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Structure Determination
How to determine what compound that you have?
One way to determine compound is to get an elemental analysis
-basically burn the compound to determine %C, %H, %O, etc.
from these percentages can determine the molecular formula
Still need to determine structure from molecular formula
We have learned various isomers can result from a given molecular formula
Consider
C3H6O
O
O
H
Could have a
ketone
Different type
of carbonyl
OH
No carbonyl
present
If we only know the molecular formula, would not know which structure is present
Structure Determination
Even if a pure sample is obtained, how do we know the actual structure of the compound?
The development and improvement of analytical instruments to determine structure has been
one of the biggest advancements in organic chemistry during the past 60 years
Today almost any structure can be determined with these instruments
The important part is to recognize what information each instrument provides, and if deciding between possible isomers which technique can be used to differentiate
Techniques to be learned:
Mass Spectrometry
UV-vis Spectroscopy
-mass of compound
-conjugation present
-isotopes present
-distinguish some atoms
IR Spectroscopy
NMR Spectroscopy
-functional groups
-bond connectivity of
structure
-symmetry
-most important for
structure determination
Mass Spectrometry
Can determine the molecular weight of a sample and some information about the structure
A key part of a mass spectrometry is the need to create a charged species
The most common method to create the charged species is electron impact ionization
e
H
H
H
H
C
C
C
H
H
H
H
H
H
H
H
C
C
C
H
H
H
e
H
e
An electron is accelerated toward a gaseous sample of the compound under consideration
Due to the high energy of the electron moving at high speed, an electron is expelled
The sample thus is now positively charged, due to the loss of one electron, and is a radical/cation structure
Mass Spectrometry
The compound (R) thus becomes a radical/cation when bombarded with electrons
magnet
e
R(•+)
detector
R
The radical/cation continues along a path until it reaches a magnetic field
Charged species become deflected (are attracted to one magnet) in the presence of the
magnetic field and hence the path direction is bent
The radius of curvature is dependent upon the mass of the species (m/z),
lighter mass species are deflected more and heavier species are deflected less
Only a certain mass can thus deflect the correct amount with the curvature of the instrument,
heavier species will hit one wall while lighter species will hit the other wall
The magnet strength is changed and depending upon when species hit the detector the mass
of the compound can be determined
Mass Spectrometry
The parent ion is called the molecular ion peak (M+)
m/z 72
Can find molecular ion, but what are the other peaks?
Mass Spectrometry
The molecular ion peak can fragment
Due to the high energy of the radical/cation generated, this species can fragment
CH3CH2
m/z 72
m/z 43
CH3
m/z 57
Remember only the charged species will be detected
(the radical species will not be affected by the magnetic field)
The probability of obtaining a given fragment is due to the STABILITY of the cations produced
Effect of Isotopes
Remember that an isotope has the same number of protons and electrons, but a different number of neutrons
Since neutrons and protons are the “heavy” parts of an atom,
the extra number of neutrons will cause a greater mass
In a mass spectrometer we can see the effect of this by peaks above the molecular ion peak
(M, M+1, M+2, etc.)
The ratio of these peaks is diagnostic for which atoms are present
The natural abundance of isotopes is well known
M
M+1
M+2
H
100%
C
98.9%
1.1%
S
95%
0.8%
Cl
75.5%
24.5%
Br
50.5%
49.5%
I
100%
4.2%
Effect of Isotopes
Can distinguish atoms by the ratio of peaks above the molecular ion
Especially useful to distinguish which halogen is present
Cl
Br
I
m/z 78
M/M+2 = 3
m/z 122
M/M+2 = 1
m/z 170
~ 3/1
= 1
M/M+2
Mass Spectrometry
Nitrogen
Nitrogen is also diagnostic in a mass spectrum due to the odd/even parity of the mass
Consider small molecules and their corresponding mass
CH4
NH3
m/z = 16
m/z = 17
The molecular ion peak for a molecule with one nitrogen is always odd,
all other common atoms in an organic compound yield an even mass
Fragmentation Behavior of Common Functional Groups
Alkenes
With an alkene the common fragmentation is to create an allylic carbocation
m/z 70
m/z 55
Alcohols
Two common effects
1) Loss of water
H2 O
OH
m/z 74
m/z 56
Alcohols
2) α-cleavage OH
OH
OH
CH2CH3
m/z 74
m/z 45
McLafferty Rearrangement
Any ketone containing a γ-hydrogen can rearrange to the enol form in a MS
O
H
m/z 100
O
H
m/z 58
Ketones
Ketones can also do α-cleavage similar to alcohols
O
m/z 100
O
O
m/z 43
CH2CH2CH2CH3
High Resolution Mass Spectrometry (HRMS)
These high sensitivity mass spectrometers, called HRMS, can be used to determine molecular formula
a HRMS can detect particle masses with an accuracy of 1/20,000 therefore > 0.0001 amu (atomic mass units)
Can use this to distinguish compounds with a similar rough mass
but with a different molecular formula
12C
1H
16O 12.0000 amu (by definition)
1.0078 amu
15.9949 amu
Many structures may have the same integer value molecular weight, but different molecular formulas
For example:
O
HN
NH
C4H6O1
C5H10
C3H6N2
70.0418 amu
70.0783 amu
70.0531 amu
Structure Determination Using Spectroscopy
Need methods to distinguish between possible structures
A nondestructive way is to use absorption spectroscopy
In a simplified picture:
Beam
splitter
Monochromatic
light source
sample
detector
blank
The ability of the sample to absorb incident radiation is measured by the difference in
absorbance at the detector versus the blank
Electromagnetic Spectrum
All light travels at a constant speed
The difference is the wavelength of the light
(which also determines the energy of the light)
E = hν = (hc) / λ
NMR
IR
UV-vis
Infrared Region
Wavelength of infrared radiation is ~800 cm-1 to 4000 cm-1 wavenumbers
(wavenumbers correspond to number of wavelengths of light in 1 cm)
-common descriptor for IR frequencies by organic chemists
As the wavenumber becomes larger the energy increases
The energy level of infrared light corresponds to the energy required to cause molecular vibrations
Depending upon what type of bond is present determines the exact energy required to cause the vibration
The energy of light absorbed therefore indicates what functional group is present
Bond Vibration
The energy of the infrared light can interact with the resonant vibrational frequency of the bond
Since different bonds have different energies, they require different energy to cause vibration
consider acetone
O
O
H3C
CH3
The carbonyl has a strong dipole
H3C
CH3
E
When electric field aligns with
dipole, bond shortens
The absorption of the infrared light thus changes the dipole for this bond as it vibrates
Infrared Spectroscopy
Active versus Inactive
IR only causes a vibration if there is a change in dipole during vibration
Therefore symmetric bonds are inactive
CH3-CH3
the carbon-carbon bond of ethane will not observe an IR stretch
Or any other symmetric bond
An IR “active” bond is therefore a bond that changes dipole during vibration,
While an IR “inactive” bond is a symmetric bond that doesn’t change dipole during vibration
Number of Vibrations
The number of possible vibrations for a given molecule is determined by the number of atoms present
For nonlinear molecules obtain 3N-6 vibrations
(N equals number of atoms present)
3N-5 vibrations for linear molecule
For example consider acetone again (C3H6O1)
Acetone has 10 atoms and is nonlinear
Therefore expect 3(10)-6 = 24 vibrations
The other vibrations are due to different
bonds besides the carbonyl stretching,
for example the hydrogens
Or bending motions
Intensity of Absorbance
Intensity of light absorbed by a molecule is related to the dipole of the bond
The greater the dipole, the greater the absorbance intensity
C-O bond stretches are therefore more intense than C-C stretches
O
C O
Realize the intensity of absorbance is not related to the wavenumber
The wavenumber is related to the force constant for the bond vibrating
(the stiffness of the bond)
Infrared Spectroscopy
Factors to be considered in an IR spectrum
1)  Position of absorbance (wavenumber)
Energy required for absorbance
2)  Intensity of absorbance
Related to the dipole of the bond
3)  Shape of absorbance
(broad or sharp peaks)
Tells information about the type of bond
Infrared Spectroscopy
Specific functional groups
As mentioned specific functional groups have characteristic absorbance frequencies
Consider carbon-carbon bonds
Wavenumber (cm-1)
C C
~1200 cm-1
C C
~1660 cm-1
C C
~2200 cm-1
As the number of bonds increases between two atoms, the stiffness of the bond increases which results in a harder bond to stretch
Infrared Spectroscopy
Conjugation lowers the stretching frequency
(RESONANCE!!!)
Wavenumber (cm-1)
~1640-1680 cm-1
~1620-1640 cm-1
Whenever a functional group becomes more conjugated
(adjacent to double bonds for example) the stretching frequency lowers
Infrared Spectroscopy
C-H bond stretching
As the %s character increases in a bond, the bond becomes stiffer
(already saw that sp hybridized C-C bonds are stiffer than sp3 hybridized C-C bonds)
Same is true for carbon-hydrogen bonds
sp3 hybridized
sp2 hybridized
sp hybridized 2800-3000 cm-1
3000-3100 cm-1
~3300 cm-1
Key point: only sp3 hybridized C-H bond stretches are below 3000 cm-1
Infrared Spectroscopy
Alcohols and amines
Both O-H and N-H bonds are “stiff” bonds
Therefore they have a higher vibrational frequencies
Alcohol Acid
Amine RO-H RCO2-H RN-H ~3300 cm-1
~3000 cm-1
~3300 cm-1
In addition, both N-H and O-H bonds are involved in hydrogen bonding therefore each bond will experience a slightly different vibrational frequency
Therefore this causes the appearance of a broad peak
Infrared Spectroscopy
Amine peaks show the same broad features
(N-H bonds are also involved in hydrogen bonding)
Difference is that often observe a sharp peak in the midst of the broad peak
(due to one conformation of hydrogen bonding having a preferential formation)
Carbonyl Compounds
One of the best diagnostic features of IR is for carbonyl compounds
Remember there are many types of carbonyl groups
(each can be differentiated only with an IR spectrum)
O
R
R
Ketone
ν 1700-1730
(cm-1)
R
O
O
O
H
R
OH
R
O
NH2
R
O
OR
R
Cl
Aldehyde
Acid
Amide
Ester
Acid chloride
1700-1730
1700-1730
1620-1680
1735-1750
1770-1820
2700-2800
3000
Two peaks
Broad peak
In addition to the carbonyl stretch, other characteristic peaks can distinguish carbonyl groups
that display similar C=O stretching frequencies
Carbonyl Compounds
Due to the large dipole of carbonyl bonds, all carbonyl groups display strong, relatively sharp peaks
C=O
large dipole
C=C
small dipole
Most carbonyl stretching frequencies are centered around 1700-1730 cm-1 and can be
distinguished easily from alkene stretches (~low 1600’s cm-1) due to both the higher
frequency and the more intense absorbance
Carbonyl Compounds
Some carbonyl stretching frequencies are noticeably different than 1700-1730 cm-1
Esters are one type
Esters have an appreciably higher stretching frequency
O
O
ν (cm-1) = 1742
Higher frequency means a “stiffer” bond
Carbonyl Compounds
What causes a “stiffer” carbonyl bond?
Substituents on the carbonyl carbon can affect the C=O bond stretch in two ways: Inductive effect
Resonance effect
O
O
R
R
Y
O
Y
R
Y
More electronegative Y pulls electron density Lone pair of electrons on Y atom can resonate
from carbon, which then pulls electrons from to create a C=Y double bond and thus a C-O
oxygen to create a stiffer bond
single bond – therefore a weaker C-O bond
The question is which effect is larger
Generally the greater difference in electronegativity between C and Y causes inductive effect to become dominant
Y
ν (cm-1)
Stronger effect
Cl
1810
inductive
OR
1735
inductive
NH2
1660
resonance
Carbonyl Compounds
Amide group lowers the frequency due to the resonance effect
If a nitrogen is attached to the carbonyl carbon then the lone pair of electrons on nitrogen can stabilize the resonance form
O
O
NH2
NH2
Due to this lower energy resonance form the carbonyl carbon-oxygen bond is less “stiff”,
therefore the stretching frequency is LOWER
Carbonyl Compounds
Resonance with extra conjugation will also lower the stretching frequency for a carbonyl
O
H
ν = 1721 cm-1
O
H
ν = 1699 cm-1
Resonance allows delocalization of π electrons,
therefore carbonyl is less “stiff”
O
O
H
H
Carbonyl Compounds
As already observed many carbonyl groups are ~1700-1730 cm-1
How to distinguish?
O
R
O
O
R
Ketone
~1715 cm-1 for carbonyl
R
H
R
OH
Aldehyde
Acid
observe aldehyde C-H stretch
observe broad O-H stretch
Two peaks between 2700-2900 cm-1
~3000 cm-1
Small Rings
Small rings also have a shift in vibrational frequency to higher energy,
Therefore 5,4, or 3-membered rings have the carbonyl stretching frequency shifted
O
1715 cm-1
O
1745 cm-1
O
1785 cm-1
Angle strain in these rings causes the carbonyl group to have more electron density,
Therefore a “stiffer” bond
Infrared Spectroscopy
C-N bonds
C-N bonds are in similar regions to C-C bonds
Wavenumber (cm-1)
C N
~1200 cm-1
C N
~1600 cm-1
C N
>2200 cm-1
The intensity of absorbance, however is higher
due to greater dipole of C-N bond compared to C-C
Fingerprint Region
The so-called “fingerprint” region is below ~1500 cm-1
Vibrations in this region are often complex and hard to assign to a specific functional group of the molecule
-a given molecule, though, has a DISTINCT pattern in this region
(reason for this region being called the “fingerprint” region)
One common pattern – differentiating substitution isomers
Ortho
Meta
Para
CH3
One example:
Aromatic isomers
one peak 770-735 cm-1
three peaks 900-860, 810-750, 725-680 cm-1
one peak 860-800 cm-1 CH3
CH3
Cl
Cl
Cl
Fingerprint Region
CH3
Cl
Strong peak 747 cm-1
CH3
Strong peaks 863, 773, 682 cm-1
Cl
CH3
Strong peak 806 cm-1
Cl
Overtone and Combination Bands
Overtone
-when assigning IR spectra be careful to note overtone bands
(an intense peak will display a smaller peak at a multiple [2x, 3x, etc.] of that peak)
Combination Bands
Two or more vibrations can couple to cause a vibration at a different position
(vibrations must be “coupled” to observe these combination bands)
2nd Overtone
~3430 cm-1
Strong carbonyl stretch
~1715 cm-1
Ultraviolet-Visible Spectroscopy
(UV-vis)
Another analytical tool to determine organic structures is UV-vis spectroscopy
Similar to IR, this is another spectroscopic technique, therefore a sample is irradiated with light of a particular wavelength
If the compound absorbs the light, the detector will record the intensity of absorbance
In an UV-vis spectrum the light used is between ~200 nm to ~700 nm
(UV range is ~200 nm to ~370 nm, while visible light is ~370 nm to 700 nm)
Remember that in IR the wavelength of light used was 2.5 – 25 µm
(between one to two orders of magnitude larger than UV light)
Ultraviolet-Visible Spectroscopy
UV light is thus much higher in energy than IR light
Instead of causing molecular vibrations, UV-vis light causes electronic excitations
An electron is excited from the HOMO to the LUMO
Ethylene LUMO
E
h!
Required energy
Ethylene HOMO
If the correct amount of energy is applied (i.e. the correct wavelength of light),
the excitation of one electron from the HOMO to the LUMO will occur
Ultraviolet-Visible Spectroscopy
The amount of energy required is thus the energy gap between the HOMO and LUMO
As the HOMO-LUMO gap changes, the wavelength required for excitation changes
(remember that a lower wavelength is higher in energy)
The HOMO-LUMO energy gap is affected by the amount of conjugation
A conjugated diene system has a lower HOMO-LUMO energy gap than an isolated double bond
Therefore a more conjugated system has a higher wavelength of absorbance
(higher wavelength is lower in energy, therefore smaller energy gap)
Ultraviolet-Visible Spectroscopy
Information Obtained from a UV-vis
The major piece of information is the point of maximum absorbance
(called λmax)
In addition an absorbance is characterized by how strongly the molecule absorbs
Beer’s law:
A = ε•c•l
c = concentration of sample
l = path length of sample
ε = molar absorbtivity (extinction coefficient)
*characteristic of sample
If the molecule absorbs more strongly, it has a higher ε
Ultraviolet-Visible Spectroscopy
As seen earlier, the position of the λmax indicates the HOMO-LUMO energy gap
A more conjugated system has a lower HOMO-LUMO energy gap, therefore the λmax will be of a longer wavelength
λmax
171 nm
180 nm
227 nm
Only conjugated alkenes will cause a shift in λmax
Alkyl substitution causes a shift of ~5 nm, but conjugation causes shift of ~30 nm
As the conjugation increases, the shift will increase
Compounds that are colored to our eye therefore must be very conjugated
(the lowest wavelength human eyes detect is ~370 nm)
Ultraviolet-Visible Spectroscopy
Organic colored compounds:
β-carotene (λmax = 453 and 483 nm)
CO2
Br
Br
O
O
Br
O
Br
Eosin Y (λmax = 517 nm)