Unit 3 Questions MEGATHREAD :)

[luken93]

When an amino acid is subjected to acidic/basic conditions, the NH2/COOH in the Z group is affected as well isn't it? I swear I've seen two different answers in practice exams as to whether they do or not, but I have a feeling that this particular exam could be wrong...

Also, is it only when a pH isn't stated that we draw the regular amino acid (H2N - CHR - COOH)? The exam I did today said at neutral pH of 7, draw a dipeptide of two amino acids immediatly after a zwitterion question - but the answers didn't show the zwitterion form? Do dipeptides change this?

[GuessWho]

The Z group would be affected by the acidic/basic conditions. So if the Z group had a COOH/NH2 in it, you would have to adjust them accordingly.
In regard to your other question, a neutral pH of 7 doesn't necessarily mean that the amino acid is in its zwitterion form. The pH at which an amino acid is in its zwitterion form is determined by its Z group.
I think if a pH isn't stated its probably safe not to add charges to the amino acid.
Can anyone back me up on this information as I am not sure.

[Graphite]

The ionisation of an acid/base depends on the pH conditions. I would assume for VCE if external pH<7 then you can assume the basic functional groups get protonated and pH>7 the acid functional groups get deprotonated. Is this always true? No.
In reality you can only make these statements by comparing the pKa of the acid/base functional groups with the external pH. (pKa vary depending on its extended conjugation to other atoms.)

@Guesswho you made a good point. Never assume an amino acid only contains a carboxylic and amino group as the Z group may contrain acid/base functional groups.

[VivaTequila]

The ionisation of an acid/base depends on the pH conditions. I would assume for VCE if external pH<7 then you can assume the basic functional groups get protonated and pH>7 the acid functional groups get deprotonated. Is this always true? No.
In reality you can only make these statements by comparing the pKa of the acid/base functional groups with the external pH. (pKa vary depending on its extended conjugation to other atoms.)

@Guesswho you made a good point. Never assume an amino acid only contains a carboxylic and amino group as the Z group may contrain acid/base functional groups.

Does this mean we can get amino acids that contain Z groups with carbonate groups or something? Those are basic aren't they?

[luken93]

When a molecule enters a Mass Spec, do the fragments occur simultaneously with the formation of the molecular ion, or are they produced from the parent ion so to speak?

I had a question that asked to show the formation of the fragment from the parent ion, but just wanted to confirm that's how it actually worked...

[Mao]

Simultaneous. The formation of smaller fragments are independent of formation of the parent ion.

Typically, the ionization step only has enough energy to cleave one bond (generally a C-C, C-O or O-H bond, it is not strong enough to cleave C-H). You therefore don't have any 'subsequent' ionization after the initial ionization.

WRONG!

[luken93]

Cheers, the question was to show the formation of the m/z = 15 fragment from the parent ion (ethanoic acid)

The answer said:

CH3COOH+  -->   CH3+ + COOH

Whereas I wrote:
CH3COOH + e-    -->   CH3+ + COOH + 2e-

Is mine necessarily wrong then? (probably hahah)

[Vincezor]

Cheers, the question was to show the formation of the m/z = 15 fragment from the parent ion (ethanoic acid)

The answer said:

CH3COOH+  -->   CH3+ + COOH

Whereas I wrote:
CH3COOH + e-    -->   CH3+ + COOH + 2e-

Is mine necessarily wrong then? (probably hahah)

Hehe this reminds me of a question from Insight 2011 :S

But I wrote what you wrote, and I think that textbook does it like that as well.

[luken93]

You guessed right haha, did it today
This was the only Q I got wrong, gotta find out if I'm right or not!

[Mao]

Wait, no. I am wrong. Fragmentation occurs after the formation of molecular ion. The exam solutions are correct.

Sorry for the confusion.

Source: Skoog, Holler & Crouch, Principles of Instrumental Analysis 6ed, 2007, Brooks/Cole.


Some more elaboration:

There are different ways to ionize the molecule. And these different methods produce different results. The most commonly used instrument in modern labs are electron-impact (EI) MS, which promote fragmentation and is useful for organic molecules. In EI-MS, electrons are accelerated to ~10 times the bond energy, which can easily cleave the bond. However, since electrons have extremely low mass, its kinetic energy is relatively small, and upon impact not much momentum is transferred to the molecule. Instead, a lot of the excess energy in the ionizing electron is transferred to vibrational and rotational energy of the impacted molecule (molecular ion), which then dissipate this energy by fragmenting. Depending on the setup of the MS, several fragmentation steps can occur.

(which, makes your life a bit harder I guess, oops)

Typical fragmentation example:

1. Molecular ion formation:
2. Fragmentation:



(and so on)


An alternative is the field-ionization technique, which simultaneously ionizes everything. This is by using a special 'emitter', which extracts electrons from the analyte via quantum tunneling. This technique doesn't promote fragmentation, and isn't too useful for organic molecules. (There are 8 other techniques listed here on top of these two. zzzZZZ)

(and obviously, this is beyond VCE level. If I had to guess, I'd say third year level, maybe)

[luken93]

Nooooo, devo!

Ah well, thanks for the very good explanation!

[jane1234]

With sig figures:

The relative masses in the data booklet are written (mostly) to 3 significant figures. If all the other values were 4 significant figures would you round to 3 or to 4? Because the exam I just did says 4, but I used a molecular mass that had 3 significant figures in it...

[RobM8]

With sig figures:

The relative masses in the data booklet are written (mostly) to 3 significant figures. If all the other values were 4 significant figures would you round to 3 or to 4? Because the exam I just did says 4, but I used a molecular mass that had 3 significant figures in it...

I think it is because the masses are meant to be treated as a 'literary value', whereas the other data you are given is experiment data that someone has collected and isn't exact. Maybe literary value is not the best term but it is the best I can think of at the moment...

[luken93]

Hmmm, but they still aren't accurate any more than other data, as they actually have more decimal places if you had an extremely precise scale to weigh with.

I hate company exams, period.

[jane1234]

I hate company exams, period.

Couldn't agree more!!
Do you know if VCAA would take the number of significant figures of the molecular masses into account??