On the mathematical formulation and interpretation of LACO MO theory

The mathematical basis of LCAO MO theory is studied, both within the Hartree-Fock approximation and in more exact formulations. The basic LCAO expansion for molecular orbitals ¦> in terms of atomic orbitals ¦x> is conveniently written ¦> = ¦x> S ^–1 B where S is the overlap matrix for atomic orbitals and B is the matrix of atomic orbital-molecular orbital overlaps. It is suggested that matrices P and Q, defined by P=B B and Q=BnB where n is the matrix of molecular orbital occupation numbers, are appropriate to the interpretation of molecular calculations in terms of atomic orbital components, electronic populations and the degree of bonding. Implications for Hartree-Fock calculations are investigated.     

Single-molecule nanopore sensing of actin dynamics and drug binding

Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores, we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed the unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, filament-growth, and drug-binding at the single-molecule level demonstrating the promise of nanopore sensing for in-depth understanding of protein folding landscapes and for drug discovery.

Nanopipettes were used for real-time investigation into actin dynamics and drug binding at single-molecule resolution, showing promise for a better understanding of the mechanism of protein–protein interactions and drug discovery.     

Artificial metalloenzymes: The powerful alliance between protein scaffolds and organometallic catalysts

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The absolute stereochemistry of grenadamide

3-(2S-Heptylcycloprop-1S-yl)propanoic acid 2-phenylethanamide was synthesised from cis-cyclopropan-1,2-dimethanol via enzymatic desymmetrisation of the dibutyrate; it gave identical NMR spectroscopic data to those reported for grenadamide but had an equal and opposite absolute rotation, indicating that the latter is the 2R,1R-enantiomer.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-aminoethyl cation and the isomeric protonated aziridine have been optimized using ab initio molecular orbital calculations employing the split-valence shell 4-31G basis set. The protonated aziridine is computed to be the more stable ion by 46.5 kcal/mole (4-31G level) and 44.9 kcal/mole (double-zeta basis set). The profile to interconversion is found to have a barrier of less than 15 kcal/mole (relative to the 2-aminoethyl cation) and this profile is compared with those computed for the similar ions XCH₂CH ₂ ⁺ where X=OH, F, SH and Cl.     

Unexpected conversion of a polycyclic thiophene to a macrocyclic anhydride

Oxygenation of 2,5,9,12-tetra(tert-butyl)diacenaphtho[1,2-b:1′,2′-d]-thiophene (1, C₄₀H₄₄S) by peracids gave the cyclic sulfonic ester 4 (2,7,10,13-tetra(tert-butyl)diacenaphtho[1,2-c:1′,2′-e]oxathiin 5,5-dioxide, C₄₀H₄₄O₃S) which, when heated in nitrobenzene, is converted into a complex, macrocyclic anhydride 3 (C₈₀H₈₈O₃), which is derived from two molecules of 4. Further investigation found a likely intermediate in this reaction, 4,4′,7,7′-tetra(tert-butyl)-1,1′-biacenaphthylenylidene-2,2′-dione (5, C₄₀H₄₄O₂), apparently formed from 4 by additional oxidation. Anhydride 3 plausibly arises by Diels-Alder reaction of 4 and 5 followed by several ring fragmentations. The structures of 3, 4, and 5 were unambiguously established by X-ray crystallography.     

Quantum yield of the iodide-iodate chemical actinometer: dependence on wavelength and concentrations

The quantum yield (QY) of the iodide-iodate chemical actinometer (0.6 M KI-0.1 M KIO3) was determined for irradiation between 214 and 330 nm. The photoproduct, triiodide, was determined from the increase in absorbance at 352 nm, which together with a concomitant measurement of the UV fluence enabled the QY to be calculated. The QY at 254 nm was determined to be 0.73 +/- 0.02 when calibration was carried out against a National Institute of Standards and Technology traceable radiometer or photometric device. At wavelengths below 254 nm the QY increased slightly, leveling off at -0.80 +/- 0.05, whereas above 254 nm the QY decreases linearly with wavelength, reaching a value of 0.30 at 284 nm. In addition, the QY was measured at different iodide concentrations. There is a slight decrease in QY going from 0.6 to 0.15 M KI, whereas below 0.15 M KI the QY drops off sharply, decreasing to 0.23 by 0.006 M KI. Calibration of the QY was also done using potassium ferrioxalate actinometry to measure the irradiance. These results showed a 20% reduction in QY between 240 and 280 nm as compared with radiometry. This discrepancy suggests that the QY of the ferrioxalate actinometer in this region of the spectrum needs reexamination.     

On the theory of electron correlation in atoms and molecules. II. General cluster expansion theory and the general correlated wave functions method

An exact cluster expansion of many electron wave functions is derived, beginning with a finite linear combination of Slater determinants rather than the more usual single determinant. This general cluster expansion is found to apply both in the case where all possible Slater determinants from a finite set of spin orbitals are included in the linear combination, and in the case where the number of determinants is restricted. The special properties of that finite linear combination of determinants closest to the exact wave function in the least squares sense are studied. These properties lead to the derivation of a general correlated wave functions method, illustrating again the close relationship between methods of this type and cluster expansion theory. Additional approximations, necessary for practical calculations, are set out.     

Absolute rate constants for some hydrogen atom abstraction reactions by a primary fluoroalkyl radical in water

A combination of laser flash photolysis and competitive kinetic methods have been used to measure the absolute bimolecular rate constants for hydrogen atom abstraction in water from a variety of organic substrates including alcohols, ethers, and carboxylic acids by the perfluoroalkyl radical, *CF(2)CF(2)OCF(2)CF(2)SO(3)(-) Na(+). Comparison, where possible, of these rate constants with those previously measured for analogous reactions in the non-polar organic solvent, 1,3-bis(trifluoromethyl)benzene (J. Am. Chem. Soc, 1999, 121, 7335) show that the alcohols react 2-5 times more rapidly in the water solvent and that the ethers react at the same rate in both solvents. A transition state for hydrogen abstraction that is more reminiscent of an "intimate ion pair" than a "solvent separated ion pair" is invoked to explain these modest solvent effects.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-chloroethyl and ethylenechloronium cations, two possible intermediates in the electrophilic addition of chlorine to ethylene, have been fully optimized using ab initio molecular orbital calculations employing the split valence shell 4-31G basis set.These geometries were then used to compute more accurate wave functions using Dunning's double-zeta basis set. The bridged chloronium ion was found to be more stable by 9.35 kcal/mole, the opposite order of stability from the C₂H₄F⁺ ions. Interconversion of the two C₂H₄Cl⁺ cations was computed to have a barrier of 6.25 kcal/mole.The activation energy for this chlorination reaction, using the ethylenechloronium cation and a chlorine anion at infinite separation as the model for the activated complex, was computed to be 128.7 kcal/mole, showing that this is not a feasible gas phase reaction.