Chemistry 350 Organic Chemistry I

Study Guide :: Unit 12

Structure Determination: Mass Spectrometry and Infrared Spectroscopy

Unit Preview

The processes of identifying and characterizing organic compounds are of great importance to the working organic chemist. With the use of modern instrumental techniques, these tasks can now be accomplished much more readily than in the past. In this unit, you will learn about two spectroscopic techniques (mass spectroscopy and infrared spectroscopy) that are used in the identification of organic compounds. You will need to refer to the Chemistry 350 Laboratory Manual as you study certain sections in this unit.

Unit Objectives

After you have completed Unit 12, you should be able to

  1. fulfil all of the detailed objectives listed under each individual section.
  2. solve road-map problems that include mass spectral data, infrared data, or both.
  3. define, and use in context, the key terms introduced.

12.0  Introduction

Objective

After completing this section, you should be able to recognize the various spectroscopic techniques used to identify and characterize organic compounds.

Learning Activities

Read 12.0 Introduction and do any associated exercises.

12.1  Mass Spectrometry of Small Molecules: Magnetic-sector Instruments

Objectives

After completing this section, you should be able to

  1. describe, briefly, how a mass spectrometer works.
  2. sketch a simple diagram to show the essential features of a mass spectrometer.
  3. identify peaks in a simple mass spectrum, and explain how they arise.

Learning Activities

Read 12.1 Mass Spectrometry of Small Molecules: Magnetic-sector Instruments and do any associated exercises.

12.2  Interpreting Mass Spectra

Objectives

After completing this section, you should be able to

  1. suggest possible molecular formulas for a compound, given the m/z value for the molecular ion, or a mass spectrum from which this value can be obtained.
  2. predict the relative heights of the M+•, (M + 1)+•, etc., peaks in the mass spectrum of a compound, given the natural abundance of the isotopes of carbon and the other elements present in the compound.
  3. interpret the fragmentation pattern of the mass spectrum of a relatively simple, known compound (e.g., hexane).
  4. use the fragmentation pattern in a given mass spectrum to assist in the identification of a relatively simple, unknown compound (e.g., an unknown alkane).

Learning Activities

Read 12.2 Interpreting Mass Spectra and do any associated exercises.

12.3  Mass Spectrometry of Some Common Functional Groups

Objective

After completing this section, you should be able to predict the expected fragmentation for common functional groups, such as alcohols, amines and carbonyl compounds.

Learning Activities

Read 12.3 Mass Spectrometry of Some Common Functional Groups and do any associated exercises.

Go to the Introduction to Mass Spectrometry website at the University of Arizona developed by Dr. Linda Breci. Examine the site and try out a few of the quizzes to build up your mass spectrometry interpretation skills.

12.4  Mass Spectrometry in Biological Chemistry: Time-of-flight (TOF) Instruments

This section is intended only to demonstrate that mass spectrometry can be useful for the investigation of some very large molecules present in biological systems.

Objective

No objectives have been identified for this section.

Learning Activities

Read 12.4 Mass Spectrometry in Biological Chemistry and do any associated exercises.

12.5  Spectroscopy and the Electromagnetic Spectrum

Objectives

After completing this section, you should be able to

  1. write a brief paragraph discussing the nature of electromagnetic radiation.
  2. write the equations that relate energy to frequency, frequency to wavelength and energy to wavelength, and perform calculations using these relationships.
  3. describe, in general terms, how absorption spectra are obtained.

Learning Activities

Read 12.5 Spectroscopy and the Electromagnetic Spectrum and do any associated exercises.

12.6  Infrared Spectroscopy

Objectives

After completing this section, you should be able to

  1. identify (by wavelength, wave number, or both) the region of the electromagnetic spectrum which is used in infrared spectroscopy.
  2. interconvert between wavelength and wave number.
  3. discuss, in general terms, the effect that the absorption of infrared radiation can have on a molecule.

Learning Activities

Read 12.6 Infrared Spectroscopy and do any associated exercises.

12.7  Interpreting Infrared Spectra

Objectives

After completing this section, you should be able to

  1. describe how the so-called “fingerprint region” of an infrared spectrum can assist in the identification of an unknown compound.
  2. identify the functional group or groups present in a compound, given a list of the most prominent absorptions in the infrared spectrum and a table of characteristic absorption frequencies.
  3. identify the broad regions of the infrared spectrum in which occur absorptions caused by
    1. $\ce{\sf{N-H}}$, $\ce{\sf{C-H}}$, and $\ce{\sf{O-H}}$
    2. $\ce{\sf{C#C}}$ and $\ce{\sf{C#N}}$
    3. $\ce{\sf{C=O}}$, $\ce{\sf{C=N}}$, and $\ce{\sf{C=C}}$

Learning Activities

Read 12.7 Interpreting Infrared Spectra and do any associated exercises.

Note: You need not memorize infrared absorption data in detail. A table with characteristic infrared absorptions of the various functional groups will be provided for all examinations in this course and can also be found under “Exam Data Sheets” on the course homepage.

12.8  Infrared Spectra of Some Common Functional Groups

Objective

After completing this section, you should be able to use an infrared spectrum to determine the presence of functional groups, such as alcohols, amines and carbonyl groups, in an unknown compound, given a list of infrared absorption frequencies.

Learning Activities

Read 12.8 Infrared Spectra of Some Common Functional Groups and do any associated exercises.

We must again emphasize that you need not memorize the characteristic absorptions given in this section. In all Chemistry 350 examinations, you will be provided with a table of characteristic absorptions to assist you in the interpretation of a given infrared spectrum.

Summary

In this unit, you examined two spectroscopic techniques—mass spectroscopy and infrared spectroscopy—used in the elucidation of molecular structure. We shall refer to these techniques throughout the remainder of the course.