[Chemistry]- Nelexus prepares for University level Chemistry

UltimaOnline SG

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!

UltimaOnline SG

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/

UltimaOnline SG

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).