Gauge Including Projector Augmented Wave Research Articles

On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR

Solid-state nuclear magnetic resonance (ssNMR) experimental 27Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

Refined Crystal Structure of Samia cynthia ricini Silk Fibroin Revealed by Solid-State NMR Investigations.

Samia cynthia ricini is one of the wild silkworms and its silk fibroin (SF) consists of alternatively repeating poly-l-alanine (PLA) sequences as crystalline domain and glycine-rich sequences as noncrystalline domain; the structure is similar to those of spider silk and other wild silkworm silks. In this paper, we proposed a new staggered model for the packing arrangement of the PLA sequence through the use of the Cambridge Serial Total Energy Package program and a comparison of the observed and calculated chemical shifts of the PLA sequence with the Gauge Including Projector Augmented Wave method. The new model was supported by the interatomic distance information from the cross peaks of Ala Cβ dipolar-assisted rotational resonance (DARR) spectrum of the PLA sequences in S. c. ricini SF fiber. In addition, three 13C NMR peaks observed in the β-sheet region were assigned to the carbons with different environments in the same model, but not assigned to different β-sheet structures.

Pharmaceutical properties of two ethenzamide-gentisic acid cocrystal polymorphs: Drug release profiles, spectroscopic studies and theoretical calculations

The aim of this study was to evaluate the stability and solubility of the polymorphic forms of the ethenzamide (ET) – gentisic acid (GA) cocrystals during standard technological processes leading to tablet formation, such as compression and excipient addition. In this work two polymorphic forms of pharmaceutical cocrystals (ETGA) were characterized by 13C and 15N solid-state nuclear magnetic resonance and Fourier transformed infrared spectroscopy. Spectroscopic studies were supported by gauge including projector augmented wave (GIPAW) calculations of chemical shielding constants.Polymorphs of cocrystals were easily identified and characterized on the basis of solid-state spectroscopic studies. ETGA cocrystals behaviour during direct compressionand tabletting with excipient addition were tested. In order to choose the best tablet composition with suitable properties for the pharmaceutical industry dissolution profile studies of tablets containing polymorphic forms of cocrystals with selected excipients were carried out.

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1H and 13C chemical shifts are determined from two-dimensional 1H-13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles.

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P21/c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C13H9N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C12H8N2, and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C8H12N2. 13C and 19F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19F to 13C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13C and 19F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

A combined NMR crystallographic and PXRD investigation of the structure-directing role of water molecules in orotic acid and its lithium and magnesium salts

Despite the abundance of hydrates, their multifaceted nature and hydration/dehydration behaviour is still not fully understood. For the example of orotic acid monohydrate and its lithium and magnesium hydrate salts, we show how NMR crystallography, namely a combination of solid-state NMR with a focus here on 1H magic angle spinning (MAS) NMR experiments and first-principles DFT GIPAW (gauge-including projector augmented wave) calculations, can play a valuable role in the characterization of hydrate systems. Starting from lithium orotate monohydrate, a rigid system with a limited number of tightly bound water molecules, the general feasibility of this approach was demonstrated. Moving onto more complex hydrate structures, mobility in the orotic acid monohydrate was observed, while for the most complex hydrate, magnesium orotate octahydrate, a loss of associated water molecules was observed after an overnight MAS NMR experiment. A combined study by experimental MAS NMR, powder X-ray diffraction (PXRD) and thermogravimetric analysis (TGA) revealed changes after vacuum drying as well as after storage of a vacuum dried sample under ambient conditions. Specifically, TGA showed the vacuum dried sample to correspond to a dihydrate, for which no structure has yet been determined by single-crystal X-ray diffraction. An NMR crystallography analysis showed that a combination of putative symmetric and asymmetric dihydrate structures explains the observed changes in the experimental MAS NMR spectra.

Combining 27Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δiso, quadrupolar coupling constants, CQ, and asymmetry parameter, η) of Al22.5O28.5N3.5, predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the 27Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al2.811O3.565N0.435 by quantitative analysis. The experimental δiso, CQ, and η of 27Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the 27Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al2.811O3.565N0.435. The results from 27Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

Toward Routine Gauge-Including Projector Augmented-Wave Calculations for Metallic Systems: The Case of ScT2Al (T = Ni, Pd, Pt, Cu, Ag, Au) Heusler Phases

We use the gauge-including projector augmented-waves (GIPAW) method to report, for the first time, theoretical 27Al Knight shifts in metallic systems other than metallic Al. We consider metallic Al and a set of six intermetallic compounds, for which experimental chemical shifts were recently made available in the literature. The orbital and spin components of the chemical shielding tensors are computed from the same ground-state spin-polarized electronic structure, converged under the influence of a uniform external magnetic field. A linear response formalism is used to compute the orbital part, while the spin part is approximated by the linear relationship between the external field and the Fermi contact contribution to the induced magnetic hyperfine field at the nuclear position. Core spin-polarization effects are taken into account by means of a perturbative approach. Our results show that the GIPAW approach yields reasonably acceptable chemical shifts with affordable k-meshes in the irreducible Brillo...

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

A Multi-Technique Experimental and Computational Approach To Study the Dehydration Processes in the Crystals of Endomorphin Opioid Peptide Derivative

When molecular crystals undergo partial dehydration, determining the crystal contents and precise localization of the remaining water in the crystal lattice becomes challenging, especially when the quality of crystals after dehydration is not suitable for X-ray diffraction studies. In this work, we describe a methodology that allows the determination and refinement of the structures of partially dehydrated crystals employing complementary experimental (advanced solid-state NMR techniques, differential scanning calorimetry, elemental analysis) and computational (gauge-including projector-augmented wave density functional theory) techniques. We present the power of the methodology using an opioid peptide derivative, endomorphin-2-OH (EM2-OH) heptahydrate. The advanced solid state NMR techniques 2D-PASS, inv-HETCOR, and cross polarization variable contact (CP-VC) carried out with very fast magic angle spinning were used as a source of the constraints showing differences and similarities in the structures and local molecular dynamics for crystallized and dehydrated samples. A crystal structure prediction employing the gauge-including projector-augmented wave (GIPAW) method was used for the determination and refinement of dehydrated EM2-OH. After dehydration, three out of the initial seven water molecules remain in the lattice of the EM2-OH crystals, with two water molecules located in the pockets made by the pseudocyclic conformations and one forming a bridge between two independent EM2-OH molecules.

Insight into Hydrogen Bonding of Uranyl Hydroxide Layers and Capsules by Use of 1H Magic-Angle Spinning NMR Spectroscopy

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO2(OH)2] (α-UOH) and hydrated uranyl hydroxide [(UO2)4O(OH)6·5H2O (metaschoepite). For the metaschoepite material, proton resonances of the μ2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H–1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. These NMR correlations allowed characterization of local hydrogen-bond environments in uranyl U24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.

Ab Initio Molecular Dynamics Simulations and GIPAW NMR Calculations of a Lithium Borate Glass Melt.

The atomic structure of a molten 0.3Li2O-0.7B2O3 glass at 1250 K was investigated using ab initio molecular dynamics (AIMD) simulations. The gauge including projector augmented wave (GIPAW) method was then employed for computing the chemical shift and quadrupolar coupling constant of (11)B, (17)O, and (7)Li from 764 AIMD derived structures. The chemical shift and quadrupolar coupling constant distributions were directly estimated from the dynamical structure of the molten glass. (11)B NMR parameters of well-known structural units such as the three-coordinated ring, nonring, and four-coordinated tetrahedron were found to be in good agreement with the experimental results. In this study, more detailed classification of B units was presented based on the number of O species bonded to the B atoms. This highlights the limitations of (11)B NMR sensitivity for resolving (11)B local environment using the experimentally obtained spectra only. The (17)O NMR parameter distributions can theoretically resolve the bridging and nonbridging O atoms with different structural units such as nonring, single boroxol ring, and double boroxol ring. Slight but clear differences in the number of bridging O atoms surrounding Li that have not been reported experimentally were observed in the theoretically obtained (7)Li NMR parameters.

Recent advances in solid‐state NMR computational spectroscopy: The case of alumino‐silicate glasses

Solid‐state NMR spectroscopy and computational approaches such as Molecular Dynamics (MD) simulations and Density Functional Theory have proven to be very useful and versatile techniques for studying the structure and the dynamics of noncrystalline materials if a direct comparison between experiment and theory is established. In this review, the basic concepts in first‐principle modeling of solid‐state NMR spectra of oxide glasses are presented. There are three theoretical ingredients in the computational recipe. First, classical or ab initio molecular dynamics simulations are employed to generate the structural models of the glasses of interest. Second, periodic Density Functional Theory calculations coupled with the gauge including projector augmented‐wave (GIPAW) algorithm form the basis for the ab initio calculations of NMR parameters (chemical shielding and quadrupolar parameters). Finally, Spin‐effective Hamiltonian are employed to simulate the solid‐state NMR spectra directly comparable with the experimental counterparts. As an example of this methodology, the investigation of the local and medium range structure of Na‐Ca silicate and aluminosilicate glasses that are usually employed as simplified models for basaltic, andesitic and rhyolitic magmas will be reported. We will show how the direct comparison of the theoretical NMR spectra of MD derived structural models with the experimental counterparts allows gaining new insights into the atomistic structure of very complex oxide glasses. © 2016 Wiley Periodicals, Inc.

Na+ as a probe to structural investigation of dehydrated smectites using NMR spectra calculated by DFT

Ab initio calculations based on density-functional theory (DFT) were made to a large ensemble of representative models of dehydrated smectites with Na+ as counterion. The structures were generated by different isomorphic substitutions of Al3+ by Mg2+ in octahedral sheet and Si4+ by Al3+ in tetrahedral sheet followed by full optimization of the geometries. Structures were chosen among the lowest total energies to calculate nuclear magnetic resonance (NMR) parameters of 1H, 27Al, 29Si, 25Mg and 23Na by means of gauge including projector augmented wave (GIPAW) method. The calculated NMR parameters and simulated spectra suggest that Na+ can be a good probe to investigate the layer structure. The spectra shape for 23Na is more sensitive to isomorphic substitutions in the layer than the other nuclei.

Oxygen-17 NMR spectroscopy of water molecules in solid hydrates

17O solid-state NMR studies of waters of hydration in crystalline solids are presented. The 17O quadrupolar coupling and chemical shift (CS) tensors, and their relative orientations, are measured experimentally at room temperature for α-oxalic acid dihydrate, barium chlorate monohydrate, lithium sulfate monohydrate, potassium oxalate monohydrate, and sodium perchlorate monohydrate. The 17O quadrupolar coupling constants (CQ) range from 6.6 to 7.35 MHz and the isotropic chemical shifts range from –17 to 19.7 ppm. The oxygen CS tensor spans vary from 25 to 78 ppm. These represent the first complete CS and electric field gradient tensor measurements for water coordinated to metals in the solid state. Gauge-including projector-augmented wave density functional theory calculations overestimate the values of CQ, likely due to librational dynamics of the water molecules. Computed CS tensors only qualitatively match the experimental data. The lack of strong correlations between the experimental and computed data, and between these data and any single structural feature, is attributed to motion of the water molecules and to the relatively small overall range in the NMR parameters relative to their measurement precision. Nevertheless, the isotropic chemical shift, quadrupolar coupling constant, and CS tensor span clearly differentiate between the samples studied and establish a ‘fingerprint’ 17O spectral region for water coordinated to metals in solids.

Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs

The experiments of carvedilol form II, form III, and hydrate by 13C and 15N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate 13C and 15N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations.

Computational and experimental study of reversible hydration/dehydration processes in molecular crystals of natural products – a case of catechin

When employing a complementary approach that joins theoretical (crystal structure prediction, CSP, gauge-including projector-augmented wave density functional theory, GIPAW DFT) and experimental (solid-state nuclear magnetic resonance, SSNMR) techniques, we prove that detectable changes in the water content in a crystal lattice can be monitored as a continuous or quantum process by using border values of the measurable number of water molecules in the crystal, depending on the observation probe. In the case of a 13C nucleus, which “feels” the presence of water in its nearest neighbourhood, the subtle changes in the structure of the water channel during the dehydration/rehydration process are not reflected until the water loss exceeds a certain number of molecules. Here, the dehydration of (+)-catechin 4.5-hydrate with a loss of ca. 1–1.5 and 2–2.5H2O molecules leads to microcrystalline form II (partially dehydrated) or amorphous form III, respectively. The CSP calculations for the partially dehydrated (+)-catechin (form II), as verified by experimental 1H and 13C shieldings, resulted in two similar probable crystal structures, which have 2 and 2.5 water molecules in the unit cell.

Self-Assembled Oligoanilinic Nanosheets: Molecular Structure Revealed by Solid-State NMR Spectroscopy

The products obtained during the early stages of the oxidative polymerization of aniline in the “falling pH” reaction were investigated using multinuclear solid-state magic-angle spinning (MAS) NMR combined with first-principles NMR chemical shielding calculations using the GIPAW (gauge-including projector augmented wave) method. A sample was synthesized starting from a 50:50 mixture of U–13C aniline and 15N-labeled aniline; two-dimensional 13C refocused INADEQUATE, 15N–13C double CP, 15N PDSD, and 1H–13C/15N refocused INEPT MAS NMR spectra revealed the presence of quinoneimine structural units. Structural models that are consistent with the connectivities revealed by the 13C refocused INADEQUATE and 15N–13C Double CP spectra are proposed. GIPAW chemical shift calculations are performed for model structures based on the proposed oligomeric structures; noting that the model structures do not take into account intermolecular hydrogen bonding and CH−π interactions, agreement and discrepancy to experiment are discussed.

Solid-State 87Sr NMR Spectroscopy at Natural Abundance and High Magnetic Field Strength.

Twenty-five strontium-containing solids were characterized via (87)Sr NMR spectroscopy at natural abundance and high magnetic field strength (B0 = 21.14 T). Strontium nuclear quadrupole coupling constants in these compounds are sensitive to the strontium site symmetry and range from 0 to 50.5 MHz. An experimental (87)Sr chemical shift scale is proposed, and available data indicate a chemical shift range of approximately 550 ppm, from -200 to +350 ppm relative to Sr(2+)(aq). In general, magnetic shielding increased with strontium coordination number. Experimentally measured chemical shift anisotropy is reported for stationary samples of solid powdered SrCl2·6H2O, SrBr2·6H2O, and SrCO3, with δaniso((87)Sr) values of +28, +26, and -65 ppm, respectively. NMR parameters were calculated using CASTEP, a gauge including projector augmented wave (GIPAW) DFT-based program, which addresses the periodic nature of solids using plane-wave basis sets. Calculated NMR parameters are in good agreement with those measured.

NMR Investigations of Noncovalent Carbon Tetrel Bonds. Computational Assessment and Initial Experimental Observation.

Group IV tetrel elements may act as tetrel bond donors, whereby a region of positive electrostatic potential (σ-hole) interacts with a Lewis base. The results of calculations of NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen or nitrogen atoms in various functional groups. The (13)C chemical shift (δiso) and the (1c)J((13)C,Y) coupling (Y = (17)O, (15)N) across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the noncovalent interaction is demonstrated via an increase in δiso and in |(1c)J((13)C,Y)| as the tetrel bond shortens. Gauge-including projector-augmented wave density functional theory (DFT) calculations of δiso are reported for crystals that exhibit tetrel bonding in the solid state. Experimental δiso values for solid sarcosine and its tetrel-bonded salts corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.