Dataset Information

Ensemble-Based Modeling of the NMR Spectra of Solid Solutions: Cation Disorder in Y2(Sn,Ti)2O7.

ABSTRACT: The sensitivity of NMR to the local environment, without the need for any long-range order, makes it an ideal tool for the characterization of disordered materials. Computational prediction of NMR parameters can be of considerable help in the interpretation and assignment of NMR spectra of solids, but the statistical representation of all possible chemical environments for a solid solution is challenging. Here, we illustrate the use of a symmetry-adapted configurational ensemble in the simulation of NMR spectra, in combination with solid-state NMR experiments. We show that for interpretation of the complex and overlapped lineshapes that are typically observed, it is important to go beyond a single-configuration representation or a simple enumeration of local environments. The ensemble method leads to excellent agreement between simulated and experimental spectra for Y2(Sn,Ti)2O7 pyrochlore ceramics, where the overlap of signals from different local environments prevents a simple decomposition of the experimental spectral lineshapes. The inclusion of a Boltzmann weighting confirms that the best agreement with experiment is obtained at higher temperatures, in the limit of full disorder. We also show that to improve agreement with experiment, in particular at low dopant concentrations, larger supercells are needed, which might require alternative simulation approaches as the complexity of the system increases. It is clear that ensemble-based modeling approaches in conjunction with NMR spectroscopy offer great potential for understanding configurational disorder, ultimately aiding the future design of functional materials.

SUBMITTER: Moran RF

PROVIDER: S-EPMC6900218 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

Ensemble-Based Modeling of the NMR Spectra of Solid Solutions: Cation Disorder in Y2(Sn,Ti)2O7.

Moran Robert F RF McKay David D Tornstrom Paulynne C PC Aziz Alex A Fernandes Arantxa A Grau-Crespo Ricardo R Ashbrook Sharon E SE

Journal of the American Chemical Society 20191022 44

The sensitivity of NMR to the local environment, without the need for any long-range order, makes it an ideal tool for the characterization of disordered materials. Computational prediction of NMR parameters can be of considerable help in the interpretation and assignment of NMR spectra of solids, but the statistical representation of all possible chemical environments for a solid solution is challenging. Here, we illustrate the use of a symmetry-adapted configurational ensemble in the simulatio ...[more]

PMID: 31591883

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Project description:Solid-state NMR has been used to determine the structures of membrane proteins in native-like lipid bilayer environments. Most structure calculations based on solid-state NMR observables are performed using simulated annealing with restrained molecular dynamics and an energy function, where all nonbonded interactions are represented by a single, purely repulsive term with no contributions from van der Waals attractive, electrostatic, or solvation energy. To our knowledge, this is the first application of an ensemble dynamics technique performed in explicit membranes that uses experimental solid-state NMR observables to obtain the refined structure of a membrane protein together with information about its dynamics and its interactions with lipids. Using the membrane-bound form of the fd coat protein as a model membrane protein and its experimental solid-state NMR data, we performed restrained ensemble dynamics simulations with different ensemble sizes in explicit membranes. For comparison, a molecular dynamics simulation of fd coat protein was also performed without any restraints. The average orientation of each protein helix is similar to a structure determined by traditional single-conformer approaches. However, their variations are limited in the resulting ensemble of structures with one or two replicas, as they are under the strong influence of solid-state NMR restraints. Although highly consistent with all solid-state NMR observables, the ensembles of more than two replicas show larger orientational variations similar to those observed in the molecular dynamics simulation without restraints. In particular, in these explicit membrane simulations, Lys(40), residing at the C-terminal side of the transmembrane helix, is observed to cause local membrane curvature. Therefore, compared to traditional single-conformer approaches in implicit environments, solid-state NMR restrained ensemble simulations in explicit membranes readily characterize not only protein dynamics but also protein-lipid interactions in detail.

Dataset Information

Ensemble-Based Modeling of the NMR Spectra of Solid Solutions: Cation Disorder in Y2(Sn,Ti)2O7.

Publications

Ensemble-Based Modeling of the NMR Spectra of Solid Solutions: Cation Disorder in Y<sub>2</sub>(Sn,Ti)<sub>2</sub>O<sub>7</sub>.

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