Molecular Interactions

Eastern Screech Owl

Molecular Interactions
Ionic interactions

Covalent interactions
Hydrogen Bonds

Van der Waals Interactions

Hydrophobic Interactions

Chemical Bonding
Elements that have a completely filled outermost (valence) electron shell
belong to family called Noble gases (He, Ne, Ar, etc.)
Filled valence electron shells represent the most energetically stable arrangement
Other elements attempt to acquire this stable arrangement by sharing or
transferring electrons with other atoms
This is the basic reason why chemicals react with one another.
Electron transfer or sharing results in the formation of chemical bonds.
Sharing of electrons (covalent bond formation) only occurs when electron
transfer (ionic bond formation) is highly unfavorable
Ionic bonds and covalent bonds are the extremes along a continuum of electron
sharing.
covalent bonds in which there is uneven sharing of electrons are called Polar.

Ionic Bonds

Your textbook calls them electrostatic interactions. They are sometimes also
called: charge-charge interactions
ion-pairing interactions
salt bridges (when occurring in proteins between charged amino acids)
A charged group on one molecule, or a charged atom, is attracted to and binds
with a molecule carrying the opposite charge.

Ionic bonds form only when an element is able to lose one or two (rarely 3) electrons
and the other element is able to accept 1 or 2 (rarely 3) electrons.
Carbon, for example, would need to lose or gain 4 electrons to engage
in ionic interactions (so it doesnt form ionic bonds!).

Consider NaCl, common table salt:

NaCl is a solid where Na cations and Cl anions are held together by

charge-charge interactions in a crystalline array.

When exposed to water, H2O molecules solvate the ions and shield their charges from
each other.
Ionic interactions are very important in biology (recall the 5 essential ionized elements
required by life (Ca2+, K+, Na+, Mg2+, Cl-). These play a role in enzymatic reactions and
help stabilize DNA, RNA, and protein molecules.

Covalent Bonds
Result from electron sharing rather than transfer.

Two (or more) atoms may share electron pairs to attain the energetically
favorable Noble gas configuration in their valence shells.
Covalent bonds are much stronger than ionic bonds.

Type

Covalent
Ionic

Bond Strength (kJ/mol)

>210
4-80

The non-metal elements are much more likely to engage in covalent bond formation.

Notice that the non-metals include the elements most abundant in living things.
CHNOPS
Lets consider Carbon

-+

+ ++
+ +

Carbon atom
(6 protons, 6 neutrons
6 e-)

Hydrogen atom
+

--

--

-+

+ ++
+ +

-+
CH4, methane

Note that the structure of methane can also be drawn as a Lewis structure

--

--

-+

+ ++
+ +

-+

CH4, methane

- -

Various ways of depicting

methane structure
Note geometry - methane
forms a tetrahedral shape

This is because the electron pairs

in each bond repel each other.
109.5o is the maximum separation
of bonds.

Minimal repulsion means the

energy of the system (the molecule)
is lowest, and most stable.

Carbon can covalently bond with itself as well

(ethane)

(ethene)

(ethyne/acetylene)

C-C bond

# pairs

length (pm)

Bond strength (kJ/mol)

single
double
triple

1
2
3

154
134
120

355
614
839

Bond Strength
the amount of energy
required to break the
bonds

etransferred
ionic
interaction

e- shared
unevenly
polar covalent
bond

Periodic Table - Electronegativity Trends

e- shared
evenly
covalent
bond
Electronegativity is
the propensity for
an atom to attract
electrons to
itself

Electronegativity difference between interacting atoms defines the bond

0-0.4
0.4- 2.0
>2.0

Covalent bond
Polar covalent bond
Ionic bond

3.5
3.5

3.5

Electronegativity difference

+
1.0

O-Ca

3.5 - 1.0 = 2.5

2.1

O-H

3.5 - 2.1 = 1.4

3.5

O-O

3.5 - 3.5 = 0

Periodic Table - Electronegativity Trends

Characterize bonds between following elements as ionic, polar

covalent, covalent:

a) N-H
b) O-H
c) C-H

Other Non-covalent Interactions

1. Hydrogen bonds (H bonds)
2. Van der Waals interactions
3. Hydrophobic interactions
All of these are weaker than covalent bonds, but are very important
in biological structures.

Hydrogen Bonds
A functional group can become a Hydrogen bond donor whenever an H atom is
covalently bonded to an atom that is very electronegative (such as N or O)
because the H atom takes on a partial + charge, as shown below:

this separation of partial

charge is called a DIPOLE

an unequal sharing of electrons: electrons spend more time around

the strongly electronegative Oxygen making it more negative and the
hydrogen more positive (i.e. polar covalent bond)

 Hydrogen bonding involves a DONOR where the H atom has partial

+ charge and an electronegative ACCEPTOR group

dashed yellow line

is the hydrogen bond

donor

acceptor

 Hydrogen bonding is an extremely important form of bonding in biological systems

They are weaker than covalent bonds, but numerous bonds between molecules
contribute great stability.

base-pairing between
guanine and cytosine in DNA
is mediated by 3 H bonds

Hydrogen bonding contributes (a little) to formation of the DNA double helix.

They are strong enough to impart stable interaction but weak enough to be broken
when necessary (e.g. during DNA replication)

Questions: In the above diagram

1. Which groups are the H bond donors and which are the H bond acceptors?
2. Can you assign partial charges to each atom involved in the H bonds?
3. What are the names of the groups participating in the H bonding?

Van der Waals Interactions

Van der Waals forces are relatively weak but important electrostatic interactions
that arise when neutral (uncharged) groups carrying a dipole
approach each other.
This can occur even between molecules that do not have a permanent dipole
because of random fluctuations in the distribution of electrons around atoms.
They are incredibly important to the structure of all large molecules like DNA and
proteins and to all matter.
Maximum interaction strength occurs when groups are separated by a precise
distance called the van der Waals distance.
Too far apart = no interaction
Too close = repulsion takes over

Three types of Van der Waals Interactions

1. Dipole-dipole. Occur between
molecules containing permanent dipoles.
Hydrogen bonds are a special type of this
interaction.

2. Dipole - induced dipole. A permanent

dipole in one molecules induces dipole in
another resulting in attractive force.

3. Induced dipole-induced dipole. Random

fluctuations in electron distribution in one
molecule sets up temporary dipole. This induces
dipole in adjacent molecule, resulting in
interaction. Weak but very important to the
cohesiveness of everything.

The importance of van der Waals interactions

in the macroscopic world

Geico Gecko
Tokay Gecko (Gekko gecko)

How do Geckos adhere to smooth surfaces?

there are about 1 million spatulas per foot pad

Proc Natl Acad Sci U S A. Dec 19, 2006; 103(51): 1932019325.

Hydrophobic Interactions
Hydrophobic interactions occur between molecules that cannot interact with water.

Consider mixing oil and water. Oil molecules are called APOLAR because they
cannot interact with water (through Hydrogen bonding).
They therefore coalesce together (interacting with each other through
Van der Waals forces) and in doing so minimize their surface area contact
with water molecules.

Hydrophobic interactions (should really be called the Hydrophobic Effect) are

very important to structure of DNA and proteins and membranes in cells.

Type
Covalent

Bond Strength (kJ/mol)

>210

Ionic

4-80

H bonds

4-20

Van der Waals

2-4

Hydrophobic

Relative strengths of
bonding interactions

Weak though they may be, non-covalent interactions are integral to structure
and function of biomolecules like nucleic acids and proteins and many
other structures and processes in biological systems.
We will return to these interactions many times when we consider the structures
of water, nucleic acids, and proteins in future classes.

The importance of aromaticity or resonance structures

in biological structure

Adenine

Benzene

Note resonance structures represent molecules

that cannot be satisfactorily represented by a
single Lewis structure.

For both adenine and benzene, neither of the above structures exist.
In other words, they are not mixtures of two forms but rather a hybrid.
Resonance hybrids occur because they have lower energy (are more stable) than are
either of the two theoretical structures above.
Electrons are shared or distributed over as many atoms that can accept them.

The 6 p-orbital electrons form a system of (pi) bonds where the electrons are
de-localized around the ring

An aromatic ring has a net negative charge above

and below the plane of the ring.
It has a net positive charge around perimeter of ring

these are called - or -stacking interactions

Na+

These are called cation- interactions

Interactions involving the system of
aromatic structures are important
in the structures of nucleic acids and
proteins

A word on the textbook

In your textbook, the topics we are covering are addressed.

Note that much more detail is presented in class than in textbook
-this is why you should attend class.
on the matter of types of molecular interactions, textbook describes these
using the structure of DNA to illustrate the interactions.
We will talk about the structure of DNA in a later lecture, at which time we
will once again talk about some of these interactions in that molecular context.
In other words, the content of the course does not follow the textbook in lock-step.