Chem 3500

Dr. L. Dawe

Fall 2010

September 8, 2010 Lecture 1

1. Molecular Formulas and What Can Be Learned From Them 1.1 Elemental Analysis 1.2 Molecular Formulas 1.3 Index of Hydrogen Deficiency 1.4 The Rule of Thirteen

Chem 3500

Dr. L. Dawe

Fall 2010

References and Additional Resources

Our course textbook: Pavia, D.L., Lampman, G.M., Kriz, G.S., Vyvyan, J.R. Introduction to Spectroscopy. Sections 1.1-1.5 Others: Crews, P., Rodriguez, J., Jaspars, M. Organic Structural Analysis. Sections 1.1-1.4. Physical characteristics of compounds (from Dalton Transactions Guidelines for Layout of Articles for Submission A Royal Society of Chemistry Journal). http://www.rsc.org/Publishing/ReSourCe/AuthorGuidelines/ArticleLayo ut/sect3.asp Perkin Elmer Organic Elemental Analysis 2400 Series II CHNS/O Elemental Analyzer. http://las.perkinelmer.com/content/RelatedMaterials/Brochures/BRO_2 400SeriesIICHNSOelementalAnalyzer.pdf

Chem 3500

Dr. L. Dawe

Fall 2010

What do I need to know before I report something new?

Physical characteristics of compounds Yield. Melting point. Optical rotation. Refractive index. Elemental analysis. UV absorptions. IR absorptions. NMR data. Mass spectrometry data.

Chem 3500

Dr. L. Dawe

Fall 2010

What do I need to know before I report something new?

Elemental Analysis: For identification purposes for new compounds, an accuracy to within 0.3% is expected, and in exceptional cases, to within 0.5% is required.

Chem 3500

Dr. L. Dawe

Fall 2010

What do I need to know before I report something new?

UV Spectroscopy

Chem 3500

Dr. L. Dawe

Fall 2010

What do I need to know before I report something new?

NMR

Chem 3500

Dr. L. Dawe

Fall 2010

What do I need to know before I report something new?

Mass Spectrometry

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

Steps towards the determination/confirmation of a molecular formula: 1. Qualitative elemental analysis 2. Quantitative elemental analysis 3. Molecular mass/weight determination

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

Steps towards the determination/confirmation of a molecular formula: 1. Qualitative elemental analysis: determines what types of elements are present.

Numerous methods are possible, many involve analysis by X-ray sources. MUN has a scanning electron microscope (SEM) equipped with an energy discriminated X-ray (EDX) system. www.mun.ca/creait/maf/ The surface of a sample is bombarded with electrons, core shells of the atoms are ionized, X-rays are produced consistent with transitions characteristic of each element.

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

Steps towards the determination/confirmation of a molecular formula: 2. Quantitative elemental analysis: determines how much of each element is present.

C,H,N,S can be detected by combustion analysis and detection of CO2, H2O, N2 (from reduction of NOx) and SO2 respectively. O can be detected by ignition in a hydrogen atmosphere (H2O is produced)

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

2NOx

N2(g) + xO2(g)

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

Recall your high school and/or C1010/C1050 combustion analysis problems: When 9.83 mg of an unknown compound containing only carbon, hydrogen and oxygen (CxHyOz) combusts fully in the presence of oxygen, 23.26 mg of CO2 and 9.52 mg of H2O are detected via gas chromatography. What is the empirical formula of the unknown?

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis in inorganic coordination chemistry: ReOCl(C17H23N5S2)

C17H25N5S2 + (NBu4)[ReOCl4]

ReOCl(C17H23N5S2)

Reference: Nguyen et al., Inorg. Chem., 2009, 48, 9356-9364

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis in inorganic coordination chemistry: ReOCl(C17H23N5S2)

ReOCl(C17H23N5S2)

Elemental analysis: Calcd for C17H23ClN5OReS2: C, 34.08; H, 3.87; N, 11.69; S, 10.70%. Found: C, 33.95; H, 3.59; N, 11.39; S, 11.01%.

Molecular Weight Calculator by Matthew Monroe. Available for download from: http://omics.pnl.gov/software/ MWCalculator.php

Chem 3500

Dr. L. Dawe

Fall 2010

1.1 Elemental Analysis

Steps towards the determination/confirmation of a molecular formula: 3. Molecular mass/weight determination: normally determined via mass spectrometry

Chem 3500

Dr. L. Dawe

Fall 2010

1.2 Molecular Formula

Can be determined, provided the empirical formula and molecular mass. Problem: The molecular mass of the unknown C7H14O2 was determined to be 260 g/mol. What is its molecular formula?

Chem 3500

Dr. L. Dawe

Fall 2010

1.3 Index of Hydrogen Deficiency

This is the number of bonds and/or rings a molecule contains. For molecules containing only carbon, hydrogen, monovalent halogens, nitrogen, and oxygen, the index of hydrogen deficiency (unsaturation index, U) can be calculated by: U = C + 1 - 0.5 * (X - N) where C = number of carbons, X = number of hydrogens and/or halogens, and N = number of nitrogens. Note that the presence of divalent elements like oxygen and sulfur does not effect the calculation of U.

Chem 3500

Dr. L. Dawe

Fall 2010

1.3 Index of Hydrogen Deficiency

Problem: Calculate the index of hydrogen deficiency for nicotine, C10H14N2. Is this consistent with its structure? U = C + 1 - 0.5 * (X - N)

N N

Chem 3500

Dr. L. Dawe

Fall 2010

1.3 Index of Hydrogen Deficiency

Problem: Calculate the index of hydrogen deficiency for chloral hydrate, C2H3Cl3O2. Is this consistent with its structure? U = C + 1 - 0.5 * (X - N)
Cl Cl HO Cl OH H

Chem 3500

Dr. L. Dawe

Fall 2010

1.4 The Rule of Thirteen

This is a useful method for generating a possible molecular formula, given the molecular mass.
M r = n+ 13 13

Where M = Molecular mass, n = whole number numerator, r = remainder, 13 = mass of one carbon + one hydrogen For a simple hydrocarbon, this leads to the base formula: CnHn+r

Chem 3500

Dr. L. Dawe

Fall 2010

1.4 The Rule of Thirteen

Another useful relationship relates the index of hydrogen deficiency (U) to the rule of thirteen:
( n r + 2) U= 2

Problem: Given a simple hydrocarbon with a molecular mass of 94 amu, propose a base formula, determine the index of hydrogen deficiency, and draw a possible structure.