Loading...

CHEM104: Organic Chemistry II

Unit 11: Spectroscopy   After you perform a reaction in a chemistry lab, how do you know whether it actually worked?  Spectroscopy is the answer!  Spectroscopy is the method by which chemists elucidate the structures of a molecule.  Proton NMR (also known as Hydrogen-1 Nuclear Magnetic Resonance (NMR) or 1H NMR) is by far the most powerful tool an organic chemist uses to study molecular structures, and is used on a daily basis in a synthetic laboratory.  However, proton NMR alone might not be able to distinguish between very similar molecules, such as hexadecylamine (C16H35N) and octadecylamine (C18H37N).  Therefore, chemists use other spectroscopy tools in conjunction with proton NMR.  Mass Spectrometry can easily discriminate between hexadecylamine and octadecylamine, for example.  IR spectroscopy can confirm the presence of the amino group (primary amine), and UV-VIs might be able to estimate the concentration of these molecules in solution.

Unit 11 Time Advisory
This unit will take you 16.25 hours to complete.

☐    Subunit 11.1: 0.5 hour

☐    Subunit 11.2: 4 hours
☐    Reading: 1 hour

☐    Web Media: 1 hour

☐    Assignment: 2 hours

☐    Subunit 11.3: 3 hours

☐    Subunit 11.4: 3 hours

☐    Subunit 11.5: 5.75 hours
☐    Sub-subunit 11.5.1: 4.25 hours

☐    Reading: 2 hours

☐    Web Media: 2.25 hours

☐    Sub-subunit 11.5.2: 1.5 hours

Unit11 Learning Outcomes
Upon successful completion of this unit, the student will be able to:
- Describe the principles behind mass spectrophotometry. - Recognize fragmentation patterns and isotope patterns in mass spectra. - Utilize mass spectra to identify unknown molecules. - Describe the principles behind UV-Vis spectrophotometry. - Interpret absorption spectra. - Understand how conjugation affects the line shape of UV-Vis spectra. - Describe the principles behind infrared spectroscopy. - Recognize and assign specific bands of absorption to functional groups. - Utilize IR spectra to identify the structure of an unknown compound. - Describe the principles behind nuclear magnetic resonance spectroscopy. - Know which isotopes have active NMR nuclei. - Describe the concepts of "chemical shifts," "equivalent protons/carbons," and "coupling constants." - Utilize the chemical shift and "splitting patterns" to derive the structure of an unknown molecule using proton-NMR, carbon-NMR, or both.

11.1 Introduction to Spectroscopy   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Introduction to Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Introduction to Spectroscopy” (HTML)

 Instructions:  Please click on the link above, and read the entire
section, “Introduction to Spectroscopy,”on the webpage.  The various
spectroscopy methods covered in this unit have been and are still
being used today by chemists and other scientists to determine the
structural formulas of the vast number of organic compounds
discovered.  Chemists primarily use laboratory spectroscopic
experiments to provide credible evidence for the structures of
organic compounds.  The major spectroscopic techniques will be
demonstrated in the following topics: mass spectrometry,
ultraviolet-Visible (UV-Vis) spectroscopy, infrared spectroscopy,
and nuclear magnetic resonance (NMR) spectroscopy.  This resource
covers the topics outlined for subunits 11.2-11.5.  

 This reading should take approximately 30 minutes to complete.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.                

11.2 Mass Spectrometry   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Mass Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Mass Spectrometry” (HTML)

 Instructions: Please click on the link above, and read the entire
chapter on the webpage.  A mass spectrometer measures the
characteristics of individual molecules.  To accomplish this, a
molecule is first broken down into its component ions.  Then, the
mass spectrometer used external electric and magnetic fields to move
and orient the ions for structural analysis.  The characteristics of
a mass spectra, isotopes, fragmentation patterns, and high
resolution spectra will be demonstrated.  

 Reading and taking notes should take approximately 1 hour to
complete.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.   
  • Assessment: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Practice Problems" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Practice Problems" (HTML)

    Instructions: Please click on the link above.  Choose a practice problem from the drop down menu (at the bottom of the page). Complete each of the eight problems.  These problems will give you some practice with determining the molecular formula of organic molecules using mass spectrometry.

    You should dedicate approximately 2 hours to practicing these problem sets.
              
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above. 

  • Web Media: YouTube: Freelanceteach’s “Introduction to Mass Spectrometry (1)" Link: YouTube: Freelanceteach’s “Introduction to Mass Spectrometry (1)"  (YouTube)  
     
    Instructions:  Watch this video (#1) in its entirety (10:48 minutes).  The video gives an introduction to mass spectrometry with a focus on the molecular/parent ion / base peak.
     
    Viewing this lecture and pausing to take notes should take approximately 15 minutes to complete.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above. 

  • Web Media: YouTube: Freelanceteach’s “Introduction to Mass Spectrometry (2);” “Introduction to Mass Spectrometry (3);” “Introduction to Mass Spectrometry (4);” “Introduction to Mass Spectrometry (5)” Links: YouTube: Freelanceteach’s “Introduction to Mass Spectrometry (2);” (YouTube) “Introduction to Mass Spectrometry (3);”(YouTube) “Introduction to Mass Spectrometry (4);” (YouTube) and “Introduction to Mass Spectrometry (5)” (YouTube)
     
    Instructions: Please note that these video lectures are optional.  For more detailed information about mass spectrometry, you may choose to click on the links above and watch lectures 2-5.  The run times for these videos range from 5-11 minutes.  This material is not required for successful completion of this course.
      
    Viewing these optional lectures should take approximately 45 minutes to complete.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpages above.

11.3 Ultraviolet-Visible (UV-Vis) Spectroscopy   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Ultraviolet-Visible Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Ultraviolet-Visible Spectroscopy” (HTML)

Instructions: Read the entire chapter on the webpage linked above.  UV radiation is invisible to the human eye and occurs next to the visible region of the electromagnetic spectrum, on the high energy side.  This high energy contributes to the incidence of cancer and other harmful effects of the sun’s UV rays.  UV-Visible spectroscopy is most useful in determining the concentration of a sample (Beer’s Law) and in determining if conjugation is present in the molecule.  The Electromagnetic Spectrum, UV-Vis Absorption Spectra, and the importance of conjugation will be demonstrated.
 
This reading should take approximately 2 hours to complete.

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.  
  • Lecture: Khan Academy’s “Spectrophotometry Introduction” and “Spectrophotometry Example” Links: Khan Academy’s “Spectrophotometry Introduction” (YouTube) and “Spectrophotometry Example” (YouTube)

    Instructions: Please click on the links above, and watch the two video lectures to reinforce the material covered in the reading. 

    Viewing these lectures and pausing to take notes should take approximately 45 minutes to complete.

    Terms of Use: These videos are licensed under a Creative Commons Attribution-NonCommercial-NoDerives United States License 3.0.  They are attributed to the Khan Academy. 

  • Web Media: YouTube: Freelanceteach’s “Electrophilic Attack on Conjugated Dienes" Link: YouTube: Freelanceteach’s “Electrophilic Attack on Conjugated Dienes" (YouTube)
     
    Instructions:  Please click on the link above, and watch this video (#11) in its entirety (10:48 minutes).  The video covers the effect of conjugation on UV-Vis (ultraviolet-visible) spectroscopy.  The conjugated system demonstrated is the electrophilic attack on conjugated dienes (1,2- and 1,4-addition) covered previously in Unit 3.  This resource also covers subunit 11.2.

    Viewing this lecture and pausing to take notes should take approximately 15 minutes to complete.
     
    Terms of Use: Please respect the copyright and terms of use on the webpage displayed above.

11.4 Infrared Spectroscopy   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Infrared Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Infrared Spectroscopy” (HTML)

[](http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/MassSpec/masspec1.htm#ms1)  
 Instructions: Read the entire chapter linked above.  While
ultraviolet radiation (covered in Subunit 11.3) occurs next to the
visible region of the electromagnetic spectrum on the high energy
side, infrared radiation occurs on the low energy side.  The lower
energy infrared radiation produces harmless heat energy for warmth.
 In Infrared Spectroscopy, the characteristic absorption vibrational
and group frequencies of functional groups aid in the identification
of organic compounds.   
    
 Reading and taking notes should take approximately 1 hour to
complete.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.                
  • Web Media: YouTube: Royal Society of Chemistry’s "Infra-Red Spectroscopy (IR)" Link: YouTube: Royal Society of Chemistry’s "Infra-Red Spectroscopy (IR)" (YouTube)
     
    Instructions:  Please click on the link above, and watch this video in its entirety (6:32 minutes). 
     
    Viewing this lecture and pausing to take notes should take approximately 15 minutes to complete.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above. 

  • Web Media: YouTube: Freelanceteach’s “Infrared (IR) Spectroscopy Problems (1)" Link: YouTube: Freelanceteach’s “Infrared (IR) Spectroscopy Problems (1)" (YouTube)
     
    Instructions: Please click on the link above, and watch this video (#1) in its entirety (about 10:59 minutes).  The video will give you some practice using IR spectroscopy to determine the presence of a specific functional group in an organic molecule.
     
    Viewing this lecture and pausing to take notes should take approximately 15 minutes to complete.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Web Media: YouTube: Freelanceteach’s “Infrared (IR) Spectroscopy Problems (2)” and “Infrared (IR) Spectroscopy Problems (3)”  Links: YouTube: Freelanceteach’s “Infrared (IR) Spectroscopy Problems (2)” (YouTube) and “Infrared (IR) Spectroscopy Problems (3)” (YouTube)
     
    Instructions: Please note that these video lectures are optional.  For more practice using infrared spectroscopy, you may choose to click on the links above and watch lecture 2 (10:38 minutes) and lecture 3 (4:19 minutes).  This material is not required for successful completion of the course.
     
    Viewing these optional lectures should take approximately 30 minutes to complete.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpages above.

  • Assessment: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Four Spectroscopy Problems" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Four Spectroscopy Problems" (HTML)

    Instructions: Please click on the link above, and work through the four problems at the bottom of the page.  Each problem presents an unknown compound along with their respective infrared and mass spectra.  You will use the given infrared and mass spectra to determine the structure of the unknown.  This resource covers the topics outlined in subunits 11.2-11.4.
     
    You should dedicate approximately 1 hour to practicing these problem sets.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

11.5 Nuclear Magnetic Resonance (NMR) Spectroscopy   11.5.1 Proton (1H) NMR   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Proton NMR Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Proton NMR Spectroscopy” (HTML)

Instructions: Read the entire chapter on the webpage linked above.  Nuclear Magnetic Resonance Spectroscopy, or NMR for short, is one of the most useful techniques used to determine the structure of organic compounds.  Unlike the other spectroscopic methods, only NRM can stand alone for the complete analysis of a sample and identification of the structure.  NMR makes use of the chemical shifts of protons in a molecule.  The presence of equivalent and nonequivalent protons, splitting and coupling of nonequivalent protons, and coupling constants are assessed to make an identification of the compound.
 
Reading and taking notes should take approximately 2 hours to complete.

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.      

11.5.2 Carbon (13C) NMR   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: “Carbon NMR Spectroscopy" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry:Carbon NMR Spectroscopy” (HTML)

 Instructions: Read the entire section titled “Carbon NMR
Spectroscopy” on the webpage linked above.  The shortcoming of
proton NMR spectroscopy is that when there is a lack of C-H bonds in
significant parts of a molecule, there are no protons for proton
chemical shift analysis.  In these cases, Carbon NMR can be useful
for spectral analysis via the analysis of equivalent and
nonequivalent carbon atoms. This resource covers sub-subunits 11.5.1
and 11.5.2.  
    
 This reading should take approximately 30 minutes to complete.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above. 
  • Assessment: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Practice Problems" Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: "Practice Problems" (HTML)
     
    Instructions: Please click on the link above, and scroll down to the bottom of the webpage.  Choose a practice problem from the drop down menu, and practice on the topic you need.  Work through the problems on proton NMR to get some practice with ‘equivalent’ hydrogen and carbon groups, ‘spin-spin coupling,’ and interpreting proton NMR spectra in general.  This resource coversthe topics outlined in sub-subunits 11.5.1 and 11.5.2.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.