Shapes & Structures Of Molecules Part 1 Flashcards
What is important to note when drawing tetrahedral structure of molecules?
If you are to draw 2 lines at right angles, one line should rest on top of the two bonds in the plane of the paper, and the other should separate the remaining two bonds (pie,wedge). Thus there is one bond in each quadrant.
Multiple tetrahedral centres should also be drawn from the same perspective.
Me
Methyl, -CH3
Et
Ethyl, -CH2CH3
nPr
Normal propyl, -CH2CH2CH3
iPr
isopropyl, -CH(CH3)2
nBu
Normal butyl, -(CH2)3CH3
tBu
Tertiary butyl, -C(CH3)3
Ac
Acetyl, CH3O-
Ph
Phenyl, -C6H5
R
Any alkyl group
Ar
Any aromatic group
What is the trivial name for methylbenzene?
Toluene
What is diffraction?
When a beam of light or wave system passes through a narrow aperture or across an edge, and spreads out as a result.
Describe how X-ray crystallography produces a diffraction pattern?
The wavelength of X-rays is typically the same size as the spacing between each ‘scatterer’ in a compound (atoms’ electrons). Thus a beam of X-rays focussed onto a crystals is diffracted as an X-ray striking an electron produces secondary spherical waves emanating from the electron.
What is the typical wavelength of an X-ray?
~1 angstrom
What are X-rays?
A form of EM radiation composed of photons.
How is an electron density map produced from diffraction patterns?
Diffraction patterns are collected at different orientations by mounting the crystal on a goniometer.
A 3D picture of electron density (contour plot) can be built by measuring the angles and intensities of these diffracted beams in the various orientations and mathematical Fourier transform.
How is the crystal structure determined from the electron density map?
Regions of high electron density represent the positions of atoms.
The bigger the electron cloud, the higher the atomic number of the element (i.e. hydrogen atoms tend not to show up).
What do atomic displacement parameters show?
The uncertainty in the position of atoms in the crystal structure, related to the fact that atoms oscillate around a mean position.
This uncertainty is reduced by streaming a jet of cold nitrogen onto the crystal to reduce vibrations.
What information is given in the crystal structure?
Mean positions of atoms
Bond length
Bond angles
Unit cell (repeating structure) of crystal.
Ads of x Ray crystallography?
Gives location of atoms
Disads of x ray crystallography?
Hard to locate H atoms.
Good quality crystals necessary.
Why is a regular crystalline structure necessary in X-ray crystallography?
Atoms of the same type in the same place will result in CONSTRUCTIVE interference of diffracted photons, rather than destructive interference, and so a more regular picture of photon intensities.
If atoms were not in the same positions fuzzy patterns would be produced with poor resolution- difficult to interpret.
Techniques used to ionise a sample for weighing via mass spectrometry?
ELECTRON IMPACT (dated)- high energy electrons fired at vaporised sample, knocking out electron and producing M+. ELECTROSPRAY (gentle, effective)- sample forced through fine hollow needle connected to +ve terminal of high voltage supply, forming charged aerosol. Solvent evaporates in vacuum leaving charged molecules (e.g. MH+, MNa+, MeO-, CH3COO-).
What is the molar mass of an electron?
0.00055 g/mol
Why might the mass spectrum of a single molecule contain more than one peak?
Isotopes
Fragmentation (i.e. particularly macromolecules).
How can the fragmentation pattern of a molecule be used to find out the identity and structure of a molecule?
Complexity is unique to the compound, so like a fingerprint.
MS/MS- certain fragmented ions can be isolated and seeing how these parent ions fragment into daughter ions (can work backwards, seeing which parent ions might fragment to form a particular daughter ion).
Ads of mass spec?
Gives molecular formula for a compound.
Analysis of mixtures.
Only small sample needed (few million molecules).
Very sensitive (measure to 1 part per 10million).
Disads of mass spec?
Difficult to interpret for unknown molecules.
What does it mean to say that the energy levels of electrons are quantised?
An electron in an atom can only have certain energies; to promote it to another level requires a fixed amount of energy.
Of the translational, vibrational and rotational energies possessed by a molecule, which of those are quantised?
Vibrational & rotational.
Thus can be promoted between these by absorbing light energy, the different given by deltaE = h*v.
Different molecules absorb different frequencies (v)- the basis of spectroscopic techniques.
What type of transition is caused when a molecule absorbs light of the radio frequency?
Transitions in the alignments of nuclear spin
What type of transition is caused when a molecule absorbs light of the microwave frequency?
Rotational
What type of transition is caused when a molecule absorbs light of the infrared frequency?
Vibrational
Which frequencies of light cause electronic transitions within a molecule?
Visible light
UV
X-rays
What type of transition is caused when a molecule absorbs light of the gamma frequency?
Electronic
Those concerning fundamental nuclear processes
When it is said that electrons/some nuclei possess spin, what is this actually referring to?
One of the two types of angular momentum (the other being orbital angular momentum).
What happens when nuclei with spin are placed in a strong magnetic field?
Nuclei with spin have a very weak local magnetic field which interacts with the external one. This gives rise to a set of nuclear spin energy levels (ie. spin up/parallel, spin down/antiparallel). Most nuclei will align with the magnetic field; few will be in the higher energy, antiparallel state.
In NMR, low frequency radio waves cause nucleic transitions between these energy levels resulting in a signal as nuclei relaxing back down emit photons.
How can the number of different energy levels of a nucleus placed in a magnetic field be determined from its nuclear spin quantum number, I?
2I + 1
What does the value of I depend on (although its exact vale cannot be predicted)?
~Odd protons OR odd neutrons = half-integer spin
~Odd protons AND odd neutrons = integer spin
~Even protons AND even neutrons = zero spin
What is significant about nuclei with zero spin?
1 energy level, so no transitions…not NMR active (e.g. carbon12, oxygen16).
What does the difference in energy between spin states depend on?
- Strength of magnetic field (increases diff- no diff with no magnetic field).
- Nucleus concerned.
Thus the resonance frequency of a nucleus (frequency of radio waves required for a particular nucleus to flip between spin states) depends on factors above.
[remember deltaE=hv]
Why is it that not all nuclei of the same type (i.e all carbon-13 nuclei) resonate at the same frequency in NMR?
Nuclei experience a local magnetic field.
This depends on the ELECTRON DENSITY surrounding a nucleus (electronic environment)- movement of electrons (current) sets up a magnetic field to oppose the applied one.
[more electrons=more shielded from applied field… smaller energy gap / resonant frequency].
What frequency does CDCl3 resonate at in carbon13 nmr?
77ppm
How is chemical shift calculated and why is it used?
10^6 x (Kfrequency of resonance - Kfrequency of reference compound)/ Kfrequency of reference compound
It dispels any difference in resonant frequencies arising from differences in the strength of the applied magnetic field used. K cancels
What reference compound is used in NMR and why?
Tetramethylsilane
- Inert
- All carbons/hydrogens equivalent so one peak
- Carbons very shielded (Si more electronegative) so signal low and out of the way.
Give the approximate chemical shifts for different types of carbon in carbon NMR.
0-50 sp3 carbons / C—N
50-100 sp3 + electro-ve / sp carbons
100-150 sp2 carbons
150-200 sp2 carbons + electro-ve
What are the resonant frequencies of the different types of carbonyl compounds?
Just over 200ppm: ketones
Just under 200ppm: aldehydes
160-170ppm: carboxylic acids, esters, acid chlorides, amides
What feature can be used to identify quaternary carbons in carbon NMR?
Peaks appear much smaller
[note, weak signals could also be due to impurities]
In NMR, what is meant by spin-spin coupling?
A through-bond interaction between neighboring, non-equivalent NMR-active nuclei (non-zero spin).
The peak of a nucleus will split into the number of different spin states possessed by the nucleus it couples with.
What is the coupling constant, J (Hz)?
The magnitude of the separation between lines that have split due to coupling between two particular nuclei.
Denoted by xJ(Y-Z) where x is no. of bonds.
Its value gets smaller the more bonds there are between the coupling nuclei.
Why does this splitting of the peak occur when nuclei couple?
The nucleus it couples with exerts a magnetic field:
- Those that are spin up reinforce the magnetic field experienced by the carbon nuclei so they resonate at a higher frequency
- Spin down decrease local magnetic field experienced by carbon nuclei so they resonate at a lower frequency
Why isn’t C—H coupling usually observed
Carbon13 spectra are usually proton decoupled
Why isn’t C—C coupling usually observed?
Low abundance of carbon13
If a carbon 13 nucleus couples to two different nuclei each with spin 1/2 , what is the resultant set of peaks named?
A doublet of doublets
[note, if different spin states then the splitting with the larger coupling constant is mentioned first]
How many peaks is a resonance signal split into when a nucleus couples to n equivalent nuclei of spin I?
2nI + 1
What is an NMR satellite?
Small peaks seen at the bases of main peaks in NMR spectra caused by nuclei of low natural abundance coupling to the nucleus in question.
e.g. peak appears as a triplet but is actually a weak doublet superimposed on a singlet.
What does it mean if a 13C spectrum is proton decoupled?
Protons are spin 1/2 so couple to carbon nuclei. Broadband proton decoupling ensures this does not appear:
The protons are irradiated over a range of frequencies so as to cause them to flip rapidly between spin states. Ultimately the coupling averages to zero.
What are the disads of a proton coupled spectrum ?
Signal strength is weaker so some peaks may get lost in background noise.
Multiplets could overlap making it difficult to assign them to a specific carbon
What does the Attached Proton Test (APT) do?
Peaks from carbons with even no. of protons attached point one way (same as deuterated solvent-down for CDCl3) and those with odd point the other.
What is geminal coupling?
Coupling through 2 bonds
What is vicinal coupling?
Three-bond coupling (as observed in proton nmr)
What is the typical value of a vicinal coupling constant between two protons when free rotation of the central bond is possible?
7Hz
What is the typical value of a vicinal coupling constant between two protons when there is no free rotation of the central bond possible?
Cis protons, 0-12Hz
Trans protons, 12-18Hz
What are the typical values of geminal coupling constants between protons?
Tetrahedron 8-18Hz (provided other groups attached are different)
Square planar 0-3Hz
What is roofing?
If two nuclei are coupling to each other, the intensity of their outer peaks decreases whilst the intensity of their inner peaks increases.
The effect of this on the signals depend on how close their resonant frequencies are.
H NMR chemical shifts
~Methyl group protons 0.5ppm less than those in alkyl chain
~Protons in three membered ring low and highly complex
~Protons bonded to sp2 carbon have shift around 2.5ppm
~Connected to oxygen have shift 1ppm greater than those connected to nitrogen; conjugation to carbonyl increases this further.
~Aldhydes>formate esters
~Aromatic ring>Alkene protons (due to mag field set up by electrons moving in ring currents)
For protons bonded to electronegative elements (rather than carbon) what do their H NMR shifts depend on?
The amount of hydrogen bonding for the proton concerned- depends on solvent, conc of sample and temp.
Signals usually much broader than other signals.
What is a D2O shake?
NMR sample is shaken with some deuterated water, so eventually all N—H and O—H in the sample will have their protons exchanged for D…signals from these protons disappear so they can be identified.
Why isn’t coupling observed with protons bonded to O or N?
They hydrogen bond in solution and therefore have exchangeable protons. Protons rapidly swap and are equally likely to be spin up or spin down, so any coupling is essentially to a proton with just one spin state (so no peak splitting).
Why do nuclei with spin greater than 1/2 generally not couple to nuclei such as carbon 13?
Relaxation- spin states interconvert particularly rapidly.
Why does solvent CDCl3 appear as a triplet at shift 77ppm?
Carbon couples to deuterium, which has spin 1 and unusually relaxes sufficiently slowly for coupling to happen. It has three spin states, so peak is split into three.
What type of energetic transitions does IR spectroscopy look at?
Vibrational (types of bonds present)
How are the x and y axes labelled in an IR spectrum?
x- wavenumbers, cm-1 (no of whole waves in 1 cm, directly proportional to frequency v=cxwavenumber)
y- transmission, %
What is hookes law (frequency of oscillation for a weight on a spring)?
v œ sqrt(Kf/m)
Where Kf is the force constant, how hard it is to stretch the spring.
How is hookes law adapted to represent the frequency a bond oscillates about its equilibrium, lowest energy bond length?
Wavenumber= (sqrt(Kf/mu))/2pic
Where mu is the reduced mass= m1m2/(m1+m2)
Or if m1»m2, mu= m1m2/m1 ~~ m2
Reduced mass is approximately mass of H atom when bond is X-H. Where does this form of bond lie in the IR spectrum?
2500-4000cm-1 (N-H sharp around 3300, C-H just less than 3000).
Otherwise double bonds lie 1500-2000cm-1, and triple bonds lie 2000-2500cm-1.
Why might a single absorption correspond to multiple bonds vibrating at once?
Molecules vibrate in a complex way that involves all atoms moving at once. These different vibrational motions are described by normal modes. E.g for ethyne C-H symmetric stretch 3374 C-H antisymmetric stretch 3287 C-C stretch 1974 Trans bend 612 Cis bend 729
What determines the size of the peak in an IR spectrum?
The dipole moment of the bond, which light can interact with. The larger the dipole, the stronger the absorption; if no dipole moment, no absorption.
How are the frequencies for symmetrical vibrations with no change in dipole Moment determined if they can’t be by IR?
Raman spectroscopy
An intense laser beam is fired at the sample, and the frequencies of light scattered is measured.
Homonuclear and heteronuclear diatomics are both Raman active; only heteronuclear diatomics are also IR active.
NH2 groups
Two adjacent absorption’s
Symmetric stretch @ 3300
Antisymmetric stretch @ 3400
Phenyl group
Two sharp peaks, 1500 and 1600
O-H alcohol
3300+
Broad when H bonding is present (varies the possible strengths of the bond)
O-H cabroxyluc acid
~3000
V shaped
CN nitrile
Strong 2250
CC triple bond
Weak 2100-2250
CC double bond
Weak 1635-1690
Benzene
Number of medium/weak peaks in range 1625-1450
NO2
Symmetric 1350
Antisymmetric 1530
Ketone CO
1715
Acid chloride CO
Cl withdraws electrons, strengthening bond.
~1750-1820
Amide CO
N donates electrons, weakening bond.
~1640-1690
Carboxylic acid CO
1730
Ester CO
1745
Aldehydes
Replacement of alkyl group by hydrogen means fewer electrons donated, so bond strengthened.
~1730
Acid anhydrides
Two stretches
Symmetric 1820
Antisymmetric 1750
How does conjugation affect the absorption frequency of a carbonyl bond?
Weakens the bond so lowers it by 20-30cm-1.
Conjugated if carbonyl separated from C=C by just one single bond.
How does ring strain affect the stretching frequency of a CO bond?
The smaller the ring, the higher the stretching frequency- smaller C-C-C bond angle requires greater compression of C-C bonds as CO stretches, needing more energy.
6 carbons 1715
5 carbons 1745
4 carbons 1780
3 carbons 1815
