Research highlights

QM/MM simulations help to resolve the sodium pumping mechanism of a light-driven ion transporter

Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven sodium pump that actively transports small cations across cellular membranes. Such pumps are used by microbes to convert light into a membrane potential and have become useful optogenetic tools with applications in neuroscience.

QM/MM studies of molybdenum and vanadium nitrogenases

The iron-molybdenum (FeMoco) and iron-vanadium cofactors (FeVco) in the molybdenum/vanadium nitrogenase enzymes catalyze the reduction of dinitrogen at ambient temperature and pressure to ammonia according to the reaction equation: N2 +8H+ 8e- +16MgATP→ H2 + 2NH3+16MgADP. How this complex 8-electron process is carried out by these enzymes is still a mystery.

Defects in the wide gap semiconductor GaN

GaN is a wide gap semiconductor that is a crucial component of blue light emitting diodes (LEDs), which are essential for solid state lighting. Both n- and p-type layers are required for LEDs, but achieving p-type GaN is very difficult; the only successful method is to very heavily dope GaN with Mg. Why no other dopants result in significant hole concentrations is not well understood. Moreover, there are many photoluminescence peaks observed from a broad range of differently prepared GaN samples whose origin is a major source of debate.

Determining the energy band alignment between different TiO2 polymorphs

TiO2 is a key material for photocatalytic water splitting, where it has been found that samples composed of mixtures of the anatase and rutile polymorphs outperform the pure phase samples. Several explanations for this observation were proposed with no consensus being reached until, using the ChemShell code to perform hybrid QM/MM embedded cluster calculations, we showed that it is a consequence of the fundamental band alignment between the two phases.

Nitrite binding in three-domain haem-Cu nitrite reductase

Copper-containing nitrite reductase enzymes (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO2) to nitric oxide (NO). CuNiRs come in two-domain and three-domain forms, where the former have one cupredoxin domain and the latter have an additional cupredoxin or haem c domain. In two-domain CuNiRs, nitrite binding at the “T2Cu” active site is observed crystallographically, but in three-domain RpNiR it is experimentally elusive.

Understanding how oxygen vacancies affect conductivity in transparent conducting oxides

The role of oxygen vacancies in the transparent conducting oxides (TCOs) In2O3, SnO2 and ZnO has remained controversial, with some studies indicating that they act as shallow donors, but many computational studies using plane-wave supercell techniques claiming that they act as deep traps. Using the hybrid QM/MM embedded cluster technique via the ChemShell code, we calculated the formation and thermal ionisation energies of oxygen vacancies in the three TCOs.

Water formation in the interstellar medium

Chemical reactions in the interstellar medium occur at low temperature, often on ice surfaces. Those are found to enhance chemical reactivity. In combination with atom tunnelling, reactions with a significant activation barrier can take place even at the cryogenic temperatures of outer space.

Unravelling of the reaction mechanism and tunnelling contributions in Taurine Dioxygenase

The biochemical turnover of taurin is catalysed by taurine dioxygenase, aided by molecular oxygen and alpha-ketogluterate. The rate-limiting step is a hydrogen atom transfer for which a significant kinetic isotope effect was found experimentally. To study it with high predictive power, quantum mechanics is needed for the chemical transformations at the catalytic centre, but the protein environment also needs to be taken into account. Since a full quantum description is computationally infeasible, a QM/MM approach was used.

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