Welcome to Organic Chemistry II

Erika Bryant, [email protected]

Class Syllabus

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CHAPTER 12: STRUCTURE DETERMINATION

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What is this solution

Soda

Tea

Coffee

???

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• What is this solution– Soda

– Tea

– Coffee

– ???

• What is its size and formula

• What functional groups are present

• What is its carbon-hydrogen framework

• Are conjugate systems present

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• What is this solution– Soda

– Tea

– Coffee

– ???

• What is its size and formula

• What functional groups are present

• Are conjugate systems present

• What is its chemical structure

Determine using mass

spectrometry

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What is mass spectrometry

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Mass Spectrometry

Gives sample an electrical charge

Separates ions by its mass-to-

charge ratio (m/z)

Detects and records separated

ions

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Mass Spectrometry

Set up for one of the most common mass spectrometers

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Mass Spectrometry

1. Inject sample

2. Sample is vaporized

3. Gaseous sample bombarded by high-energy electrons

• Energy of electron beam is commonly ~70 eV or 6700 kJ/mol

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Mass Spectrometry

4. Cation radical is produced

1. High energy electron strikes molecule

2. A valence electron is dislodge from the molecule

3. A radical cation is produced1. Radical: molecule with an

unpaired electron

2. Cation: a positive ion

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Mass Spectrometry

5. Cation radicals fragments due to energy transfer from electron bombardment

• Smaller pieces are cations and neutral molecules

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Mass Spectrometry

6. Fragments flow through a curved pipe in a magnetic field

7. Fragments are deflected into different paths according to their m/z

• Neutral charges are not deflected and collide with pipe walls

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Mass Spectrometry

8. Positively charged fragments are detected

9. Detected results are recorded as peaks at varying m/z ratios

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Mass Spectrometry

10. m/z value is equal to the fragments mass

• Charge is usually 1

• Up to ~2500 amu can be analyzed by this type of instrument

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Mass Spectrometry

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Mass Spectrometry

A common type of mass spectrometerQuadrupole mass analyzer

http://www.murr.missouri.edu/images/ac_quadrpl.gif 18

Bars parallel to the ion beam

Mass Spectrometry

•Oscillating electrostatic field is generated between bars

•For a given field, only one m/z value will make it through the charge region

http://www.murr.missouri.edu/images/ac_quadrpl.gif 19

Bars parallel to the ion beam

• Magnetic-sector mass spectrometer and quadrupole mass analyzer have a similar resolution– Mass spectrometry can easily distinguish between molecular weights

within ones place

• High resolution spectrometry can distinguish between molecules within 0.0005 amu (as with specific isotopic compositions)– Double-focusing mass spectrometers: has two magnetic sections

• Example MW “72” is ambiguous: C5H12 and C4H8O but:– C5H12 72.0939 amu exact mass C4H8O 72.0575 amu exact mass

– Result from fractional mass differences of atoms 16O = 15.99491, 12C = 12.0000, 1H = 1.00783

Mass Spectrometry

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Mass spectrometry

• Mass spectrometry may be used to

– Measure mass

– Determine molecular weight

– Gain structural information

– Determine the identity of an unknown substance

• By molecular fingerprinting

• Each organic compound fragments in a unique way

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Interpreting Mass Spectra

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Mass Spectrometry Results

• Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (roughly corresponding to the number of ions) (y-axis)

• Tallest peak assigned 100% intensity– Called base peak– Other peaks listed as percentage of base peak

• Parent peak is the unfragmented cation radical– Also called molecular ion (M+ or M)

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Propane

C

C

C

HH

H

H

H

H

H

H

Mass Spectrometry

• Not all compounds shows a molecular ion– 2,2-dimethylpropane fragments easily and no molecular

ion is observed– If parent ion not present due to electron bombardment,

“softer” methods such as chemical ionization are used– (M+1) from 13C that is randomly present

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2,2-dimethylpropane

How do you determine what fragmentation occurs

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• Fragmentation occurs by spontaneous cleavage of chemical bond– One fragment retains the positive charge (charge

remains on more stable fragment)

– Other fragment is its neutral radical

Interpreting Mass-Spectral Fragmentation Patterns

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• The way molecular ions break down can produce characteristic fragments that help in identification

– Serves as a “fingerprint” for comparison with known materials in analysis (used in forensics)

– Positive charge goes to fragments that best can stabilize it


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• Difficult to assign structures to fragment ions because fragmentation patterns are complex

• Especially true in hydrocarbons

– Most hydrocarbons fragment in many ways

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• Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29

Mass Spectral Fragmentation of Hexane

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• Difficult to assign structures to fragment ions because fragmentation patterns are complex

• Especially true in hydrocarbons

– Most hydrocarbons fragment in many ways

• Mass spectral fragmentations of functional groups can be interpreted to provide structural information

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Alcohols:

• Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C

Mass Spectrometry of Some Common Functional Groups

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• Amines undergo -cleavage, generating radicals

Nitrogen rule: compounds with an odd number of nitrogen have an odd numbered molecular

weight(Nitrogen is trivalent)

Mass Spectral Cleavage of Amines

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Mass Spectral Cleavage of Halides

• Elements with two common isotopes give a distinctive appearance

• 35Cl and 37Cl have a 3:1 ratio

– Moleclar ion peaks are M:M + 2 (Figure 12-11)

• 79Br and 81Br have a nearly 1:1 ratio

– Molecular ion peaks are M:M + 2 (Figure 12-12

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• A C-H that is three atoms away leads to an internal transfer of a proton to the C=O, called the McLafferty rearrangement

• Carbonyl compounds can also undergo cleavage

Fragmentation of Carbonyl Compounds

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Fragmentation of Carbonyl Compounds

• Most biochemical analyses by MS use:

- Soft ionization methods (produce charges with little framentation

- Electrospray ionization (ESI)

- Matrix-assisted laser desorption ionization (MALDI)

- Linked to a time-of-flight mass analyzer

- More sensitive than the magnetic sector alternative

- Separate fragments to an accuracy of 3 ppm

- Biologists use the unit dalton (Da) instead of amu

- 1 dalton = 1 amu35

SPECTROSCOPY AND THE ELECTROMAGNETIC SPECTRUM

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Spectroscopy and the Electromagnetic Spectrum

• Nondestructive spectroscopic techniques

– Infrared (IR)

– Ultraviolet (UV)

– Nuclear magnetic resonance (NMR)

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• Nondestructive spectroscopic techniques

– Infrared (IR)

– Ultraviolet (UV)

– Nuclear magnetic resonance (NMR)

What wavelength of electromagnetic radiation do these techniques use?

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• Electromagnetic spectrum is divided into regions

• Different types are classified by frequency or wavelength ranges

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• Radiant energy is proportional to its frequency (cycles/s = Hz) as a wave (Amplitude is its height)


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• Electromagnetic radiation has a dual behavior

– Properties of a particle (called a photon)

– Behaves as an energy wave

• Characterized by a wavelength, frequency and amplitude

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c = speed of light = 3.00 X 108 m/s

= frequency (s-1)

= wavelength (m)

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E= energy

NA = Avogadro’s number = 6.022 1023 number of particles/mol

h = Planck’s constant = 6.62 X 10-34 J.s; = frequency (s-1)

c = speed of light = 3.00 X 108 m/s; = wavelength (m)43

Energy of Avogadro’s number of photons of wavelength

Absorption Spectra

• An organic compound exposed to electromagnetic radiation can absorb energy of only certain wavelengths (unit of energy)– Transmits energy of other wavelengths

• Changing wavelengths to determine which are absorbed and which are transmitted produces an absorption spectrum

• Energy absorbed is distributed internally in a distinct and reproducible way

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Infrared Spectroscopy

• IR region lower energy than visible light (below red – produces heating as with a heat lamp)

• 2.5 106 m to 2.5 105 m region used by organic chemists for structural analysis

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Infrared Spectroscopy

• IR energy in a spectrum is usually measured as wavenumber (cm-1), the inverse of wavelength and proportional to frequency

• Specific IR absorbed by an organic molecule is related to its structure

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• IR energy absorption corresponds to specific modes, corresponding to combinations of atomic movements, such as bending and stretching of bonds between groups of atoms called “normal modes”

• Energy is characteristic of the atoms in the group and their bonding

• Corresponds to vibrations and rotations

Infrared Energy Modes

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• Most functional groups absorb at about the same energy and intensity independent of the molecule they are in

• Characteristic higher energy IR absorptions in Table 12.1 can be used to confirm the existence of the presence of a functional group in a molecule

Interpreting Infrared Spectra

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• IR spectrum has lower energy region characteristic of molecule as a whole (“fingerprint” region)

• Let’s examine Figure 12-20

Interpreting Infrared Spectra

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Figure 12.20

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• 4000-2500 cm-1 N-H, C-H, O-H (stretching)

– 3300-3600 N-H, O-H– 3000 C-H

• 2500-2000 cm-1 CC and • C N (stretching)

• 2000-1500 cm-1 double bonds (stretching)

– C=O 1680-1750– C=C 1640-1680 cm-1

• Below 1500 cm-1

“fingerprint” region

Regions of the Infrared Spectrum

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• Molecules vibrate and rotate in normal modes, which are combinations of motions (relates to force constants)

• Bond stretching dominates higher energy modes

• Light objects connected to heavy objects vibrate fastest: C–H, N–H, O–H

• For two heavy atoms, stronger bond requires more energy: C C, C N > C=C, C=O, C=N > C–C, C–O, C–N, C–halogen

Differences in Infrared Absorptions

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Alkanes, Alkenes, Alkynes

• C-H, C-C, C=C, C C have characteristic peaks

– absence helps rule out C=C or C C

Infrared Spectra of Some Common Functional Groups

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• Weak C–H stretch at 3030 cm1

• Weak absorptions 1660 - 2000 cm1 range

• Medium-intensity absorptions 1450 to 1600 cm1

• See spectrum of phenylacetylene, Figure 12.15

IR: Aromatic Compounds

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• O–H 3400 to 3650 cm1

– Usually broad and intense

• N–H 3300 to 3500 cm1

– Sharper and less intense than an O–H

IR: Alcohols and Amines

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• Strong, sharp C=O peak 1670 to 1780 cm1

• Exact absorption characteristic of type of carbonyl compound

– 1730 cm1 in saturated aldehydes

– 1705 cm1 in aldehydes next to double bond or aromatic ring

IR: Carbonyl Compounds

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• 1715 cm1 in six-membered ring and acyclic ketones

• 1750 cm1 in 5-membered ring ketones

• 1690 cm1 in ketones next to a double bond or an aromatic ring

C=O in Esters• 1735 cm1 in saturated esters

• 1715 cm1 in esters next to aromatic ring or a double bond

C=O in Ketones

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Let’s Work a Problem

Propose structures for a compound that fits the following data: It is an alcohol with M+ = 88 and fragments at m/z = 73, m/z = 70, and m/z = 59

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Answer

Answer: We must first decide on the the formula of an alcohol that could undergo this type of fragmentation via mass spectrometry. We know that an alcohol possesses an O atom (MW=16), so that leads us to the formula C5H12O for an alcohol with M+ = 88, with a structure of:

One fragmentation peak at 70 is due to the loss of water, and alpha cleavage can result in m/z of 73 and 59.

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Welcome to Organic Chemistry II

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