Level 2

Organic

Monocarbonyls, TCG

"Monofunctional Carbonyl Compounds and Carbanion Chemistry"

Carbanions
Organolithium reagents e.g. BuLi, LDA
Grignard reagents
Enol, enolate anion
Keto-enol tautomerism
Silyl enol ether (from Me₃SiCl with Et₃N), enamines, aza-enolates
Aldol reaction, incl. silyl enol ether aldol reactions
Reformatsky reaction
Henry reaction (nitro aldol)
Claisen condensation
Mannich reaction and Mannich bases
Haloform reaction
E1cB elimination reaction

Dicarbonyls, PJW

"Difunctional Carbonyl Compounds"

Diketone
Hard and soft nucleophiles and electrophiles
Michael reaction, nucleophilic conjugate addition, Gilman reagents
Dithianes (hard nucleophile at carbonyl carbon)
Claisen condensation
Nef reaction
McMurry reaction
Darzens reaction
Benzoin condensation
Acyloin condensation
Pinacol coupling reaction
Robinson annulation: ChemTube3D animation
OsO₄: Upjohn dihydroxylation

Aromatics and amines, TJS

"Aromatic Compounds and Amines"

CLW for amines: Gabriel synthesis, sodium azide amine synthesis, reductive amination (with NaBH₃CN), Hofmann rearrangement, nitrosation
Electrophilic aromatic substitution
Activating group. deactivating groups
Arene substitution patterns
Inductive effect, mesomeric effect
Friedel-Crafts reaction (alkylation and acylation)
Gattermann-Koch reaction
Wolff-Kishner reduction (KOH, N₂H₄)
Clemmensen reduction (Zn, HCl)
Nitrosation of aryl amines to diazonium salts
Baeyer-Villiger oxidation
Naphthalene EAS
Birch reduction
Claisen rearrangement
Fries rearrangement

Heterocycles, KIBM

"Heterocyclic Compounds"

Retrosynthesis, CLW

"Organic Synthesis"

Books:

Chris Willis and Martin Wills, Organic Synthesis (Oxford Chemistry Primer) (1995) (on Amazon.co.uk)
Stuart Warren and Paul Wyatt, Organic Synthesis: The Disconnection Approach (2008) (on Amazon.co.uk)
Stuart Warren, Organic Synthesis: The Disconnection Approach (1983) (on Amazon.co.uk)

Stereochemistry, APD

"Stereochemistry and Conformation"

Stereochemistry
Cahn–Ingold–Prelog priority rules
Chirality (chemistry)
Absolute configuration
Enantiomer
Diastereomer
Molecular configuration
Conformational isomerism
Alkane stereochemistry
Bürgi-Dunitz angle
Baeyer strain
Pitzer strain
Cycloalkanes
Cyclopropanes - planar by definition
Cyclobutanes - puckered to avoid eclipsing interactions
Cyclopentanes - envelope conformation
Cyclohexane conformation - chair form, boat form, twist boat, twist chair
Anomeric effect
Steric effects

Rearrangements, CPB

"Rearrangements involving Carbocationic or Polar Intermediates"

Carbocations
Carbon radicals (e.g. Ph₃C·)
Carbenes
Carbanions
Inductive effect
Mesomeric effect (e.g. allyl, benzyl C⁺)
Hyperconjugation, Beta-silicon effect
Non-classical ions
Synchronicity of mechanisms: stepwise reaction, concerted reaction, reaction intermediate,
Rearrangement reaction
1,2-rearrangement
Pinacol rearrangement
Demjanov rearrangement
Wagner-Meerwein rearrangement
Arndt-Eistert synthesis
Hofmann rearrangement
Curtius rearrangement
Lossen rearrangement
Schmidt reaction
Beckmann rearrangement

Proteins, DNW

"Amino Acids, Peptides and Proteins: Chemistry, Structure and Function"

Nylon (polyamides) from condensation polymerisation, e.g.

nH₂N-(CH₂)₆-NH₂ + nClOC-(CH₂)₄-COCl → (-HN-(CH₂)₆-NH-CO-(CH₂)₄-CO-)_n (nylon 6,6 with amide bond in bold) + 2nHCl

Aramids e.g. Kevlar
Amino acids
Peptide bonds
Peptides
Proteins
Hormones, signaling molecules
Peptide synthesis, Protein synthesis, Protein biosynthesis
Protein structure, Protein folding, Protein structure prediction, Membrane protein
Keratin
π-π stacking interactions
Ubiquitin (PDB 1UBQ ubiquitin), Proteasomes
Chemical polarity of amino acids: F A M I L Y V W - hydrophobic, D E H K N Q R S T - polar, G P C - special
Proline (Pro, P) is special:

It's a secondary amino acid (AKA imino acids, although this nomenclature is disputed)

It's conformationally locked (backbone dihedral angle φ fixed to about −75°) → very rigid, loses less conformational entropy upon folding, found in turns

Protein structure:
- Primary structure: sequence of amino acid backbone (plus cross-linking such as disulfide bonds)
- Secondary structure: alpha helices, beta strands (plus rare others)
- Tertiary structure: three-dimensional structure (full set of atomic coordinates in 3D space) - determined by protein crystallography or protein NMR
- Quaternary structure: arrangement of multiple folded protein molecules in a multi-subunit complex - XRD again
Ramachandran plot
UV-Vis spectroscopy can be used to determine protein concentration - aromatic amino acid side chains (K, Y, W, H) absorb UV
Supersecondary structure:
- Plastocyanins - Cu redox centre converts between Cu(I) and Cu(II), coordination geometry of Cu is not optimal for either oxidation state, making neither favoured and thus interconversion facile. Structures: PDB 3BQV, PDB 1PNC.

Ribbon diagram of plastocyanin
Residues coordinating Cu in plastocyanin
Cu coordination geometry

- EF hand - chiral, right-handed enantiomer only (with one exception). Aspartic acid residues bind Ca²⁺ (important in calcium signaling) in loop between two alpha helices.
- Beta hairpin - major structural unit, two beta strands antiparallel
- βαβ motif - two beta strands parallel, chiral (alpha helix either above or below plane of beta strands), only right-handed enantiomer found in nature
- Coiled coil - left-handed(!) - HPPHPPP repeat gives 3.5 not 3.6 residues per turn, so hydrophobic seam slowly curves - myosin, keratin
- Polyproline helix?
- Collagen helix?
Tertiary structure:
- all α-structures (αα) - buffers, triggers, allostery
  - calbindin - (2 × EF hand) mops up loose Ca²⁺
  - myoglobin - baby brother of haemoglobin - 8 helices, haem group binds Fe and thus O₂
- all β-structures (ββ) - hard-as-nails brick walls → rigidity
  - viral capsids
  - plastocyanin
  - antibodies
TIM barrel

OCPCs

RJC: Organic redox reactions
- Manganese dioxide oxidation of isopropanol to acetone
- Dess-Martin periodinane
- Baeyer-Villiger oxidation
- Swern oxidation
- Jones oxidation
- pyridinium chlorochromate oxidation
- ozonolysis
- epoxidation of olefins
- osmium tetroxide dihydroxylation
- hydrogenation
- NaBH₄ and LiAlH₄ reductions
- DIBAL-H reduction
- hydroboration-oxidation
- Birch reduction
PJW: Reversibility in reactions
KIBM: Planning organic synthesis
MCG: Protecting groups
VKA: Mechanism
- Acetal formation
RJC: Why reactions go wrong

Inorganic

NMR, CJA

"Introduction to NMR Spectroscopy"

Main group 1, NCN

"Chemistry of the Main Group Elements, Part 1"

Chlorides

Main group chlorides
group → period ↓	13	14	15	16	17
2	B B₂Cl₄ BCl₃	C C₂Cl₄ CCl₄	N - NCl₃	O - -	F - -
3	Al - AlCl₃	Si - SiCl₄	P PCl₃ PCl₅	S S₂Cl₂ SCl₂	Cl - -
4	Ga GaCl Ga₃Cl₇, GaCl₂ GaCl₃	Ge - GeCl₂ GeCl₄	As - AsCl₃ AsCl₅	Se Se₂Cl₂ SeCl₄ -	Br BrCl - -
5	In InCl In₅Cl₉, In₂Cl₃, In₇Cl₉ InCl₃	Sn - SnCl₂ SnCl₄	Sb - SbCl₃ SbCl₅	Te Te₂Cl, TeCl₂ Te₃Cl₂ TeCl₄	I ICl ICl₃ -
6	Tl TlCl TlCl₂, Tl₂Cl₃ TlCl₃	Pb - PbCl₂ PbCl₄	Bi - BiCl₃ -	Po PoCl₂ PoCl₄ -	At ? - -

Oxides

Main group chlorides
group → period ↓	13	14	15	16	17
2	B B₂O₃ B₆O	C CO_x CO CO₂ CO₃ C₃O₂ C₂O	N NO_x N₂O NO NO₂ N₂O₄ N₂O₃ N₂O₅	O O₂ O₃	F F₂O F₂O₂
3	Al Al₂O₃	Si SiO₂ SiO	P P₂O₅ P₂O₃	S SO_x SO₂ SO₃	Cl ClO_x ClO₂ Cl₂O₇ Cl₂O Cl₂O₃ Cl₂O₆
4	Ga Ga₂O₃ -	Ge GeO GeO	As As₂O₅ As₂O₃	Se SeO₂ SeO₃	Br - -
5	In In₂O₃ -	Sn SnO SnO₂	Sb Sb₂O₅ Sb₂O₃	Te TeO₂ TeO₃	I IO_x I₂O₄ I₂O₅ I₄O₉
6	Tl TlO₂ Tl₂O Tl₂O₃ -	Pb PbO_x PbO PbO₂ Pb₃O₄	Bi Bi₂O₃ -	Po PoO₂ PoO₃	At - -

Organometallics, DFW

"Organo-Transition Metal Chemistry" http://www.ilpi.com/organomet/

Transition metals 1, CAR

"Coordination Chemistry of the Transition Metals, Part 1"

Solid state, SRH

Solid State Chemistry

Close-packing of spheres, HCP, CCP
Unit cell, Miller indices
Common structure types: Cubic diamond, NaCl, CsCl, NiAs, β-ZnS, α-ZnS, CdCl₂, CdI₂, TiO₂, CaF₂, CaTiO₃, ReO₃
Molybdenum disulfide
Lattice energy: Born-Landé equation, Madelung constant, Kapustinskii equation
Cation-anion radius ratio, Pauling's rules
Solid-state synthesis: ceramic method (heat and beat, shake and bake)
Free electron model, Density of states
Band theory
Fermi energy, Fermi level
Coprecipitation, Solid-state reaction, fr:Chimie douce, Redox, Comproportionation, Electrolysis
Intercalation: potassium graphite
Ionic conductivity: fast ion conductors
Lattice defects: Schottky defects
Atomic wires - cyanoplatinates
Electron magnetic dipole moment
Magnetic structure: magnet, diamagnetism, paramagnetism, magnetic susceptibility, Curie–Weiss law, ferromagnetism, antiferromagnetism, ferrimagnetism, antiferrimagnetism, Néel temperature
- Other magnetism stuff: spin glass, photomagnetism, metamagnetism, superparamagnetism
Superexchange: MnO, FeO, CoO, NiO;
Superconductivity: zero resistance + Meissner effect, Heike Kamerlingh Onnes, high-temperature superconductivity, yttrium barium copper oxide

Semiconductors

Transition metals 2, FCM

"Co-ordination Chemistry of the Transition Metals, Part 2"

Trans effect
Eigen-Wilkins mechanism (de:Eigen-Wilkins-Mechanismus, Manfred Eigen and R. G. Wilkins)
Associative, dissociative and interchange reaction mechanisms: Dissociative substitution, Associative substitution, Sn1CB mechanism
Marcus theory
Eyring equation
Electron transfer: Inner sphere electron transfer, Outer sphere electron transfer

Main group 2, IM

"Chemistry of the Main Group Elements, Part 2: Rings, Chains and Macromolecules, Based on Main Group Elements"

Boron–nitrogen chemistry

Boron nitride
Amine-borane complexes, e.g. H₃N→BH₃ ammonia borane
Aminoboranes
Iminoboranes: tBu-B≡N-tBu Chem. Ber. (1984) 117, 1089-1102 (Shelf 20 in library)
Borazine

Boron–phosphorus chemistry

Phosphine-borane adducts
Phosphinoboranes, e.g. [Ph₂P-BH₂]₄
Boraphosphabenzenes, e.g. cyclo-(BMes)₃(PCy)₃
Polyphosphinoboranes, e.g. (PHPh-BH₂)_n

Boron–oxygen chemistry

B₂O₃
Borosilicate glass
Borates
Molecular B-O species, e.g. hydrolysis of chlorosilanes leading to boronic acids RB(OH)₂, and boroxines

Silicon–oxygen chemistry

- Silicon dioxide – α-quartz
- Siloxanes and polysiloxanes, e.g. PDMS, Rochow-Müller process, silicone gum, silicone rubber, thermal anionic ring-opening polymerization

Organosilicon chemistry

Organosilicon chemistry
Hexamethyldisilane
Polysilanes, sigma delocalisation c.f. polyacetylene, lithography
Polysilynes
Polycarbosilanes

Disilenes: Adv. Organomet. Chem. (2006) 54, 73-148 (review, including π-σ* mixing MO diagram accounting for pyramidalization of Si)

- First disilene, tetramesityldisilene (R. West, 1981): Organometallics (1984) 3, 793–800, Heteroat. Chem. (1990) 1, 1-7

- Recent calculated structures of disilene itself, Si₂H₄: Chem. Phys. Lett. (2008) 466, 11-15, Jmol structure

Disilynes: Science (2004) 305, 1755-1757

Silabenzenes

Physical

Thermodynamics, PWM

"Chemical Energy II"

Chemical energy
Chemical thermodynamics, thermochemistry
Specific heat capacity
enthalpy
entropy
Van 't Hoff equation
Clausius-Clapeyron relation
Trouton's rule
Gibbs–Duhem equation
Third law of thermodynamics: the entropy of all perfect crystals at 0 K is zero, i.e. S₀ = 0, residual entropy in non-perfect crystals
chemical potential
Raoult's law
Henry's law
Boiling-point elevation
Freezing-point depression
Osmotic pressure

Photochemistry, AJOE

"Introduction to Photochemistry"

Chemical interactions, DMS

"Chemical Interactions"

Interfaces, JPR

"Interfaces"

Kinetics, DES

"Kinetics"

Equilibria, PB

"Equilibria"

Equilibrium electrochemistry, DJF

"Equilibrium Electrochemistry"

Category:Electrochemistry
Electrochemistry
Chemical potential
Fundamental equation of chemical thermodynamics (see PWM):

dG=VdP-SdT+\sum _{i}\mu _{i}dn_{i}\,

Electrochemical potential
Activity of ions in solution
Faraday constant
Volta potential
Galvani potential
Liquid junction potential
Electrochemical cell
Half cell
Galvanic cell
Redox electrode
Absolute electrode potential
Reference electrode
Standard hydrogen electrode
Silver chloride electrode
Potentiometric titration
Glass electrodes
Ion selective electrodes
Batteries: Leclanché cell, Alkaline battery, Lead-acid battery, Nickel-cadmium battery, Lithium-ion battery (e.g. Lithium cobalt oxide-Graphite),
Fuel cells
Double layer (interfacial) / Electrical double layer: Helmholtz model, Gouy-Chapman model, Stern model, IUPAC definition of diffuse layer
Supercapacitors
Potential at the point of zero charge (p.z.c.): IUPAC definition of pzc, Point of zero charge
Molecular dynamics simulations
News reports:
- Battery that 'charges in seconds', BBC News Online, 11 March 2009 (lithium iron phosphate battery), based on Nature 458, 190-193 (12 March 2009).

Macromolecules, JSvD

"Macromolecules"

Theoretical

Quantum mechanics, FRM

"Quantum Concepts"

Molecular structure
Reactivity
Quantum chemistry
Nuclei much heavier than electrons ∴ molecules have structure
Electrostatics, internuclear repulsion
Zero-point energy
Born-Oppenheimer approximation
Potential energy surfaces: minima correspond to stable structures, saddle points correspond to transition states, reaction pathways correspond to mechanisms
Conformation of ethane, nitrogen inversion
de Broglie wavelength
Schrödinger equation
Hamiltonian operator
Wavefunctions
Particle in a box
Boundary conditions
Heisenberg uncertainty principle
Hydrogen atom
Spherical polar coordinates
Electron spin: Stern-Gerlach experiment suggested electrons have intrinsic, quantized spin angular momentum. It is now known that the spin angular momentum quantum number s = ½, and the spin projection quantum number, m_s = ±½.
Molecular Schrödinger equation
Molecular orbital approximation, molecular orbital theory (ignores electronic correlation)
Normalization of wavefunctions
Orthogonality:
In quantum mechanics, two eigenstates of a wavefunction, $\psi _{m}$ and $\psi _{n}$ , are orthogonal if they correspond to different eigenvalues. This means, in Dirac notation, that $\langle \psi _{m}|\psi _{n}\rangle =0$ unless $\psi _{m}$ and $\psi _{n}$ correspond to the same eigenvalue. This follows from the fact that Schrödinger's equation is a Sturm–Liouville equation (in Schrödinger's formulation) or that observables are given by hermitian operators (in Heisenberg's formulation).
Expectation value (quantum mechanics):
$\left\langle {\hat {\Omega }}\right\rangle =\int {\psi ^{*}{\hat {\Omega }}\psi }{\text{ d}}\tau$
Variational principle
Linear combination of atomic orbitals molecular orbital method
Vibrational spectroscopy: molecular vibration, harmonic approximation cf. classical oscillator
Quantum tunnelling
Kinetic isotope effect, e.g. in amine dehydrogenase
Reaction coordinate
Transition state theory
Morse potential

Molecular orbitals, NLA

"Understanding Structure and Reactivity, Part 1"

Hückel, AJM

"Understanding Structure and Reactivity, Part 2": http://www.chm.bris.ac.uk/pt/ajm/sb04/

Secular equations - see Quantum Concepts lectures by FRM's predecessor Prof. Balint-Kurti: GGBK lecture 6
Hückel method
Hückel's rule: aromaticity and antiaromaticity
Pericyclic reactions: ChemTube3D - Jmol animations of pericyclic reactions
Came up in the exam: the non-Kekulé molecule trimethylenemethane

Environmental

Geochemistry, RPE

"Origin and Fate of Organic Matter in the Geosphere"

Biogeochemistry
Oxygen evolution and history of life on Earth:
- 3700-2000 Ma - banded iron formations (alternating Fe₃O₄/Fe₂O₃ and silicate (chert) layers) due to early marine photosynthesis: O₂ causes Fe²⁺ → Fe³⁺
- 2000 Ma - Great Oxidation Event - O₂ started to evolve from cyanobacteria in the oceans into the atmosphere
- 2000 Ma-present - Continental Red Beds - widespread oxidation at Earth's surface
- 1500 Ma - Gypsum formation: atmospheric SO₂ + O₂ → SO₄²⁻, then + Ca²⁺ → CaSO₄
Isotope geochemistry
Isotope ratio mass spectrometry
- $\delta ^{13}{\text{C}}=\left[{{\frac {R_{\text{sample}}}{R_{\text{standard}}}}-1}\right]\times 1000{\text{ permil}}$
- $R_{\text{sample}}={\frac {^{13}{\text{C}}}{^{12}{\text{C}}}}$
- $R_{\text{standard}}=R_{\text{PDB}}=0.01124$ from Peedee belemnite
Carbon cycle
- Biosphere:
  - Photosynthesis: CO₂ + H₂O → CH₂O + O₂
  - Respiration: CH₂O + O₂ → CO₂ + H₂O
  - Exchange of CO₂ with oceans
Keeling Curve

Methane CH₄:
- Sources:
  - Natural: wetlands (habitat for methanogenic bacteria), termites, oceans, methane hydrates
    - Methane catastrophes, e.g. Permian–Triassic extinction event 250 Ma
  - Anthropogenic: energy, ruminants, rice paddies, landfills, biomass burning (biofuel), waste
- Arctic methane release, methane clathrates
- Sinks: tropospheric destruction, loss to stratosphere, soils (consumed by methanotrophs)
  - Low affinity (high capacity) methanotrophs - live in methanogenic environments, reoxidise ~90% of CH₄ to CO₂ before it escapes, adapted to [CH₄] up to 40 ppm

formula	CH₄	→	CH₃OH	→	HCHO	→	HCO₂H	→	CO₂
molecule	methane		methanol		formaldehyde		formic acid		carbon dioxide
C-O bonds	0		1		2		3		4

- - High affinity (low capacity) methanotrophs - live in well aerated soils (upland, forests, grasslands, farmland), adapted to [CH₄] up to 12 ppm
  - Investigate high affinity methanotrophs by following their characteristic PFLAs. Analyse ¹³CH₄-fed methanotroph colonies for ¹³C-rich PFLAs to find out which PFLAs are characteristic.
  - Methanotrophs cannot do their job if their habitats are destroyed - woodland → agricultural land means [N] ↑ so methanotrophs inhibited
  - Need to use land correctly to protect methanotrophs and allow them to help prevent [CH₄] ↑
Biochemicals:
- Carbohydrates for structure and energy storage, e.g. cellulose, polymer of ~10000 glucose monomers
- Lignins for structure of cell walls in higher plants, high m.w. polyphenolic heteropolymers of coumaryl alcohol, coniferyl alcohol, sinapyl alcohol
- Proteins for structure, catalysis (enzymes), storage - biopolymers of amino acids, 1-500 kDa
- Lipids - all biochemicals that are insoluble in water but soluble in organic solvents, <1000 Da, often fully saturated chains and rings - e.g. alkanes, wax esters, triglycerides, sterols:
  - straight-chain lipids - n-alkanes (odd numbers predominate, C_13-23 in algae, C_23-33 in higher plants), n-fatty acids and n-fatty alcohols (even numbers predominate, C₁₆ and C₁₈ everywhere, while C₂₀ and C₃₀ found in higher plant leaf waxes
  - branched-chain fatty acids (phospholipids) characteristic of bacteria, esp. C₁₅, C₁₇, plus corresponding alcohols and alkanes; acyclic isoprenoids (e.g. phytol) based on C₅ isoprene
  - sterols and hopanols are diagnostic of particular organisms - hormones and membrane rigidifiers, e.g. C₂₇ cholesterol in animals, C₂₈ campesterol and C₂₉ sitosterol in higher plants, C₂₈ ergosterol in fungi, C₃₀ dinosterol in algae and bacteriohopanetetrol in bacteria (which cannot make sterols)
C₃ and C₄ plants:
- C3 carbon fixation: C₃ plants adapted to moderate climates, use Calvin cycle to fix CO₂ as 3-phosphoglycerate, δ¹³C = −28 to −34 ‰ in alkanes (bulk tissue still −26 ‰)
- C4 carbon fixation: C₄ plants adapted to hot or dry climates, use Hatch-Slack pathway to fix CO₂ as oxaloacetate, δ¹³C = −20 to −24 ‰ in alkanes (bulk tissue still −26 ‰)
Bengal fan - an alluvial fan: may be contaminated, but very good temporal resolution. Palaesol and ocean sediment carbon isotope records match and suggest a shift from C³ to C⁴, starting 9 Ma, peaking 4 Ma, and now returning towards C₃ values.
Paleosols: in situ, so less contamination, but poor temporal resolution because mixing occurs
Biomarkers of terrestrial vegetation, e.g. C₂₇, C₂₉, C₃₁, C₃₃ n-alkanes

News reports:
- Key role of forests 'may be lost', BBC News Online, 18 April 2009

Marine chemistry, RDP

"Marine Chemistry"

Physical oceanography
Chemical oceanography
Seawater, salinity: conservative ions (99.8% of ocean solutes) are nacklecamgsok: Na⁺, Cl⁻, Ca²⁺, Mg²⁺, SO₄²⁻, K⁺
Ocean current, hydrothermal circulation
Thermohaline circulation: halocline, thermocline, pycnocline, sea surface temperature
Upwelling
Carbon cycle
Redfield–Richards ratio in marine plankton – C:H:P – 106:16:1
Nitrification, Anammox, Sulfur assimilation, Denitrification, Methanogenesis
Remineralisation
Biological pump - faecal pellet packaging (particulate) and downwelling (dissolved) transport organic carbon from the surface to the deep ocean
Paleocene–Eocene Thermal Maximum
Methane clathrate
Archaeol
Sulfate-reducing bacteria
Dissolved inorganic carbon: CO₂, CO₃²⁻, HCO₃⁻, H₂CO₃, CaCO₃
Lysocline, Carbonate Compensation Depth
Ocean acidification, UNESCO ocean acidification FAQ
Biomarkers, haptophytes, dinoflagellates, diatoms, maitotoxin
Methanogens and methanotrophs are archaea and have ether lipid membranes
- they probably developed in warm conditions, so needed lipids resistant to acid hydrolysis – an ester lipid would not do
- ether lipids are used to trace methanogenic and methanotrophic archaea

Isorenieratene

Anoxygenic photosynthesis by Chlorobium (green sulfur bacteria):
- H₂S + CO₂ + hν → SO₄²⁻ + organic C
- needs reduced sulfur so strictly anaerobic, but also needs light – rare combination of conditions, found in very stratified water columns (constrained basin with fresh water flowing in to achieve sharp density gradient), e.g. the Black Sea
- Lives ~100 m depth, so wavelength of sunlight is altered, ∴ uses its own special light harvesting pigment, isorenieratene:
- Brocks & Summons, Nature 437, 866-870: "Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea"
- Indicator of photic zone anoxia (Isorenieratene Biosynthesis in Green Sulfur Bacteria (2008))
Anoxic event

Anammox

Also from the anoxic Black Sea – anammox:
- NH₄⁺ + NO₂⁻ → (intermediates: N₂H₄, NH₂OH) → N₂ + 2H₂O
- Membrane lipids of planctomycetes: ladderanes e.g. pentacycloanammoxic acid from Brocadia anammoxidans, stack flat making an impermeable membrane to keep toxic intermediates isolated inside anammoxosome

Alkenones

E. huxleyi (a haptophyte) uses alkenones as membrane lipids:

In colder seas, it makes more triunsaturated alkenone (37:3) which is more kinked as so remains fluid at low temperatures
In warmer seas, it makes for diunsaturated alkenone (37:2), which is less kinked and would solidify in the cold
Use ratio of the two alkenones as a proxy for sea surface temperature: $U_{37}^{K}={\frac {37:2}{37:2+37:3}}$
First work on alkenones for SST done in Bristol in the 1980s:
- Br. Phycol. J. (1980) 19, 2619-2622
- Phys. Chem. Earth (1980) 12, 219-227
- Nature (1986) 320, 129-133
- Org. Geochem. (1988) 13, 727-734 – C₃₇ alkenones unexpectedly have all-trans (E) stereochemistry
Further reading:

37:2 (15E,22E)-heptatriaconta-15,22-dien-2-one, C₃₇H₇₀O:

37:3 (8E,15E,22E)-heptatriaconta-8,15,22-trien-2-one, C₃₇H₆₈O:

Tetraether lipids

Pelagic crenarchaea use tetraether lipids, which they adapt to different temperatures:
- more rings help membranes stack at stay well-ordered at high temperatures
- fewer rings help disorder membranes, so they don't freeze at low temperatures

News reports

Atmospheric chemistry, DES

"Chemistry of the Atmosphere"

O₂ + hν → 2O

O + O₂ + M → O₃ + M

O₃ + hν → O₂ + O (highly exothermic)

O + O₃ → 2O₂

{\text{ODP(X)}}={\frac {{\text{amount of O}}_{\text{3}}{\text{ destroyed by unit mass of X}}}{{\text{amount of O}}_{\text{3}}{\text{ destroyed by unit mass of CFCl}}_{\text{3}}}}

Hydroxyl radical, HO₂ radical:
Oxidation of hydrocarbons and carbon monoxide by ozone, catalysed by the OH radical, normally keeps tropospheric ozone very low:

CO + OH → CO₂ + H

H + O₂ + M → HO₂ + M

HO₂ + O₃ → OH + 2O₂

CO + O₃ → CO₂ + O₂ (net)

Volatile organic compounds
Montreal Protocol
Global warming
News reports:
- Earth warming faster than thought, BBC News Online, 12 March 2009

Techniques

"Techniques for Chemists"

Scientific writing
Chemometrics, principal components analysis
Molecular modelling
Gas chromatography
NMR spectroscopy: Correlation spectroscopy, Nuclear Overhauser effect?, J-coupling
- Typical coupling constants:
  - Benzene rings: J_ortho ≈ 8 Hz, J_meta ≈ 2 Hz, J_para ≈ 0 Hz
  - Alkenes: J_cis ≈ x Hz, J_trans ≈ x Hz, J_gem ≈ x Hz

Labs

Experiment 1 - The benzoin reaction - preparation of benzoin: Benzoin condensation
Experiment 2 - The preparation of fenbufen: Fenbufen
Experiment 3 - The Wittig reaction: Wittig reaction, Horner-Wadsworth-Emmons reaction, Peterson olefination, Julia olefination, Tebbe olefination, Petasis reagent
Experiment 4 - Cycloaddition reactions and their mechanisms: Cycloaddition, Tetracyanoethylene
Experiment 5 - The Robinson annulation: Robinson annulation
Experiment 6 - Synthesis of 4,6-diphenyl[2,2']bipyridine: Hantzsch pyridine synthesis
Experiment 7 - The preparation and use of a Wilkinson's catalyst: Wilkinson's catalyst
Experiment 8 - Chromatography in action: Chromatography, Thin layer chromatography, Retardation factor (R_f value), gas chromatography,
Experiment 9 - An electrochemical glucose sensor: Glucose meter, Glucose oxidase, Nernst equation, Cyclic voltammetry, Ferrocene
Experiment 10 - IR spectroscopy of cigarette smoke: Rovibrational coupling
Experiment 11 - Absorption and fluorescence of dye molecules: Nile Blue
Experiment 12 - Determination of mean aggregation number of a micellar system: Micelle
Experiment 13 - Kinetics of ionic reactions
Experiment 14 - Polymer-surfactant interactions: Sodium dodecyl sulfate
Experiment 15 - The solution properties of polyelectrolytes: Polyelectrolyte
Experiment 16 - Absorption spectroscopy and the uptake of acetic acid at the gas-liquid surface
Experiment 17 - The Ni catalysed isomerisation of 1-heptene: Linear alpha olefin, Isomerisation, Shell higher olefin process, Olefin metathesis,
Experiment 18 - Silicone polymers: Siloxane, Silicone, Diphenylsilanediol
Experiment 19 - Monomeric and polymeric transition metal oxides: Polyoxometallate, WO₃, Na₂MoO₄, Na₂WO₄, [nBu₄N]₂[W₆O₁₉]
Experiment 20 - Metal carbonyl complexes: Metal carbonyl
Experiment 21 - The application of liquefied gases as non-aqueous media: Ammonia, Inorganic nonaqueous solvent
Experiment 22 - Analysis of caffeine in soft drinks: Caffeine, Decaffeination, High performance liquid chromatography
Experiment 23 - Ferrocene: synthesis and reactivity: Ferrocene
Experiment 24 - Preparation of a luminescent Cu(I) complex
Experiment 25 - Modelling Real Reactions: Intramolecular Lactonisation: Iodolactonisation, Curtin-Hammett principle
Experiment 26 - Databases and Datamining: Crystallographic database, Cambridge Structural Database, Cambridge Crystallographic Data Centre, Data mining

Links

User:Benjah-bmm27/degree/1 - Level 1 (first year)

@@ Line 405: / Line 405: @@
 * [[Chemical thermodynamics]], [[thermochemistry]]
 * [[Specific heat capacity]]
+* [[enthalpy]]
+* [[entropy]]
 * [[Van 't Hoff equation]]
 * [[Clausius-Clapeyron relation]]
@@ Line 410: / Line 412: @@
 * [[Gibbs–Duhem equation]]
 * [[Third law of thermodynamics]]: the entropy of all perfect crystals at 0&nbsp;K is zero, i.e. ''S''<sub>0</sub>&nbsp;=&nbsp;0, [[residual entropy]] in non-perfect crystals
+* [[chemical potential]]
+* [[Raoult's law]]
+* [[Henry's law]]
+* [[Boiling-point elevation]]
+* [[Freezing-point depression]]
+* [[Osmotic pressure]]
 ===Photochemistry, AJOE===

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Revision as of 13:11, 22 April 2009