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Chemistry - Year One > Separation Science and Mass Spectrometry > Flashcards

Separation Science and Mass Spectrometry Flashcards

1
Q

What is chromatography?

A

A physical method of separation, in which the components to be separated are distributed between two phases, one of which is stationary, while the other moves in a definite direction

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2
Q

What is the mobile phase?

A

The liquid or gas flowing through the tube

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3
Q

What is the stationary phase?

A

A substance that holds in place and coated on the wall of the tube

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4
Q

How fast will a molecule with a high affinity for the stationary phase move through the tube?

A

Slowly

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5
Q

How fast will a molecule with a low affinity for the stationary phase move through the tube?

A

Fast

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6
Q

Name four different types of liquid chromatography

A

Paper Chromatography

Thin Layer Chromatography(TLC)

Column / Flash Chromatography

High-Performance Liquid Chromatography (HPLC)

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7
Q

What property must the molecules have when using liquid chromatography?

A

They must be soluble

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8
Q

What property must the molecules have when using gas chromatography?

A

They must be volatile

This can also be used if the molecules are not themselves volatile, but can easily be derivatised (converted) into volatile versions of themselves

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9
Q

What does ‘partition’ refer to when talking about chromatography?

A

When both of the phases are liquids, the solute will dissolve more in one phase than the other

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10
Q

What does ‘adsorption’ refer to when talking about chromatography?

A

When the stationary phase is solid, different molecules will ‘stick on’ to it more or less

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11
Q

What does ‘electrostatic interaction’ refer to when talking about chromatography?

A

When the solute is ionic, it can form a strong affinity with an ionic phase

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12
Q

What does ‘molecular sieving’ refer to when talking about chromatography?

A

It uses a stationary phase made of gel particles, containing cavities of defined sizes. Molecules that are too big cannot get into the cavities, and so pass through the tube more quickly

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13
Q

Why do particles of the same type not all go at the exact same speed?

A

They are subject to random thermal motion and diffusion, and therefore will travel at slightly different speeds

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14
Q

Why does separation require an input of energy?

A

It is opposite diffusion (a passive process) and is therefore going against what is wanted by the substance

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15
Q

What happens when the column length increases?

A

The gap between the peaks get larger

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16
Q

What happens when the mobile phase flow rate increases?

A

The gap between the peaks get larger as there is less opportunity for thermal motion

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17
Q

What does the gap between the peaks measure?

A

They measure how effective the separation has been

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18
Q

Why is it important to load the compound in a small volume?

A

Every molecule will start at the same place in the medium

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19
Q

What is a chromatogram?

A

It is the name for the output of a chromatography instrument

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20
Q

What is the baseline of the chromatogram?

A

The signal recorded when no compound is being eluted

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21
Q

At what time is the sample injected?

A

t₀

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22
Q

What is the retention time (tᵣ)?

A

The amount of time it takes for a specific compound to elute, measured at the height of its peak

It depends on: the relative affinity of the analyte for the different phases, the length of the column and mobile phase flow rate

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23
Q

What is the retention time proportional to?

A

Retention time is directly proportional to the length of the column

Retention time is inversely proportional to the flow rate

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24
Q

What is the peak width (W)?

A

A measure of how long it takes for all of the analyte (of one type) to pass the detector

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25
Q

What is the column length (L)?

A

The length of the chromatographic equipment

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26
Q

What is the resolution (Rₛ)?

A

A measure of how good the chromatographic method is for separating two specific components of a mixture

It depends on the retention time, peak width and column length

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27
Q

What is the formula for resolution?

A

Rₛ = (2 x (tᵣ of A - tᵣ of B)) / (W of A + W of B)

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28
Q

What is resolution directly proportional to?

A

The square root of the column length

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29
Q

What gases usually make up the mobile phase in GC?

A

Nitrogen, hydrogen or helium

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30
Q

What type of material usually makes up the stationary phase in GC?

A

A very high-boiling liquid polymer, immobilised on the inner wall of a narrow tube

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31
Q

What are the two most common types of stationary phase in GC?

A

PDMS (polydimethylsiloxane) - low polarity

PEG (polyethyleneglycol) - medium polarity

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32
Q

How does GC work?

A

A small volume of sample is injected into the start of the column and the analytes in the sample are carried along by the gaseous mobile phase, separating as they travel through the column

At the end of the column, the analytes are detected and the a chromatogram is outputted

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32
Q

How does GC work?

A

A small volume of sample is injected into the start of the column and the analytes in the sample are carried along by the gaseous mobile phase, separating as they travel through the column

At the end of the column, the analytes are detected and the a chromatogram is outputted

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33
Q

How does packed column GC work?

A

The column is filled with small particles, which are coated in the stationary phase

The mobile phase moves through the gaps between the particles

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34
Q

How does capillary column GC work?

A

The capillary walls are coated with a thin film (1-5 micrometres) of the stationary phase

The mobile phase moves through the middle of the capillary

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35
Q

What are the three different types of compound GC can be applied to?

A

Are naturally volatile e.g. gases and liquids with low boiling points

Are not very volatile at room temperature, but become more volatile when heated e.g. liquids with higher boiling points, and some solids

Are not naturally volatile, but can be chemically converted (derivatised) into volatile compounds

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36
Q

What happens if the analyte in GC has a high affinity for the stationary phase?

A

It will elute more slowly

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37
Q

What happens in the analyte in GC is more volatile?

A

Ir will spend more time in the mobile phase, making it elute more quickly

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38
Q

How are the best separation results achieved in GC?

A

When there is a good match between the polarity of the stationary phase and the polarity of the analytes to be separated - if this is the case, the order the analytes elute will reflect their boiling point

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39
Q

How can high temperatures in GC reduce the resolution of the separation?

A

It reduces the retention time of the species as they elute more quickly, therefore making the peaks closer to each other

High column temperatures also increases the random thermal motion that the analytes experience, leading to broader peaks

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40
Q

What is isothermal elution?

A

When there is a single temperature throughout the whole elution process

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41
Q

What is programmed temperature elution?

A

When there is an increase or decrease in temperature as the elution process goes on - this is useful when there are analytes with significantly different boiling points

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42
Q

Name two methods of GC detection

A

Flame Ionisation Detector (FID)

Mass Spectrometry (GCMS)

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43
Q

How does FID work?

A

The mobile phase carrying the analytes with it exits the column and is combusted in a hydrogen flame, generating a supply of CHO⁺ ions which cause a measurable current in the FID

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44
Q

How does the number of CHO⁺ ions impact the magnitude of the peaks?

A

The more CHO⁺ ions there are, the greater the peak and can therefore help to see the amount of analyte in the species

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45
Q

Why must FID be standardised when determining concentrations of analytes?

A

The constant of proportionality (or response factor) can differ significantly from one analyse to another

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46
Q

For what substances can Liquid Chromatography (LC) be used?

A

Compounds that are soluble

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47
Q

Why is LC very useful and can be applied to almost all substances?

A

The mobile phase and stationary phase can be changed greatly, reflecting any substances with differing polarities

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48
Q

Describe Paper Chromatography

A

Typically uses a strip of paper as a stationary phase, which is then dipped in a solvent acting as the mobile phase

The solvent moves up the paper, carrying the different analytes up it at different rates

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49
Q

Describe TLC

A

Typically uses silica powder as the stationary phase which is absorbed onto a thin strip of aluminium

The plate is then dipped in solvent (mobile phase) and then the solvent carries the different compounds up at different rates

This is usually used for monitoring the progress of the reaction

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50
Q

Describe Column Chromatography

A

Typically uses silica powder as a stationary phase, which is supported in a vertical glass column

A mixture can be placed at the top of the column, and then a solvent can be poured on top

The analytes then elute down the column at different rates, allowing for large scale separations and can purify reaction mixtures

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51
Q

Describe Flash Chromatography

A

It is the same as column chromatography, with the only difference is that is done under elevated pressure to speed up the elution rates

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52
Q

Describe HPLC

A

A small-scale, instrumental method for analysing and separating mixtures

It typically uses silica or chemically-modified silica as a stationary phase, with almost any type or combination of solvents being used as the mobile phase

The mobile phase is typically kept at a very high pressure (up to 400 atmospheres)

53
Q

Why is a pre-column usually used in HPLC?

A

It is the same as the main column, but is smaller and cheaper so is easier to replace if something has a very strong affinity to the stationary phase

54
Q

Describe the main column in HPLC

A

Usually made from stainless steel in order to withstand the high pressure

Typically 10-25 cm long, with an internal diameter of around 75 micrometres

55
Q

What material is usually used if a polar stationary phase is required in HPLC? Why?

A

Silica is a common choice as the surface has many polar Si-O and O-H bonds, allowing it to strongly retain polar analytes

56
Q

What material is usually used if a non-polar stationary phase is required in HPLC? Why?

A

Chemically modified silica is a common choice, with long carbon chains (such as C18) bonded to the surface

This allows it to strongly retain non-polar analytes by ‘dissolving’ them in the organic groups

57
Q

What is the mobile phase in HPLC?

A

Almost any solvent, or combination of solvents, can be used as long as they are fully miscible

Buffered aqueous solutions can be used, and salts can be added

58
Q

What are some common solvents in HPLC?

A

Hexane
Ethyl Acetate
Isopropanol
Methanol
Acetonitrile
Water

59
Q

What is ‘normal phase’ HPLC?

A

A polar stationary phase (e.g. silica) is used with a non-polar mobile phase (e.g. hexane)

60
Q

What is ‘reverse phase’ HPLC?

A

A non-polar stationary phase (e.g. C18-silica) is used with a polar mobile phase (e.g. water)

61
Q

What is isocratic elution?

A

The composition of the mobile phase is set, and does not vary

62
Q

What is gradient elution?

A

The ratio of solvents used changes over time, giving a high resolution and a quick time, making the best of both problems

63
Q

What are two types of detection when using HPLC?

A

UVvis

HPLC-MS

64
Q

What is UVvis (Ultraviolet-Visible absorption)?

A

It relies on analytes absorbing electromagnetic radiation (i.e. light) in the UVvis region, 200-800 nm, and is quantified in the Beer-Lambert Law

65
Q

What is the equation for the Beer-Lambert Law?

A

A = ε x c x l

A = absorbance
ε = molar absorption coefficient (dm³ mol⁻¹ cm⁻¹)
c = concentration (mol dm⁻³)
l = path length (m, dm, cm, mm…)

66
Q

What is the molar absorption coefficient?

A

A constant for a specified compound at a specified wavelength

It describes how much light the compound absorbs with a high number meaning that it absorbs a lot of light

67
Q

What is the path length?

A

The distance through the solution that the light beam passes, during which it is being absorbed by the analyte

Increasing the path length will result in a higher absorbance

68
Q

What are two potential problems of UVvis?

A

The analyte does not absorb in the UVvis region

The sensitivity of the detector may be too low (it is impractical to reliably measure values of A below 1 x 10⁻⁴)

69
Q

What can we do if the analyte does not absorb in the UVvis region?

A

It can potentially be overcome by derivatising the analytes e.g. by attaching a group which absorbs or fluoresces

70
Q

What can we do if the sensitivity of the detector is too low?

A

If the values of c and ε are low, the path length can be increased by using a ‘Z-cell detector’

71
Q

What is a ‘Z-cell detector’?

A

A way of increasing path length by having the incident light coming at an angle that maximises length

72
Q

What does the MS do after HPLC?

A

It yields molecular mass and structural data that can be analysed

73
Q

What are the three main principles of Mass Spectrometry (MS)?

A

Ionisation

Separation of ions by mass/charge ratios

Detection

74
Q

What are three methods of ionising a sample for MS?

A

Electron Impact (EI)

ElectroSpray Ionisation (ESI)

Matrix Assisted Laser Desorption Ionisation (MALDI)

75
Q

What is the principle of EI?

A

Involves colliding electrons with gas-phase sample molecules, and generally produces a molecular ion (a radical cation) with numerous fragment ions

76
Q

What is the principle of ESI?

A

A ‘soft’ ionisation technique in which ionisation takes place from the solution phase, making it useful for fragile or involatile species

It typically generates a protonated molecule MH⁺ ions, and does not generate fragment ions

77
Q

What is the principle of MALDI?

A

A ‘soft’ ionisation technique in which ionisation takes place from a condensed phase (solution or solid), making it useful for fragile or involatile species

Typically generates MH⁺ ions and does not generate fragment ions

78
Q

What are four different types of mass analysers?

A

Magnetic Sector

Quadrupole

Quadrupole Ion Trap (QIT)

Time of Flight (ToF)

79
Q

What is the principle of Magnetic Sector analysis?

A

Involves passing ions through a magnetic field in which the ion light path is deflected proportionally to its m/z value

It is familiar, but is less commonly used

80
Q

What is the principle of a Quadrupole mass analyser?

A

Ions pass between four parallel metal rods to which electric currents are applied which allows ions with selected m/z ratio to pass through

It is cheap and compact

81
Q

What is the principle of QIT as a mass analyser?

A

Ions pass into a cavity with metal walls to which electric currents are applied causing the ions to orbit in the space

Altering the currents allows ions with selected m/z stations to be detected from the ion trap and detected

It is cheap and very compact

82
Q

What is the principle of ToF as a mass analyser?

A

This involves accelerating ions with an electric field, and then measuring the time taken for the ions to reach a detector

It typically has an excellent mass accuracy

83
Q

What are the x and y axes of an MS spectrum?

A

Ion intensity on the y-axis

M/Z value on the x-axis

84
Q

What is the most stable ion called?

A

The base peak, and this sets the top of the scale at 100%

85
Q

How does the stability of the ions have an impact on the spectrum?

A

The higher the stability, the higher the intensity as there are more of them

86
Q

Where do very unstable ions appear in the spectrum?

A

They do not appear on the spectrum

87
Q

How do isotopes impact the MS spectrum?

A

They leave clusters of small peaks near larger peaks

88
Q

What is an isotopologue?

A

Molecules/ions which have the same formula, but differ in isotopic composition

89
Q

Where does the intensity in the clusters arise from?

A

They arise from differences in the abundance of the isotopes which contribute to the formula of the ion

90
Q

What are the main steps for EI ionisation?

A

The sample is either already in the gas phase, or is heated to volatilise it

Electrons are ejected from a heated filament and accelerated towards the electron trap

The high-energy electrons interact with the sample vapour, causing ionisation

The ionisation process creates a radical cation and two electrons

The ionised sample molecules are guided out of the ionisation chamber by the ion repeller

91
Q

Why do EI spectra not always contain a peak for the molecular ion?

A

They typically have excess energy, leading to their fragmentation

92
Q

What molecules does EI work well for?

A

Molecules that are relatively volatile as they need to be in the gas phase

93
Q

What are the main steps for ESI?

A

The sample is in solution

A small volume of the solution is sprayed through a capillary maintained at a high voltage, creating droplets containing ions in solutions

The droplets evaporate under a flow of warm, inert gas ‘curtain gas’, reducing their size

As the droplets shrink, increasing electrostatic repulsion causes the ejection of ions e.g. [MH]⁺ or [MH₂]²⁺

The ions are guided out of the ionisation chamber by electrodes into the mass analyser

94
Q

How much fragmentation occurs in ESI?

A

Very little fragmentation occurs

95
Q

What substances does ESI work on?

A

Solutions can be used, making it useful for biomolecules such as protein and DNA fragments

This is especially useful for species that are involatile, and species that would undergo decomposition if heated

96
Q

What are the main steps in MALDI?

A

The sample is in solution and mixed with a solution of matrix and dried onto a metal target

A laser pulse is directed at the target, vapourising the matrix and analyte - the matrix helps to prevent thermal decomposition here

A vaporised matrix molecule transfers a proton to a vapourised analyte molecule, forming [MH]⁺

The ions are guided out of the ionisation chamber by electrodes into the mass analyser

97
Q

How much fragmentation occurs in MALDI?

A

Very little

98
Q

What is MALDI suitable for analysing?

A

Thermolabile and involatile species, such as biomolecules and polymers

99
Q

Which detection is MALDI often paired up with and why?

A

ToF mass detection as the ionisation time can be calculated very accurately

100
Q

What is the purpose of the matrix in MALDI?

A

To absorb the laser radiation

101
Q

What are the main features of the quadrupole mass analyser?

A

Separates ions by passing them through the space between four electrically-charged metal rods

It can accept and analyse a constant steam of ions

The ions move into the space between the four parallel metal rods with opposing poles having a voltages of opposite polarity

Variable AC and DC currents are applied, with the combination of these currents constraining the direction of the ion movement in a way that depends on m/z values

102
Q

How does a QIT mass analyser work?

A

Once the ions are admitted into the ion trap, variable currents are applied to the end caps and ring electrodes, keeping the ions circulating inside the ion trap

Varying the electric currents influences the speed and direction of the ions in a way that reflects their m/z ration

Changing the currents, therefore, allows ions of a particular m/z ratio to be removed from the ion trap and detected

103
Q

What is the difference between QIT and the quadrupole mass analysing technique?

A

It uses an electronically controlled gate which opens to accept ions from the ionisation source and then shuts, making it different from the standard quadrupole

104
Q

How does the ToF mass analyser work?

A

Admits ions for the ionisation source, and then accelerates the ions with an electric field

The ions then enter the ‘flight tube’, where there is no electric field

In the flight tube, they drift towards the detector with a fixed speed, with the time taken to reach the detector depending on their m/z values

This gives very accurate results

105
Q

What is the key equation that underpins ToF MS?

A

m / z = 2ev x (t / d)²

106
Q

What different techniques can be used to promote fragmentation when doing ESI?

A

Increase the capillary voltage

Increasing the temperature of the curtain gas

Altering the curtain gas composition

Adding different additives (containing different ions) to the solution before ionisation

107
Q

What is Tandem Mass Spectrometry?

A

The ions generated from a soft ionisation method are selected using one mass analyser, and then subsequently fragmented with the fragment ions being analysed using a second mass analyser

The fragmentation is usually achieved by Collision Induced Dissociation - accelerating the ions and colliding them with unreactive neutral species (e.g. Argon)

108
Q

Why are there clusters in the mass spectrum?

A

Different isotopes of an element have different masses from each other, therefore impacting the values of m/z

109
Q

What does monoisotopic mean?

A

Elements that only have one isotope

110
Q

Using algebra, draw the mass spectrum for a sample of Cl₂

A

Assume that the ³⁵Cl : ³⁷Cl ratio is 3 : 1

(3a + b) represents the Cl chances for one atom, and so we can square this to get the algebraic ratios

This gives us a 9 : 6 : 1 ratio compared to the base peak

111
Q

What is an accurate way to measure the different peak intensities when considering isotopes?

A

We can calculate individual isotope abundance probabilities to calculate relative peak intensities

This calculates it very accurately but is time-consuming and the level of detail is not usually required

Computers are mainly used for this work

112
Q

Why does fragmentation occur?

A

Gas phase ions are put with a sufficient vibrational energy that they will fragment to produce different ions with a naturally occurring loss of uncharged species

113
Q

What type of molecular ion does EI produce?

A

Radical cations

114
Q

What type of molecular ion is generated in soft ionisation?

A

Typically protonated molecules, but can be ‘sodiated’ molecules

115
Q

Which properties change the nature and intensity of ion clusters in a mass spectrum?

A

Mainly on the stabilities of the fragments they produce

The relative rates of the fragmentation processes

116
Q

What ions are unfavourable to form?

A

Very small ions e.g. H⁺ and CH₃⁺

117
Q

What do Even Electron (EE) species not usually fragment into?

A

Two Odd Electron (OE) fragments

118
Q

Can fragment ions further fragment?

A

Yes

119
Q

How can ion stabilise itself?

A

By undergoing a rearrangement reaction e.g. McLafferty rearrangement

120
Q

Which molecules can get lost in fragmentation?

A

Stable, neutral molecules can get lost in fragmentation e.g. H₂O, CO₂, C₂H₄

121
Q

What does an even-mass molecule usually produce?

A

Two odd-mass fragments

122
Q

What must an odd-mass molecule produce?

A

An even-mass fragment, and an odd-mass fragment

123
Q

What is the nominal mass number?

A

The mass number of element of its most abundant isotope

124
Q

What is the Nitrogen rule?

A

If there is an odd number of nitrogen atoms in a molecule, the molecule will have an odd nominal mass

If the compound contains an even number of nitrogen molecules, the compound will have an even nominal mass

125
Q

Why does the Nitrogen rule take place?

A

Its principal isotope has an even mass, but an odd valence

126
Q

What do we know about the number of Nitrogen atoms if a molecular ion has an odd m/z value and is OE species?

A

It has an odd number of Nitrogen atoms

127
Q

What do we know about the number of Nitrogen atoms if a molecular ion has an even m/z value, and is an OE species?

A

It has an even number of Nitrogen atoms

128
Q

What do we know about the number of Nitrogen atoms if a soft ionisation technique is used and there is an odd m/z value?

A

It must contain an even number of Nitrogen atoms

129
Q

What do we know about the number of Nitrogen atoms if a soft ionisation technique is used and there is an even m/z value?

A

It must contain an odd number of Nitrogen atoms

Chemistry - Year One (15 decks)

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