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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

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

slide2

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

course material
Course material
  • http: // www.chem.queensu.ca/FACILITIES/NMR/nmr/chem805/
  • http: // www.chem.queensu.ca/ FACILITIES/NMR/nmr /Chem806/
reference books
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
reference books5
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.
index
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

index7
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

index8
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

index9
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

index10
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

index11
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

index12
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

index13
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

index14
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

index15
Index
  • Infrared Spectroscopy –IR
    • Interpretation of spectra
      • Nitrogen Compounds AmidesAmines, Amine salt, Amino AcidNitriles, iminesNitro
      • Sulfur CompoundsThiolsSulfidesSulfoxides and sulfones
    • Organometallic

Index

INTRO

introduction structure determination
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

characteristics of different spectrometric methods
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

electromagnetic spectrum
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

relationships
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

time scale for structural techniques
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

determination of structure
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

functional groups unsaturated
Functional groups: Unsaturated

Benzene

Alkene

Alkyne

Cumulenes

Pyridine

Imine

Nitrile

Diazo

Isonitrile

Oxime

Azide

Cyanamide

Index

functional groups
Functional groups

Alcohol

Thiol

Amine

Halides (F, Cl, Br, I)

Ether

Thioether

Peroxide

Disulfide

Hydrazine

N-Oxide

Index

functional groups carbonyl
Functional groups: carbonyl

Aldehyde

Ketone

Acid

Ester

Amide

Acid derivatives (F, Cl, Br, I)

Anhydride

Imide

Index

functional groups carbonyl25
Functional groups: carbonyl

Carbonate

Thiocarbonate

Guanidinium

Thioguanidinium

Urea

Carbamate

Thiocarbamate

Index

functional groups heteroaromatic other
Functional groups: heteroaromatic, & other

Nitro : -NO2

Nitroso : -NO

Where Z = O, NH, S

Sulfoxide

Sulfone

Index