Interpretation of Organic Spectra. Chem 4361/8361

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1 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

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

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

2 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 ppm amu cm nm 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

3 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

4 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

5 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C6H12: 6-6+1=1

6 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 :

7 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)

8 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)

9 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =3

10 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =3 Candidate structures for C4H6N2O2:

11 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =3 Candidate structures for C4H6N2O2: H 2 N OH O N (3 multiple bonds)

12 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =3 Candidate structures for C4H6N2O2: H 2 N OH N O (3 multiple bonds) O NH N O H (2 multiple bonds)

13 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =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)

14 Unsaturation Number (UN) UN = C - H/2 - X/2 + N/2 +1 For C4H6N2O2: =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)

15 Unsaturation Number (UN) Count the Rings in These Structures

16 Unsaturation Number (UN) Count the Rings in These Structures 2

17 Unsaturation Number (UN) Count the Rings in These Structures 2 3

18 Unsaturation Number (UN) Count the Rings in These Structures 2 3 4

19 Unsaturation Number (UN) Count the Rings in These Structures

20 Overview of Mass Spectrometry Process

21 Overview of Mass Spectrometry Process Introduction of Sample

22 Overview of Mass Spectrometry Process Introduction of Sample Sample can be solid, liquid, or gas

23 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

24 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

25 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

26 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

27 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

28 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

29 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

30 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

31 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

32 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)

34 Sample Introduction

35 Sample Introduction e- e e- e e- e - e- e - e- Ion Source

36 Sample Introduction Ion Source Mass Analyzer Detector m/z Abundance

38 Typical Presentation of MS Data Peak List m/z Abundance Peak Centroid Spectrum Abundance m/z

39 Common Features of MS Data

40 Isotope Patterns Common Features of MS Data

41 Common Features of MS Data Isotope Patterns Individual isotopomers are observed for each ionic species

42 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

43 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

44 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

45 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

46 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

47 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

48 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

49 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

50 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

51 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

52 Isotope Pattern C 5 H 12 O % Relative Abundance Mass (m/z)

53 Isotope Pattern C 5 H 11 O 2 Br % Relative Abundance Mass (m/z)

54 Fragmentation + OMe OH

55 Fragmentation + OMe OH 104 +

56 Fragmentation + OMe OMe + OH OH Neutral Radical is only Inferred

57 Fragmentation + OMe OMe + OH OH 45 Neutral Radical is only Inferred 59 Only 59 is Detected

58 Charge State C 30 H 30 O 3 N 3 +(H <+> ) 2 C 30 H 30 O 3 N 3 +(H <+> ) % Relative Abundance % Relative Abundance Mass (m/z) Mass (m/z)

59 C 300 H 300 O 30 N 30 +(H <+> ) Charge State % Relative Abundance Low Resolution Mass (m/z) C 300 H 300 O 30 N 30 +(H <+> ) % Relative Abundance High Resolution Mass (m/z)

60 Resolution C 16 H 22 O 4 C 15 H 18 O % Relative Abundance Mass (m/z)

61 Resolution C 15 H 18 O C H O Resolution % Relative Abundance Mass (m/z)

CHEM 241 UNIT 5: PART A DETERMINATION OF ORGANIC STRUCTURES BY SPECTROSCOPIC METHODS [MASS SPECTROMETRY]

CHEM 241 UNIT 5: PART A DETERMINATION OF ORGANIC STRUCTURES BY SPECTROSCOPIC METHODS [MASS SPECTROMETRY] 1 Introduction Outline Mass spectrometry (MS) 2 INTRODUCTION The analysis of the outcome of a reaction