ORGANIC STRUCTURE ANALYSIS INTRODUCTION

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ORGANIC STRUCTURE ANALYSISINTRODUCTION

• Prof Phil Crews, Dr Jaime Rodriguez and Dr Marcel
  Jaspars

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STRUCTURAL DRAWINGS

• 2D FRAMEWORK
• CARBON SKELETON
• FUNCTIONAL GPS
• LOCATION OF FGs

OK
But what about
3D FRAMEWORK 1 RELATIVE STEREO 2 ABSOLUTE
STEREO 3 CONFORMATIONAL FEATURES
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VERIFYING OR CREATING STRUCTURAL DRAWINGS
1. A COMMON TASK 2. MANY ELEMENTS 3. STEREO
STRUCTURES 4. CONCISE APPROACHES
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4. CONCISE APPROACHES
DESIRED OUTCOMES MOLECULAR FORMULA
FUNCTIONAL GROUPS CH, CC, CZ, OR RINGS
FUNCTIONAL GROUP POSITIONS REGIOCHEMISTRY
STEREOCHEMISTRY
FOUR TECHNIQUES NMR MS IR UV-VIS

• OBTAIN DATA
• INTERPRET
• SPECTRA

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REQUIREMENTS FOR A CONCISE APPROACH
STEP-BY-STEP ANALYSIS UNDERSTANDING OF BASIC
ORGANIC CHEM KNOW COMMON FUNCTIONAL GROUPS
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REQUIREMENTS FOR A CONCISE APPROACH
STEP-BY-STEP ANALYSIS KNOW STABLE VS. UNSTABLE
STRUCTURES DEALING WITH ALTERNATIVES
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3 TYPES OF PROBLEMS

• COMMERCIAL SAMPLES
• - VERIFYING THE LABEL
• SYNTHETIC REACTION PRODUCT
• - VERIFYING THE COURSE OF A REACTION
• UNKNOWN NATURAL PRODUCT
• - ESTABLISHING A NEW CHEMOTYPE
• MOST DIFFICULT TYPE OF APPLICATION
• O.S.A. PRINCIPLES BIOGENETIC, TAXONOMIC
  ASSUMPTIONS

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SOME MARINE NATURAL PRODUCTS.
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WHAT ABOUT PALYTOXIN?
MW 2677 MF C129H223N3054 1ST ISOLN.
1960s 1ST STRUCTURE 1980s
P 2
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PALYTOXIN
MW 2677 MF C129H223N3054 UN 20 1ST ISOLN.
1960s 1ST STRUCTURE 1980s LD50 0.025 ?g/kg
Rabbit LD50 0.45 ?g/kg Mouse WHAT STRUCTURAL
INFO FROM NMR?
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A solvable problem
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RELATIVE MERITS OF TECHNIQUES
DATA MS 29 PEAKS IR 12 PEAKS 1H NMR 1
PEAK 13C NMR 1 PEAK UV/VIS O PEAKS
More is less??
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USES OF MOLECULAR FORMULAOR PARTIAL FORMULA
UNSATURATION NUMBER (UN) OR DOUBLE BOND
EQUIVALENTS (DBE)
CnH2n2 ADD H FOR EACH X ADD CH FOR EACH N
OR P
EXAMPLES UN 1 C6H12O EVEN H COUNT C6H11Cl
ODD H COUNT C6H13N ODD H COUNT C6H14N2
EVEN H COUNT
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USES OF MOLECULAR FORMULAOR PARTIAL FORMULA
UNSATURATION NUMBER FUNCTIONAL GROUP CATEGORIES
SELECTED EXAMPLES UN 0 C-C NOT A
FUNCTIONAL GROUP UN 1 RING, ALKENE, CARBONYL,
IMINE, NITRO UN 2 TWO RINGS, POLYENE, CUMULENE,
ALKYNE NITRILE, ISONITRILE, ANHYDRIDE UN
3 NON-BENZENOID AROMATICS UN 4 ARENE, PYRIDINE
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Unsaturation number/Double bond equivalents
CaHbOcNdXe
(2a2) (b-de)
UN
2
(42)-3-1
C2H3O2Cl
1
2
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Unsaturation number/Double bond equivalents

• This is the sum of the number of multiple bonds
  of all kinds kinds (CC, C?C, CO, CN, C?N, NO,
  etc) and rings in a molecule, and is extremely
  useful in structure determination.
• A double bond has a dbe 1, a triple bond has a
  dbe 2, and a benzene ring has a dbe 4 (three
  double bonds plus one ring)
• Halogens count as hydrogen for this purpose.
• The number of oxygen atoms is immaterial.
• If you can identify securely by spectroscopic or
  other means the number of multiply bonded
  functional groups, e.g. carbonyl, present, the
  remainder will be rings. It is therefore possible
  to decide if the compound is acyclic, monocyclic,
  bicyclic, etc. and this is extremely helpful in
  imagining a structure.
• Once you have obtained the molecular formula, the
  first step in a structure determination is to
  work out the dbe.

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NOW THE QUESTION
HOW MANY STRUCTURES FIT C2H3O2Cl ?
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C2H3O2Cl
ACYCLIC
H
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C2H3O2Cl
CYCLIC
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C2H3O2Cl
SUMMARY
H
Cl
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When things go wrong.......
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Limitations in Organic Structure Analysis Horror
Stories
Even seasoned investigators sometimes experience
difficulties in analyzing the structures of
organic compounds..
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BUT
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Limitations in Organic Structure Analysis More
Horror Stories
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SUBSTRUCTURES A same Z E not same
D, C, B order different JMC
A-D-C-B-Z-E JACS A-B-C-D-Z-E
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3.2.0 3.1.1
Limitations in Organic Structure Analysis More
Horror Stories
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Limitations in Organic Structure Analysis Final
Horror Story
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Chemical shift addivity

• Predicting carbon chemical shifts

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ALIPHATICS CARBON SHIFTS GENERAL (SP3)
?10 100 UNFUNCTIONALIZED
?10 - 50
21.9
31.7
29.7
11.4
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ALIPHATICS CARBON SHIFTS GENERAL (SP3)
?10 100 UNFUNCTIONALIZED
?10 - 50
21.9

• SHIFTS ARE ADDITIVE

31.7
29.7
11.4
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ADDITIVE PATTERNS
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UNDERSTANDING THE TABLE
?
?
4
2
1
3
?
?
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1. 20
2. 10
3. -2 to -3
4. ? 0

3?
also
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SHOW 13C PREDICT!
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FUNCTIONAL GROUP ID
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PROBLEM SOLVING
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PROBLEM SOLVING
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COUPLING
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Coupling/Splitting

• Two nuclei placed close together in the same
  molecule will interact and the NMR lines will be
  split into several components.
• The splitting is also referred to as coupling and
  the resultant splitting or coupling patterns are
  also called multiplets.
• The distance between the members of each
  multiplet in Hz is the coupling constant J, and
  can be calculated from the spectrum J (Hz) Dd
  (ppm) x spectrometer frequency in MHz
• The proton proton interaction is transmitted
  through the intervening (s) electrons making up
  the chemical bonds, so the magnitude of J is an
  indication of the number and type of bonds.

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Coupling/Splitting
No coupling
Jab
Jab
Coupling
da
db
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FACTORS CONTROLLING Js

1. OF INTERVENING BONDS (1,2,3,4, etc)
2. e- DENSITY
3. ANGLE H-C-C H-C-C-H H-C-C-C H-C-C-C-H
4. BOND HYBRIDIZATION
5. ELECTRONEGATIVTY OF ATOMS ALONG PATH

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A FOCUS ON FIRST ORDER
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COMPLEX 1ST ORDER
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A FOCUS ON COMPLEX FIRST ORDER
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TERMS

1. BIG ?? A/X
2. 1ST ORDER AMX
3. NON 1ST ORDER AB
4. SPECIAL A/A
5. COUPLING 1JCH
6. VALUES IN Hz
7. 2-5 NUCLEI 21 CASES

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NON 1ST ORDER SPIN SYSTEMS

1. AB 2
2. ABC 3
3. A2B 4
4. ABCX 8
5. A2B2 9
6. AAXX 10

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P 130
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Given the 1H NMR chemical shifts and coupling
constants for allyl alcohol, explain the observed
spectrum (OH peak omitted)
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MASS SPECTROMETRY
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Mass Spectrometry

• MS is an analytical method in which molecules are
  ionised, and the ions are separated according to
  their mass. The technique is used to determine
  molecular weights and hence molecular formulas.
• MS involves chemical reactions and is therefore
  not a true spectroscopic method. However, it does
  complement information provided by

Technique What is measured EM radiation? Amount needed
NMR nuclear spin transitions yes 1-10 mg
IR bond vibrations yes lt1 mg
UV electronic transitions yes lt1 mg
MS mass to charge ratio no lt1 mg
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Processes in MS

• MS involves three distinct processes
• Volatilisation of the sample
• Ionisation of the molecules
• Separation and detection of the ions according to
  m/z ratio

Mass separation
Ionisation
Sample inlet
Source
Mass analyser
Detector
Data System
Vacuum System
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Ionisation

• Both positive and negative ions can be formed by
  MS techniques, but positive ions are most
  commonly used. The ions usually have one positive
  charge.
• There are several methods of ionisation, but the
  most common these days are electrospray (ESI,
  small/large molecules) and matrix-assisted laser
  desorption (MALDI, large molecules)

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Electron Impact (EI)

• When molecules in the gas phase are bombarded by
  a stream of electrons, an electron can be ejected
  to give the molecular ion (M.). This technique
  is the oldest method of forming cations.
• The lower energy species (M.) is much more
  favoured.
• Electrons have energies 10-70 eV (960 - 6720
  kJ/mol), so the molecular ions formed are highly
  activated, leading to fragmentation.
• M. ? Fragments (at gt 10 eV)

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Electrospray (ESI)

• This is the most popular technique for ionising
  samples soluble in polar solvents (H2O, MeOH and
  EtOH). It is therefore very important for the
  analysis of biomolecules of high molecular
  weight. A derivative of this technique,
  atmospheric pressure chemical ionisation (APCI)
  can be used to ionise samples soluble in organic
  solvents (CH2Cl2, hexanes etc).
• The main problems arise from the existence of
  multiply charged ions (which is an advantage for
  large molecules!), and the presence of other
  quasi-molecular ions
• M MeOH H, M Na, M K

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Electrospray (ESI)

• The dissolved sample is pumped through a steel
  capillary at a rate of 1-20 mL/min which is at 3
  kV. The electric field at the tip of the
  capillary charges the surface of the emerging
  droplets. The solvent is evaporated using N2,
  reducing the size of the droplet, until the
  charges come into close proximity, and a
  Coulombic explosion occurs giving rise to a
  quasi-molecular ion of the form M Hn where n
  can be gt1.

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Electrospray (ESI)
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Matrix Assisted Laser Desorption (MALDI)

• Enables gentle ionisation of very large molecules
  with a single charge
• Compound dissolved in matrix and deposited in
  target
• Irradiated by laser beam energy absorbed by
  matrix and transferred to analyte which is
  desorbed.

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Mass Analysis

• There are many types of mass analyser
• Magnetic sector/electric sector
• Quadrupole
• Ion Trap
• Time-of-flight
• Fourier Transform Ion Cyclotron Resonance (FT-MS)
• Orbitrap

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Magnetic Sector
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Magnetic Sector

• The ions formed are accelerated by a voltage V,
  and if they have mass m, velocity v and charge z
  (z is the number of electronic charges).
• Kinetic energy potential energy
• ½mv2 zV
• When a charged particle travels through a
  magnetic field B, it will travel in a circle with
  radius r. The equation relating these parameters
  is
• Combining these two equations gives
• This allows us to calculate the mass to charge
  ratio (m/z) of any ion M.. Since the charge z is
  usually 1, it is effectively the molecular mass
  we are measuring. This is extremely useful when
  trying to determine the molecular formula of a
  molecule.

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Monoisotopic masses
Isotope Mass Abundance
1H 1.008 99.99
12C 12.000 98.89
13C 13.003 1.11
14N 14.003 99.64
15N 15.000 0.36
16O 15.995 99.76
18O 17.999 0.20
32S 31.972 95.03
33S 32.971 0.76
34S 33.968 4.20
35Cl 34.969 75.77
37Cl 36.966 24.23
79Br 78.918 50.52
81Br 80.916 49.48

• For many elements, there is more than one
  isotope, each with a different natural abundance.
  For the most common elements in organic molecules

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Average atomic masses

• For instance the atomic mass of 12C is 12.000 and
  of 13C is 13.003, but the average atomic mass
  must take into account the abundance of each
  isotope.
• Average atomic mass
• Similarly the average atomic mass of Cl is given
  as 35.5
• These are used for mole calculations
• MS measures monoisotopic masses and these must be
  used to calculate molecular masses in MS.

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Calculating Molecular FormulaeUsing Low
Resolution Mass Spectra

• Rule of 13
• CH 13 amu. Most common unit in organic
  compounds
• Therefore (CH)10H6 C10H16
• Use CH4 H16 O
• CH2 H14 N
• H12 C
• Gives C9H12O, C8H8O2, C8H12N2 etc

M (molecular ion) 136 m/z
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Accurate Mass Measurement

• Experimental accurate mass measurement (from MS)
  was 136.1256 suggesting C10H16 is the correct
  formula.
• The error between calculated and experimental
  mass is
• 136.1256 - 136.1248 0.0008 0.8 mmu

Formula dbe Accurate mass
C10H16 3 136.1248
C9H12O 4 136.0885
C8H8O2 5 136.0522
C7H4O3 6 136.0159
C9H14N 3.5 136.1123
C8H12N2 4 136.0998
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Determining the Molecular Formula Using NMR and
MS Data
DEPT-135
CH3
CH3
CH
CH
CH
CH2
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Isotope Ratio Patterns

• For hydrocarbons, the height of the M 1 peak
  is given by the expression
• M 1 n x 1.1
• where n is the number of carbon atoms. The height
  of the M 1 peak can therefore be used as a
  crude measure of the number of carbon atoms in a
  hydrocarbon.
• For most other compounds, M 2 is very small,
  apart from those containing Cl or Br. The region
  around the molecular ion peak becomes more
  complex if either of these (or both) are present.

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Cl and Br

• 2 Br atoms in the same molecule
• (1 79Br 1 81Br)2
• 1 79Br79Br 2 79Br81Br 1 81Br81Br
• 2 Cl atoms present
• (3 35Cl 1 37Cl)2
• 9 35Cl35Cl 6 35Cl37Cl 1 37Cl37Cl

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Multiply Charged Ions
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Multiply Charged Ions

• Using electrospray ionization it is common to get
  multiply charged ions
• M H M 2H2 M 3H3 M nHn
• m/z M 1 (M2)/2 (M3)/3 (Mn)/n