Hi Nelexus, glad to hear you chose to read Chemistry in the
University. Btw, while both NUS and NTU Chemistry are
(approximately) equally good, the Science bookstore at NUS is
better stocked compared to the Science bookstore at NTU. Fyi.
Generally (for everyone reading this), please do not PM me
Chemistry questions (PM me only if you're interested in joining my
BedokFunland JC tuition), but post Chemistry questions on the forum
for discussion so that everyone can participate, learn and benefit
together.
Next, for Uni level Chemistry questions, please do not post them
here, as my professional interest (ie. my job) is specifically A
level Chemistry.
But no worries (this suggestion is for all JC graduate students
taking Chemistry or Chemistry related courses in the University),
I'll recommend you an excellent Chemistry forum (probably the best
on the internet) where you can get help for all your Chemistry
questions, all the way to Masters, PhDs and professional Chemical
industry questions.
Presenting.... the Chemical Forums (yeah that's the name,
strictly functional and down-to-business, nothing flowery or
fanciful).
http://www.chemicalforums.com/
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Nelexus PMed me :
Hi Ultima, I have
a few Chemistry questions that I would like to clarify with you. Am
a graduated JC student but intending to read chemistry in uni. So I
have been reading up on Chemistry before Uni starts. Some of the
questions I am asking will be covering advance concepts far beyond
the h2 chem syllabus.
1. Resonance Vs
Conjugation
What is the
difference between resonance and conjugation? From what I've read
online, a continuous overlapping of adjacent p orbitals forms a
conjugated system. The overlapping of p orbitals allows electrons
to "move" in the conjugated system, resulting in delocalisation of
electrons in that conjugated system. This is illustrated by the
diagram below I've picked up from the internet.

Therefore, from this
scenario above, conjugation allows resonance to
occur.
Now consider the
conjugate base of benzoic acid and pyruvic acid. I believe they are
all conjugated system. The thing is, for the benzoate ion, the
electrons on oxygen in the carboxyl group cannot be delocalised
into the benzene ring no matter how I draw, thus no resonance
structure forms arises for the benzoate ion. Likewise for the
pyruvic acid, the electrons cannot be delocalised into the ketone
group. So while they are conjugated, there are no resonance
structure for . This sounds abit strange, considering that for a
conjugated system with p orbitals overlapping with each other,
electrons can "move" around the system, yet this is not possible
for the electrons on the oxygen atoms of benzoate and pyruvate ion.
My point is ilustrated below (pardon the big image)

For this
amine below that I've drawn, there's a conjugated system and the
delocalisation of electrons can happen. My confusion is tha
tlogically, conjugation which is the overlapping of p
orbitals, should allow electrons to delocalise, and thus entails
resonance. Yet this is not the case for some system.
Why?

2. pH of equivalenve
points of polyprotic acids
The diagram below
shows the titration curve of sulfurous acid with sodium
hyroxide.

For he second
equivalence point where only SO3 2- is present, the equivalence
point can simply be obtained by obtaining the Kb of SO3 2-, and
then find [OH-] using Kb = [OH-]^2/ [SO3 2-] am I right?
Now the tricky part
is the first equivalence point. The species present in the first
equivalence point is HSO3- which is an amphoteric species. Meaning
HSO3- can act both as a base and an acid as follow
HSO3 - + H2O
--> SO3 2- + H3O+ Ka
HSO3 - + H2O --> H2SO3 + OH- Kb
Is it possible to
calculate the pH of the first equivalence point?
I understand that for
amino acids, theres this formula pH = 1/2 (pka1+pka2) which is used
for calculating the pI and the so called equivalence point as shown
below.

Logically amino acids
are polyprotic acids as well, so would the same formula work? Or do
I have to physically inspect whether Ka or Kb is larger, and then
proceed to using the method I used for finding the second equiv
point?
3. Amino
Acids
For amino acids, why
is it that amino acids always exist in its protonated form? For
example, in the titration of amino acids, the major species in the
beginning is always NH3+ -R - COOH at a low pH. Should it be the
case that say in the laboratory, the amino acids you work with are
powders in the form of zwitterions NH3+ - COO- and then when you
add it into water, the carboxylate group gets protonated and a
basic solution is formed. Yet this is not the case
for the examples I've seen on the internet, where the amino acids
exist as NH3+ - R - COOH at pH < 7?
Secondly, to say the
isoelectronic point of an amino acids, does it mean to have equal
concentrations of both the cation and anion, or the maximum
concentration of the zwitterions? Some textbooks obtain the formula
of pH = 1/2 (pka1+pka2) using the assumption that [cation] =
[anion], which I think does not make sense.
I quote from
Essentials of Organic Chemistry by Dewick
"The pH at which the
concentration of the zwitterion is a maximum is equal to the
isoelectric point pI, strictly that pH at which the
concentrations of cationic and anionic forms of the amino acid
are equal. With a simple amino acid, this is the mean of the
two pKa.
in the derivation, how is the statement " cation = anion " true?
Doesn't the dissociation of amino acids occur stepwise, meaning
cation --> pka1 where cation = zwitterion --> equivalence
where only zwitterion --> pka2 where zwitterion = anion -->
2nd equivalence where there is only anion.
I understand that these questions are far beyond the h2 chem
syallbus which you may not be obliged to answer, but I really hope
you do. I've scoured countless materials and resources on the
internet to find no answer. Thank you in advance!
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UltimaOnline here again. I will give brief guidance &
comments regarding Nelexus' questions. For deeper discussion,
you're advised to discuss on the Chemical Forums.
Conjugation (not to be confused with hyperconjugation) *allows*
for delocalization of electrons to occur via resonance.
In the benzoate ion, the negative formal charge on the O atom,
cannot be delocalized by resonance into the benzene ring, as
evidenced from the impossibility of drawing the required mechanism
to delocalize the negative formal charge into the benzene ring
(since resonance cannot involve the breaking or forming of sigma
bonds).
However, note that in the conjugate acid form, the pi electrons
in the benzene ring can indeed be delocalized by resonance to the
COOH group, ie. the COOH group is electron-withdrawing from the
benzene ring by resonance, and is hence deactivating and meta
directing. When deprotonated however, the COO- group, being
electron-rich, ceases to be electron-withdrawing by resonance from
the benzene ring, as the high electron charge density of the
dinegatively charged COO2- resonance contributor is excessively
destabilizing.
The real reason why the benzene ring can help to stabilize the
benzoate ion conjugate base (thus making benzoic acid a stronger
acid than say, ethanoic or propanoic acid), is because the sp2 C
atoms of the benzene ring have a higher % s orbital character, and
is thus electron-withdrawing by induction (but not by
resonance).
Yes, the formula pH = 1/2 (pKa1 + pKa2) or pH = 1/2 (pKa2 +
pKa3), is applicable for all solutions containing only an
amphiprotic species, eg. at equivalence point for polyprotic or
multiprotic acids, such as zwitterionic amino acids.
A solution at its isoelectric point contains the highest
possible molarity of its zwitterionic form (ie. no net ionic
charge), and very low and equal molarities of both the cationic
(ie. conjugate acid) and anionic forms (ie. conjugate base) forms.
The molarities of the ionic forms at pI can be calculated using the
relevant Ka values.
Amino acids can (depending on the exact amino acid's R group)
exist as dinegative anionic, uninegative anionic, neutral
zwitterionic, unipositive cationic, and dipositive cationic. So if
you were carry out a titration of an amino acid, you would usually
start with either the fully deprotonated anionic form (if you're
adding acid from burette), or the fully protonated cationic form
(if you're adding alkali from burette).