principles and application spectroscopy

VCE Professional DevelopmentModern Analytical Techniques;

IR, NMR & MS.Dr Chris Thompson

December 2007School of ChemistryMonash 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)


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 doesn’t really look like a ball, nor does a chemical bond look like a stick, right?

12

(k/1/2

frequencyreduced massk = force constant


IR Spectroscopy

12

(k/1/2

Molecule k / aJÅ-2

F2 (F−F) 4.45

O2 (O=O) 11.41

N2 (N≡N) 22.41


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 CCstretch


IR SpectroscopyThe IR Spectrum of Ethanol

Wavenumber / cm-1 Strength Vibrational mode900 w C-C stretch1080 s C-O stretch1260 m O-H bend1400 m C-H bend

2800-3000 s C-H stretch3650 m O-H stretch


IR Spectroscopy The IR Spectrum of Ethanol;

Tabulating IR data


IR Spectroscopy Identifying Functional Groups

C H stretch

ALKANES

~2850-2950 cm-1

C H bend ~1350-1450 cm-1

CH2 rock ~720 cm-1

C H stretch

ALKENES

~3000-3100 cm-1

C H bend ~800-1000 cm-1

C stretch ~1600-1700 cm-1C

C H stretch

ALKYNES

~3250-3350 cm-1

C H bend ~630 cm-1

C stretch ~2100 cm-1C

O H stretch

ALCOHOLS

~3200-3650 cm-1

O H bend ~1330-1420 cm-1

C stretch ~1000-1260 cm-1O

C C stretch

AROMATICS

~1600 & 1400-1500 cm-1

C H strecth ~3000 cm-1


IR Spectroscopy Identifying Functional Groups

O C sym. stretch

ETHERS

~1050 cm-1

O C asym. stretch ~1250 cm-1

MOLECULES WITH CARBONYL GROUPS (C=O)

N H stretch

AMINES

~3250-3450 cm-1

N H bend ~1600-1650 cm-1

C stretch ~1000-1250 cm-1N

C

C

C

O

R G

Functional groupKetoneAldehydeCarboxylic Acid

Acid Chloride

Acid Fluoride

-G

-H-OH

-Cl

-F

-R~1720-1740~1750-1770

~1775-1815

~1870

~1680-1720cm-1 Functional group

Ester/LactoneAmide/Lactam

-G

-NR-OR

~1650-1700~1735-1750

cm-1

O

OR

O

R

~1750 & 1815

Note: Conjugation in ANY of these systems results in a lowering of the carbonyl stretching frequency!


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.

H3C

CH2

O

H

H

O

CH2

H3C

H

O

CH2

H3C

H

O

CH2

H3C

H

O

CH2

H3C

H

O

CH2

H3C


IR Spectroscopy Sample Questions.

Q. The two IR spectra on the right correspond to two different molecules sharing the same molecular formula; C3H6O.a) Identify which is an alcohol and which is a ketone. b) Propose molecular structures for these two molecules!

C

O

CH3H3C

HC

CH2

H2C

OH


IR Spectroscopy Sample Questions.

Q. The three IR spectra on the right correspond to three different molecules all with a C3 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 20003000 1000

cm-14000


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. 1H, mI = ±½)

• 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.


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.


NMR SpectroscopyUnits - 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.


NMR SpectroscopyShielding - 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 (1H) in alkanes compared to alkenes.

• These differences manifest in changes to the chemical shift.


NMR Spectroscopy1H Proton NMR Spectroscopy - Chemical Shifts

• The most widely used NMR format is utilising 1H.

• 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).



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 -NH2 0.5-3.0

Ether -OCH3 3.9 Aromatic 6.0-9.0

C

O

RH2C CH2R

C OR

H


NMR Spectroscopy1H Proton NMR Spectroscopy - Sample Spectra; Ethanol

What are these 'multiplets'?


NMR SpectroscopySimple Spin Coupling - "J Splitting"

Arises through the coupling of nuclei spin (1H; mI= ±½) with the spin a neighbouring bonding electron**, which then couples to another neighbouring electron, and so on, finally coupling with another nearby nucleus (1H). **Electrons also have spin - ms=±½


NMR SpectroscopySimple Spin Coupling - "J Splitting"

• Often colloquially called "J splitting” as the derived coupling constant is labelled J.• Labelled 2J, 3J, 4J - depending on how many bonds (2, 3, 4 …) the coupling occurs through.• Basic splitting rule for I = ½ 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!


NMR Spectroscopy1H Proton NMR Spectroscopy - Sample Spectra; Ethanol

3J Coupling; n+1 = triplet

3J Coupling;n+1 = quartet


NMR Spectroscopy1H NMR - Sample Spectra; CH3CHClCOOH

3J Coupling; n+1 = doublet

3J Coupling; n+1 = quartet


NMR SpectroscopySample Question

Q. How could 1H NMR be used to distinguish between the two following isomers?

H3C

H2C

CH2

NO2

H3CC

CH3

H NO2

1-nitropropane 2-nitropropane




H3C

H2C

CH2

NO2

1-nitropropane

1.

1. Triplet @ ~1 ppm.2.

2. Sextet @ ~2 ppm.

3. 3. Triplet @ ~4 ppm.




H3CC

CH3

H NO2

2-nitropropane

1.1. Doublet @ ~2 ppm.

2.

2. Septet @ ~4 ppm.3.

3. Doublet @ ~2 ppm.



0246810

The three spectra on the right show the C6 hydrocarbons;

hexane,1-hexene,1-hexyne.

Which spectrum belongs to which? Which of these spectra is the only one to exhibit a singlet?


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


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


Mass Spectrometry

1. Ion Source2. Analyser3. Detector4. Data Acquisition

The Components of a Mass Spectrometer


Mass Spectrometry

1. Ion SourceThe 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)


Mass Spectrometry

2. AnalyserThe Components of a Mass Spectrometer

a) Magnetic deflection


Mass Spectrometry


b) Time-of flight (TOFMS)


Mass Spectrometry


c) RF fields (ie quadrupoles)


Mass Spectrometry

3. DetectorThe Components of a Mass Spectrometer

Faraday Cup


Mass Spectrometry

3. DetectorThe Components of a Mass Spectrometer

Micro-channel plates


Mass Spectrometry

1. Molecular Mass2. Molecular Structure

(fragmentation)3. Elemental composition

(ICP-MS)**Not discussed in this presentation.

What sort of information can we get from MS?


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.



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 (CnH2n).



Mass Spectrometry

1. Molecular Mass - Example Problem.


CnH2n

n = ?

84

5741

2769


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* ∴ Malkene = 84, ie. 84 = n ×12 + 2n ×1

n = 84/(12+2) n = 6* ∴ The alkene is C6H12 - hexene.

* But is it 1-hexene, 2-hexene or 3-hexene?!?!?!?



Mass Spectrometry

2. Molecular Structure - Fragmentation


CnH2n

n = ?

84

5741

2769


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!



Mass SpectrometryHyphenated 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!


Mass SpectrometryHyphenated 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!GC-MS

MS (Mass Spectrometer)

GC (Gas Chromatograph)


Mass SpectrometryOnline GC-MS Tutorial

Website:http://www.shsu.edu/~chm_tgc/sounds/sound.html

Namely:http://www.shsu.edu/%7Echm_tgc/sounds/GC-MS.movhttp://www.shsu.edu/%7Echm_tgc/sounds/gcms.movhttp://www.shsu.edu/%7Echm_tgc/sounds/SIM.mov

Now go forth and train our VCE students to be

spectroscopy specialists!

principles and application spectroscopy

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