Loading...

CHEM205: Spectroscopy

Unit 1: Mass Spectrometry   Mass spectrometry (MS) is an analytical technique that is used to determine the masses of particles for the elucidation of the chemical structures of molecules.  The technique has both qualitative and quantitative uses, including identifying unknown compounds, determining the isotopic composition of elements in a molecule, and revealing the structure of a compound by observing its fragmentation.

This unit begins with a general discussion of the theory and instrumentation of mass spectrometers.  A section on ionization and detection methods is included.  The unit continues with a discussion of isotopic distributions and fragmentation patterns of organic molecules.  This unit concludes with application of these principles for structure determination.

Unit 1 Time Advisory
This unit will take approximately 29 hours to complete.

☐    Subunit 1.1: 5.0 hours

☐    Subunit 1.2: 4.0 hours

☐    Subunit 1.3: 1.0 hour

☐    Subunit 1.4: 19.0 hours

☐    Sub-subunit 1.4.1: 1.0 hour

☐    Sub-subunit 1.4.2: 18.0 hours

☐    Reading: 8.0 hours

☐    Lecture: 0.5 hours

☐    Web Media: 2.0 hours

☐    Assignments: 2.5 hours

☐    Assessments: 5.0 hours

Unit1 Learning Outcomes
Upon successful completion of this unit, the student will be able to:

  • Identify the components of a mass spectrometer.
  • Discuss real-world applications of mass spectroscopy.
  • Describe different ionization and detection methods used in mass spectrometry.
  • Interpret both elemental and molecular mass spectra.
  • Explain fragmentation patterns and use them in structural determination.

1.1 The Mass Spectrometer   - Reading: William Reusch’s “Virtual Text of Organic Chemistry: Mass Spectrometry” Link: William Reusch’s “Virtual Text of Organic Chemistry: Mass Spectrometry”(HTML)
 
Instructions: Please read the entire webpage.  Spend time using the learning tools provided in the body of the text.  This material covers all of Unit 1. 
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Interactive Lab: OCHeM.com: Thomas Poon’s “Mass Spectrometer Simulator” Link: Web Media: OCHeM.com: Thomas Poon’s “Mass Spectrometer Simulator” (Shockwave)
     
    Instructions: Scroll down the list of “Shockwave Animations” to find a link entitled “Mass Spectrometer Simulator.”  Click on the link; it will launch an Adobe Shockwave application in a new window.  By clicking on various parts of the mass spectrometer, you will learn about each component.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: William Reusch’s “Virtual Text of Organic Chemistry: Mass Spectrometry: Practice Problems” Link: William Reusch’s “Virtual Text of Organic Chemistry: Mass Spectrometry: Practice Problems”(HTML)
     
    Instructions: Please scroll to the bottom of the page and work through the practice problems (Questions 1–8) found there.  This site is designed to require you to attempt the problems prior to obtaining the solutions from its answer key.  This material covers concepts from all of Unit 1. 
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.2 The Nature of Mass Spectra   - Reading: University of Leeds: Dr. Alison E. Ashcroft’s “An Introduction to Mass Spectrometry” Link: University of Leeds: Dr. Alison E. Ashcroft’s “An Introduction to Mass Spectrometry” (HTML)
 
Instructions: Please read the entire webpage.  This material covers the basics of mass spectrometry including its uses and analysis. 
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.3 Ionization and Detection Methods   - Reading: Connexions: Justin Law and Andrew R. Barron’s “Principles of Mass Spectrometry and Modern Applications” Link: Connexions: Justin Law and Andrew R. Barron’s “Principles of Mass Spectrometry and Modern Applications” (HTML or PDF)
 
Instructions:  Please read the entire webpage.  This material focuses on ionization techniques and detection methods (mass analyzers). You can also download this material in PDF version by clicking “Download” on the top right corner of the page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.4 Interpretation of Mass Spectra   1.4.1 Isotopes   - Reading: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Isotope Ratio Data” Link: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Isotope Ratio Data” (HTML)
 
Instructions: Click on the “Mass Spec” button on the left-hand side of the webpage, then click the link called “Common Elements in Organic Compounds” (Section III, E.1).  Please read the entire webpage.  This material presents isotopic information on elements commonly found in organic compounds, specifically C, H, N, O, Si, and S.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Bromine and Chlorine” Link: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Bromine and Chlorine” (HTML)
     
    Instructions: Click on the “Mass Spec” button on the left-hand side of the webpage, then click the link called “Bromine and Chlorine” (Section III, E.2).  Please read the entire webpage.  This material discusses the significance of the M+2 peak in mass spectra when bromine and/or chlorine are present in a compound.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.4.2 Fragment Patterns   - Reading: University of Illinois: Paul R. Young’s “Basic Mass Spectroscopy” Link: University of Illinois Paul R. Young’s “Basic Mass Spectroscopy” (HTML)
 
Instructions: Please read the material presented by following the links under “Section I: Introduction.”  This material covers some basic theory of mass spectrometry and focuses on the fragmentation patterns of functional groups.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Activity: University of Illinois: Paul R. Young’s “Basic Mass Spectroscopy” Link: University of Illinois: Paul R. Young’s “Basic Mass Spectroscopy” (HTML)
     
    Instructions: Please work through the analysis of compounds 1–5 by following the links under “Section II: Sample Mass Spectra.”
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Fragmentation Patterns for Organic Functional Groups” Link: Central Connecticut State University: Dr. Neil Glagovich’s “Mass Spectrometry: Fragmentation Patterns for Organic Functional Groups” (HTML)
     
    Instructions: Click on the “Mass Spec” button on the left-hand side of the webpage.  Scroll down to “Section IV: Fragmentation Patterns for Organic Functional Groups.”  Follow the links below each subsection (A–E) and peruse the material presented within them.  This material identifies the key spectral peaks and provides representative spectra for each organic functional group.  Subsection F presents a tabular summary of the key information covered.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Lecture: OCHeM.com: Thomas Poon’s “Mass Spectrometry” Link: OCHem.com: Thomas Poon’s “Mass Spectrometry” (QuickTime)
     
    Instructions: Scroll down the list of “PreLectures” to find a link entitled “Mass Spectrometry.”  Click on the link; it will launch a QuickTime application in a new window.  Watch the video (runtime = 32:52 minutes), which details fragmentation patterns and general trends in mass spectra.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Interactive Lab: Jean-Claude Bradley and Andrew Lang’s “Spectral Game” Link: Jean-Claude Bradley and Andrew Lang’s “Spectral Game” (HTML)
     
    Instructions: Please enter a username in the required field.  Note: You do not need to register and this does not need to be your actual name (i.e., student1).  Choose the format you prefer for your viewer and select EI for the mass spectroscopy game from the “Type” drop-down box.  A general video tutorial from the creators of the game can be found here (YouTube).  Please spend an ample amount of time using this game as a learning tool to increase your spectral analysis proficiency.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.   

  • Assessment: OCHeM.com: Thomas Poon’s “Mass Spectrometry Problems” Link: OCHeM.com: Thomas Poon’s “Mass Spectrometry Problems” (HTML or PDF)
     
    Instructions: Please work through these problems dealing with interpretation of mass spectra.  Then, click here for the answer key.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: The University of Arizona: Department of Chemistry’s “Introduction to Mass Spectrometry—Examples” Link: The University of Arizona: Department of Chemistry’s “Introduction to Mass Spectrometry—Examples” (HTML)
     
    Instructions: First use this page as a tutorial, reviewing the mass spectra for each type of functional group fragmentation.  Then take the quizzes for each of the functional groups.  There are 10 separate quizzes on this webpage.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.