V.N.

Karazin Kharkov National University

Medical Chemistry
Module 1. Lecture 2

Chemical bonding.
Coordination compounds
Natalya VODOLAZKAYA
[email protected]
7 December 2020 Department of Physical Chemistry
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 Lecture topics
√ Chemical bond.
√ Ionic bond.
√ Covalent bond.
√ Electronegativity of the elements and the type of the
bond.
√ Coordination (complex) compounds.
√ Structure of coordination compounds.
√ Stability constants.
√ Coordination compounds in living systems.
√ Amino acids and their derivatives as ligands.
√ Nucleic acids and their derivatives as ligands.
√ Coordination compounds of Fe in living systems.
√ Coordination compounds of Fe and Mg in living
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systems.
 Chemical bond
Atoms of most elements can interact with one another to form
compounds.
The forces that hold these atoms together in compounds are called
chemical bonds.
When atoms interact to form a chemical bond, only their outer electronic
shells are in contact. For this reason, when we study chemical bonding, we
are concerned with the valence electrons of the atoms.

! ! ! In general, the bonding of the atoms lowers the potential energy of the
reacting particles. As the electron configuration and the strength of the
nucleus-electron attraction determine the properties of an atom, the type
and strength of chemical bonds determine the properties of a forming
substance.

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 Ionic bond
An ionic bond is the electrostatic force that holds ions together in
an ionic compound.

For example, the reaction between lithium and fluorine to form lithium
fluoride. The electronic configuration of lithium is 1s22s1, and that of fluorine is
1s22s22p5. When lithium and fluorine atoms come in contact with each other,
the outer 2s1 valence electron of lithium is transferred to the fluorine atom. After
this process the ions with stable electronic configurations are formed. The
lithium cation (Li+) has electronic configuration like helium atom, 1s2; the
fluorine anion (F–) – like neon, 1s22s22p6. The ionic bond in LiF is formed by the
electrostatic attraction between the positively charged lithium ion and the
negatively charged fluoride ion. The compound itself is electrically neutral.

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 Ionic bond
Ionic bonding occurs between elements when the energy required to
remove the outer shell electrons (the ionization energy) of one of reacting
elements is relatively low. Elements with such low ionization energies
are metals. Non-metals generally contain more than three electrons in
the outer shells of their atoms and have high tendency to accept
electrons from another atoms. Consequently substances formed by
typical metals and nonmetals are ionic.

In the formation of an ionic compound such as LiF or CaO, it is not only the
electron transfer leads to formation of a stable substance. Much more energy
lowering value corresponds to the process of interaction of the gaseous ions giving
a crystalline solid.
The lattice energy is defined as the energy needed to separate the ions in one
mole of a solid substance to give a gaseous ions. For example, this value for NaF
equals 910 kJ/mol, for NaCl: 788 kJ/mol, for CsI: 613 kJ/mol.
The lattice energy indicates the strength of ionic interactions, which
influences melting point, hardness, solubility, and other properties of ionic crystalls.
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 Covalent bond
When two or more non-metals combine their atoms have to share
electrons forming common electronic pair and achieving the stable
electronic configuration of a noble gas. This type of bonding is called
covalent bonding.

So, in this type of chemical bond two electrons are shared by two atoms.
For the simplicity, the shared pair of electrons is often represented in the
molecule by a single line. Thus, the covalent bond in the hydrogen molecule can be
written as H–H, in hydrogen chloride molecule as H–Cl.

In a covalent bond, each electron in a shared pair is attracted to the nuclei of

both atoms. This attraction holds the two atoms in the molecule together and is
responsible for the formation of covalent bonds in other molecules. ! Covalent
bonding between many-electron atoms involves only the valence electrons.

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 Covalent bond
If two atoms are held together by one electron pair, the bond is
called a single bond.
Sometimes, more than one pair of electrons is shared. For example,
oxygen gas molecule, O2. Here, each oxygen shares two pairs of
electrons to achieve the electron configuration of neon. The structural
formula of oxygen molecule is written as O = O.
If two atoms share two pairs of electrons, the covalent bond is called
a double bond. Double bonds exist in molecules of carbon dioxide and
ethylene. In a molecular structure, where three pairs of electrons are
shared, the bond is called a triple bond, for example in nitrogen
molecule, N2. H H
H O H O C O C C N N
H H

! For the predicting whether compounds are ionic or covalent we use

general rule:
metal + non-metal → ionic bonding,
non-metal + non-metal → covalent bonding. 7
 Electronegativity of the elements
and the type of the bond
In a molecule like H2, in which the atoms are identical, the electrons to
be equally attracted by two hydrogen nucleus. However, if we have the
covalently bonded HF molecule, the H and F atoms do not share the
bonding electrons equally, because H and F atoms are characterized by
different ability to attract electrons. The bond in HF is called a polar
covalent bond, because the electrons are shifted in the vicinity of the
fluorine atom.
A property of atoms that helps us distinguish a nonpolar covalent
bond from a polar covalent bond is electronegativity, ! the ability of an
atom to attract toward itself the electrons in a chemical bond.
An atom such as fluorine, which has a high electron affinity (tends to
pick up electrons easily) and a high ionization energy (does not lose
electrons easily), has a high electronegativity. On the other hand,
sodium has a low electron affinity, a low ionization energy, and a
low electronegativity. 8
 Electronegativity
Electronegativity is a relative value, showing that an element’s
electronegativity can be measured only in relation to the electronegativity of
other elements.
L. Pauling proposed a method for calculating relative electronegativities of most
elements. These values are shown in Table. There is no sharp distinction between a
polar covalent bond and an ionic bond, but the following general rule is helpful in
distinguishing between them: an ionic bond forms when the electronegativity
difference between the two bonding atoms is 1.7 or more.

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 Coordination (complex) compounds
A complex ion is an ion containing a central metal cation bonded to
one or more molecules or ions. Complex ions are crucial to many
chemical and biological processes.

Transition metals have a particular tendency to form complex ions

because they have incompletely filled d-subshells.
This property enables them to act effectively in reactions with many
molecules or ions that serve as electron donors.

For example, a solution of cobalt (II) chloride is pink because of the

presence of the Co(H2O)62+ ions. When HCl is added, the solution turns
blue as a result of the formation of the complex ion CoCl42-:

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 Coordination (complex) compounds
A coordination compound typically consists of a complex ion and counter
ion. [Note that some coordination compounds such as Fe(CO)5 do not contain
complex ions.]

Our understanding of the nature of coordination compounds stems from the classic
work of Alfred Werner*, who prepared and characterized many coordination
compounds. In 1893, at the age of 26, Werner proposed what is now commonly
referred to as Werner’s coordination theory.
The valences of the elements in cobalt (III) chloride and in ammonia seem to be
completely satisfied, and yet these two substances react to form a stable compound
having the formula CoCl3⋅6NH3. To explain this behavior, Werner postulated that most
elements exhibit two types of valence: primary valence and secondary valence.
In modern terminology, primary valence corresponds to the oxidation number and
secondary valence to the coordination number of the element. In CoCl3⋅6NH3,
according to Werner, cobalt has a primary valence of 3 and a secondary valence of 6.

* Alfred Werner (1866–1919). Swiss chemist. Werner started as an organic chemist but became interested in
coordination chemistry. For his theory of coordination compounds, Werner was awarded the Nobel Prize in
Chemistry in 1913. 11
 Coordination (complex) compounds
Today we use the formula [Co(NH3)6]Cl3 to indicate that the ammonia
molecules and the cobalt atom form a complex ion; the chloride ions are
not part of the complex but are held to it by ionic forces. Most, but not all, of
the metals in coordination compounds are transition metals.
The molecules or ions that surround the metal in a complex ion are
called ligands. Every ligand has at least one unshared pair of valence
electrons, as these examples show:

Thus, the metal-ligand bonds are usually coordinate covalent bonds. The
atom in a ligand that is bound directly to the metal atom is known as the
donor atom. For example, nitrogen is the donor atom in the [Cu(NH3)4]2+ complex ion.
The coordination number in coordination compounds is defined as the
number of donor atoms surrounding the central metal atom in a complex ion.
For example, the coordination number of Ag+ in [Ag(NH3)2]+ is 2, that of Cu2+ in [Cu(NH3)4]2+ is
4, and that of Fe3+ in [Fe(CN)6]3- is 6.
The most common coordination numbers are 4 and 6, but coordination
numbers such as 2 and 5 are also known. 12
 Coordination (complex) compounds
Depending on the number of donor atoms
present, ligands are classified as
√ monodentate,
√ bidentate,
√ polydentate.

Bidentate and polydentate ligands are also

called chelating agents because of their
ability to hold the metal atom like a claw (from
the Greek chele, meaning “claw”).
One example is ethylenediamine-
tetraacetate ion (EDTA), a
polydentate ligand used to treat
metal poisoning (Figure 3). Six
donor atoms enable EDTA to form a
very stable complex ion with lead. In Figure 3. EDTA complex of lead. The complex
this form, it is removed from the bears a net charge of -2 because each O donor
atom has one negative charge and the lead ion
blood and tissues and excreted from carries two positive charges. Only the lone pairs
the body. EDTA is also used to that participate in bonding are shown. Note the
clean up spills of radioactive metals. octahedral geometry around the Pb2+ ion.
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 Coordination (complex) compounds
Another important property of coordination compounds is the oxidation
number of the central metal atom. The net charge of a complex ion is the
sum of the charges on the central metal atom and its surrounding ligands. In
the [PtCl6]2- ion, for example, each chloride ion has an oxidation number of
-1, so the oxidation number of Pt must be +4. If the ligands do not bear net
charges, the oxidation number of the metal is equal to the charge of the
complex ion. Thus, in [Cu(NH3)4]2+ each NH3 is neutral, so the oxidation
number of Cu is +2.

Naming Coordination Compounds

The rules for naming coordination compounds are as follows:
1. The cation is named before the anion, as in other ionic compounds.
The rule holds regardless of whether the complex ion bears a net positive or
a negative charge. For example, in K3[Fe(CN)6] and [Co(NH3)4Cl2]Cl
compound, we name the K+ and [Co(NH3)4Cl2]+ cations first, respectively.
2. Within a complex ion the ligands are named first, in alphabetical order,
and the metal ion is named last.

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 3. The names of anionic ligands end with the letter o, whereas a neutral
ligand is usually called by the name of the molecule. The exceptions are
H2O (aqua), CO (carbonyl), and NH3 (ammine). Table lists some common
ligands.

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 4. When several ligands of a particular kind are present, we use the
Greek prefixes di-, tri-, tetra-, penta-, and hexa- to name them. Thus, the
ligands in the cation [Co(NH3)4Cl2]+ are “tetraamminedichloro.” (Note that
prefixes are ignored when alphabetizing ligands.) If the ligand itself
contains a Greek prefix, we use the prefixes bis (2), tris (3), and tetrakis
(4) to indicate the number of ligands present. For example, the ligand
ethylenediamine already contains di; therefore, if two such ligands are
present the name is bis(ethylenediamine).
5. The oxidation number of the metal is written in Roman numerals
following the name of the metal. For example, the Roman numeral III is
used to indicate the +3 oxidation state of chromium in [Cr(NH3)4Cl2]+,
which is called tetraamminedichlorochromium (III) ion.
6. If the complex is an anion, its name ends in -ate. For example, in
K4[Fe(CN)6] the anion [Fe(CN)6]4- is called hexacyanoferrate (II) ion.
Note that the Roman numeral II indicates the oxidation state of iron.
Table gives the names of anions containing metal atoms.

The inner sphere of the complexes are shown in the brackets, the
outside of brackets – outer sphere.
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The names of anions containing metal atoms:

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Structure of Coordination Compounds
In studying the geometry of coordination compounds, we often find that
there is more than one way to arrange ligands around the central atom.
Compounds rearranged in this fashion have distinctly different physical
and chemical properties.
Figure 4 shows four different geometric arrangements for metal atoms
with monodentate ligands.

Figure 4. Common geometries of complex ions.

In each case, M is a metal and L is a monodentate ligand.
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 In these diagrams, we see that structure and coordination number of the
metal atom relate to each other as follows:

Stereoisomers are compounds that are made up of the same types and
numbers of atoms bonded together in the same sequence but with different
spatial arrangements.
There are two types of stereoisomers: geometric isomers and optical
isomers. Coordination compounds may exhibit one or both types of
isomerism.
Note, however, that many coordination compounds do not have
stereoisomers.

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 Geometric Isomers

Geometric isomers are stereoisomers that cannot be interconverted without

breaking a chemical bond. Geometric isomers usually come in pairs. We
use the terms ‘cis’ and ‘trans’ to distinguish one geometric isomer of a
compound from the other.
Cis means that two particular atoms (or groups of atoms) are adjacent to
each other, and trans means that the atoms (or groups of atoms) are on
opposite sides in the structural formula. The cis and trans isomers of
coordination compounds generally have quite different colors, melting
points, dipole moments, and chemical reactivities.

cis-tetraamminedichlorocobalt (III) chloride (left)

and
trans-tetraamminedichlorocobalt (III) chloride (right)

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 Note that although the types of bonds are the same in both isomers
(two Pt—N and two Pt—Cl bonds), the spatial arrangements are different.

Figure 5 shows the cis and trans isomers of diamminedichloroplatinum (II).

Figure 5. The (a) cis and (b) trans isomers of diamminedichloroplatinum (II).

Note that the two Cl atoms are adjacent to each other in the cis
isomer and diagonally across from each other in the trans
isomer.
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 Optical isomers

Optical isomers are nonsuperimposable mirror images.

(“Superimposable” means that if one structure is laid over the other, the
positions of all the atoms will match.)

Like geometric isomers, optical isomers come in pairs. However, the

optical isomers of a compound have identical physical and chemical
properties, such as melting point, boiling point, dipole moment, and
chemical reactivity toward molecules that are not optical isomers
themselves. Optical isomers differ from each other in their interactions
with plane-polarized light.

Figure 6 shows the cis and trans isomers of

dichlorobis(ethylenediamine)cobalt (III) ion and their images. Careful
examination reveals that the trans isomer and its mirror image are
superimposable, but the cis isomer and its mirror image are not.
Therefore, the cis isomer and its mirror image are optical isomers.

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 Figure 6. The (a) cis and (b) trans isomers of
dichlorobis(ethylenediamine)cobalt (III) ion and their mirror images.

If you could rotate the mirror image in (b) 90° clockwise about the vertical
position and place the ion over the trans isomer, you would find that the
two are superimposable.
No matter how you rotated the cis isomer and its mirror image in (a),
however, you could not superimpose one on the other.
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 Stability constants
Thermodynamic stability of complex ion can be characterized by
stability or formation constant which is a thermodynamic property and may
be determined in terms of equilibrium species concentrations. In general
the complexation process may be discribed by stepwise formation process
as shown (charges omitted for the simplicity):
M + L → ML,
ML + L → ML2,
ML2 + L → ML3.
For these steps stability constants is determined by the expressions:
[ML] [ML 2 ] [ML3 ]
K1 = K2 = K3 =
[M][L] [ML][L] [ML 2 ][L]

For the overall process of ML3 formation [ML3 ]

M + 3L → ML3, β3 =
[M][L]3

the overall stability constant is used β3 = K1 ⋅ K 2 ⋅ K3

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 Coordination compounds
in living systems
Coordination compounds play important roles in the living on the Earth.
They are essential in the storage and transport of oxygen, as electron
transfer agents and as parts of enzymes, etc. As a ligands in these
compounds may be present different organic molecules: carbohydrates
and polysaccharides, aminoacids and proteins, nucleotides and nucleic
acids.
Amino acids contain a central carbon, called theacarbon, to which a
hydrogen atom and three substituent groups are attached: the amine
group (–NH2), a carboxylic acid group (–COOH), a side chain (–R) group
is unique for each amino acid. The general formula of amino acids is

H
H2N C COOH
R
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 Amino acids and their derivatives
as ligands
Polypeptides are formed through the
polymerization of any combination of the
20 naturally occurring amino acids.
Relatively short polypeptide chains have
important hormonal functions in
biological species.
Proteins are classified as polypeptide
chains exceeding 50 amino acids in
length, whereas enzyme molecules
usually contain more than 100 amino
acid residues.

Metal ion bonding modes to

amino acid residues in proteins
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 Nucleic acids and their derivatives
as ligands
Nucleic acids may be divided on two groups: ribonucleic acids (RNA)
and deoxyribonucleic acid (DNA).
Nucleic acids are polymeric molecules formed by nucleotides.
The nucleotide molecule includes nitrogenous base, sugar, and
hosphate unit.
Nitrogenous base plus sugar moiety are called nucleosides.

Nitrogenous bases of nucleic acids, common metal binding sites on

nucleobases are indicated by arrows.
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 Nucleic acids and their derivatives
as ligands

Nucleotides: adenosine triphosphate (ATP), deoxyguanosine monophosphate

(dGMP) and deoxythymidine diphosphate (dTDP)

Ribose and deoxyribose

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 Coordination compounds of Fe in
living systems
The porphine molecule forms an
important part of the hemoglobin structure.
Upon coordination to a metal, the H+ ions
that are bonded to two of the four nitrogen
atoms in porphine are displaced.
Complexes derived from porphine are
called porphyrins, and the iron-porphyrin
combination is called the heme group. The
iron in the heme group has an oxidation
number of +2; it is coordinated to the four
nitrogen atoms in the porphine group and
also to a nitrogen donor atom in a ligand
that is attached to the protein. The sixth
ligand is a water molecule, which binds to
the Fe2+ ion on the other side of the ring to
complete the octahedral complex.
Possible ways for molecular oxygen
to bind to the heme group in
hemoglobin 29
 Coordination compounds of Fe and
Mg in living systems
The heme group in hemoglobin. The Fe2+ ion is
coordinated with four N atoms of the porfirine cycle and
nitrogen atom of the heme group. The ligand below the
porphyrine is the histidine group, which is attached to the
protein. The sixth ligand is a water molecule.

The heme group in cytochrome c. The ligands above

and below the porphyrin are the methionine group and
histidine group of the protein, respectively.

The chlorophyll molecule, which is necessary for plant

photosynthesis, also contains the porphyrin ring, but in this
case the metal ion is Mg2+ rather than Fe2+.
The porphyrin structure in chlorophyll. The dotted lines
indicate the coordinate covalent bonds. The electron-
delocalized portion of the molecule is shown in color.
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 References
¾ Chang R. Chemistry. 10-th edition. NY: McGraw-Hill,
2010. 1170 p.
¾ Chang R. General Chemistry: The Essential Concepts. 6-
th edition. NY: McGraw-Hill, 2011. 853 p.
¾ Crichton R.R. Biological Inorganic Chemistry: An
Introduction. Amsterdam: Elsevier, 2008. 369 p.
¾ Roat-Malone R. M. Bioinorganic Chemistry: A Short
Course. John Wiley & Sons, 2002. 348 p.
¾ S. V. Eltsov, N. A. Vodolazkaya. Practical Medical
Chemistry: manual / Kh.: V. N. Karazin Kharkiv National
University, 2018. 196 p.

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