Interpretation of Organic Spectra Chem 4361/8361
Characteristics of Common Spectrometric Methods H-1 C-13 MS IR/RAMAN UV-VIS ORD/CD X- RAY Radiation type RF RF Not relevant IR UV to visible UV to visible X-ray Spectral scale 0-15 ppm 0-220 ppm 50-4000 amu 400-4000 cm-1 200-800 nm 185-600 nm Not relevant Average sample ~ 1 mg ~50 mg < 1mg < 1 mg < 1 mg < 1 mg Single crystal 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 (by GC/IR) No No Yes (if separate) Purity information Yes Yes Yes Yes Limited Limited Limited What is measured Typical units Peak areas Chemical shifts Coupling relaxation δ (ppm) Chemical shifts Coupling relaxation δ (ppm) Singly or multiple charged ions m/z Vibrational transitions cm -1 Electronic transitions nm [α] nm Relative atom positions R/S absolute stereochemistry Typical representations ORTEP
Steps in Establishing a Molecular Structure Molecular formula Dereplicate by MF MS, NMR NMR, IR UV Functional groups Unsaturation Number (UN) Working 2D Structures Draw all isomers Pure Compound NMR Substructures List of working 2D Structures 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 C 6 H 12 :
Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C6H12: 6-6+1=1 Candidate structures for C 6 H 12 : (1 ring)
Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C6H12: 6-6+1=1 Candidate structures for C 6 H 12 : (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: H 2 N OH O N (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: H 2 N OH N O (3 multiple bonds) O NH N O H (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: H 2 N OH N O (3 multiple bonds) O NH N O H (2 multiple bonds) N O O N (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: H 2 N OH N O (3 multiple bonds) O NH N O H (2 multiple bonds) N O O N (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 77 44 73 77 44 105 7344 7728 77 73 73 9173
Sample Introduction + + + + 91 28 28 + + 77 44 + + 73 77 44 105 73 + + 44+ e- e- + 7728 + + 77 + 73 73+ e- e- + 9173+ e- e - e- e - e- Ion Source
Sample Introduction + + + + 91 28 28 + + 77 44 + + 73 77 44 105 73 + + 44+ + 7728 + + 77 + 73 73+ + 9173+ Ion Source Mass Analyzer Detector m/z Abundance 28 3 44 73 77 91 105 3 5 4 2 1
Typical Presentation of MS Data Peak List m/z Abundance 28 3 44 3 5 Peak Centroid Spectrum 73 5 4 77 4 Abundance 3 2 91 105 2 1 1 0 0 21 42 63 84 105 m/z
Common Features of MS Data
Isotope Patterns Common Features of MS Data
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 5 H 12 O 2 100.00 104.08 104.15 75.00 % Relative Abundance 50.00 25.00 0 104.0 105.0 106.0 107.0 Mass (m/z)
Isotope Pattern C 5 H 11 O 2 Br 3 100.00 339.83 342.85 75.00 % Relative Abundance 50.00 25.00 0 339.0 341.0 343.0 345.0 347.0 Mass (m/z)
Fragmentation + OMe OH
Fragmentation + OMe OH 104 +
Fragmentation + OMe OMe + OH OH 45 59 + Neutral Radical is only Inferred
Fragmentation + OMe OMe + OH OH 45 Neutral Radical is only Inferred 59 Only 59 is Detected
Charge State 100.00 241.12 C 30 H 30 O 3 N 3 +(H <+> ) 2 C 30 H 30 O 3 N 3 +(H <+> ) 1 241.30 100.00 481.24 481.59 75.00 75.00 % Relative Abundance 50.00 % Relative Abundance 50.00 25.00 25.00 0 241.0 242.0 Mass (m/z) 0 481.0 482.0 483.0 484.0 Mass (m/z)
100.00 C 300 H 300 O 30 N 30 +(H <+> ) 10 481.24 481.59 Charge State 75.00 % Relative Abundance 50.00 25.00 Low Resolution 0 481.0 482.0 Mass (m/z) C 300 H 300 O 30 N 30 +(H <+> ) 10 100.00 481.24 481.59 75.00 % Relative Abundance 50.00 25.00 High Resolution 0 481.0 482.0 Mass (m/z)
Resolution C 16 H 22 O 4 C 15 H 18 O 5 100.00 75.00 % Relative Abundance 50.00 25.00 0 278.0 279.0 280.0 Mass (m/z)
Resolution 278.1154 C 15 H 18 O 5 278.1518 C H O 16 22 4 100.00 7500 Resolution 75.00 % Relative Abundance 50.00 25.00 0 Mass (m/z)