Organic chemistry

Octet theory

"Atoms prefer to have eight electrons in their outer occupied shell." - atoms are most stable when they have filled outer shells.

Alkyl Halide

(chloride, fluoride, bromide, iodide) Alkyl halides are classified as either primary (1°), secondary (2°) or tertiary (3°) depending on whether the halogen is bound to a carbon with one, two or three attached carbon atoms. i.e. if the carbon attached to a halide group is bonded to three other carbons it is a tertiary alkyl halide. Example: trichloromethane (chloroform)

Trivial names accepted by IUPAC

-Ethylene for ethene -Propylene for propene -Vinyl for ethenyl -Vinyl chloride for (Chloroethene) -acetylene for ethyne -formaldehyde for methanal -formic acid for methanoic acid -acetaldehyde for ethanal -acetic acid for ethanoic acid -acetone for propanone

Alcohol

-Hydroxyl molecule bound -Alcohols are classified as either primary (1°), secondary (2°) or tertiary (3°) depending on whether the -OH group is bound to a carbon with one, two or three attached carbon atoms - exactly the same as alkyl halides. -ol suffix Example: ethanol

Reduction reaction

-The addition reaction can also be carried out with hydrogen in the presence of a metal catalyst such as platinum, palladium or nickel -this reaction is a special case of addition

Empirical formula

-The empirical formula gives the ratio of atoms in the smallest whole-number ratios. -not very useful

Ionic, covalent and metallic bonding

-There is an attractive force between oppositely charged ions, which leads to the formation of ionic bonds. -Compounds of oppositely charged ions held in crystal lattices by ionic bonds are called salts. -Covalent bonds are formed when electrons are shared between two atoms. By sharing electrons both atoms are able to achieve filled outer shells (octet theory).

Isolated systems

-Where the double bonds are separated by two or more single bonds C=C-C-C=C

Cumulated systems

-Where two double bonds come from the same carbon

Oxidation reaction

-addition of oxygen across a double or triple bond -or an increase in the number of bonds between oxygen and a carbon, nitrogen or sulphur. i.e. single bond to double bond e.g. Thioethers can be oxidised to sulphoxides or sulphones

Boiling point

-decreases with increased branching - the molecules do not stack together so well and there are fewer interactions between the molecules -increases with molecular weight due to increased number of interactions with increased surface area

Molecular formula

-just gives a count of the atoms present in the form CaHbNcOdSe. -For example, ethanol has the condensed formula CH3CH2OH, and the molecular formula C2H6O - the molecular formula does not give any indication about the likely properties of a molecule or the types of reactions it will undergo as it does not show the structure

Conjugated systems

-molecules with two or more double bonds and double bonds that alternate with single bonds. (or triple bonds-can be double and triple as well) -show an unusually high stability. This has been explained in terms of the overlap of pi orbitals. -there is delocalisation of the pi electrons giving lower energy orbitals and greater stability. -coloured when there are enough double bonds in the system.

Hydrogenation of Alkenes

-reduction process -Alkenes can be hydrogenated (reduced) to give alkanes, using H2 and a metal catalyst such a platinum, palladium or nickel.

Condensed formula

-still show double or triple bonds

Nomenclature of Alkanes

1. Find the parent hydrocarbon. This is the longest continuous carbon chain. 2. Number(or greek letters) the atoms in the main chain, so that the lowest substituent number is the smallest possible. That is, start at the end that is closest to a substituent. If two or more sidechains are in equivalent positions, then the one given the lowest number is the one which will come first when the substituents are listed alphabetically 3. Identify and number the substituents 4. Write out the name as a single word, using hyphens to separate numbers and prefixes, and commas to separate numbers. If two or more different substituents are present list them in alphabetical order. If two or more identical substituents are present, use the prefixes di-, tri-, tetra- etc. 5. Name any complex substituents - those with branching. Use the same procedure for the branched group as if it were a compound itself.

Methyl, Methylene and Methine

A methyl group has one atom attached that is not hydrogen, a methylene group has two atoms attached that are not hydrogen, a methine group has three atoms attached that are not hydrogen

Rearrangement reaction

A rearrangement reaction generates an isomer, and again the number of bonds normally does not change. An example of a rearrangement is the conversion of the double bond of the sunscreen octyl methoxycinnamate from the cis- to the more stable (but inactive) trans-configuration with time

Co-ordinate bonds

AKA Donor covalent bonds These are covalent bonds, where two electrons are shared between two atoms. In this case however, one atom provides both electrons. This type of bonding is usually seen in metal-ion complexes.

Nitrile

AKA cyanide C triple bonded to N Example: cyanobenzene

Stick figure

AKA skeletal structure or line drawing -Carbon atoms are not usually shown. Instead, bonds between carbons are shown as lines, with the carbon atoms assumed to be at the intersections, and at the end of each line. -Hydrogen atoms bonded to carbons are not shown. It is assumed that the correct number of hydrogens are present to bring the total number of bonds for each carbon to four. - All atoms other than carbon or hydrogen are shown. (still show hydrogen if it is not attached to carbon or need to emphasise geometry i.e. cis trans) -good practice to show what the individual molecules bond to i.e. alcohol HO-OH not OH-OH

Addition reaction

Addition across double or triple bond of alkene or alkyne respectively. Markovnikov addition - the OH of the water preferentially goes on the more substituted carbon, and the H goes on the less substituted carbon. -where Br is OH and the top is the major product with the bottom the minor product

Alkanes

Alkanes contain only carbon and hydrogen atoms, joined by single bonds, so the angles at the carbons are 109.5°. Alkanes have the formula CnH2n+2. A homologous series is one in which each one varies from the previous by a constant amount i.e. CH2 for alkanes - unbranched Alkanes are generally obtained by the fractional distillation of crude oil. Catalytic cracking and catalytic reforming under high temperature and pressure are used on an industrial scale to convert higher molecular weight petroleum products into a mixture of smaller molecules. However, laboratory production of alkanes is also possible.

Combustion of alkanes

All hydrocarbons undergo combustion in the presence of oxygen (i.e. they can be burnt). In the presence of an excess or a stoichiometrically correct amount of oxygen, the only products are carbon dioxide and water. However, if there is insufficient oxygen, carbon monoxide is produced. This is a highly toxic, odourless and colourless gas.

Phenol

Aromatic attached to a hydroxyl Example: meta-methylphenol

Thiophenol

Aromatic attached to thiol Example: meta-methylthiophenol

Bonding Forces

BONDING CHARACTERISTICS van der Waal's - weak, involving temporary partial charges from movement of electrons around the surface of a molecule Dipole-dipole - stronger, from permanent partial charges (and hence dipoles) due to electronegativity differences between atoms such as O with C Hydrogen bonding -stronger still, from permanent partial charges (and hence dipoles) between atoms such as O and N with H Ionic bonding - strongest, from atoms with full charges, typically R4N+ or COO- van der Waal's forces are weak, short-distance forces found in molecules such as alkanes. The weak attraction of polar molecules - only brief existence but can produce sufficient attractive forces to keep molecules in a liquid rather than gas state Dipole-dipole interactions interactions occur where there are permanent dipoles present in a molecule, such as in alkyl halides or aldehydes and ketones. These dipoles are the result of bonding between atoms of differing electronegativities. Hydrogen bonding is a special case of dipole-dipole interaction between the lone pair on a small electronegative atom and a hydrogen bonded to an electronegative atom. The electron cloud of an O-H (or N-H) bond is particularly distorted towards the electronegative atom, exposing the hydrogen nucleus. The resultant positive charge is strongly attracted to the negative dipole of an adjacent molecule. Hydrogen bonding is the reason that a small molecule like water has a relatively high boiling point. In organic molecules hydrogen bonding is found in alcohols, acids and amines. Acids generally have higher boiling points than alcohols of an equivalent molecular weight, as they can hydrogen bond through both oxygens of the carboxyl group.

Benzene (by itself)

Benzene has an unexpectedly high stability and does not undergo reactions characteristic of an alkene -all the carbon-carbon bond lengths in benzene are equal, and intermediate in length between single and double bonds This arrangement of pi electrons in a cyclic π system results in an unusually high stability for benzene-like compounds. Hence these compounds are particularly unreactive, and undergo substitution reactions, rather than addition reactions, which would disrupt the aromatic system 1931, Erich Hückel applied the principles of molecular orbital theory to determine why benzene was different to other cyclic conjugated systems

Hydrolysis reaction

Breaking of a bond (lysis) in the presence of water. This is most commonly seen in the cleavage (breaking) of ester and amide bonds

Ester

C double and single bonded to two Oxygens respectively -oate suffix Example: Ethyl Ethanoate Organic esters are formed from an organic acid and an alcohol. (acetic acid) Inorganic esters can be formed from any inorganic acid with one or more -OH groups, and an alcohol. In COOH, H is knocked off. nitric acid (HNO3) sulphuric acid (H2SO4) phosphoric acid (H3PO4)

Carboxylic acid

C double bonded to O and single bonded to hydroxyl -oic acid suffix -dioic acid - two carboxyl groups -acid naming is two separate words Example: Ethanoic acid(acetic acid)

Amide

C double bonded to O and single to N If N has an alkyl group attatched to it the position is indicated by an N- prefix The number of nitrogen-carbon bonds designates whether the amide is a primary, secondary or tertiary - they are as primary (1°), secondary (2°) or tertiary (3°) according to the number of carbon-nitrogen bonds i.e. number of carbons bonded to the nitrogen -amide suffix Example: pentanamide

Acid Halide

C double bonded to O and single to halide -oyl suffix Example: propanoyl chloride

Benzaldehyde

CHO bonded to a aromatic

benzoic acid

COOH bonded to a aromatic

Ketone

Carbon double bonded to oxygen -one suffix Example: Propanone

Aldehyde

Carbon double bonded to oxygen and single bonded to hydrogen -al suffix Example: propanal

Order of precedence of functional groups

Carboxylic Acid -COOH Esters -COOR Acid Halides -COX Amides -CONH2 Aldehydes -CHO Ketones >C=O Alcohols -OH (attached to an alkyl group) Phenols -OH (attached to an aromatic group) Amines -NH2 Alkenes >C=C< Alkynes -C≡C- Ether Alkyl halide Nitro Alkane CAts Eat All Army Ants; Kittens Attack Primarily All Army Ants; EAH! No Ants

Conformers of Cyclohexanes

Cyclohexane, and all larger rings, exists as a non-planar, or puckered conformation. This is necessary to achieve the tetrahedral angle of 109.5°. The most stable form of cyclohexane is the "chair" form. In this conformation, the hydrogens can exist in two positions - axial or equatorial. The "boat" conformation is a less stable form of cyclohexane, because of the steric hindrance between the bridgehead hydrogens. -The boat form is an intermediate form between two chair forms. -In this interconversion, axial hydrogens become equatorial, and equatorial hydrogens become axial. This process is called ring inversion or ring flip.

Alkene

Double bond with the example ethene -ene suffix

Electronegativity

Electronegativity is a chemical property that describes the ability of an atom to attract electrons towards itself in a covalent bond. When electrons are shared between atoms, they are seldom shared evenly - the electron density may be greater at one end of the bond than at the other. -Fluorine is the most electronegative atom -gives rise to polar bonds -A dipole occurs whenever there is a positive charge separated spatially from a negative charge. The dipole moment measures this; it is a vector. This leads to the development of permanent dipoles between atoms of different electronegativities

Elimination reaction

Elimination of a small molecule to form a double or triple bond (hence, the opposite of addition)

Functional Groups

Functional groups are sites in organic molecules which determine the physical properties of the molecules and where reactions occur. They are atoms or groups of atoms that react in characteristic ways, and allow the classification of organic compounds into different categories.

Bohr Atom

In 1913 Niels Bohr proposed a model for the atom which had a central nucleus of protons (p+) and neutrons (n°) surrounded by orbiting electrons (e-). The electrons circled the nucleus in fixed orbits called shells, which were divided into orbitals. These are further divided into sublevels.

Hückel's rule

In 1931, Erich Hückel applied the principles of molecular orbital theory to determine why benzene was different to other cyclic conjugated systems Hückel's rule: Planar, monocyclic, fully conjugated polyenes have general aromatic stability only if they possess 4n + 2 π electrons (where n is integer, 1, 2 etc.) Thus, benzene (6 π electrons, n = 1) and naphthalene (10 π electrons, n = 2) are aromatic, whereas cyclobutadiene (4 π electrons n = 0.5) and cyclooctatetrene (8 π electrons, n = 1.5) are not In summary, to be aromatic, a molecule or ion must have a pi system which is: planar; cyclic; conjugated (or with a lone pair in place of a double bond); made up of 4n + 2 π electrons (n = integer; total = 2, 6, 10, 14, 18 etc.).

Isomerism

Isomerism is possible where there are a number of different ways of organising the atoms in a molecule. Structural isomers (constitutional isomers) are compounds that have the same molecular formula, but have their atoms connected differently. Skeletal isomers - a have the same formula but different carbon skeletons.

Aromatic ions

Loss of a proton from cycloheptatriene gives the cycloheptatrienyl cation (also known as the tropylium ion). The cyclopentadienide ion is an aromatic anion. Evidence of its stability is shown by the relatively high acidity of the parent cyclopentadiene

Benzyl alcohol

Methyl and alcohol group bonded to a aromatic

Amine

N bonded to 3 groups - they are as primary (1°), secondary (2°) or tertiary (3°) according to the number of carbon-nitrogen bonds i.e. number of carbons bonded to the nitrogen -ylamine suffix Example: Methylamine

Azo compound

N double bonded to N Example: Diazobenzene

Aniline

NH2 bonded to aromatic

Amino acids

Naming via greek letters is still commonly used for amino acids; the twenty most common amino acids found in proteins are all alpha amino acids - the amine group is in the carbon alpha to the acid group. GABA - gamma-aminobuytric acid (more correctly called 4-aminobutanoic acid) - is an amino acid neurotransmitter, but in this case the amine group is on the gamma carbon Vitamin B5 is the amide formed from pantoic acid and β-alanine

Nitro compound

Nitrogen dioxide bonded to R Example: nitroethane

Solubility

Non-polar or weakly polar substances are soluble in non-polar solvents. Highly polar substances dissolve in highly polar solvents. In general terms "like dissolves like". In the process of dissolution, the bonds holding the molecules of the compound together are broken and replaced by bonds between the compound and the solvent. As a guideline, if there are four or more carbons per hydroxyl group, the molecule will have low solubility; if there a fewer than four carbons per hydroxyl group, the molecule will have high solubility.

Heterocyclic and fused-ring aromatic compounds

One lone pair on each heteroatom (usually O, N, S) can be included (if necessary) to make up the aromatic system.

Ether

Oxygen in the middle Example: diethyl ether ("ether")

Sigma and Pi bonds

Pi is the additional bond while sigma is for all single bonds plus one in each double/triple bond C=C has 5 sigmas (including the missing H bonds) and one pi

Diazonium salt

Positively charged triple bonded N Example: benzenediazonium chloride

Classification of carbon atoms

Primary (1°) carbons are those directly bonded to one other carbon (i.e., they have one carbon-carbon bond). Secondary (2°) carbons are attached to two other carbons (i.e., they have two carbon-carbon bonds). Tertiary (3°) carbons have three attached carbons (three carbon-carbon bonds). Quaternary (4°) carbons are those directly bonded to four other carbons (four carbon-carbon bonds).

Substitution reaction

Replacement of one atom or group with another

benzenesulphonic acid

SO3H bonded to a aromatic

Electron shells and orbitals

Shell Number/ Orbital/No. Electrons n s p d 2n2 1 1 0 0 2 2 1 3 0 8 3 1 3 5 18 There are two electrons per orbital - an orbital is defined as a volume in space of a particular energy that is occupied by one or two electrons -This volume is described by a probability density function Ψ2: the probability of the electron being at a specific radius in any direction from the nucleus. -s orbitals are spherical - highest probability of being found - three p orbitals. They have equal energies, but different orientations in space, at 90° to each other -P orbitals have larger energy levels than S orbitals -An orbital can hold zero, one or two electrons. -The ground state electronic configuration is the lowest energy arrangement of electrons around the atom -The aufbrau principle states that: "Lowest energy orbitals are always filled first." -The Pauli Exclusion Principle states that: "If there are two electrons in the same orbital, they must be of opposite spin." -Hund's Rule states that: "Two electrons will not occupy the same orbital if there is another vacant orbital at the same sublevel." 1s2, 2s2, 2p6 etc.

Nomenclature of cycloalkanes

Simple cycloalkanes have the formula CnH2n. 1. Find the parent hydrocarbon. Where the cyclic group has the most carbons, name the compound as an alkyl-substituted cycloalkane. However, if an alkyl side chain has more carbons than the ring, then name the compound as a ring-substituted alkane. Ring substituents are named as cycloalkyl- groups. 2. Where there are two or more substituents on the ring, number the substituents so as to give the lowest sum. List the substituents alphabetically. Where there are halogen or nitro substituents, they are treated exactly like alkyl groups.

Conformers of Alkanes

Staggered - low energy Eclipsed - High energy Gauche - intermediate energy

Ring structure

Stick figure (image) -cannot do a condensed formula Can do a full graphic

Cis - trans isomerism

Straight chain alkanes are capable of rotation about single bonds. However, in cycloalkanes the relative positions of groups attached to the ring are fixed, so that it is possible to have groups attached to either the same side of the ring, or opposite sides. Alkenes with their double bonds also have this fixed property and are unable to rotate. Same side = cis. opposite side = trans This is an example of geometric isomerism

Thioether

Sulphide Example: Diethyl Sulphide

Molecular shapes(geometry)

Tetrahedral - 4 single pairs - 109.5 Trigonal planar - 3 pairs - 120 Linear - two pairs - 180

Systemic nomenclature

The order is as follows: stereochemistry: geometry around double bonds and/or chiral centres substituents: groups attached to the main chain, listed alphabetically Amino substituents are given the N-prefix to indicate their position parent: the number of carbons in the main chain unsaturation: the presence of any double or triple bonds functional group: the most important functional group, as far as naming the compound is concerned, which also determines the end where numbering starts -hydroxy or -oxo if a aldehyde or ketone is part of the group with a higher priority e.g. trans-3-ethyl-3-methylhex-4-en-2-ol geometry of double bond substituents no. carbons double bond functional group

Lone pairs

The outer shell electrons not used for bonding are called lone pairs, and contribute to the geometry of the atom

Alkyne

Triple bonded carbon -less common in nature and are in industrial products -yne suffix Example: Ethyne

Acid anhydride

Two C's double bonded to O and joined by another O Example: Ethanoic anhydride

Condensation reaction

Two functional groups react giving a new functional group with the loss of a small molecule -Condensation polymers are formed when diacids or diacid halides react with diols or diamines:

Benzene/benzyl/phenyl

When benzene acts as a single substituent, it is called phenyl. When there are two in the chain of substituents it is called benzyl. Abbreviations for the phenyl group include Ph and Ø. Abbreviations for the benzyl group include Bn, Ph-CH2- and Ø-CH2-.

Zwitterion

a molecule with both positive and negative charges NH2CH2COOH -> NH3+CH2COO-

Heterocyclic compounds

are organic ring compounds with one or more atoms other than carbon in the ring(s). For natural compounds, the usual heteroatoms are N, O or S Examples also include cyclic esters - lactones - and cyclic amides - lactams. Aromatic heterocycles are also possible, where they satisfy Hückel's rule: Planar, monocyclic, fully conjugated polyenes have general aromatic stability only if they possess 4n + 2 π electrons, where n is integer. Thus, in compounds such as furan and pyrrole, one of the heteroatom lone pairs becomes part of the aromatic system. aromatic heterocycles make up the bases in DNA and RNA, which are derivatives of pyrimidine or purine. These are also aromatic, and hence planar. DNA contains cytosine (C), thymine (T), adenine (A) and guanine (G). In RNA, uracil (U) replaces thymine

Toluene

common name for a methyl group bonded to a aromatic ring

Styrene

ethene group attached to a aromatic

Propyl and Butyl groups

isopropyl --I is alphabetised sec-butyl -- B isobutyl -- I tertiary-butyl -- B dimethyl -- M

The position names given when two substituents are bonded to an aromatic

ortho - next to each other meta - 1 carbon apart para - opposite each other use ortho-chlorobenzoic acid rather than 2-chlorobenzoic acid If there are more than two substituents, then the positions are numbered so that the total of the numbers is the lowest possible. Substituents are listed alphabetically. If a derivative name is used (toluene; phenol, etc.) then the group that defines that derivative (methyl in toluene; hydroxyl in phenol) is given position 1

Epoxide

ring of two carbons and oxygen

Aromatic

ring with three alternating double bonds example napthalene

Thiol (mercaptan)

sulphur and hydrogen bonded Example: ethanethiol

Branched structures

we have a similar full graphic representation (image). We show the branches in brackets in a condensed formula: CH3CH2CH2CH2CH(CH3)CH3 Again, the stick figure shows only the carbon-carbon bonds