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•Simulations of any solid-state NMR experiments for any spin system (up to 15 spins).•High flexibility through scripting interface.•Fast powder averaging through efficient crystallite ...interpolation schemes.•Parallel computing on modern computer architectures, including high-performance computing clusters.•Improved optimal control algorithms.
Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden–Fletcher–Goldfarb–Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations.
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•A 1H-evolved, 1H-detected rotating-frame SLF is demonstrated under ultrafast MAS.•CP-based SLF sequence is quite sensitive to Hartmann–Hahn mismatch.•CP-based SLF sequence is ...insensitive to offset when high RF fields are used.•A constant-amplitude-CP SLF renders a better performance than a ramped-CP SLF.•1H-detection greatly enhances the sensitivity of CP-based rotating-frame SLF.
Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies of molecules in the solid-state. Though many different rotating-frame SLF sequences have been put forth, recent advances in ultrafast MAS technology have considerably simplified pulse sequence requirements due to the suppression of proton–proton dipolar interactions. In this study we revisit a simple two-dimensional 1H–13C dipolar coupling/chemical shift correlation experiment using 13C detected cross-polarization with a variable contact time (CPVC) and systematically study the conditions for its optimal performance at 60kHz MAS. In addition, we demonstrate the feasibility of a proton-detected version of the CPVC experiment. The theoretical analysis of the CPVC pulse sequence under different Hartmann–Hahn matching conditions confirms that it performs optimally under the ZQ (w1H−w1C=±wr) condition for polarization transfer. The limits of the cross polarization process are explored and precisely defined as a function of offset and Hartmann–Hahn mismatch via spin dynamics simulation and experiments on a powder sample of uniformly 13C-labeled L-isoleucine. Our results show that the performance of the CPVC sequence and subsequent determination of 1H–13C dipolar couplings are insensitive to 1H/13C frequency offset frequency when high RF fields are used on both RF channels. Conversely, the CPVC sequence is quite sensitive to the Hartmann–Hahn mismatch, particularly for systems with weak heteronuclear dipolar couplings. We demonstrate the use of the CPVC based SLF experiment as a tool to identify different carbon groups, and hope to motivate the exploration of more sophisticated 1H detected avenues for ultrafast MAS.
The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these ...membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small bicelles and the nanodiscs show increased peptide solvation and difference in peptide orientation compared to embedding in a bilayer. The large bicelle imitated a bilayer well with respect to both curvature and peptide solvation, although peripheral binding of short tailed lipids to the embedded proteins is observed, which could hinder ligand binding or multimer formation.
The Core Scientific Dataset (CSD) model with JavaScript Object Notation (JSON) serialization is presented as a lightweight, portable, and versatile standard for intra- and interdisciplinary ...scientific data exchange. This model supports datasets with a p-component dependent variable, {U0, …, Uq, …, Up-1}, discretely sampled at M unique points in a d-dimensional independent variable (X0, …, Xk, …, Xd-1) space. Moreover, this sampling is over an orthogonal grid, regular or rectilinear, where the principal coordinate axes of the grid are the independent variables. It can also hold correlated datasets assuming the different physical quantities (dependent variables) are sampled on the same orthogonal grid of independent variables. The model encapsulates the dependent variables' sampled data values and the minimum metadata needed to accurately represent this data in an appropriate coordinate system of independent variables. The CSD model can serve as a re-usable building block in the development of more sophisticated portable scientific dataset file standards.
Single-crystal NMR spectroscopy Vosegaard, Thomas
Progress in nuclear magnetic resonance spectroscopy,
April 2021, 2021-04-00, 20210401, Letnik:
123
Journal Article
Recenzirano
Odprti dostop
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•Instrumentation for single-crystal NMR spectroscopy is reviewed.•The theoretical basis for analysis of single-crystal NMR is summarized.•Software tools to analyse single-crystal NMR ...data are reviewed.•Selected applications of single-crystal NMR in materials science are presented.•Applications of single-crystal NMR to study various physical properties are presented.
Single-crystal (SC) NMR spectroscopy is a solid-state NMR method that has been used since the early days of NMR to study the magnitude and orientation of tensorial nuclear spin interactions in solids. This review first presents the field of SC NMR instrumentation, then provides a survey of software for analysis of SC NMR data, and finally it highlights selected applications of SC NMR in various fields of research. The aim of the last part is not to provide a complete review of all SC NMR literature but to provide examples that demonstrate interesting applications of SC NMR.
Solid-state magnetic resonance is a unique technique that can reveal the dynamics of complex biological systems with atomic resolution. Longitudinal relaxation is a mechanism that returns ...longitudinal nuclear magnetization to its thermal equilibrium by incoherent processes. The measured longitudinal relaxation rate constant however represents the combination of both incoherent and coherent contributions to the change of nuclear magnetization. This work demonstrates the effect of magic angle spinning rate on the longitudinal relaxation rate constant in two model compounds: L-histidine hydrochloride monohydrate and glycine serving as proxies for isotopically-enriched biological materials. Most notably, it is demonstrated that the longitudinal N15 relaxation of the two nitrogen nuclei in the imidazole ring in histidine is reduced by almost three orders of magnitude at the condition of rotational resonance with the amine, while the amine relaxation rate constant is increased at these conditions. The observed phenomenon may have radical implications for the solid-state magnetic resonance in biophysics and materials, especially in the proper measurement of dynamics and as a selective serial transfer step in dynamic nuclear polarization.
The fibril structure formed by the amyloidogenic fragment SNNFGAILSS of the human islet amyloid polypeptide (hIAPP) is determined with 0.52 Å resolution. Symmetry information contained in the easily ...obtainable resonance assignments from solid‐state NMR spectra (see picture), along with long‐range constraints, can be applied to uniquely identify the supramolecular organization of fibrils.
The fibril structure formed by the amyloidogenic fragment SNNFGAILSS of the human islet amyloid polypeptide (hIAPP) is determined with 0.52 Å resolution. Symmetry information contained in the easily obtainable resonance assignments from solid‐state NMR spectra (see picture), along with long‐range constraints, can be applied to uniquely identify the supramolecular organization of fibrils.
Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and ...other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO
production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.
Students’ skills in structure elucidation of organic molecules are developed by training them to understand advanced spectroscopic measurements and elucidate structures of small organic molecules ...from mass spectrometry (MS) and infrared (IR), ultraviolet (UV), and 1H and 13C nuclear magnetic resonance (NMR) spectroscopic data. The present work puts a specific focus on developing student skills to ensure that the students (i) are aware of the resources involved in obtaining the spectral data and (ii) obtain the skills necessary to handle spectra which have not been processed by experts, to better reflect the use of spectroscopic techniques in their later work life. This is achieved through the web-based spectroscopy activity iSpec, in which the basic idea is that every action costs resources. The cost of a resource is given in the form of resource points (RPs), such that different experimental data can be “purchased” for a number of RPs.
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