heme iron and iron-sulfur clusters.

    Nuclear Magnetic Resonance (NMR) Spectroscopy

    • NMR spectroscopic methods have been highly useful in bioinorganic chemistry.
    • NMR spectroscopy provides distance and torsion angular information about the three-dimensional structure of biopolymers, including bound metal ions.
    • The complete three-dimensional structures of small to medium-sized proteins can be determined by NMR methods.
    • Two-dimensional NMR methods have increased the applicability of NMR spectroscopy for macromolecular structural studies.

    Variants of EPR and NMR Spectroscopy

    • Electron-nuclear double resonance (ENDOR) spectroscopy is used to study substrates with EPR active metal centers.
    • Electron-spin-echo envelope modulation (ESEEM) spectroscopy is used to detect superhyperfine interactions between metal ions and ligands.
    • NMR spectroscopy can be used to study metal nuclei, such as 57Fe, 67Zn, and 113Cd, and to detect superhyperfine interactions.### NMR Spectroscopy
    • Paramagnetic metal ions can produce shifted NMR signals that facilitate identification of amino-acid side-chain ligands.
    • Line broadening without chemical shift changes occurs for ligands surrounding Mn(II) and Gd(III) and can be used to extract distance information.
    • Line broadening by paramagnetic transition metals is also useful for determining the accessibility of water to the active site of a metalloenzyme.
    • Metal nuclei having I = 1/2 are the most useful, as they do not exhibit quadrupolar line broadening.
    • Examples of useful metal nuclei include 113Cd, 195Pt, 203Tl, and 207Pb.

    Mossbauer Spectroscopy

    • This method is especially valuable for studies of 57Fe in bioinorganic chemistry.
    • The isomer shift (δ) and quadrupole splitting (ΔEQ) parameters can be obtained from the Mossbauer spectrum.
    • The isomer shift is related to the metal oxidation and spin states, as well as the types of ligands coordinated to iron.
    • The quadrupole splitting reveals the asymmetry of the electric field surrounding the metal center.

    Electronic and Vibrational Spectroscopy

    • Transitions between various electronic states lead to the absorption of energy in the ultraviolet, visible, and near-infrared regions of the electromagnetic spectrum.
    • Electronic spectra can be used to evaluate the structural and electronic properties of metallobiomolecules.
    • The three major sources of electronic spectra in metal complexes are internal ligand bands, transitions associated with metal orbitals, and charge transfer bands.
    • Selected metalloprotein chromophores have distinct spectral features, such as the Soret band in hemes.

    Magnetic Measurements

    • The magnetic moment of a metalloprotein can be measured using a SQUID susceptometer.
    • The magnetic susceptibility (χ) of a metalloprotein varies with temperature (T).
    • The magnetic moment can be used to determine the number of unpaired electrons.
    • Magnetic measurements can be used to study antiferromagnetic and ferromagnetic coupling between metal centers.

    Redox Potential Measurements

    • The redox potential of a metalloprotein can be measured using a potentiometric titration with a redox agent.
    • The redox potential is an important property of metallobiomolecules, as it affects their biological functions.
    • The redox potential can be used to study the accessibility of different redox states.

    Circular Dichroism and Magnetic Circular Dichroism Spectroscopy

    • Circular dichroism (CD) spectroscopy is a technique that measures the difference in absorption of left- and right-circularly polarized light by an optically active sample.
    • CD spectroscopy can be used to detect or resolve electronic transitions, examine the secondary structure of biopolymers, and follow folding-unfolding transitions.
    • Magnetic circular dichroism (MCD) spectroscopy is a technique that measures the circular dichroism spectrum in the presence of an applied magnetic field.
    • MCD spectroscopy can be used as a fingerprint method to identify bound ligands in certain cases.

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    Description

    This chapter provides an overview of the various physical methods used in bioinorganic chemistry to address specific questions. It discusses the different techniques available to bioinorganic chemists without delving into the underlying principles. The goal is to facilitate progress in experimental science.

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