Organic Spectroscopy Chem 744 / 754 Spring 2013 Gregory R. Cook
Web Page cook.chem.ndsu.nodak.edu 2
Resources Books on reserve in the Library Introduction to Spectroscopy 3rd Ed., Pavia, Lampman, Kriz; Saunders Publishing, 2001. Spectrometric Identification of Organic Compounds 5th Ed., Silverstein, Bassler, Morrill; Wiley, 1991. Basic one- and two-dimensional NMR Spectroscopy, Horst, Weinheim, 2005. NMR - from spectra to structures: an experimental approach, Mitchell and Costisella, Springer, 2004. Structure elucidation by modern NMR: A workbook, Duddeck, Dietrich, Toth, Springer, 1998. Other References and Texts Organic Structure Analysis, Crews, Rodríguez, Jaspars; Oxford Press, 1998 Spectrometric Identification of Organic Compounds 6th Ed., Silverstein, Bassler, Morrill; Wiley, 1998. ABCs of FT-NMR, Roberts, University Science Books, 2000. 3
744 Course Information Introduction 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. Mass spectroscopy, infrared spectroscopy, and NMR spectroscopy will be covered. If time permits, we will discuss Raman and UV spectroscopy. You are expected to have a solid understanding of physical organic chemistry and organic structure. 4
744 Course Information Introduction Grading Midterm exam (Jan 31) (25%) Final exam (Feb 28) (50%) Homework (25%) Grades will be assigned as follows (subject to change): A - 85-100% B - 70-84% C - 57-69% D - 45-56% F - <45% 5
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. Users will run known and unknown samples on the GC- Mass Spec, Infrared spectrometer, and NMR instruments. 6
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%) In analyzing the data obtained, the following approximate percentages will be applied to the various spectroscopic techniques. Mass Spec - 20%, IR - 15%, NMR ( 1 H, 13 C, etc) - 65%. 7
754 Course Information Plan Training on the instruments by March 8. 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. When you turn in your report, you will be provided with an unkown sample. The final report will be due on April 29. 8
754 Course Information Reports Reports should be typewritten in manuscript style. 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. 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. IR - Identify all functional groups in your molecule. 1 H NMR - Assign all resonances to the protons on the structure. All coupling constants should be calculated and splitting patterns explained. 13 C NMR - Assign all resonances to the carbons on the structure. Advanced NMR experiments may be necessary to correlate the peaks. 2D NMR - Explain your analysis of the data as it pertains to your structure. 9
Tentative Course Schedule Date Jan 8/10 Jan 15/17 Jan 22/24 Jan 29 Jan 31 Feb 5/7 Feb 12/14 Feb 19/21 Feb 26 Feb 28 Week of Mar 4 Topic Introduction and Basics of NMR Spectroscopy NMR Spin Coupling and Multiplet Analysis Multiplet Analysis and Multipulse NMR NMR Stereochemistry MIDTERM EXAM NMR Practical Considerations and 2D NMR Mass Spectrometry Infrared Spectroscopy UV Spectroscopy FINAL EXAM 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 10
Structure Determination
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 12
Mass Spectrometer 13
Electromagnetic Spectrum 14
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 15
Infrared Spectroscopy Vibrational (Infrared) Spectroscopy functional groups 16
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 17
Magnetic Resonance Imaging NMR is the basis for MRI 18
X-Ray Crystallography X-Ray Crystallography 3D positions of atoms 19
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 20
Empirical Formula: C11H13ClN2 Units of Unsaturation Degrees of unsaturation is the number of pi-bonds and/or rings For saturated hydrocarbons: CnH2n+2 UN = (2n+2) - #H - #X + #N 2 every halogen replaces one H every nitrogen adds one H UN = (2*11+2) - 13-1 + 2 2 = 6 H N N Cl 21
Molecular Formula from Mass Rule of 13 M / 13 = n+r/13 where CnHn+r for example - take a molecule with a M=164 164 / 13 = 12 + 8/13 therefore a MF would be C12H12+8 or C12H20 UN = (2*12+2) - 20-0 + 0 2 = 3 22
Molecular Formula from Mass What if there are other atoms besides C and H? Subtract their mass equivalents of C and H from the formula for example - take a molecule with a M=164 164 / 13 = 12 + 8/13 C12H20 O = 16 equivalent to CH4 C12H20 C11H16O Note: Be careful of invalid formulas e.g. M=32 32/13 = 2 + 6/13 C2H8 impossible UN = -1 must have another atom: CH4O CH6N 23
Identification of a Natural Product High Res. Mass Spectrometry H N Cl 210.0764 4.4% C 11 H 13 N 2 37 Cl N 208.0769 15.5% C 11 H 13 N 2 35 Cl UV Spectroscopy 217 nm and 250-280 nm indicates pyridine ring IR Spectroscopy Epibatidine J. Am. Chem. Soc. 1992, 112, 3475 Isolated from the Ecuadorian tree frog - Epibatis Tricolor Analgesic activity 500 times greater than morphine. 1428 and 1112 cm -1 suggests a pyridine ring 24
Proton NMR H N N Cl Epibatidine J. Am. Chem. Soc. 1992, 112, 3475 25
Carbon NMR H N N Cl Epibatidine J. Am. Chem. Soc. 1992, 112, 3475 26
Steps in Structure Elucidation EA, MS, NMR Molecular Formula UN Working 2D structures Pure Compound NMR, IR, UV NMR Functional Groups Substructures examine all isomers determine best possibilities NMR, MS, IR, UV X-RAY 3D structure Total Synthesis Reasonable 3D structure NMR model Best 2D structures 27