What's in a medicine?

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Acids, bases and bonding

  • Bronsted-Lowry theory says an acid is a PROTON DONOR. - They must contain hydrogen to release it as H+.
  • Bronsted-Lowry theory says a base is a PROTON ACCEPTOR - take H+ from other substances.
  • Therefore acids and bases react together by transferring protons.
  • Ionic bonding - ions stuck together by ELECTROSTATIC ATTRACTION - hold +ve and -ve ions together in a lattice.
  • Metals have giant metallic lattice structures.  Electrons in outermost shell are delocalised, leaving a positive metal ion.  Metal ions attracted to sea of delocalised ions so closely pack together to form a lattice.
  • Carbon can form giant networks of covalently bonded atoms - diamond and graphite.
  • Shape of molecule depends on number of electron pairs in outer shell.  
  • LPs repel more than BPs.
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Organic reactions - ALKENES

      • H2, Ni catalyst, 150C, high pressure
      • HBr, 20C  (Electrophilic addition)
      •  Br2, 20C (Electrophilic addition)
      •  Free radical polymerisation
      •  Steam, 300C, H3PO4 catalyst OR Water, conc H2SO4 catalyst. 
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Organic reactions - ALCOHOLS

    •  Al2O3, 400C OR reflux w/ conc H2SO4
    •  Gently heat 1 alcohol w/ acidified K2Cr2O7 w/ distillation 
    •  Reflux with acidified K2Cr2O7 
    •  Reflux 1 alcohol w/ acidified K2Cr2O7
    •  Reflux 2 alcohol w/ acidified K2CrO7
    •  Shake w/ conc HCl at room temp - 3 alcohols ONLY.
    •  Reflux w/ aq NaOH (Nucleophilic substitution)
    •  Reflux w/ excess NH3 in ethanol solvent.
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Carboxylic acids

  • Dicarboxylic acids have 2 COOH groups, one either end.
  • -dioic acid with e.  E.g pentanedioic acid.
  • CAs are weak acids as they partially dissociate into carboxylate ion and H+ ion.



  • CA + alkali ----> salt + water



  • CA + carbonate (CO  ) or hydrogencarbonate (HCO  ) ----> salt + carbon dioxide + water
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  • Esters have functional group -COO-
  • First part of name comes from alcohol, second part from carboxylic acid.
  • Alcohol + CA ---> ester + water
  • CONDITIONS: acid catalyst - conc H2SO4 + heat.
  • Ethanol + propanoic acid ----> Ethyl propanoate + water
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  • BENZENE - C6H6 - Delocalised electrons around carbon ring, making it more stable.
  • ARENES - compounds with a benzene ring.
  • Test for phenol: add IRON (III) CHLORIDE SOLUTION AND SHAKE.  If PURPLE, then phenol is present.
  • Phenol DISSOLVES to form WEAKLY ACIDIC SOLUTION, as OH group can form        H-bonds with H2O to form a phenoxide ion and an H+ ion.



  • Phenol reacts with strong bases to form salts.
  • Doesn't react with sodium carbonate as it's not a strong enough base to remove H+.
  • Phenol + NaOH ----> sodium phenoxide + H2O
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Acyl chlorides

  • Functional group -COCl
  • General formula CnH2n-1OCl
  • Acyl chloride + phenol ----> ester + HCl(g)
  • Ethanoyl chloride + phenol ----> phenyl ethanoate + HCl(g)
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Aldehydes and ketones

  • Aldehydes have carbonyl group at end of chain (-al).
  • Ketones have carbonyl group in middle of chain (-one) and have number to show which C the carbonyl group is on.
  • Aldehyde is made by heating a PRIMARY ALCOHOL with an oxidising agent.  ACIDIFIED POTASSIUM DICHROMATE (VI) used as oxidising agent.  Have to DISTIL aldehyde out of reaction to prevent further oxidation to carboxylic acids.
  • REFLUX SECONDARY ALCOHOL with an oxidising agent to form a KETONE.
  • Refluxing used as organic reactions are slow, flammable and volatile as they have low boiling points, so the vapours are condensed recycling them back into the flask, giving them time to react.
  • Distillation is used to separate liquide from impurities.  Heat impure liquid in flask with thermometer and condenser.  When liquid you want boils, place a flask at open end of condenser ready to collect product.
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Nucleophilic addition

  • Hydrogen cyanide reacts with carbonyl compounds to produce cyanohydrins (molecules with CN and OH groups).
  • Nucleophile attacks the molecule causing an extra group to be added.
  • Hydrogen cyanide is a weak acid and so partially dissociates in water to form H+ and CN- ions.


  • The CN- group attacks the carbocation and donates a pair of electrons. 2e-s from double bond transfer to oxygen.
  • H+ from HCN or H2O bonds to oxygen to form OH group.
  • HCN is highly poisonous gas - carry out in fume cupboard.
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Reaction types and atom economy

1. REARRANGEMENT - no atom added or removed.  Just change order in which connected.

2. ADDITION - molecules add together.

3. SUBSTITUTION - one functional group swapped for another.

4. ELIMINATION - atoms are removed from a molecule.

5. CONDENSATION - addition followed by elimination.  (H2O removed from combining)


  • Measure of the efficiency of a reaction - tells how wasteful a reaction is.
  • % atom economy = (Mr of DESIRED product/Sum of Mr of ALL products) x 100
  • Rearrangement and addition have 100% atom economy.
  • Elimination have lowest atom economy.
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Making medicines

  • When chemists find a molecule that has medicinal properties, they improve its properties by tweaking the molecular structure.


  • Salicylic acid relieved pain, but cased stomach ulcers.
  • Variations made = sodium salicylate - fewer side effects, but disgusting taste = vomit.
  • Best variation = acetylsalicylic acid - less irritating and not bad taste.
  • Important to test lots of similar molecules - find one with most powerful medicinal properties and least side effects.
  • Speed things up - chemists use a technique called COMBINATORIAL CHEMISTRY - make hundreds of similar molecules at same time in hope of one being safe and effective.  This set of compounds is called a LIBRARY.
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Making medicines 2

  • Before drug is licensed to be sold, goes through CLINICAL TRIALS, which answer the following questions:

1. Is it SAFE?

2. Does it WORK?


  • It's important to find reactions with high atom economy as medicine production can be damaging to the environment if it uses lots of natural resources or produces large amounts of waste chemicals.
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Infrared spectroscopy

  • Infrared spectroscopy lets you identify organic molecules.
  • Beam of IR radiation through sample, which is absorbed by the bonds, increasing their VIBRATIONAL energy.
  • Diff bonds absorb diff WAVELENGTHS and bonds in DIFF PLACES absorb diff wavelengths.
  • Can identify the molecule by referring to table and graph.
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Thin-layer chromatography

  • Used to separate and identify mixtures of molecules.
  • In TLC, stationary phase = silica fixed to glass plate.
  • Draw baseline and put drop of each mixture on the line.
  • Place plate in beaker with solvent, which is below the baseline and leave until solvent has moved up to the top of the plate.
  • Draw solvent front - where solvent moved up to, before it evaporated.
  • Use positions of chemicals to identify what the chemicals are.
  • Colourless chemicals are revealed using UV LIGHT or IODINE.  TLC plates have fluorescent dye added to silica layer that glows when UV light shines on it.  Spots of chemical cover up silica, so won't glow.  Iodine vapour sticks to chemicals, so show up as purple spots.
  • Chromatography can be used to PURIFY ORGANIC SUBSTANCES
    • Need larger scale equipment - glass column packed with silica.  Pour mixture into column and run solvent through continually.  Diff chemicals move down column at diff rates, so come out at diff times, so get pure chemicals.
  • Rf = distance travelled by spot/distance travelled by solvent
  • Rf values tells what each chemical is and are the same no matter how big plate is.
  • COMPOSITION OF TLC PLATE, SOLVENT OR TEMP CHANGE will give diff Rf values.  If suspecting mixture contains a certain chemical, run that chemical off with the mixture at the same time.
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Mass spectrometry

  • Used to find Mr of a compound.
  • To find Mr of a compound, look at molecular ion peak on spectrum.
  • Molecular ions are formed when have electrons knocked off, so put in [ ]+
  • Bombarding electrons make some of molecular ions break into fragments, which are positive ions that show up as peaks on mass spectrum, making a fragmentation pattern.
  • Differences between peaks tells you about 'lost' fragments.
  • The mass differences between peaks indicate the loss of groups of atoms, suggest the origins of peaks - e.g. peaks at masses of 15 and 77 are usually due to presence of a methyl and phenyl positive ions - loss of a methyl group would be indicated by a mass difference of 15.
  • High resolution mass spectrometers measure m/z values to at least 4dp.
  • These accurate values allow you to compare elements and compounds using relative isotopic masses - relative isotopic mass of C12 is exactly 12 - everything else measured relative to this.
  • Accurate values also help in working out formula as in low resolution mass spectrometry, an M+ peak at m/z = 28 could be produced by many different molecules - N2,CO,C2H4.
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