Basics of

Bioinorganic Chemistry

Handout

Lorenz Kienle
Max-Planck-Institut für
Festkörperforschung
Stuttgart
Outline

1. Very important terms of coordination chemistry

2. General aspects of bioinorganic chemistry
3. Coordination for uptake, transport and storage (Fe)
4. Hard ions: Na+, K+, Mg2+, Ca2+
5. Cobalamines
6. Metals in Photosynthesis
7. Fe in bio systems
Resources
Text books
• W. Kaim, B. Schwederski: Bioinorganic Chemistry: Inorganic Elements
in the Chemistry of Life, Wiley 1994, German edition: Teubner 1995
• S. J. Lippard, J. M. Berg: Bioanorganische Chemie, Spektrum- Akademischer Verlag
• D. Shriver, P. Atkins: Inorganic Chemistry, Freeman and Comp. 1999 (Chapter 19)

Internet resources
• Lectures of Prof. Rehder (University Hamburg), doc-files (german)
• Internet resources, e. g. Uni Siegen (KomplexeMaster7Sem.ppt, etc.)
• Bonding: http://wwwchem.uwimona.edu.jm:1104/courses/CFT.html
• Lectures of Prof. Klüfers (LMU, see homepage)

Papers
• S. Busch et al., Eur. J. Inorg. Chem. 1999, 1643
• E. Bäuerlein, Angew. Chem. Int. Ed. 2003, 42, 614
 1.
Very important terms
of coordination chemistry
Coordination compound (complex)- basics
• Central atom is bound to unexpectedly large number of ligands (CN)
• Usually discrete species in solution and solid
• Examples: K4[Fe(CN)6], CoCl2 * 6 H2O
• Properties of central atoms (transition metals):
• Large charge/radius ratio
• Variable oxidation states (d-electrons available)
• (Meta)stable high oxidation states, s- electrons are removed first
• Compounds are often paramagnetic (unpaired electrons)
• Formation of colored ions and compounds
• Compounds with profound catalytic activity
• Formation of stable complexes (Lewis acids, see HSAB)
• Trend to metal-metal bonding (clusters, not important in biology)

• Properties of ligands
• Monodentate or polydentate ligand
• Ambidentate ligands (nitro-, nitrito)
Electron configurations of transition metals
• Prerequisite: basic knowledge of periodic table
• Co: [Ar] 4s2 3d7, Co2+: [Ar] 3d7, Co3+: [Ar] 3d6
 Geometrical features

Pseudorotation
• Exchange of a- and e-ligand, see MgATPase
• [Ni(CN)5]3-: b) and a) in crystal structure
• Fe(CO)5: fast pseudorotation in solution

Isomerism
• Molecules have the same molecular formula
but the atoms are arranged differently
• The structures of isomers are not super imposable
• Isomers have different physical (color) and/or chemical properties.
HSAB concept

• Pearson’s concept, 1963

• Lewis concept: metal ions are acids because they accept electrons
ligands are bases because they donate electrons

• Hard acids tend to form complexes with hard bases (ionic bonds)

• Soft acids tend to form complexes with soft bases (covalent bonds)

• Hard acids: H+, Li+ (> Na+…), Cr6+ (> Cr3+)

• Intermediate acids: Fe2+, Mn2+, Cu2+, Zn2+

• Soft acids: Au+ (> Ag+, Cu+), Hg2+, Pt2+

• Hard bases: F-, OH-, NH3, PO43- (> HPO42-), MoO42-

• Intermediate bases: Cl-

• Soft bases: I- (> Br- …), S2- (> HS-, > H2S), AsS2-
Chelates
HO O
• Structure O
• Multidentate ligands (more than one bond with the central atom or ion)
N OH
• Ring structures
O
NH2 H2N N
N N O Pb N N OH
en Ni Co EDTA
N N
O N
O
NH2 H2N N O HO O

• Properties
• Multidentate ligands are much stronger complex formers than monodentate ligands
• Chelates remain stable even at very dilute concentrations (less dissociation)
• Chelate effect: Increase of entropy
ΔG = ΔH - TΔS, ΔH ~ for multi- and mono-dentate complexes
Cu(H2O)42+ + 4NH3 ↔ Cu(NH3)42+ + 4H2O
Cu(H2O)42+ + N4 ↔ Cu(N4)2+ + 4H2O
• Chelate therapy (detoxification)
Bonding in complexes- CTF
• Crystal Field Theory (Electrostatic guide to splitting of d-levels)
• Ligands regarded as point charges, ligand field splitting Δ0
• LFSE (Ligand Field Stabilization Energy)

t2 eg

e t2g
Bonding in complexes- CTF

• Spectrochemical series:
I- < Br- < S2- < Cl- < NO3- < OH- < H2O < NH3 < en < NO2- < CN- < CO

• Metal: Δ0 increases with increasing oxidation number and down a group

Mn(II) < Ni(II) < Fe(II) < V(II) < Fe(III) < Co(III) < Mn(IV) < Mo(III) < Pd(IV) < Pt(IV)

• Electronic configuration (h.s., l.s.) depend on LFSE and P (pairing energy)

• Trends for l.s:
• ligands: right end of spectrochemical series
• central atoms: 4d, 5d metals large Δ0
• geometry: octahedral coordination

• Jahn-Teller distortion: remove of degeneracy, increase of LFSE

• Splitting eg (dz2 lower energy) and t2g (dxy higher energy)
• Square coordination: dxy higher energy than dz2
Bonding in complexes- LFT (σ-bonding)
• Ligand field theory (Interaction in terms of atomic and molecular orbitals)
• Overlap atomic orbitals of similar symmetry to form molecular orbitals

nonbonding
localized on metal
Bonding in complexes- LFT (π-bonding)
• SALC of metal t2g and π-orbitals of the ligand
• Non-bonding t2g become antibonding (π -donor)
• Non-bonding t2g become bonding (π -acceptor)

π -donor ligand: completely π -acceptor ligand: incompletely

filled low-energy π-orbitals: filled low-energy π-orbitals:
Δ0 is reduced Δ0 is increased
 2.
General aspects of
bioinorganic chemistry
“Bioinorganic Chemistry” – a contradiction?

• Organic chemistry: restricted to carbon compounds

• Biochemistry: chemical components of living systems
• Inorganic chemistry: no covalent carbon components (?)
• Bioinorganic chemistry: biochemical function of “inorganic elements”
• Consequence: interdisciplinary research!

• Profit from Bioinorganic Chemistry: learning from nature

• Nature: optimized system by evolution
• Efficient collection, conversion and storage of energy
• Moderate conditions during catalytic processes supported by metal proteins
• Stereoselective synthesis

• Three main fields of research

• Enzymes, biological relevant complexes: biochemistry and coordination chemistry
• Biomineralization: biochemistry and solid state (materials) chemistry
• Synthesis and characterization (NMR, XRD, TEM, …) of model systems
 Periodic table of life

Metals Essential elements for humans (daily requirement: 25 mg)

Non metals Presumably essential elements

• Symptoms of deficiency: Mg (muscle cramps), Fe (animea), Mn (infertility)

• Toxic effects in case of high doses (therapeutic width)
• Occurrence of non essential elements (e.g. Rb: 1.1 g / 70 kg) and of contaminations (e.g. Hg)
Metal content of a human body (70 kg)

Ca 1000 g Sn 20 mg
K 140 g V 20 mg
Na 100 g Cr 14 mg
Mg 25 g Mn 12 mg
Fe 4.2 g Mo 5 mg
Zn 2.3 g Co 3 mg
Cu 72 mg Ni 1 mg

Low concentration: use for catalysis

Non metals: O (45500 g), C (12600 g), H (7000 g), N (2100 g), P (700 g)
Metal content of a human body (70 kg)
Earth’s Crust Human Body

Element % Element %

O 47 O 63

Si 28 C 25.5

Al 7.9 H 9.5

Fe 4.5 N 1.4

Ca 3.5 Ca 0.31

Na 2.5 P 0.22

K 2.5 K 0.08

Mg 2.2 S 0.06

• Week correlation to distribution of the elements in the earth’s crust (there: O > Si > Al > Fe…)
• Consequence: optimized mechanisms for uptake and storage of the inorganic elements
• Good correlation to distribution of the elements in sea water
Functions of “inorg. elements” – summary
• Assembly of structures (DNA, biomineralization), endo- and
exoskeletons. Ca, Mg, Zn, Si
• Information carriers (muscle contractions, nerve function). Na, K, Ca, Mg
• Activation of enzymes. Mg, Ca
• Formation, metabolism and degradagation of organic compounds by
Lewis acid/base catalysis. Zn, Mg
• Transfer of electrons (energy conversion), FeII/FeIII/FeIV, stable due to
bioligands
• Uptake, transport, storage and conversion of small molecules
• 3O2: Fe, Cu (conversion), Mn (generation)
• N2: Fe, Mo, V (conversion to ammonia)
• CO2: Ni, Fe (reduction to methane)
Most prominent “bioelements”
• Na+,K+: Electrolytes
• Mg2+: Chlorophyll, energy production (ATP → ADP), skeleton
• Ca2+: muscle functions, Hydroxylapatite Ca5(PO4)3(OH), CaCO3
• VIV/V, MoIV/VI, WIV/VI, MnII/III/IV, FeII/III, NiI/II/III, CuI/II: electron transfer
• Fe and Cu: transport and storage of oxygen
• FeII, FeIII: Magnetite (Fe3O4)
• Co: Cobalamine, e.g. Vitamin-B12
• Zn2+: Enzymes, zincfinger (gen. transcription), stabilization of proteins
• SiIV: bones; SiO2/silicagel
• PV: Hydroxyapatite, ATP, cell membrane, DNA
• Se-II: Selenocysteine
• F-: Fluorapatit (Ca5(PO4)3F) teeth; Cl-: besides HCO3- most important free
anion, I-: hormones of the thyroid, radiation therapy
Application of metals in medicine 1

• Li+: Treatment of depression (Li2CO3, low doses)

• Gd3+: Contrast agent (NMR)
• BaSO4: Contrast agent (radiography)
• 99mTc: radio diagnostics (thyroid)
• Au(I): Rheumatism

Well
• Sb(III): Eczema
• Bi(III): Gastric ulcer
Health
• Cd(II): Carboanhydrase
(Thalassiosira weissflogii)
Dead Concentration
Application of metals in medicine 2
O
• Pt(II): Cisplatin (cis-[Pt(NH3)2Cl2]), chemotherapy -
O
P
O
O
(inhibition of cell division, no inhibition of cell growth) CH2 H2 N
N NH
H H O
H O
N
O N NH3
H
-
O P O H
N7 of guanine Pt
O
N NH3
CH2
O N O
H H
H H N NH
H H2 N

Untreated
died day 21
tumour 3 g.

Filamentous growth Treated on day 8, tumour completely regressed by day 14.

of bacteria Died of old age 3 years later.
Terms related to bioinorganic chemistry

• Active center: Location in an enzyme where the specific reaction takes place
• Apo-enzyme: An enzyme that lacks its metal center
• ATP: Adenosine 5’-triphosphate
• Biomembrane: Sheet like assemblies of proteins and lipids (bilayer)
• Charge-transfer complex: An aggregate of two or more molecules in which charge is
transferred from a donor to an acceptor.
• Chlorophyll: Magnesium complex of a porphyrin in which a double bond in one of the
pyrrole rings (17-18) has been reduced. A fused cyclopentanone ring is also present
• Cluster: Metal centers grouped close together which can have direct metal bonding
or through a bridging ligand, e.g. ferredoxin
• Cobalamin: Vitamin B12, substituted corrin-Co(III) complex
• Coenzyme: A low-molecular-weight, non-protein organic compound (often a nucleotide)
participating in enzymatic reactions
• Cofactor: An organic molecule or ion (usually a metal ion) that is required by an enzyme for
its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
• Cooperativity: The phenomenon that binding of an effector molecule to a biological system
either enhances or diminishes the binding of a successive molecules, e.g. hemoglobin
Terms related to bioinorganic chemistry

• Entatic state: A state of an atom or group which has its geometric or electronic condition
adapted for function. Derived from entasis (Greek) meaning tension
• Enzyme: A macromolecule that functions as a biocatalyst by increasing the reaction rate
• Heme: A near-planar coordination complex obtained from iron and dianionic porphyrin
• Hemoglobin: A dioxygen-carrying heme protein of red blood cells
• Holoenzyme: An enzyme containing its characteristic prosthetic group(s) and/or metal(s)
• Ion channel: Enable ions to flow rapidly through membranes in a thermodynamically
downhill direction after an electrical or chemical impulse.
• Ionophore: A compound which can carry specific ions through membranes
• Ion pumps: Enable ions to flow through membranes in a thermodynamically uphill
direction by the use of an energy source. They open and close upon the binding and
subsequent hydrolysis of ATP, usually transporting more than one ion towards the outside
or the inside of the membrane
• Photosynthesis: A metabolic process in plants and certain bacteria, using light energy
absorbed by chlorophyll and other photosynthetic pigments for the reduction of CO2,
followed by the formation of organic compounds
• Substrates: A compound that is transformed under the influence of a catalyst
Basics of enzyme reactions (catalysis)

Catalysts…
• Accelerate chemical reactions (rate enhancement)
• Participate in reactions but are not consumed
• Stabilize the transition state (lower activation energy)
• DO NOT alter the chemical equilibrium, Δ Δ(E) ~ reaction rate
• Reduce the amount of time required to attain the equilibrium
 Catalysis- principle of complementarity

• The active sites of enzymes tend to be more complementary to the transition states than they
are to the actual substrates
• Preformation of the transition state by strained enzyme (entatic state)
• Energy aspect: small activation energy, statistical aspect: more productive encounters
between reaction partners, kinetic aspect: faster reaction
Ligands- Proteins
• Proteins consist of α-amino acids, connected via peptide bonds
R1 N-terminus
O H
H
-O
C C H N+ H
C H N C
C-terminus
O R2
H M
• Metal coordination by functional groups in the side chain (R) N
N M

H 2C
Histidine (both N atoms available, metal-metal briding H
possible, pKa ~6) N C C
O
H
Methionine
Tyrosine
Cysteine (“non-innocent ligand”)
(metal-metal bridging, pKa ~ 8)
Selenocystein Aspartic acid
(“non-innocent ligand”) pKa ~ 4
Glutamic acid
 Proteins- Structure

Primary structure:
Sequence of amino acids

Tertiary structure:
Shape of entire protein

Secondary structure:
Shapes formed within regions of the protein

Quaternary structure:
Structures formed by interaction of several subunit
Proteins- Structure representation

β-cage T-Atom-representation
Cyclic ligands- Porphyrin complexes

• Unsaturated tetradentate macrocyclic ligands

• Coordination of otherwise labile divalent metal ions
• Porphyrin complexes: chelate-effect and size selective as host
• Porphyrin: very stable, Hückel-aromatic (18 el = 4n +2), colored

Porphyrin Chlorin Corrin Metallaporphyrin

Hemoglobin Chlorophyll (Mg2+) Cobalamin (Co2+) complex
Myoglobin Fe Tunichlorine (Ni2+)
Peroxidases
Cyclic ligands- Porphyrin complexes
N C C H2 C O N H 2

H3 C H
H
C H3
C H2 C H 2 C O N H2
N H 2 C OC H2 N
N C H
R R'
+ 3
C o
H 3 C N
H
N H 2 C OC H2 C H 2
C H3 H
N
N H2 C O C H C H 3
2
H3 C
C H2 C H C ON H
N C H3 2 2

R R
H
C H2
N

N Fe N C H3

C H2
R" R' N
N C H 3
C O

H
O
N H OH O
R" R H C H2 OH

H
C H2 O H

P
O
H C C H O
3

Vitamine B12
Cyclic ligands- Porphyrin complexes

Bonding
• Most complexes are (nearly) planar → two open coordination sites (e.g. substrate…)
• Usually low spin complexes → Fe(II) high spin in deoxy-hemoglobin out-of-plane position
• Fine tuning of electronic configuration by conformation and axial ligands
• Splitting of d orbitals (CFT):

octahedron

tetragonal bipyramide
square
Cyclic ligands- Ionophores

• Bonding of hard cations by macrocycles or quasi-macrocycles

• Coordination by O, N
• Production of a lipophilic shell around hard cations
• Size, charge selective

Monesin A
Nucleobases- building units of DNA, RNA

• DNA, RNA: macromolecules consisting of nucleotides as building units

• Nucleotides: Pentose, pyrimidine- or purine base, phosphate group (1:1:1)
• Information carriers as ligands (oligo- and polynucleotides)
• Coordination by nucleobases or by phosphate groups (Zn2+, Mg2+)
O NH2 NH2 O

CH3 N HN N
HN N N

N H2N N N
O N O N N
Sugar
Sugar Sugar Sugar

Thymine Cytosine Adenine Guanine

O O
P
HO CH2 Base O O CH2 Base
H O H H O H Nucleotide
Nucleoside X = OH: Ribose
X = H Desoxiribose
H H H H
OH X OH X
 3.
Coordination for uptake,
transport and storage (Fe)
 Some basic properties of Fe
• Usually oxidation of Fe(II)aq to Fe(III)aq under in-vivo conditions

• Insalubrious function of Fe(II) high spin: formation of radicals, e.g. Fe(II) h.s. + 3O2 → Fe(III) +O2•−

• Fe(III) non soluble at pH ~7, coordination of Fe(III) by complexing agents unambiguous

• Condensation to clusters and colloids

Fe
OH2
H OH2 4+ OH2 OH2 2+ H O
+ H2 O O OH2 +
-2H H2 O OH2 O
-H2O, -2H O Fe Fe
2[Fe(H2 O)6 ]3+ Fe Fe Fe Fe O Colloids
H2 O O OH2 H2 O O OH2 HO
OH2 H OH2 OH2 OH2
Fe

• Related affinity to different ligands (S, O, N)

• Switching from high- to low spin configuration (medium strength of ligand)

• Complexation interconnected with electron and proton transfer:

[Fe3+(Ligand)3-] +3 H+ + el ↔ Fe2+ + H3(Ligand)

 Siderophores (microorganisms)

• Two groups of chelating agents Hydroxamate Catecholate

• Antibiotic function, highly active (!), octahedral coordination of Fe(III)

- -
O O O
-
-O O O 3-

Catecholate HN
O
NH
Apoenterobactin
- O
O
O O
O O O O
R Fe
- O O
O O O
O NH

-
O
-
O

O O O
NH NH
NH
NH NH NH
Mycobactin
Hydroxamate O O O Different M-X interactions
(CH2)3 (CH2)3 (CH2)3
O N O
-
N O
-
N O
-

R-C - C O C O C O
N O
CH3 CH3 CH3
R'
Ferrichrome
Proteins (complex organisms)

Transport: Transferrin

Arg NH2 Characteristics

HN
NH2
• Coordination of Fe by caboxy- and phenolate groups of residues
O
• Uptake of two Fe(III) and one HCO3-
Tyr O
O O
Fe
O
• Stability of complexes decrease with decreasing pH
O
Asp N Tyr
O • High affinity of Apotransferrin, protection against infections
NH
• Not very specific (Cr3+, Al3+, Cu2+, Mn2+…)
His
• Release of Fe(III): Reduction to Fe(II) and binding by porphyrine
 Proteins (complex organisms)

Ferritin (Storage)

Leucin Ester-groups of Glu, Asp

Characteristics
• High symmetry of Apoferritin: F432
• Hollow sphere built from proteins (inner dia.: ~ 7 nm, outer dia. ~ 13 nm)
• Capacity: up to 4500 Fe3+, biomineralization (?)
• Carboxylate groups for Fe(III) binding, core-structure related to Ferrihydrite (Fe10O6(OH)18)
• Exchange via channels (dia. 1nm), tuning of hydrophilic/hydrophobic character via residues
• Release of Fe as Fe(II) via hydrophilic channels
 4.
Hard ions: Na ,
+ K,
+

Mg ,
2+ Ca2+
Basic characteristics

Na+ K+ Mg2+ Ca2+

Antagonism
Ionic radius, Å 1.16 1.52 0.86 1.14
Charge/radius ratio 0.86 0.66 2.32 1.75
Coordination number 6 6-8 6 6-8
Preferred donors O O N,O O

multidentate chelates bidentate chelates

Concentration (mmol/kg)
Intracellular 11 92 2.5 0.1
Extracellular 152 5 1.5 2.5

Labile bonding in solution, fast diffusion along a concentration gradient

 Na, K: Inhom. distributed electrolytes

• Function
• Stabilization (membrane, nucleotides, enzymes)
• Fast information transfer by diffusion (highly volatile, diffusion control)

• Maintenance of the concentration gradient

• Pump storage model
• Active Transport:
Active
Ion pumps, proteins triggered by enzymes

membrane
• Passive transport:
Ionophores, chelating ligands
Ion channels, proteins
energy

Pump-storage model
Passive

spatial coordinate
Passive Ion transport- summary

extracellular lipophilic membran intracellular

Ionophores

Carrier
mechanism
(very slow)

Channel
pore

Gated
Channel

Neurotransmitters, toxins, Ca2+, voltage gated

Passive transport: Ionophores
• Analogs from the lab: crown ethers, cryptands (macrocycles)
• Chelate effect (thermodyn. and kinet. stable) O
O O
O O
• Size/charge selectivity N N
O O O O
O O O
• Distinct polarity inside / outside the complex Higher selectivity
• Template effect of alkali metal (conformational change of ionophore)
• Selectivity depending on number of coordination centers of ligand
• Selectivity adjusted by optimum conformation

• Natural ionophores act as antibiotics

• Transport of alkali metal through biological membranes (carrier mechanism)
• Perturbation of electrolyte level in bacteria

K-Valinomycine
Nonactin 3d coordination by folding
Passive transport: Ion channels
Transmembrane protein with tube structure

Gramicidin A: a simple example

• Formed from integral membrane proteins
• Length 3 nm, two tubes in a row can perorate a membrane

More complex channels antiparallel helical

aggregate of proteins
• Building units: 4-5 homologous membrane proteins (helices)
• Immediate lining contains polar groups (fixed charges)
• Specific due to diameter, and chemistry inside the channel

Gates of the channels

• Gate functioning important subject of pharmaceutical research
• Opening by neurotransmitters, Ca2+, electrical pulses…
• Blocking as important biological function,
e.g. blocking of K+ channels by H+ → sensing of “sour” K+ channel,
NP 2003 to Mc Kinnon
Active transport: Ion pumps- overview
Transmembrane protein acting against concentration gradient
Structure, function:
• Carboxylate groups (hydrophilic) for binding the active species
• Selectivity by formation of E1 and E2 which are produced via (de)phosphorylation
• Energy–consuming ion transport mechanism, energy production by hydrolysis of ATP

• Symport: simultaneous transport of anions and cations (K+/Cl-) in same direction

• Antiport: transport of ions of the same charge in opposite direction (H+/K+)

Example: Na+/K+/MgATPase (Mg2+-catalysis)

3 Na+(ic) + 2 K+(ic) + ATP4- +H2O → 3 Na+(ec) + 2 K+(ic) + ADP3- +H2PO4-
ic: intracellular, ec: extracellular
Na+/K+/MgATPase: Flip-Flop-mechanism
Phosphorylation, conformational change to E2

Binding of Na+ Release of Na+

Conformation E1 Conformation E2

Release of K+ Binding of K+
Conformation E1 Conformation E2

Dephosphorylation, conformational change to E1

Toxins affecting ion transport (examples)

Digitoxigenine (Foxglove)
Blocking of Na+/K+/ATPase

• Inhibition of dephosphorylization
• Increase of Na+ and Ca2+ due to antiport system
• Consequence: Muscle contraction (heart!)

Fugu fish (Tetrodotoxin)

Blocking of Na+ channels
Mg: Catalysis of phosphate transfer

• Mg2+: very hard, CN = 6, prefers multiple charged ligands (phosphates)

• Functions:
• Charge compensation, e.g. ATP (reduction of the high concentration of negative charges)
• Polarization, increase of nucleophilic character: Mg2+ + OH2 → [Mg•••OH]+ + H+
• Fixation of the reactants

• Mechanism: SN2 with pseudorotation

→ Conformational changes during Na/K pumping

On the average a human adult synthesizes and uses an amount of ATP per day
which corresponds to the body weight!
 Mg: phosphate transfer- examples

Hydrolysis of ATP (Na/K/ATPase pump) O

OH
HO P

O O O-Nu
O O O adenosyl O O adenosyl
O O
P P O P O O
P P P adenosyl
HO O HO O Nucleophile HO
P P O
O O O
O O O O
O
Mg2+ Mg2+ O
Mg2+
ATP protected ATP activated for hydrolysis

Phosphate transfer to creatine via MgATP

Phosphate transfer to glycerate (formation of 2-phosphoglycerate)

H C CO -
2 2
N MgATP/MgADP
HC NH
3 2

NH
2
Ca: great variety of functions
• Structural function
• Biomineralization (1 kg), 10g/70kg in non-solid form
• Strong influence on protein folding

• Second messenger-, trigger-, activation funftion

• Binding to acidic μ2-carboxy groups of proteins
• High coordination numbers (7, 8), irregular coordination geometry
• Lability of complexes allows fast structural changes
• High concentration gradient (Ca2+ pumps in sarcoplasmic reticulum)
• Interconnections of electrolyte transport

membrane
3Na+
ATP → ADP + P active
2K+
K+
intrac. passive extrac.
Na+
Ca2+
ADP + P → ATP active
2Na+
Ca: Activation of enzymes, energetic processes
Activation Substrate
• Calmodulin = calcium modulating protein can be fixed by
• Conformational change of Apo-Calmodulin by Ca-binding enzyme
• Recognition and activation of enzymes

Enzyme
(inactive)

Calmodulin (inactive) Calmodulin (active) Enzyme (active)

Muscle contraction (Translation of electrical stimulus into chemical stimulus)

• Depolarization of membrane, opening of Na-channels
• Release of Ca2+ from acidic storage protein: Calsequestrin
• Calsequestrin contains up to 50 Ca-binding sites, carboxylate groups (Glu, Asp)
• Uptake of Ca2+ by Troponin C, coupling with ATP Hydrolysis…
Biomineralization: CaCO3- Modifications

• Occurrence e.g. in shells, otholiths…

• Control of morphology and orientation by organic component
• Carboxy-groups of peptide side chains (Asp, Glu…)
• Oxidized carbohydrates…
• Lab-examples:
• Spindel-shaped calcite crystals in presence of malonic acid
• Presence of stearic acid supports the formation of disc shaped Vaterite crystals
• Four important modifications of CaCO3

Calcite, Calcite, {104} Aragonite

stable, structural relation to rock salt metastable, otholithes of fishes,
{104} frequently at the surface of shells coral reef, pearls

Vaterit Amorphous CaCO3

metastable, disordered (?), rare formation of spherolites
formation of sperolithes
 Biomineralization: Apatite Ca5(PO4)3X

• Occurrence e.g. in bones and teeth (enamel: larger crystals, F-substituted)

• Highly effective mechanisms for Ca-transport (humans: 0.7g/day)
• Collagen: template function, serves for defined orientation of apatite crystals
• Binding of Ca via carboxy groups of osteocalcin or via phospho-proteins (?)

Osteocalcin
Hydroxyapatite • Perfect match with apatite
collagen fiber

• Disordered structure
• OH shifted from mirror plane
• Non-polar structure (P63/m)

Collagen
• Three left handed helices combined to
one right handed super helix
• [001](Apatite) parallel to collagen helices
• Composite material, no binding sites for Ca
 5.
Cobalamines
Basic molecular features
• Organometallic compound, low-spin configuration of Co3+
• Macrocycle: Corrin (small, butterfly) + 5,6 Dimethylbenzimidazole
• Reduction: population of dz2 (σ*(Co-CH2-))
→ Decrease of axial coordination

octahedron
tetragonal
bipyramide
square

X = CH3, OH, CN (vitamin B12), 5’ deoxyadenosine

(Coenzyme B12)
Reactions- types of Co-C bond cleavages

Substitution Formation of
supernucleophile (Lewis base)

d6 d7 d8

“Carbanions” Alkyl radicals “Carbocations”

Heterolysis Homolysis Heterolysis

(Evidence via ESR)

Determination of reaction pathway: N-ligand, Substrate, redox potential

Reactions
• Mutase activity:
• 1,2-shift at saturated hydrocarbon centers (rearrangement)
• Function of apoenzyme: Decrease of Co-C bonding (el. transfer?), Protection of pr. radical
• Less amount of byproducts, stereoselectivity

Function: Reversibly acting radical carriers

Examples:
H-abstraction

1,2-shift: Stabilization
of primary radical
H-abstraction

E.g. recombination
with [CoII]

• Alkylation:
• Alkylation of electrophilic substrates by carbanions, e. g. methylation of Hg2+ ((CH3)Hg+)
• Methylation of homocystein to methionin
 6.
Metals in Photosynthesis
Mg, Mn, (Fe), (Cu), (Ca)
Fundamental aspects

• Photosynthesis: production of organic material and oxygen

• “Uphill-Catalysis” (ΔH = +470 kJ/mol), 200 billion tons of (CH2O)n / year
H2O + CO2 → 1/n (CH2O)n + 3O2

• Light induced charge separation, reduction of CO2, oxidation of H2O

• Light harvesting by antenna pigments light harvesting

• Light reactions
• One PS for bacteria (~ PS II), two PS (PS I (P700) and PS II (P680)) for green plants and algae
• Oxidation of water, oxidation of H2S, H2…, at least synthesis of ATP, production of H+ gradient

• Dark reaction: 2(NADPH + H+) + CO2 → 1/n (CH2O)n + 2 NADP+ + H2O

NADP+ NADPH

Consuming ATP
Compounds
Chromophors for light harvesting: chlorophylls, carotinoids (300!)
• Chlorophyll: absorption at short and long wavelength end of vis. spectrum
• π(HOMO), π*(LUMO)-transition, Q-band (blue) and Soret-band (red)
• Broad spectral absorption range with high absorptivity
• Exciton transport: highly efficient and orientated transfer of energy
• Spectral overlap of optical bands of exciton source and exciton acceptor

• Anchoring of molecules by phytyl side-chains and by peptide/Mg coordination

(three point fixation, spatial organization)
• Mg as light element favorable for high efficiency (small spin-orbit coupling)

Phytyl side chain

(Anchoring in the hydrophobic membrane)

Bacteriochlorophyll a, Porphyrine core (Absorption of light)

partially hydrogenated
Chlorine
Compounds

Compounds for electron and proton transfer:

• Special pairs of chlorophyll (electron donor), single chlorophyll (BC,first acceptor) Purple
• Bacteriopheophytin (BP, secondary acceptor in PS II, BC without metal) bacteria
• Quinones (third acceptor), Fe(His)4Glu center (?) located on C2 one PS
• Fe,S-cluster compounds, Fe-Heme-proteins
• Plastocyanine (Cu)
• OEC (Mn, Ca)
R = CH3 : Chl. a
= CHO: Chl. b
Dimerization
via H-bond O
H H
R Saturated for Bact. Chl.
H2C=CH O
CH2CH3
H3C
N N
Mg
N N
H3C CH3 Dimerization via H-bond
H2C
H2C O
N C=O Mg
O=C
H O
OCH3
O NH
H29C20 (His) H
Electron transfer in light reactions

e-
PS II PS I
Light: P680 → P680+ + e- Light: P700 → P700+ + e-,
2P680+ + H20 → 2P680 + ½O2 + 2H+ (cat. OEC) P700+ + e- → P700
NADP+ + 2e- + 2H+ → NADPH + H+

Plastochinon/Hydroquinon
P680 O (Cys)S
OH N(His)
Me S
light Me
e-, H+ -H+ Fe Fe
[P680 ]+ (Cys)S S N(His)
{FeN4O} Me R Me R
O OH (Fe3+ Fe 2.5+ )
[S(Met)] Rieske-Protein

S(Met) N N
Fe
N N
e- (His)N Cu
(His)N S(Cys) N
[P700]+ (Fe3+ Fe 2+)
(Cu2+ Cu1+)

Plastocyanin Cytochrome b, c
PS II: Production of H+ and electrons
Special pair: dimer of porphyrines which acts as electron donor
(determined for reaction center of a bacteriochlorophyll)

SP: Special pair

HE: Heme systems
BC: Bacteriochlorophyll
energy BP: Bacteriopheophytin (no metal)
Periplasm Q: Quinones
Membrane

1. Excited state of BC
2. Transfer of el. from SP to BC
3. Transfer of el. from BC to BP
4. Transfer of el. to Q
Membrane

5. Release of H+ and el. in cytoplasma

(ADP → ATP and NADP+ → NADPH)
6. Reconstruction of SP via He (donor)
Cytoplasm
PS II: Production of byproduct O2
• Direct production of oxygen via SP not possible
• Coupling with OEC (Oxygen Evolving Complex)
• Essential component: oxygen-bridged Mn-clusters (C-cluster, dimer of dimers)
• Combination of oxidation and deprotonation
• Important property of Mn: high flexibility of oxidation states, no complexation of 3O2
III
III Tyr radical
III as electron acceptor
IV (Asp)O
Peroxy-ligand? OH2
III H2O Mn
IV III O(Glu)
IV IV H2O
H2O O O
IV IV Mn (Asp)
V? H2O Ca O
O
(Glu)O Mn
III O O
IV
IV N(His)
Mn
IV
IV O(Glu)
IV
IV N(His)
IV
Model of OEC
 7.
Fe in bio systems
Uptake, transport and storage of O2
Compounds

• 4g Fe in humans (most common transition metal)

• Heme-proteins with Fe porphyrin complex, stoichiometric function, e.g.:
• Hemoglobin (Hb) for oxygen transport, tetrameric
• Myoglobin (Mb) for oxygen storage, monomeric

Oxy-Hb Oxy-Mb

• Binding of 3O2 via end-on coord. (less reactive as the two forms of 1O2)
Function of protein

Function of the protein ligands:

• Inhibition of irreversible oxidation (Fe(III)-μ-peroxo dimer)
• Proximal His (conformational changes of quart. structure)
• Distal His (binding of O2 via H-bonds)
• Cooperativity: Increase of affinity to oxygen during uptake by Hb (sigmoid)
T (tense, low O2 affinity) and R (relaxed, high O2 affinity)
• Binding of CO2

distal His
proximal His
σ-donor directs π-acceptor
in trans position
Configuration of Fe
• Desoxy-Mb and -Hb: High-spin Fe(II) with S = 2, out-of-plane position
• Two different theories for oxy-Mb and -Hb:

1) Pauling:
low-spin Fe(II) + 1O2 (both diamagnetic, bonding via σ, π-interactions)

2) Weiss:
low-spin Fe(III) + Superoxide radical anion (O2-). Both paramagnetic
→ Strong paramagnetic coupling for explanation of diamagnetism
→ Spectroscopical data (νO-O consistent with superoxide)
→ Charact. exchange reaction of O2- (e.g. by Cl-)

• Model systems: Protection of Fe(II),

e.g. picket fence molecules
 Cooperative binding

Domed and planar coordination of porphyrin

Fe(II) high spin too large for in-plane position

Sigmoid characteristics of Hb (T- and R-form)

conformational change
saturation Mb
Bohr effect
Hb, pH = 7.6 • Increasing O storage in Hb with increasing pH
2
• Increasing affinity of Hb to O2 with increasing pH
• Oxy-Hb is a stronger acid than Desoxy-Hb:
Hb, pH = 6.8
Hb•H+ + O2 + HCO3- → HbO2 + H2CO3
muscle lung
pressure
Conversion of O2 to water

Brutto reaction: O2 + 2(NADH + H+) → 2 H2O + 2 NAD+ (mitochondria)

NADH Ferredoxine 2H
+
Ubiquinon Rieske-Protein
Fe2.5+ Fe2.25+ 4
O
Fe3+ Fe2.5+ 2
OH
MeO Me
NAD S S N
MeO R
O OH Fe Fe
S
Stepwise electron transfer R= H
S N

• one el. transfer to Ferredoxin O2, 4H+ Me 6-10

• two el. transfer to Ubiquinon H2O Cytochrome-c-Oxidase Cytochrome-b/c

• one el. transfer to rieske protein Cu2+ 2Fe3+/Fe3+Cu2+ Fe3+ Fe2+
L
• one el. transfer to Cytochrome b/c Cu1.5+ 2Fe2+/Fe2+Cu+
N N
• four el. transfer to Cyt.-c-oxidaze N
Fe
N
N
 Alternatives: Hemerythrin and Hemocyanine

Hemerythrin

Deoxyhemerythrin, h.s. Fe(II), CN = 5, 6 Oxyhemerythrin, Fe(III) with superexchange

• Non-porphinoid metal proteins for reversible O2 uptake (spiders, etc.)

• Attachement of 3O2 at Fe with CN = 5,
• Oxidation of both Fe (Fe(III)), reduction of 3O2 to peroxide (oxo-bridge via H-transport to peroxide)

Hemocyanine
NH HN NH
HN
• Proteins with two Cu-centers N N N
N NH O NH
II II
• Reversible oxidative addition: Cu
I I
Cu N + O2 HN N Cu Cu N
HN N O
O2 → O22-, Cu+ → Cu2+ N N
N N - O2
• Side-on bridging coordination NH NH
NH NH