Lecture 3 - Molecular Interactions

8/18/2019 Lecture 3 - Molecular Interactions

1/33

Molecular Interactions

Eastern Screech Owl


2/33

Molecular Interactions

• Ionic interactions

• Covalent interactions

• Hydrogen Bonds

• Van der Waals Interactions

• Hydrophobic Interactions


3/33

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 atomsThis 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 electrontransfer (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.


4/33

Ionic Bonds

• Your textbook calls them electrostatic interactions. They are sometimes also

called: charge-charge interactionsion-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 engagein ionic interactions (so it doesn’t form ionic bonds!).


5/33

Consider NaCl, common table salt:


6/33

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 andhelp stabilize DNA, RNA, and protein molecules.


7/33

Type Bond Strength (kJ/mol)

Covalent >210

Ionic 4-80

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.

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


8/33

Notice that the non-metals include the elements most abundant in living things.

CHNOPS

Lets consider Carbon…


9/33

++

++

++- -

-

--

-

+-

Carbon atom

(6 protons, 6 neutrons

6 e-)

Hydrogen atom

++

++

++--

-

--

-

CH4, methane

+ -

+

-

+

-

+-

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=cy9it8yu4JQ8oM&tbnid=IVY7H4MZ5J58zM:&ved=0CAUQjRw&url=http://commons.wikimedia.org/wiki/File:Methane-2D-square.png&ei=EmMqUri2PIGk2gWCnIGQCQ&bvm=bv.51773540,d.aWc&psig=AFQjCNE2PN_yIqgzoCj2haufp_dehvgziA&ust=1378593489073103


10/33

+-++

++

++--

-

--

-

CH4, methane

+ -

+

-

+

-

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

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=sOVGxj9y7VAlAM&tbnid=XAQHxPtD3dd8VM:&ved=0CAUQjRw&url=http://www.masterorganicchemistry.com/2010/08/14/from-gen-chem-to-org-chem-pt-7-lewis-structures/&ei=V3crUsyKM8PV2AWj-YGQBQ&psig=AFQjCNHc2A9cI_QO0qanRgKl3NsAFAog4Q&ust=1378666649074497


11/33


12/33

This is because the electron pairs

in each bond repel each other.

109.5o is the maximum separationof bonds.

Minimal repulsion means the

energy of the system (the molecule)

is lowest, and most stable.

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=EL6bGiGrYmLJbM&tbnid=3N1mKBAP7hFF6M:&ved=0CAUQjRw&url=http://itech.dickinson.edu/chemistry/?cat=67&ei=fHkqUpqGM8KE2wX2goHYDQ&psig=AFQjCNF8K-W31QtIxSWm6q2K0TIhf4zCLw&ust=1378600836280904http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=6yVN7vTiYzowEM&tbnid=NE_DUNm8G-U0RM:&ved=0CAUQjRw&url=http://chemistry.tutorvista.com/inorganic-chemistry/ch4-molecular-geometry.html&ei=xHgqUozpIajv2QWV9IDYDQ&psig=AFQjCNF8K-W31QtIxSWm6q2K0TIhf4zCLw&ust=1378600836280904


13/33

Carbon can covalently bond with itself as well

C-C bond # pairs length (pm) Bond strength (kJ/mol)

single 1 154 355

double 2 134 614

triple 3 120 839

Bond Strength

the amount of energy

required to break thebonds

(ethane) (ethene) (ethyne/acetylene)


14/33

e-

transferred

e- shared

evenlye- shared

unevenly

ionicinteraction

polar covalentbond

covalentbond

Periodic Table - Electronegativity Trends Electronegativity isthe propensity for

an atom to attract

electrons to

itself


15/33

Electronegativity difference between interacting atoms defines the bond

3.5

2.1

1.0

3.5

3.53.5

Electronegativity difference

O-Ca 3.5 - 1.0 = 2.5

O-H 3.5 - 2.1 = 1.4

O-O 3.5 - 3.5 = 0

0-0.4 Covalent bond

0.4- 2.0 Polar covalent bond

>2.0 Ionic bond

+-

δ+δ-


16/33

Periodic Table - Electronegativity Trends

Characterize bonds between following elements as ionic, polar

covalent, covalent:

a) N-H

b) O-H

c) C-H


17/33

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.


18/33

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:

• 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)

δ- δ+

O H this separation of partialcharge is called a DIPOLE


19/33

• Hydrogen bonding involves a DONOR where the H atom has partial

+ charge and an electronegative ACCEPTOR group

δ- δ+

donor acceptor

dashed yellow lineis the hydrogen bond

δ-


20/33

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCJPH0IDu-McCFcMYHgodk-gGmQ&url=http://academic.brooklyn.cuny.edu/biology/bio4fv/page/molecular%20biology/dna-structure.html&psig=AFQjCNFcPelkdJQvHYaH_EbMVeUrxTAYSQ&ust=1442400272342210


21/33

• 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.

• 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)

base-pairing between

guanine and cytosine in DNA

is mediated by 3 H bonds


22/33

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?

V d W l I t ti


23/33

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


24/33

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 permanentdipole 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.


25/33

The importance of van der Waals interactions

in the macroscopic world

How do Geckos adhere to smooth surfaces?

Tokay Gecko (Gekko gecko)Geico Gecko


26/33

Proc Natl Acad Sci U S A. Dec 19, 2006; 103(51): 19320 –19325.there are about 1 million spatulas per foot pad

H d h bi I i


27/33

Hydrophobic Interactions

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

•

Consider mixing oil and water. Oil molecules are called APOLAR because theycannot 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.

T B d St th (kJ/ l)


28/33

Type Bond Strength (kJ/mol)

Covalent >210

Ionic 4-80

H bonds 4-20

Van der Waals 2-4

Hydrophobic 3

• 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.

Relative strengths ofbonding interactions


29/33


30/33

The 6 p-orbital electrons form a system of π (pi) bonds where the electrons are

de-localized around the ring

http://localhost/var/www/apps/conversion/tmp/scratch_7//upload.wikimedia.org/wikipedia/commons/9/90/Benzene_Orbitals.svghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.png


31/33

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 π-π or π-stacking interactions

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=FL9PKQwl9gegtM&tbnid=s0lyvhg0i-lTKM:&ved=0CAUQjRw&url=http://pipe.ibibiosolutions.com/Aromatic-Aromatic.html&ei=oLkrUrbgNafI2wW-_IGYBw&bvm=bv.51773540,d.aWc&psig=AFQjCNEFrn6fLXSEN_zIlDkcVxrbGqAXNw&ust=1378683251022333http://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.png


32/33

Na+

These are called cation-π interactions

Interactions involving the π system of

aromatic structures are importantin the structures of nucleic acids and

proteins

http://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=v85Ir26cvKckWM&tbnid=aBYlAQ1s1FKVKM:&ved=0CAUQjRw&url=http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-A/arginine.html&ei=k74rUt6iNqLD2wXn_YHwDQ&bvm=bv.51773540,d.aWc&psig=AFQjCNGj4FcpKp8dPLCEQxfSAMu4ttgENA&ust=1378684930035280http://en.wikipedia.org/wiki/File:Benzene_Quadrupole.pnghttp://en.wikipedia.org/wiki/File:Benzene_Quadrupole.png


33/33

Lecture 3 - Molecular Interactions

Documents

Transcript of Lecture 3 - Molecular Interactions