Bioinorganic Chemistry

Introduction:

• Bio-inorganic chemistry is a field that examines the role of metals in biology.

• It is the gateway of inorganic chemistry and biochemistry, i.e., it describes the mutual relationship between these two sub-disciplines, with focus upon the function of inorganic substances in living systems, including the transport, speciation and eventually, mineralisation of inorganic materials, and including the use of inorganics in medicinal therapy and diagnosis. These substances can be metal ions, composite ions, coordination compounds or inorganic molecule.

• There are a number of importantsmall ligands, apart from water and free amino acids, which include sulfide, sulfate, carbonate,cyanide, carbon monoxide, and nitrogen monoxide, as well as organic acids suchas citrate that form reasonably strong polydentate complexes with Fe(III).

• Metalloproteins: The proteins containing one or more metal ions, perform a wide range of specificfunctions.

• These functions include oxidation and reduction (for which most important elements are Fe, Mn, Cu, and Mo), radical-based rearrangement reactions andmethyl-group transfer (Co), hydrolysis (Zn, Fe, Mg, Mn, and Ni), and DNA processing(Zn).

The following list shows typical bioactive substances containing metals :

(1) Electron Carriers. Fe : cytochrome, iron-sulfur protein. Cu : blue copper protein.

(2) Metal storage compound. Fe : ferritin, transferrin. Zn : metallothionein.

(3) Oxygen transportation agent. Fe: hemoglobin, myoglobin. Cu: hemocyanin.

(4) Photosynthesis. Mg: chlorophyll.

(5)Hydrolase. Zn: carboxypeptidase. Mg: aminopeptidase.

(6) Oxidoreductase. Fe: oxygenase, hydrogenase. Fe, Mo: nitrogenase.

(7) Isomerase. Fe: aconitase. Co: vitamin B12 coenzyme.

Examples of actions of metals other than by metalloenzymes include transfer,

(1) Mg: MgATP energy Na/K ion pumping

(2) Na/K ion pumping.

(3) Ca : transfer of hormone functions, muscle contraction, nerve transfer, blood coagulation, are some of the important roles of metals

Biological functions of selected metal ions:

1. Porphyrin and Related Complex:

• The metalloporphyrins are the complexes in which a metal ion is coordinated to four nitrogen atoms inside the cavity of the porphyrin ring in a square planar geometry.

• Porphyrins are the substituted porphins which are heterocyclic macrocyclics containing 4 modified pyrrole rings inter connected at their alpha carbons via methine(=CH-)bridges.

• The simplest porphin found in Hemoglobin is called porphyrin (fig.1).

• A porpbine ring with one double bond reduced is called a chlorin. The chlorophylls are examples of compounds containing this ring(fig.2).

• Corrin ring which has one less =CH- bridge between the pyrrole rings than the porphyrins. The vitamin B12 are example of compounds containing corrin ring.(fig.3)

2. Hemoglobin (Hb) and Myoglobin (Mb) in Oxygen Transport Mechanism:

• Fe-porphyrin referred to as heme is the prosthetic group of hemoglobin (Hb) and Myoglobin (Mb).

• Each Hemoglobin (Hb) molecule has four heme groups bound to the globin on its surface.

• On each heme unit of Hemoglobin (Hb) the four square-planer coordination sites of the Fe(II) are occupied by porphyrin nitrogen atom.

• Whereas the fifth coordination site of iron occupied by the nitrogen of histidine ( distal histidine) ligand of the protein chain i.e. globin chain, and the sixth position of iron remains vacant or occupied by H2O in their deoxy forms and this site is occupied by O2 in their oxy forms.

• The water ligand in haemoglobin can be readily replaced by molecular oxygen to form the red-coloured oxyhaemoglobin this is present in the arterial blood.

• The water-coordinated complex is called deoxyhaemoglobin; it is blue, the colour characteristic of the venous blood.

• As each sub-unit can bind one O2, each haemoglobin molecule can bind up to four O2 molecules.

• In oxyhaemoglobin, the Fe(II) is in the low-spin state and is diamagnetic; but in deoxyhaemoglobin, the Fe(II) is in the high-spin state and is paramagnetic.

• The size of Fe(II) is increased by about 30 per cent, when it changes from the diamagnetic to paramagnetic state.This increase in size distorts the bonds around Fe and also the shape of the complex.

• In oxyhaemoglobin, the Fe(II) is of the right size to get into the hole at the centre of the porphyrin ring; but in deoxyhaemoglobin, because of its enlargement, it is above the plane of the ring.

• The arteries carry blood to the muscles in various parts of the body, where oxygen is required.

• In the muscles, the oxygen is transferred to a myoglobin molecule and stored, until it is required to produce energy from glucose.

• When haemoglobin loses its O2, a water molecule is again coordinated to iron. Then, the protein part of it absorbs H+.

• This indirectly helps remove CO2 from the tissues; CO2 is converted to HCO3 and H+. HCO-3 readily dissolves in blood and H+ is absorbed by the protein unit of haemoglobin.

• The impure blood returns to the heart through the veins. Then, it is pumped to the lungs where HCO3 is converted to CO2(g) and exhaled. The blood once again, picks up O2 in the. lungs and the cycle is repeated.

• The oxygen-carrying process by haemoglobin is reversible; the oxyhaemoglobin complex is not too stable to render the release of O2 at the muscles difficult.

• The transfer of O2 by haemoglobin involves only Fe(II) and not Fe(III).

• The oxidation of Fe(II) to Fe(III),which would be irreversible and O2 transport, is prevented by the protein unit.

• Hemoglobin and myoglobin are transport and storage of dioxygen respectively.

2.1) The Effect of Carbon Dioxide in the Blood

Haemoglobin can also bind carbon dioxide, but to a lesser extent. Carbaminohaemoglobin forms.

Some carbon dioxide is carried in this form to the lungs from respiring tissues.

The presence of carbon dioxide helps the release of oxygen from haemoglobin, this is known as the Bohr effect.

This can be seen by comparing the oxygen dissociation curves when there is less carbon dioxide present and when there is more carbon dioxide in the blood.

When carbon dioxide diffuses into the blood plasma and then into the red blood cells (erythrocytes) in the presence of the catalyst carbonic anhydrase most CO2 reacts with water in the erythrocytes and the following dynamic equilibrium is established :

Carbonic acid, H2CO3, dissociates to form hydrogen ions and hydrogencarbonate ions.

This is also a reversible reaction and undissociated carbonic acid, hydrogen ions and hydrogencarbonate ions exist in dynamic equilibrium with one another

Inside the erythrocytes negatively charged HCO3- ions diffuse from the cytoplasm to the plasma.

This is balanced by diffusion of chloride ions, Cl-, in the opposite direction, maintaining the balance of negative and positive ions either side. This is called the 'chloride shift'.

The dissociation of carbonic acid increases the acidity of the blood (decreases its pH).

Hydrogen ions, H+, then react with oxyhaemoglobin to release bound oxygen and reduce the acidity of the blood.

This buffering action allows large quantities of carbonic acid to be carried in the blood without major changes in blood pH.

It is this reversible reaction that accounts for the Bohr effect.

Carbon dioxide is a waste product of respiration and its concentration is high in the respiring cell and so it is here that haemoglobin releases oxygen.

Now the haemoglobin is strongly attracted to carbon dioxide molecules.

Carbon dioxide is removed to reduce its concentration in the cell and is transported to the lungs were its concentration is lower.

This process is continuous since the oxygen concentration is always higher than the carbon dioxide concentration in the lungs.

The opposite is true in respiring cells.

2.2) Hemerythrin:

• An Non-hem iron protein.

• Fe(II) oxidation state.

• It consists of eight indentical units each containing two iron atom.

• Deoxyhemerythrin is paramagnetic and high spin.

• Environment of iron atom is pseudo octahedral.

• Each dioxygen binding site contains Fe(II) atom and the reaction takes place via redox reaction to form Fe(II) peroxide O22-.

• The antiferromagnetic coupling of two Fe gives rise to diamagnetism of oxy hemerythrins at low temperature.

2.3) Hemocynin: (An oxygen uptake protein)

• Haemocyanins are O2-carrying copper-containing proteins and haemocyanins are not haem proteins.

• The deoxy-form of a haemocyanin is colourless and contains Cu(I), while O2 binding results in the blue Cu(II) form.

• In this metalloprotein are two adjacent Cu(I) centres (Cu -----Cu =354pm, i.e. non bonded), each of which is bound by three histidine residues (Figure ).

• The active site of the structurally characterized oxyhaemocyanin is the Cu2(His)6-unit (Cu ----- Cu = 360pm) resembles that in the deoxy-form.

• The O2 unit is bound in a bridging mode with an O--O bond length of 140pm, typical of that found in peroxide complexes.

• The O2-binding site is formulated as Cu(II)-[O2]2-Cu(II), i.e. electron transfer accompanies O2 binding.

• Resonance Raman spectroscopic data are consistent with this formulation:

• v(O-O)≈750cm-1 compared with ≈800cm-1 for [O2]2-.

• Oxyhaemocyanin, complex is diamagnetic as a result of antiferromagnetically coupled Cu(II) centres.

NOTE :

Deoxyhemocynin is diamagnetic, colourless , in which Cu(I) oxidation state.

Oxyhemocynin is blue in colour and Cu (II) oxidation state.

3. ELECTRON TRANSFER

A. Cytochromes:

Hemeproteins that transfer electrons belong to the family of the cytochromes, which refers to a group of intracellular hemeproteins that undergo oxidation-reduction and, upon reduction, exhibit intense absorption bands between 510 and 615 nm.

As currently used, the name appears to include all intracellular hemeproteins with the exception of hemoglobin, myoglobin, the peroxidases, catalase, tryptophan 2,3-dioxygenase, heme-thiolate proteins (P-450) and the nitrite and sulfite reductases.

Consequently, proteins of markedly different function are found in this family.

These include cytochrome-c oxidase, L-lactate dehydrogenase (cytochrome) (yeast cytochrome b2) and cytochrome P-450.

It has been customary to assign the cytochromes to the groups a, b, and c according to the nature and mode of binding of the heme prosthetic group.

Cytochrome Groups:

Four major groups of cytochromes are currently recognized and are slightly differ in their structures.

Cytochromes a.

Cytochromes in which the heme prosthetic group is heme a, i.e. the iron chelate of cytoporphyrin IX

Cytochromes b.

Cytochromes with protoheme the iron chelate of protoporphyrin IX, as prosthetic group but which lack a covalent bond between the porphyrin and the protein.

Cytochromes c.

Cytochromes with covalent thioether linkages between either or both of the vinyl side chains of protoheme side chains and the protein.

Cytochromes d.

Cytochromes with a tetrapyrrolic chelate of iron as prosthetic group in which the degree of conjugation of double bonds is less than in porphyrin, e.g. dihydroporphyrin [chlorin; heme d], tetrahydroporphyrin [isobacteriochlorins; heme d1, siroheme ]. Heme d has also been known as heme a2.

The cytochromes act as electron carriers. The iron in them is in the low-spin state and undergoes rapid, reversible redox reactions

Fe3+ + e- = Fe2+

These reactions are coupled to the oxidation of carbohydrates.

The iron atom of each cytochrome alternately accepts and releases an electron, passing it along to the next cytochrome at a slightly lower energy level; ultimately, at the end of the chain, the electrons, their solution to form water. The energy released in each step of the passage of electron is harnessed to form ATP molecules from ADP.

This formation of ATP is called oxidative phosphorylation.

B. Rubredoxins

• These are non-heme iron-sulphur proteins.

• They participate in several biological redox reactions, especially in anaerobic bacteria.

• The simplest bacterial rubredoxin contains (Cys-S)4 Fe unit as a part of its structure .

• It consists of a single peptide chain of 53 amino acid residues.

• The single iron species in this molecule is in the +3 state; it is coordinated by four sulphur atoms of cystein residues.

• This coordination is close to tetrahedral

• The sulphur atoms in it are non-labile; they are not lost on treatment with an acid.

C. Ferredoxins

• Ferredoxins are a group of non-heme iron proteins; these effect electron transfer in plants and bacteria.

• These are iron complexes and serve the same biological function that cytochromes do in animals.

• These have much lower molecular weights (6,000 - 12,000).

• A ferredoxin molecule may contain one, two, four or eight iron atoms.

• The simplest of these is bacterial rubredoxin, (Cys-S)4Fe.

• The ferredoxin, which helps photosynthesis in higher plants has a bridge structure (with Fe2S2 units) .

• Another type of ferredoxin molecule found in certain bacteria has a cubane -like cluster of four iron atoms, four labile sulphur atoms and four cysteine ligands.

D. Blue Copper Proteins

• Perhaps the three most important redox systems in bioinorganic chemistry are:

• high spin, tetrahedral Fe(II)/Fe(III) in rubredoxin, ferredoxin, etc.;

• low spin, octahedral Fe(Il)/Fe(III) in the cytochromes; and

• pseudotetrahedral Cu(I)/Cu(II) in the blue copper proteins, such as stellacyanin, plastocyanin, and azurin.

• The structure of plastocyanin is especially instructive this regard.

• Plastocyanin is found in chloroplasts of green plants and blue-green algae.

• Plastocyanin has molar mass about 10500. It contain one copper atom per molecule.

• Plastocyanin is involved in electron transfer in photosynthesis (between PS I and PS II).

• The protein chain in a plastocyanin contains 97-104 amino acid residues.

• The copper centre in plastocyanin is coordinated to two N atoms of imidazoles of histidine residues, one S of methionine and one S of thiol of cysteine residues in distorted tetrahedral arrangement (or flattened tetrahedron) (Fig.).

• The arrangement about copper centre involves three short bonds in an trigonal planar arrangement with fourth longer bond to S of methionine

• The blue copper protein azurin is found in bacteria and has molar mass about 16000.

• It also contains one Cu atom per molecule.

• The copper centre in azurin is trigonal bipyramid.

• The two N atoms of imidazole of histidine residues and one S atom of cysteine residue in trigonal planar- arrangement, one S of methionine and one O of glycine residues above and below the plane.

• There are three short bonds in the trigonal plane and two long bonds along the axis of the trigonal bipyramid Cu-S (Met) and Cu-0.

• The coordination spheres can suite for both Cu(I) and Cu(II) and therefore, facilitate fast electron transfer.

4. Catalysis

4.1) Carboxypeptidase

• The enzyme consists of a protein chain of 307 amino acid residues plus one Zn+2 ion to yield a molecular weight about 34,600.

• The molecule is roughly egg-shaped, with a maximum dimension of approximately 5000 pm and a minimum dimension of about 3800 pm.

• There is a cleft on one side that contains the zinc ion at the active site.

• The metal is coordinated approximately tetrahedrally to two nitrogen atoms and an oxygen, atom from three amino acids (His 69, Glu 72, His 169) in the protein chain.

• Carboxypeptidase is a pancreatic enzyme that catalyzes the hydrolysis of the peptide bond at the carboxyl end of proteins and peptides, with a strong preference for amino acids with an aromatic or branched aliphatic side chain.

• The zinc ion is bond in a 5- coordinate site by two histidine nitrogens, both oxygens from a glutamic acid carboxyl group, and a water molecule.

• A pocket in the protein structure accommodates the side chain of the substrate. Evidence indicates that the negative carboxyl group of the substrate hydrogen bonds to an arginine on the enzyme while the zinc bonds to the oxygen of the peptide carbonyl, as shown in (Figure).

• A Zn-OH or Zn-OH2 combination seems to be the group that reacts with the carbonyl carbon, with assistance of a glutamic acid carboxyl group from the enzyme that assists in the transfer of from H+ the bound water to the amino acid product.

• An artificial peptidase model compound has been made with a Cu(Il) bound by four nitrogens in a chain that ends in a guanidinium ion, all attached to a cross-linked polystyrenel".

• The catalytic activity is high for hydrolysis of amides with carboxyl groups attached, similar to a carboxypeptidase activity.

• The H+ on the guanidinium group can hydrogen-bond to the carboxyl group, holding the substrate in position near the Cu, which is the active site.

FIGURE : Proposed Meclianism of Carboxypeptidase Action. Transfer of several hydrogen ions is not shown.

4.2) Coenzyme B12

• A vitamin known as coenzyme B12 is the only known organometallic compound in nature.

• It incorporates cobalt into a coma ring structure, which has one less =CH- bridge between the pyrrole rings than the porphyrins (Figure ).

• This compound is known to prevent anemia and also has been found to have many catalytic properties.

• During isolation of this compound from natural sources, the adenosine group is usually replaced by cyanide, and it is in this cyanocobalamin (vitamin B12) form that it is used medicinally.

• The cobalt can be counted as Co(III) in these compounds; the four corrin nitrogens contribute electrons and a charge of 2-, the benzimidazole nitrogen contributes two electrons, and the cyanide or adenosine in the sixth position contributes two electrons and a charge of 1-.

• Without the sixth ligand, the molecule is called cobalamin.

• Methylcobalamin can methylate many compounds, including metals.

• The reactions of alkylcobalamins depend on cleavage of the alkylcobalt bond, which can result in Co(l) and an alkyl cation; Co(ll) and an alkyl radical, or Co(lll) and an alkyl anion, with the radical mechanism being the most common.

Nitrogen Fixation

Nitrogenase catalyses the reduction of nitrogen to ammonia.

N2 + 8e- + 8H+ +16MgATP ⟶ NH3 + H2 +16MgADP + Pi

All the nitrogenases consists of two subunits:

i) M-cluster (FeMo cofactor) - containing Fe, S and Mo

ii) P-cluster - containing Fe and S

According to modern view, the M-cluster is involved in the reduction of dinitrogen to ammonia. The iron centres at the middle (shown in circles) are involved in binding of dinitrogen.

(Note: These irons are just having three bonds and with open configuration)

The P-cluster contains cubane like [4Fe,4S] ferredoxins which are involved in the transfer of electrons to M-cluster.

Note: The molybdenum, may be replaced by vanadium or iron in some organisms.

5. INORGANIC COMPLEX IN MEDICINE

5.1) CISPLATIN AND RELATED COMPLEXES

• One compound that is currently being used for the treatment of certain cancers is cis- diamminedichloroplatinum(II), or cisplatin.

• This compound shares the common action of chemotherapeutic agents by preventing cell growth and proliferation.

• It also shares the common trait of affecting normal cells as well as cancerous cells, but of having a larger effect on the cancerous cells because of their rapid growth rate.

• Its effect on cell growth was discovered by B. Rosenberg, 48 when E. coli bacteria placed in an electric field stopped dividing and grew into long filaments, similar to their action when treated with antitumor agents.

• It was found that the ammonium chloride buffer and the platinum electrode were forming compounds, including cisplatin.

• Cisplatin acts on the deoxyribonucleic acid (DNA) of the cells, disturbing the usual helical structure and thus preventing duplication.

5.2) DEFICIENCY SYMPTOMS OF SOME TRACE ELEMENT

1. Zinc:

• Zinc is very important for proper functioning of the immune system.

• The body of an adult human contains about 2g of zinc. There is some zinc in every one of the cells in the body but most of it is in the skin, hair, nails and eyes and in the prostate gland for males.

• The most easily absorbed form of zinc is zinc gluconate, zinc citrate and zinc monomethionate. Zinc sulphate is likely to upset the stomach.

• Zinc is important for:

o Fighting off cold or flu: Zinc suppliments assist to reduce the cold symptoms such as runny nose, coughing and sore throat.

o Zinc makes skin, nails and hair healthy.

o Zinc helps in healing wounds.

Symptoms of Zinc Deficiency

(i) Reduced growth of children.

(ii) Reduced mental retardation.

(iii) Slow wound healing.

Zinc Works Best with

(i) Vitamin A

(ii) Vitamin B6

(iii) Insulin

(iv) Vitamin D

(v) Vitamin E

(vi) Glucose

(vii) Mg

(viii) Mn

Impacts of Excess of Zinc - Excess of zinc in the human body causes:

(i) Dysfunction fo the central nervous system

(ii) Anaemia

(iii) Diarrhoea

(iv) Dizziness

(v) Sore stomach

(vi) Vomiting

(vii) Nausea

(viii) Alcohol intolerance

(ix) Electrolyte imbalance

(x) Increase LDL cholesterol and lower HDL cholesterol

2. COPPER

• Copper is required in the formation of hemoglobin, red blood cells and bones.

• It helps in the formation of elastin and collagen making it necessary for wound healing. Copper works closely with iron for these functions.

• Copper is a vital component of a number of enzymes. Copper is essential for connective tissue formation, iron metabolism. It also acts as an antioxidant.

Copper Sources:

• Main sources of copper are: Oysters (cooked), sunflower seeds, almonds, etc.

Copper deficiency Cause:

• Deficiency of iron which can lead to anaemia, infections, osteoporoses, thining of bones, thyroid gland dysfunction, heart disease, nervous system problems and increased blood fat level. Copper works best with folic acid, vitamin B6, vitamin B12, amino acids, iron, zinc and Mn.

Excess of copper Causes:

• Fever, high blood pressure, diarrhoea, dizziness, depression, fatigue, irritability, joint and muscle pain, nausea, premature ageing, vomiting, wrinkling of skin, headache etc.

3. COBALT

• Cobalt is an essential trace mineral that is a constituent of vitamin B12.

• Cobalt is a necessary cofactor for making the thyroid hormone thyroxine.

• The most of the body's cobalt is stored in liver.

• Main sources of cobalt are liver, clams, milk, nuts, fish, red meat, oysters. Cobalt works best with vitamin B12.

Deficiency of Cobalt

A deficiency of cobalt may lead to a deficiency of vitamin B12 and lead to pernicious anaemia.

The symptoms of perniceous anaemia are:

(i) bleeding gums.

(ii) nausia, appetite loss and weight loss.

(iii) weakness and tingling in the arms and legs.

(iv) headache, confusion and poor memory.

(v) sore tongue.

Impact of Excess of Cobalt - The symptoms of excess of cobalt in the human body are:

(i) Nausea (ii) vomiting (iii) diarrhoea (iv) skin rashes

4. IRON:

• Iron is the most important transition element involved in the living systems.

• The adult human’s body contains about 4 g of iron. It plays a crucial role in the transport and storage of dioxygen and electron transport.

• The important sources of iron are : green vegetable, squash, pumpkin seeds, liver, oysters beans, pulses, nuts (cashew, peanut, almond, pine, hazel nut), beef, lamb, Pork, wheat products, corn meal, strawberries, watermelon etc.

• Deficiency of iron and oxygen causes anaemia.

The symptoms of deficiency of iron anaemia are:

difficulty maintaining body temperature, feeling tired and weak, decreased immune function which increases susceptibility to infection, fatigue, decreased memory,

Excess of iron causes stomach pain as the stomach lining becomes ulcerated, damage of internal organs particularly the brain and the liver.

• Iron poisoning can be treated by chelate therapy using chelating agent such as deferoxamine.

Main Deficiency symptoms of some trace elements are given in below Table: