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Organic and biological chemistry - Coggle Diagram
Organic and biological chemistry
Classification of chemical bonds
Ionic(G1,2,15,16,17)
Characterized by the complete donation of electrons from one atom to another
Has a giant crystal lattice structure
Held together by strong electrostatic forces of attraction
Formed between metal and non metal atoms
Covalent(G14,15,16,17)
Atoms share electrons
Formed between non metal atoms
Octet rule
General rule states that non-metal tend to gain electrons so as to fully fill their valence shell(i.e. Complete 8 e- in their outer shell
number of covalent bonds formed will depend on how many more e- are needed to complete octet
Carbon atoms can form total of 4 bonds either, 4 single bonds, 2 double bonds, 1 double bond and 2 single bonds and finally 1 triple and 1 single bond.
Significance of type of bonds
Differences in behavior due to differences in molecular bonding
Dissolved NaCL would break into their respective ions but Dissolved sugar molecules remain intact
Electronegativity and polarity
Electronegativity is the tendency of an electron being held on by an atom
In a covalent molecule, the more electronegative atom would hold onto the electron more and attain a partial negative charge while the other atoms would attain a partial positive charge
Bond polarity is a chemical property indicating the presence of dipoles(permanent partial charges) in a covalent bond between two atoms. Only applicable for covalent bonds
Polarity is directly related to EN difference where if the EN diff is 0-0.5, it will be non-polar so because there are no permanent dipole and where if EN diff is 0.5-2.0 it will be polar because there is existence of permanent dipole.
Non-polar covalent bond
Both atoms in the bond share electrons equally. But no permanent + or - charge build up. It is between two atoms that re close in position in periodic table.
Polar bonds
Electrons in polar bonds are not share equally. Between two non-metal atoms that re two or more positions apart in the periodic table. Development of dipole moments on bonded atoms.
Molecular polarity
Polarity of bonds has directions, indicated by arrows. The vectorial sum of all the individual bond arrows determine molecular polarity or dipole
Van der waals (intermolecular forces of attraction)
London-dispersion forces
The only force within non-polar molecules
Permanent Dipole-Dipole forces
Formed when there is a partial negative charge and a partial positive charge on two separate non-metal atoms.
Dipole - Induced dipole force(temp)
When a non-polar molecule attains a temporary partial charge on one of its atoms that attracts a polar molecule.
Hydrogen bonds
When hydrogen is bonded with atoms with a high electronegativity like nitrogen, fluorine or chlorine
Oxygen, Nitrogen, fluorine, chlorine, bromine in organic compounds are sure polar molecules
Lecture 3
IUPAC nomenclature of hydrocarbons
Locate main chain where we must contain the double/triple bond. Number the main chain. Carbon atom of the double/triple bond has the lowest number. Higher priority than branch. If both double and triple bond exist, double bond takes higher priority and indicate the double or triple bond. If there is more then 1 or 2 double or triple bonds, we must number them and add the relevant prefix
The prefix "iso" is used when all carbons except one form a continuous chain. This one carbon is part of an isopropyl group at the end of the chain
Isomerisms of hydrocarbons
Structural Isomers
Molecules that have the same number of atoms, but different arrangement.
They have different properties
The number of structural isomers increases as the number of C atoms in the main chain increases(OBC need to learn till 7 C atoms)
How to form structural isomers
Find a line of symmetry
Cancel either left or right side and cancel the very last carbon in the side that was not cancelled at the start
3.The purpose of crossing either left or right hand side is to expel a mirror image being formed
Cross out ALL the ends when we have 2 or more excess carbons that we want to form isomers.
Geometric Isomers
(stereoisomerism)
Single bonds between C atoms have free rotation
Rotation around a CC double bond is not possible
Geometric isomers exist when 2 or more isolated arrangements are possible due to type of bonds
Alkenes: Rigid double bond, geometric isomers possible
Alkynes: rigid triple bond but linear(1-D structure) no geometric isomers
Alkanes: free rotation about all bonds(no geometric isomers)
Geometric isomers are compounds that have same molecular and structural formulas but a different spatial arrangement of atoms or groups because of restricted rotation about double bond or ring system
Geometric isomers do not interconvert under normal conditions as they require the double bond to be broken(too much energy)
How to determine cis or trans isomers of alkenes:
Locate double bond
Determine if the compound is unsymmetrical at each C
If compound unsymmetrical, cis if the two large grps on same side and trans if two large grps are on opp side
Large groups when determining isomers would depend on atomic number if they are the same amount of atoms
Cycloalkanes geometric isomers
The C atom must be unsymmetrical where the carbon is not just connecting to the other carbons but also must not be connecting to one other atom like hydrogen only
Properties of hydrocarbon
Physical properties
Density is less then 1g/ml
C1-C4 hydrocarbons is gas at room temp
Insoluble in water but soluble in non-polar solvents like CCL4
C5-C17 is liquid at room temp
Non-polar
More than C17 is solid at room temp
Chemical properties
Alkanes are saturated with no functional group. Chemicaly unreactive or INERT
Alkenes/Alkynes are unsaturated, possesses either double or triple bond where there is a source of reactivity.
Dispersion intermolecular-forces
Solubility concept: like-dissolves-like
Effect to boiling point
Boiling point being higher, means they have stronger dispersion forces.
Reactions of hydrocarbons
Elimination
Used to prepare alkenes as atoms or functional group between two carbons would be eliminated to create a double bond
Dehydrohalogenation where a use of base to remove H-X elements(HCL ,HBr, HI) from alkyl halide
The base must be able to be dissolved in its solvent
Dehydration where water removed from adjacent carbons of alcohol using concentrated acid and heat
zaitsev rule states that asymmetrical alkanes are the reactants, elimination can result in formation of more than 1 alkene-product mixture. Major products will be the one which is most stable. Most stable product is the one which has more no. of substituents or R-groups attached to double bond
Addition
Reagents add to the compound to form a saturated compound with presence of catalyst and heat (except hydrohalogenation and halogenation)
Hydration(addition of H and OH)
presence of diluted acid or a small amount of acid
Markonikov rule where the carbon atom with the most hydrogen atom initially will receive the additional hydrogen atom only when the alkene is unsymmetrical
Halogenation(addition of 2 X)
Cannot add fluorine and iodine because its too reactive and too unreactive.
Hydrogenation(addition of 2H)
presence of catalyst(Pt, Pd, Ni) and heat
Hydrohalogenation(addition of HX)
Forms alkyl halide with acid halide as a reagent. Follows markonikov rule too.
Markonikov rule where the carbon atom with the most hydrogen atom initially will receive the additional hydrogen atom only when the alkene is unsymmetrica
Alkyne addition reaction
Can form double bond by adding 1 equivalent reagent
Can form single bond with 2 equivalent reagents
Hydrogenation, Halogenation and hydrohalogenation same as alkene
Hydration reaction
When there is a double bond and OH we call this an -Enol where the double bond would go towards to oxygen forming a carbonyl- group
Product will form aldehydes or ketones
Mono-Substitution
Substitution of alkane
Energy is needed, in the form of heat or light(UV) is necessary for halogenations
Substitution is most likely to happen for secondary and tertiary hydrogens
Intro to hydrocarbons and their classifications
Hydrocarbons are organic compounds that contains hydrogen and carbon atoms only
Saturated hydrocarbons
Alkanes
Linear
General formula is CnH2n+2
Cyclic
General formula is CnH2n
Unsaturated hydrocarbons
Alkenes(cc double bond) and Alkynes(cc triple bonds)
Linear
General formula of alkene is CnH2n while general formula of alkyne is CnH2n-2
Cyclic
Number the ring double bond 1 and 2. Numbering goes to the direction of the C atom nearest to the substituent.
Functional Groups
C-C double bond
C-C triple bonds
Reactions
Lecture 4
Nomenclature of alkyl halides
Locate and rank functional group.
2.Locate double or triple bonds.
3.Locate main chain(contains all functional groups and unsaturations)
4.Number the main chain and start naming the parent chain and substituents.
Preparation of alkyl halides
Hydrohalogenation of alkenes and alkynes
Remember markonikov rule
Aromatic substitution
Formation of aryl halides through the reaction between benzene and halogen gas.
A hydrogen on a benzene ring is replaced with X
Catalyst used is lewis acid(FeX3) or (AlX3), X identify is the same as the halogen gas reagent
Lewis acid is an electrophile[electron loving] ( e deficient, e seeking reagent)
If lewis acid halogen is not the same as halogen reagent, there will be a mixture of reagent halogen and lewis acid halogen (50%)
Free radical substitution (alkanes)
Free radical = Any atom or molecular fragment with an unpaired electron.
Radicals contain an tom with an incomplete octet and are generally unstable and reactive.
Initiation
1.Free radicals are first generated.
2.Halogen gas is broken into halide free radicals.
3.A slow reaction which requires energy in the form of radiation, heat or peroxides
Propagartion
A series of chain reactions.
1.Initial halide radicals take the H atom from alkane chain to produce alkyl radicals.
2.Alkyl radicals in turn take up halogen atom to produce 3.halogenated product and regenerate the halide radical.
Termination
A process where 2 free radicals to combine to form unreactive centers. Stops the substitution reaction by consuming the free radicals.
In the presence of more chlorine an long reaction time, more substitution occurs and a mixture of halogenated alkanes are produced.
Substitution of alcohol to akyl halides.
Reagents are anhydrous or pure alcohol with concentrated HX, Pcl3 or Pcl5(catalyst) in the dry state.
Alkyl halides properties and classification
Alkyl halides are alkanes with one of more halogens in place of hydrogen
Halogen groups treated as substituents to the main chain alkane.
Chlorine(chloro)
Bromine(bromo)
Fluorine(fluoro)
Iodine(iodo)
Melting and boiling points are higher than alkanes due to its higher polarity
Increases with higher molecular weight(increase dispersion forces) and number of halogen atoms
Not soluble in water. Soluble in non-polar solvents like alkanes and other alkyl halides
Primary secondary and tertiary alkyl grps (amine exception of pst)
Reactions of alkyl halides
Nucleophilic substitution
Replacement or substitution of the halide groups with nucleophiles.
Nucleophiles are electron-rich species that can donate electrons to electrophiles to form a new bond.
Nucleophiles can be in the form of negatively charged ions or neutral species. Nucleophiles are usually Characterized by lone pairs.
(group 5,6 and7 would probably act as nucleophiles)
C-X bond in alkyl halides are polarized.
Partial positive charge on carbon attracts negative charge in nucleophile.
When neutral nucleophiles are used, usually a small amount of base is required for faster reaction.
Older sibling giving in to younger sibling(higher group atoms being displaced by lower group atoms)
Halogen --> Sulfur group(-SH,-SR) --> Alcohol/ether group(-OH,-OR)--> Amino Group(-NH2)