IR, NMR & MS. Dr Chris Thompson December 2007 School of Chemistry Monash University Understanding & Identifying Molecular Structure Infrared Spectroscopy (IR) Nuclear Magnetic Resonance Spectroscopy (NMR) Mass Spectrometry (MS) Atomic Absorption Spectroscopy (AAS) Ultraviolet/Visible Spectroscopy (UV/Vis) Understanding & Identifying Molecular Structure IR Spectroscopy Ball and stick figure of an ethanol molecule. But exactly what is the ball, and for that matter, what is the stick? An atom doesnt really look like a ball, nor does a chemical bond look like a stick, right? n 1 2 (k/ 1/2 n frequency reduced mass k = force constant Understanding & Identifying Molecular Structure IR Spectroscopy n 1 2 (k/ 1/2 Molecule k / aJ -2
F 2 (FF) 4.45 O 2 (O=O) 11.41 N 2 (NN) 22.41 Understanding & Identifying Molecular Structure IR Spectroscopy Several Force Constants Note: IR spectra are typically presented in units called wavenumber, or more correctly, reciprocal centimetres (cm -1 ). Increasing wavenumber corresponds to increasing frequency. OH stretch CH stretch CH bend CO stretch OH bend CC stretch Understanding & Identifying Molecular Structure IR Spectroscopy The IR Spectrum of Ethanol Wavenumber / cm -1 Strength Vibrational mode 900 w C-C stretch 1080 s C-O stretch 1260 m O-H bend 1400 m C-H bend 2800-3000 s C-H stretch 3650 m O-H stretch Understanding & Identifying Molecular Structure IR Spectroscopy The IR Spectrum of Ethanol; Tabulating IR data Understanding & Identifying Molecular Structure IR Spectroscopy Identifying Functional Groups C H s t r e t c h A L K A N E S ~ 2 8 5 0 - 2 9 5 0 c m - 1 C H b e n d ~ 1 3 5 0 - 1 4 5 0 c m - 1 C H 2 r o c k ~ 7 2 0 c m - 1 C H s t r e t c h A L K E N E S ~ 3 0 0 0 - 3 1 0 0 c m - 1 C H b e n d ~ 8 0 0 - 1 0 0 0 c m - 1 C s t r e t c h ~ 1 6 0 0 - 1 7 0 0 c m - 1 C C H s t r e t c h A L K Y N E S ~ 3 2 5 0 - 3 3 5 0 c m - 1 C H b e n d ~ 6 3 0 c m - 1 C s t r e t c h ~ 2 1 0 0 c m - 1 C O H s t r e t c h A L C O H O L S ~ 3 2 0 0 - 3 6 5 0 c m - 1 O H b e n d ~ 1 3 3 0 - 1 4 2 0 c m - 1 C s t r e t c h ~ 1 0 0 0 - 1 2 6 0 c m - 1 O C C s t r e t c h A R O M A T I C S ~ 1 6 0 0 & 1 4 0 0 - 1 5 0 0 c m - 1 C H s t r e c t h ~ 3 0 0 0 c m - 1 Understanding & Identifying Molecular Structure IR Spectroscopy Identifying Functional Groups O C s y m . s t r e t c h E T H E R S ~ 1 0 5 0 c m - 1 O C a s y m . s t r e t c h ~ 1 2 5 0 c m - 1 M O L E C U L E S W I T H C A R B O N Y L G R O U P S ( C = O ) N H s t r e t c h A M I N E S ~ 3 2 5 0 - 3 4 5 0 c m - 1 N H b e n d ~ 1 6 0 0 - 1 6 5 0 c m - 1 C s t r e t c h ~ 1 0 0 0 - 1 2 5 0 c m - 1 N C C C O R G F u n c t i o n a l g r o u p K e t o n e A l d e h y d e C a r b o x y l i c A c i d A c i d C h l o r i d e A c i d F l u o r i d e - G - H - O H - C l - F - R ~ 1 7 2 0 - 1 7 4 0 ~ 1 7 5 0 - 1 7 7 0 ~ 1 7 7 5 - 1 8 1 5 ~ 1 8 7 0 ~ 1 6 8 0 - 1 7 2 0 c m - 1 F u n c t i o n a l g r o u p E s t e r / L a c t o n e A m i d e / L a c t a m - G - N R - O R ~ 1 6 5 0 - 1 7 0 0 ~ 1 7 3 5 - 1 7 5 0 c m - 1 O O R O R ~ 1 7 5 0 & 1 8 1 5 Note: Conjugation in ANY of these systems results in a lowering of the carbonyl stretching frequency! Understanding & Identifying Molecular Structure IR Spectroscopy The origin of broad -OH and -NH bands. gas liquid Hydrogen bonding results in lower electron density at each oxygen, thus lowering the force constant, k, thus lowering (& broadening) the frequency for the mode. H 3 C CH 2 O H H O CH 2 H 3 C H O CH 2 H 3 C H O CH 2 H 3 C H O CH 2 H 3 C H O CH 2 H 3 C Understanding & Identifying Molecular Structure IR Spectroscopy Sample Questions. Q. The two IR spectra on the right correspond to two different molecules sharing the same molecular formula; C 3 H 6 O. a) Identify which is an alcohol and which is a ketone. b) Propose molecular structures for these two molecules!
C O C H 3 H 3 C H C C H 2 H 2 C O H Understanding & Identifying Molecular Structure IR Spectroscopy Sample Questions. Q. The three IR spectra on the right correspond to three different molecules all with a C 3 carbon chain but different degrees of unsaturation. a) Identify which of these is propane, propene and propyne. b) Label each peak with the relevant vibrational mode. Satisfy yourself that some features unambiguously identify some kinds of functional groups 2000 3000 1000 cm -1
4000 Understanding & Identifying Molecular Structure NMR Spectroscopy Basic Principle Technique applying exclusively to nuclei with spin. I 0 In a magnetic field, these nuclei become non-degenerate (differ in energy) due to differences in spin. (eg. 1 H, m I = ) Electromagnetic radiation, at frequencies corresponding to the difference in energy, can resonate with some nuclei and it is absorbed. 'Shielding' from the local chemical environment means resonance can occur across a variety of frequencies. Understanding & Identifying Molecular Structure NMR Spectroscopy Basic Principle Therefore, these frequencies have embedded information regarding the local chemical environment - ie. the functional groups. These differences are measured on a scale of chemical shift. NMR has subsequently become one of the most powerful techniques for determining molecular structure, now extending to species as large as proteins. Understanding & Identifying Molecular Structure NMR Spectroscopy Units - Chemical Shift (ppm) The units for chemical shift usually appear as ppm, typically in the range 0-10. But what does this mean? The chemical shift is the difference in the magnitude of the precession frequency between two nuclei with different spin "" (Hz) in a some magnetic field "B (MHz). Since this is dependant on the strength of the magnetic field, we often express the chemical shift as the quotient; B (Hz/MHz, thus ppm) This allows us to compare chemical shift measured on different instruments. Understanding & Identifying Molecular Structure NMR Spectroscopy Shielding - What is it? While nuclei with spin are perturbed by a magnetic field, the electrons in the vicinity also serve to shield the nuclei to a degree. Thus, the degree of perturbation is going to be different depending on where the electrons are with respect to the nuclei. For example there will be a difference between hydrogen atoms ( 1 H) in alkanes compared to alkenes. These differences manifest in changes to the chemical shift. Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H Proton NMR Spectroscopy - Chemical Shifts The most widely used NMR format is utilising 1 H. The chemical shifts for protons with respect to different functional groups are well known. Note: Proton NMR is the underlying principle for the now common medical procedure of MRI (Magnetic Resonance Imaging). Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H Proton NMR Spectroscopy - Chemical Shifts Functional Group Chemical Shift Functional Group Chemical Shift Name Structure ppm Name Structure ppm Alkane 0-2.0 Ketone 2.0-3.0 Alkene 4.3-7.3 Aldehyde 9.0-10.0 Alkyne 2.0-3.0 Acid -COOH 10-13.5 Alcohol -OH 0.5-4.0* Amine -NH 2
0.5-3.0 Ether -OCH 3
3.9 Aromatic 6.0-9.0 C O RH 2 C CH 2 R C O R H Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H Proton NMR Spectroscopy - Chemical Shifts Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H Proton NMR Spectroscopy - Sample Spectra; Ethanol What are these 'multiplets'? Understanding & Identifying Molecular Structure NMR Spectroscopy Simple Spin Coupling - "J Splitting" Arises through the coupling of nuclei spin ( 1 H; m I = ) with the spin a neighbouring bonding electron**, which then couples to another neighbouring electron, and so on, finally coupling with another nearby nucleus ( 1 H). **Electrons also have spin - m s = Understanding & Identifying Molecular Structure NMR Spectroscopy Simple Spin Coupling - "J Splitting" Often colloquially called "J splitting as the derived coupling constant is labelled J. Labelled 2 J, 3 J, 4 J - depending on how many bonds (2, 3, 4 ) the coupling occurs through. Basic splitting rule for I = nuclei; # of peaks = n+1 where n is the number of neighbouring, equivalent nuclei.
In other words, the splitting is a clue as to the chemical structure of the local environment! Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H Proton NMR Spectroscopy - Sample Spectra; Ethanol 3 J Coupling; n+1 = triplet 3 J Coupling; n+1 = quartet Understanding & Identifying Molecular Structure NMR Spectroscopy 1 H NMR - Sample Spectra; CH 3 CHClCOOH 3 J Coupling; n+1 = doublet 3 J Coupling; n+1 = quartet Understanding & Identifying Molecular Structure NMR Spectroscopy Sample Question Q. How could 1 H NMR be used to distinguish between the two following isomers? H 3 C H 2 C C H 2 N O 2 H 3 C C C H 3 H N O 2 1-nitropropane 2-nitropropane Understanding & Identifying Molecular Structure NMR Spectroscopy Sample Question Q. How could 1 H NMR be used to distinguish between the two following isomers? H 3 C H 2 C C H 2 N O 2 1-nitropropane 1. 1. Triplet @ ~1 ppm. 2. 2. Sextet @ ~2 ppm. 3. 3. Triplet @ ~4 ppm. Understanding & Identifying Molecular Structure NMR Spectroscopy Sample Question Q. How could 1 H NMR be used to distinguish between the two following isomers? H 3 C C C H 3 H N O 2 2-nitropropane 1. 1. Doublet @ ~2 ppm. 2. 2. Septet @ ~4 ppm. 3. 3. Doublet @ ~2 ppm. Understanding & Identifying Molecular Structure NMR Spectroscopy Sample Question 0 2 4 6 8 10 The three spectra on the right show the C 6 hydrocarbons;
hexane, 1-hexene, 1-hexyne.
Which spectrum belongs to which? Which of these spectra is the only one to exhibit a singlet? Understanding & Identifying Molecular Structure Mass Spectrometry Discovery of isotopes Determination of molecular weights Characterization of new elements Qualitative and quantitative analyses Sequence identification (proteomics) Stable isotope labeling and enrichment Identification of trace elements, pollutants, and drugs Counter-terrorism, detection of chemical agents Understanding & Identifying Molecular Structure Mass Spectrometry Molecules can be ionised via a number of different methods, meaning they are either positively or negatively charged. Charged particles can be manipulated by the presence of an electric or magnetic field. This effect is dependant on several parameters including the mass (m) and the charge (z) of the particle. Mass spectrometers give us information about the molecular mass and more! Basic Principle Understanding & Identifying Molecular Structure Mass Spectrometry 1. Ion Source 2. Analyser 3. Detector 4. Data Acquisition The Components of a Mass Spectrometer Understanding & Identifying Molecular Structure Mass Spectrometry 1. Ion Source The Components of a Mass Spectrometer Atmospheric Pressure Chemical Ionisation (APCI) Chemical Ionisation (CI) Electron Impact (EI) Electrospray Ionisation (ESI) Fast Atom Bombardment (FAB) Field Desorption / Field Ionisation (FD/FI) Matrix Assisted Laser Desorption Ionisation (MALDI) Thermospray Ionisation (TSP) Understanding & Identifying Molecular Structure Mass Spectrometry 2. Analyser The Components of a Mass Spectrometer a) Magnetic deflection Understanding & Identifying Molecular Structure Mass Spectrometry 2. Analyser The Components of a Mass Spectrometer b) Time-of flight (TOFMS)
Understanding & Identifying Molecular Structure Mass Spectrometry 2. Analyser The Components of a Mass Spectrometer c) RF fields (ie quadrupoles) Understanding & Identifying Molecular Structure Mass Spectrometry 3. Detector The Components of a Mass Spectrometer Faraday Cup Understanding & Identifying Molecular Structure Mass Spectrometry 3. Detector The Components of a Mass Spectrometer Micro-channel plates Understanding & Identifying Molecular Structure Mass Spectrometry 1. Molecular Mass 2. Molecular Structure (fragmentation) 3. Elemental composition (ICP-MS)* *Not discussed in this presentation. What sort of information can we get from MS? Understanding & Identifying Molecular Structure Mass Spectrometry 1.Molecular Mass * A molecule is ionised, preferably with a known charge. * Charged particles (ions) experience a force when in the presence of an electric or magnetic field. * Using the appropriate algebraics of specific analysers, the behaviour of the particle in the field can be used to determine mass-to-charge ratio (m/z), thus indirectly the molecular mass. * The charge, z, is usually = 1. What sort of information can we get from MS? Understanding & Identifying Molecular Structure Mass Spectrometry 1. Molecular Mass - Example Problem. Q. IR & NMR data suggest an unknown molecule to be an alkene, however the molecular formula is not known. How can MS solve this problem? A. The molecular mass can unambiguously be determined using MS, which can in turn be used to determine (n) for the molecular formula of the alkene (C n H 2n ). What sort of information can we get from MS? Understanding & Identifying Molecular Structure Mass Spectrometry 1. Molecular Mass - Example Problem. What sort of information can we get from MS? C n H 2n n = ? 84 57 41 27 69 Understanding & Identifying Molecular Structure Mass Spectrometry 1. Molecular Mass - Example Problem. * The molecular ion is almost always the peak with the largest m/z value. * (Remember, MS measures m/z, but usually z = 1.) * So in this case, the molecular ion is 84 * M alkene = 84, ie. 84 = n 12 + 2n 1 n = 84/(12+2) n = 6 * The alkene is C 6 H 12 - hexene. * But is it 1-hexene, 2-hexene or 3-hexene?!?!?!?
What sort of information can we get from MS? Understanding & Identifying Molecular Structure Mass Spectrometry 2. Molecular Structure - Fragmentation What sort of information can we get from MS? C n H 2n n = ? 84 57 41 27 69 Understanding & Identifying Molecular Structure Mass Spectrometry 2. Molecular Structure - Fragmentation - Subtle differences in fragmentation patterns can be explained by the fragmentation mechanisms - Of course NMR can also be used to differentiate between these structural isomers!
What sort of information can we get from MS? Understanding & Identifying Molecular Structure Mass Spectrometry Hyphenated techniques; GC-MS * GC-MS & LC-MS ARE high resolution separation techniques, capable of detecting trace concentrations of most compounds; drugs, explosives, herbicides & pesticides, secondary metabolites - No inherent identification ability * Mass spectrometry is an identification technique capable of producing a unique 'fingerprint for any given compound. - Poor at compound separation * IN UNISON, THESE TWO TECHNIQUES FORM AN EXTREMELY POWERFUL FORENSIC TOOL!
Understanding & Identifying Molecular Structure Mass Spectrometry Hyphenated techniques; GC-MS Excellent in separation and quantitation Poor in identification Excellent in identification and quantitation Poor in separation Excellent in separation, identification and quantitation! MS (Mass Spectrometer) GC (Gas Chromatograph) Understanding & Identifying Molecular Structure Mass Spectrometry Online GC-MS Tutorial Website: http://www.shsu.edu/~chm_tgc/sounds/sound.html
Namely: http://www.shsu.edu/%7Echm_tgc/sounds/GC-MS.mov http://www.shsu.edu/%7Echm_tgc/sounds/gcms.mov http://www.shsu.edu/%7Echm_tgc/sounds/SIM.mov Now go forth and train our VCE students to be spectroscopy specialists!