BIOSPECTROSCOPY

Question 1

Hierarchy of energy from nuclear motion

Answer 1

electronic energy (highest)
vibrational energy
rotational energy (lowest)

Question 2

Equations for calculating energy

Answer 2

E = hv = (hc)/lambda = hc x wavenumber

Question 3

what is planks constant

Answer 3

6.626 x 10^-34 J s

Question 4

what is the speed of light

Answer 4

3.0 x 10^8 m/s

Question 5

What is the beer lambert law

Answer 5

A = epsilon x concentration x path length = -log(I0/I)

Question 6

what does epsilon in the beer lambert law represent

Answer 6

related to inherent transition strength B, is a property of molecules measuring how strongly a substance absorbs light at a specific wavelength.

Question 7

When is a molecule IR active

Answer 7

if it has a dipole moment that changes with bending or stretching of the molecule. A dipole changing isn’t affecting the actual electrons and therefore isn’t changing polarizability like in raman.

Question 8

what is the wavenumber force constant equation

Answer 8

wavenumber = (1/2pi)x √(k/v)

k= force constant, stronger bond is higher k

Question 9

what is the equation of reduced mass

Answer 9

mu = (m1m2)/(m1+m2)

m= mass of atom, greater mass = greater mu

Question 10

what is a fundamental energy change

Answer 10

from ground state to v=1 and also downwards

Question 11

what is an overtone energy change

Answer 11

where is goes from ground state, skips v=1 to another v.

1st overtone is ground to v=2
2nd is ground to v=3 etc

Question 12

what is a vibrational mode

Answer 12

a specific way a molecule can vibrate.

Question 13

How to calculate number of vibrational modes

Answer 13

3N - 6 where N=no. of atoms

3N - 5 for linear molecules

Question 14

What are the modes of CO2

Answer 14

v1 = symmetrical stretching

v2 = 2 equivalent bending modes

v3 = asymmetrical stretching.

These would from highest appear on a spectrum:
v3, v1, v2 however v1 would not have a signal as it has no change in dipole moment meaning not IR active.

Question 15

which gives higher readings, stretching or bending

Answer 15

stretching is higher than bending as it affects the electron density more and is therefore in a higher energy state.

Question 16

What are the spectral trends observed in IR

Answer 16

cm-1 is inversely proportional to reduced mass
cm-1 is proportional to strength of bond, force constant
strength of bond, force constant, is inversely proportional bond length
cm-1 is inversely proportional to bond length

higher cm-1 = lighter mu and larger k

Question 17

What are the differences between A and B forms of DNA

Answer 17

Lower humidity = A form
More hydrated = B form = more h bonds, less vibration, smaller cm-1

Base pair carbonyl: B(1717) > A(1712)
Antisymmetric phosphate: A(1238) > B(1225)

Question 18

Intensity of scattered light equation

Answer 18

Is proportional to a^2/lambda^4

a = polarisability

Question 19

What are the 3 different types of scattering

Answer 19

Stokes: leaving photon has less energy
Anti stokes: leaving photon has more energy
Rayleigh: leaving photon has same energy

Question 20

What is polarisability

Answer 20

polarisability is a measure of electrons being displaced relative to the nuclei.

Question 21

Molecules with high polarisability

Answer 21

show strong raman scattering

Question 22

When is a mode raman active

Answer 22

modes that cause a change in polarizability and therefore a change in the ability to form instantaneous dipoles OR a change in the electrons being displaced relative to their nuclei. Inactive IR modes are active Raman modes

Question 23

is asymmetric or symmetric higher in cm-1

Answer 23

asymmetric is higher due to the due to the change in bond length.

Question 24

What causes band broadening

Answer 24

If the bond in question can hydrogen bond it will have a broader peak

Question 25

Baseline offset

Answer 25

represents number of signals generated when no light present due to noise.

corrected by subtracting the lowest point in the spectrum from all the variables to bring the spectrum down to the baseline or fitting a linear/polynomial baseline to data

Question 26

Average spectra

Answer 26

reduces uncertainty in measurements and the effect of noise. allows comparison between 2 spectral tables collected at different resolutions (different number of raw spectra).

done by using a reducing factor to create any smaller number of spectra from the original number. Each value corresponding to the wavelength is taken and averaged to give a value.

Question 27

Mean centre

Answer 27

subtracts the mean from each variable producing a new set of axes centered around the mean.

Question 28

Savitsky-Golay smoothing

Answer 28

Smoothing is used to reduce noise without reducing the number of variables.

fits a polynomial to data. polynomial order = actual shape of peaks (parabola, cubic etc.).

Question 29

Normalisation

Answer 29

used to get all data in approximately the same scaling for good comparison.

done by dividing variables by a specific value to give relative values.

Question 30

Standard normal variate

Answer 30

Normalises the spectra by subtracting the mean and dividing by the standard deviation on each variable. Corrects path length variation

Question 31

Multiplicative Scatter Correction

Answer 31

Corrects for both baseline slope and offset. Normalises for variations in pathlength and uses a linear model of the whole data to bring each sample as close to the average

Question 32

What does MVA allow us to do

Answer 32

analyse chemical nature/composition

provide information on physical characteristics specific to samples

quantify and predict unknown things.

Question 33

What does PCA allow us to do

Answer 33

allows spectra to be represented as one point for large comparisons from variation

replace expensive and or destructive testing,

perform rapid analysis,

reveal true structure and classification of data + spectral features

Question 34

Model equation of PCA

Answer 34

X = (TPT )mode + (E) residuals

Question 35

What is an object

Answer 35

An object is an observation of the spectra, in the case of the project each observation is one spectrum collected from the sample.

Question 36

What is a variable

Answer 36

A variable is the things changing in the object, in the case of the project the variables are the absorbance values at each wavenumber of a spectrum.

Question 37

What is PC

Answer 37

A principal component is a main variation in the collect data. It can be used to contrast objects and determine significant factors affecting their data.

Question 38

What is a score

Answer 38

A score is a projected locatios of an object with reference to the principal components. A map of scores is a scores plot used to compare different objects with reference to the variation between them.

Question 39

What is a loading

Answer 39

A loading is a correlation between a variable important in association and comparison

Question 40

What is a residual

Answer 40

A residual refers to the error associated between a score and variance

Question 41

What is a dummy variable

Answer 41

A dummy variable is a variable that takes the form of a 0 or a 1 to represent the presence or absence of a specific variable.

allow us to use a single regression equation for both groups instead of having separate equations.

The ‘Switch’ to turn parameters on and off.

Question 42

What is leverage

Answer 42

High leverage refers to the ability for a score to greatly affect the variance between the data.

Question 43

What is an indirect observation

Answer 43

Collect the desired data without actually directly measuring something. Gives a correlation instead.