CHE2202, Chapter 12 Learn, 1 Structure Determination: Mass Spectrometry and Infrared Spectroscopy Chapter 12 Suggested Problems – 1- 11,14-16,18,23,26,30-

CHE2202, Chapter 12Learn, 1

Structure Determination: Mass

Spectrometry and Infrared Spectroscopy

Chapter 12

Suggested Problems – 1-11,14-16,18,23,26,30-34,41-2


• The analysis of the outcome of a reaction requires that we know the full structure of the products as well as the reactants

• In the 19th and early 20th centuries, structures were determined by synthesis and chemical degradation that related compounds to each other

• Physical methods now permit structures to be determined directly. We will examine:– mass spectrometry (MS)– infrared (IR) spectroscopy– nuclear magnetic resonance spectroscopy (NMR)– ultraviolet-visible spectroscopy (UV-VIS)

Determining the Structure of an Organic Compound


Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments

• Mass spectrometry (MS) determines molecular weight by measuring the mass of a molecule

• Components of a mass spectrometer:– Ionization source - Electrical charge assigned to

sample molecules

– Mass analyzer - Ions are separated based on their mass-to-charge ratio

– Detector - Separated ions are observed and counted


Electron-Ionization, Magnetic-Sector Mass Spectrometer

• Small amount of sample undergoes vaporization at the ionization source to form cation radicals

• Amount of energy transferred causes fragmentation of most cation radicals into positive and neutral pieces


Electron-Ionization, Magnetic-Sector Mass Spectrometer

• Fragments pass through a strong magnetic field in a curved pipe that segregates them according to their mass-to-charge ratio

• Positive fragments are sorted into a detector and are recorded as peaks at the various m/z ratios– Mass of the ion is the m/z value


The electron-ionization, magnetic-sector mass spectrometer


Quadrupole Mass Analyzer

• Comprises four iron rods arranged parallel to the direction of the ion beam

• Specific oscillating electrostatic field is created in the space between the four rods– Only the corresponding m/z value is able to pass

through and reach the detector

– Other values are deflected and crash into the rods or the walls of the instrument


The Quadrupole Mass Analyzer


Representing the Mass Spectrum

• 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 is base peak (Intensity of 100%)• Peak that corresponds to the unfragmented radical

cation is parent peak or molecular ion (M+)


Interpreting Mass Spectra

• Provides the molecular weight from the mass of the molecular ion

• Double-focusing mass spectrometers have a high accuracy rate

• In compounds that do not exhibit molecular ions, soft ionization methods are used


High Resolution Mass Spectrometry Can DistinguishBetween Compound with the Same Molecular Mass

Exact Masses of Isotopes


Natural Abundance of Isotopes


Other Mass Spectral Features

• Mass spectrum provides the molecular fingerprint of a compound– The way molecular ions break down, can produce

characteristic fragments that help in identification

• Interpretation of molecular fragmentation pattern assists in the derivation of structural information


Mass Spectral Fragmentation of Hexane

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


Worked Example

• The male sex hormone testosterone contains only C, H, and O and has a mass of 288.2089 amu, as determined by high-resolution mass spectrometry– Determine the possible molecular formula of

testosterone


Worked Example

• Solution:– Assume that hydrogen contributes 0.2089 to the mass

of 288.2089– Dividing 0.2089 by 0.00783 ( difference between the

atomic weight of one H atom and 1) gives 26.67• Approximate number of H in testosterone

– Determine the maximum number of carbons by dividing 288 by 12

– List reasonable molecular formulas containing C,H, and O that contain 20-30 hydrogens and whose mass is 288


Worked Example

– The possible formula for testosterone is C19H28O2


Mass Spectrometry of Some Common Functional Groups

• Alcohols– Fragment through alpha cleavage and

dehydration



• Amines– Nitrogen rule of mass spectrometry

• A compound with an odd number of nitrogen atoms has an odd-numbered molecular weight

– Amines undergo -cleavage, generating alkyl radicals and a resonance-stabilized, nitrogen-containing cation



• Halides– Elements comprising

two common isotopes possess a distinctive appearance as a mass spectra


Fragmentation of Carbonyl Compounds

• 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


Worked Example

• List the masses of the parent ion and of several fragments that can be found in the mass spectrum of the following molecule

2-methyl-2-pentanol


Worked Example

• Solution:– The molecule is 2-methyl-2-pentanol

• It produces fragments resulting from dehydration and alpha cleavage

• Peaks may appear at M+=102(molecular ion), 87, 84, 59


Mass Spectroscopy in Biological Chemistry: Time-of-Flight (TOF) Instruments

• Most biochemical analyses by MS use soft ionization methods that charge molecules with minimal fragmentation– Electrospray ionization (ESI)

• High voltage is passed through the solution sample• Sample molecule gains one or more protons from the

volatile solvent, which evaporates quickly

– Matrix-assisted laser desorption ionization (MALDI)• Sample is absorbed onto a suitable matrix compound • Upon brief exposure to laser light, energy is

transferred from the matrix compound to the sample molecule


MALDI–TOF Mass Spectrum of Chicken Egg-White Lysozyme


Spectroscopy and the Electromagnetic Spectrum

• Waves are classified by frequency or wavelength ranges


Absorption Spectrum

• Organic compounds exposed to electromagnetic radiation can absorb energy of only certain wavelengths (unit of energy)– Transmit energy of other wavelengths

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

• In infrared radiation, absorbed energy causes bonds to stretch and bend more vigorously

• In ultraviolet radiation, absorbed energy causes electrons to jump to a higher-energy orbital


Infrared Energy Modes

• Molecules possess a certain amount of energy that causes them to vibrate

• Molecule absorbs energy upon electromagnetic radiation only if the radiation frequency and the vibration frequency match


Interpreting Infrared Spectra

• IR spectrum interpretation is difficult as the arrangement of organic molecules is complex – Disadvantage - Generally used only in pure

samples of fairly small molecules

– Advantage - Provides a unique identification of compounds

• Fingerprint region - 1500cm-1 to 400 cm-1 (approx)

• Complete interpretation of the IR spectrum is not necessary to gain useful structural information– IR absorption bands are similar among compounds


Characteristic IR Absorptions of Some Functional Groups


IR Spectra of Hexane, 1-Hexene, and 1-Hexyne


Regions of the Infrared Spectrum

• Region from 4000 to 2500 cm-1 can be divided into areas characterized by:– Single-bond stretching motions

– Triple-bond stretching motions

– Absorption by double bonds

– Fingerprint portion of the IR spectrum


Worked Example

• Using IR spectroscopy, distinguish between the following isomers:– CH3CH2OH and CH3OCH3

• Solution:– CH3CH2OH is a strong hydroxyl bond at

3400–3640 cm-1

– CH3OCH3 does not possess a band in the region 3400–3640 cm-1


Infrared Spectra of Some Common Functional Groups

• Alkanes– No functional groups

– C–H and C–C bonds are responsible for absorption

– C–H bond absorption ranges from 2850 to 2960 cm-1

– C–C bonds show bands between 800 to 1300 cm-1



• Alkenes– Vinylic =C–H bonds are responsible for

absorption from 3020 to 3011cm-1

– Alkene C=C bonds are responsible for absorption close to 1650cm-1

– Alkenes possess =C–H out-of-plane bending absorptions in the 700 to 1000 cm-1 range



• Alkynes– C≡C stretching absorption exhibited at 2100 to

2260 cm-1

• Similar bonds in 3-hexyne show no absorption

– Terminal alkynes such as 1-hexyne possess ≡C–H stretching absorption at 3300 cm-1


Some Vibrations are Infrared Inactive

A bond absorbs IR radiation only if its dipole moment changes when it vibrates.


Aromatic Compounds

• Weak C–H stretch at 3030 cm1

• Weak absorptions at 1660 to 2000 cm1 range

• Medium-intensity absorptions at 1450 to 1600 cm1


Alcohols and Amines

• Alcohols– O–H 3400 to 3650 cm1

• Usually broad and intense

• Amines– N–H 3300 to 3500 cm1

• Sharper and less intense than an O–H


The IR Spectrum of an Alcohol


The IR Spectrum of an Amine


Carbonyl Compounds

• Strong, sharp C=O peak in the range of 1670 to 1780 cm1

• Exact absorption is characteristic of type of carbonyl compound

• Principles of resonance, inductive electronic effects, and hydrogen bonding provides a better understanding of IR radiation frequencies


Carbonyl Compounds

• Aldehydes– 1730 cm1 in saturated aldehydes– 1705 cm1 in aldehydes next to double bond or

aromatic ring– Low absorbance frequency is due to the

resonance delocalization of electron density from the C=C into the carbonyl


The IR Spectrum of an Aldehyde

The carbon—hydrogen stretch of an aldehyde hydrogen occursat 2820 cm–1 and at 2720 cm–1.


Ketones

• Saturated open-chain ketones and six-membered cyclic ketones absorb at 1715cm-1

• Five-membered ketones absorb at 1750cm-1

– Stiffening of C=O bond due to ring strain

• Four members absorb at 1780cm-1


This C═O Bond Is Essentially a Pure Double Bond


This C═O Bond Has Significant Single Bond Character

The less double bond character, the lower the frequency.


Carbonyl Compounds

• Esters– Saturated esters absorb at 1735 cm-1

– Esters possess two strong absorbances within the range of 1300 to 1000 cm-1

– Esters adjacent to an aromatic ring or a double bond absorb at 1715 cm-1


The IR Spectrum of an Ester


The IR Spectrum of a Carboxylic Acid


Hydrogen Bonded OH Groups Stretch at a Lower Frequency

It is easier to stretch a hydrogen bonded OH group.


The IR Spectrum of an Amide


Worked Example

• Identify the possible location of IR absorptions in the compound below


Worked Example

• Solution:

– The compound possesses nitrile and ketone groups as well as a carbon–carbon double bond

– Nitrile absorption occurs at 2210–2260 cm-1

– Ketone exhibits an absorption bond at 1690 cm-1

– Double bond absorption occurs at 1640–1680 cm-1

Documents

CHE2202, Chapter 12 Learn, 1 Structure Determination: Mass Spectrometry and Infrared Spectroscopy Chapter 12 Suggested Problems – 1- 11,14-16,18,23,26,30-