Small Student made study guide: Addressing the issues frequently asked about Mass Spec, IR, H1 NMR

Pictures and slides found online and compiled for your use.

Mass Spectrometry: How does this mass spectrometer work? Well we put in a small sample of a substance that is in most cases comprised of one particular molecule into a mass spectrometer and it gives us a mass spectrum graph which we must interpret. How does this equipment work While in Chem 14c we might not be working directly with a mass spectrometer it is important to conceptually understand what occurs in the process of producing the reading we will interpret. 1) we introduce a sample to the spectrometer 2) this sample undergoes ionization, this is done by using an electron gun that shoots out electrons at the molecules ( not yet charged) then this interaction between the incoming electrons and the substance result in ionization. One important distinction is that it can result in ionization which produces a molecular ion which can be analyzed later by the detector or it can cause cleavage of one or more bonds which results in the production of fragment ions. These fragment ions are NOT molecular ions but are still charged and therefore can be detected by the detector. So all those little lines not the M, M+1 or M+2 are readings from other charged particles. This is a good time to introduce the base peak~ this is the ion which presents on the graph to have the highest relative abundance. So why isnt the molecular ion that derives from the original molecule we are interested always the base peak or the ion which has the highest abundance? Well in some cases a molecule can fragment more readily than others and therefore the fragments produced are not the molecular ion but product ions that in some cases are quite abundant in an easily fragmentable molecule. 3) Then the ions produces are passed through an accelerator which allows the positively charged particles to pass through to the electromagnet 4) this electromagnet then works to deflect ions or manipulate the flight path of the ions passing through, those ions with smaller m/z ratio are more likely to not make it to the detector and those with large m/z value will. This is one of the reasons we often see the base peak, or the peak with

the highest relative abundance present as the M or molecular ion. But why not M+1 or M+2? Well remember a molecule is comprised of various atoms and those atoms have isotopes with natural abundance. As Aston discovered that there are stable isotopes of different elements the same concept applies in which the molecule can be comprised of different atoms which can have different molecular weights due to the different atoms that comprise them and the isotopes present. BUT we must recognize that there is also a natural abundance of these isotopes we must take into consideration. The M is representative of the molecular ion made of isotopes that are of the lowest molecular weight. Why? Well these are the most abundant as see in the table on page 99 of your course reader. So now understanding the mass spectrometer, some good questions to consider... Why do we need a sample and not just a molecule? Well this process of spectrometry produces product ions which could be molecular ions or fragment ions and we cannot obtain an accurate reading if our one lil molecule never made it through the spectrometer, or if it only gave us a reading for one of the molecular ions of the molecule in question. So having multiple molecules of a substance allows for a graph that not only shows the M value but also the M+2, M+1 and also those fragment ions that are produced. While in chem 14c we dont analyze these fragment ions it could be applicable in other areas of chemistry as well.

Base Peak: ion peak with the highest relative abundance, often, but not always M. Why? The base peak simply has the highest relative ion abundance on the graph. If the molecule fragments the base peak could represent a fragment ion rather than the molecular ion. Mass Spectrum Graphs: X axis: m/z: mass to charge ration, not simply the molecular weight as depicted by the periodic table Y axis: Relative ion abundance, the amount of that particular ion present in sample. M: What is it It is the molecular ion in question, usually has a high m/z value on the graph. This depicts the mass of the molecular ion comprised of the isotopes with the lowest molecular weight. M+1: This is the M value with one amu added. This indicates that there is likely to be an isotope which varies by 1 amu or by one neutron. We can see that these are commonly c (1.1% abundance) N ( .37%) and S (.76%) We will most commonly see C as it has the highest abundance
13 15 33 13

How is this M+1 value used to determine presence of these atoms or the molecular formula of the molecular ion in question? Well since M+1 is most commonly an indicator of the presence of the isotope of carbon we can use this to determine an approximate amount of carbons in the formula. HOW to do this and not screw up the calculations: If we take the M+1 relative intensity/ 1.1% = approximate number of carbons When M is 100 on the y axis in the relative abundance then the M+1 value is already indicating the M+1 relative intensity but what if M doesnt have 100% relative abundance

This equation could be useful (relative abundance of M +1)X (100) / ( relative abundance of M) = The intensity of M+1 as if the M value was 100 Then take this value and plug it into the equation above. Also recognize that there could be presence of the other atoms such as sulfur and nitrogen present and one must take this into account before definitively deciding on a molecular formula. M+2 so what is M+2? Again it is one unit over from M+1 and two units over from M, It is representative of a molecular ion which differs by 2 amus and therefore has some isotope of an atom it is comprised of within it. For the purposes of this course these atoms could be SCl BrHow to determine presence? Compare the relative intensity of the M+2 line. Remember if M isnt 100 you must manipulate the M+2 value to give you the correct value simply take (M+2 relative abundance/ M relative abundance) X 100 = relative intensity of M+2 Presence by relative intensity of M+2 S - 4% Cl - 33% Br-100% Note: if two halogens are present in the formula then the relative intensities are added as the probability of having one of those halogens in the formula or sulfur differing by 2 amus compounds so 2 Cls would have a relative intensity of 66% about, obviously make sure it fits the mass that we expect the molecular ion to have.
33 37 81 33 37 81

Challenge: Check this out! Divide the natural abundance of this isotope by the more abundant isotope and check those numbers. How do they correlate to the numbers above? This was based on a discussion board question If you are having issues understanding what all these relative ions, abundances, and natural abundances mean this should help!

Relative ion abundance: the abundance of a particular molecular ion We are interested in the M, M+1, and M+2 peaks Relative intensity: The intensity of one molecular ion, we should scale M to 100% if not already done But how to? And why? Well M has the highest relative molecular ion abundance of the peaks of the 3 highest molecular weights (depicted on the Y-axis) By scaling M to 100 % we can also scale each of the natural abundance percentages of isotopes depicted on page 99 of the think book to allow the M contributors to be the 100% and the rest of the isotopes scaled from there. This allows us to compare the M+1 line and

M+2 line to M easily and correlate the percentages of each with the natural abundances percentages when scaled to let the M contributors have 100% and the others scaled from there. Pretty much we want to scale everything equally easier to compare. Also DO NOT get confused relative intensity of each of the molecular ion lines (M, M+1, and M+2) will not correspond to the relative ion abundance depicted on the y axis unless M is scaled to 100% Also unless you scale the percentages of the natural abundances of isotopes so that the M contributors are 100 percent and you base the rest of the percentages off of that. You cant compare the natural abundance to the relative ion intensities directly I suggest: 1) Make sure M has 100% relative ion abundance on graph, if it doesnt scale it and the other M+1 and M+2 peaks so that this is the case. This can be done by (M+1 or M+2 /M) X 100 = relative intensity of M+1 or 2 when M is 100 2) Make sure the relative intensities you are comparing to the natural abundances of isotopes ( in order to determine presence) also allow M contributors to be the 100% abundance and from there scale the rest for easier comparison Since usually the most abundant isotope (for our purposes) are the ones with the lowest molecular mass and the M value depicts the molecular ion with the lowest molecular mass by scaling to 100% for M and then scaling M+2 and M+1 we can get an idea of the chances of an isotope or isotopes with higher molecular mass (1 amu for M+1 and 2amus for M+2) appearing. Sometimes more than one isotope is indicated on the M +1 orM+2 lines Like for M+1 we could have two or more M +1 contributors (see p 99) Or we could have two or more M+2 contributors present (see owls 3 answer) Surprisingly this is applicable for why we divide the M+1 relative intensity by 1.1% This might be an abstract concept but let me try to explain it this way lets use the example of C6H6 predicted relative intensity of M+1 is 6.66% See page 100 of the think book. But why? Well in this situation we have 6 carbon atoms, all of them could differ by 1 amu unit but they all cant differ at once that would be the M+6 line! But think if we have 6 carbon atoms and the abundance of that M+1 molecular ion line depends on just one little carbon in the formula differing by 1 amu unit the probability of this happening increases by 1.1% for each addition carbon because for 100 12Cs we have 1.1 13Cs!

Why? Well we still have 100 12Cs for 1.1 13C but as the formula has more carbons the chance of one of those carbons being an isotope increases and a molecular ion that is 1 amu heavier than the molecular ion comprised of the lowest mass isotopes (this is the M+1) has a greater relative intensity and greater possibility of occurring If there was magic in the world right (we are at Hogwarts or something) Taking this concept and I am going to go elementary school on you!

Before I go over this example try this. Divide C natural abundance percent by the 12C percent and then multiply by 100 This will get you 1.107% X 100 = 1.1 ish 98.893% ^ This part of the calculation yields a ratio that says for every .011123 13C we have 1 12C isotope. Then by multiplying by 100 we can deal with the number a bit better and then we can have the abundance ratio 1.1:100 Mull over this While you think lets try this trivial analogy:
13

So we have these ducks they will help us understand the M+1/M value, what this value means, why we scale to 100, and why in the heck we divide by 1.1? We have ducks white ducks; skinny white ducks aka 12 C isotopes

For every 100 ducks Of Isotope of 12C

.1
We have 1.1 fatter (like the M+1 has 1.1 13C isotopes which are a little heavier) brown ducks.

Now lets say we have these groups of ducks we will create (like molecules ducks like to form groups) and in this case these groups will only have 1 duck differ at a time (we could have more like if we were talking about the M+2 isotope in which we could have 2 ducks carbons differing at a time but this is M+1 example) In this case we just need one of those ducks to differ at a time for it to be classified as the M+1 group if we have 6 ducks and each has a 1.1% chance of being brown and all we need is 1 to be brown in order to classify into the M+1 group. SOOOO we can say for every for every 100 times all the ducks are white (M) then 6.6 times one duck is brown (M+1) This example considers a 6 carbon compound This example is very trivial but it might help a bit!

Infrared Spectroscopy:

A students approach to understand what is going on 1st a diagram of an IR Spectrometer, in the simplest way I have found:

What could this IR stuff tell us? Well like mass spectroscopy it can tell us what atoms are in a molecule but unlike mas spectroscopy we now can determine through analysis of an IR spectra graph which functional groups are present in the molecule. (Could be present not definitive as we must have a correct analysis in order to assure we have identified the right functional groups) ` Each molecule has various bonded atoms which make up different functional groups from alkanes to aldehydes. Although we might simply receive a graph and analyze it is important to understand what is occurring and why. We receive this graph from performing IR Spectroscopy on a molecule that plots the stretching frequency (x axis) against the number of photons absorbed (y axis) while this graph is very useful lets first understand how this graph is obtained and the concepts behind it: First lets ask... Whats this Infrared Spectrum?

The Infrared Region

Infrared radiation is of slightly shorter frequency than visible light. Typical IR wavelengths range from 8x10-5 cm to 1x10-2 cm, and this corresponds to energies of around 1-10 kcal. This energy is sufficient to make atoms vibrate, but not enough to cause electronic transitions.

How this relates to IR spectroscopy? Well Infrared spectroscopy uses infrared light. By shooting photons of frequencies within the infrared part of the spectrum different parts of a molecule vibrate at different points within the spectrum. When these molecular vibrations occur at a certain point in the spectrum the atoms within the bond within the molecule absorb the photons and therefore there are a high number of photons absorbed. In other places of the spectrum where there are no photons absorbed we see smaller or no peaks.

These absorption spectrums for the molecule show us what functional groups the molecule might consist of. Remember none of this is definitive as we must account for the fact that there are other forces which effect bond strength, length, and such within a molecule which might increase or decrease the stretching frequency which the particular function group undergoes molecular vibrations at, hence the use of ranges for each functional group. * Note: molecular vibration transitions (ground -> excited state) are NOT synonymous with electronic transitions, these would not occur when using lower frequency/lower energy infrared photons. Electronic transitions would require much higher frequency/energetic photons.

Why would this apply to functional groups? Well each functional group has atoms that are bonded these bonds have different characteristics from bond length, strength, and dipole. Now that we see that bonds differ, understand that in order to cause a molecular vibration or a transition between the ground and excited state requires a specific amount of energy. *remember all the way back from 14a that energy comes in discrete packets, therefore vibration energy is quantized and can only occur if the energy is the specific energy that will cause a molecular vibration.

How does molecular structure control Intensity of the peak/ amount photon absorption?

(Y axis) Intensity of absorption in the IR spectrum relates to the change in dipole movement which occurs during molecular vibrations. A bond that has a large initial dipole will have a greater change in dipole movement and therefore will absorb more of the incoming photons assuming the frequency of these photons corresponds to the stretching frequency of that particular bond. Dipole is greater if and when The atoms bonded have a larger electronegativity difference (delta EN) i.e.: C-H bond less dipole than O-H bond The bond length is longer (distance between the atoms) Makes sense as if the bonded atoms were closer it would be harder to unequally share electrons, therefore decreasing the dipole. If the atoms bonded were farther from each other than its easier to isolate electron density to one area and therefore increase the polarity of the bond. Remember Dipole up, Intensity of Absorption UP

How does molecular structure affect the stretching frequency X AXIS that a particular part of the molecule undergoes molecular vibrations?
1) As the bond strength goes up so does the stretching frequency. Why? Well the stiffer the spring the faster it will vibrate when you stretch it and release it. Same concept, In order to cause a molecular vibration which occurs when bond goes from the ground to the excited state, the bond must vibrate but just like we must put a certain amount of energy into stretching a stiff spring there is also a certain amount of energy that must be receive in a quantized packet by the stiff/strong bond. 2) As the mass of one of the atoms participating in the bond goes up the stretching frequency will go down (must consider change in the bond strength as well) and Vis versa, when there are lighter atoms participating in a bond this requires a higher frequency. I know this analogy has its flaws but it helped me, If you had a hippo (big, larger) it would jiggle easier If you had a lighter hippo, one that was skinny, lighter, and had a smaller mass it wouldnt jiggle as easy

Remember this is just a way to remember not the actual situation

The IR graph notes and important concepts : Some have asked about the fingerprint region Dr. Hs tutorial on IR explains why we dont analyze past the finger print region and the types of molecular vibrations that occur in this region Please go here http://www.chem.ucla.edu/harding/notes/notes_14C_IR.pdf

Characteristic IR Absorption Values Functional Group Bond Stretching, cm Zone 1: 3700 3200 cm alcohol O-H 3650 3200 alkyne ~3300 C-H amine, amide N-H 3500 3300 Zone 2: 3200 2700 cm alkane sp3 C-H 2960 2850 aryl, vinyl sp2 C-H 3100 3000 aldehyde sp2 C-H ~2900, ~2700 carboxylic acid O-H 3000 2500 Zone 3: 2300 2100 cm alkyne CC 2260 2100 CN nitrile 2260 2220 Zone 4: 1950 - 1650 cm C=O 1740 1720 aldehyde amide C=O 1690 1650 aryl ketone C=O 1700 1680 carboxylic acid C=O 1725 1700 ester C=O 1750 1735 ketone C=O 1750 1705 enone (C=C-C=O) C=O 1685 1665 aromatic overtones 1950 1750 Zone 5: 1680 1450 cm alkene C=C 1680 1620 aromatic C=C ~1600, 1500-1450 Fingerprint region: < 1450 cm

Intensity variable; usually broad strong medium, often broad variable variable medium, 2 bands strong, broad variable variable strong strong strong strong strong strong strong 3 or 4 small peaks variable variable; 1600 often 2 bands

( ^^Credit to Dr. Hardinger, this is off his tutorial on IR)

NMR Spectroscopy:

So the process of NMR is the first thing we should understand. First we apply a magnetic field to a sample this allows the nuclei in question whether H or C13 to become aligned with the magnetic field this doesnt mean that their spin aligns but rather that there orientation is no longer random. Some nuclei are parallel or aligned with the magnetic field applied some are not aligned and are antiparallel to the direction of the applied magnetic field. The nuclei themselves have their own magnetic environment, as the specific ones we are dealing with ( H1 and C13) have an odd number of protons or neutrons and therefore have an l quantum number or a spin that is not equal to zero. This allows us to apply the magnetic field and photons to induce the nuclei to be in resonance between the lower and higher energy states when a certain frequency photon is applied. The electromagnetic signal they give off when this occurs can be detected and graphed.

A little Alpha and Beta the Greek life of NMR

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/nmr/nmr1.htm

- Alpha The nuclei in the lower energy state are said to be in the alpha state spin state In this state the spin has a value of +1/2 and the poles are oriented in the same way as the magnetic field from South to North or they are parallel (as we said earlier). These nuclei can make the transition to the higher state BetaThe nuclei in the higher energy state are said to be in the Beta spin state. In this state the spin has a value of -1/2 and the poles of the nucleus are oriented in the opposing direction of the magnetic field (North to south rather than south to north) or they are antiparallel to the direction of the magnetic field.

This transition occurs when the nuclei accept a photon of a given frequency (Radio waves) which has a specific energy. As energy is quantized this happens at a specific value on the chemical shift scale. The applied magnetic field strength will alter the magnetic field strength at the nucleus. The greater this magnetic field strength the greater the energy required to induce a spin flips. Each spectrometer is a bit different and therefore when we receive an NMR graph it must be normalized so the chemical shift values dont vary dramatically for the same molecule.

Taking this normalization into account now the question is what effects the photon frequency or the energy required to induce a spin flip for certain protons, we know the values are different for protons in different environments but why?

Various factors can and should be taken into account when considering what effects a particular chemical shift The first thing one should discuss is the shielding or deseeding around the nuclei in question... Why does this affect the chemical shift value of particular nuclei? First the definitions required to understand this section: Shielded: When a nucleus is surrounded by electrons in this case shielding them from feeling the full strength of the applied magnetic field Deshielded: When the nucleus is not surrounded by electrons, the electron density is centered elsewhere, and therefore the strength of the applied magnetic field is felt more so by the nuclei.

The electrons around the proton create a magnetic field that opposes the applied field. Since this reduces the field experienced at the nucleus, the electrons are said to shield the proton. It can be useful to think of this in terms of vectors.... But why? The electrons have a magnetic moment opposite to that of the applied magnetic field!

Found this online

So as we said, the energy difference between the lower and higher energy states is effected by the magnetic field strength at the nucleus but the shielding from electrons with the opposite magnetic moment allows reduction of this magnetic field and in turn a reduction of the E between lower and higher energy spin states. This shielding can occur when the nuclei Are neighboring or attached to an atom with a lower electronegativity value, therefore it doesnt hog electrons and the nucleus is more shielded.

These hydrogen nuclei chemical shifts should occur up field, or at a lower chemical shift value Also these nuclei are said to be high field often and I would look out for this when reading other sites and supplementary materials When the hydrogen nucleus is deshielded it is neighboring or attached to other atoms that the electron density is centered around. These atoms draw electrons away from the hydrogen nuclei and therefore their nuclei are subjected to feeling more the applied magnetic field. The energy or photon frequency required to induce a spin flip is higher and therefore the chemical shift is higher Here is this little handy chart so that you can compare what I am saying to the shift values

This can occur when: The hydrogen nuclei is neighboring more electronegative atoms The hydrogen nuclei is around (less than three spaces away) from a higher electronegative atom and therefore these hog the electrons Or if we are comparing the hydrogen nuclei in question are attached to an atom that is within the chain versus terminal on the chain but has the same/ similar surrounding attachments such as this. You can see this demonstrated by the characteristic chemical shift value of a methyl group which is the lowest.

***These chemical shifts of deshielded nuclei occur downfield or at a higher chemical shift value and therefore require more energy to induce spin flip. These are also said to be low field which I believe refers to the low field of magnetic moment induced by the electrons that arent shielding the nuclei in question.

Something to consider: Magnetic induction: H- NMR

This concept is confusing as it comes into play often. Heres a graph that shows some pi bonded and aromatic sections of molecules and there characteristic chemical shift range in H-NMR. Note: When you see only one H bonded off the carbon chair where there could be more what the diagram is trying to show is that this is the H in question that they are talking about. Anisotropy means the un-uniform distribution of the magnetic field. This occurs when magnetic induction is present. When does this happen and what does this mean for the hydrogens!? Well we know we have a couple magnetic fields already the shielding field of the electrons around the nuclei & the applied magnetic field. But now if the molecule in question has pi bonds or aromatic rings, in the presence of an external magnetic field these electrons in the pi bonds or rings are forced to rotate around the bond axis and therefore cause their own, and a third magnetic field.

If you see the pi electrons induced magnetic field opposes the direction of B0 in certain areas and then is in the same direction as B 0 in other areas. When the induced magnetic field is in the direction of B it reinforces it and causes more affect magnetic field strength at the nuclei in question. When the magnetic field magnetic field is NOT in the same direction of B0 then the magnetic field generated by the electron circulating around the pi bonds at a particular place are able to reduce the effective magnetic field strength in that area and around the nuclei in that area. Also one must consider where this circulation of electrons is around and in what direction it is compared to the magnetic field. The diagram above shows the areas in which a (+) indicates the direction of the magnetic field is going against the external or applied magnetic field, this causes shielding. Conversely the (-) negative signs denote the areas where the magnetic field generated by circulating pi electrons is in the direction of B 0 and therefore causes deshielding This is where the characteristic chemical shift values can be derived from for many nuclei around or participating in ring and pi bonds. Below are some pictures I have found helpful in explaining this.

NMR: Little Side Notes we probably will forget about.

First we know that we have this n +1, number of neighbors +1. This begs the question why!? Why is this case? Lets take the simplest case: This is a doublet which we will consider:

What I think is important to consider is that we have our peaks one which is shifted somewhat up and somewhat down. If you havent noticed by now the subatomic particles we know and love have a spin and they can also have a magnetic field in the direction of the applied magnetic field or against it. Why this applies to coupling??? In this case the neighboring nuclei can have one of the two. They can be oriented parallel or anti parallel to the magnetic field. Note this is kind of interesting the protons spin is the same direction as its magnetic field. Unlike the electron in which the magnetic moment is opposite to the spin. So if these neighboring nuclei are parallel or oriented with the magnetic field then the strength of the B effective is increased and the nuclei in question lets say its A in this case above has a higher applied magnetic field at the nucleus and therefore is shifted downfield a bit. Then what if the neighboring nuclei were antiparallel or oriented against the magnetic field. Well then there opposing magnetic moment would reduce the applied or effective magnetic field at the nucleus in question in this case A. So we will see due to the orientation of the neighboring proton (or protons) spin there can be a shift up or downfield of the chemical shift. Both of these are then displayed on the NMR graph. Odd Ball out : Non- first order coupling For this course we will mainly be dealing with neighbors that have equal J distance but there are often exceptions in which different neighbors, aka nonequivalent Hs have chemical shifts that are different and cause non first order splitting. Here are some examples to refer to if you get stuck. Doublet of doublets:

For HA the splitting pattern would be a triplet normally but the difference in chemical shift values Hx and HM are to large and therefore the coupling constants denoted by J arent equivalent. We see this in benzene rings that are disubstituted fairly often. See owls for C-NMR for some examples Doublet of Triplets Below is an example of an aldehyde with a doublet of triplets.
SpinWorks 2.5: 1D Proton

1.924 2.48 2.46 2.44 2.42 2.40

PPM

9.86

9.84

9.82

9.80

9.78

9.76

9.74

9.72

9.70

file: C:\Documents and Settings\Weitu\Desktop\AlkemystNMR\cs-nonanalsm\1\fid expt: <zg30> transmitter freq.: 300.131853 MHz time domain size: 32768 points width: 6172.84 Hz = 20.567092 ppm = 0.188380 Hz/pt number of scans: 16

freq. of 0 ppm: 300.130000 MHz processed size: 32768 complex points LB: 0.000 GB: 0.0000

When it comes to benzene rings some people have had issues this should assist with explaining why we might see the doublet of doublets or triplets in these cases.

While you might not have to know the background and simply be able to recognize what this means for the structure this might have discern what is going on.