Coordination compounds in nature

W.D.S.S. Pemasinghe

BS/2004/233

What is a coordination compound?

It is a compound which has one or more

co-ordinate bonds In a coordination bond there is a species which

donates a lone pair of electrons (ligand) and a species which receives the lone pair of electrons

Most of the time the receiver of the lone pair of electrons is a metal ion (or a metal atom in rare cases) in which case we call it a metal ligand complex.

A characteristic feature of the coordination compounds is their ability to retain their identity in solution (which distinguishes them from double salts like carnallite-KCl.MgCl2.6H2O )

Coordination number- number of ligands bound to the central metal ion (or atom)

Coordination sphere- the group comprising the metal ion and the ligands

Polynuclear complex- complex containing more than one central metal atom

Classification of coordination compounds in nature according to various aspects of nature

Coordination compounds in plants and animals

Coordination compounds in soil Coordination compounds in reservoirs Coordination compounds in air

*Coordination compounds are extremely rare in the air*In reservoirs metal ions that are available in higher percentages are ions like Na+,K+,Ca2+

*These ions are not good at making coordination compounds due to the lack of empty orbitals with comparable energy to that of the available ligand orbitals to accept lone pairs of electrons *Although some strong coordination complexes of ions like Fe3+ and Al3+ are brought to reservoirs with rainwater, due to the large organic ligands with which they are incorporated, they become insoluble in water and get deposited in the bottom of the reservoirs.

Coordination compounds in soil There are three mineral components of soil

Sand Silt Clay

The clay particles in soil play a major role in retaining cations in the soil by making coordination and ionic bonds with them, thus preventing them from being carried away with the rain-water

The alkaline cations(Na+, K+, Ca2+, Mg2+) are held primarily by simple cation exchange with COOH groups (RCOONa, RCOOK etc.).

The surfaces of these clay particles are usually negatively charged, largely due to the presence of COO- groups (which are ligand groups)

There are some other ligand groups also attached to these clay particles which have been altogether arranged according to the decreasing affinity for metal ions

-O- > -NH2 > -N=N- > =N > -COO- > -O- > C=O

enolate amine azo ring N carboxylate ether carbonyl

These ligands act as chelating agents to retain transition metal cations which have been arranged below according to the decreasing ability for chelating

Fe3+>Cu2+>Ni2+>Co2+>Zn2+>Fe2+>Mn2+

The chemical reactions in cation exchange and chelation make it possible for calcium and the other elements to be changed into water-soluble forms that plants can use for food. Therefore, a soil's cation exchange and chelation capacity is an important measure of its fertility.

Since organic anions are normally repelled from negatively charged clay surfaces, adsorption of humic and fulvic acids by clay minerals such as montmorillonite occurs only when polyvalent cations are present on the exchange complex.

Unlike Na+ and K+, polyvalent cations are able to maintain neutrality at the surface by neutralizing both the charge on the clay and the acidic functional group of the organic matter (e.g. COO-)

The main polyvalent cations responsible for the binding of humic and fulvic acids to soil clays are Ca2+, Fe3+ and Al3+.

The divalent Ca2+ ion doesn't form strong coordination complexes with organic molecules.

In contrast Fe3+ and Al3+ form strong coordination complexes with organic compounds.

The polyvalent cations act as a bridge between two charged sites.

For a long chain organic molecule, several points of attachment to the clay particle are possible.

Coordination compounds(complexes) in plants and animals

The porphyrin ring-related compounds(complexes) Compounds involved in catalysis Compounds involved in chemotherapy

Porphyrin*Porphyrin is a tetradentate ligand*It is a nitrogen donor*Action of Porphyrin

Porphyrin related complexes Heme

Hemoglobin and myoglobin Cytochromes and iron-containing enzymes

Chlorophyll Corrin

Heme Heme-unit is part of Hemoglobin, Myoglobin, Cytochromes and several enzymes. They differ by the proteins surrounding the heme

Hemoglobin and myoglobin

The site at which oxygen binds to both hemoglobin and myoglobin is the heme

In hemoglobin and myoglobin the fifth coordination site of the iron is occupied by the nitrogen of a histidine, which is part of a protein.

The sixth coordination site can reversibly bind oxygen. Hemoglobin is constituted of four heme units. Hemoglobin transports oxygen from the lungs to the cells of the body and there it transfers the oxygen to myoglobin which contains only one heme unit. The myoglobin makes the oxygen available to the respiratory reactions of the cell.

Carbonmonoxide and cyanide make very stable iron complexes. They block the sixth coordination site of heme and therefore are extremely toxic.

Cytochromes and iron-containing enzymes

Cytochromes are generally membrane-bound hemoproteins that contain heme groups and carry out electron transport

In cytochromes and many other irons containing enzymes of redox catalytic activity proteins are bound to the two free coordination sites of heme.

In these complexes the Fe(III)/Fe(II) redox couple is protected of chemical reactions. Its redox-potential depends on the coordination proteins

Chrophyll

Porphyrin is also part of the chlorophyll, the key substance for the photosynthesis of green plants, some algae and some bacteria.

Chlorophyll absorbs mainly violet-blue and orange-red light and reflect green colour which give plants their green colour

Several kinds of chlorophyll exist (chl a,chl b etc.). They differ from each other in details of their molecular structure and absorb slightly different wavelengths of light.

Corrin The ligand corrin is very similar to porphyrin. The

coenzyme B12 contains a cobalt-corrin-complex. B12 is the most chemically complex of all the

vitamins. The structure of B12 is based on a corrin ring, which is similar to the porphyrin ring found in heme, chlorophyll, and cytochrome.

The central metal ion is Co (cobalt). Four of the six coordination sites are provided by the corrin ring, and a fifth by a dimethylbenzimidazole group.

The sixth coordination site, the center of reactivity, is variable, being a cyano group (-CN), a hydroxyl group (-OH), a methyl group (-CH3) or a 5'-deoxyadenosyl group (here the C5' atom of the deoxyribose forms the covalent bond with Co), respectively, to yield the four B12 forms mentioned above.

The covalent C-Co bond is one of first examples of carbon-metal bonds in biology.

Vitamin B12 is important for the normal functioning of the brain and nervous system and for the formation of blood. It is involved in the metabolism of every cell of the body, especially affecting the DNA synthesis and regulation but also fatty acid synthesis and energy production. Its effects are still incompletely known.

Catalysis

*Enzymes containing zinc Zinc plays an important role in many

enzymes. The only stable oxidation state of zinc in water is Zn2+ . Therefore zinc is not participating in redox-reactions, but thanks to its Lewis-acidity it can activate substrates by polarization.

By activating H2O carboanhydrase accelerates the following reaction by a factor of 107 .

In a simplified way the reaction may be described as:

The above reaction is vital for the elimination of CO2 produced by the metabolism.

The toxicity of cadmium and mercury are interpreted as being caused by the replacement of enzymatic zinc by these metals. Their complexes being more stable than those of zinc they block the enzyme and slow down the exchange of substrates.

Catalytic action of magnesium The hydrolysis of adenosine triphosphate

(ATP) into adenosine diphosphate (ADP) and phosphate is catalyzed by Mg2+, especially by Mg2+. The following structures of the ATP-magnesium-complex have been proposed:

Coordination compounds involved in chemotherapy

Cisplatin – an anti-cancer drug Auranofin – an oral rheumatoid arthritis drug Cardiolyte – a heart imaging agent

Cisplatin Once cisplatin is in the bloodstream, it remains intact due the

relatively high concentration of chloride ions (~100 mM). The neutral compound then enters the cell by either passive diffusion or active uptake by the cell. Inside the cell, the neutral cisplatin molecule undergoes hydrolysis, in which a chlorine ligand is replaced by a molecule of water, generating a positively charged species, as shown below and in Figure 1. Hydrolysis occurs inside the cell due to a much lower concentration of chloride ion (~3-20 mM)—and therefore a higher concentration of water.

inside the cell: PtII(NH3)2Cl2 + H2O -> [PtII(NH3)2Cl(H2O)]+ + Cl-

[PtII(NH3)2Cl(H2O)]+ + H2O -> [PtII(NH3)2(H2O)2]2+

Interaction of cisplatin with DNA Cisplatin coordinates to DNA mainly through

certain nitrogen atoms of the DNA base pairs; these nitrogen atoms (specifically, the N7 atoms of purines) are free to coordinate to cisplatin because they do not form hydrogen bonds with any other DNA bases.

Many types of cisplatin–DNA coordination complexes, or adducts, can be formed. The most important of these appear to be the ones in which the two chlorine ligands of cisplatin are replaced by purine nitrogen atoms on adjacent bases on the same strand of DNA; these complexes are referred to 1,2-intrastrand adducts. The purine bases most commonly involved in these adducts are guanines; however, adducts involving one guanine and one adenine are also found. The formation of these adducts causes the purines to become destacked and the DNA helix to become kinked (thus causing DNA damage)

The cell detects DNA damage by the action of damage recognition proteins

Researchers have been able to isolate several proteins that bind to cisplatin–DNA adducts. These proteins all contain a common portion (that is, similar or even identical sequences of amino acids, which are the building blocks of proteins) called a high mobility group (HMG);

Two theories explain the possible role of HMG-domain proteins in cisplatin’s cytotoxic activity.

Theory1:-Many HMG-domain proteins are transcription factors, meaning that they are required for the synthesis of RNA from a DNA template. If HMG-domain-containing transcription factors bind preferentially to the cisplatin–DNA adducts, they could wreak havoc with the transcriptional machinery, possibly leading to cell death.

Theory2:-When HMG-domain proteins bind to the cisplatin–DNA adducts, the adducts would not be recognized by the repair machinery. DNA repair would then be slower than normal thus causing cell death.