pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMDMSλD). In the CPHMDMSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMDMSλD simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMDMSλD framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules – proteins and nucleic acids is now possible.

We present the compound K 2 Sn 3 O 7 , a Sn 4+ ­containing oxide with a unique structure type among oxides. A combination of X-ray and neutron diffraction was essential to solve the structure of this compound from powder data. The compound is orthorhombic and reminiscent of an offset hollandite, where open channels hold a row of four K + per channel per cell. UV-visible spectroscopy indicates a wide band gap semiconductor, which is confirmed by first-principles electronic-structure calculations of band structures, densities of states, and optical properties. The continued discovery of new structure types in ternary tin oxides should remain a priority for the identification of prospective ion conductors and transparent conducting compounds.

The effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO2, including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.

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Characterization of the thermal expansion in the rare earth di-titanates is important for their use in high-temperature structural and dielectric applications. Powder samples of the rare earth di-titanates R 2Ti2O7 (or R 2O3·2TiO2), where R = La, Pr, Nd, Sm, Gd, Dy, Er, Yb, Y, which crystallize in either the monoclinic or cubic phases, were synthesized for the first time by the solution-based steric entrapment method. The three-dimensional thermal expansions of these polycrystalline powder samples were measured by in situ synchrotron powder diffraction from 25°C to 1600°C in air, nearly 600°C higher than other in situ thermal expansion studies. The high temperatures in synchrotron experiments were achieved with a quadrupole lamp furnace. Neutron powder diffraction measured the monoclinic phases from 25°C to 1150°C. The La2Ti2O7 member of the rare earth di-titanates undergoes a monoclinic to orthorhombic displacive transition on heating, as shown by synchrotron diffraction in air at 885°C (864°C–904°C) and neutron diffraction at 874°C (841°C–894°C).