Terms Flashcards
Conformation Isomers (Conformers)
Arise from free rotation about a σ-bond. Vary in stability due to differences in steric interactions. Staggered conformers are more stable than eclipsed conformers, while anti arrangements are more stable than gauche.
Cycloalkanes
Have a cyclic structure and vary in stability and strain energies based on sized and bond angles. Rings prevent free rotation about single bonds. Therefore substituent isomers that do not interconvert exist
What is the most stable conformation of cycloalkanes?
Chair conformation, which results in axial and equatorial positions (ring-flips can exchange these). Equatorial substituents result in more stable conformations due to reduces steric interactions.
Enantiomers
Molecules that are non superimposable mirror images - chiral.
Racemic Mixture
1:1 mixture of enantiomers
How can enantiomers be separated?
By converting them into diastereomers (different 3D shapes), separating them, then retransforming them into enantiomers
Stereochemistry of Alkenes
Stereoisomers due to lack of rotation about the C=C bond.
- diastereomers - non mirror image stereoisomers, named using E/Z nomenclature
Addition Reactions
Overall replacement of a weak π-bonds with a strong σ-bond
- hydrogenation, halogenation, hydrohalogenation, hydration
- σ-bond is a nucleophile, supplies e-, produces a carbocation intermediate
- rate increases with acidity
Stability of Carbocations
3° > 2° > 1°
stability increases with variety of substituents
Markovnikov’s Rule
Predicts the regiochemistry of HX addition to unsymmetrically substituted alkenes
H will preferentially end up on the side that has more Hs, while X will end up on the side with more substituents.
Alkene addition reactions with no nucleophile
Can result in polymers
Aromaticity requirements
Cyclic
conjugated
planar
4n + 2 π-electrons (n=integer)
Nomenclature for disubstituted benznes
Ortho (1,2-)
Meta (1,3-)
Para (1,4-)
Nucleophilic Substitution Reaction
- replacement of a leaving group by a nucleophile
- nucleophile attacks carbon of an organic molecule and displaces a leaving group, which carries away its bonding e-
- Two mechanisms
First Order Nucleophilic Substitution (SN1)
Two distinct steps: - ionisation - nucleophilic attack Reaction proceeds via an intermediate and rate depends only on substrate concentration. Results in a racemic mixture. Ease parallels carbocation stability.
Second Order Nucleophilic Substitution (SN2)
Making/Breaking of bonds is concerted. There is no intermediate and rate depends on both substrate and nucleophile concentrations. Able to interconvert enantiomers.
Ease is the reverse of carbocation stability
Elimination Reactions
The loss of an atom or group of atoms resulting in the formation of a multiple bond (opposite of addition reactions). Require reagents that are strong bases and relatively weak leaving groups. Two distinct mechanisms.
First Order Elimination (E1)
Two distinct steps:
- ionisation
- deprotonation
Proceeds via an intermediate with a rate dependent only on substrate concentration
Second Order Elimination (E2)
One step with simultaneous making/breaking of bonds. Rate dependent on concentration of substrate and base.
Regiochemistry of Elimination
Often more than one product possible (placement of double bond and rotation around it). The transition state for E2 reactions dictates the stereochemical outcome. Newman projections are needed.
Zaitsev’s Rule
In the elimination of H-X from an alkyl halide, the more highly substituted alkene product predominates. (less sterically crowded)
Carbonyl Functional Group
Carbonyl bond strongly polarised - electrophilic at the carbon and can undergo nucleophilic addition reactions.
Most carbonyl reactions involve the breaking of π-bonds
Formation of Aldehydes and Ketones
Can be formed via oxidation of primary and secondary alcohols.
1° alcohols oxidise to aldehydes and then to carboxylic acids
2° alcohols oxidise to ketones
3° alcohols are not oxidised
Jones Reagent
Oxidising agent (Cr)3/H2SO4)
Reduction of Carbonyls
Addition of hydride leads to an alkoxide, protonation of the alkoxide affords an alcohol
Common reducing agents
(H- sources)
LiAlH4 - Lithium aluminium hydride
NABH4 - Sodium borhydride
Reduction of Carboxylic Acids
Lithium aluminium hydride will reduce carboxylic acids directly to alcohols. It is not possible to stop at the intermediate aldehyde as these are more reactive than the acid.
Sodium borohydride does not reduce carboxylic acids
Nucleophilic Addition Reactions with CArbonyls
Addition of water affords hydrates - creates an acid base equilibrium
Addition of alcohols (catalysed by acids) affords hemiacetals; SN2 substitution then affords acetals
Carboxyl Group
Highly polarised and undergoes nucleophilic substitution through an addition/elimination mechanism
Nucleophilic Substitution of Esters
Nucleophilic substitution of esters by hydride results in reduction to primary alcohols
Preparation of Acid Chlorides
Acid Chlorides can be prepared from carboxylic acids and thionyl chloride (SOCl2).
Preparation of Esters
Acid Chlorides react readily with alcohols to yield esters. Nucleophilic Substitution via addition/elimination mechanism.
Preparation of Amides
Amides can be prepared via nucleophilic substitution (addition/elimination mechanism) of acid chlorides with primary or secondary amines. Tertiary amines are unreactive.
Reaction of Anhydrides
Carboxylic anhydrides have similar reactivity to acid chlorides.
- can produce esters via substitution with alcohols
- can produce amides by substitution with amines.
One equivalent of carboxylic acid is released.
Carbohydrates
Polyhydroxy aldehydes and ketones of general formula Cn(H2O)m
Energy storage material that also plays important roles in the social behaviour of cells and organisms.
Stereochemistry of Carbohydrates
Indicated by (D)- or (L)- descriptors. (L)- indicates highest numbered stereogonic sentre has hydroxyl on the left.
Nomenclature of Carbohydrates
Named according to:
- whether they are an aldehyde or a ketone
- number of carbons
- suffix ‘ose’
- D or L descriptor
Chemistry of Sugars
Dominated by intramolecular interaction of the alcohol and carbonyl functional groups
- aldehyde –> hemiacetal of aldehyde –> acetal of an aldehyde
- ketone –> hemiacetal of ketone –> acetal of ketone
Cyclisation of Aldoses
Aldoses are able to form cyclic hemiacetals. Hydroxide on second last carbon binds to carbonyl - addition of alcohol to carbonyl group).
This produces a new stereocentre called the anomeric centre.
Anomeric Isomers
Stereoisomer found in carbohydrate chemistry. Able to interconvert - mutarotation.
Cyclisation of Ketoses
Ketoses are able to form cyclic hemiacetals via addition of last hydroxyl group to oxygen.
Pyranose and Furanose
Used to denote 6 and 5 membered rings.
α- and β-anomers
For sugars of the D-series, in a standard Haworth projection, α-anomers have the anomeric hydroxyl pointing down while β-anomers have it pointing up.
This is the opposite for L-sugars
Reduction of Carbohydrates
The carbonyl group is readily reduced as the ring forms are in equilibrium with the open chain forms
Tautomers
Two molecules with the same molecular formula but different connectivity - constitutional isomers, in other words - which can interconvert in a rapid equilibrium
Oxidation of Carbohydrates
Can be used as a diagnostic method (reducing/non-reducing sugars).
Both aldoses and ketoses react because of tautomerism, if a sugar cannot mutarotate it is anon-reducing sugar (glycocsides)
Glycosides
A molecule (acetal) in which a sugar is bound to another functional group via a glycosidic bond. Produced from hemiacetal monosaccharides upon treatment with an alcohol and catalytic acid. Do not mutarotate and are not reducing sugars.
Maltose
Formed from joining the anomeric centre of one D-glucose and the 4-position of another (α-D-glucapyranosyl-1,4-β-glucapyranose) A reducing Sugar.
Sucrose
Formed from joining the anomeric centres of D-glucose and D-fructose. As both anomeric centres are acetals, sucrose is a non reducing sugar. (α-D-glucapyranosyl-1,1-β-fructafuranose)
Cellulose
Polymer of D-glucose
β-linkage between 1 and 4 positions
Starch
Comprised of amylose and amylopectin
α-linkage
Amylose
Exists in a helical conformation
Core of helix can form characteristic inclusion complexes
Amylopectin
linear chains of 24-30 α-1,4-linked D-glucopyranose interupted by α-1,6-branch points
Nucleosides
N-glycosides formed from a sugar and a nucleobase
Nucleotides
Formed from nucleosides by phosphorylation
Oligo and polynucleotides form the structure of DNA
Base pairing allows the double helix to form - need donor to form hydrogen bond
Keto-enol tautomerism
Each of the bases in DNA can appear as different tautomers, which are in equilibrium.
The keto form of each base normally present in DNA - critical for correctly matching the base pairs.
The imino and enol forms are rare.
The wrong tautomer of one base results in a mispairing
Amino Acids
Contain a basic amino group an acidic carboxyl group
20 naturally occurring α-amino acids, which can be classified according to their side chain
All are chiral except glycine.
Take (L)- and (D)- descriptors (proteins derived exclusively from L)
Amide Bonds
Form between -NH2 and of one amino acid and -CO2H of the next
Can be broken to establish amino acid sequence - acid hydrolysis (can be non-selectively or selectively broken, involves nucleophilic substitution via addition/elimination)
Synthesis of Proteins
Peptides can be synthesized chemically using nucleophilic substitution reactions of the carboxyl group.
Requires protecting the carboxylic acid of one amino acid and the amine of the other (and sometimes the R group)
Steps to make a peptide bond
- Amino group of one amino acid 1 is protected by the BOC derivative (via substitution)
- Carboxyl end of amino acid 2 is protected as the methyl ester
- The two protected amino acids are coupled using DDC
- The BOC protecting group is removed by acid treatment
- The methyl ester is removed by basic hydrolyisis
The Nernst Equation
Allows for calculation of cell potential under non-standard conditions
Concentration Cells
At unequal concentrations, current will flow until the concentration in each beaker is equal. At equilibrium, cell potential = 0V
The Stability Field of Water
Species with a potential more positive than the top line will liberate Oxygen from water - oxidation
Species with a potential more negative than the bottom line will liberate hydrogen from water - reduction.
Transition Metal Cation
Have strong attractions in water leading to metal water interactions approaching strength of covalent bonds - thus results in acid-base interactions.
A strong transition metal acid can bind up to 6OH2 ligands - an aqua complex, discrete and soluble
Bio availability
Requires concentration of at least 10^-6M
Availability of Fe
Ferric Ion soluble and available under acidic conditions, but not at the surface of natural fresh water bodies.
Iron enters the food chain in deep waters via the metabolisms of anaerobic bacteria.
Ligands
Natural molecules or anions that have a lone pair of electrons which is donated towards a metal ion - donor atoms
Coordination Number
The number of donor atoms bound to the metal ion. This determines geometric shape.
Charge on Metal Complexes
- If ligands are all neutral, the charge on the complex will equal the charge on the metal ion - the complex is cationic.
- If the total charge on the ligands equals the charge on the metal ion then the complex then the complex is neutral.
- if the total charge on the ligands exceeds the charge on the metal ion then the complex is anionic
Ligand name for water
aqua
Ligand name for ammonia
Ammine
Ligand name for carbon monoxide
carbonyl
Ligand name for Nitric Oxide
Nitrosyl
Ligand name for hydroxide
Hydroxido
Ligand name for oxide
oxido
Ligand name for Cyanide
cyanido
Ligand name for carbonate
Carbonato
Coordination Isomerism
Compound has the same formula but the formula of the complex ion is different
(structural)
Linkage Isomerism
The complex has the same formula but a ligand binds through different donor atoms
(Structural)
Complex Ion
A metal plus its ligands
Bidentate
A ligand that can form two bonds to a metal ion (e.g. oxalato
Chelate
A ligand that can bind to a metal ion through more than one donor atom to form a ring (e.g. catechol, ethylendiamine)
Geometric Isomerism
Occurs when atoms or groups of atoms can assume different positions in a complex (cis/trans, fac/mer)
(stereoisomerism)
Optical Isomers
Non-superimposible mirror images (chiral)
Enterobactin
A compound produced by aerobic bacteria that can extract iron from rust.
A cyclic ester with amide links to three catechol-type ligands
Catechol
A dianionic chelating ligand. Upon deprotonation can chelate metal ions.
Siderophores
Chelating molecules secreted by microorganisms that are able to bind iron ions very strongly.
Transferrin
An iron transport protein in the blood
- two identical subunits
- Fe ligands: 2 tyrosine, 1 histidine and 1 aspartic acid
- coordination environment completed by an anion (e.g. carbonate)
- drop in pH causes release of Fe2+
- acts as an iron scavanger
Ferritin
An iron storage protein
- rust covered with protein
- 24 subunits
- Fe ions enter through channels
Haem Group
An Fe2+ at the centre of a porphyrin ligand. Binds oxygen in oxygen carrying proteins.
Haemogloin
An oxygen binding protein α2,β2 with 4 haem units.
Exhibits cooperativity - binding of oxygen to one haem group causes conformational change that increases affinity of other haem groups (histidine is moved up)
The Bohr Effect
Low pH decreases haemoglobin’s affinity for oxygen
Zinc in Biological systems
Catalyses acid-base reactions
Zinc enzymes can act as OH- reagents - allow it to act as a base in biological systems
Carbonic Anhydrase
Catalyses formation of bicarbonate from carbon dioxide and water, and the reverse reaction.
- active site: zinc bound to three histidines
- binds water first, loses proton, nucleophilic O attacks C of carbon dioxide, bicarbonate formed
- bicarbonate can displace the water ligand, but not the coordinated OH-
Internal Energy (U)
The sum of the energies for all of the individual particles in a sample of matter.
Enthalpy (H)
A function related to the heat adsorbed or evolved by a chemical system.
Entropy (S)
A measure of the number of ways energy is distributed throughout a chemical system.
Gibbs Energy (G)
The energy from a reaction that is available to do work.
Heat (q)
A transfer of thermal energy due to a temperature difference.
First Law of Thermodynamics
The only way we can change the total energy of a system is through the transfer of heat or work to the surroundings.
Energy cannot be created or destroyed
Reaction Enthalpy
The sum of the enthalpies of any sequence of reactions into which the overall reaction may be divided.
Standard Enthalpy of Formation
The enthalpy change when 1mol of substance is formed at 10^5Pa and specified T from its elements in their standard states.
Second Law of Thermodynamics
The entropy of the universe increases in the course of a spontaneous change. Thus spontaneous processes tend to disperse energy.
Boltzmann Equation
S = klnW (W - microstates into which energy can be dispersed)
Spontaneous Process
A process is spontaneous if the change in Gibbs energy is less than 0 at constant p and T
Chemical Equilibrium
At equilibrium the rates of the forward and reverse reactions are equal and there is no net change to the overall reaction mixture.
Equilibrium concentrations are independent of direction of approach
Change in Gibbs Energy = 0, T=change in H/change in S can be used to find when a non-spontaneous process becomes spontaneous.
At equilibrium deltaG = -RTlnK
Reaction Quotient
An expression for systems that are not necessarily at equilibrium.
How do we derive rate laws for reactions?
Rate laws must always be derived experimentally using the method of initial rates.
What is Collision Theory?
The rate of reaction is proportional to the number of effective collisions per second among the reactant molecules. This requires sufficient energy and correct orientation.
How can Ea be determined?
Using the Arrhenius Equation:
- graphically: when ln(k) is plotted against 1/T the slope is -Ea/R
- using two temperatures: ln(k1) - ln (k2)
What is a homogenous catalyst?
A catalyst in the same phase as the reactants. Usually reacts with the reactants.
What is a heterogenous catalyst?
A catalyst in a different phase to the reactants. Commonly a solid and promotes reactions on surface through adsorption of one or more reactants.
How are Enzyme Kinetics modelled?
Using the Michaelis-Menten Model.
How do we derive rate laws for reactions?
Rate laws must always be derived experimentally using the method of initial rates.
What is Collision Theory?
The rate of reaction is proportional to the number of effective collisions per second among the reactant molecules. This requires sufficient energy and correct orientation.
How can Ea be determined?
Using the Arrhenius Equation:
- graphically: when ln(k) is plotted against 1/T the slope is -Ea/R
- using two temperatures: ln(k1) - ln (k2)
What is a homogenous catalyst?
A catalyst in the same phase as the reactants. Usually reacts with the reactants.
What is a heterogenous catalyst?
A catalyst in a different phase to the reactants. Commonly a solid and promotes reactions on surface through adsorption of one or more reactants.
How are Enzyme Kinetics modelled?
Using the Michaelis-Menten Model.
What are some common oxidising agents?
Hydrogen Peroxide Potassium Permaganate Chromium Trioxide Potassium Dichromate Jones Reagent
What are some common reducing agents?
Lithium aluminium hydride
sodium borohydride
