Hydrogen Bonding

The Essence of Life

 Introduction:
We are going to speak about some of the aspects of hydrogen bonding:
 Formation and Evidence.
 Occurrences in Nature (Including Water, DNA and Proteins).
 Applications in the field of medicine.
Section 1:-
Formation and Evidence
 Formation Of A Hydrogen Bond:
A Hydrogen bond is a special type of dipole-dipole attraction that
occurs when:
 A hydrogen atom is bonded to a highly electronegative atom such as
Nitrogen, Oxygen or Fluorine.
 This hydrogen atom is in close vicinity to another molecule containing a
Nitrogen, Oxygen or Fluorine atom with a lone pair.

An example of a hydrogen bond:

Hydrogen bonds are one of the strongest types of intermolecular

forces. However, they are weak relative to ionic and covalent bonds.
 Evidence Of Hydrogen Bonding:
One of the biggest proofs of the existence of hydrogen bonding is the
abnormally high boiling points of compounds in which it occurs:

Hydrides of atoms that are highly electronegative have higher boiling points
compared to hydrides that have higher molecular weight, and the only
explanation is the presence of an extra intermolecular force.

See Graph in next slide for comparison between boiling points of hydrides
formed by elements in the same group.
It should be noted that the reason why water has a higher boiling than hydrogen
fluoride, even though fluorine is more electronegative than oxygen, is due to the
fact that each water molecule forms 2 hydrogen bonds while each hydrogen
fluoride molecule only forms 1.
Section 2:-
Hydrogen Bonding In Water
Uniqueness Of Water:
Hydrogen bonding is most prominently found between water
molecules, and this provides water with a number of unique
properties that make it undoubtedly the predominant
biochemical on Earth since without it life would not exist.
Some of the special abilities of water:
 A Universal Solvent.
 High Specific Heat Capacity.
 Less Dense as a Solid than as a Liquid.
 High Surface Tension and Cohesion.
A “Universal” Solvent:
Water is always described as a wonderful solvent, which enables it
to act as a transportation and reaction medium.
For ionic and polar substances the above statement is true,
because water molecules are attracted to these particles,
surrounding and separating them from each other. This allows
particles to react with each other, and allows for movement of
these materials in animals (blood and lymph), and in plants
(vascular tissues).

How water molecules dissolve Sodium Chloride:

For non-polar substances water is a terrible solvent, simply

because they are not attracted to each other. However, this is to
our benefit because if lipids were soluble in water, plasma
membranes would simply disintegrate.
High Specific Heat Capacity:
This simply means that the temperature of water does not
change easily.
As we saw before, hydrogen bonding is an additional
intermolecular force in the case of water, and this makes its
molecules more attracted to each other, thus more energy is
required to overcome these forces to allow the molecules to
move at a faster rate and cause a rise in temperature.
This allows water to store more energy, and this is vital for living
organisms:
 Keeps their temperatures more constant, not easily affected by
the surrounding environment, this results in metabolic reactions
going at a relatively regular rate.
 Moreover, this provides stable habitats for aquatic organisms, as
the temperatures of large bodies of water, such as oceans and
seas, do not change significantly, by the presence or absence of
the sun.
Less Dense as a Solid than as a Liquid:
This is because as water is cooled (Below 4 ℃ ):
 Molecules are less able to overcome hydrogen bonds between them.
 A crystalline tetrahedral structure, maintained by the hydrogen
bonds, starts to form.
 This structure is less dense than water due to an increase in the
amount of empty space between the molecules.

Comparison between arrangement of molecules

in ice and water:
This causes ice to float on water and therefore act as an insulator of the
water below it. This is particularly important in the north and south
poles, where the bodies of water do not freeze, making organisms in
those regions more likely to survive in the harsh cold conditions.
High Surface Tension and Cohesion:
Hydrogen bonding makes water molecules stick to each other –
which we can describe as “Water molecules are cohesive”.
This property is utilized in nature, examples include:
In plants, as why long unbroken columns of water can move
from the roots up to the leaves through vascular tissues.
Cohesion allows for high surface tension at the surface of
water, which some tiny organisms, such as pond skaters,
exploit to make use of the surface as a habitat.
Section 3:-
Hydrogen Bonding In DNA
Basic Structure of a DNA molecule:
A polymer made up of many repeating units called nucleotides,
where each nucleotide consists of:
 Phosphate Group
 Deoxyribose Sugar
 Nitrogenous base – Either Adenine, Guanine, Thymine or Cytosine
It is made up of two chains of nucleotides, connected by hydrogen
bonds.
 Description of the Hydrogen Bonds in DNA:
The hydrogen bonds occur between the nitrogenous bases:
 Adenine pairs with Thymine with 2 hydrogen bonds.
 Guanine pairs with Cytosine with 3 hydrogen bonds.

These hydrogen bonds are much weaker compared to the covalent bonds
present in each strand of the molecule. However, this is advantageous as it
makes the process of replication easier.
Hydrogen bonds are the main cause of the double helix structure of DNA,
which stabilizes the molecule preventing it from being easily destroyed.
Section 4:-
Hydrogen Bonding In Proteins
Formation of the Secondary Structure:
After the amino acids combine to form a polypeptide, these residues
interact by forming hydrogen bonds; the oxygen from –CO- group of
one amino acid forms a hydrogen bond with the hydrogen of the –NH-
group of another amino acid.
This bonding results in the formation of one of two shapes:
 An -helix, where the polypeptide chain will turn around itself.
 A -pleated sheet, where the polypeptide will fold.

These structures stabilize the polypeptide.

 Formation of the Tertiary Structure:
Hydrogen bonds are also involved in the formation of the three-
dimensional coiling of the already folded polypeptide.
This happens between polar side chains of the amino acid residues, and
leads to further stabilization of the protein.

Bond 2 in the figure resembles a hydrogen

bond in tertiary structure:
Section 5:-
Hydrogen Bonding In Drugs
 How are Hydrogen Bonds Utilized in Drugs?
Drugs target macromolecules in the body, such as nucleic acids and proteins.
Drugs bind to their targets molecules in regions known as binding sites or
receptors. One way to bind to receptors is through hydrogen bonding as
shown in the diagram.
In this example, target molecule
is Hydrogen Bond Acceptor (HBA) and
drug is Hydrogen Bond Donator (HBD).

Since hydrogen bonding is very common in the human body, Pharmacists have
found ways to use the properties of hydrogen bonds to elicit the same
reaction of natural ligands but with stronger effects. This can be done by
achieving the desired strength and bond length of hydrogen bonding to get
the intended effect of the drug.
Conclusion:
We have seen that hydrogen bonding is one of the most crucial
aspects of life, as it contributes to abilities of water, and stabilizes
structures of macromolecules such as proteins and DNA.
And how it has also been utilized in the field of pharmacy to
control the effects of many synthesized medicines.
 References:
 Cambridge International AS and A Level Biology Coursebook / Mary
Jones, Richard Fosbery, Jennifer Gregory and Dennis Taylor / Oriental Press
/ Dubai, United Arab Emirates / Fourth Edition / 2015.
 Cambridge International AS and A Level Physics / Mike Crundell, Geoff
Goodwin, Chris Mee, Wendy Brown and Brian Arnold / Hodder Education /
United Kingdom / Second Edition / 2014.
 Cambridge International AS and A Level Chemistry Coursebook / Lawrie
Ryan and Roger Norris / Cambridge University Press / United Kingdom /
Second Edition / 2014.
 Principles of Biochemistry / Albert L. Lehninger, David L. Nelson and
Michael M. Cox / W. H. Freeman / United States of America / Fourth Edition
/ 2004.
 http://mysite.science.uottawa.ca/sites/default/files/sgambarotta/CHM%2
01311F/Course%20info/a-CHM1311%20Syllabus%202016.pdf
 https://pharmafactz.com/introduction-to-medicinal-chemistry/
 References:
 https://chem.libretexts.org/Textbook_Maps/Physical_and_Theoretical_Che
mistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical
_Chemistry)/Physical_Properties_of_Matter/Atomic_and_Molecular_Propert
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 https://biology.stackexchange.com/questions/23851/importance-of-
double-helix-dna-structure
 http://www.els.net/WileyCDA/ElsArticle/refId-a0003011.html
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