optical spec 4 - vibrational spectroscopy

8/8/2019 Optical Spec 4 - Vibrational Spectroscopy

http://slidepdf.com/reader/full/optical-spec-4-vibrational-spectroscopy 1/8

Physical Biochemistry Vibrational Spectrosco py

[]

In general, molecules can undergo three types of motion

Translational ² moving along a line

Rotation

Vibrational (bonds expand / contract)

All of these motions have energy associated with then, but only rotation and vibrational motion have

quantised energies (they have specific values)

Under certain circumstances, the vibrational and rotational motion energies can exchange EMR

They can emit or absorb EMR

EMR can interact with the vibrational or rotational motion of the molecule

Born-Oppenheimer approximation makes use of the fact that these phenomena take place at very different

timescales and energies.

Molecular rotation: 10-11s (360r rotation)

Molecular vibration: 10-13s (to expand and contract)

Electron transition: 10-15 (from ground state to excited state) - femtosecond scale

This is useful, for example if we are looking at vibrational motion then we can assume that the molecule is

¶still· in terms of rotation. The influence of these phenomena can be studied separately.

Separation between energy levels:

Rotational < Vibrational < Electronic

A molecular energy state describes the electronic, vibrational and rotational states of the molecule. It is the

sum of these 3 energy components.

In this example, each electronic state has 3 vibrational states.

The total energy levels represent all three parameters.

Molecular Rotation:




[]

Can be probed with microwave radiation in molecules with electric dipole moments e.g. Heteronuclear (non-

identical masses) diatomic molecules. In order for EMR to interact with a molecule, the molecule must have a

permanent electric dipole moment (heteronuclear only).

Can be used to determine bond length in small molecules in rotational spectroscopy.

m = mass

c = centre of mass (the point at which the molecule is rotating)

r 0 = bond length

Ramen spectroscopy is an easier indirect way to study rotation

Vibrational Rotation:

Simple Harmonic Oscillator (classical)

Represents a vibrating diatomic molecule

The bond is treated a spring, stretching and compression store equal amounts of energy

m = mass

r eq = equilibrium bond distance

Intermolecular distance (x) / Energy (y)

Parabolic curve

When bond is at equilibrium distance, there is no energy stored in the spring.

If you assume that the potential energy is changing

Simple Harmonic Oscillator (quantum)

v = vibrational energy level. Associated with quantum numbers (non-negative integers).

The E between consecutive vibrational energy levels is always the same.




[]

Even when v = 0, there is still energy in the system, the molecule is

always vibrating. If a molecule is not vibrating, its location can be

accurately determined; this breaks fundamental quantum laws

(Heisenberg uncertainty principle). In order to measure something

you need to disturb it, if you disturb something you cannot measure

it with complete precision.

The potential energy has no defined limits

The graph shows wave functions, showing distribution of one of the

atomse.g. In v = 0, the atom is likely to be at r eq. The wave function is

not a physical location, more a distribution of possible locations. 2

gives the probability distribution of the atom. In the higher vibrational states, curves 2 show the atom is not

likely to be found at the equilibrium distance.

The max compression / stretch are ¶turning points·, the molecule is more likely to be found at these points

than at the equilibrium distance. Atoms are moving the slowest at the turning points as they are changing

direction (they need a velocity of 0 to change direction). Conversely, the atoms are moving fastest at r eq.

It should be noted that the simple harmonic oscillator is not a fair description of molecular vibration. The

compression and stretching of a bond are not actually equivalent, however we assume this in the simple

harmonic oscillator model (quantum).

In reality, a bond behaves more like an anharmonic oscillator.

If a bond stretches beyond a certain point, the bond will break and the atoms will dissociate (dissociation

energy = D).

De = E between 0 and dissociation energy

D0 = E between v = 0 and dissociation energy

The spacing between energy levels decreases with increasing , it is no longer constant

Compression brings changes into the system ² e- repulsion, nuclear repulsion etc.




[]

he Morse potential follows a different path to that of the

simple harmonic oscillator (left).

here is a lot of overlap between the two for v = 0 & 1. At

room temperature, most molecules will be found at

vibrational state 0, making the simple harmonic oscillator

appropriate for biochemistry.

Normal H2O Modes:

Wavenumber [cm-1] = 1/ (wavelength)

Proportional to frequency: Higher wavenumber corresponds to a higher energy

he EM ¡ that can interact with vibrational energy transitions is usually in the I ¡ region (2.5 - 20).

Vibrational spectroscopy is often called infrared spectroscopy.

A water molecule is vibrating.

hree different types of vibration are shown:

Antisymmetric stretch ² one compresses while the other bond stretches (3756 cm-1)

Symmetric stretch ² both bonds are stretching and compressing at the same time(3651 cm-1)

Symmetric bend ² the bond is undergoing angular movement(1595cm-1)

All molecules have a small group of vibrations, known as normal vibrational modes. Each mode has an

independent energy level. By using EM ¡ of different wavelengths, each vibrational mode can be studied

independently.




[]

The amount of energy put into the system will influence the amplitude of vibration.

Any molecular vibration can be described as a linear combination of the normal modes.

In order for a vibrational mode to interact with electromagnetic radiation the dipole of a molecule needs to

change as the molecule vibrates, but does not require a permanent dipole (rotational spectroscopy requires a

permanent electric dipole moment).

The symmetric stretch in CO2 will not produce a vibrational spectra using EMR (there is no varying dipole

moment), but the antisymmetric stretch and symmetric bend will.

Skeletal vibrations usually occur in the fingerprint region of a vibration spectrum (600 ² 1500cm-1)

A complex region, can be used to identify compounds (forensics) as different molecules have characteristic

vibrational spectra.

Functional Group Vibrations:

Functional group vibrations (related to specific bonds) have typical absorbances in the region of 1000 -

4000cm-1

v = Vibrational frequency

Groups with light atoms have a higher frequency than groups with heavier atoms.

Stretching modes usually have higher frequencies than bending modes

The stronger the bond the higher the frequency (triple > double > single bond)

N²H: One or two sharper peaks at 3500-3300cm-1

O²H:Broad peak between 3650-3200cm-1

Analysis in this region can be difficult as peaks overlap.

C=O: Strong and sharp peak between 1820-1660cm-1

IR Spectrometer:

Measurement is alternated between sample and n0-sample to minimize environmental effects and background

radiation. If the sample is contained within a solvent, a reference cell is used to cancel out the solvent

absorption spectrum.




[]

¢

he light

is

initially

polychromatic (many different wavelengths)¢

he monochromator ensures only the desired light comes out (effectivelya prism)¢

he beam splitter allows some light to pass through the sample, and some light to reach the detector without

passing through the sample (this would allow a reference cell to be placed).

Sample Handling:

Solvents: Water and alcohol are rarely used as they absorb in I £ and attack cell window materials. CCl4 and

chloroform are commonly used, however no solvents are completely invisible in the I £ region.

Liquid samples are often analysed in their pure form for this reason.

Cells: NaCl and KBr are often used as a transparent material to hold the sample. 0.1-1mm thick. Glass and

quartz are opaque in the I £ region.

Attenuated¢

otal £ eflection (A¢

£ ) Infrared Spectroscopy:

Used to study samples

without using water.¢

he

aqueous solution is passed

through the flow cell. Uses

total internal reflection.

¢

otal internal reflection

occurs when light crosses a




[]

boundary of different refractive indices (n), an angle that is greater than the critical angle.

With each internal reflection, the beam penetrates 1-10m into the sample (evanescent wave), and is

attenuated depending on what is in this thin layer. Multiple reflections (~7 bounces) help to amplify the signal.

Useful for studying thin layered samples such as membranes.

Fourier Transform Infrared (FTIR) Spectroscopy:

Does not use a monochromator, the sample is irradiated by the full IR spectrum of the source. Studies using a

monochromator are slow; it can take minutes to scan the entire spectrum.

1. A beam of light passes through the beamsplitter, passes through the sample then is reflected back through

the sample and beamsplitter, then hits the detector.

2. The second beam of light passes straight through the beamsplitter, and is reflected back to the detector,

without passing through the sample.

The second mirror can be moved, for each position of this mirror a reading is taken using the detector.

There will be both constructive and destructive interference at different wavelengths between these beams.

Movement of mirror 2 will suppress or accentuate other wavelengths.

The interference imposes a cosine modulation on the spectrum, which has a periodicity that is dependant on

path difference.




[]

The detector will detect the Fourier transform of the spectrum, which is a type of encoding of the spectrum. In

order to reconstruct the absorption spectrum, the signal needs to be ¶decoded· as a function of path

difference.

The ¶decoding· can be carried out computationally in order to obtain the spectrum (Inverse FT).

This process is much faster than conventional means.

Interference:

The frequency of the modulation imposed on the spectrum is increased with the path difference (dx).

Advantages of FT

Full spectrum is obtained in one go

Less noise

Faster (10s) ² real time measurements much easier to carry out

Uniform resolution over entire spectrum. When using a monochromator, resolution is not constant at

different wavelengths.

Isotope editing can be used to enhance results. Using a different isotope will specifically shift the absorption

frequency for a specific group. Spectra of edited and unedited molecules are compared. Helpful analysing

overlapping carbonyl groups.

optical spec 4 - vibrational spectroscopy

Documents