Lab Techniques and IR spec

[priam18]

So I'll be taking the MCATs soon (um, 7 days anyone?) and was going over some of my weak areas. I orginally took Orgo 1 in undergrad, didn't do so well, and had to drop before I retook it post-bacc. I got through most of the lab part of Orgo 1, but I never retook the lab in post-bacc (least not yet), so I may be a little weak in the lab-ish areas of the MCAT and wanted to know if my intuitiv understanding of the following topics was correct:

A. Techniques used to separate organic molecules

1. Extraction I'm thinking would be used to separate an organic substance (can't think of an example right now, just something with lots of Carbons and Hydrogens) from a substance that can dissolve in an aqueous solution (such as an acid?). More importantly, extraction would be used when confronted with two compounds of different solubilities in a solution.

2. Distillation's all about boiling points. Substances with large differences in boiling points can be separated using simple distillation, while substances with small differences in boiling points can be separated using fractional distillation. Vacuum distillation is used when you have a substance that has such a high boiling point that applying so much heat to it to boil it could possibly denature the substance. Therefore, you vacuum, lower the boiling point, and use either of the above techniques.

3. From my understanding, chromatography is used more to find the mass of a substance, since it's based on the idea that different substances will have different rates of movement across a stationary phase. Heavier substances will travel slower and will appear near the bottom of the phase, while lighter substances will travel faster and appear near the top of the phase. Now I understand there are 3 different types of chromatography, but why? Is there really a significant difference between each type of chromatography as there is with distillation? Also, is there a type of chromatography that's better for substances that have similar masses? And does chromatography work with ions also?

4. Recrystallization is used to purify an impure substance. By boiling the crystal, then slowly cooling it down, one can obtain a purer substance. I'm assuming though, that it's important to *slowly* cool and collect the crystal as it forms; otherwise, you'll just end up with the same impure substance you started out with.


B. IR Absorption for organic bonds

Now this one I'm stumped about. I *could* just memorize the absorption frequencies for each type of functional group, but I really want to try to understand *why* a group has a specific absorption frequencies. There's a whole chapter on it in my Orgo book, but I'm hoping for a simpler, more basic explanation of this.

The only trend I've noticed regarding the absorption frequencies, though I'm not sure if it really means anything is that for functional groups with a C=O group, the absorption frequency is 1600-1800 if the carbon is connected to non-H groups.

So, please feel free to expand my understanding of these things, and if there are any other lab issues that'll be covered (I'm okay with proton NMR), please share

Thanks

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[MundaneMD]

B. IR Absorption for organic bonds

Now this one I'm stumped about. I *could* just memorize the absorption frequencies for each type of functional group, but I really want to try to understand *why* a group has a specific absorption frequencies. There's a whole chapter on it in my Orgo book, but I'm hoping for a simpler, more basic explanation of this.

The only trend I've noticed regarding the absorption frequencies, though I'm not sure if it really means anything is that for functional groups with a C=O group, the absorption frequency is 1600-1800 if the carbon is connected to non-H groups.
Thanks

Basically, the stronger a bond, the higher the absorption frequency. Think of a spring that is stiff; it will oscillate much faster than a spring which is not so stiff.

In terms of bond strength,
Single Bond < Double Bond < Triple Bond

Now compare this to the stretching frequency of specific bonds:
C-O ~1000-1250
C=O ~1630-1820

C=C ~1600-1680
C=C ~2100-2250

The strength of the bond clearly shows a correlation to the stretching frequency. So if you ever get stuck, you can always make educated guesses for certain stretches.

In addition, if you see a broad peak, it is due to interactions between hydrogens and electronegative elements (Hydrogen bonding). Broad peaks are often (not always) the result of H--F, H--O, and H--N interactions.

One more general rule: the intensity of an IR stretch is related to the change in dipole. If the dipole of a bond is greatly changed, the IR peak will be very intense. On the other hand, a bond that is more symmetrical will produce a peak with a lower intensity.

I'm sure you can find some more general rules for IR by combing through your Orgo book, but these rules have been enough for most problems.

I think you should really memorize some of the common stretches:
CH
CH3
C=C
C=C
OH
C=O
NH

These are, in my experience, enough for solving most IR problems in organic chemistry.

There are better ways of understanding IR, but instead of taking a whole course on spectroscopy, I think it will be much easier for you to just memorize certain IR values.

 

[Phlame217]

The above is pretty accurate but if your a hands on/visual thinker, think of IR this way.

You have springs that are tightly wound of varying lengths. When you have a large atom such as Carbon and a small atom such as Hydrogen, their bond length (aka spring length) is very very short due to difference in electronegativity. So visualized a pool ball(C) connected via a 1.38"(short bond) spring to a marble(H). Now see how hard it is to get that spring to stretch or compress, or move side to side in a "deflection" motion.

It should take alot of energy to get any motion out of it.

Compare that to a C-C bond.

So visualize two pool balls connected by say a 2.10" spring. It should be much easier to deflect the spring (bend side to side etc) or stretch/compress it.

Should help you out some with the stuff above.

 

[PRodulous]

The previous responses are correct on the description of IR spectrum. I'd like to add to the correlation to energy. As they previously said,the higher the energy needed , the higher the absorption. This can be reaffirmed if you look at the units of the wavenumber (1/cm or 1/wavelength):

Increase wavenumber, decrease wavelength
Decrease wavelength, increase frequency (by v=wavelength*frequency)
Increase frequency, increase energy (by E=hf)

Relating this logic of energy helped me remember the functional group frequencies better.

3. From my understanding, chromatography is used more to find the mass of a substance, since it's based on the idea that different substances will have different rates of movement across a stationary phase. Heavier substances will travel slower and will appear near the bottom of the phase, while lighter substances will travel faster and appear near the top of the phase. Now I understand there are 3 different types of chromatography, but why? Is there really a significant difference between each type of chromatography as there is with distillation? Also, is there a type of chromatography that's better for substances that have similar masses? And does chromatography work with ions also?

Chromatography works a little differently than you mentioned. This process is either to analyze or separate the products of a reaction. thin layer chromatography is purely a quantitative way of identifying substances. The sample is placed on a very polar silica. After the procedure is complete, the more polar substances will move less and the less polar substances will move higher up.

Column chromatography works on the same principle of polarity, but is often done to physically separate chemicals based on polarity.

Gas Chromatography separates the chemicals on basis of volatility (more volatile, less time in the machine). Many factors (such as mass) determine the volatility. The results of GC is a graph where you can determine the relative amounts of a substances in a mixture.

To answer you question on what is best for masses: chromatography is often used to determine if diastereomers or enatiomers are produced in a reaction. Enatiomers have the same Rf Value because they have the same physical properties (Having only 1 Rf Value). On the other hand, diastereomers have different physical properties (resulting in 2 Rf values).

Hopefully this helps, I tried not getting in too much detail.

 

[priam18]

No, it's great..I actually had a question about polarity and chromatography on one of the practice MCATs, but got it wrong cuz I didn't realize it had anything to do with polarity.

Thanks again!

 

[priam18]

Sorry to bug you guys again, but I'm still trying to get my head around the whole IR thing...I've memorized all of the specs, but I'm just wondering if my thinking (in light of what you've posted is correct)

So the reason why -CH bonds have a high reading is because of the difference in electronegativity, and this in turn makes it harder for the bond to be moved. Okay..but what about ester bonds? There's a similar difference in electronegativity between the C=O and the C-O bond. In fact, one can argue that the C=O bond both has a shorter bond angle *and* is bonded to a more electronegative atom, and this should cause it to have a higher reading than a -CH bond.

I'm assuming, and again, please correct me if I'm wrong, that because the C is also bonded to another O, reasonance comes into play, and as such, the bond strength is between that you get for a single and a double bond. In addition, because carbon is basically being pulled by elements that are more electronegative than it, it's already somewhat stretched, making it easier to break that bond (again, compared to a CH bond). I guess this could also explain why aldehydes have a high reading too, as because carbon is bonded to an O and to an H, the CH sort of act together (dont know if that makes sense) and most of the electronegativity is still drawn towards the O (as it is in say, an alcohol).

Thoughts?

 

[PRodulous]

I don't think I have an absolute answer to your question, but remember what the absorbency spectrum means. When the line dips down (often the y-axis is %transmittance), this represents when the IR machine does NOT receive any energy from the IR waves that it bombards the substance with. Where does the energy go? To the molecules of the substance. It uses the energy to vibrate and rotate. Though this doesn't answer your question, I feel that the readings are the result of forces within the molecule. Maybe someone can further address your question.

 

[BerkReviewTeach]

Sorry to bug you guys again, but I'm still trying to get my head around the whole IR thing...I've memorized all of the specs, but I'm just wondering if my thinking (in light of what you've posted is correct)

So the reason why -CH bonds have a high reading is because of the difference in electronegativity, and this in turn makes it harder for the bond to be moved. Okay..but what about ester bonds? There's a similar difference in electronegativity between the C=O and the C-O bond. In fact, one can argue that the C=O bond both has a shorter bond angle *and* is bonded to a more electronegative atom, and this should cause it to have a higher reading than a -CH bond.

I'm assuming, and again, please correct me if I'm wrong, that because the C is also bonded to another O, reasonance comes into play, and as such, the bond strength is between that you get for a single and a double bond. In addition, because carbon is basically being pulled by elements that are more electronegative than it, it's already somewhat stretched, making it easier to break that bond (again, compared to a CH bond). I guess this could also explain why aldehydes have a high reading too, as because carbon is bonded to an O and to an H, the CH sort of act together (dont know if that makes sense) and most of the electronegativity is still drawn towards the O (as it is in say, an alcohol).

Thoughts?

If you by any far off chance have a BR organic chemistry book, page 118 gives a good explanation for this. If not, let me do my best to paraphrase.

As mentioned before, the IR absorbance is an energy term for all intent and purpose (cm-1 is proprtional to photon energy). So, we expect at face value that stronger bonds have higher absorbances. Comapring C-C to C-N to C-O or C=C to C=N to C=O or C-H to N-H to O-H all confirm this. However, having C-H (a single bond) around 3000 cm-1 versus a C=O (stronger double bond) around 1700 cm-1 appears to violate the rule.

It doesn't actually violate it; we are just half-thinking about the model. We use a spring system as a model. The potential energy of a spring depends on k and ?x2. The C-H bond, because H is so light, experiences a very large ?x when it stretches (you may recall that the center of mass is constant during vibration of a spring, so if H is 1/12th the mass of carbon, it must move 12x as far during a stretch). The result is that while the k for a C-H is small, the ?x2 term is large, so the stretch has a high change in potential energy and thus a high-energy absorbance of 3000 cm-1.

For spectroscopy, I strongly suggest you give BR orgo a look. It explains things in a clear, MCAT-friendly way. I'm not saying this to promote either; it's just a really great way to look at o chem... different than everything I've read before.