Practical Approaches to Biological Inorganic Chemistry

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Practical Approaches to Biological Inorganic Chemistry
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List of Contributors
1 An overview of the role of metals in biology
	Introduction
	Essential metal ions and their functions
	Toxic metals
	Metals in diagnosis and therapeutics
	References
	Further reading
2 Introduction to ligand field theory and computational chemistry
	Introduction
	Introduction to quantum chemistry
		Approximations in quantum chemistry
	Electronic structure of atoms
		Hydrogen atom
			Angular momentum
			Electron spin
		Many-electron atoms
			Periodic system of elements
		Pauli principle
		Two electrons in two orbitals
		Electronic terms
	Symmetry
	Ligand field theory
		Some qualitative considerations
		Symmetry in ligand field theory
		Some quantitative considerations
			Tanabe–Sugano diagrams
	Introduction to computational chemistry
		The wave function–based methods
			The Hartree–Fock method
			Post-Hartree–Fock methods
		Density functional theory
			Density functional approximations
			Density functionals and spin states
		Computational methods for excited states
		Computational methods for biological systems containing transition metal
	Concluding remarks
	Acknowledgments
	References
3 Molecular magnetochemistry
	Introduction
		Origin of magnetism
		Contributions to angular momentum in free atoms and ions
			Term symbols for free atoms and ions with one electron outside a closed inner shell
				Spin–orbit coupling
			Term symbols for free atoms and ions with more than one electron outside a closed inner shell
	Units and definitions
		Magnetic moment and the Bohr magneton
		Magnetic field and magnetization
		Zeeman effect
			Normal Zeeman effect
			Anomalous Zeeman effect
		Magnetic susceptibility, effective magnetic moment and magnetization saturation
		Curie law for noninteracting paramagnets
		Boltzmann treatment of magnetization
			Langevin paramagnetism
			Brillouin function
			Van Vleck equation
			Curie constant and spin-only effective magnetic moment
			Temperature-independent paramagnetism and the second-order Zeeman effect
	Contributions to magnetism in biologically relevant ions
		Orbital splitting of transition metal ions in crystal field
		Effect of crystal field on magnetic properties of 3d compounds
	Dimeric sites: exchange mechanisms and J values
		Curie–Weiss law
		Superexchange
		Spin Hamiltonian
		Bleaney–Bowers equation
	Diamagnetism
	Experimental methods
		Magnetometry
			Force methods
			SQUID—super conducting quantum interference device
				What is measured in the SQUID?
		Evans NMR method
		Magnetic circular dichroism
	Conclusion
	Problems
	Answers
	References
	Further reading
4 EPR spectroscopy
	Why electron paramagnetic resonance spectroscopy?
	What is electron paramagnetic resonance spectroscopy?
	Anisotropy
	A comparison of electron paramagnetic resonance versus NMR
	Electron paramagnetic resonance spectrometer
	What (bio)molecules give electron paramagnetic resonance?
	Basic theory and simulation of electron paramagnetic resonance
	Saturation
	Concentration determination
	Hyperfine interactions
	High-spin systems
	Applications overview
	Test questions
	Answers to test questions
	References
5 Introduction to biomolecular nuclear magnetic resonance and metals
	Introduction
	Properties of the matter relevant to nuclear magnetic resonance
	Energy of nuclear magnetic resonance transitions
	Macroscopic magnetization
	Acting on magnetization
		Pulses
		The rotating frame
	Relaxation
		What are the physical mechanisms of relaxation?
	An nuclear magnetic resonance experiment
	The chemical shift
		Carrier frequency
		Sampling bandwidth and the Nyquist theorem
		Measuring T1
	Coupling: the interaction between magnetic nuclei
		Decoupling
	The nuclear Overhauser effect
	DOSY: sizing up molecules
	Chemical exchange
	Multidimensional nuclear magnetic resonance
		How do the correlations arise and how are cross-peaks generated?
		The COSY
		The NOESY
		The HSQC
	Metals in biomolecular nuclear magnetic resonance spectra
		Transition metals and interaction with the unpaired electron(s)
	Hyperfine scalar coupling
	Dipolar coupling
		Relaxation
	Contact relaxation
	Dipolar relaxation
	Curie relaxation
	Residual dipolar couplings
	Nuclear magnetic resonance of (semi-)solid samples
		Direct observation of metals by nuclear magnetic resonance
	In-cell nuclear magnetic resonance
	An nuclear magnetic resonance spectrometer: measuring macroscopic magnetization and relaxation
	Care in obtaining nuclear magnetic resonance spectra of paramagnetic samples
		Water eliminated Fourier transform and super-water eliminated Fourier transform sequences: catching up with fast relaxing s...
		Evan’s method: measuring magnetic susceptibility
	Conclusions
	Further reading
	Useful physical constants
	Exercises
	Answers
6 57Fe-Mössbauer spectroscopy and basic interpretation of Mössbauer parameters
	Introduction
	Principles
		The Mössbauer light source
		γ-Emission and absorption—recoil is a problem
		Recoilless emission and absorption—the Mössbauer effect
		The Mössbauer experiment
		The Mössbauer spectrometer
	57Fe hyperfine interactions
	Isomer shift as informative hyperfine interaction
	Electric quadrupole splitting
	Magnetic hyperfine splitting
	Combined hyperfine splitting
	Applications—selected examples
		Oxidation and spin states in a nonheme diiron center
		Reaction intermediates and low- and high-valent iron complexes
		The heme enzyme horseradish peroxidase
		Nonheme model compounds
			Synthetic iron(III) complexes with the macrocyclic ligand cyclam
		Iron(II) complexes
		Mixed-valence iron(III)–iron(IV) dimers and iron(IV) monomers
		Iron(V) complexes
		Four-coordinated iron(IV) and iron(V) compounds
		The first molecular iron(VI) compound
	Perspectives
	Exercises
	References
7 X-ray absorption and emission spectroscopy in biology
	Outline of the X-ray absorption and emission spectroscopy in biology
	An introductory biological X-ray absorption spectroscopy example: Mo, Cu, and Se in CO-dehydrogenase from Oligotropha carbo...
	X-ray absorption (near-)edge structure
	X-ray emission spectroscopy in biology
	Time-resolved X-ray absorption spectroscopy
	X-ray absorption spectroscopy: X-ray–induced electron diffraction
	Phase shifts and effect of atom type
	Plane wave and muffin-tin approximation
	Multiple scattering in biological systems
	Strategy for the interpretation of EXAFS
	Validation and Automation of EXAFS data analysis
	X-ray absorption near-edge structure simulations with three-dimensional models
	Metal–metal distances in metal clusters
	Nonmetal trace elements: halogens
	Summary: strengths and limitations
	Conclusions: relations with other techniques
	Exercises
	Hints and answers to exercises
	References
8 Resonance Raman spectroscopy and its application in bioinorganic chemistry
	Introduction
	The fundamentals of vibrational spectroscopy
		The classical oscillator, Hooke’s law, the force constant, and quantization
		Quantization and the nature of a quantum excitation
	Permanent, induced, and transition electric dipole moments
		Electric dipole moments
		Transition dipole moments
		Polarizability, induced dipole moments, and scattering
			What is ∫φvf*(x)φvidx?
		Relative intensities of Stokes and anti-Stokes Raman scattering
		What is a virtual state?
	The (resonance) Raman experiment
		Raman cross-section and the intensity of Raman bands
		Raman scattering is a weak effect; but how weak?
	Resonance enhancement of Raman scattering
		The Raman spectroscopy of carrots and parrots
		Classical description of Rayleigh and Raman scattering
		The Kramer–Heisenberg–Dirac (KHD) equation
		A-, B-, C-term enhancement mechanisms, overtones, and combination bands
		Assigning electronic absorption spectra
		Heller’s time-dependent approach
	SERS and SERRS spectroscopy
	Experimental and instrumental considerations
		Isotope labeling and band assignment
		Resolution and natural linewidth
		Confocality, the inner filter effect, and quartz
	Applications of resonance Raman spectroscopy
		Resonance enhanced Raman spectroscopy in the characterization of artificial metalloenzymes based on the LmrR protein
		Reaction monitoring with resonance Raman spectroscopy
		Transient and time-resolved resonance Raman spectroscopy
	Conclusions
	Questions
	Answers to Questions
	References
	Further reading
9 An introduction to electrochemical methods for the functional analysis of metalloproteins
	Introduction
	Basics
		Redox thermodynamics: the Nernst equation
		Reference potential and reference electrodes
		The biological redox scale
		Influence of coupled reactions (e.g., protonation or ligand binding) on reduction potentials
		Electron transfer kinetics
		Kinetics of proton-coupled electron transfer: stepwise versus concerted mechanisms
	Electrochemistry under equilibrium conditions: potentiometric titrations
	Dynamic electrochemistry
		Distinction between equilibrium and dynamic electrochemistry
		Electrodes for electron transfer to/from proteins
		Electrochemical equipment
		Vocab and conventions
		The capacitive current
	Diffusion-controlled voltammetry
		Diffusion-controlled voltammetry at stationary electrodes
		Diffusion-controlled voltammetry at rotating electrodes
	Voltammetry of adsorbed proteins: protein film voltammetry
		Noncatalytic voltammetry at slow scan rates to measure reduction potentials
		Fast-scan voltammetry to determine the rates of coupled reactions
	Catalytic protein film voltammetry and chronoamperometry
		Principle and general comments
		Mass-transport controlled catalytic voltammetry
		Chronoamperometry to measure Michaelis and inhibition constants
		Chronoamperometry to resolve rapid changes in activity
		Determining the reduction potentials of an active site bound to substrate
		The effect of slow intramolecular electron transfer
		Slow interfacial electron transfer
		Slow substrate binding
		Slow, redox-driven (in)activation
	Exercises
	Appendices
		Notations and abbreviations
		Derivation of Eq. (9.9)
	References
10 Structural biology techniques: X-ray crystallography, cryo-electron microscopy, and small-angle X-ray scattering
	Questions and purposes
	Preamble
	X-ray crystallography
	Protein crystallization
		Protein production and sample preparation
		Protein quality assessment
			Protein concentration
			Crystallization techniques and initial screens
			Analysis of crystallization trials
			Salt or protein crystals?
			Crystal optimization and seeding
			Cocrystallization and soaking
			Membrane proteins
			Harvesting and mounting of crystals
	Data collection
	Phase determination
		Molecular replacement
		Isomorphous replacement
		Anomalous scattering
		Direct methods
		Heavy-atom derivatization
	Model building and refinement
	Structure analysis and model quality
		Content of crystallographic models
		Validation
	X-ray free electron lasers
	Cryo-electron microscopy
	Small-angle X-ray scattering
	General conclusion
	References
11 Genetic and molecular biological approaches for the study of metals in biology
	Introduction and aims
	Basic genetics and molecular genetics: origins and definitions
		The origins, evolution, and speciation
		Grouping the species: classification, taxonomy, phylogeny
		The fundamental molecular biological information molecules: deoxyribonucleic acid and ribonucleic acid
		The central dogma
		The genetic code
		What is a gene?
		How big are genes and genomes?
		Replicons
		Gene organization
		Insertion elements, transposons, and repetitive deoxyribonucleic acid
		How deoxyribonucleic acid moves and can be moved around between organisms: transformation, transduction, conjugation
		Homologous recombination
		Promoters, transcription initiation, and transcriptional regulation
		Translation initiation
	Setting up: regulations, equipment, methods, and resources
		Regulation and approvals
	Approaches and systems
		Model systems
	Molecular biology tools and methods
		Preparation of deoxyribonucleic acid
		Agarose gel electrophoresis
		Pulse-field/orthoganol electrophoresis
		Blotting techniques
		Molecular cloning/recombinant deoxyribonucleic acid technology
		The polymerase chain reaction
		Deoxyribonucleic acid sequencing
	Genetic and molecular genetic methods
		Cloning vectors and hosts
		Gene libraries
		Libraries intended for genome deoxyribonucleic acid sequencing
		Cosmid libraries
		Mobilizable and broad-host range vectors and cosmids
		Bacterial artificial chromosomes
		Yeast artificial chromosomes
		Deoxyribonucleic acid copy (cDNA) libraries
		Protein overexpression and purification
		The T7 ribonucleic acid polymerase-T7 promoter system in Escherichia coli
		The Pichia pastoris system
		Tags for protein purification, correct folding, improved stability
		Mutagenesis
			Mutants: general considerations
			Chemical and physical mutagenesis
			Transposable elements and their use in mutagenesis
			Site-directed mutagenesis
			Site-directed point mutants
			CRISPR/CAS9 mutagenesis (“gene-editing/engineering”)
	Bioinformatics
		General bioinformatics websites
		Sequence searching sites
		Multiple sequence alignment
		Comparative gene organization
		Identification of potential domains in proteins
		Genome sites
		Cross-relational databases for genomes and metabolic and other pathways
		Molecular phylogenies and tree drawing programs
		Visualization of molecular structures
	The OMICS revolution
		Genomics
		Transcriptomics
		Proteomics
		Structural genomics
		Omniomics
		Metabolomics
		Economics
	Illustrative examples in the genetics and molecular biology of N2-fixation
	References
	Further reading
Index
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