BedokFunland JC's 'A' Levels H2 Chemistry Notes on :
Chemical Bonding (intermolecular interactions) and Proteins
(tertiary structure)
Many Singapore JC teachers still subscribe to the outdated idea
of regard van der Waals strictly as purely instantaneous dipole -
induced dipole between non-polar molecules or parts of molecules.
This is outdated, and the correct updated version that Cambridge
uses today is : Van der Waals forces are a collective term for all
3 types : instantaneous dipole - induced dipole, permanent dipole -
permanent dipole, and permanent dipole - induced dipole.
Increasing number of electrons, and/or increasing size of
atom/ion/molecule, and/or increasing polarizability of electron
clouds; any and all of these (which are intimately related) will
result in greater magnitude of the dipoles (whether permanent or
induced) and partial charges, and hence stronger or more extensive
van der Waals interactions, stronger instantaneous dipole - induced
dipole interactions, stronger permanent dipole - permanent dipole
interactions, and stronger permanent dipole - induced dipole
interactions, all of these.
For hydrophobic interactions of non-polar or weakly polar 'R'
groups (ie. groups not capable of hydrogen bonding or ionic
bonding) of amino acid residues of a polypeptide chain in a protein
: as hydrogen bonds are significantly stronger, water would rather
hydrogen bond amongst themselves (because the stronger the bonds or
interactions formed, the more stable the resulting
structure/product/species), hence pushing or repelling away
non-polar 'R' groups. These non-polar 'R' groups subsequently get
pushed until they come within close proximity of each other,
whereupon the consequent van der Waals forces of attraction
(whether they be permanent dipole - permanent dipole, or permanent
dipole - induced dipole, or instantaneous dipole - induced dipole)
will hold these non-polar or weakly polar 'R' groups together,
contributing to the protein's tertiary structure.
The exam-smart student will include both key phrases
"hydrophobic" and "van der Waals" in his answer on the nature of
the interaction betwen non-polar or weakly polar 'R' groups in a
protein.
Disulfide bridges, or disulfide bonds, are covalent bonds
between two S atoms, usually present in proteins as occurring
between cysteine amino acid residues of the polypeptide. These are
the covalent bonds that are involved in the perming and rebonding
of hair. (the term "rebond" means to recreate the disulfide
covalent bonds that allow hair to hold its shape, whether it be
curly or straight.)
If your hair is curly, the disulfide bonds are cleaved (via
adding of hydrogen; a reduction process for sulfur since the OS of
the sulfur atoms is decreased; since sulfur is more electronegative
than hydrogen), then your hair is straightened, and the disulfide
bonds are recreated (hence "rebond") (via removal of hydrogen; an
oxidation process for sulfur since the OS of the sulfur atoms are
increased; since sulfur and sulfur have equal electronegativity)
these newly recreated disulfide bonds hold your hair straight after
a rebonding session.
Hydrogen bonds, belong to a class on its own. They are stronger
than permanent dipole - permanent dipole forces of attraction, but
weaker than covalent bonds. They are therefore neither, but possess
some characteristics of both.
Hydrogen bonds have similar strength to ion-dipole attractions
(of which there are two types : ion - permanent dipoles are
naturally usually stronger than ion - induced dipoles), though
(depending on the charge densities of the ions involved) ion -
dipole attractions are usually slightly stronger than hydrogen
bonds.
An illustrative example of this, is that phenol precipitate or
benzoic acid precipitate, dissolves when aqueous sodium hydroxide
is added : deprotonation of phenol or benzoic acid, which only had
limited hydrogen bonding with water, results in the phenoxide anion
or benzoate anion which experiences the somewhat stronger (than
hydrogen bonding) ion - (permanent) dipole interactions with water,
allowing the precipitate to dissolve. An upgrade in the class of
inter-species physical interactions, so to speak, resulting in
greater solubility in water.
An interesting case in point, would be whether amino-acids in
zwitterionic form have hydrogen bonds or ionic bonds with each
other. The answer is : the forces of attraction that results
between the R-NH3+ group on one zwitterionic amino acid, and the
R-COO- group on the next zwitterionic amino acid, may be regarded
as either. Again, the exam-smart candidate would write both, but
with brief qualifications or explanations, so the examiner
understands, "this candidate really knows his stuff!" and award the
full marks.
The interaction between R-NH3+ and R-COO-, may be regarded as
hydrogen bonding, because the interaction is between a partially
positively charged hydrogen on R-NH3+ and a formally negatively
charged oxygen on R-COO-. But because R-NH3+ may also be regarded
as cationic (though the positive formal charge is on N, not H; more
on that in a while) and the R-COO- group may be regarded as
anionic; hence one may argue ionic bonding occurs between
zwitterionic amino acids. Either way, this explains why amino acids
are least soluble in water, at their isoelectric point.
Related to the above discussion, is whether ammonium cations and
hydroxide anions experience hydrogen bonding or ion-dipole
attractions with water. Both are acceptable (some chemists would
label such as the former, while other chemists would label such as
the latter), and the exam-smart student will again, write both, but
with brief qualifications and explanations.
Technically, NH4+ experiences hydrogen bonding rather than
ion-dipole interactions with water. This is because :
1) the tetrahedral geometry of the NH4+ ion will result in water
molecule physically interacting with the partially positively
charged H atoms, rather than the N atom.
2) the positively formally charged N atom would be even more
strongly electron-withdrawing by induction, resulting in a larger
magnitude of a partial positive charge on the H atoms, resulting in
stronger hydrogen bonding with water (compared to say, ammonia with
water).
The hydroxide ion, consists of a partially positively charged H
atom, and a formally negatively charged O atom. The H atom
therefore experiences hydrogen bonding with water molecules, while
the O atom experiences what may be regarded as ion - permanent
dipole interactions with water, or what may be regarded as
especially strong hydrogen bonding with water.
For hydrogen bonding to occur, there must be :
#1 - a partially positively charged H atom; the magnitude of the
partial positive charge must be significant enough, this occurs
naturally when H is covalently bonded to electronegative F, O or N
atoms.
#2 - a partially or formally negatively charged F, O or N atom with
at least one available lone pair; because hydrogen bonding is
mainly electrostatic in nature, hence there needs to be a partial
or formal negative charge on the F, O or N atom for hydrogen
bonding to occur with the partially positively charged H atom.
Because hydrogen bonding is also somewhat covalent in nature, there
needs to be at least one available lone pair for donation of the
hydrogen bond (which may be viewed as almost dative in nature, but
not quite, since H atoms only has one 1S orbital and cannot violate
its duplet, ie. a H atom can have at most only one lone pair or one
bond pair at any time).
Therefore, the negatively formally charged O atom in hydroxide
ion experiences particularly strong hydrogen bonding, which
accordingly may arguably also be labelled as an ion - permanent
dipole interaction.
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Warning :
Being exam smart, means to write both possible answers if the
question is ambiguous, or the context or concepts involved, allow
for such. This will greatly increase the exam candidate's chances
of successfully scoring the allocated marks. However, the exam
smart student *must* qualify and explain (at least briefly) why
both answers may be argued to be correct or relevant. If this
qualification or explanation is not done, the examiner/marker may
think the student is trying to smoke/bluff his way through, by
giving multiple answers to a single question; which will result in
the student losing the marks.
Example of an ambiguous question : "What is the product formed
when the following compound is reacted with KMnO4(aq)?".
The exam smart candidate would write : "Dear Examiner Sir/Mdm,
because the question failed to specify umambiguously the conditions
(eg. temperature) at which the reaction is carried out, therefore I
will explore both alternative possibilites as follows."
"If hot, concentrated, acidified KMnO4(aq) is used, oxidative
cleavage of the alkene double bond would occur, and the structure
of the product would be... If cold, dilute, alkaline KmNO4(aq) is
used, then two OH groups would be added across the alkene double
bond, and the structure of the product would be..."