Physical organic chemistry
Physical organic chemistry – the study of the interplay between structure and reactivity in organic molecules – underpins organic chemistry, which cannot be imagined as a subject without knowledge of mechanism and reactivity. Applications to complex reactions in biology, polymer chemistry and electronic materials are ever more prevalent, and add to contributions in ‘small molecule’ chemistry. Novel experimental techniques combined with the revolution in computational chemistry give new impetus to physical organic chemistry and contribute to its continuing importance, which is reflected in the large number of international meetings in physical organic chemistry in the past two years.
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- Published 05 Jul 2010
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Figure 1: Neutral organic electron donors 1 and 4–10.
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Figure 2: Formation of donors and oxidation to form diiodide salts, together with the ORTEP diagram of diiodi...
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Figure 3: Cyclic voltammograms vs Fc/Fc+ of 17′ ↔ 8 (red) and 16′ ↔ 14 (blue).
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Figure 4: (a) Cyclic voltammograms vs. Fc/Fc+ of 17′ ↔ 8 (red) and 18′ ↔ 15 (blue) and (b) of 17′ ↔ 8 (red) a...
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Figure 5: Electron donors, their oxidized dications and their reactions with 27.
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Figure 6: Cyclic voltammograms vs Fc/Fc+ (a) of 17′ ↔ 8 (red) and 21′ ↔ 23 (blue) and (b) of 17′ ↔ 8 (red) an...
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- Full Research Paper
- Published 09 Aug 2010
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Scheme 1: Organic azides studied.
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Scheme 2: Reaction of 4-substituted-phenyl azides with GaCl3.
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Figure 1: EPR spectra after treatment of azide 2 with MCl3. (a) AlCl3 in DCM; 1st derivative spectrum at 300 ...
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Figure 2: EPR spectrum after treatment of tetra-deuterated azide 3 with AlCl3. Top: 2nd derivative spectrum a...
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Figure 3: EPR spectra after treatment of azide 1 with AlCl3. (a) 1st derivative spectrum in DCM at 280 K. (b)...
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Figure 4: EPR spectra after GaCl3 and InCl3 reactions of azide 6. (a) 1st derivative spectrum from 6 and GaCl3...
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Scheme 3: Dimer and trimer radical cations.
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Figure 5: EPR spectra after GaCl3- and InCl3-promoted reactions of 2-methoxyphenyl azide 5. (a) 1st derivativ...
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Figure 6: EPR spectra after In-, Ga- and Al-promoted reactions of azide 8. (a) intermediate from InCl3 treatm...
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Figure 7: Experimental and simulated Davies ENDOR spectrum after the Ga-promoted reaction of azide 6 recorded...
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Figure 8: DFT structures and SOMOs for dimer and trimer radical cations.
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Scheme 4: Possible mechanism of formation of aromatic amines.
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Scheme 5: Possible mechanism for dimer and trimer formation.
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Kinetic studies and predictions on the hydrolysis and aminolysis of esters of 2-S-phosphorylacetates
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- Published 16 Aug 2010
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Scheme 1: Use of 2-bromoacetic acid esters as heterobifunctional cross-linking agents.
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Scheme 2: Cross-linking between thiophosphate 4, D-glucosamine (GlcNH2) and bromoacetyl-N-hydroxybenzotriazol...
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Scheme 3: Ligation of 2-bromoacetic acid esters 1 (R = pNP or mNP) to thiophosphate 4.
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Scheme 4: Displacement of p- or m-nitrophenolate ions from nitrophenyl esters 7 (R = pNP) and 7 (R = mNP).
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Figure 1: log khydrol vs pH for the hydrolysis p-nitrophenyl ester 7 (R = pNP) and m-nitrophenyl ester 7 (R = ...
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Figure 2: log kaminol vs pH for the combined aminolysis and hydrolysis of p-nitrophenyl ester 7 (R = pNP) and ...
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Scheme 5: Kinetic model for competing hydrolysis and aminolysis processes of nitrophenyl esters 7 (R = pNP) a...
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Figure 3: Predicted concentration-time profile for the reaction between starting concentrations of 0.05 M p-n...
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Figure 4: Predicted concentration-time profile for the reaction between starting concentrations of 0.05 M m-n...
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Figure 5: Predicted leaving group pKaH values required for user-defined conversion levels of starting concent...
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Scheme 6: (A) Direct aminolysis of the ester carbonyl group; (B) intramolecular nucleophilic catalysis of est...
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Figure 6: 2-nitrophenyl 2-(ethylthio)acetate.
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- Commentary
- Published 03 Nov 2010
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Figure 1: Free energy profiles for reactions of substrate S uncatalysed and catalysed by enzyme E, showing ho...
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Scheme 1: SN2 methyl transfer from SAM to catechol catalysed by COMT.
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Figure 2: Energetic analysis of the compression hypothesis for enzyme-catalysed methyl transfer.
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Figure 3: Catalyst design for methyl transfer: (a) the reaction to be catalysed; (b) dipoles favourably align...
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Scheme 2: SN2 methyl transfer (a) uncatalysed and (b) within a cryptand cavity.
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Figure 4: Free energy analysis of COMT catalysis.
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Scheme 3: Formation of glycosyl-enzyme covalent intermediate COV.
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Figure 5: Conformational change of the xylose ring from chair (via envelope) with long OYHY…Oring hydrogen bo...
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Figure 6: AM1/OPLS potentials of mean force for formation of glycosyl-enzyme covalent intermediate between 4-...
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Figure 7: Hydrogen-bond distances HY…Oring (red) and HY…Onuc (blue) to boat conformer of RC, TS and glycosyl-...
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- Full Research Paper
- Published 03 Nov 2010
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Scheme 1: Mechanism of dehydration of benzene-1,2-dihydrodiol.
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Figure 1: Reactivity ratios for acid-catalyzed reaction of arene dihydrodiols.
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Figure 2: Substrates for solvolysis measurements.
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Scheme 2: Products of solvolysis and (ester) hydrolysis of trans-1-trichloroacetoxy-2-methoxy-1,2-dihydronaph...
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Scheme 3: Products of solvolysis of trans-1-chloro-2-hydroxy-1,2,3,4-tetrahydronaphthalene.
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Figure 3: Rate constants for aqueous solvolyses.
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Figure 4: Cis/trans reactivity ratios for β-hydroxycarbocation forming reactions.
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Figure 5: Comparison of the effect of a β-hydroxy group on the reactivity of cis and trans di- and tetrahdron...
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Scheme 4: ‘Aromatic’ hyperconjugation for the benzenium ion.
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Scheme 5: Stereochemistry of carbocation formation from solvolysis of cis-1-trichloroacetoxy-2-hydroxy-1,2-di...
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Kinetics and mechanism of vanadium catalysed asymmetric cyanohydrin synthesis in propylene carbonate
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- Published 03 Nov 2010
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Scheme 1: Synthesis and transformation of nonracemic silyl-protected cyanohydrins.
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Figure 1: Highly active metal(salen) complexes for asymmetric cyanohydrin synthesis.
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Scheme 2: Synthesis of cyclic carbonates.
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Scheme 3: Synthesis of cyanohydrin trimethylsilyl ethers and acetates.
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Scheme 4: Equilibrium between bimetallic and monometallic Ti(salen) complexes.
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Figure 2: Second-order kinetics plot for the addition of TMSCN to benzaldehyde at 0 °C catalysed by complex 2...
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Figure 3: Plot of k2obs against [2], showing that the reactions are first order with respect to the concentratio...
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Figure 4: Eyring plot to determine the activation parameters for catalyst 2 in propylene carbonate. The red a...
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Figure 5: 51V NMR spectra of complex 2 recorded at 50 °C. a) Spectrum in CDCl3; b) spectrum in CDCl3 with 500...
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Figure 6: Structures consistent with the 51V NMR spectra.
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Figure 7: Bimetallic aluminium(salen) complex for asymmetric cyanohydrin synthesis.
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Figure 8: Rate determining transition states for asymmetric cyanohydrin synthesis: a) when Lewis base catalys...
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Figure 9: Hammett correlations with catalyst 2 at 0 °C. Data in red are obtained in dichloromethane [52], whilst ...
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- Full Research Paper
- Published 11 Nov 2010
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Scheme 1: Unimolecular reactivity of hydroxycarbenes under cryogenic conditions: [1,2]H-Tunneling of 1 and 3 (...
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Scheme 2: A selection of heterocarbenes that undergo intramolecular C–H insertions.
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Scheme 3: Attempted generation of 5 and d-5 as well as their corresponding insertion products.
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Scheme 4: Proposed mechanism for the generation of 8 and 9. The [1,2]H-tunneling process apparently cannot co...
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Figure 1: Unmodified matrix IR spectrum (Ar, 11 K) of the pyrolysis (600 °C) of 5. Traces of 9 are indicated ...
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Figure 2: Unmodified matrix IR spectrum (Ar, 11 K) of the pyrolysis (600 °C) of d-5. Traces of 9 are indicate...
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Scheme 5: Decay of the 2,3-dihydrobenzofuran-3-ol molecular radical cation (8+•).
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Scheme 6: Attempted generation of 12 and the actual pyrolysis product 11.
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Scheme 7: Unanticipated reaction of 6 upon heating in xylenes.
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Scheme 8: Potential energy hypersurface of (o-methoxyphenyl)hydroxycarbene (5) (not drawn to scale; ZPVE incl...
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Scheme 9: Acid-catalyzed generation of 7 by unreacted 6.
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- Full Research Paper
- Published 17 Mar 2011
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Figure 1: 1,8-disubstituted naphthalene model systems.
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Scheme 1: The general reaction for the preparation of the 1,8-disubstituted naphthol derivatives 1–5 [31].
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Figure 2: X-ray structure of 8-(4-methylphenyl)-1-naphthol derivative 4.
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Figure 3: Potentiometric titration data for compound 1 and TBAH.
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Figure 4: Structures (a) with the hydrogen atom pointing into the ring, as seen in the crystal structure of 4...
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Scheme 2: Titration of the acids 1–5 to generate the corresponding anions 8–12, respectively.
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Figure 5: Plot of pKa' values for compounds 1–5 versus the corresponding R-substituent σp Hammett parameter. ...
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Figure 6: Anion density (HOMO) for the phenyl-derivative 8, illustrating no conjugation of the anion with the...
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Figure 7: Bond critical points (red), ring critical points (yellow) and bond paths illustrated for the anion 8...
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- Review
- Published 23 Mar 2011
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Scheme 1: Superelectrophilic activation of the acetyl cation.
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Scheme 2: Ring opening of diprotonated 2-oxazolines.
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Scheme 3: AlCl3-promoted ring opening of isoxaolidine 16.
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Scheme 4: Ring-opening reactions of cyclopropyl derivatives.
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Scheme 5: Condensations of ninhydrin (28) with benzene.
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Scheme 6: Rearrangement of 29 to 30.
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Scheme 7: Superacid promoted ring opening of succinic anhydride (33).
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Scheme 8: Reaction of phthalic acid (36) in FSO3H-SbF5.
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Scheme 9: Ring expansion of superelectrophile 42.
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Scheme 10: Reaction of camphor (44) in superacid.
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Scheme 11: Isomerization of 2-cyclohexen-1-one (48).
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Scheme 12: Isomerization of 2-decalone (51).
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Scheme 13: Rearrangement of the acyl-dication 58.
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Scheme 14: Reaction of dialkylketone 64.
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Scheme 15: Ozonolysis in superacid.
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Scheme 16: Rearrangement of 1-hydroxy-2-methylcyclohexane carboxylic acid (79) in superacid.
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Scheme 17: Isomerization of the 1,5-manxyl dication 87.
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Scheme 18: Energetics of isomerization.
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Scheme 19: Rearrangement of dication 90.
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Scheme 20: Superacid promoted rearrangement of pivaldehyde (92).
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Scheme 21: Rearrangement of a superelectrophilic carboxonium ion 100.
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Scheme 22: Proposed mechanism for the Wallach rearrangement.
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Scheme 23: Wallach rearrangement of azoxypyridines 108 and 109.
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Scheme 24: Proposed mechanism of the benzidine rearrangement.
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Scheme 25: Superacid-promoted reaction of quinine (122).
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Scheme 26: Superacid-promoted reaction of vindoline derivative 130.
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Scheme 27: Charge migration by hydride shift and acid–base chemistry.
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Scheme 28: Reactions of 1-hydroxycyclohexanecarboxylic acid (137).
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Scheme 29: Reaction of alcohol 143 with benzene in superacid.
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Scheme 30: Reaction of alcohol 148 in superacid with benzene.
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Scheme 31: Mechanism of aza-polycyclic aromatic compound formation.
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Scheme 32: Superacid-promoted reaction of ethylene glycol (159).
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Scheme 33: Reactions of 1,3-propanediol (165) and 2-methoxyethanol (169).
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Scheme 34: Rearrangement of superelelctrophilic acyl dication 173.
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- Full Research Paper
- Published 15 Apr 2011
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Figure 1: Quinone imine structural relationships.
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Figure 2: Numbering and structure of oxazine dyes studied in this work (counterions not shown).
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Figure 3: Directions of solvated (a) dipole moments and (b) transition moments from origin (0,0,0).
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Figure 4: Error between experimental and calculated λmax values for each dye at the different levels of theor...
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Figure 5: The orbital overlaps (Λ) for each dye at the different levels of theory investigated. All structure...
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- Full Research Paper
- Published 29 Apr 2011
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Figure 1: Molecular structures of syn-isobutyl chloroformate (1), syn-isobutyl chlorothioformate (2), phenyl ...
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Scheme 1: Stepwise addition–elimination mechanism through a tetrahedral intermediate for solvolysis of chloro...
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Scheme 2: Unimolecular solvolytic pathway for the dithioformate esters.
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Figure 2: The plot of log (k/k0) for iBuOCOCl (1) against log (k/k0) for PhOCOCl (3).
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Figure 3: The plot of log (k/k0) for isobutyl chloroformate (1) against 1.82 NT + 0.53 YCl in eighteen pure a...
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Figure 4: The plot of log (k/k0) for isobutyl chlorothioformate (2) against 0.42 NT + 0.73 YCl in 15 pure and...
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