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Chem-805 Basic course on Identification of organic and inorganic compounds by spectroscopy

Chem-805 Basic course on Identification of organic and inorganic compounds by spectroscopy. Mass Spectrometry NMR Infrared. Given by: Françoise Sauriol (sauriolf@chem.queensu.ca) - CHE-108, phone: 32260 Chemistry Dept., Queen's University. Summary: 6 weeks lecture (3 hrs / week)

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Chem-805 Basic course on Identification of organic and inorganic compounds by spectroscopy

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  1. Chem-805Basic course onIdentification of organic and inorganic compounds by spectroscopy Mass Spectrometry NMR Infrared Given by: Françoise Sauriol (sauriolf@chem.queensu.ca) - CHE-108, phone: 32260 Chemistry Dept., Queen's University

  2. Summary: 6 weeks lecture (3 hrs / week) This course will teach the organic and organometallic chemist how to identify relatively simple compounds using Mass Spectrometry (MS), Nuclear Magnetic Resonance (NMR) and Infrared (IR) techniques. The focus is on using the various techniquesin a practical way and therefore will not discuss in details the theoretical aspects behind the various techniques. Index

  3. Course material • http: // www.chem.queensu.ca/FACILITIES/NMR/nmr/chem805/ • http: // www.chem.queensu.ca/ FACILITIES/NMR/nmr /Chem806/

  4. Reference books • Robert M. Silverstein and Francis X. Webster, "Spectrometric Identification of Organic Compounds", John Wiley & Sins, inc., sixth edition (or later). • Joseph B. Lambert, Herbert F. Shurvel, David A. Lightner, R. Graham Cooks, “ Organic Structural Spectrocopy” , Prentice Hall inc., 1998. • Harald Günther, “NMR Spectroscopy, Basic principles, concepts, and applications in chemistry”, second edition, John Wiley & Sins, inc., 1995. • Jeremy K.M. Sanders, Brian K. Hunter, “Modern NMR Spectroscopy, A Guide for Chemists”, Oxford University Press, 1987

  5. Reference books • Phillip Crews, Jaime Rofriguez, Marcel Jaspars, “Organic Structure Analysis”, Oxford University Press, 1998. • Tetrahedron Organic Chemistry Series Volume 19, Thimothy D.W. Claridge, “ High-Rosolution NMR techniques in Organic Chemistry” , Pergamon, 1999.

  6. Index • Mass Spectrometry –MS • InstrumentationMSResolution (low and high)Ionization techniques • Determination of the Molecular formulaIsotopic composition (M+1) (M+2)... PeaksMolecular formula vs Index of Hydrogen deficiency (insaturation)High Resolution Hydrogen deficiencyIonization techniques (IE, CI, FAB..)Separation of charged particulesDetectionOrganometallic compoundsIsotope patternmetastable ion Index

  7. Index • Fragmentation rules in MS : Illustrated with different chemical classesHydrocarbons (alkanes, Alkenes, Aromatics)Oxygen containing compoundsNitrogen containing compoundsSulfur containing compoundsHalogens containing compounds • Mass Spectrometry of Organometallicsisotope patternsdoubly charged ionsFragmentationMigration of H, X and Alkyl groupsMcLafferty rearrangementInfluence of operating conditions on MSMetal Carbonyls Index

  8. Index • NMR Nuclear Magnetic Resonance Spectroscopy • Instrumentation and Basic conceptsBasic conceptsField Dependance of a spectraMultinuclear NMRFree Induction DecayPulse angleRelaxationLab Frame vs Rotating FrameDigitalizationPulse NMR spectrometerAbsolute and Relative Chemical shiftParameters in NMR Index

  9. Index • Proton NMR basics • Chemical Shift(d)Inductive effectAnisotropyElectronic effectProtons on heteroatoms (exchangeability) Chemical Shift and Coupling • Coupling Constants (J)The sign of couplingGeminal coupling (2J)Vicinal coupling (3J)Long range coupling (4J, 5J)Spin system: Pople NotationSecond Order spectra • Organometallics Index

  10. Index • Proton NMR Symmetry • Chemical Shift Equivalence • Magnetic Equivalence • Chiral centers • Pople Notation • Virtual Coupling • Calculating Shifts in Proton NMR • Proton and Heteronuclear NMR • Coupling of protons with other nuclei (13C, 19F, 31P, 2H, 195Pt, ...) • Other nuclei coupled to proton Index

  11. Index • Carbon-13 NMR • NOE and Decoupling proton • C-13 ShiftsAlkanesAlkenesAromaticsCarbonyls • Couplings with Carbon Nuclei 1JCH, 2JCH, 3JCHCoupling with other nuclei • NMR of N-15, Fluorine-19, Silicon-29 Nuclei • Conformational exchangeKeto-Enol interconversionRestricted RotationRing Interconversion Index

  12. Index • NMR and Organometallic compounds • Spin ½ nuclei • Quadrupolar Nuclei • Chemical Shift • Symmetry • Proton NMR and other Nuclei in Organometallics • Chemical shift of C-13 • Chemical Shift of F-19 • Chemical Shift of P-31 • Effect of coupling with Exotic spin ½ Nuclei • Coupling with Quadrupolar Nuclei • Si-29 NMR • Coupling In General (1J, 2J, 3J) • Multinuclear Approach • Dynamic NMR • Paramagnetic compounds Index

  13. Index • More specialized topics in 1D-NMR • Relaxation • Molecular Motion • Dipole Relaxation • Quadrupolar Relaxation • Inversion Recovery: Measure T1 • Spin-Spin Relaxation T2 • Spin Decoupling • Homonuclear decoupling • Heteronuclear Decoupling • NOE • Multiplicity detection • APT • INEPT • DEPT Index

  14. Index • Infrared Spectroscopy –IR • Introduction • Theory • Hydrogen Bonding • Instrumentation • Interpretation of spectra • Alkanes, Alkenes, Alkynes, Aromatics • Oxygen compounds Alcohols and phenolsEtherKetones, Aldehydes, Acids, Esters Index

  15. Index • Infrared Spectroscopy –IR • Interpretation of spectra • Nitrogen Compounds AmidesAmines, Amine salt, Amino AcidNitriles, iminesNitro • Sulfur CompoundsThiolsSulfidesSulfoxides and sulfones • Organometallic Index INTRO

  16. Introduction: Structure Determination • Need information on: • Molecular Formula • Functional groups • Carbon Connectivity • Position of substitution on the carbon framework • Stereochemical properties including Dynamic and static aspects. Index

  17. Characteristics of different Spectrometric methods 1H-NMR 13C-NMR MS IR Scale 0-15 ppm 1-220 ppm 50-4000 amu 400-4000 cm-1 Sample 1-2 mg 10-20 mg < 1 mg < 1 mg Molecular formula Partial Partial Yes No Functional group ~ yes ~ yes limited Yes yes yes yes Very limited Substructure yes yes No Very limited C-Connection Stereochem. & regiostereo-chemistry yes yes No Very limited

  18. Electromagnetic spectrum E kJ/mol 105 103 101 10-1 10-3 10-5 10-7 l cm 10-8 10-6 10-4 10-2 1 102 104 Radio wave: Nuclear Spin transition UV: Electron. transition IR: vibration g Rays X-Rays Microwave: rotation motion UV Visible 200 nm 400 nm Blue 800 nm Red n, cm -1 10000 1000 100 Near IR Middle IR Far IR 1 10 100 l, m Index

  19. Relationships Photon energy: e =h n=h c /l Energy per Mol: E = N h c /l Where: h =Plank’s constant = 1.58 10-37 kcal sec = 6.63 10-34 J sec c = 3 1010 cm/sec N = Avogadro’s Number = 6.023 1023 l = Wavelength (cm) Energy per Mol: E = 1.20 10-2/l (cm) kJ/mol 2.86 10-3 /l (cm) kcal/mol Index

  20. Time Scale for structural techniques Technique Approximate time scale (seconds) Electron Diffraction 10-20 Neutron Diffraction 10-18 X-Ray Diffraction 10-18 UV (ultraviolet) 10-15 Visible 10-14 IR (Infra Red) / Raman 10-13 Electron Spin Resonance 10-4 – 10-8 Nuclear Spin Resonance 10-1 – 10-9 Quadrupole Resonance 10-1 – 10-8 Experimental separationof isomers > 102

  21. Determination of structure • First priority:NMR • Provides info on C=O groups • Aromatic / olefinic • Aliphatic • Presence of oxygen (alcohol / ether ..) • Second priority : MS • Help determining molecular formula • Atomic composition • Fragmentation pattern can also help … • Third priority: IR • Identify Functional groups Index

  22. Functional groups: Unsaturated Benzene Alkene Alkyne Cumulenes Pyridine Imine Nitrile Diazo Isonitrile Oxime Azide Cyanamide Index

  23. Functional groups Alcohol Thiol Amine Halides (F, Cl, Br, I) Ether Thioether Peroxide Disulfide Hydrazine N-Oxide Index

  24. Functional groups: carbonyl Aldehyde Ketone Acid Ester Amide Acid derivatives (F, Cl, Br, I) Anhydride Imide Index

  25. Functional groups: carbonyl Carbonate Thiocarbonate Guanidinium Thioguanidinium Urea Carbamate Thiocarbamate Index

  26. Functional groups: heteroaromatic, & other Nitro : -NO2 Nitroso : -NO Where Z = O, NH, S Sulfoxide Sulfone Index

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