Section 3: Spectroscopy Structure elucidation

How to identify a new molecule?
New Natural products (drugs)

How to identify the products of a reaction? How to tell if a reaction is complete? How do we know what a molecule looks like?

Taxol (Paclitaxel)
Pacific yew tree (Taxus brevifolia) Ovarian, Breast lung, head and neck cancers 3 full mature trees (100 years old) provides 2 g (one treatment)
O O OH O O NH O HO O O O H O O O

Tree Bark

200 – 300 g

Extract with Organic Solvent Could be hundreds of molecules!

Crude Extract
Assay For Biological Activity

Chromatographic Separation
O O OH O O NH O HO O O O H O O O

Pure Molecule! 1 or 2 g

Daldinia loculata

Fungal Culture 2,000 mL
Extract with Organic Solvent Evaporate Solvent

Isolated from soil collected in Wapusk National Park

Crude Extract ~0.5 g
Assay For Biological Activity

Several Steps

Chromatographic Separation

OH
New Natural Product with antibiotic activity

O
Pure Molecule! 0.0050g 5.0 mg

O

Tree Bark How to do this step? Crude Extract Chromatographic Separation O O OH O O NH O HO O O O H O O O .

Tree Bark Crude Extract Chromatographic Separation O O OH O O NH O HO O O O H O O O How to identify molecule? .

Chromatographic Separation TLC Column Chromatography .

Thin Layer Chromatography Solvent Front Rf = 0.5 Distance travelled by compound Rf = Distance travelled by solvent front Origin .

Column Chromatography Solid phase = Silica gel Very finely ground sand Solvent pushed through By air pressure (Flash column) Solid Phase Solvent Sample Mobile phase = Organic Solvent Hexane and ethyl acetate mixtures Interactions based on polarity of molecule and solvent Silica = polar .

Column Chromatography C B A B C C C A B A A B A B C .

Column Chromatography Pure Molecules Least Polar Not so Polar A B C Most Polar .

Column Chromatography A B C .

Gas Chromatography High Performance Liquid Chromatography (HPLC) – common O O OH O O NH O HO O O O H O O O .Other Methods Tree Bark Crude Extract Distillation. Crystallization. Sublimation.

Tree Bark Crude Extract Chromatographic Separation O O OH O O NH O HO O O O H O O O How to identify molecule? .

Klein Chapter 15 & 16 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

.

Klein Chapter 15 p 695 – 710 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

21 .Schematic of a mass spectrometer Charge is deflected in magnetic field according to mass Figure 15.

Mass Spectrum e O H O H Chemical Formula: C7H6O• m/z: 106.04 (100.0%) .

High resolution mass spectrum .

2 Exact Mass: 182.10955 Chemical Formula: C12H10N2 Molecular Weight: 182.High resolution mass spectrum N N Chemical Formula: C14H14 Molecular Weight: 182.08440 Uses the presence of isotopes of carbon and oxygen and hydrogen .2 Exact Mass: 182.

0%).Mass Spectroscopy Chemical Formula: C10H8 Molecular Weight: 128.06 (100.17052 m/z: 128. .

04186 m/z: 77 .e O H O H Mass Spectroscopy -Fragmentation m/z: 106 H H H H H m/z: 105 O Chemical Formula: C7H6O• Exact Mass: 106.

Mass Spectroscopy Conclusion: Can get molecular formula (ONLY!) There is other information present in Mass Spectrum (fragmentation patterns) but it is difficult to interpret and we have more useful techniques. .

Klein Chapter 15 p 672 – 694 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

IR Spectroscopy Low energy Long wavelength Chemical bond vibrations .

000 nm to 15.700 cm–1) H H C O H H ~ 3000 cm–1 H H C O H H .000 nm Usually expressed in wavenumber (5000 .IR Spectroscopy Stretching of bonds Energy = 60 kJ / mole to 8 kJ / mole Wavelength = 2.

IR Spectroscopy The IR Spectrum .

No Useful Functional Group Information .IR Spectroscopy The IR Spectrum Diagnostic Functional Group Region ‘Fingerprint’ Region Can get some functional group information An additional piece of evidence for deducing chemical structure.

IR Spectroscopy Hydrocarbons C—H Stretch = 2900 cm-1 .

IR Spectroscopy Hydrocarbons C—H Stretch = 2900 cm-1 .

IR Spectroscopy Hydrocarbons C—H Stretch = 2900 cm-1 .

IR Spectroscopy Hydrocarbons C—H Stretch = 2900 cm-1 .

IR Spectroscopy Hydrocarbons C—H Stretch = 2900 cm-1 .

IR Spectroscopy Hydrocarbons C—H Stretch = 3000 cm-1 CH3 .

IR Spectroscopy Alcohol Groups OH R R Characteristic stretching at ≈ 3200 cm-1 Very broad and very strong absorption .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 OH CH3 .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 OH .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 OH .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 OH .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 OH .

IR Spectroscopy Alcohols O—H absorption ≈ 3250 cm-1 H HO H H .

3000 cm-1 Somewhat broad and usually strong absorption .IR Spectroscopy Amine Groups NH2 R R Characteristic stretching at ≈ 3500 .

3000 Somewhat broad and usually strong absorption cm-1 NH2 .IR Spectroscopy Amines Characteristic stretching at ≈ 3500.

3000 cm-1 Somewhat broad and usually strong absorption NH2 “Doublet” shape indicates primary amine .IR Spectroscopy Amines Characteristic stretching at ≈ 3500.

3000 cm-1 Somewhat broad and usually strong absorption H N CH3 No longer a “doublet” .IR Spectroscopy Secondary Amines Characteristic stretching at ≈ 3500.

IR Spectroscopy Amines Characteristic stretching at ≈ 3500.3000 cm-1 Somewhat broad and usually strong absorption NH2 “Doublet” shape indicates primary amine .

3000 cm-1 Somewhat broad and usually strong absorption H N CH3 No longer a “doublet” .IR Spectroscopy Amines Characteristic stretching at ≈ 3500.

IR Spectroscopy Carbonyl Groups O R R Characteristic stretching at ≈ 1780 – 1640 cm-1 Very sharp and very strong absorption .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1718 cm-1 Ketones O CH3 CH3 .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1730 cm-1 Ketones O .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1740 cm-1 Ketones O .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1691 cm-1 Ketones O CH3 .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1730 Aldehyde Hydrogen = 3450cm–1 cm-1 Aldehydes O H .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1757 Aldehyde Hydrogen ~ 3400 cm-1 Aldehydes O H .

IR Spectroscopy Carbonyl Groups Esters Carbonyl absorption = 1740 cm-1 C—O Stretch = 1228 cm-1 O O .

IR Spectroscopy Carbonyl Groups Esters Carbonyl absorption = 1723 cm-1 C—O Stretch = 1270 cm-1 O O .

IR Spectroscopy Carbonyl Groups Acids Carbonyl absorption = 1695 cm-1 O—H Stretch = 3200 cm-1 O H O .

IR Spectroscopy Carbonyl Groups -1 Carbonyl absorption = 1700 cmAcids O—H Stretch = 3200 cm-1 O OH .

IR Spectroscopy Carbonyl Groups -1 Carbonyl absorption = 1707 cmAcids O—H Stretch = 3150 cm-1 O H O .

IR Spectroscopy Carbonyl Groups Carbonyl absorption = 1651 cm-1 N—H Stretch = 3100 cm-1 Amides O NH2 .

IR Spectroscopy Alkynes Triple Bond Stretch = 2120 cm-1 Alkyne C—H Stretch = 3100 cm-1 H .

IR Spectroscopy Nitriles Triple Bond (CN) Stretch = 2237 cm-1 C N .

IR Spectroscopy The IR Spectrum – C–H Stretch Hydrocarbons C—H Stretch = 2900 cm-1 Present in all organic molecules .

IR Spectroscopy The IR Spectrum – O–H Stretch R O H Alcohols Characteristic stretching at ≈ 3500 cm-1 Very broad and very strong absorption .

3000 cm-1 Somewhat broad and usually strong absorption .IR Spectroscopy The IR Spectrum – N–H Stretch R NH2 Amines Characteristic stretching at ≈ 3500.

IR Spectroscopy The IR Spectrum – The Carbonyl Carbonyl Characteristic stretching at ≈ 1800 – 1600 cm-1 Very sharp and very strong absorption O R R .

IR Spectroscopy The IR Spectrum – The Carboxylic acid O R OH Carbonyl Characteristic stretching at ≈ 1700 .1680 cm-1 Very sharp and very strong absorption AND Very Broad Very Strong OH Stretch ≈ 3300 – 3000 cm-1 .

3000 cm-1 Somewhat broad and usually strong absorption Aldehyde C–H Bond Ester C–O Bond Acid O–H Bond Amide N–H Bond Alkynes Triple Bond Stretch = 2120 cm-1 Alkyne C—H Stretch = 3100 cm-1 Hydrocarbons C—H Stretch = 2900 cm-1 Present in all organic molecules Carbonyl Characteristic stretching at ≈ 1800 – 1600 cm-1 Very sharp and very strong absorption Nitriles Triple Bond (CN) Stretch = 2237 cm-1 .IR Spectroscopy Alcohols Characteristic stretching at ≈ 3500 cm-1 Very broad and very strong absorption Amines Characteristic stretching at ≈ 3500.

IR Spectroscopy Conclusion: Functional Group Information ONLY!! Cannot tell you how those functional groups are connected. We need 1H and 13C NMR for that! .

Wednesday!! NMR Spectroscopy Klein Chapter 16 .

Last Time Klein Chapter 15 p 672 – 694 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

700 cm–1) H H C O H H ~ 3000 cm–1 H H C O H H .000 nm Usually expressed in wavenumber (5000 .IR Spectroscopy Last Time Stretching of bonds Energy = 60 kJ / mole to 8 kJ / mole Wavelength = 2.000 nm to 15.

3000 cm-1 Somewhat broad and usually strong absorption Aldehyde C–H Bond Ester C–O Bond Acid O–H Bond Amide N–H Bond Alkynes Triple Bond Stretch = 2100 cm-1 Alkyne C—H Stretch = 3100 cm-1 Hydrocarbons C—H Stretch = 2900 cm-1 Present in all organic molecules Carbonyl Characteristic stretching at ≈ 1800 – 1600 cm-1 Very sharp and very strong absorption Nitriles Triple Bond (CN) Stretch = 2200 cm-1 .IR Spectroscopy Alcohols Characteristic stretching at ≈ 3500 cm-1 Very broad and very strong absorption Amines Characteristic stretching at ≈ 3500.

IR Spectroscopy Conclusion: Functional Group Information ONLY!! Cannot tell you how those functional groups are connected. We need 1H and 13C NMR for that! .

Klein Chapter 16 p 718 – 767 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

NMR The radio-frequency region (rf) energy) 1H .

Not necessarily ½ .NMR Nuclear Spin 1H Quantum numbers ms = ½ or – ½ Electron spin =½ Nucleus of atom can have spin as well.

NMR Recall Isotopes 1H AX Z e- X = element symbol A = mass number z = Atomic Number en e- n n 3H 1 1H 1 2H 1 Hydrogen Deuterium Tritium .

NMR Table of nuclear spins Nucle u s 1 H (Proton) 2 H (Deuterium) 3 H (Tritium) 10 B 11 B 12 C 13 C 16 O 31 P 73 Ge 197 Au 235 U Spin 1 3 3/2 0 0 9/2 3/2 7/2 1H .

NMR Behavior of nuclei in a magnetic field 1H e- Spinning electric charge generates a magnetic vector 1H Hydrogen .

NMR Behavior of nuclei in a magnetic field

1H

e-

In absence of external magnetic field all nuclear magnetic vectors are randomly oriented.

1H

Hydrogen

NMR Behavior of nuclei in a magnetic field

1H

e-

In presence of external magnetic field (B0) all nuclear magnetic vectors are aligned with or against the field.

1H

Hydrogen

B0

NMR Behavior of nuclei in a magnetic field
Magnetic field strength = 1 Tesla

1H

Takes a photon of light with a frequency of 42.5 MHz to cause the spin of a proton in a hydrogen nucleus to ‘flip’ from aligned with to aligned against.

Note: other nuclei have different frequencies

FM Radio = 88 to 108 MHz

NMR Behavior of nuclei in a magnetic field
Magnetic field strength = 2 Tesla Spin state transition (1H) = 85 MHz Magnetic field strength = 7 Tesla Spin state transition (1H) = 300 MHz

1H

Magnetic field strength = 20 Tesla Spin state transition (1H) = 850 MHz

4 – 24 T) (Superconducting Magnets) Technique referred to as Nuclear Magnetic Resonance (NMR) Also referred to as Magnetic Resonance Imaging (MRI) .NMR Strength of magnets Strength of magnets usually expressed in terms of the frequency for a 1H transition 1H Early Magnets (1950’s) = 60 MHz (1.4T permanent magnets) Later Magnets (1960’s) = 80 MHz (2T electromagnets) Current Magnets (1970’s to now) = 100 MHz – 1000 MHz (2.

NMR Picture of an NMR 300 MHZ (7.05 T Field Strength) Open to all third year organic students Also a 500 MHz and a 600 MHz NMR Tank filled with liquid He and N2 1H .

NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H CH3 CH2 I Expectation: One signal for all of the protons in the molecule .

Observation: 2 Peaks! NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H CH3 CH2 Why 2 Peaks?!?! Shouldn’t all protons be the same? I .

. This effect is sometimes referred to as shielding.CH3 CH2 NMR NMR Spectra Answer = NO! The chemical environment of each proton is unique! I 1H Referred to as the chemical shift.

This is referred to as the chemical shift (δ). . The effective frequency affected by ‘chemical environment’.NMR NMR Spectra Sample of Et–I in a magnetic field Result: 2 Signals 1H CH3 CH2 Physics: Irritating Chemistry: Gold Mine! I Shielding of individual protons by local field of electrons. Allows us to determine ‘types’ of protons in molecule.

This chemical shift can be correlated to structure. .NMR NMR Spectra Sample of Et–I in a magnetic field Result: 2 Signals 1H CH3 CH2 Conclusion: I Protons (1H) in unique chemical environments will generate a unique chemical shift.

(TMS is now never added to a sample – therefore no signal at 0 ppm) Note: The spectrometer operating frequency is part of the above equation. so that the position of the signals are field independent. (if a signal is at 1 ppm on a 300 MHZ NMR it will be at 1 ppm on a 500 MHZ NMR) . Original reference standard was TMS Tetramethylsilane = (CH3)4Si This is set to 0 ppm and almost all resonances (in organic molecules) are at a lower frequency relative to TMS therefore have a larger chemical shift.NMR NMR Spectra 1H CH3 CH2 OH Chemical shift from TMS in Hz Chemical Shift (δ) in ppm = Spectrometer frequency in MHz Frequency shifts are expressed in parts per million (ppm) from a reference standard.

24 ppm and is present in all of the 1H NMR that we Placed in a glass tube and placed in a magnet. Area under the peak (integration) can tell how many protons .NMR NMR Spectra 1H How an NMR spectrum is collected: Sample is dissolved in a suitable solvent (usually CDCl3) CH3 CH2 OH (Deuterium absorbs at a different frequency — residual signal from trace of CHCl3) This residual CHCl3 has a chemical shift of 7. (hits all the rf frequencies at once uses a Fourier Transform to decide where the energy is ‘missing’ [absorbed]) Computer plots from 0 ppm to ~ 10 ppm and shows where rf energy has been absorbed. Computer collects spectrum.

NMR Schematic of an NMR 1H .

NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H CH3 CH2 Residual CHCl3 I .

NMR NMR Spectra Chemical Equivalence 1H CH3 CH2 Why does each proton not generate a unique signal? I .

.Why does each proton not generate a unique signal? ANSWER: Symmetry NMR NMR Spectra Chemical Equivalence 1H CH3 CH2 I We will see more examples of chemically equivalent protons.

I .NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H CH3 CH2 In Alkyl Groups: The more electronegative the environment the higher the chemical shift.

NMR NMR Spectra 1H .In Alkyl Groups: The more electronegative the environment the higher the chemical shift.

NMR NMR Spectra Direct observation of the inductive effect.In Alkyl Groups: The more electronegative the environment the higher the chemical shift. 1H .

8 ppm . 1H ‘Aromatic Protons’ usually occur between 6.5 .NMR NMR Spectra In Functional Groups Containing π-bonds: The anisotropic effect “shields” protons.

‘Correlation’ table NMR NMR Spectra Will be provided on exam 1H .

1H . Signals experiencing this effect appear with a characteristic chemical shift.NMR NMR Spectra Chemical Shift: Tells us about the chemical environment of the protons Number of unique chemical environments = Number of signals Chemical shift (δ) in ppm relative to TMS The more electronegative the environment = higher chemical shift Anisotropic effect also has an effect on chemical shift.

NMR NMR Spectra Why are peaks split?? Sample of Iodoethane in a magnetic field 1H CH3 CH2 I .

NMR NMR Spectra 1H Answer: Spin – Spin coupling. . CH3 CH2 OH Each proton ‘feels’ the effect of the neighboring protons Or: Each spin is coupled to the spin of the neighbour The number of lines in the splitting pattern based on the number of nearest neighbors The pattern is referred to as the multiplicity of the peak.

NMR NMR Spectra

1H

Ha ‘feels’ the effect of Hb and can align ‘with’ or ‘against’ spin of Hb.

NMR NMR Spectra

1H

NMR NMR Spectra

1H

NMR Expected splitting pattern The n+1 rule Number of lines = n+1
Where n = nearest neighbours

1H

NMR Expected splitting pattern Pascal’s Triangle 1H .

NMR Expected splitting pattern

1H

NMR Expected splitting pattern

1H

NMR Ethyl Group

1H

CH3 CH2
Quartet

I
Triplet

Last time

Klein Chapter 16 p 718 – 767 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons

How to identify molecule?
O O OH O O NH O HO O O O H O O O

Note: other nuclei have different frequencies FM Radio = 88 to 108 MHz .5 MHz to cause the spin of a proton in a hydrogen nucleus to ‘flip’ from aligned with to aligned against.Last time NMR Behavior of nuclei in a magnetic field 1H Magnetic field strength = 1 Tesla Takes a photon of light with a frequency of 42.

Last time NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H CH3 CH2 In Alkyl Groups: The more electronegative the environment the higher the chemical shift. I .

Last time NMR NMR Spectra 1H .

Last time NMR NMR Spectra Sample of Iodoethane in a magnetic field 1H Why are peaks split?? CH3 CH2 I .

Last time NMR NMR Spectra 1H Multiplicity: Number of adjacent protons .

Last time NMR Ethyl Group 1H CH3 CH2 Quartet I Triplet .

Friday afternoon help session cancelled for today only! There will be a help session next Friday and every Friday till the end of term. You are responsible for everything in Lecture and in Textbook sections that we have covered. . Mid-Term: Sample Mid-Term posted on ANGEL Nov 2nd @ 7:00 pm (2 hours long) MC and Long Answer Everything up to and including Oct 31st lecture. (Buller 207) AND: I will run a help session on Oct 31st in the late afternoon (~ 5 – 7 pm) depending on room booking.

NMR Coupling is a three-bond process 1H O O This is a singlet it does not ‘see’ the spin of the CH2 on the ethyl group This is a quartet. It only ‘sees’ the spin of the neighbouring CH3 and not the acetate CH3 .

1H NMR O O .

NMR Coupling is a three-bond process 1H O H H 5 H1 H 2 3 O H 4 1 2 3 H H H .

NMR Coupling is a three-bond process 1H H 1 HH 2 4 H 1 2 3 H O 3 H H H Expected Pattern = quartet. triplet and a singlet O .

1H NMR Symmetry and NMR: Protons in identical chemical environments will have identical chemical shifts OH .

Predict the 1H NMR spectra for isopropanol One proton broad singlet Six identical protons split by one proton two lines One proton split by six identical protons seven lines OH OH H H H H H H .

OH .

NMR Exchangeable Protons Exchangeable Protons = Protons directly attached to oxygen or nitrogen 1H OH “Exchangeable proton” OH + D2O OD + HOD Exchangeable protons Variable chemical shift NO .spin-spin coupling! Proton now ‘disappears’ in NMR .

NMR Exchangeable Protons 1H OH .

OH NMR Exchangeable Protons 1H OH + D2O OD + HOD Proton now ‘disappears’ in NMR 1H 1H 1H .

1H NMR .

NMR Look at Pyridine 1H H H H N H H .

NMR NMR Spectra 1H How an NMR spectrum is interpreted: Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Multiplicity: Number of adjacent protons .

NMR Integration 1H O O Singlet Quartet Triplet .

NMR NMR Spectra 1H How an NMR spectrum is interpreted: Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Multiplicity: Number of adjacent protons Integration: Number of protons responsible for a signal .

O O NMR Integration 1H How to interpret these lines Integral: Area under the curve .

1H NMR How to Integrate: Measure the integral ∫ = area under the curve 4.5 cm 3 cm 4.5 cm 3 cm = 1.5 : 1 (or 3 : 2) O O 4.5 cm .

NMR NMR Spectra 1H How an NMR spectrum is interpreted: Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Multiplicity: Number of adjacent protons Integration: Number of protons responsible for a signal .

NMR The usefulness of NMR: An Example 1H Can give us conclusive determination of molecular structure .

NMR The usefulness of NMR: An Example Molecular formula = C4H10O 1H Molecular Ion (usually highest peak) m/z = 74 .

NMR The usefulness of NMR: An Example Molecular formula = C4H10O Some Possibilities 1H OH O O OH .

Molecular formula = C4H10O NMR The usefulness of NMR: An Example Interpreting the IR 1H OH O O OH .

Molecular formula = C4H10O NMR The usefulness of NMR: An Example Interpreting the IR 1H OH X O OH X O .

1H NMR This is 1H NMR of our “unknown” sample OH OH .

1H

NMR

Use Integration To Determine # of Protons 2H 1H 2H
OH

2H

3H

OH

NMR An Expansion

1H

OH

OH

NMR Some Real NMR

1H

HO

1H

NMR

CH3

CH3 OH CH3

1H NMR CH3 CH3 OH CH3 .

HO .NMR The usefulness of NMR 1H OH Vs.

HO Same Molecular formula in Mass Spectrum Nearly Identical IR spectrum (only broad OH peak) ONLY 1H NMR can tell the difference between these two .NMR The usefulness of NMR 1H OH Vs.

Klein Chapter 16 p 718 – 767 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

13C NMR Nucle u s 1 H (Proton) 2 H (Deuterium) 3 H (Tritium) 10 B 11 B 12 C 13 C 16 O 31 P 73 Ge 197 Au 235 U 12C Spin 1 3 3/2 0 0 9/2 3/2 7/2 and 13C are Isotopes of Carbon .

NMR Behavior of nuclei in a magnetic field In presence of external magnetic field (B0) all nuclear magnetic vectors are aligned with or against the field. 13C B0 Magnetic field strength = 7 Tesla Spin state transition (1H) = 300 MHz Spin state transition (13C) = 125 MHz .

NMR NMR Spectra 13C How a 13C NMR spectrum is interpreted: CH3 CH2 OH Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Chemical shift range is from 0 ppm to ~220 ppm Where 0 ppm is (CH3)4Si (but we don’t put it in anymore) .

108 % Compare: Natural Abundance of 1H is 99. Sensitivity is ~ 1/5700 .9 % Natural Abundance of 13C is 1.98 % Result: 13C NMR is harder to collect.13C NMR Natural Abundance of 12C is 98.

99 mg have 1H .NMR NMR Spectra 13C CH3 CH2 OH 60 mg of EtOH 59.

32 mg have 13C .NMR NMR Spectra 13C CH3 CH2 OH 60 mg of EtOH 1.

NMR NMR Spectra 13C CH3 CH2 OH Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Same general trend in correlations as in 1H NMR The more electronegative the environment The higher the chemical shift .

Last Time Klein Chapter 16 p 718 – 767 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

HO Same Molecular formula in Mass Spectrum Nearly Identical IR spectrum (only broad OH peak) ONLY 1H NMR can tell the difference between these two .Last Time NMR The usefulness of NMR 1H OH Vs.

Last Time Klein Chapter 16 p 718 – 767 Mass Spectrum InfraRed Spectrum 1H NMR 13C NMR = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O OH O O NH O HO O O O H O O O .

B0 Magnetic field strength = 7 Tesla Spin state transition (1H) = 300 MHz Spin state transition (13C) = 125 MHz .Last Time Nucle u s H (Proton) 2 H (Deuterium) 12 C 13 C 1 NMR Behavior of nuclei in a magnetic field Spin 1 0 13C In presence of external magnetic field (B0) all nuclear magnetic vectors are aligned with or against the field.

Last Time NMR NMR Spectra 13C How a 13C NMR spectrum is interpreted: CH3 CH2 OH Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Chemical shift range is from 0 ppm to ~220 ppm Where 0 ppm is (CH3)4Si (but we don’t put it in anymore) .

9 % Natural Abundance of 13C is 1.Last Time 13C NMR Natural Abundance of 12C is 98.98 % Result: 13C NMR is harder to collect.108 % Compare: Natural Abundance of 1H is 99. Sensitivity is ~ 1/5700 .

99 mg have 1H .Last Time NMR NMR Spectra 13C CH3 CH2 OH 60 mg of EtOH 59.

Last Time NMR NMR Spectra 13C CH3 CH2 OH 60 mg of EtOH 1.32 mg have 13C .

NMR NMR Spectra 13C CH3 CH2 OH Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Same general trend in correlations as in 1H NMR The more electronegative the environment The higher the chemical shift .

NMR NMR Spectra 13C CH3 CH2 OH ? .

–1) that the spin 1/2 carbon nucleus can couple to. Three states (1. . 13C Chemical Shift of CDCl3 = 77. 0 .0 ppm Peak is split into three lines because of coupling to the Deuterium Nucleus. We can ignore this signal.NMR NMR Spectra 13C Cl Cl C D Cl Present in all of the NMR spectra we will look at.

NMR NMR Spectra 13C CH3 CH2 OH Why aren’t carbon signals in EtOH split because of coupling to protons? .

.NMR NMR Spectra 13C CH3 CH2 OH Why aren’t carbon signals in EtOH split because of coupling to protons? Answer: They are! Coupling between 13C and 1H nuclei directly attached.

.NMR NMR Spectra – Broadband Decoupling 13C CH3 CH2 OH Why don’t we see this coupling in our 13C Spectra? Reason: We use a special rf ‘broadband’ generator to saturate this signal. This is referred to as decoupling. All of the 13C NMR that we will see are decoupled.

NMR NMR Spectra – Broadband Decoupling 13C O O .

NMR NMR Spectra 13C CH3 CH2 OH Question: Why don’t we see 13C — 13C coupling? Answer: Natural Abundance and Statistics! .

1% of the adjacent carbons will be 13C.000 molecules only 121 molecules would be doubly labeled.NMR NMR Spectra Question: Why don’t we see 13C — 13C coupling? Answer: Statistics! 13C CH3 CH2 OH Consider this carbon 1. 13C—13C—OH) Example: If we had 1. 13CH 3 13CH 2 OH So: Our 60 mg sample of EtOH will have 0.0121%) of all EtOH molecules will have adjacent 13C (i.e.1% X 1.00726 mg of 13C—13C—OH! ALL OTHER CARBON ATOMS are 12C and ! do not couple (or generate NMR signals) . This means that (1.1% of this Carbon are 13C isotopes AND of those only 1.1% = 0.000.

NMR NMR Spectra 13C CH3 CH2 OH Question: Why don’t we see 13C — 13C coupling? Answer: Natural Abundance and Statistics! Result: All signals are singlets!!! .

1% of all carbon atoms in the molecule we can’t integrate.NMR NMR Spectra 13C CH3 CH2 OH Question: What about integration? Answer: Because we only see 1. .

NMR NMR Spectra 13C How a 13C NMR spectrum is interpreted: CH3 CH2 OH Chemical Shift: Chemical environment of proton More electronegative higher chemical shift Chemical shift range is from 0 ppm to ~220 ppm Multiplicity: All peaks are singlets Integration: Can’t integrate like we could with 1H NMR .

NMR Some Examples 13C O O .

55 ppm –CH3 10 .160 ppm C OH 50 – 90 ppm —CH— C C O 160 – 220 ppm 30 .150 ppm R R . Chemical Shift: Chemical environment of proton More electronegative higher chemical shift C 30 – 40 ppm 100 .60 ppm –CH2— 20 .30 ppm CDCl3 100 .NMR NMR Spectra Correlation Table 13C Adapted from: Silverstein. Bassler and Morrill. Spectrometric Identification of Organic Compounds 5th ed.

210 ppm Aldehydes: 200 .220 ppm O R O R OH O R O R R O H O 160 – 220 ppm R R R CDCl3 . Bassler and Morrill. Chemical Shift: Chemical environment of proton More electronegative higher chemical shift O R NH2 Amides: 150-175 ppm Esters: 150 . Spectrometric Identification of Organic Compounds 5th ed.NMR NMR Spectra 13C Adapted from: Silverstein.180 ppm Ketones: 185 .175 ppm Acids: 165 .

NMR Some Examples 13C CH3 CH3 OH CH3 vs OH .

NMR Some Examples Note: Even carbons with no hydrogens appear in 13C NMR 13C CH3 CH3 OH CH3 .

NMR Some Examples 13C OH .

NMR Some Examples 13C .

NMR Some Examples 13C Note: 4 Aromatic Signals CH3 .

NMR Some Examples 13C N .

OH O O NH O HO O O O H O O .Klein Chapter 15 & 16 !Mass Spectrum !InfraRed Spectrum !HCNMR ! NMR 1 13 = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O O How to solve structures.

Solving Spectral Problems Use all of the information presented in a systematic manner For example if there is no carbonyl stretching in the IR Don’t propose an ester for your structure. . OR: If the correlation table for IR makes you think that there is an aromatic ring then double check the 13C NMR and look for carbon signals in the armoatic region (~120 – 150 ppm) Use the mass spectrum to put the pieces together until the mass matches.

Solving Spectral Problems Molecular Formula (Weight) A flow chart approach Check IR for Functional groups (Alcohol and Carbonyl) 13C NMR —Chemical Shift: Number and type of carbon. sp2 and sp3 (electronegative environment) 1H NMR — Chemical shift. coupling and integration Chemical Shift: Chemical environment (Oxygen atom?) Coupling: Recognize a pattern? Integration: How many hydrogen atoms for each signal .

coupling and integration Chemical Shift: Chemical environment (Oxygen atom?) Coupling: Recognize a pattern? Integration: How many hydrogens for each signal . sp2 and sp3 (electronegative environment) 1H NMR — Chemical shift.Solving Spectral Problems Molecular Formula (Weight) IMPORTANT: Does ALL the evidence agree? Check IR for Functional groups (Alcohol and Carbonyl) 13C NMR —Chemical Shift: Number and type of carbon.

Solving Spectral Problems Use of molecular formula Unsaturation number: H+N = C+1— 2 Example: C6H14 = UN of 0 C6H12 = UN of 1 OR C6H6 = UN of 4 High UN (4 or higher) suggests aromatic ring .

Solving Spectral Problems Use of Mass Spectrum IF molecular weight is an odd number there is a nitrogen atom Eg. Ethanol = C2H6O MW = 46 But EthylAmine = C2H7N = 45 Or Benzene = C6H6 MW = 78 But Pyridine = C6H5N MW = 79 Can use this in addition to other evidence that N is present .

Solving Spectral Problems Let’s do some problems! Again we will do as an IClicker exercise .

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Conclusion: Molecular Weight = 60 mass units .

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Conclusion: OH Group present NO Carbonyl group .

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Conclusion: Only 2-Kinds of carbon atoms One is in an electronegative environment (O atom?) NO sp2 hybridized carbon atoms. .

Conclusion: Shift: An electronegative group Coupling: 7 lines and 2 lines (i–Propyl?) Integration: 1:1:6 .

Exchanges with D2O = OH (or NH2) group .

A OH O B OH C OH D Br E .

A OH O B OH C OH D Br E .

OH O O NH O HO O O O O H O O .Klein Chapter 15 & 16 Mass Spectrum InfraRed H NMR Spectrum  C NMR  1 13 = Molecular Formula = Functional Groups = Protons = Carbons How to identify molecule? O O How to solve structures.

sp2 and sp3 (electronegative environment) 1H NMR — Chemical shift.Solving Spectral Problems Molecular Formula (Weight) IMPORTANT: Does ALL the evidence agree? Check IR for Functional groups (Alcohol and Carbonyl) 13C NMR —Chemical Shift: Number and type of carbon. coupling and integration Chemical Shift: Chemical environment (Oxygen atom?) Coupling: Recognize a pattern? Integration: How many hydrogens for each signal .

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A B C O OH O H O D O O E .

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A B C O OH O O D O O E .

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A B O O O O C O D E HO OH O O .

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O A O O O O B O O O O O O O C D E O O O O .

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