Oxford IBDP Chemistry Course Book 2014 Part 2

allosteric activation 612 random errors 266, 267 crude oil 658–70 allosteric inhibition 612 systematic errors 266–7 Franklin, Rosalind 624 allosteric sites 611 esterification 256 free-radicals 250–1, 535 biological detergents 597, 600–1 esterification reaction 529–30 freeze-drying 4 competitive inhibition 612 esters 256 freezing 4 enzyme action and kinetics 611–14 ethane 452 fuel cells 230–1, 687, 701 enzyme inhibition and negative feedback 612 ethanol 721, 781 alkali fuel cells 693–4 enzyme-substrate complex 561 ethene 253 biological fuel cells 230, 430 induced fit model 561, 611 formation of sp2 hybrid orbitals in ethene direct methanol fuel cells 694–5 lock-and-key model 561, 611 350–1 electrolytes 693 Michaelis–Menten equation 612–13 ethylenediamineteraacetate see EDTA hydrogen fuel cells 693–6 non-competitive enzyme inhibition 611–12 ethyne 351–2 hydrogen–oxygen fuel cells 230, 430 pharmaceutical drugs 721 evaporation 4 methanol fuel cells 230, 430 product inhibition 612 exothermic processes 4, 140, 141 microbial fuel cells 430, 687, 700–1 reverse transcriptase enzymes 748 experiments 261 PEM (proton exchange membrane) fuel cell saturated enzymes 612 effect of changing experimental conditions on 693, 694 sharing knowledge 614 the equilibrium constant separators 693 substrates 561 185–7 fuels 9, 664 epimers 645 energetics experiments 146 “green” fuels and the carbon footprint 663 equations 1 experimental conditions for paper greener energy 661–2 Arrhenius equation 384–6 chromatography 553 motor octane number (MON) 246, 660 balancing the equation for the combustion of experimental determination of strength of octane number 246 butane 10 acids and bases 202 octane rating 660–1 Bragg equation 523 experimental errors 266–7 research octane number (RON) 246, 660 de Broglie equation 293 experimental evidence for electron fullerenes 119, 502, 503 expressing redox reactions using half- configurations 64 C60 fullerene 119–20 equations 217–18 experimental measurements of reaction rates inclusion complexes 120 Henderson–Hasselbach equation 608, 741 162–3 functional groups 236, 242 how to balance chemical equations 8 experimental methodology errors 266 aliphatic compounds 244 ideal gas equation 29–30, 165 experimental yield 20, 23, 24 converting one functional group to another ionic equations 89 OPERA experiment 263 249 Michaelis–Menten equation 612–13 reproducibility of results 674–5 unsaturated hydrocarbons 242–3 Nernst equation 687, 697–9 risk assessment 598 fusion reaction 666 nuclear equations 767 Rutherford’s gold foil experiment 40–1, 42 oxidation overall equation 309 exponential notation 264 Galvani, Luigi 227, 688 Planck’s equation 279–80 extinction coefficient 615 galvanic cells see voltaic cells rate equation 165, 375, 376–7, 378–9, 379–83 gamma knife 769 Rydberg equation 295 Fahrenheit scale 3, 139 gamma radiation 545, 769 Schrödinger wave equation 56, 294 Faraday’s constant 432 gas chromatography (GC) 554 thermochemical equations 145, 271 Faraday’s first law of electrolysis 432 gas laws 26 writing and balancing equations 7 Faraday’s second law of electrolysis 432 Boyle’s law 26–7, 307 equilibrium 4, 7, 179, 190, 394 fats 316–17, 565, 568, 578–9 Charles’s law 27–8 calculating the equilibrium constant using cis-fats 647 combined gas law 29 concentration data 390–2 health 571–2 Gay-Lussac’s law 29 chemical systems 181–2 neoglucogenesis 574 gases 1, 3 combining equilibrium constants 184 rancidity of fats 570–1 kinetic theory of gases 24, 161, 165, 170 dynamic equilibrium 180 trans-fats 647–8 Gay-Lussac, Joseph 24–5, 29 dynamic equilibrium: computer simulations fatty acids 565, 566, 647–8 gel electrophoresis 551, 610 182 degree of unsaturation 569 genetic code 626 effect of a catalyst on equilibrium reactions essential fatty acids 567–8 genetic diseases 626 189 monounsaturated fatty acids 565, 566 genetic engineering 619, 627 effect of changing experimental conditions on physical properties of fatty acids 566–7 Geobacter 687 the equilibrium constant polyunsaturated fatty acids 565, 566 metallireducens 700–1 185–7 saturated fatty acids 565, 566 Gibbs free energy 357, 369–70 effect of pressure on reactions in the gas phase unsaturated fatty acids 565, 566 calculating Gibbs free energy change of a 187 vaccenic acid 648 reaction from enthalpy and equilibrium constant 179, 182–3, 185–7, 389 Fehling’s solution 583 entropy data 370–1 equilibrium law 182–4, 389, 390 female sex hormones 577 cell potential 418–21 equilibrium reactions in chemistry 180–1 Fenton reactions 535 Gibbs free energy and chemical equilibrium Gibbs free energy and chemical equilibrium Feynman, Richard 42, 501 372, 392–3 372, 389, 392–3 Fibonacci sequence 464 Gibbs free energy change of formation 370 Haber process 186–7 first order reactions 670 glaciers, retreating 366 heterogeneous equilibrium 183 fission 44, 187 global dimming 679, 685–6 heterogeneous equilibrium and solubility heterolytic fission 250, 251 global warming 361, 366, 679, 686 180–1 homolytic fission 250 glucose 583 heterogeneous equilibrium partition coefficient see nuclear fission control of glucose metabolism 583 779 flame tests 52 glycerophospholids 573 homogeneous equilibrium 183 Fleming, Sir Alexander 725, 728, 729 glycogen 588 law of chemical equilibrium 182 fluorine 98 glycosidic links 580, 584, 585 Le Châtelier’s principle 185–6, 389 food labelling 147 Graham’s law of effusion 705–6 position of equilibrium 390–2 foods 571–2 graphene 118–19 reaction quotient 189 calculating energy content 573 graphite 117 temperature and the equilibrium constant food additives and the law 572 electrolysis of aqueous copper sulfate using 187–8 food fortification 595 inert graphite (carbon) writing equilibrium constant expressions 183– formal charge (FC) 329, 330–1, 355–6 electrodes 425–6 4 calculation of FC 330 graphs 261, 272, 274–6 equivalence point 405 different interpretations of “charge” 331–2 dependence 272 half-equivalence point 405 fossil fuels 230, 245, 430, 657 dependent variables 272 errors 266–7 coal 662–4 effect 272 crash of the Mars Climate Orbiter spacecraft crude oil 245, 658–70 equation of a line 274 263 fossil fuels store reduced carbon 658 extrapolation 274 OPERA experiment 263 fractional distillation 238, 779–80 graphical representations of first order 795

INDE X reactions 380, 381–2 physical properties of a homologous series intermolecular forces of attraction 123 graphical representations of second order 236–8 London forces 124–8 reactions 380, 382–3 Hooke’s law 281 van der Waal’s forces 124 graphical representations of zero order hormones 44–5, 576 International Atomic Energy Agency 754 reactions 380, 381 host–guest complexes 597, 601–2 International Bureau of Weights and Measures graphs and correlation 272–3 Howrah Bridge, Calcutta 211 (BIPM) 13, 267 idea of a “best-fit” line 274 Human Genome Project 625 International Energy Agency 654 independent variables 272 Hund’s rule of maximum multiplicity 60, 304 International Organization for Standards (ISO) intercept 274, 386 hybridization 329, 345, 347, 348, 352–4, 355–6 267 scatter plots 272 formation of sp hybrid orbitals in ethyne 351– International Renewable Energy Agency (IRENA) slope or gradient of a line 273–4 2 656 x-axis 272 formation of sp2 hybrid orbitals in ethene International Space Station (ISS) 230 y-axis 272 350–1 International Union of Pure and Applied Gratzel cells 714 formation of sp3 hybrid orbitals in methane Chemistry see IUPAC green chemistry 317, 443, 509, 597, 603, 605, 349–50 Inuit diet 574 752, 755 hybrid orbitals 348 iodine 45 atom economy 603, 755–6 hydration 362, 363 iodine number 569 costs of green chemistry 603–4 hydration shells 363 iodine test for starch 587–8 greenhouse gases 250, 679, 680, 686 hydrocarbons 10, 236 ionic bonding 93, 94–5, 102, 103, 472 agriculture and deforestation 685 aromatic hydrocarbons 242 differences between ionic and covalent carbon sinks: role of the oceans 683–4 saturated and unsaturated hydrocarbons 242 bonding 101 global dimming 685–6 hydrogen ionic compounds 95 greenhouse gas emissions from human index of hydrogen deficiency (IHD) 277–9 deduction of formula and name 96 activities 682 uses of hydrogen 424 lattice structures 93, 95, 357 industry and energy production 684–5 hydrogen bonding 122, 124, 129–30 Lewis (electron dot) structures 106 measures to reduce greenhouse gas emissions definition of the hydrogen bond 129 physical properties of ionic compounds 96–7 684–5 example of the effect of hydrogen bonding ionic equations 89 natural sources of greenhouse gases 681–3 130 ionic liquids 97 guanine 621 hydrogen bonding and water 130 ionic radius 75 gyres 509 key point 129 periodic trends in ionic radius 79–80 representation of hydrogen bonds 129 ionization 201 Haber process 179, 186–7, 316 hydrogen cells 430–1 emission spectra and ionization 294–6 Haber–Weiss reactions 535 hydrogen fluoride 99–100, 331–2 ionization of water 199 Haber, Fritz 186, 187, 535 hydrogen fuel cells 693–4 ionization energy 75, 80, 291, 300i, 359 half-life (t) 45 comparing fuels 695–6 first ionization energy 80, 294 th half-life of a nuclear process 670–1 hydrogen fuel sources 694 n ionization energy 294 half-life calculations 671 hydrogen fusion 666–7 periodic trends in ionization energy 80–2, halides 89, 444 hydrogen–oxygen fuel cells 230, 430 296–9 halogenation of alkanes 250–1 hydrogen peroxide 213 second ionization energy 294 halogenation of alkenes 253–4 hydrogenation 247 transition metals 311 halogenoalkanes 245, 248, 442 hydrogenation of alkenes 253, 316 ionizing radiation 766, 767 halogens 75, 88, 441–2 hydrogenation of oils 316–17 ions 7, 79, 93, 95 reaction between halogens and alkali metals hydrolysis 542 coloured compounds of transition metals and 89 peptides hydrosis 556 their ions 311–16 reaction between halogens and halides 89 salt hydrosis 404 electron configurations of first-row d-block covalent network solids 117 triglycerides hydrosis 570 elements and their ions Hawking, Stephen 166 hydrolytic rancidity 315 304–7 Haworth projections 580, 582 hydronium cation 121 iron 476 heat 139 hydronium ion 191, 193–4 isoelectric focusing 560, 610 chemical potential energy, heat and entropy hydrophilic molecules 779 isomers 241, 451 140 hypotheses 70, 148 cis-/trans-isomers 641 heavy metals 534, 538 configurational isomers 451, 453–4 adsorption 537 ibuprofen 728 conformational isomerism in cyclic chelating effects 535–6 ideal gases 20 hydrocarbons 453 solubility product constant 536–7 ideal gas equation 29–30, 165 conformational isomers 451–2, 452 toxicity 599–600 molar volume of an ideal gas 24–6 eclipsed conformations 452, 453 Heisenberg’s uncertainty principle 56, 171, 293 index of hydrogen deficiency (IHD) 277 ethane 452 hemoglobin 632 working out from the molecular formula 278– Newman projections 452 carbon monoxide poisoning 634 9 optical isomerism 455–8, 641 cooperative binding in hemoglobin 632–4 working out from the structure 278 staggered conformations 452, 453 fetal hemoglobin 633 indicators 403, 405, 408–9 stereoisomers 451, 641–2 other factors affecting affinity of hemoglobin selection of an indicator 409 structural isomers 241 for oxygen 633–4 indices 15 see also stereoisomerism Henderson–Hasselbach equation 608, 741 indigestion 738, 740 isotactic addition polymers 494 heredity 619–20 inductive reasoning 70, 390 isotopes 14, 43 heroin 734, 735 Inductively Coupled Plasma (ICP) 480–2 calculations involving non-integer relative Hess’s law 139, 148, 357 infrared radiation 280 atomic masses and overall and net reactions 148–51 infrared spectroscopy (IR) 261, 280 abundances of isotopes 48–9 hexoses 581 fingerprint region 283 isotope enrichment 44 Higgs boson 292 molecular dipole moment 282–3 isotope separation 44 high density polyethene, 494, 496 spring model 280–1 radioisotopes 44–6 high pressure carbon monoxide vibration mode 281–2 IUPAC 1, 6, 46, 82, 117, 121, 124, 125, 129, 214, disproportionation (HiPCO) 501, 502, 504, initial rate of reaction 15, 164 216, 235, 240, 262, 263, 266, 267, 302, 505 initiation 251 337, 363, 405, 414 high resolution 1H NMR spectroscopy 462–4 injections spin–spin coupling 462–4 intramuscular 718 Kekulé, August 115, 246, 247 high-performance liquid chromatography (HPLC) intravenous 718 kelvin (K) 3, 139 554, 616–17 subcutaneous 718 Kelvin scale 3, 139, 171 histones 620 insecticides 598 keratin 559 HIV (human immunodeficiency virus) 748–9 intermolecular forces 122, 123–4, 131–2 ketoses 580, 581 homologous series 235, 236 dipole–dipole forces 128–9 Kevlar 492, 558 functional groups 236 hydrogen bonding 129–30 kinetic theory of gases 24, 161, 165, 170 796

kinetic–molecular theory 384 773 molar absorptivity 615 kwashiorkor 561 multinuclear MRI 773 molar concentration 20, 31, 221 male sex hormones 577 molar mass 12, 14, 15 lactase 585 malleability of metals 71, 134–5 determining molar mass 30–1 lactose intolerance 585 manganese 308–9 percentage composition by mass 19 language of chemistry 1, 6, 7, 216 Markovnikov’s rule 444 molar volume 20 language of mathematics 199 mass 1 molar volume of an ideal gas 24–6 lanthanoids 72–3, 302 mass defect 666–7 mole 1, 12, 13–14 Large Hadron Collider 292 mass spectrometry (MS) 261, 285–6, 480 mole calculations 16–18 laser ablation 504, 505 fragmentation pattern 285 molecular electrostatic potential 332 lattice enthalpies 358, 359, 361 molecular ion peak 285 molecular formulae 12, 18, 239 Lavoisier, Antoine 2, 192 mass spectrometers 47 molecular geometry 109, 338–42, 355–6 Le Châtelier’s principle 179, 185–6, 187, 188 materials 471, 474 axial positions 333 Leucippus 38 classifying materials 472–3 bond angles in molecular geometries 109–10 Lewis (electron dot) structures 98, 99, 104, designer materials 473 equatorial positions 333 105–6, 239, 329, 355 materials science 472 method to deduce Lewis (electron dot) cations and anions and ionic compounds 106 mathematics 1, 21, 199 structures and electron domain method to deduce Lewis (electron dot) significant figures 264–6 and molecular geometries 110–14 structures and electron domain matter 2–3 molecular geometries based on five and six and molecular geometries 110–14 elements, compounds, and mixtures 6 electron domains 333–4 use of square brackets 106 Maxwell–Boltzmann energy distribution curve molecular orbital theory (MOT) 319, 335, 346, Lewis acids and bases 395, 396 161, 170 347–8 Lewis symbols 98, 105 temperature effects on kinetic energies 171 anti-bonding molecular orbitals 347 Lewis, Gilbert N. 98, 396 measurement 261, 289–90 bonding molecular orbitals 347 Libby, Willard 45 absolute and relative uncertainty 268–71 molecular orbital diagrams 347–8 ligands 312 experimental errors 266–7 molecular orbits 347 bidentate ligands 314 graphical techniques 272–6 molecular polarity 115–16 chelate ligands 313, 314–15 qualitative and quantitative analysis 262 molecular self-assembly 501, 502 classification of ligands 313–15 spectroscopic identification of organic molecular substances 117 ligand field theory (LFT) 319 compounds 277–88 molecularity 377–8 monodentate ligands 313, 314 uncertainty in measurement 262–6 bimolecular 377 nature of the ligands 322–3 medical waste 751–2, 757 termolecular 377, 378 polydentate ligands 313, 314–15 nuclear waste 753–4 unimolecular 377 spin-free configuration 322 pharmaceutical industry 754–5, 756 molecules 95, 99 spin-paired configuration 322 medicinal chemistry 717, 718 actual shapes 105–6, 127–8 strong-field ligands 322 natural products in medicine 725 classifying molecules: primary, secondary, and weak-field ligands 322 Meissner effect 516, 517 tertiary compounds limiting reagents 20, 21 melanin 638 245–6 determining limiting reagent 21–2 eumelanin 638 hydrophilic molecules 779 lipases 570 pheomelanin 638 molecules of life 540–2 lipids 565, 578–9 melting points 4 monomers 254–5, 495 dietary choices 576 covalent network solids 117 identifying monomers 498–9 energy values of lipids 571 ionic compounds 96 monosaccharides 580–2 lipids and health 571–2 Mendeleev, Dmitri 67, 68–9, 76, 658 cyclic forms 581, 645–6 lipids in living organisms 565 mercury 71 morphine 732, 733, 734 lipoproteins and health 576 metabolic pathways 540 Moseley, Henry 67, 69 phospholipids 573–5 metabolism 540, 541 multidrug resistance (MDR) 730 steroids 575–6, 576–7 metallic bonding 133–6, 472 animals and humans 753 lipophilic drugs 779 alloys 134, 136, 478–9 multiplication 265 lipoproteins 576 delocalized electrons 134 mutagens 626 high-density lipoproteins (HDL) 576 melting points of metals 135 mutations 625, 626 low-density lipoproteins (LDL) 576 non-directional bonds 134–5, 136 point mutation 626 liquefied petroleum gas (LPG) 10 metallic substances 472 liquid crystals 489, 492–3 metalloids 67, 71–2 nano scale 120 discovery of liquid crystals 489 metals 67, 71, 136, 475 nanocatalysts 487 LCD displays 491–2 periodic trends in metallic and non-metallic nanoparticles 487, 714, 710 lyotropic liquid crystals 491 character 75, 85–7 molecular self-assembly 502 nematic liquid crystals 491 production of aluminium 477–8 nanotechnology 501–2, 508 properties of liquid crystals 490 reactions of acids with metals, bases, and atomic force microscopy (AFM) 506 thermotropic liquid crystals 491 carbonates 196–7 bottom-up approach 502 liquid–liquid extraction 778 reduction by a more reactive metal 476–7 electron-beam-induced deposition 507 LNGS (Laboratori Nazionali del Gran Sasso) 263 reduction of iron ore in the blast furnace 476 implications and applications of logarithms 265–6 reduction of metals 475–6 nanotechnology 507 characteristic 265 spectroscopic methods 479–82 scanning probe techniques 506 mantissa 265–6 metathesis 9 scanning tunnelling microscopy 507 Lomonosov, Mikhail 658 methane 349–50 top-down approach 501–2 London forces 117, 122, 128 methanogenesis 250 nanotubes 501, 502 dispersion forces 124 methanol fuel cells 230, 430 carbon nanotubes 119, 120 instantaneous dipole 124–5 direct methano fuel cells 694–5 constructing nanotubes 502–5 instantaneous induced dipole-induced dipole methodologies 193 how do nanotubes grow? 503 forces 124 micelles 491–2 narcotic analgesics 733 number of electrons 126 Michaelis–Menten equation 612–13 natural compounds 242 polarizability 125 Michaelis constant 612 negative indices 15 shapes of molecules 127–8 turnover number 613 neoglucogenesis 574 size (volume) of electron cloud 126–7 microbial fuel cells 430, 687, 700–1 Nernst, Walther Hermann 699 low density polyethene, 494, 496 microscopic properties 183 net charge 332 Lowry, Thomas 193, 396 microwaves 102, 103, 280 neutralization 202–3 lustre of metals 71 mild analgesics 727, 728 standard enthalpy change of neutralization mixtures 1, 5–6 15, 196 macroscopic properties 183 heterogenous 1, 6 neutrons 42, 766 magnetic quantum number 58 homogenous 1, 6 boron neutron capture therapy (BNCT) 765, magnetic resonance imaging (MRI) 285, 765, models 345–6 768–9 797

INDE X Newlands, John 68 SN1 reactions and tertiary halogenoalkanes background to designing a synthetic route 448 Newman projections 452 440–1 retro-synthesis 448–50 Newton, Sir Isaac 51 SN2 reactions and primary halogenoalkanes summary reaction pathways 450 nicotine 721 439–40 oseltamivir (Tamiflu) 747–8, 756 nitrobenzene 447 nucleotides 619, 620, 621–2 overvoltage 423 nitrogen 99 nucleus 40, 41 oxidation 209, 210, 542 Nobel Prize in Chemistry 45 daughter nucleus 767 anodes (CROA) 226, 227, 415, 417, 422, 423, noble gas electron configuration 94–5, 98 lead nucleus 767 425, 426, 428, 429 nomenclature 216 nylon 530, 558 corrosion 210–11 nomenclature of alkanes 240–2 overall equation 309 oxidation states and the nomenclature of obesity 146–7, 571 oxidation and reduction in terms of electron transition metal compounds observation 90 transfer (OILRIG) 211–12 215–16 Occam’s razor 161, 166, 197, 198, 329, 330 oxidation and reduction in terms of oxidation Stock nomenclature system 215 octaves, law of 68, 69 states 213 non-biodegradable materials 602 octet rule 95, 104, 329, 330 oxidation half-reaction 309 non-directional bonds 134–5 incomplete and expanded octets 114, 331, oxidation number 214 alloys 136 344–5 oxidation of alcohols 255 non-metals 67, 71 oil 245 oxidation state 331 periodic trends in metallic and non-metallic fractionating and cracking 658–70 oxidation states and the nomenclature of character 75, 85–7 net exporters 245 transition metal compounds non-narcotic analgesics 727 net importers 245 215–16 non-steroidal anti-inflammatory drugs (NSAIDS) OILRIG 211 oxidizing agents 214 727 oligosaccharides 586 rules for assigning oxidation states 213 nuclear charge 767 opiates 732–3, 736 variable oxidation states 309, 214–15 effective nuclear charge 77–8 crossing the blood–brain barrier 732, 733–4 oxidative rancidity 315 nuclear energy 44, 703–4, 708–9 cultural views on drugs 735 oxides 75 background to nuclear technology 702–3 development of synthetic opiates 734 metal oxides 196 radioactive decay 706–7 diamorphine (heroin) 734, 735 non-metal oxides 196 risks associated with nuclear energy 707–8 side effects and withdrawal symptoms 733 oxidization 85, 94, 209, 543 uranium enrichment 704–6 opioid receptors 733 oxidizing ability 89, 90 nuclear equations 767 opium 732 reaction with water 90 atomic number 767 opsin 649–50 some interesting oxides 87 mass number 767 optical emission spectroscopy (OES) 480 trends in the properties of metal and non- nuclear fission 665, 668–9, 673, 702 optical isomerism 455 metal oxides 86 critical mass 669 diastereomers 451, 455, 458 oxoanions 86, 95, 113 half-life of a nuclear process 670–1 optical isomers and plane-polarized light 456– oxygen 2, 211, 343 radioactive waste 672, 753–4 7 biochemical oxygen demand (BOD) 209, types of subatomic particle 669–70 physical and chemical properties of optical 223–5 nuclear fusion 665, 667–8, 673, 702 isomers 457 covalent bonding 98–9 discovery of nuclear fusion 666 optometry 212 hydrogen–oxygen fuel cells 230, 430 hydrogen fusion 666–7 orbitals 56–7 other factors affecting affinity of hemoglobin mass defect 666–7 d orbitals 319 for oxygen 633–4 types of subatomic particle 669–70 d-to-d electronic transmissions 324 ozone 220 nuclear magnetic resonance spectroscopy (NMR) degenerate orbitals 60 catalysis of ozone depletion 343 280 frontier orbitals 319 ozone layer 9, 10, 155, 156, 167–9, 680 nuclear magnetic resonance spectrometers hybrid orbitals 348–52 wavelength of light required to dissociate 285 orbital diagrams 58, 62, 63–4 oxygen and ozone 343 nuclear medicine 765, 774 see atomic orbitals; molecular orbital theory availability of nuclear medicine 768 (MOT) paclitaxel 758–60 decay constant 772–3 orbits 52–3, 75 paper chromatography 552–4 gamma knife 769 organic chemistry 235, 236, 259–60, 437–8, biological pigments 636 magnetic resonance imaging (MRI) 765, 773 459–60 eluent 552 radiodiagnostics 769–72 alcohols 255–7 experimental conditions for paper radionuclides in nuclear medicine 765 alkanes 249–51 chromatography 553 radiotherapy 765, 766–8 alkenes 252–5 mobile phase 552 techniques in nuclear medicine 768–9 aromatic hydrocarbons 246–7 retention factors 552–3 nuclear symbol 43, 44 chemical formulae of organic compounds 239 stationary phase 552 nuclear waste 753 classifying molecules: primary, secondary, and paracetamol 728 Goiânia accident, Brazil 754 tertiary compounds paradigm shifts 2 high-level waste (HLW) 754 245–6 paramagnetic materials 64, 318, 479 low-level waste (LLW) 753 conversion of nitrobenzene to phenalymine partial charges 331–2 nuclear weapons 44 (aniline) 447 partial pressure 780 nucleic acids 619, 628i electrophilic addition reactions 443–5 particles 1 adenosine triphosphate (ATP) 622 electrophilic substitution reactions 257–8, changes of state 4 complementary base pairs 621 445–6 distribution of velocities 170 DNA replication 625–6 factors affecting the rate of nucleophilic fundamental particles 292 heredity and the storage of biological substitution 441–3 Higgs boson 292 information 619–20 functional groups 242–4, 248, 249 Rutherford’s gold foil experiment 40–1 intermolecular bonding 625 homologous series 236–8 subatomic particles and descriptions of the nitrogenous bases and nucleotides 620–2 Markovnikov’s rule 444 atom 42–4 primary structure 624 nomenclature of organic compounds 240–2 partition coefficient 779 RNA and DNA 623–4 nucleophilic substitution reactions 257, 439– Pascal’s triangle 463, 464 structure of DNA 624–5 41 patterns 201 transcription 626–7 organic synthesis 439 Pauli exclusion principle 60 nucleophiles 257, 397 saturated and unsaturated hydrocarbons 242 Pauling scale 83, 101 what makes a good nucleophile? 443 organic compounds 235, 236 Pauling, Linus 83, 85, 101, 319, 593 nucleophilic substitution reactions 257, 437, chemical formulae of organic compounds 239 Pauling’s electroneutrality principle 312–13 438, 439 classes 242 PCBs (polychlorinated biphenyls) 510–11, 599 drawing mechanisms for SN1 reactions 441 nomenclature of organic compounds 240–2 PEM (proton exchange membrane) fuel cells drawing mechanisms for SN2 reactions 440 spectroscopic identification 277–88 693, 694 factors affecting the rate of nucleophilic organic solvents 754 penicillin 725, 729, 730 substitution 441–3 organic synthesis 439, 448 antibiotic resistance 729, 730, 752–3 798

benzylpenicillin 729–30 pharmaceutically active compounds (PACs) 600, effect of pressure on reactions in the gas phase beta-lactam ring 729 751 187 development of penicillin into a drug 729 pharmacodynamics 456 partial pressure 780 mechanism of action of penicillin 729–30 pharmacokinetics 456 primary compounds 245–6 penicillin G 729 phenalymine 447 primary solutions 33 side-chain (R) 729 phenol–methanal plastics 530 primary standards 16 penicillinase 729 philosophy 307 principal quantum number 57 pentoses 581 phlogiston 2, 192 probability density 56 peptides 548 phonons 519 products 1 C-terminal 555 phospholipids 565, 573–5 proligands 312 dipeptides 555 amphiphilic 574 propagation 251 example of peptide 555 photochromic lenses 212 how many peptides can we make? 555 photons 52, 53, 292 hydrolysis of peptides 556 photosynthesis 540, 543, 544–5, 658, 678 N-terminal 555 harnessing solar energy by chlorophyll 675–7 naming peptides 555 photosynthesis, respiration, and the prophylactics 730 peptide bonds 554 atmosphere 544–5 prosthetic groups 559, 613 peptide linkage 554 photosystems 635 proteins 213, 547, 548, 563–4, 606, 617–18 peptides in the human body 556 photovoltaic cells 710, 712–13 properties of peptides 556 pi bonds 113, 334–6 acid–base of proteins 560 percentage yield 20, 23 picometre (pm) 41 acid–base properties of 2-amino acids 606–8 perfumes 455 placebos 718 amino acids and peptides 548–9 periodic law 68–9, 69 double-blind tests 719 amino acids as zwitterions 550 periodic table 67, 68–9, 76 placebo effect and clinical trials 718–19 biuret test 560, 616 actinoids 72–3, 302 Planck’s equation 279–80 central role of proteins in biochemistry 547–8 d-block elements 72–3, 303 plasma 480–2 denatured proteins 559 electron configurations and the periodic table Inductively Coupled Plasma (ICP) 480–2 enzymes 560–3 73–4 plasticizers 494 fibrous proteins 558–9 f-block elements 72–3, 302, 303 plasticizers and chlorine-free plastics 511 gel electrophoresis 551, 610 lanthanoids 72–3, 302 PVC and the use of plasticizers 496–7 globular proteins 558 main-group elements 72–3 plastics 509, 515 isoelectric focusing 560, 610 metals, non-metals and metalloids 71–2 biodegradable plastics 597, 602 native states/structures 559 p-block elements 72–3 effect of plastic waste and POPs on wildlife predicting secondary structures 557 period number 67, 71 510 primary structure 556 periodic table today 70–1 phenol–methanal plastics 530 prosthetic groups 559, 613 periods 71 plastics and polymers 602 protein assay 614–17 s-block elements 72–3 recycling of plastics 511–13 protein deficiency 561 transition elements 72, 302–3 resin identification code (RIC) 512–13 protein sequencing 556 periodic trends 75, 91–2 sorting plastics 514 protein subunits 559 periodic trends in atomic radius 78–9 see also polymers proteins and heredity 547 periodic trends in electron affinity 82 polarizability 125 proteins as biological buffers 610–11 periodic trends in electronegativity 84 Poliakoff, Martyn 76 quaternary structure 559 periodic trends in ionic radius 79–80 polychloroethene see PVC scleroproteins 559 periodic trends in ionization energy 80–2, polyethene, 494, 496 secondary structure 556–7 296–9 polymers 248, 472, 494, 500 tertiary structure 558–9 periodic trends in metallic and non-metallic addition polymerization 254, 529 proteomics 556, 560 character 75, 85–7 atom economy of polymerization reactions proton beam therapy (PBT) 769 periodicity 67, 68 499, 529 proton nuclear magnetic resonance spectroscopy perms 559 condensation polymerization 528–9 (1H NMR) 261, 283–5, 462 pH curves 404–8 cross-linking polymer chains 531 chemical shift 283 pH scale 191, 197, 198 elastomers 496 high resolution 1H NMR spectroscopy 462–4 calculating pH 198–9 high density and low density polyethene 495 integration trace 285 ionization of water 199 identifying monomers 498–9 magnetic resonance imaging (MRI) 285 pH and acid–base titrations 200 ion implantation 531 tetramethylsilane 465–9 pH changes 75 isotactic, atactic, and syndiotactic addition protons 42, 766 pharmaceutical drugs 717, 718, 724 polymers 497–8 Proust, Joseph 38 administration 718 modifying polymers 531–2 Proust’s law of constant composition 6 clinical trials 718–19, 720, 723 plastics and polymers 602 PTFE (polytetrafluoroethene) 244 drug action and development of new drugs polymerization of alkenes 254–5 puckering 453 721–3 polymers in society 496 pure sciences 472 drug design 722 polystyrene 497 pure substances 5 effective dose 717, 719 PVC and the use of plasticizers 496–7 purines 620, 621 effectiveness and safety 719–20 thermoplastics and thermosets 495–6 PVC 496–7, 509 lead compounds 722 vulcanization 531 pyrimidines 620 lethal dose 717, 719 see also plastics new chemical entities (NCEs) 722 polypeptides 548 qualitative analysis 18, 262 phase IV trials 723 polysaccharides 586–7 quantitative analysis 18, 33, 262 placebo effect 718–19 polystyrene 497 quantitative measurements 1 post-clinical studies 723 polyurethanes 530–1 mole 13–14 preclinical trials 722–3 polyvinyl chloride see PVC si units, 3, 12–13 receptors and inhibitors 717, 721 POPs (persistent organic pollutants) 510, 598 quantization 52–4 risks and benefits 719 dioxins and PCBs 510–11 quantization and atomic structure 55–8 side effects 719 porphyrins 631–2 quantum mechanics 187 social implications of the pharmaceutical porphin 631 quantum mechanical model of the atom 56–8 industry 752 positron emission tomography (PET) 45, 770 quantum numbers 58 therapeutic effects 718 postulates 24, 38 azimuthal quantum number 58 therapeutic index 717, 719 potassium permanganate 308–9 magnetic quantum number 58 therapeutic window and bioavailability 717, potential energy profile 167, 171 principal quantum number 58 719–20 powers 15 spin magnetic quantum number 58 tolerance and addiction 717, 720–1 precision 263–4, 267 quartz 120 toxic dose 717, 719 predictions 201 waste products 754–5, 746 pressure 20, 25 racemic mixtures 456 799

INDE X optically inactive mixtures 762 activity series 218–19 semiconductor oxide sensors 310 radiation 754 chlorine and ozone 220 silicon semiconductor photovoltaic cells 710, alpha particles 766 electron book-keeping 212 712–13 beta particles 766 expressing redox reactions using half- sensory perceptions 203 gamma radiation 545, 769 equations in acidic or neutral sequestration 685 infrared radiation 280 solutions 217–18 serendipitous discoveries 120, 244, 489, 725, 728 ionizing radiation 766, 767 hydrogen peroxide 213 sex hormones 577 neutrons 766 optometry 212 shielding 77, 78 positrons 766 oxidation states and the nomenclature of shikimic acid 756 protons 766 transition metal compounds SI units 3, 12 radioactive decay 706–7 215–16 accuracy 13 decay chain 768 redox titration reactions 221–2 base units 13 decay constant 706, 772–3 variable oxidation states 214–15 International System of Units 267 radioactive waste 672, 753–4 Winkler method 222–5 physical constants and unit conversions 13, 25 radiodiagnostics 769–70 reducing sugars 583–4 prefixes, abbreviations and scales 13 technetium-99m 770–2 reduction 85, 94, 209, 542, 543 units of pressure 24 radioisotopes 44 cathodes (CROA) 226, 227, 415, 417, 422, sigma bonds 113, 334–6 carbon-14 in cosmic, geological, and 423, 425, 426, 428, 429 significant figures 264–6 archaeological dating 45–6 oxidation and reduction in terms of electron logarithms 265–6 cobalt-60 in radiotherapy 45 transfer (OILRIG) 211–12 operations involving addition or subtraction iodine radioisotopes as medical tracers 44–5 oxidation and reduction in terms of oxidation 265 Turin Shroud 46 states 213 operations involving multiplication or division radionuclides 753, 765 reducing agents 214 265 radiopharmaceuticals 765 reduction half-reaction 309 rounding off 265 radiotherapy 766 removal of oxygen or addition of hydrogen silicon dioxide 120 cobalt-60 in radiotherapy 45 211 silicon semiconductor photovoltaic cells 710, external radiotherapy 765 reflux 256, 447 712–13 internal radiotherapy 765 refrigerants 9 single replacement reaction 9 types of radiation 766–8 Reinitzer, Friedrich 489 single-photon emission computed tomography radiotracers 770 relative abundance 14 (SPECT) imaging 45 radiowaves 280 relative atomic mass 12, 14, 15, 46–7 Slater’s rules 77, 78 rancidity 570–1 atomic mass unit 42, 46 slow step 377–8 hydrolytic rancidity 570 calculations involving non-integer relative soap 491, 570 microbial rancidity 570 atomic masses and sodium chloride 5 oxidative rancidity 570 abundances of isotopes 48–9 sodium hydroxide, uses of 424 random errors 261, 266, 267 mass spectrometers 47 solar cells 713, 716 Raoult’s law 780 relative molecular/formula mass 12, 14 advantages and disadvantages of DSSCs 715 rate equation 165, 375, 376–7 renewable energy 368 developing the technology 715 deduction of rate equation from proposed reproducibility of results 674–5 dye-sensitized solar cells (DSSCs) 710, 713–15 reaction mechanism 378–9 resin identification code (RIC) 512–13 solar energy 674 graphical representations of first order resonance 104, 113, 329, 337 energy conversion in solar cells 710, 713 reactions 380, 381–2 delocalization and resonance 336–7 photosynthesis 675–7 graphical representations of second order resonance energy 247 solubility reactions 380, 382–3 resonance forms 115, 337 covalent network solids 117 graphical representations of zero order resonance hybrids 115, 337 heterogeneous equilibrium and solubility reactions 380, 381 resonance structures 115, 247, 337, 675 180–1 method of initial rates 376, 379–80 respiration 540 ionic compounds 97 orders 376 aerobic respiration 543 solutions 20, 31 overall reaction order 376 anaerobic respiration 543 solvation 362, 363, 442 rate law 376 photosynthesis, respiration, and the solvation shells 363 rate-determining step (RDS) 377–8 atmosphere 544–5 solvents 31, 442–3, 542 reactants 1, 20, 542 respirators 23 specific heat capacity 142 in excess 21 retinal 649–50 spectrochemical series 322–3 reaction intermediate 378, 383, 485 retro-synthesis 448–50 spectroscopy 280, 286–8, 289–90, 461, 470, reaction mechanism 377–8, 379 retroviruses 748 479–80, 483, 672 deduction of rate equation from proposed reverse transcriptase enzymes 748 advances in analytical techniques 462 reaction mechanism 378–9 rhodopsin 649–50 atomic emission spectroscopy (AES) 480 evaluation of proposed reaction mechanisms ribosomes 626 high resolution 1H NMR spectroscopy 462–4 383 rimantadine 746–7 infrared spectroscopy 261, 280–3 reaction quotient 179, 189 ring strain 453 mass spectrometry (MS) 261, 285–6, 480 reaction rates 161, 162, 375, 387–8i risk assessment 598 nuclear magnetic resonance spectroscopy average rate 163–4 RNA 620, 623–4 (NMR) 280, 285 experimental measurements of reaction rates RNA polymerase 626 optical emission spectroscopy (OES) 480 162–3 secondary structure 626 plasma 480–2 factors that affect the rate of a chemical strands 623 proton nuclear magnetic resonance reaction 172 Rohrer, Heinrich 41 spectroscopy (1H NMR) 261, initial rate 164 Rutherford, Ernest 40–1, 42, 43 283–5, 462–4 instantaneous rate 164 Rydberg equation 295 spectroscopic identification of drugs 775–6 measuring the rate of a chemical reaction UV-vis spectroscopy 280, 614–16 172–6 salt hydrolysis 404 spin–spin coupling 462–3 molecularity and rate-determing step (slow salts 196 chemical shift 463 step) of a reaction 377–8 saponification 570 combinations 463 monitoring the rate of a reaction 203 scanning tunnelling microscope (STM) 41 rules 464 overall order of reaction 376 scholasticism 307 shielding and deshielding 463 rate equation 165, 375, 376–7 Schrödinger wave equation 56, 294 upfield and downfield 463 rate of reaction 162 Schrödinger, Erwin 56, 294 spontaneity 364 reactions 1, 2, 5, 7, 8 scientific notation 264 non-spontaneous reactions 364 types of reaction 9 scleroproteins 559 spontaneous reactions 364 real gases 20, 24, 30 screening 77 spring constant 281 recycling 150 secondary compounds 245–6 spring model 280–1 recycling of plastics 511–13 self-ordering 502 standard cell potential 414–16 redox reactions 209, 210–13, 233–4, 688 semiconductors 72 Gibbs free energy 418–21 800

standard conditions 144 instrumentation errors 266 explanation of the colour of transition metal standard hydrogen electrode (SHE) 416–18 personal errors 266 complexes 323–6 gas electrode 416 Système International d’Unités 3, 12 Haber–Weiss and Fenton reactions 535 standard electrode potential 416–17 systems 140 heavy metals 534–7 Standard Model 292 chemical systems 181–2 key characteristics 307 standard solutions 20, 33 closed systems 140 magnetic properties of transition metals 318 standard temperature and pressure (STP) 20, 25 isolated systems 140 successive ionization energies 311 starch 586–7 open systems 140 transition metals as catalysts 316–18, 487–8 iodine test for starch 587–8 Type A 308 state function 139, 141 Tamiflu 747–8, 756 Type B 308 state symbols 1, 7 targeted alpha therapy (TAT) 765, 768 Type C 308 states of matter 2 Taxol 758, 763–4i variable oxidation states 308–11 gas 3 chiral auxiliaries 761–2 transition state 167 liquid 3 clinical use 760–1 translation 626 solid 3 discovery of paclitaxel 758–60 transmutation 669 statins 576 environmental considerations of Taxol transpeptidase 729 Statue of Liberty, NY 210 production 760 triads, law of 68, 69 stereocentres 455 semi-synthetic production 760 triglycerides 565, 566, 568–9 stereoisomerism 451, 459–60, 641–2, 651–2 technetium-99m 770–2 hydrolysis of triglycerides 570 configurational isomers 453–4, 641 temperature 1, 3, 139 iodine number 569 conformational isomerism in cyclic temperature and the equilibrium constant triglycerides in chocolate 568 hydrocarbons 453 187–8 triplets 626 conformational isomers 452 temperature dependence of Kw 400–1 Turin Shroud 46 optical isomerism 455–8 temperature effects on kinetic energies 171 stereoisomerism in carotenoids 455 temperature scales 144 ultraviolet (UV) light 280 stereoisomerism in medicine 456 teratogens 457, 762 uncertainty 262 types of isomerism 451–2 termination 251 absolute and relative uncertainty 268–71 see also isomers terminology 181, 182, 193, 358 percentage error 268–9 steroids 565, 575–6, 579 tertiary compounds 245–6 percentage relative uncertainty 268 anabolic steroids 577, 780–1 tetrahedral structures 107, 108–9 precision and accuracy 263–4 steroid hormones 576–7 wedge-and-dash notation 122 propagation of uncertainty 268–71 steroidal backbone 565, 575 tetramethylsilane 465–9 significant figures 264–6 Stock nomenclature system 215 thalidomide 457, 762 unified atomic mass unit 46 stoichiometry 20–1 theoretical yield 20, 23, 24 unit cells 516, 520–2 stoichiometry coefficients 221, 376 theories 70 unsaturated hydrocarbons 242–3 stoichometric relationships 1, 14, 34–6 thermochemistry 141, 157–60, 271 test for unsaturation 252 stomach acid 737–8, 744 chemical potential energy, heat and entropy unsaturation, degree of 277–9 active metabolites 737, 740 140 uracil 620 antacids 738–9 endothermic and exothermic reactions 141 uranium enrichment 704–5 discovery of gastric acid 739 enthalpy and thermochemistry 141–6 Graham’s law of effusion 705–6 gastric proton pump 740 thermodynamics 140 UV-vis spectroscopy 280, 614–16 H2-histamine receptors 740 first law of thermodynamics 364 omeprazole and esomeprazole 740 second law of thermodynamics 364, 365 nern valence bond theory (VBT) 319, 346–7 regulation of acid secretion 739–40 third law of thermodynamics 699 valence shell electron pair repulsion see VSEPR Stoney, George Johnstone 39 thermoplasticity 242, 494 theory strong analgesics 733 thermoplastics 495–6 van der Waal’s forces 124 structural formulae 239 thermoset plastics 494, 495–6, 530 van der Waal’s radius 77 condensed structural formulae 239 thin-layer chromatography (TLC) 553 vaporization 4 full structural formulae 239 Thomson, J.J. 39, 40, 42, 50 standard enthalpy change of vaporization of skeletal formulae 239 thymine 620 water 123 sublevels 57, 72 titrations 33, 403 vibration mode 281–2 sublimation 4 acid–alkali titration 32 viruses 745–6, 750 substitution 250–1 acid–base titrations 197 antiviral drugs 746–8 electrophilic substitution reactions 257–8 indicators and end point 405 capsids 745 nucleophilic substitution reactions 257 pH and acid–base titrations 200 retroviruses 748 subtraction 265 redox titration reactions 221–2 visible light 280 sucrose 584 titration of strong acid with strong base 405 vision chemistry 649–50 sulfuric acid 377 titration of weak acid with strong base 405–6 visual cycle 650 superconductors 516–17, 525–7 titration of weak base with strong acid 407 vitalism 236 applications of superconductors 519 titration of weak base with weak acid 408 vitamins 590, 596 Bardeen–Cooper–Schrieffer (BCS) theory 516, tobacco 721 classification of vitamins 590 518–19 torsional strain/energy 453 decomposition of vitamins 595 Cooper pairs 516, 519 total energy 139, 140 deficiency diseases 591 Meissner effect 516, 517 transcription 626–7 fat-soluble vitamins 591 strange metals” 519 transesterification 676 food fortification 595 superconductivity 517 transition elements 72, 214, 301, 302–3, 327–8 primary and secondary deficiencies 591 type 1 and type 2 superconductors 516, 517– actinoids 302 vitamin A: retinoids and carotenes 592–3, 18 characteristics of transition elements 307 649, 650 supercritical fluids 755 electron configurations of first-row d-block vitamin C: ascorbic acid 84, 593–4 supersymmetry (SUSY) 348 elements and their ions vitamin D: cholecalciferol 594–5 supramolecules 601 304–7 vitamin poisoning 591 sustainable energy 368 inner transition 302 water-soluble vitamins 591 symbols 6 lanthanoids 302 vitrification 754 alchemical symbols 306–7 transition metals 214, 215–16, 303 volatility 97 symmetry 321, 348 Aufbau principle 304–5 Volta, Alessandro 227, 688 syndiotactic addition polymers 497–8 bonding models of transition metal complexes voltage 687, 692 Synroc 754 312–13 voltaic cells 226, 227, 413 synthesis 9 classification of ligands 313–15 cell diagrams 229 synthetic compounds 242 coloured compounds of transition metals and Daniell voltaic cell 228–9 synthetic polyamides 558 their ions 311–16 EMF and the standard cell potential 414–16 systematic errors 142, 143, 261, 266–7 complexes of transition metals 312 metal/metal-ion electrode 227–8 experimental methodology errors 266 coordination numbers 314, 216 spontaneous cell 415 801

INDE X voltaic pile 688 volumes 1 volumetric analysis 1, 33 VSEPR theory 104, 106–9, 329 bond angles in molecular geometries 109–10 electronegativity differences 110 how to handle π bonds 113 interpreting the VSEPR model 110 linear arrangement 107, 108–9 method to deduce Lewis (electron dot) structures and electron domain and molecular geometries 110–14 multiple bonds 110 tetrahedral arrangement 107, 108–9 trigonal planar arrangement 107, 108–9 vulcanization 531 Warner, John 603, 755 water 3–4 auto-ionization 199 chlorine and ozone as disinfectants in drinking water 220 hydrogen bonding and water 130 ion product constant 199 solvent, reactant, and product 542 standard enthalpy change of vaporization of water 123 Watson, James 348, 624 wavefunctions 56 wavenumber 281 websites 44, 58, 70, 76, 302, 320, 354, 377, 560 wedge-and-dash notation 122 Wilkins, Maurice 624 Winkler method 209, 222–4 measuring BOD using the Winkler method 224–5 Winter, Mark 44, 58, 70, 302 work 140, 226 World Health Organization 223 writing organic mechanisms 250 (”curly arrows”) X-ray crystallography 37, 41, 280, 522–3, 525–7 covalent and atomic radii 524 finding the atomic radius from X-ray crystallography data 524–5 single-crystal X-ray crystallography 464 X-rays 37, 280 xenobiotics 597, 598, 751 metabolism of xenobiotics 599 yew, European (Taxus baccata) 760 Pacific (Taxus brevifolia) 758, 760 zanamivir 747–8 zeolites 488 zero current 414 zidovudine 747 zwitterions 550, 607 802

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