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HANDOUT

SPECTROSCOPY ANALYSIS OF CHEMISTRY

bY:

Drs. Tri Santoso ,M.Si

PROGRAM STUDI PENDIDIKAN KIMIA

JURUSAN MATEMATIKA DAN ILMU PENGETAHUAN ALAM

FAKULTAS KEGURUAN DAN ILMU PENDIDIKAN

MARCH, 2010

1. Introduction:
Modern spectroscopic methods have largely replaced chemical tests as the standard means of identifying chemical structures, and for a practising practical organic chemist 1H-NMR has become a routine tool for identifying the products of reactions.

Spectroscopic techniques are based on the absorption of specific forms of energy by a molecule and monitoring the affect that this has on the molecule.

Spectroscopy:

Theoretical Background:

Since spectroscopy is based on the interaction of electromagnetic radiation (EMR) with a molecule, an understanding of electromagnetic radiation is a must.

Spectroscopy monitors the changes in energy states of a molecule, so one must be familiar with the important energy states and concept of quantisation of energy within a molecule.

The part of the electromagnetic radiation spectrum that you are most familar with is "visible light" but this is just a small portion of all the possible types.
Can you think of common applications of other regions of the electromagnetic spectrum ?

Electromagnetic radiation has both particle and wave properties.  Can you think of an example of each ?

Wave-like properties:
It is important to understand wavelength and frequency and how they relate to one another.

Particle-like properties:
A particle of energy is called a photon.  Each photon has a discrete amount of energy : a quantum.

Energy States:
There are many energy 'states' in a molecule.  Of particular interest to the organic chemist will be those relating to the energy associated with the nuclear spin state, the vibration of a bond or an electronic energy levels (orbitals)

Quantisation of Energy:

 The absorption of energy causes an atom or molecule to go from an initial energy state (the ground state) to another higher enrgy state (an excited state)   The energy changes are frequently described using an energy level diagram. The energy states are said to be quantised because there are only certain values that are possible, there is not a continuous spread of energy levels available.

Spectroscopic methods:

• Ultra-Violet (UV-VIS)

• Infra red (IR)

• Nuclear Magnetic Resonance (1H-NMR and 13C-NMR)

• Mass Spectrometry (MS)

• Getting Structures fromSpectra

1. Ultraviolet-Visible (uv-vis) Spectroscopy

Basics
 Ultraviolet-visible spectropscopy (uv = 200-400 nm, visible = 400-800 nm) corresponds to electronic excitations between the energy levels that correspond to the molecular orbitals of the systems.  In particular, transitions involving  orbitals and lone pairs (n = non-bonding) are important and so uv-vis spectroscopy is of most use for identifying conjugated systems which tend to have stronger absorptions. The lowest energy transition is that between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) in the ground state.  The absorption of the EM radiation excites an electron to the LUMO and creates an excited state. The more highly conjugated the system, the smaller the HOMO-LUMO gap, E, and therefore the lower the frequency and longer the wavelength, .  The colours we see in inks, dyes, flowers etc. are typically due to highly conjugated organic molecules. The unit of the molecule that is responsible for the absorption is called the chromophore, of which the most common are C=C ( to *) and C=O (n to *) systems.

The following table contains some data for polyenes and demonstrates how the wavelength of the absorbance increases as the conjugated system becomes more extended.

 H(CH=CH)nH max / nm max 1 170 15,000 2 217 21,000 3 258 35,000

Terminology

 Absorbance A, a measure of the amount of radiation that is absorbed Band Term to describe a uv-vis absorption which are typically broad. Chromophore Structural unit responsible for the absorption. Molar absorptivity , absorbance of a sample of molar concentration in 1 cm cell. Extinction coefficicent An alternative term for the molar absorptivity. Path length l, the length of the sample cell in cm. Beer-Lambert Law A = c.l    (c = concentration in moles / litre) max The wavelength at maximum absorbance max The molar absorbance at max HOMO Highest Occupied Molecular Orbital LUMO Lowest Unoccupied Molecular Orbital

1. Infra Red Spectrophometry

Basics:
Infra red (IR) spectroscopy deals with the interaction between a molecule and radiation from the IR region of the EM spectrum (IR region = 4000 - 400 cm-1). The cm-1 unit is the wave number scale and is given by 1 / (wavelength in cm).

IR radiation causes the excitation of the vibrations of covalent bonds within that molecule. These vibrations include the stretching and bending modes.

An IR spectrum show the energy absorptions as one 'scans' the IR region of the EM spectrum.  As an example, the IR spectrum of butanal is shown below.

In general terms it is convienient to split an IR spectrum into two approximate regions:

• 4000-1000 cm-1 known as the functional group region, and

• < 1000 cm-1 known as the fingerprint region

• Most of the information that is used to interpret an IR spectrum is obtained from the functional group region.

• In practice, it is the polar covalent bonds than are IR "active" and whose excitation can be observed in an IR spectrum.

• In organic molecules these polar covalent bonds represent the functional groups.

• Hence, the most useful information obtained from an IR spectrum is what functional groups are present within the molecule (NMR spectroscopy typically gives the hydrocarbon fragments).

• Remember that some functional groups can be "viewed" as combinations of different bond types.  For example, an ester, CO2R contains both C=O and C-O bonds, and both are typically seen in an IR spectrum of an ester.

• In the fingerprint region, the spectra tend to be more complex and much harder to assign.

MOST IMPORTANT THING TO REMEMBER.....

When analysing an IR spectrum avoid the temptation to try to assign every peak.
The fingerprint region, however, can be useful for helping to confirm a structure by direct comparison with a known spectra.

Infra-Red (IR) Spectroscopy
Hookes' Law
 To help understand IR, it is useful to compare a vibrating bond to the physical model of a vibrating spring system.  The spring system can be described by Hooke's Law, as shown in the equation given on the left.  Consider a bond and the connected atoms to be a spring with two masses attached. Using the force constant k (which reflects the stiffness of the spring) and the two masses m1 and m2, then the equation indicates how the frequency, , of the absorption should change as the properties of the system change.

Consider the following trends:
1. for a stronger bond (larger k value),  increases.

As examples of this, in order of increasing bond strength compare:
CC bonds: C-C (1000 cm-1), C=C (1600 cm-1) and CC (2200 cm-1),
CH bonds: C-C-H (2900 cm-1), C=C-H (3100 cm-1) and CC-H (3300 cm-1),

(n.b. make sure that you understand the bond strengths order)

2.  for heavier atoms attached (larger  value),  decreases.

As examples of this, in order of increasing reduced mass compare:

C-H  (3000 cm-1)
C-C  (1000 cm-1)
C-Cl (800 cm-1)
C-Br (550 cm-1)

The following diagram reflects some of the trends that can be accounted for using Hookes' Law.  It also gives an approximate outline of where specific types of bond stretches may be found.

Infra-Red (IR) Spectroscopy

Important absorptions:

The more important absorptions that you should probably learn to recognise, in order of importance are:

 Bond Base Value Strength / Shape Comments 1 C=O 1715 s, "finger" Exact position depends on type of carbonyl 2 O-H 3600 s, brd Broad due to H bonding 3 N-H 3500 m Can tell primary (two peaks) from secondary (one peak) 4 C-O 1100 s Also check for OH and C=O 5 C=C 1650 w alkene  m-s aromatic Alkene weak due to low polarity  Aromatic usually in pairs 6 CC 2150 w, sharp Most obvious in terminal alkynes 7 C-H 3000 s As hybridisation of C changes sp3-sp2-sp, the frequency increases 8 CN 2250 m, sharp Characteristic since little else around it

abbreviations :  "s" = strong, "m" = medium and "w" = weak

If you know these, then you can identify most of the functional groups of interest. Note that it is rarely useful to look for C-C since the large majority organic molecules will have them.

You should also be aware that the exact substitution pattern of a particular bond causes shifts in the position of the absorption and, therefore, ranges of values are typically given in most tables.

It is possible to rationalise the shifts of absorbances based on electronic effects due to proximal groups, conjugation and / or ring strain.

In general, when you are trying to work out what a molecule is, you will not just have the IR spectrum, but you will have other information as well, such as the formula or most likely the NMR. Always cross check between these sets of information For example, if the molecular formula indicates only one O, then you can not have an ester (CO2R) or a carboxylic acid (CO2H) !

Sample IR Spectra :
By looking at IR spectra that contain known functional groups and comparing and contrasting them with other IR spectra, one can develop the skills required to be able to "interpret" an "unknown" IR spectra.  Remember that for an organic chemist, the primary role of IR is to identify the functional groups that are present. A few examples reflecting some of the more important functional groups are provided below.
Compare them to try to appreciate the subtle differences, comparing frequency, intensity and shape.
In the first example, of the aromatic hydrocarbon, toluene, we can see both the aromatic and aliphatic CH stretches, and two absorptions for the aromatic C=C stretches.

Acetone (2-propanone) is the "classic" carbonyl containing compound with the obvious C=O stretch in the middle of the spectra. Note that the peak is a very strong absorption. Compare it with the C=C in the previous case which are weaker and sharper.

The characteristic absorption of the alcohol, 2-propanol, is the broad band due to the hydrogen bonded -OH group.

Carboxylic acids contain both C=O and OH groups. Note the broadness of both absorptions due to the hydrogen bonding and that the C=O is typically at slightly lower frequency than that of a ketone.

An ester has the following key absorptions, the C=O and typically two bands for the C-O (not always easy to identify) since there are both sp3 C-O and sp2 C-O bonds.

1. Nuclear Magnetic Resonance (NMR) Spectroscopy

Basics:
Nuclei with an odd mass or odd atomic number have "nuclear spin" (in a similar fashion to the spin of electrons). This includes 1H and 13C (but not 12C). The spins of nuclei are sufficiently different that NMR experiments can be sensitive for only one particular isotope of one particular element.  The NMR behaviour of 1H and 13C nuclei has been exploited by organic chemist since they provide valuable information that can be used to deduce the structure of organic compounds. These will be the focus of our attention.

Since a nucleus is a charged particle in motion, it will develop a magnetic field.  1H and 13C  have nuclear spins of 1/2 and so they behave in a similar fashion to a simple, tiny bar magnet.  In the absence of a magnetic field, these are randomly oriented but when a field is applied they line up parallel to the applied field, either spin aligned or spin opposed.  The  more highly populated state is the lower energy spin state spin aligned situation.  Two schematic  representations of these arrangements are shown below:

 In NMR, EM radiation is used to "flip" the alignment of nuclear spins from the low energy spin aligned state to the higher energy spin opposed state. The energy required for this transition depends on the strength of the applied magnetic field (see below) but in is small and corresponds to the radio frequency range of the EM spectrum.

 As this diagram shows, the energy required for the spin-flip depends on the magnetic field strength at the nucleus. With no applied field, there is no energy difference between the spin states, but as the field increases so does the separation of energies of the spin states and therefore so does the frequency required to cause the spin-flip, referred to as resonance.

 The basic arrangement of an NMR spectrometer is shown to the left.  The sample is positioned in the magnetic field and excited via pulsations in the radio frequency input circuit. The realigned magnetic fields induce a radio signal in the output circuit which is used to generate the output signal.  Fourier analysis of the complex output produces the actual spectrum. The pulse is repeated as many times as necessary to allow the signals to be identified from the background noise.

Chemical Shift

• An NMR spectrum is a plot of the radio frequency applied against absorption.

• A signal in the spectrum is referred to as a resonance.

• The frequency of a signal is known as its chemical shift.

The chemical shift in absolute terms is defined by the frequency of the resonance expressed with reference to a standard compound which is defined to be at 0 ppm. The scale is made more manageable by expressing it in parts per million (ppm) and is indepedent of the spectrometer frequency.

It is often convienient to describe the relative positions of the resonances in an NMR spectrum.  For example, a peak at a chemical shift, , of 10 ppm is said to be downfield or deshielded with respect to a peak at 5 ppm, or if you prefer, the peak at 5 ppm is upfield or shielded  with respect to the peak at 10 ppm.

Typically for a field strength of 4.7T the resonance frequency of a proton will occur around 200MHz and for a carbon, around 50.4MHz.  The reference compound is the same for both, tetramethysilane (Si(CH3)4 often just refered to as TMS).

What would be the chemical shift of a peak that occurs 655.2 Hz downfield of TMS on a spectrum recorded using a 90 MHz spectrometer

At what frequency would the chemical shift of chloroform (CHCl3, =7.28 ppm) occur relative to TMS on a spectrum recorded on a 300 MHz spectrometer ?

A 1 GHz (1000 MHz) NMR spectrometer is being developed, at what frequency and chemical shift would chloroform occur ?

Shielding in H-NMR

The magnetic field experienced by a proton is influenced by various structural factors.
Since the magnetic field strength dictates the energy separation of the spin states and hence the radio frequency of the resonance, the structural factors mean that different types of proton will occur at different chemical shifts. This is what makes NMR so useful for structure determination, otherwise all protons would have the same chemical shift.

The various factors include:

• inductive effects by electronegative groups

• magnetic anisotropy

• hydrogen bonding

Electronegativity

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....

 Since the field experienced by the proton defines the energy difference between the two spin states, the frequency and hence the chemical shift, /ppm, will change depending on the electron density around the proton. Electronegative groups attached to the C-H system decrease the electron density around the protons, and there is less shielding (i.e. deshielding) so the chemical shift increases. This is reflected by the plot shown in the graph to the left which is based on the data shown below.
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