Course Evaluation Last semester the average response rate for the on-line form was 54% as compared to about 80% for the old paper forms. Let’s do better ! https:/coursevals.drew.edu/ We are going to do the course evaluation in class on Fri., Dec., 5, 2014 Please bring your laptop. Thanks !

Structure Determination Chemistry 250-02 Organic Chemistry I Fall, 2014 Day 36 12/1/14 Chapter 12 Structure Determination Infrared Spectroscopy (IR) Chem Activity L-01 Mass Spectrometry (MS) Chem Activity L-02

Great Spectroscopy Sites http://www.chem.ucla.edu/~webspectra/ http://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

Substitution vs. Elimination How can you tell which reaction occurs ?

The Electromagnetic Spectrum 25

The Electromagnetic Spectrum

Molecular Motions ν ≈ k/m # IR bands = 3n – 6 for n non co-linear atoms Peak Intensity related to Δ in dipole moment

The Infrared Spectrum ȳ (cm-1) = 10,000/ λ in μm

Functional Groups in the IR

Chem Act L-01 The Infrared Spectrum

Model 5

Model 5

Model 5

Model 5 1715 cm-1

Exercise 1 # 1

Exercise 1 # 1 R-NH2 3350 asym 3250 sym

Exercise 1 # 2

Exercise 1 # 2 3340 broad

Exercise 1 # 3

Exercise 1 # 3 3300 H-CΞ stretch 2100 CΞC 630 H-CΞ bend

Exercise 1 # 4

Exercise 1 # 4 3050 H-C=C sp2 C-H 1660 C=C weak 1690 C=O unsat

Exercise 1 # 5

Exercise 1 # 5 1125 C-O

Alkanes, Alkenes, Alkynes

Infrared Spectra - Hydrocarbons

Cyclohexane and Cyclohexene which is which?

Benzenoid Aromatics =C-H ca. 3030 cm-1 C=C ca. 1600 cm-1

Alcohols

Carbonyls C=O

What functionality ?

mono substituted

Problems 12. 34, 12. 35 How can you distinguish by IR Problems 12.34, 12.35 How can you distinguish by IR ? What distinguishing peaks in the IR ?

ChemAct S-16 Exercise Part A

Problem 12.41 page 453

Problem 12.42 page 453

What are the possible products?

What are the possible products?

What is the best way to prepare the ether ?

Chemistry 250-02 Organic Chemistry I Fall, 2014 Day 37 12/3/14 Chemistry 250-02 Organic Chemistry I Fall, 2014 Day 37 12/3/14 Chapter 12 Chem Activity L2 Structure Determination Q: How do we know the structure of an organic molecule ? A: MS, IR, UV-Vis, NMR !

epibatidine ↓

A Mass Spectrometer

History of Mass Spectrometry Mass Spectrum of Neon Showing Major and Minor Natural Isotopes 20Ne 90.48% rel. int J.J. Thompson, the discoverer of the electron in 1912, showed there are 2 neon isotopes that are deflected differently by a magnet. His student, F. Aston, designed more elaborate instruments. 22Ne 9.25% 21Ne 0.27% m/z

Electron Impact (EI) Mass Spectrometry ≈ MW !

base peak parent peak fragment analyte none of these In mass spectrometry, what is the term used to describe the ion that results from the ejection of one electron from a molecule? base peak parent peak fragment analyte none of these

What EI Mass Spectra Look Like

What quantity is detected in mass spectrometry? the energy of a molecule the number of electrons ejected from a molecule the number of ions of a particular mass to charge (m/z) ratio the number of electrons needed to ionize a molecule the number of hydrogen atoms in a molecule

Chem Activity L2 Mass Spectrometry Do Model 1 - 4 page 270-271

Peak at m/z > MW ?!

Problem 12.1 Given the EI MS of Testosterone What is the molecular formula ?

Problem 12.1 Given the EI MS of Testosterone What is the molecular formula ? C19H28O2

Which of the following reasons explains why some peaks are larger than others in a mass spectrum? The larger peaks represent fragments that are more stable. The larger peaks represent fragments that are less stable. Cations tend to give larger peaks than radical cations. Radical cations tend to give larger peaks than cations. None of these

Problem 12.41 page 453

Problem 12.42 page 453

High Resolution MS Masses measured to 1 part in 20,000 ! Masses measured to 1 part in 20,000 ! A molecule with nominal mass of 44 could be C3H8, C2H4O, CO2, or CN2H4. If a more exact mass is, for example 44.029, pick the correct structure from: C3H8 C2H4O CO2 CN2H4 44.06260 44.02620 43.98983 44.03740

Mass Spectra 1-Bromopropane CH3-CH=CH2 + HBr in air  CH3-CH2-CH3

1-bromopropane  propene  2-bromopropane 1-bromopropane  propane  2-bromopropane 43 CH3CH2CH2-Br (CH3)2CH+

Mass Spectrometry The presence of Bromine in a compound The two (2) principal Bromine Isotopes in nature are Br-79 and Br-81 (2 additional Neutrons in Br-81) The relative abundance ratio of 79Br to 81Br is 100 : 97.1 or 50.5 : 49.5 or  1 : 1 Molecules containing a single Bromine atom will also show two molecular ion peaks one for Br-79 (M+) and one for Br-81 M+2). Based on the natural abundance ratio of 100 / 97.1 (about 1:1), the relative intensity of the Br-79 peak will be about the same as the Br-81 peak. Note: Fluorine exists in nature principally as a single isotope - 19F9 Therefore, single Molecular Ion peak (assuming no other Halogens present.

bromotoluene  Methylbenzene  benzylbromide

Mass Spectra 1- and 2-Chloropropane 43 CH3CH2CH2-Cl

Mass Spectrometry The Presence of Chlorine in a Compound The two (2) principal Chlorine Isotopes in nature are Cl-35 and Cl-37 (2 additional Neutrons in Cl-37) The relative abundance ratio of 35Cl to 37Cl is 100 : 32.6 or 75.8 : 24.2 or  3 : 1 Therefore, a Molecule containing a single Chlorine atom will show two Mass Spectrum Molecular Ion peaks, one for Cl-35 (M+) and one for Cl-37 (M+2) Note: M+2 denotes 2 more neutrons than M+ Based on the natural abundance ratio of 100 / 32.6 (about 3:1), the relative intensity (peak height) of the Cl-35 peak will be 3 times the intensity of the Cl-37 peak.

EI MS – Alkanes n-Hexane (C6H14) 57 41, 43 27, 29 71

Mass Spectra C5H12 pentane 2-methylbutane 2,2-dimethylpropane

EI MS 2,2-dimethylpropane is the parent ion detected ?

Problem 12.24 43 29 71 57 86

Worked Example 12.1 EI MS methylcyclohexane and ethylcyclopentane

Mass Spectra - Alkenes

Mass Spectra - Alkenes

Problem 12.2 EI MS 2-methylpent-2-ene and hex-2-ene

EI Mass Spectra - Alkynes 1-Pentyne

 2-bromobutane  CH3CH2CH=CH2 CH3CH=CHCH3

Mass Spectra - Ketones

EI MS 2- and 3-Pentanone CH3-CH2-CH2-CO-CH3 CH3-CH2-CO-CH2-CH3

Mass Spectra - Alcohols

1-propanol  propene  2-propanol CH3-CH2-CH2-OH CH3-CH(OH)-CH3

EI MS 1-Butanol

EI MS 2-Hexanol

Problem 12.2 (worked)

MALDI TOF MS of the Protein Insulin and an Enzyme Lysozyme MW 14,307.7578

GC-MS Gas Chromatography - Mass Spectrometry

MS in Natural Products

MS and C60 !