Neil L. Allan

Experimental access to the thermodynamic landscapes underlying individual catalytic steps remains limited because ensemble measurements average over transient intermediates. Here we combine single-molecule optoplasmonic measurements with macromolecular rate theory to resolve activation thermodynamics for individual catalytic transitions. Using adenylate kinase as a model system, we extract activation heat capacities for individual catalytic and conformational transitions from temperature-dependent single-molecule kinetics. Temperature-dependent single-molecule measurements enable extraction of rate constants for individual steps along the reaction coordinate, from which activation parameters are determined across 10–35 °C. Analysis yields distinct activation heat capacities ($\Delta C_p^\ddagger$), including negative values for catalytic transitions and positive or near-zero values for substrate binding and product release. Single-molecule kinetic parameters are in good agreement with ensemble measurements, and molecular dynamics simulations demonstrate that immobilisation on the optoplasmonic sensor preserves the folded structure and catalytically relevant conformational states of the enzyme. The value obtained for the reopening step is in quantitative agreement with ensemble measurements, validating the approach. Importantly, the single-molecule measurements resolve a longstanding ambiguity in MMRT by directly linking negative activation heat capacities to ordering of a specific conformational substate during catalysis. These results provide experimental support for a central mechanistic assumption underlying MMRT and establish a general experimental framework for mapping catalytic heat-capacity landscapes with step-level resolution.

The energy landscapes and electronic properties of non-polar and polar nanofilms of silicon carbide are studied using periodic hybrid density functional calculations. Relative energies and electronic properties are reported as a function of film thickness for a set of structures derived from those of wurtzite, zinc blende and graphite. The energy landscape of the films is complex with pronounced nano-polymorphism. Across polar films different mechanisms in different cases remove or reduce the dipole moment, including charge transfer and phase transitions to the graphitic-like structures which are stable for the thinnest films. Graphitic structures are lowest in energy for the thinnest films. For ten layers non-polar films—zinc blende (110) and wurtzite( 10 1 ― 0 ) with tetrahedrally-coordinated Si and C in Si ₃ C ₃ rings in chair conformations—are lowest in energy, followed, ≈0.1 eV per formula unit higher in energy, by a body-centered tetragonal structure containing Si ₃ C ₃ rings in boat conformations. In the planar graphene structure the energy of the anti-site defect C _Si -Si _C (≈0.3 eV)) is more than an order of magnitude lower than in the bulk, suggesting a much higher degree of disorder in such films. One staggered graphitic-like structure with ABC stacking, a local minimum in the energy landscape, is of particular interest, since it lies in a regime of uncompensated polarity and possesses a direct band gap that decreases linearly with film thickness., from ≈2 eV (3 layers) to zero (6 layers).

With increasing number of primary knock on atoms the damage decreases much more slowly.

Molecular 3-point turns are seen in molecular dynamics simulations of methanol and promoters of the CH ₃ OH to CH ₃ OCH ₃ reaction. The more catalytically active aromatic aldehydes limit methanol diffusion less than other promoters.

Multilevel ab initio calculations reveal the role of promoters in the dehydration of methanol in H-ZSM-5.

The diffusion in ZSM-5 zeolite of methanol and of two series of promoters of the methanol to dimethyl ether reaction (linear methyl esters, benzaldehyde, 4-n-alkyl benzaldehydes) has been studied using classical molecular dynamics in the NVT ensemble. Whereas promoter diffusion coefficients decrease with increasing alkyl chain length in methyl esters, the aromatic aldehyde promoters all have similar diffusion coefficients. The lowest diffusion coefficient is that of benzaldehyde. All the promoters exhibit a preference for moving in the straight pore, a preference that is most pronounced for the 4-n-alkyl benzaldehydes and least for the longest aliphatic esters. A novel diffusion mechanism, a molecular ’3-point turn’, is observed. The diffusion coefficient of methanol is larger than that of all the promoters. The more catalytically active aromatic aldehyde promoters limit methanol diffusion less than the aliphatic esters.

The ability to tune band gaps of semiconductors is important for many optoelectronics applications including photocatalysis. A common approach to this is doping, but this often has the disadvantage of introducing defect states in the electronic structure that can result in poor charge mobility and increased recombination losses. In this work, density functional theory calculations are used to understand how co-doping and solid solution formation can allow tuning of semiconductor band gaps through indirect effects. The addition of ZnS to GaP alters the local environments of the Ga and P atoms, resulting in shifts in the energies of the P and Ga states that form the valence and conduction band edges, and hence changes the band gap without altering which atoms form the band edges, providing an explanation for previous experimental observations. Similarly, N doping of ZnO is known from previous experimental work to reduce the band gap and increase visible-light absorption; here we show that, when co-doped with Al, the Al changes the local environment of the N atoms, providing further control of the band gap without introducing new states within the band gap or at the band edges, while also providing an energetically more favourable state than N-doped ZnO. Replacing Al with elements of different electronegativity is an additional tool for band gap tuning, since the different electronegativities correspond to different effects on the N local environment. The consistency in the parameters identified here that control the band gaps across the various systems studied indicates some general concepts that can be applied in tuning the band gaps of semiconductors, without or only minimally affecting charge mobility.