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CHM2942 > Biospectroscopy > Flashcards

Biospectroscopy Flashcards

1
Q

What state of matter has rotational energy?

A

Gas only

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2
Q

What are the challenges of Raman spectroscopy?

A

Can be highly effected by fluorescence

Laser can destroy sample if power is too high

May require several modes of operation and different laser wavelengths to cover all applications

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3
Q
A
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4
Q

Define

Symmetric stretching

A

Simultaneous vibration of two bonds, in which the bonds elongate together and contract together

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5
Q

What happens when PCA is applied to spectroscopic data?

A

When applied to spectroscopic data, scores proved a map of the sample similarities/dissimilarities and the loadings represent the spectral features that cause the samples to group the way they do

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6
Q

Definition

Map of samples: Projected locations of objects onto the principal components

A

Scores (T)

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7
Q

Draw a FT/Raman Spectrometer

A
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8
Q

Define

Vibrational energy

A

The energy in a vibrating system, otherwise at rest; especially that in a molecule due to the vibrations of its atoms

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9
Q

What is the equation for Beer’s law?

A

A = ελ c l

Where:

A = Absorbance

  • c* = concentration
  • l* = path length

ελ = Extinction coefficient

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10
Q

Draw a Michelson Interferometer

A
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11
Q

Definition

a measure of the degree to which electrons are displaced relative to the nuclei (i.e. how much to the electrons slosh about)

A

Polarizability

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12
Q

Which has a higher frequency (and wavenumber)?

Stretching or Bending modes

A

Stretching modes

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13
Q

What are the two types of light scattering?

A

Rayleigh scattering: elastic - same frequency - weak

Raman scattering: inelastic - changed frequency - weaker

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14
Q

Definition

One of the possible Raman interactions that leads to the material losing energy and the emitted photon has a higher energy than the absorbed photon

A

Anti-Stokes Raman scattering

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15
Q

Definition

finds a data value by averaging the values within a segment of data points

A

Moving average

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16
Q

Why are the spectra for the same molecule different?

A

Different chemophores are enhancing different excitation wavelengths

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17
Q

Define

De-trending

A

Removing unwanted baseline effects by estimating a polynomial baseline

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18
Q

Which mode has the strongest absorbance?

A

Asymmetric stretching

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19
Q

What is the relationship between number of double bonds and the position of v(C=C)?

A

↑ congugation

=

↓ frequency v(C=C)

because

↑ electron delocalisation

=

↓ strength of double bonds

=

↓ force constant

↓ wavenumber

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20
Q

What two components make up molecular energy levels?

A

Electronic

Nuclear motion

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21
Q

Do all CO2 modes give rise to IR transitions?

A

No. The electric component of the electro-magnetic radiation must interact with an oscillating dipole of the same frequency. Asymmetric stretching and bending modes do but symmetric stretching does not.

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22
Q
  1. The fundamental transition of a diatomic molecule that is a harmonic oscillator is found at 3000 cm-1. Where would you expect to observe the 2nd overtone? (1 mark)
A

9000 cm-1

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23
Q

Which of the following statements about DNA is correct?

  1. DNA has a strong bands assigned to the symmetric phosphodiester stretching and the asymmetric stretching vibration at 1080 cm-1 and 1220 cm-1, respectively.
  2. In the hydrated state the B-DNA asymmetric stretch appears at 1240 cm -1 whereas in A-DNA the band appears at 1220 cm -1
  3. The A-DNA conformation is adopted by bacteria under hydrating conditions
  4. The B-DNA form is a more narrow and disordered form compared to A-DNA
  5. The A-DNA conformation is observed when DNA is hydrated
A

Which of the following statements about DNA is correct?

  1. DNA has a strong bands assigned to the symmetric phosphodiester stretching and the asymmetric stretching vibration at 1080 cm-1 and 1220 cm-1, respectively.
  2. In the hydrated state the B-DNA asymmetric stretch appears at 1240 cm -1 whereas in A-DNA the band appears at 1220 cm -1
  3. The A-DNA conformation is adopted by bacteria under hydrating conditions
  4. The B-DNA form is a more narrow and disordered form compared to A-DNA
  5. The A-DNA conformation is observed when DNA is hydrated
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24
Q

How can fluorescence be prevented?

A

Choosing an appropriate wavelength

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25
Q

What is chemimetrics?

A

Chemometrics is the science of relating measurements made on a chemical system or process to the state of the system via application of mathematical or statistical methods

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26
Q

What does a molecules eletronic energy level depend on?

A

The arrangement of electrons in molecular orbitals

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27
Q

Why does the loadings of a PCA model matter?

A

The loading plot is useful to understand the correlations between the variables

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28
Q

What is the Boltzman distribution?

A

The number of molecules in the ground state compared to the number of molecules in the excited state

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29
Q

What does a high residual indicate?

A

That it is an outlier

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30
Q

What are the four types of smoothing?

A

Moving average

Gaussian Filter

Median Filter

Savitzky-Golay

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31
Q

Definition

a row-oriented transformation used to get all data in approximately the same scaling

A

Normalisation

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32
Q

Define

Rotational energy

A

kinetic energy due to the rotation of an object and is part of its total kinetic energy

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33
Q

Define

Anti-Stokes Raman scattering

A

One of the possible Raman interactions that leads to the material losing energy and the emitted photon has a higher energy than the absorbed photon

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34
Q

The amide I mode is a complex mode made up of 3 modes and appears at ~1650 cm-1 depending on the protein secondary structure.

What are the main modes in order of importance that make up the Amide I mode?

  1. C=O stretch, C-N stretch and NH2 in plane bend
  2. C-N stretch, C=O stretch, NH2 in plane bend
  3. NH2 in plane bend, C=O stretch, C-N stretch
  4. C-C stretch, C=O stretch, NH2 in plane bend
A

The amide I mode is a complex mode made up of 3 modes and appears at ~1650 cm-1 depending on the protein secondary structure.

What are the main modes in order of importance that make up the Amide I mode?

  1. C=O stretch, C-N stretch and NH2 in plane bend
  2. C-N stretch, C=O stretch, NH2 in plane bend
  3. NH2 in plane bend, C=O stretch, C-N stretch
  4. C-C stretch, C=O stretch, NH2 in plane bend
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35
Q

What is a score plot (T)?

A

A 2D plot of the projected objects using PC1 and PC2 as a new coordinate system

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36
Q

What does Principal Component Analysis (PCA) do?

A
  • Extract information and remove noise
  • Reduce dimensionality/compression
  • Exploratory data analysis
  • Classification/identification
  • Variable reduction
  • Process monitoring
  • Visual Analysis of Variance
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37
Q

Definition

used to reduce the nise in the data without reducing the number of variables. It is a row-oriented transformation, that is to say the contents of a cell are likely to be influenced by its horizontal neighbours

A

Smoothing

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38
Q

Definition

uses a diffraction grating spectrometer (essentially operating like a prism) to disperse the light scattered from a sample and then will detect this upon a multi-channel detector such as a CCD. The wavelengths of light detected are the Raman spectrum

A

Dispersive Raman spectrometer

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39
Q

Define

Fluorescence

A

Signal noise on a Raman spectrometer that occurs due to real electronic transitions

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40
Q

The force constant increases with what?

A

Increased bond strength

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41
Q

What does the intensity of overtone and combination bands depend on?

A

The intensity of fundamentals

The anharmonicity of the molecule

Resonance with strong fundamentals

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42
Q

What is the difference between A-DNA and B-DNA?

A
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43
Q

What is the difference between a molecules’ IR and Raman wavenumers?

A

They occur at the same frequency but at different intensities

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44
Q

Low frequencies (wavenumber) correlate with what?

A

Vibrational motion of heavy masses and low force constants

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45
Q

Definition

the scattering of light by particles in a medium, without change in wavelength. It accounts, for example, for the blue colour of the sky, since blue light is scattered slightly more efficiently than red

A

Rayleigh scattering

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46
Q

What happens is you increase the number of smoothing points when using Savitzky-Golay Derivatives?

A

Increasing the number of smoothing points reduces the amount of noise, but can also eliminate important chemical information through reduced resolution

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47
Q

What are category variables?

A

Strictly qualitative variables without order and non-overlapping

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48
Q

What are the disadvantages of FT/Raman?

A

High laser power required

Low sensitivity

Not very useful for microspectroscopy

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49
Q

Below a Scores Plot and Loadings Plot for FTIR transflection spectra of cancer versus normal liver tissue

  1. How much variance is explained by PC1 and PC2? (1 mark)
A

94%

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50
Q

__________: For each sample, the value of the lowest point in the spectrum is subtracted from all the variables

_____________: Transforms a sloped baseline into a horizontal baseline. The rechnique is to point out two variables, both defined as o, which should define the new baseline

____________: Removes unwanted baseline effects by estimating a polynomial baseline

A

Baseline offset: For each sample, the value of the lowest point in the spectrum is subtracted from all the variables

Linear Baseline Correction: Transforms a sloped baseline into a horizontal baseline. The rechnique is to point out two variables, both defined as o, which should define the new baseline

De-trending: Removes unwanted baseline effects by estimating a polynomial baseline

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51
Q

Define

B-DNA

A

the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn

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52
Q

Define

Frequency

A

the number of occurrences of a repeating event per unit of time

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53
Q

A fundamental frequency of 5Hz would seen overtones at what frequencies?

A

10Hz, 15Hz, 20Hz etc.

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54
Q

Define

Virtual states

A

a very short-lived, unobservable quantum state

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55
Q

Define Residual variance

A

Variance remaining in E

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56
Q

Definition

the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn

A

B-DNA

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57
Q

Definition

an alcohol and ether attached to the same carbon

A

Hemiacetal

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58
Q

What are the advantages of Dispersive micro-Raman spectrometers?

A

Multiplex advantage as for FT/Raman

High sensitivity detector

Low power OK

Choice of laser frequency

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59
Q

How many modes does CO2 have?

A

3x3-5 = 4 modes

(CO2 is linear)

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60
Q
  1. Why are symmetric stretches generally lower in wavenumber value than asymmetric stretches? (2 marks)
A

In symmetric stretching, two or more bonds vibrate in and out together. In asymmetric stretching, some bonds are getting shorter at the same time as others are getting longer. Longer bonds mean lower wavenumber value because the force constant is smaller. Therefore symmetric stretches are lower in wavenumber value.

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61
Q

When should you use a second derivative?

A

When the spectra is not noisy and you want to minimise broad features and highlight inflection points

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62
Q

Define

Boltzman distribution

A

a probability distribution or probability measure that gives the probability that a system will be in a certain state as a function of that state’s energy and the temperature of the system

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63
Q

What does Multiplicative scatter correction do?

A

Removes offset and divides by slope to normalise

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64
Q

What is the loading (p) of a variable?

A

The cosine of the angle that the PC makes with the original variables

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65
Q

Definition

an oscillating system is a pattern of motion in which all parts of the system move sinusoidally with the same frequency and with a fixed phase relation

A

Normal modes

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66
Q

What happens is you use a higher degree polynomial when using Savitzky-Golay Derivatives?

A

A higher degree polynomial will fit better to the data, giving a more precise derivative. However, noise sensitivity increases

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67
Q

What are the benefits of Near-IR spectroscopy?

A

Non-destructive

Minimal sample preparation

Can be easily integrated into processes

Chemical and physcial information

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68
Q

Definition

Error of the data

A

Residuals (E)

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69
Q

Define

Michelson Interferometer

A

a device that produces interference between two beams of light

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70
Q

Consider the following diagram

Why does the position of ν(C=C) shift to lower wavenumber as the number of double bonds (0-12) increases?

A

Delocalisation

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71
Q

What factors determine the intensity of an IR band in a spectrum?

A

∂μ/∂x that is the change in electric field over the change in bond length

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72
Q
  1. Sketch the main fundamental modes of CO2 (2 marks)
  2. Which of these are infrared and Raman active? (2 marks)
A

The asymmetric stretching mode and the bending modes ae IR active while the totally symmetric mode is Raman active

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73
Q

Why are bending modes generally lower in wavenumber value than stretching modes?

A

It is easier to bend a bond than to stretch it because the nuclei are not moving against the attraction of the bonding electrons.

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74
Q
  1. How many fundamental modes of vibration will CO2 have? (1 mark)
A

3N-5 = 4 modes of vibration

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75
Q

Where are beta-sheet bands found?

A

1635 cm-1

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76
Q

Define

FT Raman spectrometer

A

A type of Raman designed to eliminate the fluorescence problem encountered in conventional Raman spectroscopy

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77
Q

Definition

the spatial frequency of a wave, measured in cycles per unit distance or radians per unit distance

A

Wavenumber

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78
Q

How can the size of a data table be reduced?

A

Averaging samples or variables

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79
Q

What are the advantages of FT/Raman?

A

Highly fluorescent samples usually not a problem

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80
Q

What are second derivatives used for?

A

To correct for both linear and quadratic baseline effects such as scatter dues to particle size

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81
Q

What are ordinal variables?

A

Qualitative variables with an inherent rank (e.g. small, large)

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82
Q

What happens at each end of the data after Savitzky-Golay smoothing? What does it depend on?

A

After smoothing, the data will be slightly truncated at both ends. Truncation depends on segment size

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83
Q

Define Residuals, E

A

Error. The data can be divided into structure (Xstruct) and residual (E) : X = Xstruct + E

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84
Q

Which PC line accounts for the most variation?

A

The lowest (i.e. PC1)

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85
Q

Definition

the number of occurrences of a repeating event per unit of time

A

Frequency

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86
Q

Define

Dispersive Raman spectrometer

A

uses a diffraction grating spectrometer (essentially operating like a prism) to disperse the light scattered from a sample and then will detect this upon a multi-channel detector such as a CCD. The wavelengths of light detected are the Raman spectrum

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87
Q

Define Principal components

A

Main data variations, also known as ”latent variables”, ”factors” and ”eigenvectors”. The first PC accounts for the majority of the varaince with each successive PC accounting for less varaince in the data set.

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88
Q

Define

Smoothing

A

used to reduce the nise in the data without reducing the number of variables. It is a row-oriented transformation, that is to say the contents of a cell are likely to be influenced by its horizontal neighbours

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89
Q

List in order from highest to lowest wavenumber value the following functional groups

C-Cl, C-O, C=O, C-F, C-H and Fe-O

A

C-H, C=O, C-O, C-F, C-Cl and Fe-O

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90
Q

Convert 3100 cm-1 into wavelength (micron mm), frequency (s-1) and energy (KJ).

A

v= c/λ = 3 x108 ms-1/3.226 10-6 m = 9.299 x 1013 Hz

E = hv = 6.62 x 10-34 Js x 9.299 x 1013 s-1 = 6.16 x 10-20 J = 6.16 x 10-23 KJ

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91
Q

Define

Multivariate analysis

A

a subdivision of statistics encompassing the simultaneous observation and analysis of more than one outcome variable

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92
Q

What does the intensity of hot bands depend on?

A

Boltzman distribution

Temperature

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93
Q

What is residual variance?

A

Variance remaining in the residuals

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94
Q

What are the benefits of Raman spectroscopy?

A

Non-destructuve

Minimal sample preparation

Can be easily integrated into processes

Can provide enhanced chemical information over NIR

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95
Q

What is usually the first preprocessing step?

A

Mean centering of data

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96
Q

How many modes does a linear molecule have?

A

3N-5 (where N=number of atoms)

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97
Q

What is a disadvantage of using an FT-Raman system? (2 marks)

A

Less energy means more power is required to produce a spectrum because the scattered intensity of the light is smaller at longer wavelenghts

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98
Q

Definition

a non-destructive identification method that measures the vibrational energy in a compound

A

Vibrational spectroscopy

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99
Q

Definition

The energy in a vibrating system, otherwise at rest; especially that in a molecule due to the vibrations of its atoms

A

Vibrational energy

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100
Q

Define

Hot band

A

a band centred on a hot transition, which is a transition between two excited vibrational states

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101
Q

Which of the following functional would have the lowest wavenumber value in the mid-infrared spectrum?

C-H

C-C

C-O

C-Cl

C-Br

A

Which of the following functional would have the lowest wavenumber value in the mid-infrared spectrum?

C-H

C-C

C-O

C-Cl

C-Br

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102
Q

Define

Scores (T)

A

Map of samples: Projected locations of objects onto the principal components

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103
Q

Definition

define the curvature of a data set and are best applied to data with quadratic (curved) baselines

A

Second derivative

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104
Q

What does a bond require to be IR active?

A

A dipole moment

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105
Q

Definition

a change of wavelength exhibited by some of the radiation scattered in a medium. The effect is specific to the molecules which cause it, and so can be used in spectroscopic analysis

A

Raman effect

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106
Q

Definition

used to remove linear baseline effects in continuous spectral data

A

First derivative

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107
Q

Consider resonance from of amide I mode. Why does the amide I mode appear at ~1650-1630 cm-1 And not ~1730 cm-1

A

Resonance structures for an amide. Remember that the molecule does not actually switch between these structures. Instead, the actual structure is somewhere in between the structures shown. It can be thought of as some average of these structures.

108
Q

The nitrile group is another reliable functional group that generally is easy to identify. There is a significant dipole moment associated with the C ≡N bond which leads to a significant change when it interacts with infrared radiation usually leading to an intense sharp peak at 2200-2280 cm-1 Very few other groups absorb at this region with this intensity.

Why is the C ≡N band more intense than the C ≡C band?

A

The C ≡N bond has a larger dipole moment compared to the C ≡C bond due to the electronegativity of the nitrogen atom

109
Q
  1. List the molecules HC≡CH, H2C=CH2 and H3CCH3 in descending order of their C–C vibrational stretching frequencies. (2 marks)
A

HC≡CH> H2C=CH2>H3CCH3

110
Q

What is Dark DNA?

A

The phenomenon that describes the nucleosomes of an inactive nucleus appearing as “black” strings or dots that yield no spectral information from the DNA

111
Q

How many normal modes of vibration are there in the molecule CH4 ? (2 marks)

A

3N – 6 =9 modes of vibration

112
Q

Definition

A type of Raman designed to eliminate the fluorescence problem encountered in conventional Raman spectroscopy

A

FT Raman spectrometer

113
Q

Why does the scores of a PCA model matter?

A

The score plot shows how the data are distributed, Sample patterns, groupings, similarities and differences can be studied

114
Q

Define

Hemiacetal

A

an alcohol and ether attached to the same carbon

115
Q

What are the yellow and green lines?

A

Fluorescence

116
Q

What are the challenges of Near-IR spectroscopy?

A

Spectra features are broad and undefined

Suffers highly from scatter effects

Requires multivariate analysis for complete understanding

117
Q

Raman spectroscopy involves the scattering of light.

  1. Explain the difference between Stokes, anti-Stokes and Rayleigh scattering using an energy diagram and list in order from highest to lowest the intensity of the scattering from these three processes. (6 marks)
A

Stokes scattering is totally elastic scattering where the incoming photon leaves at the same energy as the scattered photon. It is the most intense form of scattering.

Anti-Stokes scattering results when the incident photon is scattered from a molecule in an excited vibrational state. The scattered photon leaves at a higher energy than the initial photon and is the weakest type of scattering.

Stokes scattering results when the incident photon interacts with a molecule in the ground vibrational state and the photon scatters at a lower energy than the initial photon. The intensity of the scattered light is less than Rayleigh scattering but more than anti-Stokes scattering.

In both Stokes and anti-Stokes the energy difference between the incident and scattered photon is equal to wavenumber of the vibrational mode.

118
Q

Why doesn’t symmetric stretching result in a IR transition?

A

There is no change in dipole

119
Q

What must occur in the molecule for a Raman spectrum to be generated?

A

Application of an electric field (laser) can induce a dipole moment. If this induced dipole moment varies during a vibrational motion, a Raman spectrum will be produced

i.e. the “mean” polarizability (α) must vary during the vibrational motion

120
Q

Define

Linear baseline correction

A

A transformation of a sloped baseline into a horizontal baseline. The technique is to point out two variables, both defined as o, which should define the new baseline

121
Q

Definition

The first preprocessing step that involves subtraction of the mean for each variable

A

Mean centering

122
Q

What caused the peaks between 3400 and 3900?

A

Overtones

123
Q
  1. List the molecules HF, HI, HCl and HBr in descending order of their vibrational frequencies. (2 marks)
A

HF>HCl>HBr>HI

124
Q
  1. Why are bending modes lower in wavenumber value than stretching modes? (2 marks)
A

It is easier to bend a bond than to stretch it because the nuclei are not moving against the

attraction of the bonding electrons.

125
Q

Definition

a normalisation of spectra to remove effect of variations between samples due to differences in pathlength. Corrects for both baseline slope and offset

A

Multiplicative scatter correction

126
Q

Definition

one of the possible double helical structures which DNA can adopt. It is thought to be one of three biologically active double helical structures. It is a right-handed double helix fairly similar to the more common form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in the common form

A

A-DNA

127
Q

Below a Scores Plot and Loadings Plot for FTIR transflection spectra of cancer versus normal liver tissue

  1. Along which PC is the separation between cancerous and normal spectra of cells? (1mark)
A

PC1

128
Q

What does Raman measure?

A

Scattering of UV, vis or near IR laser light (or X-ray etc.)

129
Q

Definition

finds a data value by making a polynomial fit to the data points using a number of data points on each side

A

Savizky-Golay smoothing

130
Q

Draw a diagram illustrating the difference between Rayleigh, Stoke and Anti-Stokes scattering

A
131
Q

What does the wavenumber of a bond depend on? State the equation

A

The wavenumber depends on the force constant and the mass of the atoms. An increase in bond strength and/or a decrease in mass causes an increase in wavenumber

v = (1/2π)*sqrt(k/μ)

Where:

v = wavenumber

k = force constant

μ = mass

132
Q

What allows Raman microprobes to rapidly line map?

A

Line of laser diodes the give high laser energy output

133
Q

How many modes does a non linear molecule have?

A

3N-6 (where N=number of atoms)

134
Q

Definition

an analytical technique to study the electronic structure and its dynamics in atoms and molecules

A

Electronic spectroscopy

135
Q

Define

Moving average

A

finds a data value by averaging the values within a segment of data points

136
Q

Definition

concerned with the measurement of the energies of transitions between quantized rotational states of molecules in the gas phase

A

Rotational spectroscopy

137
Q

What are the max number of PC lines?

A

n - 1

Where:

n = number of spectra

138
Q

List in order of magnitude:

Evib, Erot, Eelec

A

Eelec >> Evib >> Erot

139
Q

What are first derivatives used for?

A

To remove linear baseline effects in continuous spectral data

140
Q

How is FT/Raman different to FTIR?

A
  • Scatter of Nd-YAG laser
  • Requires Rayleight filter
  • Requires different materials for:
    • Beamsplitter
    • Windows
    • Detector
    • Mirror coating
141
Q

What is an issue with higher PC lines?

A

They pick up noise in the sample

142
Q

Consider the following carboxylate group. Would you expect the carbonyl group to be at ~1730 cm-1 as seen in esters, aldehydes and ketones?

A

The carbonyl frequency for a bond and a half would be expected to fall halfway between 1735 and 1200 or at approximately 1465 cm-1. The carboxyl group has the same symmetry as the nitro and CH2 groups. Both a symmetric and asymmetric stretch should be observed. An asymmetric and symmetric stretch is observed at 1410 and 1560 cm-1 in sodium benzoate that averages to 1480 cm-1, in good agreement with the average frequency predicted for a carbon oxygen bond with a bond order of 1.5.

143
Q

Definition

kinetic energy due to the rotation of an object and is part of its total kinetic energy

A

Rotational energy

144
Q

Define

Rotational spectroscopy

A

concerned with the measurement of the energies of transitions between quantized rotational states of molecules in the gas phase

145
Q

Definition

corrects each spectrum by subtracting the mean and dividing by the standard deviation for that spectrum

A

Standard normal variate

146
Q

Definition

Signal noise on a Raman spectrometer that occurs due to real electronic transitions

A

Fluorescence

147
Q

Define

Loadings (P)

A

Map of variables: Correlation between variables (regression of X on 1)

148
Q

What is a virtual state?

A

A continuum of vibrational states that occurs when there is not enough energy to be an electronic state change

149
Q

Definition

a probability distribution or probability measure that gives the probability that a system will be in a certain state as a function of that state’s energy and the temperature of the system

A

Boltzman distribution

150
Q

Spectroscopic transformations let you switch between _________and _________units and transform reflectance data into __________ units

A

Spectroscopic transformations let you switch between absorbance and reflectance units and transform reflectance data into Kubelka-Munk units

151
Q
A
152
Q

Define

Second derivative

A

define the curvature of a data set and are best applied to data with quadratic (curved) baselines

153
Q

What can happen to light that hits a sample?

A

Transmitted, absorbed or scattered

154
Q

Define

Resonance Raman

A

occurs when excitation laser frequency is chosen in such a way that it crosses the frequencies of electronic excited states and resonates with them. The intensity of Raman bands, which originate from electronic transitions between those states, are enhanced three-to-five orders of magnitude

155
Q

Why are lipids good biomarkers?

A
  • Lipids change in response to disease conditions
    • e.g. cholesterol, which, has been used in risk calculations for heart disease
    • Triglycerides are also used clinically for risk assessmet of heart disease and diabetes
    • Lipids can be used as infrared biomarkers for malaria diagnosis
156
Q

When should you not use a second derivative?

A

Don’t use it when the spectra is noisy becauase it will amplify the noise

157
Q

Define

Overtone bands

A

the spectral band that occurs in a vibrational spectrum of a molecule when the molecule makes a transition from the ground state (v=0) to the second excited state (v=2), where v is the vibrational quantum number (a non-negative integer) obtained from solving the Schrödinger equation for the molecule

158
Q

What does averaging samples and variables do?

A

Reduce the size of the data table

Reduces uncertainty in the measurements

Reduces the effects of noise

159
Q

Define

Biospectroscopy

A

The spectroscopic examination of specimens of living tissue or body fluids

160
Q

Consider the following spectrum.

What type of molecule is this?

Aldehyde, ketone, carboxylate, organic halide, carboxylic acid, aliphatic, aromatic?

A

Hexanoic acid

The carbonyl stretch C=O of a carboxylic acid appears as an intense band from 1760-1690 cm-1. The exact position of this broad band depends on whether the carboxylic acid is saturated or unsaturated, dimerized, or has internal hydrogen bonding.

O–H stretch from 3300-2500 cm-1
C=O stretch from 1760-1690 cm-1
C–O stretch from 1320-1210 cm-1
C-O–H bend from 1440-1395 and 950-910 cm-1

161
Q

Define

Asymmetric stretching

A

Simultaneous vibration of two bonds, with opposite atomic motions. While one bond is elongating the other is contracting

162
Q

Define

Raman effect

A

a change of wavelength exhibited by some of the radiation scattered in a medium. The effect is specific to the molecules which cause it, and so can be used in spectroscopic analysis

163
Q

Write down an expression for the PCA model equation. (1 mark)

A
164
Q

Define PCA Loadings

A

Map of variables: Correlation between variables (regression of X on T). Explains what variables are causing the seaparation observed on the Scores Plot

165
Q

Define Explained variance

A

The % variance explained by Xstruct

166
Q

Definition

the spectral band that occurs in a vibrational spectrum of a molecule when the molecule makes a transition from the ground state (v=0) to the second excited state (v=2), where v is the vibrational quantum number (a non-negative integer) obtained from solving the Schrödinger equation for the molecule

A

Overtone bands

167
Q

What state of matter has vibrational energy?

A

All states (above 0K)

168
Q

What are the disadvantages of Dispersive micro-Raman spectrometers?

A

Possible fluorescence

Requires calibration

169
Q

How do you work out the score (t) of a sample?

A

The distance from the mean along th PC is the score

170
Q

Define

Mean centering

A

The first preprocessing step that involves subtraction of the mean for each variable

171
Q

List these types of spectroscopy in order of increasing size of wavelengths detected:

Electronic, rotational and vibrational

A

Rotational > vibrational > electronic

172
Q

Haemoglobin has 87% alpha helices while IgG has only 3%. Which would have a high Amide I band?

A

Haemoglobin (1651 cm-1; IgG 1632 cm-1)

173
Q

Define

Standard normal variate

A

corrects each spectrum by subtracting the mean and dividing by the standard deviation for that spectrum

174
Q

Definition

Simultaneous vibration of two bonds, with opposite atomic motions. While one bond is elongating the other is contracting

A

Asymmetric stretching

175
Q

Definition

the science of relating measurements made on a chemical system or process to the state of the system via application of mathematical or statistical methods

A

Chemometrics

176
Q

Definition

observed when more than two or more fundamental vibrations are excited simultaneously

A

Combination bands

177
Q
  1. What happens to maxima bands when a first derivative of the spectrum is calculated? (1 mark)
A

The maxima lie on the Y=0 axis

178
Q

Define

Residuals (E)

A

Error of the data

179
Q

Definition

occurs when excitation laser frequency is chosen in such a way that it crosses the frequencies of electronic excited states and resonates with them. The intensity of Raman bands, which originate from electronic transitions between those states, are enhanced three-to-five orders of magnitude

A

Resonance Raman

180
Q

Definition

One of the possible Raman interactions that leads to the material absorbing energy and the emitted photon has a lower energy than the incident photon

A

Stokes Raman scattering

181
Q

Define

Stokes Raman scattering

A

One of the possible Raman interactions that leads to the material absorbing energy and the emitted photon has a lower energy than the incident photon

182
Q

What is the explained variance?

A

The % variance explained by Xstruct

183
Q

What are the four modes of CO2?

A

Symmetric stretching

Asymmetric stretching

2 equivalent bending

184
Q

What are the three types of spectroscopic transformations available in The Unscrambler?

A
  1. Absorbance to reflectance or Absorbance to transmittance
  2. Reflectance to absorbance or Transmittance to absorbance
  3. Reflectance to Kubelka-Munk
185
Q

__________: finds a data value by averaging the value within a segment of data points

____________: applies a normally distributed weighting function across the spectral region

__________: finds the median value within a segment of data points

__________: finds a data value by making a polynomial fit to the data points using a number of data points on each side

A

Moving average: finds a data value by averaging the value within a segment of data points

Gaussian Filter: applies a normally distributed weighting function across the spectral region

Median Filter: finds the median value within a segment of data points

Savizky-Golay: finds a data value by making a polynomial fit to the data points using a number of data points on each side

186
Q

Define

Combination bands

A

observed when more than two or more fundamental vibrations are excited simultaneously

187
Q

What is the criteria for selecting the appropriate number of PCs?

A
  • Explained variance/Residual variance
  • Clear global maximum/minimum
  • First local maximum/minimum
  • Plateau
188
Q

Definition

a very short-lived, unobservable quantum state

A

Virtual states

189
Q

Define

Wavenumber

A

the spatial frequency of a wave, measured in cycles per unit distance or radians per unit distance

190
Q

Define

Rayleigh scattering

A

the scattering of light by particles in a medium, without change in wavelength. It accounts, for example, for the blue colour of the sky, since blue light is scattered slightly more efficiently than red

191
Q

Draw a diagram illustrating the difference between Resonance Raman, Pre-Resonance Raman and Fluorescence scattering

A
192
Q

What is the most common application of Beer-Lambert Law?

A

UV-vis determination of component concentrations in unknown solutions

193
Q

Which of the following statements is correct in relation to Principle Component Analysis?

  1. The first PC accounts for the lowest variance in the data set
  2. Loadings plots show the projected samples onto the scores plot
  3. The PCA matrix is decomposed into a scores and loadings matrix
  4. The inclusion of outliers can improve the models predictive capacity
A

Which of the following statements is correct in relation to Principle Component Analysis?

  1. The first PC accounts for the lowest variance in the data set
  2. Loadings plots show the projected samples onto the scores plot
  3. The PCA matrix is decomposed into a scores and loadings matrix
  4. The inclusion of outliers can improve the models predictive capacity
194
Q

Which region of the spectrum are fundamental, overtone and combination bads found?

A

Fundamental: IR region

Overtones and Combination: IR or near-IR region

195
Q

Definition

The spectroscopic examination of specimens of living tissue or body fluids

A

Biospectroscopy

196
Q

Define

Savizky-Golay smoothing

A

finds a data value by making a polynomial fit to the data points using a number of data points on each side

197
Q

Define

Multiplicative scatter correction

A

a normalisation of spectra to remove effect of variations between samples due to differences in pathlength. Corrects for both baseline slope and offset

198
Q

Define

Normalisation

A

a row-oriented transformation used to get all data in approximately the same scaling

199
Q

A spectrum shows a band at 750 cm-1. What is the main functional group contributing to this vibrational mode? (1 mark)

  1. ν(C=O)
  2. δ(NH2)
  3. ν(C-Cl)
  4. ν(N-H)
A

A spectrum shows a band at 750 cm-1. What is the main functional group contributing to this vibrational mode? (1 mark)

  1. ν(C=O)
  2. δ(NH2)
  3. ν(C-Cl)
  4. ν(N-H)
200
Q

A spectrum of an unknown compound shows a small distinct band at 3010 cm-1 plus strong bands between 3000-2800 cm-1 and a medium band at 1740 cm-1. The spectrum is likely to be from:

  1. B-DNA
  2. Protein
  3. Unsaturated lipid
  4. Saturated lipid
  5. None of the above
A

A spectrum of an unknown compound shows a small distinct band at 3010 cm-1 plus strong bands between 3000-2800 cm-1 and a medium band at 1740 cm-1. The spectrum is likely to be from:

  1. B-DNA
  2. Protein
  3. Unsaturated lipid
  4. Saturated lipid
  5. None of the above
201
Q

Definition

Removing unwanted baseline effects by estimating a polynomial baseline

A

De-trending

202
Q

Definition

a device that produces interference between two beams of light

A

Michelson Interferometer

203
Q

What is PC1?

A

The line that points in the direction of the maximum data variation

204
Q

Which one of the following statements is incorrect for infrared spectroscopy: (1 mark)

  1. The absorbance is directly proportional to the concentration
  2. The stronger the dipole moment the higher the wavenumber value
  3. The larger the reduced mass the lower the wavenumber value

Hydrogen boning gives rise to broad OH stretching modes

A

Which one of the following statements is incorrect for infrared spectroscopy: (1 mark)

  1. The absorbance is directly proportional to the concentration
  2. The stronger the dipole moment the higher the wavenumber value
  3. The larger the reduced mass the lower the wavenumber value

Hydrogen boning gives rise to broad OH stretching modes

205
Q

What is PC2?

A

The line perpendicular to PC1 that explains the perpendicular variation

206
Q

True or False:

The PCs are orthogonal to each other

A

True

This means that they are independent of one another

207
Q

Why are the C=C bonds generally have a higher wavenumber value than C-C bonds?

A

C=C bonds are more electron rich and thus have a higher bond order than C-C bonds therefore they have a greater force constant and thus higher wavenumber value

208
Q

True or False:

Water is a good Raman scatterer

A

False

Water doesn’t scatter

209
Q

Why does the number of components of a PCA model matter?

A

The number of components in the model characterises the structure of the data: the fewer PCs needed, the simpler the model

210
Q

Which one of the following molecules is a strong Raman scatterer?

  1. Asymmetric CO2
  2. HCl
  3. water
  4. HF
  5. benzene
A

Which one of the following molecules is a strong Raman scatterer?

  1. Asymmetric CO2
  2. HCl
  3. water
  4. HF
  5. benzene
211
Q

What are the two types of nuclear motions?

A

Rotational and vibrational energy

212
Q

Define

Polarizability

A

a measure of the degree to which electrons are displaced relative to the nuclei (i.e. how much to the electrons slosh about)

213
Q

Definition

a subdivision of statistics encompassing the simultaneous observation and analysis of more than one outcome variable

A

Multivariate analysis

214
Q

Definition

Map of variables: Correlation between variables (regression of X on 1)

A

Loadings (P)

215
Q

Given this fundamental absorption frequency, what are the overtones?

A
216
Q

How does Standard Normal Variate (SNV) correct each spectrum?

A

SNV corrects each spectrum by subtracting the mean and dividing by the standard deviation for that spectrum

217
Q

Define

Principal Component Analysis (PCA)

A

a method of analysis which involves finding the linear combination of a set of variables that has maximum variance and removing its effect, repeating this successively

218
Q

What is the model equation of PCA?

A

X = TPT + E

Where:

X = data matrix

T = score matrix

P = matrix of loadings

219
Q

What is smoothing used for?

A

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

220
Q

Where are alpha helix bands found?

A

1650 cm<span>-1</span>

221
Q

What are the general guidelines for pre-processing spectral data?

A
  • Baseline correction
  • Scatter correction
  • Derivatives
  • Normalisation
222
Q

Definition

states that the quantity of light absorbed by a substance dissolved in a fully transmitting solvent is directly proportional to the concentration of the substance and the path length of the light through the solution

A

Beer-Lambert Law

223
Q

Definition

Simultaneous vibration of two bonds, in which the bonds elongate together and contract together

A

Symmetric stretching

224
Q

Define

First derivative

A

used to remove linear baseline effects in continuous spectral data

225
Q

True or False:

Both C-C and C-F would be IR active

A

False

C-F would be but C-C would not since it does not have a dipole moment

226
Q

Consider the following spectrum. Is this molecule aromatic, alkane, alkene, alkyne?

=C-H stretch between 3100-3000 cm-1

C–H stretch from 3000–2850 cm-1
CH2 bend or scissoring from 1470-1450 cm-1
C–H rock, methyl from 1380-1350 cm-1
C–H rock, methyl, seen only in long chain alkanes, from 725-720 cm-1

A

Alkene

227
Q
  1. What type of data would you avoid the use of a second derivative and why? (2 marks)
A

Data that is noisy because small spikes become large bands in the second derivative (large rise over small run).

228
Q

Label the major bands in the spectrum of normal epithelial cell and cancer cell

A
229
Q

Define PCA Scores

A

Map of samples: Projected locations of objects onto the principal components

230
Q

Define

Beer-Lambert Law

A

states that the quantity of light absorbed by a substance dissolved in a fully transmitting solvent is directly proportional to the concentration of the substance and the path length of the light through the solution

231
Q

What does the force constant depend on?

A

The strength of the bond

232
Q

Why is the O-H stretching mode at a higher wavenumber value than the C-H stretching mode?

A

Although the mass of oxygen is higher than carbon. The force constant for the O-H bond is stronger because the oxygen is more electronegative and forms a stronger bond than the C-H producing a larger force constant.

233
Q

Consider the following spectrum of ethanol. Why is the OH so broad?

A

In any sample where hydrogen bonding occurs, the number and strength of intermolecular interactions varies greatly within the sample, causing the bands in these samples to be particularly broad.

234
Q

What is polarizability?

A

A measure of the degree to which electrons are displaced relative to the nuclei

i.e. how much do the electrons slosh about

235
Q

Define

Chemometrics

A

the science of relating measurements made on a chemical system or process to the state of the system via application of mathematical or statistical methods

236
Q

Which one of the following molecules will show an infrared spectrum?

  1. oxygen
  2. nitrogen
  3. symmetric CO2 vibration
  4. Br2
  5. carbon monoxide
A

Which one of the following molecules will show an infrared spectrum?

  1. oxygen
  2. nitrogen
  3. symmetric CO2 vibration
  4. Br2
  5. carbon monoxide
237
Q

What does Multiplicative Scatter Correction (MSC) correct?

A

Corrects for both baseline slope and offset

238
Q

Draw a Dispersive micro-Raman spectrometer

A
239
Q

Define

A-DNA

A

one of the possible double helical structures which DNA can adopt. It is thought to be one of three biologically active double helical structures. It is a right-handed double helix fairly similar to the more common form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in the common form

240
Q

High frequencies (wavenumber) correlate with what?

A

Vibrational motion of light masses and molecules with large force constants

241
Q

Definition

a band centred on a hot transition, which is a transition between two excited vibrational states

A

Hot band

242
Q

Define

Electronic spectroscopy

A

an analytical technique to study the electronic structure and its dynamics in atoms and molecules

243
Q

Definition

a technique, where for each sample, the value of the lowest point in the spectrum is subtracted from all the variables

A

Baseline offset

244
Q

Why does a longer wavelength mean less fluorescence?

A

There is less energy so there is less scattering of light

245
Q

In which region of the electromagnetic spectrum is radiation of wavenumber 10000 cm‑1?

Near-IR

Visible

far IR

microwave

infrared

UV

A

In which region of the electromagnetic spectrum is radiation of wavenumber 10000 cm‑1?

Near-IR

Visible

far IR

microwave

infrared

UV

246
Q

Define

Normal modes

A

an oscillating system is a pattern of motion in which all parts of the system move sinusoidally with the same frequency and with a fixed phase relation

247
Q

Definition

A transformation of a sloped baseline into a horizontal baseline. The technique is to point out two variables, both defined as o, which should define the new baseline

A

Linear baseline correction

248
Q

Define

Vibrational spectroscopy

A

a non-destructive identification method that measures the vibrational energy in a compound

249
Q

The total energy of a molecule is made up of what components?

A

Electronic energy

Vibrational energy

Rotational energy

250
Q

Why are asymmetric modes generally higher in wavenumber than symmetric modes?

A

In symmetric stretching, two or more bonds vibrate in and out together. In asymmetric stretching, some bonds are getting shorter at the same time as others are getting longer. Shorter bonds mean higher wavenumber value because the force constant is greater.

251
Q
  1. The Michelson Interferometer is an essential piece of apparatus in the FT Raman spectrometer. Sketch and label the basic components of an FT-Raman spectrometer including the Michelson Interferometer . (5 marks)
A
252
Q

Define

Baseline offset

A

a technique, where for each sample, the value of the lowest point in the spectrum is subtracted from all the variables

253
Q

How do you choose an appropriate wavelength for Raman?

A
254
Q

Below a Scores Plot and Loadings Plot for FTIR transflection spectra of cancer versus normal liver tissue

  1. Assuming the spectra have been processed using a second derivative. What are the wavenumber values for the strong loadings (bands) associated with cancer cells? (2 marks)
  2. What is the likely origin of these bands? (2 marks)
A

1153, 1084, 1026 and 995 cm-1

DNA

255
Q

Definition

a method of analysis which involves finding the linear combination of a set of variables that has maximum variance and removing its effect, repeating this successively

A

Principal Component Analysis (PCA)

256
Q
  1. What are some advantages of using FT-Raman spectrometer compared to conventional visible/UV dispersive Raman spectrometer ? (2 marks)
A

Using a longer wavelength can minimise fluorescence (not enough energy to cause electronic transitions). Damage from shorter wavelengths (high energy) is possibly reduced depending on the applied power.

257
Q

Which nucleotide is the most acidic?

A

Cytosine

258
Q

List the nucleotides in terms of nucleophilicity

A

G > A >> T > C

259
Q

___________ between aromatic rings of base pairs stabilises DNA double helix

A

π- stacking between aromatic rings of base pairs stabilises DNA double helix

260
Q

What happens to the melting point of DNA as the GC content increases?

A

Tm increases

261
Q

What is the formula for the melting point of DNA?

A

Tm = 2(#ATbp)+4(#GCbp)

262
Q

What are the three ways of targeting DNA with cytotoxic drugs?

A
  • Thymine biosynthesis
  • DNA replication
  • Inhibition of mitosis (alkylating agents)
263
Q

What are the steps of thymine biosynthesis?

A
  1. Remove 2’ OH
  2. Remove 5’ diphosphate
  3. Add 5-CH3
264
Q

Why do drugs targer thymine synthesis instead of other nucleotides?

A

Thymine does not form spontaneously; it requires enzymes

Targeting thymine prevents targeting of RNA

265
Q

How are alkylating agents mutagenic?

A

They react as electrophiles to form stable covalent bonds, intercalating with the DNA causing mutation

266
Q

Cyclophosphamide is the most commonly prescribed alkylating agent used for the treatment of cancer. It is converted to an active metabolite in the liver, which is capable of cross-linking DNA. Draw a curved arrow mechanism for the formation of the double stranded DNA adduct (Note: onlt the mechanism for the second step is required)

A

CHM2942 (3 decks)

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