Chemistry of Oxygen

Group 16 contains two of the most important elements for life.

Oxygen- is most commonly found as water and in the atmosphere, both of which are
essential for almost all life forms. Dioxygen is produced from water by photosynthesis
and recycled in respiration by higher organisms.
Sulfur - is also essential to all life forms and even selenium is required in trace amounts.
Sulfur and selenium exhibit a tendency to catenation and form rings and chains.

Chalcogens: The Group 16 elements- oxygen, sulfur, selenium, tellurium, and polonium

Oxygen is the most electronegative element in Group 16 and is the only gas; exist as
diatomic molecules under normal conditions; coordination numbers of its compounds are
generally lower

Allotropy and polymorphism are important features of Group 16 and sulfur occurs
in more natural allotropes and polymorphs than any other element

group electron configuration of ns2np4 suggests a group maximum oxidation number of

+6: Oxygen never achieves this maximum oxidation state, the common [O].st. is -2
 Chemistry of Oxygen
Oxygen: the second most electronegative element in the periodic table and significantly
more electronegative than its congeners.

Why Oxygen is different from other congeners?

1. High electronegativity
2. small atomic radius of O and absence of accessible d orbitals- O seldom has a
coordination number greater than 3 in simple molecular compounds.
3. Dioxygen (O2) oxidizes many elements and reacts with many organic and inorganic
compounds under suitable conditions- except He, Ne, Ar
4. Even though the O=O bond energy of 494 kJ mol1 is high, many exothermic combustion
reactions occur because the resulting EO covalent bond enthalpies or MOn lattice
enthalpies are also high.
5. One of the most important reactions of dioxygen is the coordination to the oxygen-
transport protein haemoglobin

Abudnace: Most abundant element in Earth’s crust at 46 percent by mass.

The average human is two-thirds oxygen by mass.
Oxygen is also the third most abundant element in the Sun, and the most abundant element
on the surface of the Moon (46 per cent by mass).
Oxygen also occurs as ozone, O3, a highly reactive pungent- it shields the surface from solar
ultraviolet radiation
 Chemistry of Oxygen

NMR active nuclei and isotopes as tracers: Despite its low abundance, 17O has been used
in studies of, for example, hydrated ions in aqueous solution and polyoxometallates

NMR active nuclei (% abundance, nuclear spin)

17O (0.04, I = 5/2 )
77Se (7.6, I = 1/2 )
123Te (0.9, I = 1/2 )
125Te (7.0, I = 1/2 )
 Chemistry of Oxygen
Simple compounds: The elements of Group 16 form simple binary compounds with
hydrogen, halogens, oxygen, and metals.

H2O: Water is the only Group 16 hydride that is not a poisonous, malodorous gas.
Its melting and boiling points (0oC and 100oC, respectively) are both very high compared to
compounds of similar molecular mass and the analogous molecules in Group 16
- extensive hydrogen bonding between H and the highly electronegative oxygen, OH...O.
Oxygen also forms hydrogen peroxide, H2O2, which is also a liquid (from 0oC to 150oC)
on account of extensive hydrogen bonding.

Oxygen forms oxides with most metals, and peroxides and superoxides with Group 1 and
2 metals.
 Chemistry of Oxygen
Oxygen has two allotropes, dioxygen and ozone

Dioxygen is a biogenic gas (that is, one that has been produced by the action of
organisms)- photosynthesis, some is produced by the action of ultraviolet radiation on
water.
The solubility of O2 in organic solvents is approximately ten times greater than in water.
-The high solubility of O2 makes it necessary to purge all solvents used in the synthesis of
oxygen sensitive compounds.
Oxygen is readily available as O2 from the atmosphere and is obtained on a massive scale
by the liquefaction and distillation of liquid air.
Convenient laboratory preparations of O2 are the electrolysis of aqueous alkali using Ni
electrodes, and decomposition of H2O2

A mixture of KClO3 and MnO2 used to be sold as ‘oxygen mixture’ and the thermal
decompositions of many other oxo salts (e.g. KNO3, KMnO4 and K2S2O8) produce O2.
 Dioxygen

The main commercial motivation is to recover O2 for steel making, in which it reacts
exothermically with coke (carbon) to produce carbon monoxide. The high temperature is
necessary to achieve a fast reduction of iron oxides by CO and carbon. About 1 tonne (1 t =
103 kg) of oxygen is needed to make 1 tonne of steel.

Oxygen is also required by industry in the production of the white pigment TiO2 by the
chloride process:
TiCl4 (l) + O2 (g) → TiO2 (s) + 2Cl (g)
 Dioxygen

Dioxygen is a colourless gas, but condenses to a pale blue liquid or solid.

In all phases, it is paramagnetic with a triplet ground state, i.e. the two unpaired electrons
have the same spin, with the valence electron configuration being:
The molecular orbital description of O2 implies the existence of a double bond; the outermost two electrons occupy
different antibonding π orbitals with parallel spins; as a result, the molecule is para- magnetic

The MO diagram of O2
 Dioxygen
it is paramagnetic with a triplet ground state, i.e. the two unpaired electrons have the same spin,
with the valence electron configuration being:

This triplet ground state is designated by the term symbol 3Σg

In this state, O2 is a powerful oxidizing agent. but fortunately, the kinetic barrier is often high.
The O2 molecule possesses two excited states that lie 94.7 and 157.8 kJ mol–1 above the ground
state. The first excited state is a singlet state (designated by the term symbol1Δg) with two spin-
paired electrons in the pg* level occupying one MO:

In the higher excited state (singlet state, 1+), the two electrons occupy different MOs as in the
ground state, but have opposite spins.

Of the two singlet states, the former has much the longer excited state lifetime (its
return to the ground state is spin-forbidden) and O2(1Δg) survives long enough to
participate in chemical reactions. When it is needed for reactions, O2(1Δg) can be
generated in solution by energy transfer from a photoexcited molecule.
The blue colour of liquid and solid O2 arises from the simultaneous excitation by a single
photon of two O2 molecules from their ground to excited states. The associated
absorption of energy corresponds to absorption of light in the red to green region of the
visible part of the spectrum.

Singlet dioxygen (the (1Δg) state) can be generated photochemically by irradiation of O2

in the presence of an organic dye as sensitizer, or non-photochemically by reactions such
as
H2O2 + NaOCl → O2 + NaCl + H2O

Thus [Ru(bpy)3]2 can be excited by absorption of blue light (452 nm) to give an
electronically excited state, denoted *[Ru(bpy)3]2+, and this state transfers energy to
O2(3Σg):
 Chemistry of Oxygen

Another efficient way to generate O2(1Δg) is through the thermal decomposition of an

ozonide:

In contrast to the radical character of many O2(3Σg) reactions, O2(1Δg) reacts as an

electrophile. This mode of reaction is feasible because O2(1Δg) has an empty π* orbital,
rather than two that are each occupied by a single electron. For example, O2(1Δg) adds
across a diene, thus mimicking the DielsAlder reaction of butadiene with an electrophilic
alkene:

Singlet oxygen is implicated as one of the biologically hazardous products of

photochemical smog.
 Chemistry of Oxygen

At high temperatures, O2 combines with most elements, exceptions being the halogens and noble
gases, and N2 unless under special conditions.
Reactions with the group 1 metals are of particular interest, oxides, peroxides, superox- ides and
suboxides being possible products.

Bond lengths in O2, [O2]- and [O2]2- are 121, 134 and 149 pm, consistent with a weakening of the bond
caused by increased occupation of the p* MOs

Assignment: Try the MO diagram for [O2]- and [O2]2- and explain why there is an increase in
the bond order.

The first ionization energy of O2 is 1168 kJmol-1 and it may be oxidized by very powerful
oxidizing agents such as PtF6.

The bond distance of 112 pm in [O2]+ is in keeping with the trend for O2, [O2]- and [O2]- .
 Chemistry of Oxygen
Ozone

The other allotrope of oxygen, ozone, O3, boils at 112oC and is an explosive and highly
reactive endoergic blue gas
(fGO 163 kJ mol1). It decomposes into dioxygen
2O3 (g) → 3O2(g)
-but this reaction is slow in the absence of a catalyst or ultraviolet radiation.

-Ozone has a pungent odour; this property is reflected in its name, which is derived
from the Greek ozein, to smell.
-The O3 molecule is angular, in accord with the VSEPR model and has bond angle 117; it
is diamagnetic.
-Gaseous ozone is blue, liquid ozone is blue-black, and solid ozone is violet-black.

Ozone is produced from electrical discharges or ultraviolet radiation acting on O2.

 Chemistry of Oxygen

Ozone reacts with unsaturated polymers, causing undesirable cross-linking and

degradation.

Reactions of ozone typically involve oxidation and transfer of an O atom. Ozone is very
unstable in acidic solution and much more stable in basic conditions:

Ozone is exceeded in oxidizing power only by F2, atomic O, the OH radical, and
perxenate ions.
Ozone forms ozonides with Group 1 and 2 elements.
They are prepared by passing gaseous ozone over the powdered hydroxide, MOH or
M(OH)2, at temperatures below -10oC. The ozonides are red-brown solids that
decompose on warming:
MO3 → MO2 + ½ O2
The ozonide ion, O3-, is angular, like O3, but with the slightly larger bond angle of 119.5o.
 Chemistry of Oxygen
Ozone is much more reactive than O2

Ozonides are explosive, but [Me4N]O3 is relatively stable, decomposing above 348K

Phosphite ozonides, (RO)3PO3, have been known since the early 1960s, and are made
in situ as precursors to singlet oxygen. The ozonides are stable only at low
temperatures, and it is only with the use of modern low temperature crystallographic
methods that structural data are now available.
 Chemistry of Oxygen

Reactivity of oxygen: The reactions of dioxygen are often thermodynamically favourable

but sluggish.

Oxygen is by no means an inert molecule, yet many of its reactions are sluggish,
For example, a solution of Fe2+ is only slowly oxidized by air even though the reaction is
thermodynamically favourable.

Several factors contribute to the appreciable activation energy of many reactions of O2.
-with weak reducing agents, single-electron transfer to O2 is mildly unfavourable
thermodynamically:

A single-electron reducing reagent must exceed these potentials for the reaction to be
thermodynamically viable and must exceed them to achieve a significant rate.

-Second, the ground state of O2, with both π* orbitals singly occupied, is neither an
effective Lewis acid nor an effective Lewis base, and therefore has little tendency to
undergo displacement reactions with p-block Lewis bases or acids.
-Finally, the high bond energy of O2 (497 kJ mol1) results in a high activation energy for
reactions that depend on its dissociation.
 Chemistry of Oxygen

In metalloenzymes O2 coordinates to metals such as Fe and Cu, and the enzyme

catalyses the four-electron reduction of O2 to water.

Hydrogen peroxide: Hydrogen peroxide is susceptible to decomposition by disproportionation

at elevated temperatures or in the presence of catalysts.

Hydrogen peroxide is a very pale blue, viscous liquid. It has a higher boiling point than
water (150oC) and a greater density (1.445 g cm-3 at 25oC).

It is miscible in water and is usually handled in aqueous solution.

H2O2 is a good oxidizing agent, but it is unstable with respect to disproportionation:

This reaction is slow but is explosive when catalysed by a metal

surface or alkali dissolved from glass.
For this reason, hydrogen peroxide and its solutions are stored in
plastic bottles and a stabilizer is added.
 Chemistry of Oxygen
This reaction can be considered in terms of the reduction half-reactions

Any substance with a standard potential in the range 0.70-1.68 V that has suitable binding
sites will catalyse this reaction. As can be inferred from these standard potentials,
hydrogen peroxide is a very powerful oxidizing agent in acid solution:

However, in basic solution hydrogen peroxide can act as a reducing agent:

The underlying reason for the oxidizing nature of hydrogen peroxide lies in the weakness
of the O-O single bond (146 kJ mol1).
Fenton Reaction: Hydrogen peroxide reacts with d-metal ions such as Fe2+ to form the
hydroxyl radical:
 Chemistry of Oxygen

The Fe3+ product can react with a second H2O2 to regenerate Fe2+, so that the production of
hydroxyl radical is catalytic.

The hydroxyl radical is one of the strongest oxidizing agents known (E 2.85 V) and the
reaction is used to oxidize organic matter. In living cells, its reaction with DNA has
potentially lethal consequences.

Hydrogen peroxide is a slightly stronger acid than water:

H2O2(aq) + H2O(l) → H3O+(aq) + HO2-(aq) pKa = 11.65

Deprotonation occurs in other basic solvents such as liquid ammonia, and NH4OOH has
been isolated and found to consist of NH4+ and HO2- ions.

The oxidizing ability of hydrogen peroxide and the harmless nature of its byproducts
lead to its many applications. It is used in water treatment to oxidize pollutants, as a
mild antiseptic, and as a bleach in the textile, paper, and hair-care industries
 Chemistry of Oxygen

H2O2 has a trans-planar conformation

Tracer studies using 18O show that in these redox reactions H2(18O)2 is converted to (18O)2,
confirming that no oxygen from the solvent (which is not labelled) is incorporated and
the O-O bond is not broken.
 Chemistry of Halogens

Fluorine, chlorine, bromine and iodine- The group 17 elements are called the halogens.

Except for fluorine and the highly radioactive astatine, the halogens exist with oxidation
numbers ranging from -1 to +7; the small and highly electronegative fluorine atom is
effective in oxidizing many elements to high oxidation states.
The valence electron configuration ns2np5-
-high ionization energies
-high electronegativities
-high electron affinities: because the incoming electron can occupy an orbital of an
incomplete valence shell and experience a strong nuclear attraction.

The effective Nuclear charge Zeff increases progressively across the period
But F has a lower electron affinity than Cl. it stems from the larger electron–electron
repulsion in the compact F atom as compared with the larger Cl atom.

This electron–electron repulsion is also responsible for the weakness of the F-F bond
in F2.
 Chemistry of Halogens

Iodine is a purple–grey solid that sublimes to a violet vapour. The violet colour persists when
it is dissolved in nonpolar solvents such as CCl4. However, in polar solvents it dissolves to give
red–brown solutions, indicating the presence of polyiodide ions such as I3- .

All the halogens form hydrogen halides; HF is a liquid and HCl, HBr, and HI are gases. All
the Group 17 elements form oxo compounds and oxoanions.

Fluorine never found in a positive oxidation state- because it is most electronegative of

all elements.

With the possible exception of At, the other halogens occur with oxidation numbers ranging
from -1 to +7. Compounds of Br(VII) are very unstable compared to those of Cl and I.

The high electronegativity of F leads to enhanced Bronsted acidity in compounds containing

the element compared to nonfluorine analogues.
A combination of high electronegativity and small atomic radius, which means that many
atoms can pack round a central atom, results in F being able to stabilize high oxidation states
of most elements, for example UF6 and IF7.

The metal fluorides in low oxidation states tend to be predominantly ionic whereas extensive
covalent character is found in metal chlorides, bromides, and iodides.
 Chemistry of Halogens

Fluorocarbon compounds:
Polytetrafluoroethene (PTFE)- great technological importance because these compounds
are useful in applications ranging from coatings for nonstick cookware and halogen-
resistant laboratory vessels to the volatile fluorocarbons used as refrigerants in air
conditioners and refrigerators.
Hydrofluorocarbons are used as replacements for chlorofluorocarbons as refrigerants and
propellants.
Tetrafluorethane, CHF2CHF2, is an important solvent for the extraction of natural products
such as vanilla and taxol, which is used in chemotherapy.

Hydrogen Halides:
The properties of HF contrast starkly with those of the other hydrogen halides- its ability
to participate in extensive hydrogen bonding.
Because hydrogen bonding is extensive, HF is a volatile liquid whereas HCl, HBr, and HI are
gases at room temperature.
All the hydrogen halides are Bronsted acids: aqueous HF is a weak acid (‘hydrofluoric acid’)
whereas HCl, HBr, and HI are all essentially fully deprotonated in water
 Chemistry of Halogens

Although hydrofluoric acid is a weak acid it is one of the most toxic and corrosive substances
known, being able to attack glass, metals, concrete, and organic matter.
Very readily absorbed through the skin, and even brief contact can lead to severe burning and
necrosis of the skin and deep tissue, and damage to bone by decalcification by formation of
CaF2 from calcium phosphate.
Oxygen difluoride, OF2, is the most stable oxide of F but decomposes above -100oC.
Chlorine occurs with many different oxidation numbers in its oxides- ClO2, in which Cl has the
unusual oxidation number +4, and Cl2O6, which exists as a mixed oxidation state ionic solid,
[ClO2+][ClO4-].
There are fewer oxides of Br than Cl-- Br2O, Br2O3, and BrO2.
The oxides of I are the most stable halogen oxides. The most important of these is I2O5.
 Molecular structure and properties

The F-F bond is weak relative to the Cl-Cl bond; bond strengths decrease down the group
from chlorine.
In the vapour they range from the almost colourless F2, through yellow–green Cl2 and
red–brown Br2, to purple I2.

The progression of the maximum

absorption to longer wavelengths
reflects the decrease in the
HOMO–LUMO gap on descending
the group.
- Elcetronic transitions in which
an electron is promoted from the
highest filled 2sg and 1pg orbitals
into the vacant antibonding 2su
orbital
 Molecular structure and properties

Except for F2, the analysis of the UV absorption spectra gives precise values for the
dihalogen bond dissociation energies.
The lack of discrete absorption bands makes it difficult to estimate the dissociation
energy spectroscopically, and thermochemical methods are complicated by the
highly corrosive nature of this reactive halogen.

The simplest explanation (like the explanation of the low electron affinity of fluorine) is
that the bond is weakened by the strong repulsions between nonbonding electrons in
the small F2 molecule.

There is a weak intermolecular bonding interactions that strengthen on going from

Cl2 to I2
 Pseudohalogens

Pseudohalogens and pseudohalides mimic halogens and halides, respectively; the

pseudohalogens exist as dimers and form molecular compounds with nonmetals and
ionic compounds with alkali metals.

A number of compounds have properties so similar to those of the halogens that they
are called pseudohalogens
 Pseudohalogens

like the dihalogens, cyanogen, (CN)2, undergoes thermal and photochemical dissociation in
the gas phase; the resulting CN radicals are isolobal with halogen atoms and undergo
similar reactions, such as a chain reaction with hydrogen:

Another similarity is the reduction of a pseudohalogen:

The anion formally derived from a pseudohalogen is called a pseudohalide ion; An example
is the cyanide anion, CN-

Pseudohalogen ions are not spherical, so the structures of their ionic compounds often
differ
The thiocyanate ion, SCN-, for instance, acts as an ambidentate ligand with a soft base site,
S, and a hard base site, N
 Chemistry of Halogens
The interhalogens
All the halogens form compounds with other members of the group.
The binary interhalogens are molecular compounds with formulas XY, XY3, XY5, and XY7,
where the heavier, less electronegative halogen X is the central atom.
They also form ternary interhalogens of the type XY2Z and XYZ2, where Z is also a halogen
atom. The interhalogens are of special importance as highly reactive intermediates and
for providing useful insights into bonding.

All the F interhalogen compounds are exergonic. The least labile interhalogen is ClF,
but ICl and IBr can also be obtained in pure crystalline form.

Their physical properties are intermediate between those of their component

elements. For example, the deep red α-ICl (m.p. 27C, b.p. 97C) is intermediate
between yellowish–green Cl2 (m.p. -101oC, b.p. 35oC) and dark purple I2 (m.p. 114oC,
b.p. 184oC).

Most of the higher interhalogens are fluorides. The only neutral interhalogen
with the central atom in a +7 oxidation state is IF7, but the cation ClF6+ a compound of Cl(VII),
is known.
The absence of a neutral ClF7 - reflects the destabilizing effect of nonbonding
electron repulsions between F atoms
 Chemistry of Halogens
The interhalogens
Most of the higher interhalogens are fluorides. The only neutral interhalogen with the central
atom in a +7 oxidation state is IF7, but the cation ClF6+ a compound of Cl(VII), is known.

The absence of a neutral ClF7 - reflects the destabilizing effect of nonbonding electron
repulsions between F atoms.

Reactions of F2 with the later halogens at ambient temperature and pressure give ClF, BrF3
or IF5, but increased temperatures give ClF3, ClF5, BrF5 and IF7.

• F is always in oxidation state -1;

• highest oxidation states for X reached are Cl < Br < I;
• combination of the later halogens with fluorine leads to
the highest oxidation state compounds.

With the exception of I2Cl6, the higher interhalogens contain F and are extremely
reactive, exploding or reacting violently with water or organic compounds; ClF3 even
ignites asbestos.
 Chemistry of Halogens

Shapes of interhalogen molecules: in accord with the VSEPR model

ClF3 compounds (such as) have five valence The Lewis structure of XF5 has five
electron pairs around the Cl atom in a bonding pairs and one lone pair on the
trigonal–bipyramidal arrangement central X atom and, as expected from
C2v bent T shape. the VSEPR model, XF5 molecules are
square pyramidal.

The only known XY7 compound is IF7- pentagonal bipyramidal.

 Chemistry of Halogens

Polymeric interhalogens may also be formed and may be cationic or anionic.

- Examples of cationic polyhalides are I3+ and I5+.

The I3- ion is the most stable but others with the general formula [(I2)nI-] are formed.
Other anionic polyhalides include Cl3- and BrF4-.
 Chemistry of Halogens
Among the interhalogens, ‘ICl3’ is unusual in being dimeric and possesses structure; the
planar I environments are consistent with the VSEPR model.

The most stable of the diatomic molecules are ClF and ICl.
IBr dissociates somewhat into its elements, while BrCl is substantially dissociated

Chlorine monofluoride acts as a powerful fluorinating and oxidizing agent

It may behave as a fluoride donor

or as a fluoride acceptor

Iodine monochloride and monobromide are less reactive than ClF, but of importance
is the fact that, in polar solvents, ICl is a source of I+ and iodinates aromatic compounds.
 Chemistry of Halogens

Reactivity decreases in the general order ClFn > BrFn > IFn, and within a series having
common halogens, the compound with the highest value of n is the most reactive,
e.g. BrF5 > BrF3 > BrF.

In line with these trends is the use of IF5 as a relatively mild fluorinating agent in organic
chemistry.

There is some evidence for the self-ionization of IF5, but little to support similar
processes for other interhalogens.
 Chemistry of Halogens
Bonding in [XY2]- ions
In terms of valence electrons, XeF2 is isoelectronic with [ICl2]-, [IBr2]-, [ClF2]- and related
anions, and all have linear structures.
The bonding in these anions can be viewed as being similar to that in XeF2, and thus
suggests weak X-Y bonds- Evidence for weak bonds comes from the X-Y bond lengths
(e.g. 255 pm in [ICl2]- compared with 232 in gas phase ICl) and from X-Y bond stretching
wavenumbers (e.g. 267 and 222 cm-1 for the symmetric and asymmetric stretches of
[ICl2]- compared with 384cm-1 in ICl).
 Chemistry of Halogens
Polyhalogen cations
[Br2]+, [I2]+, [Cl3]+, [Br3]+, [I3]+, [Br5]+, [I5]+ and [I4]2+ are well established.
The cations [Br2]+ and [I2]+ can be obtained by oxidation of the corresponding
halogen
Under special strongly oxidizing conditions, such as in fuming sulfuric acid, [I2]+ is
oxidized to the blue paramagnetic diiodinium cation, [I2]+.

The dibrominium cation, Br2+, is also known. The bonds of these cations are shorter than
those of the corresponding neutral dihalogens, which is the expected result for loss of an
electron from a π* orbital and the accompanying increase in bond order from 1 to 1.5

Another class of polyhalogen cations of formula XFn is obtained when a strong Lewis
acid, such as SbF5, abstracts F from interhalogen fluorides:
ClF3 + SbF5 → [ClF2+][SbF6-]
 Chemistry of Halogens

Polyhalides: Polyiodides, such as I3- are formed by adding I2 to I-; they are stabilized by
large cations. Some of the most stable polyhalogen anions contain fluorine as the
substituent; their structures usually conform to the VSEPR model.

I2 + I - → I3 - + I5 -

These polyiodides are Lewis acid-base complexes in which I- and I3- act as the bases and
I2 acts as the acid.

An I3- ion can interact with other I2 molecules to yield larger mononegative polyiodides
of composition [(I2)nI-].
I3- ion: most stable ion, In combination with a large cation, such as [N(CH3)4], it is
symmetrical and linear with a longer I-I bond than in I2.
 Chemistry of Halogens
Oxoacids and oxoanions: The halogen oxoanions are thermodynamically strong
oxidizing agents; perchlorates of oxidizable cations are unstable.

The strengths of the oxoacids vary systematically with the number of O atoms on the
central atom

Periodic acid, H5IO6, is the I(VII) analogue of perchloric acid- there is only
one I=O group

H4IO6-(aq) → IO4-(aq) + 2H2O(l)

IO4- is the dominant ion.

The halogen oxoanions, like many oxoanions, form metal complexes, including the
metal perchlorates and periodates.

HClO4 is a very strong acid and H5IO6 is a weak acid, it follows that ClO4- is a very
weak base and H4IO6- is a relatively strong base.

The ClO4- ion is used as a weakly coordinating ion that can readily be displaced from a
complex by other ligands, or as a medium-sized anion that might stabilize solid
salts containing large cationic complexes with easily displaced ligands.
Chemistry of Halogens
 Bioinorganic chemistry: S and P-block elements in biology

The major biological elements are oxygen, hydrogen, carbon, nitrogen, phosphorus, sulfur,
sodium, magnesium, calcium, and potassium. The trace elements include many d metals,
(V, Cr, Mn, Fe, Co, Ni, Cu, Zn and Mo) as well as fluorine, selenium, iodine, silicon, and
boron.

V: accumulated by a few organisms, and has been shown to be essential for growth in
rats and chicks;
Cr: essential
Mn, Fe, Cu, Ni, Zn: essential to all organisms
Co: essential to mammals and many other organisms
Mo: essential to all organisms although green algae may be an exception;
B: essential to green algae and higher plants, but its exact role is unknown
Si: exoskeletons of marine diatoms composed of hydrated silica, but its role in other
biological systems is less well defined;
Se: essential to mammals and some higher plants;
F: its role is not fully established but its deficiency causes dental caries;
I: essential to many organisms.
 Bioinorganic chemistry: S and P-block elements in biology

Amanita muscaria
 The organization of cells

Living cells and organelles are enclosed by membranes; the concentrations of specific
elements may vary greatly between different compartments due to the actions of ion pumps
and gated channels.

Cells, the basic unit of any living organism, range in complexity from the simplest types
found in prokaryotes (bacteria and bacteria-like organisms now classified as archaea) and
the much larger and more complex examples found in eukaryotes (which include animals
and plants).

Cytoplasm of eukaryotic cells contains

subcompartments (also enclosed within lipid
bilayers) known as organelles, which have highly
specialized functions.
Organelles include the nucleus (which houses DNA),
mitochondria (the ‘fuel cells’ that carry out
respiration), chloroplasts (the ‘photocells’ that
harness light energy), the endoplasmic reticulum
(for protein synthesis), Golgi (vesicles containing
proteins for export), lysosomes (which contain
degradative enzymes and help rid the cell of waste),
peroxisomes (which remove harmful hydrogen
peroxide), and other specialized processing zones.
The inorganic composition of cells
 The inorganic composition of cells

Compartmentalization: Different elements are strongly segregated inside and outside a

cell and among different internal compartments.
-is the distribution of elements inside and outside a cell and between
different internal compartments.

The maintenance of constant ion levels in different biological zones is an example of

‘homeostasis’ and it is achieved as a result of membranes being barriers to passive ion
flow.

K+ and Na+ ions across cell membranes- large difference in concentration

For eg: In the cytoplasm, the K+ concentration may be as high as 0.3 M whereas outside it
is usually less than 5 x 10-3 M.
-Na is abundant outside a cell but scarce inside.
Ca2+, which is almost absent from the cytoplasm (its free concentration is below 1 . 107
m) yet is a common cation in the extracellular environment and is concentrated in certain
organelles, such as mitochondria.
 Sodium and potassium transport
Transport across a membrane is active (energized) or passive (spontaneous); the flow of
ions is achieved by proteins known as ion pumps (active) and channels (passive).

Elements are selected by Nature for their inherent useful properties and their availability
Na+ and K+, two ions that are very similar except for their radii

Na, K, and Li The ions of these elements are characterized by weak binding to hard
ligands and their specificity is based on size and hydrophobicity that arises from a lower
charge density.
crown ethers and cryptands, with dimensions appropriate for coordination to one
particular kind of ion.

Ionophores: Organisms use this principle in the molecules known as ionophores, which
have hydrophobic exteriors that make them soluble in lipids.

antibiotic valinomycin: high selectivity for K+ It enables K to pass

through a bacterial cell membrane and thereby dissipate the electrical potential difference,
so causing the bacterium’s death

ion channels, which are large membrane-spanning proteins that allow selective transport
of K+ and Na+ (as well as Ca2+ and Cl-) and are responsible for electrical conduction in
nervous systems as well as in coupled transport of solutes
 Sodium and potassium transport
Moving from the inside surface of the membrane, the enzyme has a pore (which can open
and close on receipt of a signal) leading into a central cavity about 1 nm in diameter; up to
this stage K+ ions can remain hydrated.

selectivity filter consisting of helical ladders of closely spaced peptide carbonyl-O donors
that form a sequence of four cubic eightfold coordination sites. During operation of the
channel these sites are occupied, at any one time, by a queue of two K ions and two H2O
molecules in alternate fashion, as in …K+…H2O…K+…H2O….

This mechanism is not effective for Na because

the cavity is too large, which accounts for the
104-fold selectivity of the channel for K+ over
Na+.
The binding is weak and fast because it is
important to convey but not to trap K+.
▪ Charged groups on the molecule move in response to a change in the membrane potential and cause
the intracellular pore to open, so allowing entry of hydrated K ions.
▪ Selective binding of dehydrated K ions occurs in the filter region, a potential drop across the
membrane is sensed, and the cavity closes.
▪ At this point the filter opens up to the external surface, where the K concentration is low and the K ions
are hydrated and released.
▪ This release causes the protein to switch back to the original conformation and K ions again enter the
filter.
 Sodium and potassium transport

Compared to Na+, K+ is more likely to be found coordinated within a protein and is more
easily dehydrated.
Both Na+ and K+ are important agents in controlling cell structure through osmotic
pressure, but whereas Na+ is ejected from cells, K+ is accumulated, contributing to a
sizeable potential difference across the cell membrane.
This differential is maintained by ion pumps, in particular the Na+, K+ -ATPase, also
known as the Na-pump.
 Calcium signaling proteins
Calcium ions are suitable for signalling because they exhibit fast ligand exchange and a
large, flexible coordination geometry.
Calcium ions play a crucial role in higher organisms as an intracellular messenger

Fluxes of Ca2+ trigger enzyme action in cells in response to receiving a hormonal or

electrical signal from elsewhere in the organism- because it has fast ligand-exchange rates,
intermediate binding constants, and a large, flexible coordination sphere.
Calcium signaling proteins are small proteins that change their conformation depending
on the binding of Ca2+ at one or more sites
Every muscle movement we make is stimulated by Ca2+ binding to a protein known as
troponin C.
The best-studied Ca2+ -regulatory protein is calmodulin (17 kg mol–1, Fig. 27.8): its roles
include activating protein kinases that catalyse phosphorylation of proteins and activating
NO-synthase, a Fe-containing enzyme responsible for generating the intercellular signalling
molecule nitric oxide.
 Calcium signaling proteins

Calmodulin has four Ca2-binding sites (one is shown as 12) with dissociation constants lying
close to 10-6. The binding of Ca2+ to the four sites alters the protein conformation and it is then
recognized by a target enzyme.

Calcium signalling requires special Ca2+ pumps, which are large,

membrane-spanning Enzymes-pump Ca2+ out of the cytoplasm,
either out of the cell altogether or into Ca-storing organelles such
as the endoplasmic reticulum or the mitochondria.

the energy for Ca2+ pumping comes from ATP hydrolysis

Although Ca2+ is invisible to most spectroscopic methods, some Ca

proteins, such as calmodulin or troponin C, are small enough to be
studied by NMR.
the lanthanoid ions have been used as probes for Ca binding-
chemical shift reagents in NMR spectroscopy

Intracellular concentrations of Ca are monitored by using

special fluorescent polycarboxylate ligands
 Magnesium enzymes
The major direct catalytic function of magnesium is as the catalytic centre of ribulose
bisphosphate carboxylase.
Mg2+ is ‘weaker acid’ than Zn2+; confers less polarization of coordinated ligands than Zn2+
cells contain high concentrations of uncomplexed Mg2+ ions.
Mg–ATP complex (1), which is the substrate in kinases, the enzymes that transfer
phosphate groups thereby activating the target compound or causing it to change its
conformation.
Kinases are controlled by calmodulin-so they are part of the signalling mechanism in
higher organisms.
Rubisco (ribulose 1,5-bisphosphate carboxylase): An important example of an Mg enzyme, in
which Mg acts separately from ATP is

▪ most abundant in the biosphere

▪ responsible for the production of biomass by oxygenic photosynthetic organisms and
removal of CO2 from the atmosphere
Rubisco is an enzyme of the Calvin cycle: the stages of photosynthesis that can occur in the
dark, in which it catalyses the incorporation of CO2 into a molecule of ribulose 1,5-
bisphosphate

The reactive enolate will

also react with O2, in
which case the result is an
oxidative degradation of
substrate: for this reason
the enzyme
is often called ribulose
1,5-bisphosphate
carboxylase-oxygenase
 Biological significance of phosphates

Phosphates play an enormously important role in biological systems.

-The genetic substances deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are
phosphate esters.
-Bones and teeth are constructed from collagen (fibrous protein) and single crystals of
hydroxyapatite, Ca5(OH)(PO4)3.

Tooth decay involves acid attack on the phosphate, but the addition of fluoride ion to
water supplies facilitates the formation of fluoroapatite, which is more resistant to decay.

All living cells contain adenosine triphosphate, ATP, which consists of adenine, ribose and
triphosphate units.
Hydrolysis results in the loss of a phosphate group
and converts ATP to ADP (adenosine diphosphate),
releasing energy which is used for functions such as
cell growth and muscle movement.
Conversely, energy released by, for example, the
oxidation of carbohydrates can be used to convert
ADP to ATP; thus, ATP is continually being reformed,
ensuring a continued supply of stored energy in the
body.
The d-block Elements
 d-block metal and transition metal

Transition element is that it is an element that has an incomplete d subshell in either the
neutral atom or its ions.
Group 12 elements (Zn, Cd, Hg) are members of the d block but are not transition
elements.

F block, the inner transition elements

Early and Late transition metals

➢ Each group of d-block metals consists of three members and is called a triad;
➢ Metals of the second and third rows are sometimes called the heavier d-block
metals;
➢ Ru, Os, Rh, Ir, Pd and Pt are collectively known as the platinum-group metals.
Chemically soft members of the block occur as sulfide minerals and are partially oxidize to obtain
the metal; the more electropositive ‘hard’ metals occur as oxides and are extracted by reduction.
Physical Properties
The properties of the d metals are largely derived from their electronic structure, with
the strength of metallic bonding peaking at Group 6; the lanthanide contraction is
responsible for some of the anomalous behaviour of the metals in the 5d series.

(n1)s orbitals to give an s band and of the nd orbitals to give a d band

Ti (3d24s2) has four bonding electrons

V (3d34s2) five
Cr (3d54s1) six, and so on
 Chemical Properties
Oxidation states across a series electronic properties of many solid compounds
in catalysis interesting role in biochemical processes

High oxidation states

The group oxidation state:
Sc, Y, and La in Group 3, with
configurations nd1(n1)s2, are found in
aqueous solution only in oxidation state 3

The group oxidation state is never achieved

after Group 8 (Fe, Ru, and Os)
-increase in ionization energy -noble character
Intermediate [O] states in 4d and 5d series
 Structural trends
The 4d- and 5d-series elements often exhibit higher coordination numbers than
their 3d-series congeners; compounds of d-metals in high oxidation states tend to have
covalent structures.
ionic radii of d-metal ions-decrease across each period

low-spin complexes, high-spin complexes

small F ligand, these 3d-series metals tend to form six

coordinate complexes but that the larger 4d- and 5d-
series metals in the same oxidation state tend to form
seven-, eight-, and nine-coordinate complexes

[Mo(CN)8]3-
 Noble Metals

With the exception of Group 12, the metals at the lower right of the d block are resistant to
oxidation-strong intermetallic bonding and high ionization energies
Aqua regia, a 3:1 mixture of concentrated hydrochloric and nitric acids, is an old but
effective reagent for the oxidation of gold and platinum.
the NO3- ions provide the oxidizing power and the Cl- ions act as complexing agents
Au(s) + 4H(aq) + NO3 (aq) 4Cl(aq) [AuCl4](aq) NO(g) 2H2O(l)
The active species in solution are thought to be Cl2 and NOCl,
3HCl(aq) + HNO3(aq) Cl2(aq) + NOCl(aq) + 2H2O(l)
Metal Complexes:
Mostly associated with electronegative ligands
-Halogens, Oxygen, Nitrogen and Sulfur

Metal Halides
Monohalide: Group 11, CuCl, AgCl and AuCl
Binary Metal halides
Low oxidation states metals: Iodides and bromides
Many different oxides of the d-block elements exist, with a wide variety of structures, varying
from ionic lattices to covalent molecules.

Metal Oxides:
Oxides of elements in low oxidation states exist.

Vanadyl complex
Mononuclear oxido complexes
The conversion of an aqua ligand to an oxido ligand is favoured by a high pH and by a high
oxidation state of the central metal atom; in vanadium complexes in oxidation state 4 or 5,
the site trans to the oxido ligand may be vacant or occupied by a weakly coordinating ligand.

Elements in high oxidation states typically occur as oxoanions in aqueous solution,

such as MnO4-, which contains Mn(VII), and CrO42-, which contains Cr(VI). The
existence of these oxoanions contrasts with the existence of simple aqua ions for
the same metals in lower oxidation states, such as [Mn(OH2)6]2 for manganese(II)
and [Cr(OH2)6]3 for chromium(III).
Polyoxometallates:

The tendency for Cr(VI) to form polyoxo species is limited by the fact that the O
tetrahedra link only through vertices: edge and face bridging would result in too close
an approach of the metal atoms.
It is often convenient to represent the structures of the polyoxometallate ions by polyhedra,
with the metal atom understood to be in the centre and O atoms at the vertices.
 The structures for this series of polyoxometallates contain terminal O atoms (those
projecting out from a single metal atom) and two types of bridging O atoms: two-metal
bridges, MOM, and one hypercoordinated O atom in the centre of the structure that is
common to all six metal atoms.

Polyoxometallate anions can be prepared by carefully adjusting pH and concentrations,

for example polyoxomolybdates and polyoxotungstates are formed by acidification of
solutions of the simple molybdate or tungstate:

Metal Sulfides and Sulfide complexes:

Monosulfides and Disulfides
Clusters of Fe and S atoms (‘FeS clusters’) are cofactors in many enzymes, including
nitrogenase, which converts N2 to NH3 under ambient conditions
Nitrido and alkylidyne complexes
The nitrido ligand (N≡) and alkylidyne ligand (RC≡ previously known as carbido) are
present formally as N3- and RC3-.
(Me3CO)3W ≡ W(OCMe3)3 + PhC ≡ N → (Me3CO)3W ≡ CPh + (Me3CO)3W ≡ N
Like the O2 group, these ligands are strong donors and weaken the trans metal- ligand
bond.
The order of this influence is RC ≡ > N ≡ > O=
Metal-metal bonded compounds and clusters
Metal-metal (MM) bond distances comparable to or shorter than those in the elemental
metal- cluster compounds
- bond orders up to five are formed by many d metals in low oxidation states
Hg22+ ion - first d-block metal-metal bonded species to be identified

-a bond between two metal atoms can arise from the overlap of a dz2 orbital from
each atom
-two bonds can arise from the overlap of dzx or dyz orbitals
-two bonds can be formed from the overlap of two face-to-face dxy or dx2-y2 orbitals.

quintuple bond- if all the bonding orbitals are occupied to give the electron
configuration σ2π4δ4
The two Cr atoms are separated by a very short distance
of 183.5 pm

Assignment: [Re2Cl8]2- explain the Metal Metal bond.

Many other species with multiple metal metal bonds, where the dx2-y2 orbital is involved
in bonding to ligand species, are known.

A well-known example is the quadruply bonded compound molybdenum(II) acetate,

which is prepared by heating Mo(CO)6 with acetic acid:
2Mo(CO)6 + 4CH3COOH → Mo2(O2CCH3)4 + 2H2 + 12CO

Mo2(O2CCH3)4(aq) + 4H(aq) 8Cl(aq) → [Mo2Cl8]4-(aq) + 4CH3COOH(aq)

The reaction product can be regarded as containing a 3c,2e MHM bridge and an
iodide anion bonding by two conventional 2c,2e bonds, one to each Mo atom.

Larger metal clusters can be synthesized by addition to a metal metal multiple bond.
 Clusters

Metal clusters may be formed; for early d-block elements they are favored by good donor
ligands, whereas for later d-block elements -acceptor ligands are needed.