Chemistry of biogenic elements.
Complexing.
Chemistry of biogenic elements
The basis of all the living systems is
constituted
by
six
organogenic
elements: carbon, hydrogen, oxygen,
nitrogen, phosphorus, sulfur.
macroelements (>10-2 %),
microelements (<10-2 %)
Irreplaceable elements: H, Ca, O, K,
Na, Mg, N, P, S, Cl, C, I, Mn, Cu, Co, Fe,
Zn, Mo, V
Deficiency of the maintenance of
these elements leads to infringement
of ability to live of an organism.
Doped elements: Sr, Be, Li, Ba, Rb, Ra,
Cs, Ga, Sb, Br, F, B, Si, Sn, As, Ge, Pb,
Bi, Se, Cd, Cr, Ni, Ti, Ag, Th, Hg,
Biological role is not always found
out or is a little studied yet
1
Periodic Table
2
Periodic Table
3
Covalent bond.
Covalent bond is a chemical bond between two atoms arising at
expense of shared electron pair.
Total number of electron pairs taking part in formation of covalent bond is
called multiplicity of bond.
+
Н
Н
Н
+
Н
Н
.*
.N* : Н
.*
Н
.*
     :
.*
.N* : +
Н
donor-acceptor mechanism
π-bond
σ-bond
δ-bond
4
Covalent bond.
Oxidation number is a hypothetical charge which would arise on atom
of an element, if pairs of electrons connecting it with other atoms in a
molecule, completely pass to atoms of more electronegative elements.
Term “oxidation state” is often used synonymously to term “oxidation
number”.
+1 +7
-2
+1
+1 +5 -2
KMnO4
-1
H2O2
HNO3
oxidation number of individual numbers in simple substances is equal to zero;
oxidation number of an atom in simple ion is equal to charge of the ion;
oxidation number of fluorine atom in its compounds is equal -1;
in majority of oxygen compounds, its oxidation number is equal −2, with exception of
2
1
1
 F2
  
hydrogen in majority of its compounds has oxidation number +1, with exception of
compounds with alkali and alkali-earth metals (hydrides), where oxidation number of
hydrogen is −1;
alkali metals in all compounds have oxidation number +1; alkali-earth metals and Be,
Mg, Zn, Cd have it +2, and aluminium have it +3.
5
S-elements. Biological role, application
Small values of ionisation energy
Big radiuses of atoms and ions
Ionic bonds (except for hydrogen)
low values of electronegativity
in solutions in a kind of E+(H2O)x
Hydrogen - H
The distilled water is applied as
solvent of drugs. Mineral waters,
which contains mineral, radioactive
substances enriched by gas often
apply with medical purpose
The hydrogen bond is caused by donor-acceptor interaction where the atom of
an electronegative molecule is the donor, and hydrogen atom of another
molecule is the acceptor.
Structure of organic substances often depends in a large extent on presence of
hydrogen bond.
6
S-elements. Biological role, application
Sodium and potassium – Na, K
sodium-potassium ionic pump transfer of ions through a
membrane against a gradient of
concentration at
expense of
energy: three Na+ are taken out
from the cell, and two K+ get deep
into the cell. It causes the potential
difference on the plasmatic
membrane
Hypokaliemia - deficiency of potassium salts (K+ activate endocellular enzymes)
Sodium ions (Na+) regulate the water exchange and influence work of enzymes.
Other ions of S-elements – Li+, Rb+, Cs+, Fr+, Be2+, Mg2+, Ca2+, Sr2+
Magnesium ions (Mg2+) activate many enzymes (phosphatase, kinase, etc.)
Hydroxilapatite Са10(РО4)6(OH) 2 - basic substance of bone and tooth tissues
7
S-elements. Biological role, application
8
S-elements. Biological role, application
9
P-elements. Biological role, application
Relatively small values
of ionization energy
Medium values of
ionization energy
Big values of ionization energy
Small radiuses of atoms and ions
Carbon, Oxygen, Nitrogen - C, N, O
Ionic bonds, both cations, and anions
(Al, Ga, Tl, Ge, Sn, Pb, Sb, Bi)
Covalent bonds
(B, C, Si, N, P, As, O, S, Se, Te)
Ionic bonds, anions
(F, Cl, Br, I, At )
Bromide salt are a class of
tranquilizers that were withdrawn
from market due to their toxicity.
10
P-elements. Biological role, application
11
P-elements. Biological role, application
12
P-elements. Biological role, application
13
d-elements
•
d-elements differ from s-elements by smaller regenerative ability and
bigger chemical inertness;
• d-elements have two or more degrees of oxidation that causes a big
variety of oxidation-reduction reactions is characteristic;
• typical feature of d-metals is ability to form various complex compounds
Free ions of d-metals do not exist in an organism only as part bioinorganic
metal complexes
Cu2+
Vital elements Zn, Cu, Fe, Mn, Co, Mo are called life metals. 14
d-elements
15
Complexation
Coordination compounds have crystal lattice consisting of complex
groups formed owing to interaction of ions or molecules.
Werner’s Theory: Structure
of coordination compounds
Denticity (coordination capacity) is defined by the number of sites occupied
by ligands in the internal sphere of coordination compound.
16
Complexation
Monodentate ligands (literally “one tooth”) - F−, Cl−, Br−, I−, CN−, NH3, H2O,
Polydentate (“many tooth”) ligands - CO32−, SO42−, H2N–CH2–CH2–NH2, that
can form more than one bond with complexing agent
Bioorganic
molecules
(proteins, enzymes and
nucleonic acids) are
polydentate ligands.
Common for d10 metal
ions: Cu+, Ag+, Au+, and
Hg2+. ([Au(CN)2]− )
Uncommon
coordination number
(e.g. [HgI3]−
17
Geometrical structure of complexes
Tetrahedral structure for d10 ions (e.g., [ZnCl4]2−),
first-row transition metals (e.g.[FeCl4]− , [FeCl4]2−).
Square structures is observed for d8 ions, such as
[PdCl4]2− and in some complexes of Ni2+ and Cu2+.
This coordination number is less common than 4, 6
This coordination number is the most common.
The six ligands are almost always at the vertices of
an octahedron or a distorted octahedron. The
trigonal prism is very uncommon in simple metal
complexes.
18
Geometrical structure of complexes
This relatively uncommon coordination number is
generally encountered for only large metals
The square antiprism and the dodecahedron are
common for larger metal ions.
This coordination number is also found in larger
metal ions, as in [Nd(H2O)9]3+.
19
Clasification
Depending on electric charge of inner sphere
•Coordination compounds containing complex cations ( e.g. [Zn(NH3)4]Cl2
•Coordination compounds containing complex anions (e.g.K3[AI(OH)6].
•Natural complexes. ( e.g.[Pt(NH3)2Cl2]).
Depending on nature of ligands
•Acidocomplexes containing residues of acids as ligands. (e.g. [Fe(CN)6]4−.
•Aquacomplexes containing H2O as ligands. (e.g. [Cr(H2O)6]3+).
•Hydrocomplexes containing hydroxide ions as ligands. (e.g. [Zn(OH)4]2-.
•Amminecomplexes containing ammonia molecules. (e.g. [Cu(NH3)4]2+.)
20
Nature of chemical bonds
Mechanism of covalent bond formation between complexing agent and ligands
is donor-acceptor. Zn2+, Ag+, Au+, Cu+, Hg2+, Co3+, Fe2+, Fe3+ with vacant
orbitals are acceptors of electrons. Molecules (H2O, NH3, ethylenediamine) or
ions (F–, Cl–, Br–, I–, CN–, CO32–, C2O42– etc.) can be donors of electrons.
An example of formation of donor-acceptor bond in [Zn(NH3)4]2+:
ZnSO4 + NH3∙H2O → Zn(OH)2↓ + (NH4)2SO4;
Zn(OH)2↓ + 4NH3 → [Zn(NH3)4](OH)2 + 4H2O.
Zn: 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p0.
Zn2+: 1s2 2s2 2p6 3s2 3p6 3d10 4s0 4p0
4p
4s
..
NH3
..
.. ..
NH3 NH3NH3
21
Characteristic of some metalloenzymes
Metallo-enzyme Central
Ligands
Content
Carbo-anhydrase Zn2+
Amino
acid Erythro-cytes
residues
Carboxypeptidase
Zn2+
Amino
acid Pancreas,
residues
intestines
Enzyme action
Catalyzes reversible hydration of
carbondioxide: CO2 + H2O ↔ H2CO3
↔ H+ + HCO3−
Catalyzes splitting of proteins by
hydrolysis of peptide groups.
O
Н2N CH C N CH COOH
Н R2
R1
R1
CH
COOH + R2
NH2
Catalase
Fe3+
Peroxidase
Fe3+
Cytochrome
oxydase
Pyruvate
carboxylase
Cu2+,
Fe3+
Mn2+
Ribonucleoti-de
reductase
Co2+
Amino
acid Blood
residues
Proteins
Tissues, blood
CH
COOH
NH2
Catalyzes
hydrogen
peroxide
decomposition:H2O2 = H2O + O
Catalyzes oxidation of substrates
(RH2) by hydrogen peroxide:
RH2 + H2O2 = R + 2H2O
Amino acids Heart,
liver, Catalyzes reduction of oxygen in
residues
kidneys
respiratory chain of mitochondria.
Tissues’
Liver,
thyroid Catalyzes process of pyruvic acid
proteins
gland
carboxylation.
Tissues’
proteins
Liver
Takes part in
ribonucleic acids.
biosynthesis
of
22
Chelation effect
The heightened stability of complexes with polydentate ligands over
complexes with monodentate ligands is known as chelation effect.
Therefore
polydentate ligands
(complexones)
are
widely
used
for
maintenance of metal-ligand homeostasis and removing of toxic metals ions
and radioactive isotopes from the organism. In medical practice salts of
ethylenediaminetetraacetic acids (EDTA) are widely used as antidotes.
23
TEST
Point out oxidation number of the underlined elements:
a) Na2SO3;
b) K2Cr2O7
c) KFeO2
24