rganic Structure Determination Analytical hemistry Instrument-based methods for determination of structure of organic molecules 1) Infrared Spectroscopy - yields functional groups 2) M Spectroscopy - very important, yields structure - described in the next section of the notes 1 Infrared Spectroscopy molecules at room temperature are very hot, they don't seem to be very hot, but relative to absolute zero (where molecules have essentially no energy), molecules at room temperature have a lot of energy (they are hotter by 273 degrees ), and this energy has to "go" somewhere. In molecules, this energy goes into kinetic energy if they are in the gas or liquid phase, but importantly also into bond vibrations. Electromagnetic adiation (light!) Electromagnetic radiation consists of an oscillating orthogonal (right angles) electric and magnetic fields the energy in electromagnetic radiation is determined by the oscillation frequency of the electric (and magnetic) field vectors, and is given the symbol Greek n (pronounced "nu" and which looks sort of like a v) the energy in electromagnetic radiation is ALS determined by the wavelength of the electric (and magnetic) field vectors, and is given the symbol Greek l (pronounced "lambda" and which looks sort of like a v) the wavelength and frequency of electromagnetic radiation are related via the speed of light we do not need to get into these equations in detail (although they are quite simple), what we need to know is that energy in electromagnetic radiation is DIETLY proportional to frequency, and IVESELY proportional to wavelength, i.e., energy increases with increasing frequency. Electric Field λ = wavelength M ag ne t ic i e l d f Energy (E) = Direction λ (wavelength) = c (speed of light) ν (frequency) c = speed of light h = Plank constant h c λ Energy (E) = hν The Electromagnetic Spectrum wavelength, λ (meters) 10 3 1 10-5 5x10-7 5x10-8 5x10-8 5x10-10 frequency, ν (s -1 ) 10 5 10 9 5x10 13 10 14 10 14 10 17 10 19 increasing energy radio micro visible ultraviolet X-ray gamma ν (s -1 ) infrared ~ 10 13 ~ 10 14 E (kcal/mol) ~ 0.8 ~ 8 "frequency" (cm -1 ) ~ 300 ~ frequencies match frequencies for bond vibrations The range of frequencies of the electromagnetic radiation in the infrared matches the range of frequencies of vibrations of bonds in molecules. If the frequency of the infrared radiation exactly matches that of a particular bond vibration in a molecule, then the electric field vector of the radiation can interact with the dipole moment of the vibrating bond, the radiation can be absorbed by the molecule and used to increase the bond vibration amplitude. Spectroscopy : page 1
frequency too high, no absorption electric field vector ν > 5x10 13 X higher vibrational state correct frequency, energy absorbed! electric field vector ν = 5x10 13 bond dipole vibration frequency 5x10 13 s -1 ΔE = hν lower vibrational state frequency too low, no absorption electric field vector ν < 5x10 13 X The electromagnetic frequency must EXATLY match the frequency of VIBATI of the bond (I absorption is quantized), if the frequency is higher or lower than the bond vibration frequency it will not be absorbed for I radiation to interact with a vibrating bond, the bond MUST AVE A DIPLE MMET 1.1 A eal Infrared Spectrum many vibrations I absorbance - stretching vibrations WEAK 3 = stretching vibration STG ~5 x 10 13 s -1 3 ν 2 2000 increasing vibration frequency Infrared Vibrations are often localized on bonds or groups of atoms (the more useful vibrations are localized on specific bonds) Different bonds vibrate with different frequencies, this is important as this is the basis for identifying different bonds/functional groups in a spectrum, and hence in a structure We need to know about how many bond vibrations are possible, what their frequencies are also how STG or WEAK the absorptions are, i.e. how "big" they appear in actual spectra 1) ow Many Bond Vibrations Are Possible in a Molecule? For n atoms, there are MAY PSSIBLE vibrations, in fact (3n 6)! owever, many of these are complex, i.e. are not localized on individual bonds, and occur with lower frequencies (less than 1 cm-1) in the "fingerprint ", which is the area that has signals that are specific to a particular molecule, not to a specific functional group, in this class we ignore the fingerprint 2) What are the BD Vibrational Frequencies? Vibrational frequencies are determined by bond strength and atomic mass A bond as "spring" analogy is useful Bonds have IG VIBATI FEQUEIES if they are STG, and have consist of LIGT ATMS Bonds have LW VIBATI FEQUEIES if they are WEAK, and have consist of EAVY ATMS Spectroscopy : page 2 1
bond (vibrating spring) atom atom A strong bond (spring) vibrates with a higher frequency stronger bond (spring) higher frequency vibration bond BDE (kcal/mol) ν (s -1 ) E (cm -1 ) IEASIG bond strength ~85 3 x 10 13 1200 ~145 5 x 10 13 1600 ~200 6 x 10 13 2100 IEASIG frequency A bond (spring) with small/light atoms attached will vibrate with a higher frequency higher frequency vibration lighter smaller atom bond BDE (kcal/mol) ν (s -1 ) E (cm -1 ) DEEASIG mass ~85 3 x 10 13 1200 D ~100 6 x 10 13 2100 ~100 10 14 IEASIG frequency Visualize the how stronger bonds and lighter atoms result in higher vibrational frequencies Approximate egions in the Infrared Spectrum Spectroscopy : page 3
stronger bonds stronger bonds - light atom - - triple bond double bond single bond (fingerprint) vibrations are "mixed" 3 2000 1750 1 increasing vibrational frequency cm -1 decreasing vibrational frequency Bonds to the very light atom have the highest vibrational frequencies, stronger bonds to having the highest frequencies. Triple bonds to heavier atoms come next. Double bonds to heavier elements come next, with higher frequencies for stronger bonds. Single bonds to heavier elements have the lowest frequencies, usually in the fingerprint where identifying functional groups is difficult, and is not included in this course. 3) ow strong are the Absorption Peaks (how big are the peaks in the spectra)? The electric field vector of the electromagnetic radiation interacts with dipole moment of the vibrating bond When the DIETI F TE electric field (vector) of the I electromagnetic radiation is ALIGED with the DIETI F TE BD DIPLE MMET the field can "pull" the atoms apart (if the frequency is matched) and thus increase the amplitude of the vibration (the atoms separate more), in this way the I energy is absorbed into the molecule, the energy is "used" to make the bind vibrate with a larger amplitude It may seem unlikely that the electric field and the bond dipole line up exactly, but in fact there are billions of molecules that are constantly tumbling in space which means that there will be plenty of bonds in the correct alignment, especially because the alignment doesn t have to be perfect Large (change in) dipole moment results in stronger interactions with the electric field vector, which result sin absorption of a lot of I radiation which in turn results strong I absorptions I ν = bond frequency E field vector in paper plane bond dipole AD electric field vector must be ALIGED bond in paper plane larger amplitude vibration I ν ABSBED by the molecule into the - bond as vibration energy To be observed in an I spectrum a bond has to have a dipole moment. Bonds with LAGE DIPLE moments interact more strongly with the electric field vector of the electromagnetic radiation and have STGE (LAGE) absorption signals in an I spectrum. Examples: large dipole moments, STG (large) absorptions small dipole moments, WEAK absorptions very small dipole moment, but there are many, so observed! symmetrical zero dipole moment, no absorption! Spectroscopy : page 4
1.2 eal Absorption Bands Vibrations of - bonds around cm -1 : (2700-3 cm -1 = bonds to atoms) atoms are LIGT, bonds to atoms tend to be high frequency (large nu), ca. 2700-3 cm-1 stronger - bonds will vibrate with higher frequencies, weaker - bonds will vibrate with lower frequencies We KW SMETIG about - bond strengths sp3 sp2 sp increasing bond strength increasing expected vibrational frequency We EXPET that stronger - bonds will have higher frequency absorption in I spectroscopy, and they do! sp 3 < cm-1 for -(sp3) 3 2 2000 peaks due to - vibrations that are found at frequencies less than cm-1 are due to atoms that are attached to sp3 hybridized carbons. Bonds from hydrogen to sp3 carbons are somewhat weaker than bonds to, e.g. sp2 hybridized carbons, and thus are found at somewhat lower frequencies the dipole moments for - bonds are very small, WEVE, there are usually LTS of - bond vibrations, and so they "add up" so that the peaks can still be observed in the spectrum 1 stronger bond sp 2 sp 3 > weaker bond < 3 2 2000 peaks due to - vibrations that are found at frequencies just above cm-1 are due to atoms that are attached to sp2 hybridized carbons. Bonds from hydrogen to sp2 carbons are somewhat stronger than bonds to sp3 hybridized carbons, and thus are found at somewhat higher frequencies 1 Spectroscopy : page 5
weaker absorption ca. 2200 cm -1 only if "terminal" symmetrical internal alkynes very weak usually not observed 3 2 2000 - vibrations around 3300 cm-1 are due to atoms that are attached to sp hybridized carbons. These are stronger bonds with higher vibrational frequencies. They are distinguished from - and - bonds by the fact that they are not broad Vibrations greater than cm -1 : (2700-3 cm -1 = bonds to atoms) Bonds between hydrogen and other elements are also expected to have high frequency vibrations AD, bonds to more electronegative elements than carbon are stronger and are thus expected to vibrate with higher frequencies We therefore EXPET that bonds to more electronegative elements should have higher vibration frequencies because they are stronger similar increasing bond strength increasing vibrational frequency increasing DIPLE MMET - and - bonds ALS AVE larger dipole moments; their I absorption peaks should be stronger 1 large bond dipole, STG absorption 100 95 90 broad 85 80 75 centered ~ 3300 cm -1 1 - vibration as strong as several - vibrations 70 3 2 2000 variable hydrogen-bonding broadens vibrational frequency Spectroscopy : page 6 1
The - bond vibration IS at higher frequencies than - bond vibrations, ca. 3300 cm-1, AD it is strong due to the large bond dipole moment, one - bond is equivalent to many - bonds in absorption strength The alcohol - stretching vibration is broad due to hydrogen-bonding, ydrogen-bonding "pulls" the "away" from the, resulting in a lower frequency vibration, a distribution in ydrogen-bonding results in a distribution in frequencies which results in a broad absorption band The absorption is centered at ca. 3300 cm-1, which distinguished alcohols from carboxylic acids (see later) broad due to variable -bonding 2 "spikes" must be 1 amine centered ~ 3300 cm -1 primary 2 - bonds 2 "spikes" secondary 1 - bond 1 "spike" 3 2 2000 The amine - stretching vibration is also broad due to hydrogen-bonding, but - hydrogen bonding is WEAKE than - ydrogen bonding (nitrogen is less electronegative than oxygen), and some non-hydrogen bonded - vibrations can be observed as small sharp peaks on top of the broad absorption The - bond dipole is also smaller than the - bond dipole ( less electronegative than ) and so - absorptions tend to be somewhat weaker than - absorptions There are usually 2 small (non hydrogen-bonding) peaks for a primary amine that has two - bonds There is usually 1 small (non hydrogen-bonding) peak for a secondary amine that has one - bond f course, a tertiary amine has no - bonds and no signals at all are observed in this in this case. Vibrations of other bonds to ydrogen around cm -1 : (2700-3 cm -1 = bonds to ) 1 WEAKE ydrogen-bonding therefore sharp - vibration peaks A be observed 100 95 90 85 80 75 2 - peaks ca. 2730 and 2820 AD = ca. 1700 70 65 60 3 2 2000 1 Aldehydes have 2 small peaks around 2730 and 2820 for the single - bond that is attached to the = Spectroscopy : page 7
These are sometimes difficult to distinguish, and can range between ca. 2720-2740 and ca. 2810-2830, but the aldehyde also has the strong = stretching vibration at ca. 1700 cm-1 (see further below). bservation of BT vibrational features helps to identify an aldehyde The aldehyde - stretching vibration has a lower frequency than other - bonds due to electron withdrawal from the - bond by the electronegative oxygen VEY broad alcohol ~3300 cm-1 acid ~ cm-1 lower vibration frequency STGE -bonding ~ cm-1 - AD = for acids 3 2 2000 1 ote: Two absorption peaks are observed for carboxylic acids corresponding to - and = vibration arboxylic acids have a broad - peak for the same reason that alcohols do, hydrogen bonding, however, the hydrogen bonding is stronger in carboxylic acids, which results in a lower frequency - stretching vibration compared to an alcohol due to a larger "pull" on the atom away from the oxygen The stronger hydrogen bonding also results in a very broad absorption band broad absorption band that is distinguished from the alcohol - in that it is centered around cm-1, basically right in top of the usual - arboxylic acids are also distinguished from alcohols by having the = stretching vibration at ca. 1700 cm-1 that is very strong (see later). Vibrations around 2-1700 cm -1 : (2000-2 cm -1 = triple bond ) Bonds to atoms heavier than hydrogen vibrate with lower frequencies, the strongest of these are triple bonds There are only two kinds of vibrations observed in this, the - triple bond of the nitrile functional group and the - triple bond of the alkyne functional group ALS - vibration larger DIPLE MMET large bond dipole strong absorption ca. 2250 cm -1 3 2 2000 1 Spectroscopy : page 8
The - triple bond absorptions due to nitrile tend to be strong because the dipole moment associated with this bond is VEY large! weaker absorption ca. 2200 cm -1 X X X X only if "terminal" X X X X symmetrical internal alkynes very weak X X X X X X usually not observed 3 2 2000 cm-1 1 arbon-carbon triple bond absorptions tend to be somewhat weak (the bonds have very small dipole moments) and are only usually observed for the asymmetrical terminal alkynes (alkynes in which one carbon is attached to hydrogen, the other to an alkyl or aryl group). Internal alkynes that have alkyl groups attached to both ends of the triple bond are too symmetrical, too small dipole moments and are usually not observed For terminal alkynes of course, the -(sp) vibration is also observed at ca. 3300 cm-1. Vibrations Around 1850 1600 cm -1 : (1600-1850 cm -1 = double bond ) This is an important of the I spectrum, as usual, stronger bonds vibrate at higher frequencies, which means that = double bonds are expected higher vibrational frequencies than = double bonds, and they do stronger bond: expect higher frequency larger DIPLE MMET: expect stronger absorption weaker bond: lower frequency expect weaker absorption = bonds also have larger bond dipole moments than = bonds, and should have stronger absorptions than = bonds, and they do aldehyde/ketone VEY strong and ~1710 cm-1 3 2 2000 1 Vibrations of the = bond in aldehydes and ketone are VEY strong and occur close to 1700 cm -1, often ca. 1710-1715 cm -1. Aldehydes can be distinguished from ketones because they also have the 2 peaks due to - vibration at ca. 2730 and 2820 cm -1 (which means the spectrum above must be of a ketone because these peaks are absent) Spectroscopy : page 9
small dipole moment, often weak ~1610-1650 cm -1 3 2 2000 = double bonds tend to have small dipole moments and are usually have weak (small) absorptions, the bonds are also weaker than = bonds and vibrate with lower frequencies, ca. 1620 cm -1. Different = Vibrations Around 1730 1680 cm -1 : (1600-1850 cm -1 = double bond ) Small changes in the = bond strength can be detected in small changes in the = vibration frequency These small changes can be quite reliable and can be used to distinguish various kinds of = bonds 1 3 stronger bond means higher frequency ester strong close to 1730 = bond is strong due to TIS electronegative oxygen 2 2000 1 The electronegative oxygen that is connected to the = bond in the ester makes all of the bonds stronger, including the = bond, thus, ester = vibrations occur at relatively high frequencies, around 1720-1730 cm-1 Even though this is only slightly higher than the normal frequencies for = bond vibrations in aldehydes and ketones it is diagnostic enough to distinguish most esters from ketones increases single bond character minor "conjugation" decreases double bond character, weakens bond, lowers = vibration frequency to ~ 1680 cm -1 3 2 2000 1 Spectroscopy : page 10
"onjugated" ketones have a = bond adjacent to the = bond, the minor resonance contributor illustrates that the = bond has some single bond character in these cases. The more important the minor resonance contributor, the more single bond character (the = is less of a pure double bond), the weaker the bond, the lower the vibrational frequency conjugated aldehydes and ketones have vibration frequencies around 1680 cm-1, the difference compared to non-conjugated aldehydes and ketones (ca. 1710 cm-1) is reliable enough to distinguish these cases minor resonance ME important than conjugated example above even LWE vibration frequency minor ~1640 cm -1 3 2 2000 1 The minor resonance contributor for the amide also shows that the = bond has some single bond character In the case of an amide the minor resonance contributor is even more important than the minor contributor in the conjugated system above, because the electrons that are involved in resonance "start" as nonbonding on the nitrogen and are thus higher energy than those in the double bond above, and are thus more "available" for resonance, the minor contributor here is "less minor" the vibration frequency is thus further decreased to ca. 1640 cm-1. Just like amines, the amide will have - vibrations (with peaks) in the 3300 cm-1. MLEULA vibration at 1600 cm -1 : (1600-1850 cm -1 = double bond ) There is one final vibration that is unusual in that it is not of a single bond, but is associated with a stretching motion of an entire benzene ring that is useful to us. 100 90 80 > cm-1 70 60 50 3 2 2000 very sharp, close to 1600 cm-1, very characteristic (but often weak). The peak is often not very strong (because of a small dipole moment again), but is usually sharp and very close to 1600 cm -1, and is thus often easily identified. If there is a benzene ring there should almost always also be (sp2)- bond vibrations, and these will be observed at > cm -1. 1 Spectroscopy : page 11
eturn to eal Spectra: Example: Acetophenone fingerprint (ignore < 1 cm -1 ) 2 ignore sp 2 sp 3 3 ignore conjugated 3 ote that you will need to be able to distinguish "real" peaks from peaks due to impurities or other artifacts, such as water as a contaminant, which is often seen as a weak peak around 3300 cm -1 (any real peaks in this would be strong). ote that a benzene ring adjacent to a = bond represents a common example of a the more generic conjugated = adjacent to =. Example: A hydroxy ketone 2 2000 1 T aldehyde, no 2730 2820 peaks centered ~3300 therefore not acid sp3 all <, therefore no = ignored ca. 1700, therefore ketone or aldehyde 3 2 2000 1 The strong peak at 1710 cm -1 must be an aldehyde or a ketone, in this case it must be a ketone because the two - aldehyde peaks at ca. 2700 and ca. 2800 are not observed. Spectroscopy : page 12
The chart below is what you are provided with on a test to help you assign peaks 4000 small range range of values broad peak 3250-3300 broad with spikes ~3300 broad ~3300-3400 3100 2850 2960 broad ~ 2730 2820 2 peaks usually strong 2200 2200 1600 1660 1680 1710 2 1650 3 2 2000 1 wavenumber, cm -1 1730 1600 Spectroscopy : page 13