Download Coordination compounds in nature

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.
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 A characteristic feature of the coordination
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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
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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
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There are three mineral components of soil
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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.).
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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-
enolate
> -NH2
amine
> -N=N- > =N
azo
ring N
> -COOcarboxylate
> -Oether
> C=O
carbonyl
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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.
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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+.
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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
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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
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Heme
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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
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Hemoglobin and myoglobin
The site at which oxygen binds to both
hemoglobin and myoglobin is the heme
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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.
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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.
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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
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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
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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
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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.
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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
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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.
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By activating H2O carboanhydrase
accelerates the following reaction by a factor
of 107 .
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In a simplified way the reaction may be
described as:
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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
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The hydrolysis of adenosine triphosphate
(ATP) into adenosine diphosphate (ADP) and
phosphate is catalyzed by Mg2+, especially by
Mg2+. The following structures of the ATPmagnesium-complex have been proposed:
Coordination compounds involved in
chemotherapy
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Cisplatin – an anti-cancer drug
Auranofin – an oral rheumatoid arthritis drug
Cardiolyte – a heart imaging agent
Cisplatin
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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
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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.
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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)
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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);
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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.
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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.