Chapter 1 Introduction to Organic Analytical Chemistry

Introduction Chemistry of carbon Analytical Chemistry Application Case Study

Introduction

Organic Chemistry
Organic is the study of matter that contains ______ Organic chemists study the structure, function, synthesis, and identity of carbon compounds Useful in petroleum industry, pharmaceuticals, polymers

Analytical Chemistry
Analytical chemistry is the study of high precision measurement Find composition and identity of chemicals Forensics, quality control, medical tests

Scientific Method

Chemistry of Carbon

Basic Questions
Organic chemistry: What is it? The study of molecules containing carbon Why all this fuss about carbon? Carbon is unique in its ability to form stable chains and rings

Basic Questions
Why should I study organic chemistry? Broadly applicable to other fields: biochemistry, pharmaceuticals, biology, etc. Skills learned useful elsewhere: information organization, critical/analytical thinking, etc. How often should I study organic analytical chemistry? Monday, Tuesday, Wednesday, Thursday, Friday, Saturday, Sunday

CH3

CH3

Cholesterol

HO

Carbon compounds basis for life (as we know it)

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Properties of typical organic and inorganic compound

Property Bonding with molecule Forces between molecules Normal physical state Flammability Solubility in water Conductivity Rate of chemical reaction Organic compound Usually covalent Generally weak (Intermolecular force) Inorganic compound Often ionic Quite strong (Electrostatic force)

Position of Carbon

Gases, liquids or lowUsually highmelting-point solids. melting-point solids. Often flammable Insoluble Nonconductor Slow and complex Usually nonflammable Soluble Conductor Fast and simple

Information in the table

Basic

Importance of Carbon
for all life

C
Carbon 12.01

Atomic number Name of the element Elemental symbol Atomic mass (weight)

Form stable covalent bonds to other carbon atoms catenation Can form single, double, triple bonds Long carbon chain can be produced Will bond to many other element A huge number of chemicals are posibble

Naturally Occurred Organic Compounds

Name Of Organic Compounds Proteins Example : a) Enzymes b) Hormones Fats and Oils Example : a) Triglyceride b) Paraffin Oils c) Almond Oils Vitamins Example : A,B Complex, C, D, E and K Origin From animals Usage

Synthetic Organic Compounds

Items Examples
Poly (ethene), Perspex. Tranquilizer, Analgesic and Bactericide. Dichlorodiphenyl trichloroethane ( DDT ) Methylene blue

Usage
For packaging, plastic bags, as a substitute for glass. To treat tropical diseases such as Trypanosomiasis or Sleeping Illness and Malaria. To kill houseflies and other insects. Give colour to the material.

a) As a structural materials. b) As a biological catalyst and regulators. To store energy.

Plastics

From animals and vegetables

Medicines and Drugs Pesticides

From food

For healthy growth and functioning.

Dyes

Functional groups and Homologous Series

DEFINATION : Functional groups:

Classifying of Organic Compounds

is an atom or group of atom which determine the chemical and physical properties of an organic compound. Homologous Series: is a series of compounds where each member differs from the next member by a constant CH2-

Classifying compounds by functional group

Functional group Specific combination of atoms that gives a known type of behaviors Hydrocarbons Alkohols Acids Amines Ketones Aldehydes C and H only R - OH R - COOH R NH2 R ( C = O ) R R CHO
(C-C double bond) (C-C triple bond) (halogen) (hydroxyl) (alkoxy) (amino) (carbonyl) (carbonyl) (carboxyl) (carboxylalkonxy) (amide)

FUNCTIONAL GROUPS
are important for three reasons:
They are the units by which we divide organic compounds into classes. They are sites of chemical reaction; a particular functional group, in whatever compound it is found, undergoes the same types of chemical reactions. Functional groups serve as a basic for naming organic compounds.

HOMOLOGOUS SERIES General characteristic : All the member of a particular homologous series have: 1. the same general formula eg : CnH2n+1OH 2. Same functional group : same chemical reactions. Eg : all alcohols contain OH group. 3. each member differs from the next member by a constant CH2. 4. As the molecular size increase, the boiling points increase.

Alkane Nomenclature

Type of organic compound

Organic compound

Aliphatic Alicyclic

Aromatic

Saturated
24.2

Unsaturated

Aliphatic
OPEN chains of Carbon atoms. Unbranched or Branched Contain Single, Double or Triple bonds. Example: ethane (CH3CH3) ethene / ethylene (CH2=CH2) ethyne / acetylene ( HC CH )

Saturated
Compound that contains only single bond. Example: alkane

H H H H H H C H

H C H H
ethane

Aromatic
CLOSE rings of Carbon atoms.

H H

Contain a benzene ring. Example: Benzene

Unsaturated
Compound that contains multiple bond. Example: alkene, alkyne

Alicyclic
CLOSE rings of Carbon Atoms.

H
ethene

Rings form the shape of POLYGON (triangle, square, rectangle or etc). Example: Epoxide C C

HC

CH H

ethyne

Classification of isomers
Isomers

Structural isomers

C5H12

Structural isomers

Stereoisomers
n-pentane 2-methylbutane

Isomers are different compounds that have the same molecular formula.

2,2-dimethylpropane

Example

C6H14
CH3CH2CH2CH2CH2CH3 n-hexane

Stereoisomer
Compound with the same molecular formula and structural formula but with different arrangement of their bond in space.
cis-2-butene (CH3CH2)2CHCH3 3-Methylpentane trans-2-butene

(CH3CH2)2CHCH3 2-Methylpentane

H3C C C

CH3

H3C C C

(CH3)3CCH2CH3 2,2-Dimethylbutane 2,2-

(CH3)2CHCH(CH3)2 2,3-Dimethylbutane 2,3-

CH3

cis (large groups on same side)

trans (large groups on opposite sides)

Naming of organic compound according to IUPAC system.

Step 1) Find the longest continuous carbon chain and use the IUPAC name of the unbranched alkane as the basis. Add name of substituent as a prefix. Use base name with yl ending. Use replicating prefixes (di-, tri-, tetra-, etc.) according to the number of substituents attached to the main chain. Number the chain from the end nearest the substituent, and identify the carbon to which the substituent is attached by number. List substituents in alphabetical order.

Base Names
prefix Meth Eth Prop But Pent Hex Hept Oct Non Dec Length of Carbon 1 2 3 4 5 6 7 8 9 10

Step 2)

Step 3)

Step 4)

Example

Example

C6H14
CH3CH2CH2CH2CH2CH3 n-hexane

Longest C chain has 4 carbon used But All C and H with single bonds used Parent name : Butane ane

(CH3CH2)2CHCH3 2-Methylpentane

(CH3CH2)2CHCH3 3-Methylpentane

CH3 on 2nd Carbon methyl

2 methyl butane

(CH3)3CCH2CH3 2,2-Dimethylbutane 2,2-

(CH3)2CHCH(CH3)2 2,3-Dimethylbutane 2,3-

Type of Organic Reactions

General

Type of Reactions

Addition

Substitution

Elimination

Rearrangement

Specific Hydrogenation Esterification Oxidation Hydrolysis

Addition
Two substances react together to form a single substance. Addition of HBr to an alkene
Hydrogen bromide

Substitution
An atom or a group (leaving group) in a molecule is replaced by another atom or group (nucleophile / electrophile). SN2 reaction
Hydroxide ion (nucleophile)

(leaving group)

Ethene

Bromoethane

Bromobutane

Butanol

Bromide ion

Elimination
Removal of atoms or groups of atoms from a saturated molecule to form an unsaturated molecule. Dehydration of alcohol
H2SO4

Rearrangement
Migration of an atom, a group of atoms or a bond from one atom to another within molecule to form its isomer. Tautomerism of keto-enol
CH3C CH2 CH3CCH3 O Propanone

CH3CH2CH2CH2OH Butanol

CH3CH2CH=CH2 + H2O Butene

OH Propenol

Hydrogenation
Addition of hydrogen to a multiple bond to form a single bond substance. Hydrogenation of alkane
H C H Ethylene C H H + H HH Hydrogen
Pt

Specific Reaction
H C H

H H C

H H Ethane

Esterification
Acid-catalyzed ester formation between alcohol and carboxylic acid. Fischer esterification
O CH3COH + CH3CH2OH Ethanoic acid Ethanol
H2SO4 reflux

Oxidation
An increase in the number of bonds between carbon and oxygen and/or a decrease in the number of carbon-hydrogen bonds. Chlorination of methane

CH4 + Cl2
CH3COCH2CH3 + H2O Ethyl ethanoate Methane Chlorine

CH3Cl + HCl
Chloromethane Hydrogen chloride

Hydrolysis
Chemical process in which a molecule is split into two parts by the addition of a molecule of water.

The Importance of Organic Chemistry

Many areas rely on organic chemistry :
Biology and Biochemistry Petroleum

(CH3)3CBr + H2O tert-Butyl bromide

(CH3)3COH + HBr tert-Butyl alcohol Hydrogen bromide

Polymers Genetic Engineering Agriculture Pharmacology Consumer Products

Introduction to Chemical Analysis Analytical Chemistry

The Art and Science of Chemical Analysis Chemical analysis includes any aspect of the chemical characterization of a sample material. Analytical Chemistry?
Science of Chemical Measurements

Areas of Chemical Analysis and Questions They Answer

Quantitation:
How much of substance X is in the sample?

What do Chemical Analyst Do?

Analyst: Applies known measurement techniques to well defined compositional or characterization questions. Research Analytical Chemist

Detection:
Does the sample contain substance X?

Identification:
What is the identity of the substance in the sample?

Separation:
How can the species of interest be separated from the sample matrix for better quantitation and identification?

What do Chemical Analyst Do?

Senior Analyst: Develops new measurement methods on existing principles to solve new analysis problems.

What do Chemical Analyst Do?

Research Analytical Chemist: Creates and /or investigates novel techniques or principles for chemical measurements. or Conducts fundamental studies of chemical/physical phenomena underlying chemical measurements.

What is Analytical Science?

Analytical Chemistry provides the methods and tools needed for insight into our material world for answering four basic questions about a material sample? What? Where? How much? What arrangement, structure or form? Fresenius J. Anal. Chem. 343 (1992):812-813

Qualitative analysis is what. Quantitative analysis is how much.

Gary Christian, Analytical Chemistry,

6th Ed. (Wiley)

Table 1: Methods of Analysis

Qualitative Method Qualitative analysis: Is identification method established the chemical identity of species in the samples such analysis does not report the amount of substance Quantitative Method Quantitative analysis : determine the relative amount of these species or analyte, in numeral terms undertaken when the identity of the component is already known and when it is important to also know the quantities of these Example: Analysis of soil reported that potassium concentration present is at 342 ppm

An analysis involves several steps and operations which depend on: the particular problem your expertise the apparatus or equipment available. The analyst should be involved in every step.

Example: Identify the present of sugar in soft drink

Gary Christian, Analytical Chemistry, 6th Ed. (Wiley)

Fig. 1.1. Steps in an analysis

Classification of Analytical Methods

Classical Methods

Instrumental Methods

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Classical Methods
Analyte is separated from Sample by : precipitation, extraction or distillation. Qualitative analysis: The analyte is then treated with reagents that yield product that could be recognised by Colour, melting point, solubilities, odours etc. Example: Qualitative analysis of common ions ( Pb2+,Hg2+,Ag+) Quantitative analysis: Amount of Analyte can be determined by gravimetric and titrametric method

Instrumental Method

SPECTROSCOPIC INSTRUMENTS

Structural Features we can address Spectroscopically

Molecular weight Chemical Formula Functional groups Skeletal Connectivity, structural isomers Spatial-geometric arrangements, stereoisomerism, symmetry Presence and location of chromophores Chirality issues Some of these are more central than others. Sometimes we can stop when the answer is fit to purpose.

UV VIS Spectrophotometer

Atomic Absorption Spectroscopy (AAS)

FT IR Spectrometer

CHROMATOGRAPHIC INSTRUMENTS

Chromatographic Methods
What is Chromatography? Chromatography is one of the separation technique The main purpose of chromatography is to separate, to identify and to quantify the target sample in matrix

Gas Chromatography (GC)

High Performance Liquid Chromatography (HPLC)

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PLANAR CHROMATOGRAPHY

Thin Layer Chromatography (TLC)

How can the separation be carried out?

Comparison between Analytical Methods

Figure: (a) Diagram showing the separation of a mixture of component A and B by column elution chromatography. (b) The output of the signal detector at the various stages of elution in (a).

Different methods provide a range of precision, sensitivity, selectivity, and speed capabilities.

Gary Christian, Analytical Chemistry,

6th Ed. (Wiley)

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Biology

Chemistry

Physics

Geology A ALYTICAL CHEMISTRY Engineering

Case Study

Environmental Science Medicine

Agriculture

Social Science

Material Science

Deer Kill
Case Study # : Deer Kill Problem: Dead whitetail deer near pond in the Land Between the Lakes State Park in south central Kentucky. Chemist state veterinary diagnostic laboratory helped find the cause

Site Investigation
Careful visual observation of a two acre area around the site: Observation: grass around nearby powerpoles was wilted and discolored. Speculation: Herbicide used on grass. Ingredient: Arsenic in a variety of forms
CH3AsO(OH)2 very soluble in water.

Select Method
Association of Official Analytical Chemists (AOAC) Distillation of arsenic as arsine which is then determined by colorimetric measurements.

Representative Sample
Dissect both deer. Removed kidneys for analysis. Laboratory Sample. Preparation Cut kidney into pieces and blend in a high speed blender to homogenize the sample.

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Defining Replicate Samples

Three 10-g samples of the homogenized tissue were placed in porcelain curcibles and dry ashed. Dry ashing serves to free the analyte from organic material and convert the arsenic present to As2O5. Samples of the discolored grass were treated in a similar manner.

Dissolving the Samples

The dry solid in each of the sample crucibles was dissolved in dilute HCl, which converted the As2O5 to soluble H3AsO4.

Eliminating Interferences
Reactions to Eliminate Interferences:
H3AsO4 + SnCl2 + 2HCl --> H3AsO3 + SnCl2 + H2O H3AsO3 + 3Zn + 6HCl --> AsH3(g) + 3ZnCl2 + 3H2O Bubble gas into collectors with silver diethyldithiocarbamate to form a colored complex compound shown below.

Measuring the Amount of Analyte

Spectrophotometer: Highly colored complex of arsenic was found to absorb light at a wavelength of 535 nm.

Conc. ppm 0 5 10 15 20 25 deer 1 deer 2

Absorbance 0 0.16 0.28 0.41 0.595 0.7 0.61 0.43

Absorbance vs Concentration
0.8 0.6 0.4 0.2 0 0 y = 0.0282x + 0.005 R2 = 0.9961 A bs orba nc e

Calculating the Concentration

ppm = (Absorbance -.005)/0.0282 Deer 1: (0.61 - 0.005)/0.0282 = 22 ppm Deer 2: (0.43 -0.005)/0.0282 = 15 ppm Arsenic in the kidney tissue of animals is toxic at levels above about 10 ppm. Grass Samples showed about 600 ppm arsenic.

10

15 Conc., ppm

20

25

30

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Reliability of the Data

The data from these experiments could be analyzed using the statistical methods

Where Do We Begin?
Review of Basic Tools and Operations of Analytical Chemistry
The Laboratory Notebook Analytical Balances, Volumetric Glassware Laboratory Safety

Error Analysis
Concepts Terminology Evaluation of Data Experimental Design Units Concentration Calculations Stoichiometry Balanced Chemical Reactions

Review of Solution Chemistry

Laboratory safety is a must! Learn the rules. See Lab Manual for Detail.

Gary Christian, Analytical Chemistry, 6th Ed. (Wiley)

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