Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography

Predicting 35-Cl electric field gradient tensors in crystalline solids using cluster and fragment-corrected planewave density functional theory

Planewave-corrected methods have proven effective for accurately modeling nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent work extended the application of planewave-corrected calculations beyond the second row, predicting EFG tensor parameters for 35Cl using a simple molecular correction to projector augmented-wave (PAW) density functional theory (DFT). Here we extend this work using fragment and cluster-based calculations coupled with polarizable continuum (PCM) methods to improve further the accuracy of planewave-corrected 35Cl EFG tensor calculations. Benchmark data from a test set comprised of 105 individual 35Cl EFG tensor principal components for chlorine-containing molecular crystals and crystalline chloride salts shows fragment-corrected planewave calculations using the PBE0 hybrid density functional improve the accuracy of predicted EFG tensor components by 30 % relative to traditional planewave calculations. We compare the influence of different geometry optimization methods and density functionals on the accuracy of predicted 35Cl EFG tensor parameters. Four cases of spectral assignment are presented to demonstrate the utility of improving the accuracy of predicted 35Cl EFG tensor parameters.

Ab initio study of stability and quadrupole coupling constants in borophosphates

The DFT method was used to predict the formation energies and quadrupole coupling constants CQ in a series of borophosphates: Li3BP2O8, Li2NaBP2O8, Na3BP2O8, Li2B3PO8, Na5B2P3O13, LiNa2B5P2O14 and Na3B6PO13 composed of different networks and different amounts of borate and phosphate units. The change in formation energies with increasing number of B atoms in this series is attributed to the multiplicity of boron sites and is explained by density of states calculations. The calculated CQ values of 7Li, 23Na and 11B are correlated with the coordination and distortion of polyhedra to elucidate the influence of local and more distant environments. As for the CQ of 11B, it should be in the ranges of 0.26-0.36, 0.48-0.84 and ∼1 MHz for boron tetrahedral distortion indices of 0.004-0.013, 0.015-0.019 and 0.033, respectively, whereas CQ ∼3.0 MHz corresponds to boron in a triangular site. The obtained numerical relationships make it possible to predict the quadrupole frequencies for these nuclei based only on their local environment, and vice versa, to propose structural models from NMR data. These results provide guidance for studying similar characteristics of other borophosphates, the structure of which varies depending on the initial reaction, composition and temperature.

Understanding Cu(i) local environments in MOFs via63/65Cu NMR spectroscopy

The field of metal-organic frameworks (MOFs) includes a vast number of hybrid organic and inorganic porous materials with wide-ranging applications. In particular, the Cu(i) ion exhibits rich coordination chemistry in MOFs and can exist in two-, three-, and four-coordinate environments, which gives rise to many structural motifs and potential applications. Direct characterization of the structurally and chemically important Cu(i) local environments is essential for understanding the sources of specific MOF properties. For the first time, 63/65Cu solid-state NMR has been used to investigate a variety of Cu(i) sites and local coordination geometries in Cu MOFs. This approach is a sensitive probe of the local Cu environment, particularly when combined with density functional theory calculations. A wide range of structurally-dependent 63/65Cu NMR parameters have been observed, including 65Cu quadrupolar coupling constants ranging from 18.8 to 74.8 MHz. Using the data from this and prior studies, a correlation between Cu quadrupolar coupling constants, Cu coordination number, and local Cu coordination geometry has been established. Links between DFT-calculated and experimental Cu NMR parameters are also presented. Several case studies illustrate the feasibility of 63/65Cu NMR for investigating and resolving inequivalent Cu sites, monitoring MOF phase changes, interrogating the Cu oxidation number, and characterizing the product of a MOF chemical reaction involving Cu(ii) reduction to Cu(i). A convenient avenue to acquire accurate 65Cu NMR spectra and NMR parameters from Cu(i) MOFs at a widely accessible magnetic field of 9.4 T is described, with a demonstrated practical application for tracking Cu(i) coordination evolution during MOF anion exchange. This work showcases the power of 63/65Cu solid-state NMR spectroscopy and DFT calculations for molecular-level characterization of Cu(i) centers in MOFs, along with the potential of this protocol for investigating a wide variety of MOF structural changes and processes important for practical applications. This approach has broad applications for examining Cu(i) centers in other weight-dilute systems.

An unusual ionic cocrystal of ponatinib hydrochloride: characterization by single-crystal X-ray diffraction and ultra-high field NMR spectroscopy

This study describes the discovery of a unique ionic cocrystal of the active pharmaceutical ingredient (API) ponatinib hydrochloride (pon·HCl), and characterization using single-crystal X-ray diffraction (SCXRD) and solid-state NMR (SSNMR) spectroscopy. Pon·HCl is a multicomponent crystal that features an unusual stoichiometry, with an asymmetric unit containing both monocations and dications of the ponatinib molecule, three water molecules, and three chloride ions. Structural features include (i) a charged imidazopyridazine moiety that forms a hydrogen bond between the ponatinib monocations and dications and (ii) a chloride ion that does not feature hydrogen bonds involving any organic moiety, instead being situated in a "square" arrangement with three water molecules. Multinuclear SSNMR, featuring high and ultra-high fields up to 35.2 T, provides the groundwork for structural interpretation of complex multicomponent crystals in the absence of diffraction data. A 13C CP/MAS spectrum confirms the presence of two crystallographically distinct ponatinib molecules, whereas 1D 1H and 2D 1H-1H DQ-SQ spectra identify and assign the unusually deshielded imidazopyridazine proton. 1D 35Cl spectra obtained at multiple fields confirm the presence of three distinct chloride ions, with density functional theory calculations providing key relationships between the SSNMR spectra and H⋯Cl- hydrogen bonding arrangements. A 2D 35Cl → 1H D-RINEPT spectrum confirms the spatial proximities between the chloride ions, water molecules, and amine moieties. This all suggests future application of multinuclear SSNMR at high and ultra-high fields to the study of complex API solid forms for which SCXRD data are unavailable, with potential application to heterogeneous mixtures or amorphous solid dispersions.

Benchmark accuracy of predicted NMR observables for quadrupolar 14 N and 17 O nuclei in molecular crystals

Nuclear quadrupole resonances for 14 N and ¹⁷ O nuclei are exquisitely sensitive to interactions with surrounding atoms. As a result, nitrogen and oxygen solid-state nuclear magnetic resonance (ssNMR) provides a powerful tool for investigating structure and dynamics in complex systems. First-principles calculations are increasingly used to facilitate spectral assignment and to evaluate and adjust crystal structures. Recent work combining the strengths of planewave density functional theory (DFT) calculations with a single molecule correction obtained using a higher level of theory has proven successful in improving the accuracy of predicted chemical shielding (CS) tensors and ¹⁷ O quadrupolar coupling constants ( C q ). Here we extend this work by examining the accuracy of predicted ¹⁴ N and ¹⁷ O electric field gradient (EFG) tensor components obtained using alternative planewave-corrections involving cluster and two-body fragment-based calculations. We benchmark the accuracy of CS and EFG tensor predictions for both nitrogen and oxygen using planewave, two-body fragment, and enhanced planewave-corrected techniques. Combining planewave and two-body fragment calculations reduces the error in predicted ¹⁷ O C q values by 35% relative to traditional planewave calculations. These enhanced planewave-correction methods improve the accuracy of ¹⁷ O and ¹⁴ N EFG tensor components by 15% relative to planewave DFT but yield minimal improvement relative to a simple molecular correction. However, in structural environments involving either high symmetry or strong intermolecular interactions, enhanced planewave-corrected methods provide a distinct advantage.

Exploring the Potential of Multinuclear Solid-State 1 H, 13 C, and 35 Cl Magnetic Resonance To Characterize Static and Dynamic Disorder in Pharmaceutical Hydrochlorides

Crystallographic disorder, whether static or dynamic, can be detrimental to the physical and chemical stability, ease of crystallization and dissolution rate of an active pharmaceutical ingredient. Disorder can result in a loss of manufacturing control leading to batch-to-batch variability and can lengthen the process of structural characterization. The range of NMR active nuclei makes solid-state NMR a unique technique for gaining nucleus-specific information about crystallographic disorder. Here, we explore the use of high-field ³⁵ Cl solid-state NMR at 23.5 T to characterize both static and dynamic crystallographic disorder: specifically, dynamic disorder occurring in duloxetine hydrochloride (1), static disorder in promethazine hydrochloride (2), and trifluoperazine dihydrochloride (3). In all structures, the presence of crystallographic disorder was confirmed by ¹³ C cross-polarization magic-angle spinning (CPMAS) NMR and supported by GIPAW-DFT calculations, and in the case of 3, ¹ H solid-state NMR provided additional confirmation. Applying ³⁵ Cl solid-state NMR to these compounds, we show that higher magnetic fields are beneficial for resolving the crystallographic disorder in 1 and 3, while broad spectral features were observed in 2 even at higher fields. Combining the data obtained from ¹ H, ¹³ C, and ³⁵ Cl NMR, we show that 3 exhibits a unique case of disorder involving the ⁺ N-H hydrogen positions of the piperazinium ring, driving the chloride anions to occupy three distinct sites.

Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction

Nesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO₂ . Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO₃  ⋅ 3H₂ O], or a hydroxy- hydrated- magnesium bicarbonate [Mg(HCO₃ )OH ⋅ 2H₂ O]. The resolution of this controversy is central to understanding this material's thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational-echo double-resonance ¹³ C{¹ H} (REDOR), ¹³ C-¹ H distances are determined with precision, and the combination of ¹³ C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO₃  ⋅ 3H₂ O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H-bonding stabilizes this structure against dehydration to MgCO₃ . More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X-ray diffraction is inconclusive.

Hydrates of active pharmaceutical ingredients: A 35Cl and 2H solid-state NMR and DFT study

This study uses ³⁵Cl and ²H solid-state NMR (SSNMR) spectroscopy and dispersion-corrected plane-wave density functional theory (DFT) calculations to characterize the molecular-level structures and dynamics of hydrates of active pharmaceutical ingredients (APIs). We use ³⁵Cl SSNMR to measure the EFG tensors of the chloride ions to characterize hydrated forms of hydrochloride salts of APIs, along with two corresponding anhydrous forms. DFT calculations are used to refine the crystal structures of the APIs and determine relationships between the ³⁵Cl EFG tensors and the spatial arrangements of proximate hydrogen bonds, which are particularly influenced by interactions with water molecules. We find that the relationship between ³⁵Cl EFG tensors and local hydrogen bonding geometries is complex, but meaningful structure/property relationships can be garnered through use of DFT calculations. Specifically, for every case in which such a comparison could be made, we find that the hydrate has a smaller magnitude of C_Q than the corresponding anhydrous form, indicating a chloride ion environment with a ground-state electron density of higher spherical symmetry in the former. Finally, variable-temperature ³⁵Cl and ²H SSNMR experiments on a deuterium-exchanged sample of the API cimetidine hydrochloride monohydrate are used to monitor temperature-dependent influences on the spectra that may arise from motional influences on the ³⁵Cl and ²H EFG tensors. From the ²H SSNMR spectra, we determine that the motions of water molecules are characterized by jump-like motions about their C₂ rotational axes that occur on timescales that are unlikely to influence the ³⁵Cl central-transition (+1/2 ↔︎ -1/2) powder patterns (this is confirmed by ³⁵Cl SSNMR). Together, these methods show great promise for the future study of APIs in their bulk and dosage forms, especially variable hydrates in which crystallographic water content varies with external conditions such as humidity.

Multi-Component Crystals Containing Urea: Mechanochemical Synthesis and Characterization by 35Cl Solid-State NMR Spectroscopy and DFT Calculations

Mechanochemical synthesis provides new pathways for the rational design of multi-component crystals (MCCs) involving anionic or cationic components, which offer molecular-level architectures unavailable to MCCs comprised of strictly neutral components....

A toolbox for improving the workflow of NMR crystallography

NMR crystallography is a powerful tool with applications in structural characterization and crystal structure verification, to name two. However, applying this tool presents several challenges, especially for industrial users, in terms of consistency, workflow, time consumption, and the requirement for a high level of understanding of experimental solid-state NMR and GIPAW-DFT calculations. Here, we have developed a series of fully parameterized scripts for use in Materials Studio and TopSpin, based on the .magres file format, with a focus on organic molecules (e.g. pharmaceuticals), improving efficiency, robustness, and workflow. We separate these tools into three major categories: performing the DFT calculations, extracting & visualizing the results, and crystallographic modelling. These scripts will rapidly submit fully parameterized CASTEP jobs, extract data from the calculations, assist in visualizing the results, and expedite the process of structural modelling. Accompanied with these tools is a description on their functionality, documentation on how to get started and use the scripts, and links to video tutorials for guiding new users. Through the use of these tools, we hope to facilitate NMR crystallography and to harmonize the process across users.

Nutraceuticals in Bulk and Dosage Forms: Analysis by 35Cl and 14N Solid-State NMR and DFT Calculations

This study uses ³⁵Cl and ¹⁴N solid-state NMR (SSNMR) spectroscopy and dispersion-corrected plane-wave density functional theory (DFT) calculations for the structural characterization of chloride salts of nutraceuticals in their bulk and dosage forms. For eight nutraceuticals, we measure the ³⁵Cl EFG tensor parameters of the chloride ions and use plane-wave DFT calculations to elucidate relationships between NMR parameters and molecular-level structure, which provide rapid NMR crystallographic assessments of structural features. We employ both ³⁵Cl direct excitation and ¹H→³⁵Cl cross-polarization methods to characterize a dosage form containing α-d-glucosamine HCl, observe possible impurity and/or adulterant phases, and quantify the weight percent of the active ingredient. To complement this, we also investigate ¹⁴N SSNMR spectroscopy and DFT calculations to characterize nitrogen atoms in the nutraceuticals. This includes a discussion of targeted acquisition experimental protocols (i.e., acquiring a select region of the overall pattern that features key discontinuities) that allow ultrawideline spectra to be acquired rapidly, even for unreceptive samples (i.e., those with long values of T₁(¹⁴N), short values of T₂^eff(¹⁴N), or very broad patterns). It is hoped that these experimental and computational protocols will be useful for the characterization of various solid forms of nutraceuticals (i.e., salts, polymorphs, hydrates, solvates, cocrystals, amorphous solid dispersions, etc.), help detect impurity and counterfeit solid phases in dosage forms, and serve as a foundation for future NMR crystallographic studies of nutraceutical solid forms, including studies using ab initio crystal structure prediction algorithms.

35 Cl-1 H Heteronuclear correlation magic-angle spinning nuclear magnetic resonance experiments for probing pharmaceutical salts

Heteronuclear multiple-quantum coherence (HMQC) pulse sequences for establishing heteronuclear correlation in solid-state nuclear magnetic resonance (NMR) between ³⁵ Cl and ¹ H nuclei in chloride salts under fast (60 kHz) magic-angle spinning (MAS) and at high magnetic field (a ¹ H Larmor frequency of 850 MHz) are investigated. Specifically, recoupling of the ³⁵ Cl-¹ H dipolar interaction using rotary resonance recoupling with phase inversion every rotor period or the symmetry-based SR4² ₁ pulse sequences are compared. In our implementation of the population transfer (PT) dipolar (D) HMQC experiment, the satellite transitions of the ³⁵ Cl nuclei are saturated with an off-resonance WURST sweep, at a low nutation frequency, over the second spinning sideband, whereby the WURST pulse must be of the same duration as the recoupling time. Numerical simulations of the ³⁵ Cl-¹ H MAS D-HMQC experiment performed separately for each crystallite orientation in a powder provide insight into the orientation dependence of changes in the second-order quadrupolar-broadened ³⁵ Cl MAS NMR lineshape under the application of dipolar recoupling. Two-dimensional ³⁵ Cl-¹ H PT-D-HMQC MAS NMR spectra are presented for the amino acids glycine·HCl and l-tyrosine·HCl and the pharmaceuticals cimetidine·HCl, amitriptyline·HCl and lidocaine·HCl·H₂ O. Experimentally observed ³⁵ Cl lineshapes are compared with those simulated for ³⁵ Cl chemical shift and quadrupolar parameters as calculated using the gauge-including projector-augmented wave (GIPAW) method: the calculated quadrupolar product (P_Q ) values exceed those measured experimentally by a factor of between 1.3 and 1.9.

Modeling Small Structural and Environmental Differences in Solids with 15 N NMR Chemical Shift Tensors

The ability to theoretically predict accurate NMR chemical shifts in solids is increasingly important due to the role such shifts play in selecting among proposed model structures. Herein, two theoretical methods are evaluated for their ability to assign ¹⁵ N shifts from guanosine dihydrate to one of the two independent molecules present in the lattice. The NMR data consist of ¹⁵ N shift tensors from 10 resonances. Analysis using periodic boundary or fragment methods consider a benchmark dataset to estimate errors and predict uncertainties of 5.6 and 6.2 ppm, respectively. Despite this high accuracy, only one of the five sites were confidently assigned to a specific molecule of the asymmetric unit. This limitation is not due to negligible differences in experimental data, as most sites exhibit differences of >6.0 ppm between pairs of resonances representing a given position. Instead, the theoretical methods are insufficiently accurate to make assignments at most positions.