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
Reformatsky reaction
Henry reaction (nitro aldol)
Claisen condensation
Mannich reaction
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

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"

Stereochemistry, APD

"Stereochemistry and Conformation"

Stereochemistry
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, 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 - 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⁺
  - myosin - 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

Inorganic

NMR, CJA

"Introduction to NMR Spectroscopy"

Main group 1, NCN

"Chemistry of the Main Group Elements, Part 1"

Organometallics, DFW

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

Transition metals 1, CAR

"Coordination Chemistry of the Transition Metals, Part 1"

Ligand field theory

Solid state, SRH

Solid State Chemistry

Unit cell
Lattice energy: Born-Landé equation, Madelung constant, Kapustinskii equation
Pauling's rules
Solid-state synthesis: ceramic method (heat and beat, shake and bake)
Free electron model
Band theory
Fermi energy
Lattice defects
Magnetic structure: magnet, diamagnetism, paramagnetism, ferromagnetism, antiferromagnetism, ferrimagnetism, antiferrimagnetism, Néel temperature
Superconductivity
Atomic wires - cyanoplatinates
Fast ion conductors?
Semiconductors

Transition metals 2, FCM

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

Trans effect
Eigen-Wilkins mechanism (de:Eigen-Wilkins-Mechanismus)
Associative, dissociative and interchange reaction mechanisms
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"

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
Siloxanes

Physical

Thermodynamics, PWM

"Chemical Energy II"

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

Macromolecules, JSvD

"Macromolecules"

Theoretical

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
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)
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/

Environmental

Geochemistry, RPE

"Origin and Fate of Organic Matter in the Geosphere"

Marine chemistry, RDP

"Marine Chemistry"

Atmospheric chemistry, DES

"Chemistry of the Atmosphere"

Techniques

"Techniques for Chemists"

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, Tungsten trioxide, Sodium molybdate
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 432: / Line 432: @@
 * [[Isotope ratio mass spectrometry]]
 * [[C3 carbon fixation]], [[C4 carbon fixation]]
-* [[Carbon cycle]]
+* [[Carbon Cycle]]
+* [[Methanotroph]]
 ===Marine chemistry, RDP===

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Revision as of 15:56, 11 March 2009