Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor $\Phi$ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds we calculate $\Phi$ as a function of the proton donor-acceptor distance $R$. For numerical results, we use a parameterization of the model for symmetric O-H.... O bonds. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunnelling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total $\Phi$ as a function of $R$ with NMR experimental results for enzymes, and in particular with an empirical parametrisation $\Phi(R)$, used previously to determine bond lengths.Comment: Final version, accepted for publication in Journal of Chemical Physics. Minor changes, including more extensive discussion of relevant of model to protein

Three-dimensional modelling on the hydrodynamics of a circulating fluidised bed

The rapid depletion of oil and the environmentalimpact of combustion has motivated the search for cleancombustion technologies. Fluidised bed combustion (FBC)technology works by suspending a fuel over a fast air inletwhilst sustaining the required temperatures. Using biomassor a mixture of coal/biomass as the fuel, FBC provides alow-carbon combustion technology whilst operating at lowtemperatures. Understanding the hydrodynamic processes influidised beds is essential as the flow behaviours causing heatdistributions and mixing determine the combustion processes.The inlet velocities and different particle sizes influence theflow behaviour significantly, particularly on the transitionfrom bubbling to fast fluidising regimes. Computationalmodelling has shown great advancement in its predictive capabilityand reliability over recent years. Whilst 3D modellingis preferred over 2D modelling, the majority of studies use2D models for multiphase models due to computational costconsideration. In this paper, two-fluid modelling (TFM) isused to model a 3D circulating fluidised bed (CFB) initiallyfocussing on fluid catalytic cracker (FCC) particles. Thetransition from bubbling to fast fluidisation over a rangeof velocities is explored, whilst the effects on the bubblediameter, particle distributions and bed expansion for differentparticle properties including particle sizes are compared. Dragmodels are also compared to study the effects of particleclustering at the meso-scale

Absolute Dynamical Limit to Cooling Weakly-Coupled Quantum Systems

Cooling of a quantum system is limited by the size of the control forces that are available (the "speed" of control). We consider the most general cooling process, albeit restricted to the regime in which the thermodynamics of the system is preserved (weak coupling). Within this regime, we further focus on the most useful control regime, in which a large cooling factor, and good ground-state cooling can be achieved. We present a control protocol for cooling, and give clear structural arguments, as well as strong numerical evidence, that this protocol is globally optimal. From this we obtain simple expressions for the limit to cooling that is imposed by the speed of control.Comment: 4 pages, Revetex4-1, 2 png figure

Coexistence of antiferrodistortive and ferroelectric distortions at the PbTiO3_3 (001) surface

The c(2$\times$2) reconstruction of (001) PbTiO$_3$ surfaces is studied by means of first principles calculations for paraelectric (non-polar) and ferroelectric ([001] polarized) films. Analysis of the atomic displacements in the near-surface region shows how the surface modifies the antiferrodistortive (AFD) instability and its interaction with ferroelectric (FE) distortions. The effect of the surface is found to be termination dependent. The AFD instability is suppressed at the TiO$_2$ termination while it is strongly enhanced, relative to the bulk, at the PbO termination resulting in a c(2x2) surface reconstruction which is in excellent agreement with experiments. We find that, in contrast to bulk PbTiO$_3$, in-plane ferroelectricity at the PbO termination does not suppress the AFD instability. The AFD and the in-plane FE distortions are instead concurrently enhanced at the PbO termination. This leads to a novel surface phase with coexisting FE and AFD distortions which is not found in PbTiO$_3$ bulk

Photophysics of phycoerythrocyanins from the cyanobacterium Westiellopsis prolifica studied by time-resolved fluorescence and coherent anti-Stokes Raman scattering spectroscopy

Three building blocks of the antenna complexes of the cyanobacterium Westiellopsis prolifica were studied: PEC(X), which is similar to the α-subunit of phycoerythrocyanin (PEC), trimers of PEC and monomers derived from these by deaggregation with KSCN. The fit of the fluorescence decay curve of PEC(X) requires at least four exponentials, although it supposedly contains only one chromophore. The coherent anti-Stokes Raman scattering (CARS) spectra indicate that the heterogeneity observed is due to geometrical isomers, which are in part generated by photoinduced processes. A similar heterogeneity in chromophore structure and properties is also found in the monomers, where four exponentials are needed to fit the fluorescence decay curve. As in trimers, there is a long-lived, low-amplitude component, which can be assigned to impurities and/or oxidation products. The energy transfer time between the two phyocyanobilin chromophores in the β-subunit is about 500 ps; the lifetime of the fluorescing β-chromophore is 1.5 ns. The phycoviolobilin chromophore in the α-subunit adopts different geometries characterized by fluorescence lifetimes of about 240 and 800 ps. No evidence was found for energy transfer between the α-chromophore and the β-chromophores. This energy transfer occurs in trimers on a time scale of less than 20 ps; the energy transfer time between the two different types of β-chromophore is about 250 ps and the lifetime of the terminal emitter is about 1.5 ns. The excited state kinetics are therefore similar to those of PEC trimers from Mastigocladus laminosus, as are the CARS spectra, indicating a similar chromophore—protein arrangement. In comparison with phycocyanin, the ordering of the excited states of chromophores β84 and β155 may be changed. Although PEC trimers of Westiellopsis prolifica show almost as good a photostability as trimers of Mastigocladus laminosus, monomers are so photolabile that no CARS spectra could be recorded