Organic
Spectroscopy
Chem 744 / 754
Spring 2013
Gregory R. Cook
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
Web Page
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cook.chem.ndsu.nodak.edu
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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Resources
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Books on reserve in the Library
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Introduction to Spectroscopy 3rd Ed., Pavia, Lampman, Kriz; Saunders Publishing, 2001.
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Spectrometric Identification of Organic Compounds 5th Ed., Silverstein, Bassler,
Morrill; Wiley, 1991.
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Basic one- and two-dimensional NMR Spectroscopy, Horst, Weinheim, 2005.
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NMR - from spectra to structures: an experimental approach, Mitchell and Costisella,
Springer, 2004.
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Structure elucidation by modern NMR: A workbook, Duddeck, Dietrich, Toth,
Springer, 1998.
Other References and Texts
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Organic Structure Analysis, Crews, Rodríguez, Jaspars; Oxford Press, 1998
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Spectrometric Identification of Organic Compounds 6th Ed., Silverstein, Bassler,
Morrill; Wiley, 1998.
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ABCs of FT-NMR, Roberts, University Science Books, 2000.
©2013 Gregory R. Cook, NDSU
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744 Course Information
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Introduction
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This course is designed to provide a theoretical and
practical working knowledge of modern
spectroscopic techniques as applied to the elucidation
of the structure of organic compounds.
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Mass spectroscopy, infrared spectroscopy, and NMR
spectroscopy will be covered. If time permits, we will
discuss Raman and UV spectroscopy.
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You are expected to have a solid understanding of
physical organic chemistry and organic structure.
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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744 Course Information
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Introduction
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Grading
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Midterm exam (Jan 31) (25%)
Final exam (Feb 28) (50%)
Homework (25%)
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Grades will be assigned as follows (subject to change):
A - 85-100%
B - 70-84%
C - 57-69%
D - 45-56%
F - <45%
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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754 Course Information
‣
Introduction
‣
The lab course is designed to train users on the various
instruments for spectroscopic determination of organic
compounds and to interpret data.
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Users will run known and unknown samples on the GCMass Spec, Infrared spectrometer, and NMR
instruments.
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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754 Course Information
‣
Grading
‣
Grades will be assigned as follows:
‣
A - 90-100%
B - 80-89%
C - 70-79%
D - 60-69%
F - <60%.
‣
Grades are based upon two laboratory reports;
report on a known sample (40%)
report on an an unknown sample (60%)
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In analyzing the data obtained, the following approximate
percentages will be applied to the various spectroscopic
techniques.
Mass Spec - 20%, IR - 15%, NMR (1H, 13C, etc) - 65%.
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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754 Course Information
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Plan
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Training on the instruments by March 8.
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You will be provided with a known sample.You must
obtain all the data and analyze it. The first report is due
on April 1.
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When you turn in your report, you will be provided
with an unkown sample.
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The final report will be due on April 29.
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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754 Course Information
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Reports
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Reports should be typewritten in manuscript style.
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A good model to follow would be a paper on the
structure determination of a natural product found in J.
Nat. Prod. or J. Am. Chem. Soc.
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MS - Determine the m/e peak and m+1 and m+2 if present. Explain the fragmentation
patterns observed for as many peaks as possible. You should include the structure of the
fragments as well as the fragmentation pathway from which it arose.
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IR - Identify all functional groups in your molecule.
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1H
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13C
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2D NMR - Explain your analysis of the data as it pertains to your structure.
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
NMR - Assign all resonances to the protons on the structure. All coupling constants
should be calculated and splitting patterns explained.
NMR - Assign all resonances to the carbons on the structure. Advanced NMR
experiments may be necessary to correlate the peaks.
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Tentative Course Schedule
Date
Jan 8/10
Introduction and Basics of NMR Spectroscopy
Jan 15/17
NMR Spin Coupling and Multiplet Analysis
Jan 22/24
Multiplet Analysis and Multipulse NMR
Jan 29
NMR Stereochemistry
Jan 31
MIDTERM EXAM
Feb 5/7
NMR Practical Considerations and 2D NMR
Feb 12/14
Mass Spectrometry
Feb 19/21
Infrared Spectroscopy
Feb 26
UV Spectroscopy
Feb 28
FINAL EXAM
Week of Mar 4
Chem 754 - Make appointments with Dan Wanner and
John Bagu to be trained on the instruments. You will be
given a known sample to work with and analyze
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
Topic
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Structure
Determination
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
How to determine the structure of molecules?
‣ Probe physical properties
‣ Elemental Analysis
‣ atomic composition (relative ratios)
‣ empirical formula
‣ Mass Spectrometry
‣ molecular formula
‣ element identification (isotopes)
‣ connectivity
©2013 Gregory R. Cook, NDSU
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Mass Spectrometer
©2013 Gregory R. Cook, NDSU
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Electromagnetic Spectrum
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Ultraviolet - Visible Spectroscopy
‣ Electronic (UV-VIS) Spectroscopy
‣ energy to excite an electron to a higher
excited state
‣ More conjugation, lower energy
220 nm
258 nm
455 nm
©2013 Gregory R. Cook, NDSU
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Infrared Spectroscopy
‣ Vibrational (Infrared) Spectroscopy
‣ functional groups
©2013 Gregory R. Cook, NDSU
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Nuclear Magnetic Resonance Spectroscopy
‣ NMR probes the spin transitions of nuclei
‣ energy in the radio frequency range
‣ NMR provides a wealth of information about
structure
‣ Functional Groups
‣ Atom Connectivity
‣ Stereochemistry
‣ Higher Order Structure
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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Magnetic Resonance Imaging
‣ NMR is the basis for MRI
©2013 Gregory R. Cook, NDSU
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X-Ray Crystallography
‣ X-Ray Crystallography
‣ 3D positions of atoms
©2013 Gregory R. Cook, NDSU
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Empirical Formula from Elemental Analysis
C - 63.31%
H - 6.28%
Cl - 16.99%
N - 13.42%
Assume 100 g of analyte
% composition proportional to grams
Moles of C = 6.331 g / 12.011 g/mol = 5.27 / 0.48 = 11
Moles of H = 6.28 g / 1.008 g/mol = 6.23 / 0.48 = 13
Moles of Cl = 16.999 g / 35.453 g/mol = 0.48 / 0.48 = 1
Moles of N = 13.42 g / 14.007 g/mol = 0.96 / 0.48 = 2
Empirical Formula: C11H13ClN2
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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Units of Unsaturation
Empirical Formula: C11H13ClN2
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Degrees of unsaturation is the number of pi-bonds and/or
rings
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UN =
UN =
For saturated hydrocarbons: CnH2n+2
(2n+2) - #H - #X + #N every halogen replaces one H
2
(2*11+2) - 13 - 1 + 2
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
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every nitrogen adds one H
=6
H
Cl
N
N
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Molecular Formula from Mass
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Rule of 13
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M / 13 = n+r/13
where
CnHn+r
for example - take a molecule with a M=164
164 / 13 = 12 + 8/13
C12H20
UN =
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
therefore a MF would be C12H12+8 or
(2*12+2) - 20 - 0 + 0
2
=3
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Molecular Formula from Mass
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What if there are other atoms besides C and H?
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Subtract their mass equivalents of C and H from the
formula
for example - take a molecule with a M=164
C12H20
164 / 13 = 12 + 8/13
O = 16 equivalent to CH4
C12H20
C11H16O
Note: Be careful of invalid formulas
e.g. M=32
32/13 = 2 + 6/13
must have another atom:
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
CH4O
C2H8 impossible UN = -1
CH6N
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Identification of a Natural Product
‣ High Res. Mass Spectrometry
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210.0764 4.4% C11H13N2 Cl
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208.0769 15.5% C11H13N2 Cl
‣ UV Spectroscopy
217 nm and 250-280 nm indicates
pyridine ring
H
Cl
N
N
Epibatidine
J. Am. Chem. Soc. 1992, 112, 3475
Isolated from the Ecuadorian tree
frog - Epibatis Tricolor
‣ IR Spectroscopy
Analgesic activity 500 times
greater than morphine.
-1
1428 and 1112 cm suggests a pyridine ring
©2013 Gregory R. Cook, NDSU
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Proton NMR
H
Cl
N
N
Epibatidine
J. Am. Chem. Soc. 1992, 112, 3475
©2013 Gregory R. Cook, NDSU
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Carbon NMR
H
Cl
N
N
Epibatidine
J. Am. Chem. Soc. 1992, 112, 3475
©2013 Gregory R. Cook, NDSU
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Steps in Structure Elucidation
EA, MS, NMR
Molecular
Formula
Working
2D
structures
UN
NMR, IR, UV
examine
all isomers
Functional
Groups
determine best
possibilities
Pure
Compound
NMR
X-RAY
©2013 Gregory R. Cook, NDSU
Friday, January 4, 13
NMR, MS, IR, UV
Substructures
3D
structure
Total
Synthesis
Reasonable
3D
structure
NMR
model
Best 2D
structures
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