1. Structure and Formulae

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Carbon ChemistryStructure and FormulaeScience Year 2

1.1 Explain the occurrence of carbon compounds with straight chains, branched chains and ringsRevisionWhat are atomic orbitals?What atomic orbitals are present in carbon?What are the shapes of these orbitals?3Atomic OrbitalsA region of space around the nucleus within which the probability of finding an electron is high (~95%)

This region can be calculated using advanced mathematical procedures (Schredinger)There is no way of determining the exact location of an electron within an atomThere is a definite 3 dimensional area around the nucleus within which an electron is most likely to be found

4Atomic Orbitals in Carbons orbitals are spherical1s and 2s orbitals are similar in shape however electron density is closer to the nucleus for the 1s orbital

p orbitals are dumbbell shapedThere are three p orbitals - 2px, 2py and 2pz

5Shapes of Orbitals

6The Carbon Atom

http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter__1%3A_Chapter_1%3A_Introduction_to_organic_structure_and_bonding_I/Section_1.5%3A_Valence_bond_theory%3A_sp,_sp2,_and_sp3_hybrid_orbitals7Organic CompoundsCarbon forms a vast number of compounds because of:Tetravalency each carbon atom forms four bondsCatenation - carbon has the ability to form strong covalent bond with other carbon atomsHybridisation -2s and 2p orbitals mix and rearrange to form hybrid orbitals; can form multiple bonds [single (sp3), double (sp2), triple bonds (sp)]CatenationThe ability for carbon to bond to itself, gives rise to:

Straight chains

Branched chains

Rings

You can also get a combination of rings and chains

Catenation and TetravalencyCarbon can also form single, double or triple bonds with itself

Different atoms or groups of atoms can be attached to the carbon atom

The basic atom is HYDROGEN but groups containing OXYGEN, NITROGEN, HALOGENS and SULPHUR may be attached to the carbon atom or chainThis group attached to the carbon chain, called the functional group, may determine the chemistry of an organic compound

Why does carbon form four bonds?

Carbon forms four bonds (instead of two)

Simple model of carbon does not help in explaining the phenomenon

Explanation found using actual illustration of atomic orbitals11Bonding

The ground state configuration of carbon is unsuitable for bonding

In the ground state carbon can only form bonds of unequal length and strength For correct bonding to occur some changes have to be made in the orbitals

12Hybridisation2s electrons spontaneously promoted to empty 2p orbital

s orbital and the THREE p orbitals mix to form FOUR hybrid orbitals (sp3)

number of orbitals is conserved during hybridisation

13The Excited Carbon AtomFour identical sp3 orbitals formed

All the same shape, size and energy

14sp3 hybridized orbitals

s and p orbitalssp3 orbitals

Arranged in a tetrahedral conformation

Gives minimum repulsion between orbitals

Angle of 109 from each other

Can form bonds by overlapping with orbitals of other atoms15Bonding in Methane (CH4)Overlap of s and sp3 orbitals form sigma () bond

Carbon atom is sp3 hybridized

Bonds are formed by overlapping of the 1s orbitals of four hydrogen atoms with the sp3 orbitals of the carbon atom

Methane has 4 bonds 16

Note that each bond contains 2 electrons:1 from s orbital of hydrogen1 from sp3 orbital of carbon17Bonding in Ethene (C2H4)Ethene contains a double bondIn carbon of double bond there are three sp2 hybrid orbitals and one unused p orbitalEach carbon in the double bond is sp2 hybridisedUnused p orbital overlaps above and below the plane to form a pi () bond

http://www.citycollegiate.com/hybridization2.htmBonding in Ethyne (C2H2)Ethyne contains a triple bondIn carbon of triple bond there are two sp hybrid orbitals and two unused p orbitalEach carbon in the triple bond is sp hybridisedThe two unused p orbitals overlap above and below the plane to form two pi () bonds

The triple bond consists of one sigma bond and two pi bonds The geometry around each carbon is linear with a bond angle of 180o http://pages.towson.edu/ladon/carbon.html22

Some molecules cannot be adequately represented by a single Lewis structure

For example, two valid Lewis structures can be drawn for the anion (HCONH)These structures are called resonance structures or resonance formsA double headed arrow is used to separate the two resonance structuresSome carbon compounds can display Resonance

22

1.2 Explain the meaning of the term homologous series

eg. First three members of the ALCOHOLs homologous series CH3OH C2H5OH C3H7OHMETHANOL ETHANOL PROPAN-1-OLHomologous SeriesA series of compounds of similar structure in which each member differs from the next by a common repeating unit, CH2 All members share the same general formulaMolecular formula of each member differs from its neighbour by CH2 (e.g. CH4, C2H6, ...)Each member contains the same functional groupEach member has similar chemical properties Each member shows a gradual change in physical properties as molar mass increasesEach member of the series can usually be prepared by similar methods

Functional GroupsLarge number of organic compounds, so it is easier to split them into small sections for studyThis is done by studying compounds which behave in a similar way because they have a particular atom, or group of atoms, Functional Group, in their structureFunctional groups can consist of one atom, a group of atoms or multiple bonds between carbon atoms

Each functional group has its own distinctive properties which means that the properties of a compound are governed by the functional group(s) in it

H H H H HH C C C C C OH H H H H H H H H H HH C C C C C NH2 H H H H HCarbon Functional Carbon Functionalskeleton Group = AMINE skeleton Group = ALCOHOLCOMMON FUNCTIONAL GROUPSGroupSuffixGeneral FormulaExample (name)Example (molecular formula)Alkane- aneCnH2n+2EthaneC2H6Alkene- eneCnH2nEtheneC2H4Alkyne- yneCnHnEthyneC2H2Alcohol- olCnH2n+1OHEthanolC2H5OHHalogenoalkaneAldehydeKetoneCarboxylic AcidCOMMON FUNCTIONAL GROUPSGroupSuffixGeneral FormulaExample (name)Example (molecular formula)AmineAmideEsterNitrileEtherAcyl chloride

1.3 Distinguish between empirical, molecular and structural formulae Depiction of Organic MoleculesEmpirical formula is the simplest whole number ratio of atoms in a compound e.g. CH2

Molecular formula is the actual number of atoms in a compound e.g. C2H6 for ethene

Structural formula is the diagrammatic representation of an organic molecule showing the arrangement of atomsStructural FormulaeMay be represented as:Displayed formula

Condensed formula

Skeletal formula carbon atoms and hydrogens are not shown; An open end represents a CH3 group while a bend represents a CH2 group

http://www.ivy-rose.co.uk/Chemistry/Organic/How-to-draw-skeletal-formulae-of-organic-molecules.phpDepiction of Organic Molecules eg. ButaneMOLECULAR FORMULA The exact number of atoms of eachelement present in the molecule

EMPIRICAL FORMULA The simplest whole number ratioof atoms in the molecule

STRUCTURAL FORMULA The minimal detail using conventionalgroups, for an unambiguous structure

DISPLAYED FORMULAShows both the relative placing of atoms and the number of bonds between them

C4H10C2H5CH3CH2CH2CH3 CH3CH(CH3)CH3 ***there are two possible structures

1.4 Determine formulae from experimental data

Determining Empirical FormulaeWhat is the empirical formula for a compound containing 38.8% carbon, 16.2% hydrogen and 45.1% nitrogen?

Find the empirical formula of a compound containing 4g of hydrogen and 32g of oxygen

When 3.79 grams of an organic compound is burned, 6.61 grams of CO2 and 3.59 grams of H2O are produced. What is the empirical formula of this compound?

http://thechemguys.blogspot.com/2010/12/calculating-emperical-formula-of.htmlAns: CH5NAns: H2OAns: C3H8O2Determining Molecular FormulaeThe empirical formula of hexane is C3H7. Its molecular weight is 86.2 amu. What is the molecular formula of hexane?Calculate the formula weight of C3H7

Calculate the ratio between the molecular weight and the empirical weight:

The molecular formula must be twice the empirical formula: (C3H7)2or C6H14

Determining Molecular FormulaeThe compound ethylene glycol is often used as an antifreeze. It contains 38.7% carbon, 9.75% hydrogen, and the rest oxygen. The molecular weight of ethylene glycol is 62.07 g. What is the molecular formula of ethylene glycol?

The compound dioxane contains only carbon, hydrogen, and oxygen. When 0.956 g dioxane is burned, 1.91 g carbon dioxide and 0.782 g water are formed. In another experiment, it was determined that 6.04x10-3 mol dioxane weighs 0.532 g. What is the molecular formula of dioxane?

1.5 Write structural formulae

Structural FormulaeMay be represented as:Displayed formula

Condensed formula

Skeletal formula carbon atoms and hydrogens are not shown; An open end represents a CH3 group while a bend represents a CH2 group

http://www.ivy-rose.co.uk/Chemistry/Organic/How-to-draw-skeletal-formulae-of-organic-molecules.phpStructural FormulaExamples of structural formulae for ring compounds:

HomeworkWrite the following using the (a) displayed formula and (ii) skeletal formula:CH3CH2CH(OH)CH2CH2CH3

CH3CH2CH(OH)CH2CH(CH3)2

CH3CH2CH(OH)CHBrCH3

C6H6

C6H5Br

1.6 Apply the IUPAC rules to named organic compounds

NomenclatureTwo ways to name organic compounds:Systematic based on IUPAC rules for naming organic compounds eg. Ethanoic acidTrivial based on some characteristic of compound or historical aspect eg. Acetic acid (from acetum; latin for vinegar)

IUPAC NomenclatureA systematic way of naming organic compounds. The name consists of two parts:Stem - based on the carbon skeleton (backbone)Suffix based on the functional group present (homologous group)

Nomenclature1. STEM Based on the carbon skeleton

Carbon skeleton is named using the number of carbon atoms in longest chain bearing the functional group + a prefix showing the position and identity of any side-chain substituents/groups

Apart from the first four the number of carbons atoms is indicated by a prefix derived from the Greek numbering system

Working out which is the longest chain can pose a problem with larger molecules

Prefix C atomsmeth- 1eth- 2prop- 3but- 4pent- 5hex- 6hept- 7oct- 8non- 9dec- 10Nomenclature2. SUFFIX The last part of the name tells you which functional group is presentThe relevant suffix is added to the end of the basic stemIn many cases the position of the functional group must be given to avoid any ambiguity

Substituents Many compounds have substituents (additional atoms, or groups) attached to the main chainTheir position is numbered

Functional group SuffixALKANE - ANEALKENE - ENEALKYNE - YNEALCOHOL - OLALDEHYDE - ALKETONE - ONEACID - OIC ACID

1-CHLOROBUTANE 2-CHLOROBUTANENomenclature - AlkanesIdentify the main carbon chain/skeleton - the carbon chain containing the most carbon atomsRemember:It is too complicated to draw molecules with the correct bond anglesSingle covalent bonds are free to rotateA simple way to check the length of carbon chain is to run a pencil along the chain and see how many carbon atoms can be covered without reversing direction or taking the pencil off the pageFor eg. in all the compounds below, there are five carbon atoms in the main chainAll the structures are of the same molecule - Pentane C5H12CH2CH3CH2CH2CH3CH2CH2CH2CH3CH3CH3CH2CH2CH2CH3CH2CH2CH2CH3CH3CH2CH3CH2CH2CHCH3CH3CH2CH3CH3CHCH2CH3CH3CH3CHCH2CH2CH3CHCH3LONGEST CHAIN = 5LONGEST CHAIN = 6LONGEST CHAIN = 6Nomenclature - AlkanesHow long is the longest chain?Look at the structures and work out how many carbon atoms are in the longest chain.

Alkyl radicals methylCH3 - CH3ethylCH3- CH2- C2H5propylCH3- CH2- CH2- C3H7Nomenclature - AlkanesWhat if the stem (or carbon backbone) has a side group or substituent on it?

SIDE-CHAIN - carbon based substituents are placed before the chain name they have the prefix -yl added to the basic stem (e.g. CH3 is methyl)

Number the principal chain from one end to give the lowest numbers.Side-chain names appear in alphabetical order - butyl, ethyl, methyl, propylEach side-chain is given its own numberIf identical side-chains appear more than once, prefix with e.g. di, tri, tetra, penta Numbers are separated from names by a HYPHEN e.g. 2-methylheptaneNumbers are separated from numbers by a COMMA e.g. 2,3-dimethylbutanechloroCl bromoBriodoI nitroNO2 methoxy OCH3aminoNH2Examples of SubstituentsNomenclatureExample: longest chain 8 (it is an octane)3,4,5 are the numbers NOT 4,5,6order is ethyl, methyl, propyl3-ethyl-5-methyl-4-propyloctane

CH3CH2CH3CHCH2CH2CH3CHCHCH2CH2CH3CH2CH3I.U.P.A.C. NomenclatureCH2CH3CH2CH2CHCH3CH3CH2CH3CH3CHCH2CH3CH3CH3CHCH2CH2CH3CHCH3Longest chain = 5 ; so it is a pentaneA CH3, methyl, group is attached to the third carbon from one end...3-methylpentaneLongest chain = 6;so it is a hexaneA CH3, methyl, group is attached to the second carbon from one end...2-methylhexaneLongest chain = 6 so it is a hexaneCH3, methyl, groups are attached to the third and fourth carbon atoms (whichever end you count from). 3,4-dimethylhexane

1.7 Define, with examples, structural isomerism

Structural IsomerismStructural isomerism (or constitutional isomerism), is a form of isomerism in which molecules have the same molecular formula but different bonding arrangement

Chain isomerism eg. C4H10

***isomers have different arrangements of the carbon chain

Structural IsomerismPositional isomerism eg. C4H9OH

P.I contain same carbon skeleton but the functional group is in different positions on the carbon chain

Structural IsomerismFunctional group isomerism eg. C3H6O

F.G. isomers contain different functional groups ClassworkDraw and name all the possible isomers for C5H12C8H18

Draw two positional isomers with the molecular formula C3H7Br

Draw two functional group isomers with the molecular formula C3H6O

1.8 Explain stereoisomerism StereoisomerismStereoisomerism occurs when isomers have identical molecular formulae and the atoms are linked together in the same order, but have different relative positions in space

Stereoisomers may be classified as geometric isomers or optical isomers

Geometric (or cis-trans) isomerism eg. alkenes bond restricts rotation around a bond eg. double bondcis isomer identical groups are on the same side of the double bondtrans isomer - identical groups are on opposite sides of the double bondGeometric IsomerismGeometric (or cis-trans) isomerism eg. butene cis isomer vs. trans isomer

The identical groups in question MUST be on two different carbons in order to display cis-trans isomerism

Geometric IsomerismThere are two requirements for cis-trans isomerism:Rotation must be restricted in the moleculeThere must be two non-identical groups oneachdoubly bonded carbon atomCis-trans isomerism also occurs in cyclic compounds (ring structures) since groups are unable to rotate about any of the ring carboncarbon bonds. In cyclic compounds, groups can be either on the same side of the ring (cis) or on opposite sides of the ring (trans).

Geometric IsomerismAlkenes with a C=CH2unit do not exist as cis-trans isomers.

Alkenes with a C=CR2unit, where the two R groups are the same, do not exist as cis-trans isomers.

Alkenes of the type RCH=CHR can exist as cis and trans isomers; cis if the two R groups are on the same side of the carbon-to-carbon double bond, and trans if the two R groups are on opposite sides of the carbon-to-carbon double bond.

StereoisomerismOptical isomerism exists for compounds which are mirror images of each other; non-superimposable on each other

Molecules possess a CHIRAL centre

Optical isomers show similar physical and chemical propertiesHow can we distinguish between two optical isomers?

http://astrobiology.berkeley.edu/Mars101/definitions.htmOptical isomers Differ in the direction in which they rotate plane polarized light

D-isomer (dextrorotary) rotates light in clockwise (+) direction

L-isomer (laevorotary) rotates light in anticlockwise (-) direction

The isomers are called enantiomers

Racemic mixture optically inactive; contains equal amounts (50:50) of each enantiomer

http://www.chem.yale.edu/~chem125/125/thalidomide/thalidomide.html

1.9 determine the possible isomers from given molecular formulaeClassworkDraw and name all the possible isomers for the following molecular formula:C5H11Br

C6H14

C4H8

C6H12

For the molecular formulae above, state the type of isomerism which may exist