Shapes + Structures of Molecules I Flashcards
Michaelmas
acetyl fragment
CH3C(=O)-
toluene
benzene w methyl branch
chloroform
CHCl3
X ray crystallography is used to / shows
determine structure of crystals
bond lengths and angles
positions of atoms
packing of molecules
outline how x-ray crystallography works
beam of X-ray focused on crystal diffracts due to interactions with electrons
diffraction pattern analysed through electron density maps
why do H not show up on electron density maps?
H have very little e- density, do not significantly diffract x-rays in crystallography
disadvantages of x ray crystallography
good quality crystals needed
may be difficult to locate H’s
in solutions, crystals often have different structure
mass spectrometry is used to
find the weight of a molecule
mass spec method
sample vaporised, ionised
ions focused onto detector using mag/elec fields
two methods of ionising the sample for mass spec
- knock e- off by firing high energy e- at vapour
- electrospray: charged aerosol, ion attaches to molecule
IR spectroscopy is used to ___ by measuring _____
identify functional groups present in molecules
by measuring changes in molecular vibrational energy levels
molecules always possess what three types of energy?
translational, vibrational, rotational
all are quantised
transitions in what type of energy correspond with infrared radiation?
vibrational transitions
relationship between wavenumber and energy for transition
proportional as E=hv
higher wavenumber, more energy needed
frequency of a vibration depends on:
- mass 2. stiffness
faster freq = stiffer spring, lighter mass
reduced mass
in a diatomic, both atoms vibrate
µ = m1m2 / m1+m2
for m1»m2, µ=m2 (esp for H)
fingerprint region
500-1500 (RHS)
double bonds region
1500-2000
triple bonds region
2000-2500
X-H single bonds region
2500+
there is only absorption of IR if…
there is a significant change in dipole moment, ie asymmetric stretch
which is why N2 in air doesn’t give rise to peaks, symmetric
define Raman spectroscopy
for homonuclear diatomics (symmetric, doesn’t absorb IR)
looks at frequency of light scattered by a sample
(heteronuclear diatomics are also Raman active)
N-H absorption
about 3300 cm-1
-NH2 group absorption feature, explain
usually two peaks (3300, 3400 ish)
due to the sym / asymm N-H stretches respectively
why is the O-H stretch often broad?
H bonding between molecules possible, results in many slightly different strengths of O-H bonds
C triple bond N and C peaks
C-N > C-C due to greater dipole
C-N 2250
C-C 2100-2250
C=C peak
1635-1690, weak
C=C peaks for benzene ring
multiple peaks between 1625-1450
medium-weak
-NO2 group IR spec
TWO peaks (sym/asym)
1350 (fingerprint), 1530
C=O peak
in KETONE, 1715
strengthen C=O bond –> higher
weaken –> lower
(“stiffer” spring = higher freq)
what causes strengthening / weakening of the C=O bond
EWG (eg. Cl) strengthen
EDG (eg. NH2) weaken
(dipole)
acyl chloride IR
1750-1830 cm-1
EWG strengthens C=O, higher than 1715
amide IR
1640-1690 cm-1
EDG weakens C=O, lower than 1715
carboxylic acid IR
1730 cm-1
weakly EWG
ester IR
1745 cm-1
weakly EWG
aldehyde IR
1730 cm-1
bc ketone (1715) alkyl groups weakly EDG compared to H of ald
acid anhydride IR
TWO stretches (Sym/asym)
BUT sym 1820 > asym 1750
(vs asym>tym for NH2 / NO2)
how does conjugation affect the frequency of the C=O bond?
LOWERS base freq by 20-30 cm-1
as e- density spread over system
how does ring size affect freq of C=O
smaller ring, higher freq
35 cm-1 step
what does NMR measure?
transitions between energy levels of nuclear spin
how does NMR work?
radio waves of appropriate frequency cause transitions in energy levels of nuclei in a strong magnetic field
what is nuclear spin quantum number and how does it relate to energy levels?
I = 0, 1/2, 1, 3/2, …
nucleus spin I gives rise to 2I+1 different energy levels when placed in mag field, given by -ve to +ve m(I) in integer steps
eg. I=1, m(I)= -1,0,1
I=3/2, m(I)= -3/2, -1/2, 1/2, 3/2
rules for I based on nuclei mass number
odd mass # = 1/2-integral spin
odd #prot and neutron = integral
even #prot and neutron = 0
energy difference between spin states depends on
strength of mag field, both supplied and local (e-dens, other nuclei)
the nucleus itself
how does electron density impact the strength of the local magnetic field`
electrons move to oppose the mag field
more e- = more shielding, lower freq
e-neg atoms DESHIELD other atoms by withdrawing e-dens, higher freq
chemical shift scale NMR
ppm, relative to a reference compound
shift = diff in freq / ref freq
standard reference compound used for NMR
TMS, tetramethylsilane
inert, one signal, away from other peaks (to the right)
C NMR shift for sp3 C’s
0-100 ppm
more e-withdrawing (e-neg) groups attached –> higher freq
C NMR shift for sp2 C’s
100-200 ppm
more EWG, higher shift
C NMR shift for sp C triple bond C
70-80 ppm
what groups have shift around 200ppm?
ketones - just over
aldehydes - just under
what groups have shift around 160-170ppm?
carboxylic acids, esters, acyl chlorides, amides, acid anhydrides
note - LOWER shift than ald/ket despite more EWG attached! unexpected
how can quaternary C’s be identified in C NMR?
much smaller line
how does coupling between atoms work?
if neighbouring atom also has spin states, a through bond interaction
up reinforces mag field experienced by the C nuclei –> slightly higher freq
down reduces –> slightly lower
=> doublet
why is C-C coupling not seen in C NMR?
low abundance of spin active C-13
tiny chance of C-13 - C-13 coupling lost in the noise
could see if artificially enriched
when are splittings due to couplings of spin active nuclei NOT seen?
when the nuclei are EQUIVALENT (often symmetric)
they still interact but the effects are not seen in splitting
how is a triplet splitting formed?
C couples to two other identical nuclei with spins
general rule splitting for coupling to multiple nuclei
coupling to n equivalent nuclei with spin I
splits into 2nI+1 lines
for I=1/2, pascals triangle
define equivalent nuclei (for coupling)
not only the same atom but also interchangeable positions!
axial and equatorial are DIFFERENT for T-shape molecules
how is C NMR decoupled from protons?
by broadband proton decoupling - irradiating over a range of frequencies so all protons rapidly interconvert spin states, couplings to C average 0
what is the APT?
Attached Proton Test
run on NMR spectrometer
C with even# and odd# protons attached point up/down
determine by solvent peak (CDCl3=0, even)
what are satellites in NMR?
some isotopes with spin that have low natural abundance
this portion couples –> doublet (satellites), the rest appears as a singlet
looks like a triplet (if the proportion is high enough) but really is a singlet w satellites
define vicinal coupling
the main difference between C NMR coupling and H NMR
Coupling between protons easily seen separated by three bonds (vicinal) or more
H NMR shift scale
approx 0-14ppm (NOT the same scale as the CNMR ofc!)
vicinal coupling constant rough value
about 7 Hz
vicinal coupling constant value across C=C
cis about 8Hz
trans about 15Hz
shift on protons on three-membered rings
unusually low, close to 0ppm
proton shift for H on C attached to double bonded C (C=C, C=O, Ar ring)
around 2.5
shift of H on C attached to N
around 2.5
shift on C attached to amide (N side)
3.5 ish
C=O increases shift of H on C attached to N by 1
shift of H on C attached to O
around 3.5
shift of H on C attached to ester (O side)
around 4.5
C=O increases shift of H on C attached to O by 1
shift of H on C attached to Cl
3.7-4ish
H on C=C
4.5-6 ppm
shift of H on benzene ring
6-9ppm
shift of terminal H on aldehyde
9.5-10.5 ppm
shift of H on formate ester
8 ppm (a bit counterintuitive that this shift is lower than terminal H on aldehyde given there’s another O)
feature of proton shifts of H attached to non-C atoms
they tend to be a lot broader than other signals but exact position is difficult to guess
D2O shake
identifying N-H and O-H protons by shaking NMR sample prepared in CDCl3 with D2O, which exchange these H for D
signals of exchangeable protons disappear
define relaxation in spin states
rapid interconversion of spin states, most rapid in nuclei with spins greater than 1/2
also the reason why coupling to spins greater than 1/2 is not observed (eg. Cl, I=3/2)
Deuterium spin states
I=1
hence three spin states
solvent CDCl3 split into triplet
