Various spectrometry queries (and miscellaneous chemistry qualms)

[ahat]

I think I have some flaws (many flaws) in my fundamental understanding of spectrometry, and other topic of Chemistry. This is a bucketload of questions, but I would really appreciate it if you could impart your knowledge and help me improve my understanding. Thank you so much:

Ultraviolet-Visible Spectrometry:
- What produces the absorbance graph in UV-VS: Light is shone through a molecular solution and electrons (in the 3d subshell) will absorb a quantised amount of energy. This will allow them to jump to a higher energy level (because UV radiation has enough energy to cause an electrical change).
I read this statement:The spectrum is the result of electrons falling back from higher to lower energy levels.
Can someone please explain this?

Atomic Absorption Spectrometry
- Used for metals
- Light is shone through a solution of metal exposed to a flame. This light is absorbed by the excited atoms which absorb specific wavelengths of light.
I read this statement: The flame is green (copper sulfate solution) due to electron transitions from a higher energy state to a lower energy state. Can you please explain this too?

What do the graphs for using both of these techniques tell us? Is the only difference between these two techniques that one is for metals/metalloids and the other for molecular solutions?

Infrared Spectroscopy
- Bonds between atoms have natural vibrations. They can absorb a specific amount of Infrared Radiation (Radio waves) that amplify their natural vibrations. Specific bonds are subject to polarity etc. (what else?) and therefore absorb different amounts of energy.
What is the cause of phenomena such as 'Bond Stretching', 'Bond Contracting' and 'Bond Bending'?
I read this statement: The IR wave number for bond stretching in a C-O bond (1000 - 1300 cm^-1) is lower than for a C-H bond (2850 - 3300 cm^-1). This is because (out of four options) Oxygen atoms have a greater atomic mass than hydrogen atoms.
How does one discern this?

Mass Spectrometry
- If we look at a mass spectrometer readout, what is it exactly that the height of each of the peaks tell us? Does the highest peak tell us which fragment is most energetically stable?

NMR - ¹H and ¹³C
Is the C-13 isotope used opposed to the more abundant C-12 isotope due to the odd number of nuclei? Why does this matter?

Amino Acids
Why do they form specific ions based on pH change? What's the chemical reason. And also, will a pH change denature the protein?

Biochemical Fuels
My book has little to no info on this. Where can I get some?

These are my queries so far. Thank you (in advance) for taking the time.
I think I'll have a few more for Unit 4

[Aurelian]

I think I have some flaws (many flaws) in my fundamental understanding of spectrometry, and other topic of Chemistry. This is a bucketload of questions, but I would really appreciate it if you could impart your knowledge and help me improve my understanding. Thank you so much:

Ultraviolet-Visible Spectrometry:
- What produces the absorbance graph in UV-VS: Light is shone through a molecular solution and electrons (in the 3d subshell) will absorb a quantised amount of energy. This will allow them to jump to a higher energy level (because UV radiation has enough energy to cause an electrical change).
I read this statement:The spectrum is the result of electrons falling back from higher to lower energy levels.
Can someone please explain this?

Electrons can only occupy discrete energy levels in atoms and molecules. When an electron falls from a higher energy level E₁ to a lower energy level E₂, an energy change will occur given by ∆E = E₁ - E₂. However, because of the principle of conservation of energy, this energy can't just "disappear" from the universe. It is instead released as a photon of light of a particular frequency corresponding to the magnitude of the energy change ∆E.

Atomic Absorption Spectrometry
- Used for metals
- Light is shone through a solution of metal exposed to a flame. This light is absorbed by the excited atoms which absorb specific wavelengths of light.
I read this statement: The flame is green (copper sulfate solution) due to electron transitions from a higher energy state to a lower energy state. Can you please explain this too?

Same deal as above. The fact that the emitted light is green indicates that the energy change ∆E corresponds to a frequency of light in the green part of the visible spectrum.

What do the graphs for using both of these techniques tell us? Is the only difference between these two techniques that one is for metals/metalloids and the other for molecular solutions?

The fundamental principle of each technique is the same, in that light will be absorbed by the atoms or molecules being analysed. Both techniques can be used qualitatively, to identify substances according to their absorption characteristics over a range of light wavelengths/frequencies. Both techniques can also be used quantitatively to determine concentrations of substances present, using calibration curves constructed from standards of known concentrations. Refer to your textbook for more detail...

There are slight differences in the practical execution of each technique. Furthermore, as you have pointed out AAS is suitable for examination of metals whereas UV-Vis is suited to the examination of things like organic molecules.

Infrared Spectroscopy
- Bonds between atoms have natural vibrations. They can absorb a specific amount of Infrared Radiation (Radio waves) that amplify their natural vibrations. Specific bonds are subject to polarity etc. (what else?) and therefore absorb different amounts of energy.
What is the cause of phenomena such as 'Bond Stretching', 'Bond Contracting' and 'Bond Bending'?
I read this statement: The IR wave number for bond stretching in a C-O bond (1000 - 1300 cm^-1) is lower than for a C-H bond (2850 - 3300 cm^-1). This is because (out of four options) Oxygen atoms have a greater atomic mass than hydrogen atoms.
How does one discern this?

The proper answers to your questions here are well beyond the scope of the VCE course. In brief, though, light can be modelled as a wave with an oscillating electric field component. For IR radiation, this electric field "pushes" electrons in bonds up and down, causing those bonds to exhibit vibrational/oscillatory motion. Drawing an analogy, consider a small metal ball hanging from a spring. If you grab the spring and wave it up and down, and then let go, you will observe the mass to now be oscillating up and down on the spring.

If we model this oscillatory motion according to the laws of classical physics, it can be shown that the frequency of vibration of two atoms is given by:



...where k = some constant and m = the mass of the lighter atom.

(Strictly speaking we should use something called the "reduced mass", µ, instead of m, but don't worry about that).

From the above relation it should be obvious that the smaller the masses involved in the vibration, the greater the frequency of vibration. A hydrogen atom is much smaller/lighter than an oxygen atom, and so a C-H stretch will occur at a higher frequency of vibration than C=O stretch. (These frequencies of vibration also correspond to the frequencies of light so absorbed).

At VCE level, this isn't really something you can "discern". As far as I am aware, you just sort of need to "know" how mass affects IR absorption frequencies...

Mass Spectrometry
- If we look at a mass spectrometer readout, what is it exactly that the height of each of the peaks tell us? Does the highest peak tell us which fragment is most energetically stable?

The height of each peak describes the relative abundance of the (charged) fragments to which they correspond. More stable fragments are going to be more abundant, so yes I suppose peak height does tell us about relative stabilities of fragments.

NMR - ¹H and ¹³C
Is the C-13 isotope used opposed to the more abundant C-12 isotope due to the odd number of nuclei? Why does this matter?

In order to interact with magnetic fields in the way required for NMR, the nuclei under examination must possess a net "spin", where spin is an intrinsic property of the nucleons in the nuclei (i.e. of the protons and neutrons). Protons and neutrons each have spin 1/2, but these "spins" can be oriented in two different directions - either "upwards" (spin +1/2) or "downwards" (spin -1/2). In nuclei with an even number of nucleons, these spins will typically cancel out - there will be just as many +1/2 spins as -1/2 spins. Hence C-12, which contains 6 protons and 6 neutrons, is invisible to NMR techniques. However, C-13 has an odd number of nucleons. The extra nucleon contributes a 1/2 spin to the nucleus which isn't cancelled out by some other nucleon. Therefore it is visible to NMR techniques.

Amino Acids
Why do they form specific ions based on pH change? What's the chemical reason. And also, will a pH change denature the protein?

For the first question, think about the principles covered in Unit 4 concerning equilibrium. If there is a high concentration of H⁺, for example, it is going to be more likely at any given moment in time that a -COO^- or -NH₃ groups on amino acids will be protonated. As a result, the more protonated form will be more abundant at low pHs.

As for the second question, yes - substantial enough pH changes will denature a protein.

[ahat]

Aurellian, thank you so much. This was really helpful.

[Aurelian]

No problem =)

[ahat]

Could you give me a hand with this question please? I have to find the mass of manganese in the original sample.

The concentration of MnO₄^- in the 100 mL solution is 35 mg/L.

I applied this to get to the concentration originally (in the 1L flask, where all the manganese is):
35 x (100/25) x (1000/25)
 (100/25) to get from the 100 mL flask back to the 25 mL sample and then (1000/25) to get from the 25 mL sample back to the 1L vessel that all of the manganese was dissolved in. This multiplication wasn't done though (1000/25), could you please explain why? (If we didn't, wouldn't we be finding the concentration of the 25 mL sample? Or would the concentration be the same for the 1L vessel and 25 mL sample it was taken from because the reduction in mole would be proportional in the reduction in volume?)

Thankyou!

[jgoudie]

Yep, it was not a dilution from 1L to 25ml, it was just a 25ml sample taken from the 1L. 

Think about having a 1L jug of cordial, if you pour 25ml of that 1L out, it still tastes the same as it is the same concentration. 

Yes smaller number of mole, however you have a smaller volume, and the number of mole:volume ratio is the same, thus same concentration (as it is a solution we always assume it is a homogenous (fully mixed solution).

Could you give me a hand with this question please? I have to find the mass of manganese in the original sample.

The concentration of MnO₄^- in the 100 mL solution is 35 mg/L.

I applied this to get to the concentration originally (in the 1L flask, where all the manganese is):
35 x (100/25) x (1000/25)
 (100/25) to get from the 100 mL flask back to the 25 mL sample and then (1000/25) to get from the 25 mL sample back to the 1L vessel that all of the manganese was dissolved in. This multiplication wasn't done though (1000/25), could you please explain why? (If we didn't, wouldn't we be finding the concentration of the 25 mL sample? Or would the concentration be the same for the 1L vessel and 25 mL sample it was taken from because the reduction in mole would be proportional in the reduction in volume?)

Thankyou!

[ahat]

Thank you
And *sweet* anecdote

[ahat]

Hey, I'm back

Could you please help me with this question. For the solution VCAA posted, they've used the K_a value for Methanoic acid in their calculations, which I don't get, because if you were combining the two different acids, would you be allowed to use that K_a value? (which is 1.8 x 10^-4 for reference). It would be reallyyyy appreciated if you could explain this, with some theory as well. I am shocking at U4 compared to U3.

Also, they made a little note that some students (incorrectly) used: – the equilibrium [H3O+] = the equilibrium [HCOO-] When do we do this? Let concentrations equal each other that is?

Thank you so much in advance.

[lzxnl]

Here you have methanoate ions and methanoic acid. Just an acid and its conjugate base; forget the sodiums, which do nothing.

So from the equilibrium expression,
Work out the concentrations of the methanoic acid and methanoate ion and then plug into this expression. That's it.

As for why you can do this, it's because we don't have two acids. One is the acid HA, one is the conjugate base A^-.

Also, the equilibrium assumption that [H+]=[A-] for a generic acid HA works when you dissolve a concentration of acid in water, and that's the only substance in the water (aside from water and the ions produced from auto-ionisation of water). Here, as the H+ formed is formed by the dissolution of the acid HA, from the mole ratios in HA <=> A- + H+, the concentrations of H+ and A- are the same. Now replace HA with HCOOH and A- with HCOO- and you should be able to see what I mean. In this example, we added HA AND A- to the solution.

[ahat]

Thanks for the reply Nilu, but I still have some questions, sorry :/

Here you have methanoate ions and methanoic acid. Just an acid and its conjugate base; forget the sodiums, which do nothing.

This makes sense, should have realised this.

equilibrium expression,

For this though, I'm not sure how we set this expression up. The question says that Methanoic acid and its conjugate base were added together, i.e. reactants in the equation. So why isn't the concentration for these both in the denominator?
What I mean is, the reaction would look something like this

HCOOH + HCOO^- A + B (where what A and B might be allude me)

So

I guess my logic is probably convoluted, but this question is really stumping me.

Btw Nilu, when we're calculating standard cell potentials for a spontaneous redox reaction, do we read the E^o values straight from the e/c series or do we flip the equations first to represent oxidation/reduction? When I flipped the equations, I got the wrong answer, so I assume it was the latter.

[lzxnl]

Thanks for the reply Nilu, but I still have some questions, sorry :/

This makes sense, should have realised this.

For this though, I'm not sure how we set this expression up. The question says that Methanoic acid and its conjugate base were added together, i.e. reactants in the equation. So why isn't the concentration for these both in the denominator?
What I mean is, the reaction would look something like this

HCOOH + HCOO^- A + B (where what A and B might be allude me)

So

I guess my logic is probably convoluted, but this question is really stumping me.

Btw Nilu, when we're calculating standard cell potentials for a spontaneous redox reaction, do we read the E^o values straight from the e/c series or do we flip the equations first to represent oxidation/reduction? When I flipped the equations, I got the wrong answer, so I assume it was the latter.

Erm...why would methanoic acid and methanoate react? Just because they're added together doesn't mean they react. I mean, we can add sodium hydroxide solution to an equivalent sodium hydroxide solution. Do they react? On a more extreme example: let's add lithium metal to sodium metal. They don't react directly with each other. "Adding" means "put together in the same container". For all we know they may not react. In this case, they're on opposite sides of the reaction.

As for cell potentials AT STANDARD CONDITIONS, you take the higher cell potential (which corresponds to the positive cathode) and the lower cell potential (the one corresponding to the negative anode) and subtract the smaller from the larger. That's your cell potential. Note, this will only work if you have predicted a spontaneous reaction to actually occur, and these cell potentials are only valid at standard conditions.

[ahat]

"Adding" means "put together in the same container". For all we know they may not react. In this case, they're on opposite sides of the reaction.

The logic, I see it. Thanks.

[ahat]

For condensation polymerisation (a polyester specifically), is it always between a diol and diacid? Thanks.

Btw, sort of an irrelevant question, but which is more important, per mole or per gram, say in the context of fuels? For example, Methane releases 49.39 kJ/g and 889 kJ/Mole and Octane releases 47.93 kJ/g and -5464 kJ/Mole so what kinds of considerations goes into these decisions?

[brightsky]

In general, synthetic polymers are made from monomers with two of the same functional group, whilst natural polymers are made from monomers with both functional groups. So, no, not all condensation polymerisation reactions are between a diol and a diacid.

Normally, in the context of fuels, people are more interested in kJ/g, because no one knows how to measure out 1 mol of octane. The unit for energy density is kJ/g, if you recall. The greater the energy density, the better.