KHS ChemistryUnit 3.4 Structural Analysis1 Structural Analysis 3 Adv Higher Unit 3 Topic 4 Gordon Watson Chemistry Department, Kelso High School

KHS Chemistry Unit 3.4 Structural Analysis 1

StructuralStructuralAnalysis 3Analysis 3

Adv Higher Unit 3 Topic 4Adv Higher Unit 3 Topic 4

Gordon WatsonGordon Watson

Chemistry Department, Kelso High SchoolChemistry Department, Kelso High School


IntroductionIntroduction

This topic continues to explore methods used in the Structural Structural AnalysisAnalysis of organic molecules including NMR SpectroscopyNMR Spectroscopy and X-Ray CrystallographyX-Ray Crystallography.


Nuclear SpinNuclear Spin

Nuclei with an odd mass or odd atomic number, eg 1H, have “nuclear spinnuclear spin” (in a similar fashion to the spin of electrons).

+ +

Since a nucleus is a charged particle in motion, it will develop a magnetic fieldmagnetic field.

The The magnetic fieldmagnetic field generated by a nucleus of spin +generated by a nucleus of spin +11//22 is is opposite opposite

in directionin direction from that generated by a nucleus of spin – from that generated by a nucleus of spin –11//22..


OrientationOrientation

+

+

+

+

+

The distribution of The distribution of nuclear spins is nuclear spins is randomrandom in the in the absence of an absence of an externalexternal magnetic magnetic field.field.


Magnetic FieldMagnetic FieldWhen a field is applied they line up parallelline up parallel to the applied field, either spin alignedspin aligned or spin spin opposedopposed.

+

++

+

+

MagneticField, Ho


Energy LevelsEnergy LevelsEnergy levelsEnergy levels between the spin alignedspin aligned and spin spin opposedopposed states are slightly different.

+

++

+

+

MagneticField, Ho

There is a slight excessslight excess of nuclear magnetic moments spin alignedspin aligned parallel to the applied field, (lower energylower energy).


Magnetic Field StrengthMagnetic Field Strength

EE E E ''

increasing field strengthincreasing field strength

+

+

The splitting of the energy levels is proportional to the strengthstrength of the magnetic field. Low energy - radio wavesradio waves


Proton ResonanceProton Resonance

APPLIED FIELD

E

RadioFrequency

in

RadioFrequency

out


NMR SpectrometerNMR Spectrometer

The basic arrangement of an NMR spectrometerNMR spectrometer is shown above.


RelationshipsRelationships

The frequency of absorbed electromagnetic radiation is The frequency of absorbed electromagnetic radiation is different for different for

different elementsdifferent elements, and for different isotopes of the same element., and for different isotopes of the same element.

For a field strength of 4.7 T (4.7 x 10For a field strength of 4.7 T (4.7 x 1044 gauss): gauss):11HH absorbs radiation having a frequency of 200 MHz (200 x 10 absorbs radiation having a frequency of 200 MHz (200 x 1066 s s-1-1))1313CC absorbs radiation having a frequency of 50.4 MHz (50.4 x 106 s-1)

The frequency of absorbed electromagnetic radiation for a particular The frequency of absorbed electromagnetic radiation for a particular

nucleus (such as nucleus (such as 11H) depends on its H) depends on its molecularmolecular environmentenvironment..

This is what makes NMR spectroscopy such a useful tool.


Molecular EnvironmentMolecular Environment

H

HH

H H

HH

O

H

H

H

HH

HH

H

butanone


Reference MoleculeReference Molecule

TMS is given a value of 0.

CH3

C H3

C H3

C H3

Si

TetramethylsilaneTetramethylsilane, TMS, is used as a reference molecule.

All the hydrogens are in an identical environmentidentical environment and, more importantly, are far enough apart (with a Si shieldingshielding them) to have no coupling effect on no coupling effect on each othereach other.

The values for hydrogen atoms in other molecules will be shiftedshifted, due to the deshieldingdeshielding effect of other atoms in the molecule.

The values for equivalent hydrogen atoms can be slightly different due to the coupling coupling effect of adjacent adjacent hydrogen atoms.


NMR SpectrumNMR Spectrum

These hydrogens have been shiftedshifted least, and their signal has been split split into 3 by the coupling coupling effect of the 2 adjacent hydrogens2 adjacent hydrogens.

O

H

H

H

HH

HH

H

3H2H

3H

03 2 1

CH3

CH3

CH3

CH3SiThese hydrogenshydrogens have been shiftedshifted more, but their signal has not been split split due to the absence of adjacent hydrogensadjacent hydrogens.

These hydrogenshydrogens have been shiftedshifted most, and their signal has been split split into 4 due to the presence of 3 adjacent hydrogensadjacent hydrogens.


More VocabularlyMore Vocabularly

It is often convienient to describe the relative positions of the resonancesresonances in an NMR spectrum.

For example, a peak at a chemical shift, , of 10 ppm is said to be downfielddownfield or deshieldeddeshielded with respect to a peak at 5 ppm, or if you prefer, the peak at 5 ppm is upfieldupfield or shieldedshielded with respect to the peak at 10 ppm.


ShieldingShielding

Since this reducesreduces the field experienced at the nucleus, the electrons are said to shieldshield the proton

appliedmagnetic

fieldinduced

magnetic field

sigmaorbital

The electrons around the proton create a magnetic field that opposesopposes the applied field.


DeshieldingDeshielding

H C X

X = electronegative atom

Anything that pulls electronspulls electrons away from the hydrogen atom will reduce the shieldingreduce the shielding effect of the sigma electrons.


ElectronegativityElectronegativityCHCH33FF 4.3 ppm4.3 ppm least shielded H least shielded H big shiftbig shift

CHCH33OOCHCH33 3.2 ppm 3.2 ppm

CHCH33NN(CH(CH33))22 2.2 ppm 2.2 ppm

CHCH33CHCH33 0.9 ppm 0.9 ppm

CHCH33SiSi(CH(CH33))33 0.0 ppm 0.0 ppm most shielded Hmost shielded H no shiftno shift

TMSH3C-IH3C-F H3C-Cl

H3C-Br

The more electronegative the group, the greater the shift.The more electronegative the group, the greater the shift.


Quantity & DistanceQuantity & Distance

CHCHClCl33 7.3 ppm 7.3 ppm

CHCH22ClCl2 2 5.3 ppm 5.3 ppm

CHCH33ClCl 3.1 ppm 3.1 ppmThe larger the number of electronegative groups present, the The larger the number of electronegative groups present, the greater the shift.greater the shift.

TMSH3C-Cl H3C-C-Cl

The closer to the electronegative group, the greater the shift.The closer to the electronegative group, the greater the shift.


More DeshieldingMore Deshielding

The magnetic field goes downdown through the centre of the ring and up up through the hydrogen atoms on the outside.

HHH

HHCH3applied

magneticfield

induced magnetic fieldPi electronsPi electrons (in muliple bonds) are perpendicular to sigma electrons.


Pi BondsPi Bonds

Spectrum of methylbenzene (toluene).

TMS

3H

5H

2

IntegrationIntegration of the peaks will supply you with the number number of hydrogens.

HH HH

HHHH

HH

HH

CC CC

HHHH

HH HHCCHH33CCHH33

7.3 ppm7.3 ppm 5.3 ppm5.3 ppm 0.9 ppm0.9 ppm


IntegrationIntegration

CH3 CH2 I

Most of the time you can expect to be told the number of H atoms at each position. Alternatively, the relative heightsrelative heights of the integrations, (along with molecular formula), can be used.


H-NMR Chemical ShiftsH-NMR Chemical ShiftsIn ‘Theory’ Shifts can be used to identify which typetype of molecule the hydrogens are in.

In reality, IR spectroscopy will have identified the type of molecule. NMR is mainly used to help identify the position of the hydrogens.


Splitting - CouplingSplitting - Coupling

O

H

H

H

HH

HH

H

3H2H

3H

03 2 1

Protons have themselves small magnetic fields. These can increase, or decrease, slightly the magnetic field experienced by adjacent adjacent hydrogens. This is called couplingcoupling.

Any effect on Hydrogens on the same carbonsame carbon is already part of the value measured by the NMR spectrometer, while Hydrogens 3 bonds away, —C—C—H, are too far to feel an effect.


Coupling - 1 hydrogenCoupling - 1 hydrogen

An isolated H atom would produce a single peak C

HA

If a single hydrogensingle hydrogen is present on the adjacent carbon then two possibilitiestwo possibilities exist.C

HA

C

HX

or

The field of the hydrogen can align withalign with or against against the magnetic field - two slightly different shifts - a doubletdoublet.


Coupling - 2 hydrogensCoupling - 2 hydrogens

If two hydrogenstwo hydrogens are present on the adjacent carbon then four possibilitiesfour possibilities exist.

Three slightly different shifts - a triplettriplet.

C

HA

C

HX

HX

or or or

These two combinations would have same effect.


A Pattern EmergesA Pattern Emerges

0 adjacent hydrogens 0 adjacent hydrogens - a singletsinglet produced

1 adjacent hydrogen 1 adjacent hydrogen - a doubletdoublet produced

2 adjacent hydrogens 2 adjacent hydrogens - a triplet triplet produced

3 adjacent hydrogens 3 adjacent hydrogens - a quadruplet quadruplet produced

4 adjacent hydrogens 4 adjacent hydrogens - a quintuplet quintuplet produced


Information in NMR SpectrumInformation in NMR Spectrum

number of signalsnumber of signals - - number of different typesdifferent types of hydrogens.

their intensitytheir intensity (as measured by relative areas under peak

….called integration,gives integral values) - numbernumber of each

type of hydrogen.

their shift, their shift, - proximity to electronegativeproximity to electronegative groups/

pi electrons etc.

splitting patternsplitting pattern (couplingcoupling) - how many hydrogens on

adjacent carbons.


Spectrum ExplainedSpectrum Explained

O

H

H

H

HH

HH

H

3H2H

3H

03 2 1


Spectrum 1Spectrum 1












Spectrum 7aSpectrum 7aA more ‘realistic’ problem:

C11H14O2Elemental analysis has shown that the empirical formula of a compound is

178 amuMass Spectrum shows the molecular ionmolecular ion to be:

C=O

aromatic

The IR Spectrum shows the presence of a carbonyl groupcarbonyl group, , no hydroxyl group, no aldehyde hydrogens, and a busy fingerprint region idicative of aromaticaromatic :

Molecular FormulaMolecular Formula CC1111HH1414OO22

Phenyl group (CPhenyl group (C66HH55) , ester group COO, leaving C) , ester group COO, leaving C44HH99..


Spectrum 7bSpectrum 7b3H at 0.9 must be CH3 next to CH2 (triplettriplet)

2H at 2.1 must be CH2 next to CH3 (quadrupletquadruplet)

2H at 2.8 must be CH2 next to CH2 (triplettriplet)


H’s at 0.9 and 2.1 must be —CH2CH3 - low shift suggests attached to C=O rather than —O—.

5H at 7.2 must be aromaticaromatic

H’s at 2.8 and 4.4 must be —CH2CH2 - highest shift (4.4) probably attached to —O— while lower shift (2.8) is attached to phenyl group.


Spectrum 7bSpectrum 7b3H at 0.9 must be CH3 next to CH2 (triplettriplet)

2H at 2.1 must be CH2 next to CH3 (quadrupletquadruplet)



H’s at 0.9 and 2.1 must be —CH2CH3 - low shift suggests attached to C=O rather than —O—.

5H at 7.2 must be aromaticaromatic

H’s at 2.8 and 4.4 must be —CH2CH2 - highest shift (4.4) probably attached to —O— while lower shift (2.8) is attached to phenyl group.


X-RaysX-Rays


X-Ray CrystallographyX-Ray Crystallography

x-rays scatteredby crystal

x-ray source

beam of x-rays

crystal

x-ray sensitivephotographic film


ScatteringScattering

The layers of atoms in the molecules make the crystal act like a diffraction gratingdiffraction grating causing the x-rays to scatterscatter.

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H

O

Cl

Cl

Cl

H


Diffraction PatternDiffraction Pattern

The diffraction patterndiffraction pattern of spots that is obtained is then used to create an electron density mapelectron density map.


Electron Density MapElectron Density Map

O

Cl

Cl

Cl

H

Electron density mapElectron density map of trichlorophenol compared with the structural formula


End of Topic 4End of Topic 4

StructuralStructuralAnalysis 3Analysis 3

Documents

KHS ChemistryUnit 3.4 Structural Analysis1 Structural Analysis 3 Adv Higher Unit 3 Topic 4 Gordon Watson Chemistry Department, Kelso High School