Spectroscopy and proof of structure Flashcards
Use of Mass Spectrometry
- molecular ion gives molecular weight (MW)
- exact MW and isotope patterns may give molecular formula
- fragmentation pattern may suggest molecular fragments
Use of Infrared Spectroscopy
- look for peaks characteristic of functional groups
Use of HNMR
- Integrals give number of equivalent protons
- Chemical shifts can be correlated with functional groups
- J couplings give connectivity between groups of protons
Strengths of HNMR spectroscopy
- quick to determine type of H sites and their relative numbers
- chemical shifts correlate well with chemical functionality
- coupling patterns are useful in determining connectivity between H types
- different isomers give very different spectra
Limitations of HNMR spectroscopy
- no info about overall molecular weight
- no direct info about atoms other than H
Strengths of Mass Spectrometry
- quick to determine molecular mass
- isotope patterns may reveal presence of e.g. halogens, approx number of C atoms, odd numbers of N, etc
- some chemical groups (e.g. benzyl) give identifiable fragment ions
- fragments can also confirm the presence of some functional groups (being lost)
Limitation of mass spectrometry
- fragmentation patterns may be complex
Strengths of IR Spectroscopy
- easy to check presence/ absence of certain chemical groups
- the precise vibrational frequencies of some groups can distinguish between other similar groupings, e.g. carbonyl, carboxylic acid and amide.
Limitation of IR Spectroscopy
- molecular vibration can be complex - do not over-interpret
Photon and energy relationship
photon energy = molecular energy gap
Degenerate States
Two different states (defined by different quantum numbers) can have the same energy
Units for wavelength, λ
metres, m
Units for Frequency, v
s -1 , Hz
Units for wavenumber, ṽ
cm -1
A “state” definition
defines an atom or molecule by its quantum numbers
A “transition” definition
the process by which one state turns into another state, usually by the exchange of energy with the surroundings by electromagnetic radiation
What do the selection rules do?
They tell us which transitions are allowed and which are not
How is data recorded in spectroscopy?
In the frequency domain - scanning the frequency of radiation we pass through the sample and seeing what is absorbed
What causes a shadow?
When samples containing the atoms are placed between the lamp and a screen due to the atoms absorbing the specific atomic line spectrum
Define the functional group region
4000-1500 cm -1
In this region, there is localised vibrational motion of atoms with functional groups which is helpful in indicating the general molecular structure.
Define the fingerprint region
1200-100 cm -1
In this region, there is global vibrational movement involving extended parts of the molecule. These are unique to a particular structure and act as a ‘fingerprint’. Isomers with the same functional groups will show different fingerprint spectra.
(many atoms move at the same time)
Factors that determine vibrational frequencies
- bond strength
- types of bonds
- stretching v bending
How does bond strength impact force constant and vibrational wavenumber
As bond strength becomes weaker, force constant decreases and vibrational wavenumber decreases
How does type of bonding effect vibrational wavenumber and frequency?
Vibrational wavenumber:
Bonds to hydrogen > Bonds between first row atoms > bonds to heavier atoms
How does vibrational frequency vary from stretching and bending?
symmetric stretch = not IR active
asymmetric stretch > degenerate bends
What is the impact of isotopic substitution?
It changes the reduced mass and shifts vibrational frequencies.
Force constants remain the same.
What is the result of anharmonicity?
energy levels get closer together as v increases
(v = vibrational quantum number)
NMR outline on nuclei acting as magnets
- nuclei can interact with an applied magnetic field giving rise to sets of energy levels and can induce transitions
- magnetic moments on different nuclei within a molecule can interact with each other
What do energy levels refer to?
they describe the energy of the entire molecule in that state
What does Fourier Transforms (FT) do?
Allows a time-domain spectrum to be calculated into a frequency domain spectrum
Measuring wavelength of absorption
- tend to be broad
- gives information on the energy gap between ground and excited states
Measuring intensity of absorption
- not all transitions have the same probability and therefore strength (sometimes referred to as a cross- section, σ)
What are chromophores?
they are molecules in a given material that absorb particular wavelengths of visible light
What length molecule is favourable for absorption?
the longer the molecule, the greater the wavelength therefore greater the absorption
(longer the molecule, closer the energy levels)
Why are transition metal ions coloured?
transitions between d-orbitals
Isosbestic points
absorbence doesn’t change
What does electronic spectroscopy involve?
electrons moving between molecular orbitals (changing the electronic structure)
Why is electronic spectroscopy useful?
to measure the concentration of a known chromophore or to follow the course of a reaction.
What is the harmonic oscillator in terms of energy?
a potential energy curve showing potential energy as a function of displacement
- total energy is constant, but interconverts between potential and kinetic energy
Selection rules for IR spectroscopy
- ΔV = ± 1
- a vibrational mode is only IR active if the molecular dipole moment changes during the vibration
(IR spectra are only observed for heteronuclear diatomics, not homonuclear ones)
What sort of vibrational frequencies is greater: stretching or bending
stretching frequencies > bending frequencies
*can have symmetric or antisymmetric stretches
If a molecule has n atoms, how many vibrations (degrees of vibrational freedom), for linear molecules?
3n - 5
If a molecule has n atoms, how many vibrations (degrees of vibrational freedom), for non-linear molecules?
3n - 6
Functional group vs molecule vibrations
- functional group vibrations are found in the functional group region
- whole molecule vibrations are found in the fingerprint region
How does isotopic substitution affect vibrational frequencies?
changes the reduced mass and shifts vibrations, but force constants remain the same
What does anharmonicity mean for when v (vibrational quantum number) increases?
it causes the energy levels to get closer together
What does nuclear spin mean for the nucleus?
it gets a magnetic moment
In an applied magnetic field, in how many ways can the magnetic moment align with the field?
2I +1
What do you need for NMR?
- big magnet (very high field strength, superconducting magnet)
- sample placed in magnet
- radiofrequency (RF) transmitter to obtain spectra
Basic interpretation of NMR spectra
expect to see a separate peak for each magnetic nucleus in a chemically distinct environment
Why is the magnetic field experienced at each nucleus in a molecule not identical?
it is affected by electron density around the nucleus which shields it from the applied magnetic field
How to calculate effective magnetic field?
B eff = app (1-σ)
where σ is the shielding constant
Why does electron density impact effective magnetic field?
- when electron orbital is put into a magnetic field, it induces motion of the electrons which generates an induced field
- greater the electron density around the proton, the greater the shielding and the lower the B eff
Factors affecting chemical shift?
- electron density
- electronegativity of neighbouring groups
- magnetic anisotropy
- aromatic and other pi-bonding
What do correlation charts show?
typical ppm ranges for different functional groups
What essentially is the cause of spin-spin coupling?
when the magnetic moments of two protons interact
What is the chemical shift?
a ratio of the peak position in Hz to the operating frequency in MHz
- it’s independent of the magnetic field strength and it’s reported in ppm
What is the coupling constant?
- it is a measure of the interaction between a pair of protons
- it is independent of the magnetic field strength
- reported in Hz
What is coupling like to equivalent protons?
if the nuclei (spin 1/2) are equivalent, there are characteristic ‘multiplets’ of n+1 lines:
1H: 1:1 doublet
2H: 1:2:1 triplet
3H: 1:3:3:1 quartet
etc
Why is C13 NMR much less sensitive than H1 NMR?
C13 is in such low natural abundance (about 1.1%) thus gives very weak signals.
(& lower gyromagnetic ratio)
Why does 13C NMR have higher chemical shift?
Why does 13C NMR only show single line per site in molecule?
13C - 13C coupling is negligible due to 13C being in such low abundance
What is the basic scheme of mass spectrometry?
- Vaporise and ionise molecule
- Accelerate ions
- Separate ions by mass (mass filters, time-of-flight)
- Detect ions
Hard vs soft ionisation techniques
Hard: electron impact - suitable for small/ volatile molecules
Soft: electrospray - for delicate molecules
Electron impact ionisation
- leads to extensive fragmentation
- sample must be thermodynamically stable since it undergoes harsh conditions
parent peak (M+) corresponds to molecular mass of compound
Matrix assisted laser desorption and ionisation (MALDI)
- good for polymers and biological macromolecules
- prepare sample in a matrix that absorbs light (soft technique)
- minimal fragmentation
- ions can be +ve or -ve and may include a metal ion attached (e.g. Na+)
Time-of-flight
- ions are accelerated with equal kinetic energy
- m/z is proportional to V acc t 2
- recording time between ion generation and arrival time at the deterctor, m/z can be deduced
What can be lost in fragmentation?
both radicals and neutrals but only ions are detected
What does fragmentation do?
it follows a pathway that leads to the most stable ions thus giving these as strong peaks in the mass spectrum
Molecular ion peak (M+)
M+ peak is the highest possible mass from a molecule, M (molecular mass)
*M+ peak may be weak or absent if molecular ion is very unstable
Nitrogen rule
odd number of nitrogen atoms = odd molecular mass
- molecular weight is always even from molecules made up on the common elements
For the ring + double bond rule, what does RDB = 4 may mean?
it is aromatic
What are the key isotopes of C, Br and Cl?
C13 and C12
Br79 and Br81
Cl35 and Cl37
Peaks for bromine in mass spec
51% Br79 and 49% Br81 so approximately equal intensity
Peaks for carbon in mass spec
98.9% C12 and 1.1% C13 so clusters of peaks for all large organic molecules
What is a quick way to estimate the number of C’s in mass spec?
Divide M+1:M ratio by 1.11%
Peaks for chlorine in mass spec
75% Cl35 and 25% Cl37 so a 3:1 ratio
Peaks for boron in mass spec
20% B10 and 80% B11
Stable fragments: molecules containing benzyl
gives strong stabilised fragment ion at 91 units, which can rearrange to stable “tropylium ion” by resonance
Stable fragments: Carbonyl containing compounds
they often give the stable ‘acylium ion’ fragment
