Interpretation of Organic Spectra
Chem 4361/8361
Characteristics of Common Spectrometric Methods
MS
IR/RA MAN
UV-VIS
ORD/CD
X- RAY
RF
Not relevant
IR
UV to visible
UV to visible
X-ray
0-220 ppm
50-4000 amu
400-4000 cm-1
200-800 nm
185-600 nm
Not relevant
~50 mg
< 1 mg
< 1 mg
< 1 mg
< 1 mg
Single crystal
H-1
C-13
•Radiation type
RF
•Spectral scale
0-15 ppm
mg
•Average sample
~1
•Molecular formula
Partial
Partial
Yes
No
No
No
Yes
•Functional groups
Yes
Yes
Limited
Yes
Very limited
Very limited
Yes
•Substructures
Yes
Limited
Yes
Limited
Limited
No
Yes
•Carbon Connectivity
Yes
Yes
No
No
No
No
Yes
•Substituent
regiochemistry
Yes
Yes
No
Limited
No
No
Yes
•Substituent
stereochemistry
Yes
Yes
No
Limited
No
No
Yes
•Analysis of isomer
mixtures
Yes
Yes
Yes
(by GC/MS LC/MS)
Yes
No
No
(by GC/IR)
Yes
(if separate)
•Purity information
Yes
Yes
Yes
Yes
Limited
Limited
Limited
•What is measured
Peak areas
Chemical shifts
Coupling
relaxation
Chemical shifts
Coupling
relaxation
Singly or multiple
charged ions
Vibrational
transitions
Electronic
transitions
[α]
Relative atom
positions
R/S absolute
stereochemistry
cm -1
nm
nm
•Typical units
δ (ppm)
δ (ppm)
m/z
•Typical
representations
ORTEP
Steps in Establishing a Molecular Structure
Dereplicate by MF
Molecular
formula
Unsaturation
Number
(UN)
MS, NMR
NMR, IR
UV
Functional
groups
Working
2D
Structures
Draw all isomers
Pure
Compound
NMR
List of
working
2D Structures
Substructures
Dereplicate
by structure
NMR, MS, IR, UV
X-RAY
Very Secure
3D molecular
Structure
Total
Synthesis
Reasonable
3D molecular
structure
NMR
ORD
Molecular
Modeling
New 2D
molecular
Structure
Known
Molecular
Structure
Unsaturation Number (UN)
for
CCHHOOXXNN
Given the molecular formula of an unknown, can guess
the combined number of rings and multiple bonds
(called the “unsaturation number”).
UN = C - H/2 - X/2 + N/2 +1
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C6H12: 6-6+1=1
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C6H12: 6-6+1=1
Candidate structures for C6H12:
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C6H12: 6-6+1=1
Candidate structures for C6H12:
(1 ring)
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C6H12: 6-6+1=1
Candidate structures for C6H12:
(1 ring)
(1 double bond)
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Candidate structures for C4H6N2O2:
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Candidate structures for C4H6N2O2:
OH
H2N
N
O
(3 multiple bonds)
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Candidate structures for C4H6N2O2:
O
OH
H2N
NH
N
O
(3 multiple bonds)
N
H
O
(2 multiple bonds)
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Candidate structures for C4H6N2O2:
O
OH
H2N
N
NH
O
N
O
(3 multiple bonds)
O
N
N
H
O
(2 multiple bonds)
(1 multiple bond)
Unsaturation Number (UN)
UN = C - H/2 - X/2 + N/2 +1
For C4H6N2O2: 4-3+1+1=3
Candidate structures for C4H6N2O2:
O
OH
H2N
N
NH
O
N
O
(3 multiple bonds)
O
N
N
H
O
(2 multiple bonds)
(1 multiple bond)
N
N
O
O
(0 multiple bonds)
Unsaturation Number (UN)
Count the Rings in These Structures
Unsaturation Number (UN)
Count the Rings in These Structures
2
Unsaturation Number (UN)
Count the Rings in These Structures
2
3
Unsaturation Number (UN)
Count the Rings in These Structures
2
3
4
Unsaturation Number (UN)
Count the Rings in These Structures
2
3
4
5
Overview of Mass Spectrometry Process
Overview of Mass Spectrometry Process
• Introduction of Sample
Overview of Mass Spectrometry Process
• Introduction of Sample
•
Sample can be solid, liquid, or gas
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
Ions are formed from molecules by a variety of methods
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
•
Gas-phase Ions are separated by electric and/or magnetic fields
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
•
•
Gas-phase Ions are separated by electric and/or magnetic fields
Ions can be separated in space, time, or frequency
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
•
•
Gas-phase Ions are separated by electric and/or magnetic fields
Ions can be separated in space, time, or frequency
• Detection of Ions
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
•
•
Gas-phase Ions are separated by electric and/or magnetic fields
Ions can be separated in space, time, or frequency
• Detection of Ions
•
Ions can be detected by impact on an electron multiplier or multichannel plate
Overview of Mass Spectrometry Process
• Introduction of Sample
•
•
Sample can be solid, liquid, or gas
Sampling can occur at atmospheric pressure or in a vacuum
• Ionization of Sample
•
•
Ions are formed from molecules by a variety of methods
Sampling can occur at atmospheric pressure or in a vacuum
• Mass Selection of Ions
•
•
Gas-phase Ions are separated by electric and/or magnetic fields
Ions can be separated in space, time, or frequency
• Detection of Ions
•
•
Ions can be detected by impact on an electron multiplier or multichannel plate
Ions can also be detected as an image current (FTMS)
Sample Introduction
91 28 28
7744 73 77 44
105 7344
77 28
77
73 73
9173
Sample Introduction
+ 28+ 28+
+
+
91
+
44
44
+ 77 +73 77 +
+ 105 7344+
e- e- + 77 28+ ++ 77
e- e- + 73 73
+ 9173+
e
e- eee-
Ion Source
Sample Introduction
+ 28+ 28+
+
+
91
+
44
44
+ 77 +73 77 +
+ 105 7344+
+ 77 28+ + 77
+
73
+ 73
+ 9173+
Ion Source
Mass Analyzer
Detector
m/z
Abundance
28
44
73
77
91
105
3
3
5
4
2
1
Typical Presentation of MS Data
Peak Centroid Spectrum
5
Abundance
4
3
2
Peak List
m/z Abundance
28
3
44
3
73
5
77
4
91
2
105
1
1
0
0
21
42
m/z
63
84
105
Common Features of MS Data
Common Features of MS Data
• Isotope Patterns
Common Features of MS Data
• Isotope Patterns
•
Individual isotopomers are observed for each ionic species
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
Degree of fragmentation can be controlled by choice of ionization conditions
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
•
Multiple charge states can be observed, especially in electrospray ionization
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
•
•
Multiple charge states can be observed, especially in electrospray ionization
Often, software must be used to deconvolute charge states in mixtures
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
•
•
Multiple charge states can be observed, especially in electrospray ionization
Often, software must be used to deconvolute charge states in mixtures
• Mass Accuracy/Resolution
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
•
•
Multiple charge states can be observed, especially in electrospray ionization
Often, software must be used to deconvolute charge states in mixtures
• Mass Accuracy/Resolution
•
Depending on the mass analyzer used, resolution and accuracy vary widely
Common Features of MS Data
• Isotope Patterns
•
•
Individual isotopomers are observed for each ionic species
Isotope distribution can aid in the determination of molecular formula
• Fragmentation Patterns
•
•
Degree of fragmentation can be controlled by choice of ionization conditions
Fragmentation can be used to identify structural elements or as a fingerprint
• Charge States
•
•
Multiple charge states can be observed, especially in electrospray ionization
Often, software must be used to deconvolute charge states in mixtures
• Mass Accuracy/Resolution
•
•
Depending on the mass analyzer used, resolution and accuracy vary widely
High resolution and accuracy can uniquely identify a molecular formula
Isotope Pattern
C H O
5 12 2
104.08
104.15
100.00
% Relative Abundance
75.00
50.00
25.00
0
104.0
105.0
Mass (m/z)
106.0
107.0
Isotope Pattern
C H O Br
5 11 2 3
339.83
342.85
100.00
% Relative Abundance
75.00
50.00
25.00
0
339.0
341.0
343.0
Mass (m/z)
345.0
347.0
Fragmentation
+
• OMe
OH
Fragmentation
+
• OMe
OH
104
+
Fragmentation
+
• OMe
+
OMe
•
OH
45
•
59 +
Neutral Radical
is only
Inferred
OH
Fragmentation
+
• OMe
+
OMe
•
OH
OH
45
•
Neutral Radical
is only
Inferred
59
Only 59 is Detected
Charge State
C30H30O3N3+(H<+>)1
C30H30O3N3+(H<+>)2
241.12
481.24
241.30
100.00
75.00
% Relative Abundance
75.00
% Relative Abundance
481.59
100.00
50.00
50.00
25.00
25.00
0
0
241.0
242.0
Mass (m/z)
481.0
482.0
483.0
Mass (m/z)
484.0
C
H
O N +(H<+>)
300 300 30 30
10
481.24
Charge State
481.59
100.00
% Relative Abundance
75.00
Low Resolution
50.00
25.00
0
481.0
482.0
Mass (m/z)
C
O N +(H<+>)
300 300 30 30
10
481.24
H
481.59
100.00
% Relative Abundance
75.00
High Resolution
50.00
25.00
0
481.0
482.0
Mass (m/z)
Resolution
C16H22O4
C15H18O5
100.00
% Relative Abundance
75.00
50.00
25.00
0
278.0
279.0
280.0
Mass (m/z)
Resolution
278.1154
C15H18O5
278.1518
C H O
16 22 4
100.00
7500 Resolution
% Relative Abundance
75.00
50.00
25.00
0
Mass (m/z)