Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates.

Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic MD trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure the R1 relaxation rates of uniformly 13C-labeled and site-specific 2H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal the following: (a) for the incoherent component of 13C relaxation, the nearest-neighbor spin interactions dominate, while the 1H-1H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine Cγ-Cδ bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the 2H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the Cß and Cα nuclei; and (d) 13C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.

Proton Transfer and Ionicity: An 15N NMR Study of Pyridine Base Protonation.

Protic ionic liquids (PILs) are made by proton transfer from a Brønsted acid to a base and are of interest for their solvent and electrolyte properties such as high ionic conductivity. Unfortunately, many PILs have been misnamed, because their ionic content is minimal due to an insufficient driving force for the proton transfer. Here we review this problem and introduce a new method, using 15N NMR spectroscopy, of characterizing the relation between the extent of proton transfer to a given base and the strength of the proton-donating acid. The experimental data reveal a sigmoid "titration type" curve that indicates clearly the acid strength, at which molecule bases, of substituted pyridine type, are fully protonated. We compare results for two bases of similar shape but different basicity, protonated by equimolar amounts of the different acids. The extent of protonation is also reflected in the ionic conductivity, and we show that the important part of the protonation sigmoid is quantitatively reproduced by data for conductivity and viscosity displayed in the form of a Walden plot (log equivalent conductivity vs log fluidity). The acid strength, for this study, is based on gas phase proton affinities, but we note that a similar sigmoid is obtained if we use the condensed phase Hammett acidity functions instead. Our findings allow us to rank the AlCl4- anion as the weakest proton acceptor in use in IL studies, consistent with its role in the most conductive ILs.

Thermal and Structural Properties of Silk Biomaterials Plasticized by Glycerol.

The molecular interactions of silk materials plasticized using glycerol were studied, as these materials provide options for biodegradable and flexible protein-based systems. Plasticizer interactions with silk were analyzed by thermal, spectroscopic, and solid-state NMR analyses. Spectroscopic analysis implied that glycerol was hydrogen bonded to the peptide matrix, but may be displaced with polar solvents. Solid-state NMR indicated that glycerol induced ß-sheet formation in the dried silk materials, but not to the extent of methanol treatment. Fast scanning calorimetry suggested that ß-sheet crystal formation in silk-glycerol films appeared to be less organized than in the methanol treated silk films. We propose that glycerol may be simultaneously inducing and interfering with ß-sheet formation in silk materials, causing some improper folding that results in less-organized silk II structures even after the glycerol is removed. This difference, along with trace residual glycerol, allows glycerol extracted silk materials to retain more flexibility than methanol processed versions.

NMR Characterization of Ionicity and Transport Properties for a Series of Diethylmethylamine Based Protic Ionic Liquids.

The ionicity and transport properties of a series of diethylmethylamine (DEMA) based protic ionic liquids (PILs) were characterized, principally utilizing nuclear magnetic resonance (NMR) spectroscopy. PILs were formed via the protonation of DEMA by an array of acids spanning a large range of acidities. A correlation between the (1)H chemical shift of the exchangeable proton and the acidity of the acid used for the synthesis of the PIL was observed. The gas phase proton affinity of the acid was found to be a better predictor of the extent of proton transfer than the commonly used aqueous ΔpKa. Pulsed field gradient (PFG) NMR was used to determine the diffusivity of the exchangeable proton in a subset of the PILs. The exchangeable proton diffuses with the acid if the PIL is synthesized with a weak acid, and with the base if a strong acid is used. The ionicity of the PILs was characterized using the Walden analysis and by comparing to the ideal Nernst-Einstein conductivity predicted from the (1)H PFG-NMR results.

Solid-State NMR Characterization of Mixed Phosphonic Acid Ligand Binding and Organization on Silica Nanoparticles.

As ligand functionalization of nanomaterials becomes more complex, methods to characterize the organization of multiple ligands on surfaces is required. In an effort to further the understanding of ligand-surface interactions, a combination of multinuclear ((1)H, (29)Si, (31)P) and multidimensional solid-state nuclear magnetic resonance (NMR) techniques was utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methylphosphonic acid (MPA) and phenylphosphonic acid (PPA). (1)H → (29)Si cross-polarization (CP)-magic angle spinning (MAS) solid-state NMR was used to selectively detect silicon atoms near hydrogen atoms (primarily surface species); these results indicate that geminal silanols are preferentially depleted during the functionalization with phosphonic acids. (1)H → (31)P CP-MAS solid-state NMR measurements on the functionalized silica nanoparticles show three distinct resonances shifted upfield (lower ppm) and broadened compared to the resonances of the crystalline ligands. Quantitative (31)P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. When fumed silica nanoparticles were functionalized with an equal molar ratio of MPA and PPA, the MPA bound the nanoparticle surface preferentially. Cross-peaks apparent in the 2D (1)H exchange spectroscopy (EXSY) NMR measurements of the multiligand sample at short mixing times indicate that the MPA and PPA are spatially close (≤5 Å) on the surface of the nanostructure. Furthermore, (1)H-(1)H double quantum-single quantum (DQ-SQ) back-to-back (BABA) 2D NMR spectra further confirmed that MPA and PPA are strongly dipolar coupled with observation of DQ intermolecular contacts between the ligands. DQ experimental buildup curves and simulations indicate that the average distance between MPA and PPA is no further than 4.2 ± 0.2 Å.

Characterizing mixed phosphonic acid ligand capping on CdSe/ZnS quantum dots using ligand exchange and NMR spectroscopy.

The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd.

Type I Clathrates as Novel Silicon Anodes: An Electrochemical and Structural Investigation.

Silicon clathrates contain cage-like structures that can encapsulate various guest atoms or molecules. An electrochemical evaluation of type I silicon clathrates based on Ba8Al y Si46-y as the anode material for lithium-ion batteries is presented here. Postcycling characterization with nuclear magnetic resonance and X-ray diffraction shows no discernible structural or volume changes even after electrochemical insertion of 44 Li (≈1 Li/Si) into the clathrate structure. The observed properties are in stark contrast with lithiation of other silicon anodes, which become amorphous and suffer from large volume changes. The electrochemical reactions are proposed to occur as single phase reactions at approximately 0.2 and 0.4 V versus Li/Li+ during lithiation and delithiation, respectively, distinct from diamond cubic or amorphous silicon anodes. Reversible capacities as high as 499 mAh g-1 at a 5 mA g-1 rate were observed for silicon clathrate with composition Ba8Al8.54Si37.46, corresponding to ≈1.18 Li/Si. These results show that silicon clathrates could be promising durable anodes for lithium-ion batteries.

Benzene-derived carbon nanothreads.

Low-dimensional carbon nanomaterials such as fullerenes, nanotubes, graphene and diamondoids have extraordinary physical and chemical properties. Compression-induced polymerization of aromatic molecules could provide a viable synthetic route to ordered carbon nanomaterials, but despite almost a century of study this approach has produced only amorphous products. Here we report recovery to ambient pressure of macroscopic quantities of a crystalline one- dimensional sp(3) carbon nanomaterial formed by high-pressure solid-state reaction of benzene. X-ray and neutron diffraction, Raman spectroscopy, solid-state NMR, transmission electron microscopy and first-principles calculations reveal close- packed bundles of subnanometre-diameter sp(3)-bonded carbon threads capped with hydrogen, crystalline in two dimensions and short-range ordered in the third. These nanothreads promise extraordinary properties such as strength and stiffness higher than that of sp(2) carbon nanotubes or conventional high-strength polymers. They may be the first member of a new class of ordered sp(3) nanomaterials synthesized by kinetic control of high-pressure solid-state reactions.

Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments.

The composition of the Sutter's Mill meteorite insoluble organic material was studied both in toto by solid-state NMR spectroscopy of the powders and by gas chromatography-mass spectrometry analyses of compounds released upon their hydrothermal treatment. Results were compared with those obtained for other meteorites of diverse classifications (Murray, GRA 95229, Murchison, Orgueil, and Tagish Lake) and found to be so far unique in regard to the molecular species released. These include, in addition to O-containing aromatic compounds, complex polyether- and ester-containing alkyl molecules of prebiotic appeal and never detected in meteorites before. The Sutter's Mill fragments we analyzed had likely been altered by heat, and the hydrothermal conditions of the experiments realistically mimic early Earth settings, such as near volcanic activity or impact craters. On this basis, the data suggest a far larger availability of meteoritic organic materials for planetary environments than previously assumed and that molecular evolution on the early Earth could have benefited from accretion of carbonaceous meteorites both directly with soluble compounds and, for a more protracted time, through alteration, processing, and release from their insoluble organic materials.