Organic Chemistry. O1: Ways of representing organic molecules. Dr Amanda Rousseau C Molecular formula

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1 O1: Ways of representing organic molecules Organic Chemistry Dr Amanda Rousseau C503 Chemistry the Central Science - Brown (Chapter 24) Extra reading: Organic Chemistry McMurry (any edition) Self study: Background notes green booklet 1. Molecular formula Indicates composition Gives no indication of how the atoms are bonded or connected 2. Condensed structural formula Shows groupings of atoms in a condensed or compact manner Introduction - Organic chemistry The study of carbon compounds, their reactions and structure Often with These compounds are known as Known as hydrocarbons if only C & H are present Can also contain O, N, S, P (heteroatoms) and almost always H 3. 2-D projection formula / expanded formula Shows connectivity between atoms Geometry may be unrealistic gives no indication of 3-D shape Organic compounds form the basis of life Biology at a molecular level = organic chemistry Also important in: food, dyes, paints, pharmaceuticals, agrochemicals, fuel, glue, flavourings, perfumes, cosmeceuticals, plastics

2 4. 3-D structural formula / perspective drawing Compare: Best representation gives indication of geometry But, cumbersome for large molecules 5. Line drawing Short-hand stick formulae = OH = = O2: Trivial and IUPAC nomenclature 1. Trivial names Common names Often based on historical origins Non-systematic O

3 2. Systematic name Follows IUPAC rules International Union of Pure and Applied Chemistry C C C C IUPAC rules for systematic names: C C O2&3: Trivial and IUPAC nomenclature & structural features Branches containing C and H only CH 4 CH 3 CH 3 CH 3 CH 2 CH 3 CH 3 CH 2 CH 2 CH 3 Methane 1 Ethane Propane Butane C 5 C 6 C 7 Substituents containing other kinds of atoms C 8 C 9 C 10

4 Examples: Use the IUPAC rules to name the following: CH 3 CH 2 CH(CH 3 )CH 2 CH 2 CH 3 1) Draw the molecule 2) Count the carbons in the longest chain Note: If there is more than one substituent: Each must have its own number you may have to repeat a number Number the longest chain from the end that gives the lowest numbers for substituents TWO methyl groups = THREE propyl groups = FOUR ethyl groups = Substituents are listed alphabetically, BUT, ignore di-; tri-; tetra etc Other substituents called heteroatoms: 3) Identify and name the substituent F Fluoro Cl Chloro Br Bromo I Iodo NO 2 Nitro NH 2 - Amino Examples: Use the IUPAC rules to name the following: 4) Identify position of substituent by a number 5) Name the compound

5 O3: Structural features of organic molecules Molecules with rings

6 More Terminology 1. Acyclic O5: Isomerism Isomers are compounds which have the same: 2. Cyclic but differ in: 3. Polycyclic Leads to structural diversity and a vast number of compounds 4. Straight Chain 5. Branched Chain There are two classes of isomers: 1. Structural Isomers 2. Stereoisomers 6. Saturated 7. Unsaturated 8.. Heteroatom O6: Isomerism 1. Structural isomers Different connectivity between atoms: sequence of bonds between atoms is different Different physical properties (and in some cases, different chemical properties) 9. Heterocycle 10. Aromatics with heteroatom (heteroaromatic) 11. Aromatic hydrocarbon

7 1. Structural isomers cont. O7: Isomerism 2. Stereoisomers Same bonding sequence of atoms BUT: Shape is important! We often need to use 3-D projection formulae 3 different classes of stereoisomers: e.g. How many structural isomers of C 6 H 14 can you find? Can you name them? 2a. Conformational Isomers Require: No bond is broken, Two conformers:

8 2a. Conformational Isomers cont. eg: Cyclohexane Not a flat ring - puckered 2b. Geometric Isomers cont. Alkane All single or σ bond Fully saturated Rotation about C-C bond: Alkene C=C bond one σ bond and one π bond Unsaturated Rotation about C=C bond: H H H H Two types of geometric isomers Cis Trans Different physical properties (similar chemical properties) Example: But-2-ene 2b. Geometric Isomers Require: For example: Example: 1,2-dimethylcyclobutane Interconversion of isomers requires

9 2b. Geometric Isomers cont. Example: How many isomers of C 4 H 8 are there? Can you name them? 2c. Enantiomers cont. Enantiomers are known as chiral (handed) compounds Hint: General formula for alkanes: C n H 2n+2 i.e. a relationship between the number of carbons and hydrogens Does C 4 H 8 fit this formula? If YES, compound is an alkane If NO, then compound either contains double or triple bonds, or is cyclic. Bergman, J. Why the Miller Urey research argues against abiogenesis; 2c. Enantiomers Require: These molecules are non-superimposable but are mirror images of one another. Have virtually identical: Physical properties are identical EXCEPT: They have optical activity and are known as: Optical activity measured using a polarimeter Enantiomers rotate plane polarised light to the: Right Dextrorotatory (+) Left Laevorotatory (-) This was discovered in 1849 by Pasteur. A mixture of 50% (+) and 50% (-) = Racemic mixture and the mixture is optically INACTIVE, but the individual molecules are still optically active

10 O8: Chirality A molecule that exists as a pair of nonsuperimposable mirror images (enantiomers) is called chiral. O8: Chirality cont. Examples: Do these molecules contain a stereogenic centre? If so, identify the asymmetric carbon & draw both enantiomers. A carbon atom attached to four different atoms or groups is called a: Remember: Molecules with one stereogenic centre exist as a pair of: The enantiomers are nonsuperimposable mirror images. If two enantiomers are placed in a solution in equal amounts, then the mixture is optically inactive and is called: Many pharmaceuticals are chiral molecules. Example: Ibuprofen * COOH

11 Example Pentan-2-ol is chiral but pentan-3-ol is not. Explain. Thalidomide (S) Sedative, painkiller, antiemetic, antidepressant (R) Teratogen intercalates DNA & affects limb & ear development Sold as a racemate ( ) Caused 10,000 birth defects Examples of compounds with more than one stereogenic centre: Stereoisomerism is very important in biology Ephedrine Pseudoephedrine Stimulant, appetite suppressant, Nasal/sinus decongestant decongestant O9: Structural vs stereoisomers Isomers Structural isomers Stereoisomers Anon. Fundamentals of Drugs I, Chapter 4;

12 O10: Stereoisomers O11: Classification of organic molecules Stereoisomers Conformational isomers Geometric isomers Organic compounds Enantiomers C and H Hydrocarbon Saturated Unsaturated C and H plus Heteroatoms Saturated H H CH3 CH3 O10: Comparison of stereoisomer properties Sigma (σ)bonds free rotation Example: To which broad class do the following belong? Pi (π) bond or ring no free rotation Carbon with 4 different substituents Optically active Unsaturated

13 O12: Functional groups Thiol Definition: An atom, or group of atoms, that imparts characteristic chemical properties to an organic compound Functional Groups (FGs) include hetero-atoms (not H or C) & multiple bonds Ether FGs are the most reactive sites in a molecule YOU NEED TO LEARN THE FGs!!! GREEN BOOKLET!!! Thioether Alkene Amine Alkyne Nitrile Haloalkane Aromatic ring Alcohol Carboxylic acid Carboxylic acid chloride

14 Carboxylic ester Example: Identify the functional groups in Candarel Carboxylic amide Aldehyde Ketone Example: Identify the functional groups in methotrexate Example: Identify the functional groups in lopinavir O O NH O HN N HN O OH

15 O12: Trivial and IUPAC nomenclature Trivial names Historical Can be ambiguous O12: Trivial and IUPAC nomenclature cont. What about these alcohols? IUPAC Follows a set of internationally accepted rules Unambiguous Primary alcohol Secondary alcohol Tertiary alcohol Examples: Carbon atom carrying Carbon atom carrying Carbon atom carrying the OH is attached to: the OH is attached to: the OH is attached to: Carboxylic acids Alcohols Examples: Name the hydrocarbon Suffix = anol not ane Number the carbons and note the position of the OH Examples: Contain a COOH group Name the hydrocarbon Suffix = anoic acid, not ane

16 Carboxylic esters Derived from a carboxylic acid & an alcohol Contain a COOR group Responsible for many flavours and fragrances Amines Contain N 1, 2, 3 amines Other examples: You will need to know how to name simple organic molecules with no more than 2 FGs Use the following table and the green booklet to guide you

17 Useful websites: AND_FACTS_OF_ORGANIC_CHEMISTRY_-_Must_Have_514.html O13: SPECTROSCOPY A set of techniques in which the response of molecules to the absorption or emission of energy is measured. i.e., supply electromagnetic radiation to compounds, observe the interaction. The picture of the response is called: In this topic, we shall deal with the effect of infra-red (IR) radiation on molecules. Name the following organic molecules

18 Reminder: Symbols and Equations Regions of the electromagnetic spectrum: QUANTITY SYMBOL UNITS Wavelength Velocity Frequency Energy Infrared (IR) radiation induces: Wavenumber Different bonds vibrate in different regions of the IR range So IR spectroscopy gives one an idea of what kinds of bonds (and hence functional groups!) are present in molecules.

19 SOME FACTS ABOUT VIBRATIONS 1. Vibrations can be: Note small λ values ( m = cm). Using wavenumbers instead (= 1/ λ) ) gives numbers that are more convenient to work with. Typical wavenumber range for IR spectroscopy: cm -1. The higher the wavenumber, the higher the energy of the radiation. OBTAINING IR SPECTRA 1. Radiation of known wavenumber in the IR range passes through sample. 2. Sample absorbs energy. Beam s intensity decreases as it emerges. STRETCHES - BENDS Stretching requires more energy than bending i.e. Stretching occurs at a higher ν than bending NORMAL MODES OF VIBRATION EXAMPLES 3. Detect the emerging beam and measure its intensity (i.e.,, what % is transmitted?) 4. Do this sequentially at all wavenumbers in the infrared range. 5. Graph of % light transmitted vs wavenumber is the infra-red spectrum (plural: spectra) 2. Bonds behave like springs: 6. Get information from: peak intensities (strong, medium, weak); peak shapes (sharp, broad); most important: peak positions on the ν axis Hooke s law describes the properties of springs. It includes terms for the stiffness of the spring, and the load on it. In chemical terms: Stiffness relates to: Load relates to:

20 In other words: Strong bonds are stiffer, and need more energy to induce vibration: they absorb at: e.g. Approx energy (kj mol -1 ): C C 348 C=C 611 CºC 837 Typical wavenumbers (cm -1 ): ~2200 Bonds with lighter atoms (less load ) vibrate faster than bonds with heavier atoms (i.e., higher frequency, higher energy): they also absorb at: e.g. C=O P=O Typical wavenumbers (cm -1 ): SOME FACTS ABOUT VIBRATIONS cont. 4. Polyatomic molecules: Vibrations in one bond influence vibrations in neighbouring bonds a knock-on effect This lets one deduce information about the environment in which atoms find themselves e.g. C C H C=C H C C H Typical wavenumbers (cm -1 ): ~3300 e.g. 3. IR signals are seen only if the dipole moment changes during vibration. Result: different functional groups have very characteristic IR absorption signals! Average positions from many examples are listed in correlation tables or charts EXAMPLE OF AN IR CORRELATION CHART

21 EXAMPLE OF AN IR CORRELATION TABLE WHAT SHOULD YOU MEMORISE? Try to assign everything above 1500 cm -1 Note: complete assignment of every signal is difficult, if not impossible! USEFUL INFORMATION FROM THE FINGERPRINT REGION Some specific substitution patterns have characteristic bending vibrations e.g. Alkenes with 2 H atoms:

22 IR SPECTRA OF (a) HEXANE; (b) 1-HEXENE; (c) 1-HEXYNE Examples: Using the data from the table provided, decide which isomer belongs with which spectrum

23 Example: Spectra of propan-1-ol, propanal and propanoic acid.decide which is which.