Solid-state NMR and computational studies of 4-methyl-2-nitroacetanilide

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.

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured ¹³C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (¹H, ¹³C, ¹⁵N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct ¹³C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental ¹³C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of ¹³C shift tensors and the observation of residual dipolar coupling between ¹³C and ¹⁴N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD₁₆ = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD₁₆ = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

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 (13)C and (15)N 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 (13)C and (15)N 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.

Can the conformation of flexible hydroxyl groups be constrained by simple NMR crystallography approaches? The case of the quercetin solid forms

Hydrogen atoms in systems with many flexible hydroxyl side-groups are difficult to be exactly located from experimental X-Ray diffraction and/or solid-state NMR data, thus often leading to wrong conclusions with respect to the hydrogen bonding network established in crystal lattice. A simple computational method is proposed in the present work to tackle this problem, which may be readily incorporated in conventional NMR crystallography protocols. The method is based on ranking all possible conformations of the flexible hydroxyls according to their lattice energy in crystalline environments. Its effectiveness is investigated on two distinct solid forms of quercetin, for which only two out of the five hydroxyl side-groups can be well constrained from experimental/theoretical data. For this purpose, first-principle quantum-mechanical computations were combined with calculations at the molecular mechanics (MM) level of theory, and previous ss-NMR and X-Ray diffraction data. To assess accuracy in ranking the identified conformers, tests have been performed first on quercetin dihydrate, for which an X-Ray single-crystal structure is available. The possibility of applying this method in a real NMR crystallography context has been investigated finally on anhydrous quercetin, for which only powder X-Ray crystal structure has been reported so far.

Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations

A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.

Applications of solid-state NMR to pharmaceutical polymorphism and related matters

Magic-angle spinning NMR is now making a significant contribution to our understanding of the structure of polymorphs and solvates of pharmaceutical significance. This personal review article discusses a range of applications, with particular emphasis on information about crystallography, for which NMR can address problems that cannot be readily solved by diffraction techniques (such as dynamic disorder and non-stoichiometric hydration). Unlike diffractograms, NMR spectra yield immediate chemical information. Moreover, heterogeneous samples can be investigated and amorphous content provides no significant barrier to studies. Furthermore, NMR can be an effective technique for quantitation (down to the level of ca. 1%). Additional strength is being derived from computation of chemical shifts in solids, using a code that takes account of the spatial repetition inherent in crystalline materials.

A structure refinement strategy for NMR crystallography: an improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors

A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si-O, O-O, and Si-Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si-O, O-O, and Si-Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this "NMR crystallography" structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods.

Chemical shift computations on a crystallographic basis: some reflections and comments

Computations for chemical shifts of molecular organic compounds using the gauge-including projector augmented wave method and the NMR-CASTEP code are reviewed. The methods are briefly introduced, and some general aspects involving the sources of uncertainty in the results are explored. The limitations are outlined. Successful applications of the computations to problems of interpretation of NMR results are discussed and the range of areas in which useful information is obtained is illustrated by examples. The particular value of the computations for comparing shifts between resonances where the same chemical site is involved is emphasised. Such cases arise for shifts between different crystallographically independent molecules of the same chemical species, between polymorphs and for shift anisotropies and asymmetries.

Structural Study of Polymorphs and Solvates of Finasteride

NMR and XRD data are reported for several new forms of finasteride, including the results of complete structure determinations for three solvates. Form III of finasteride, hitherto only mentioned in the patent literature, and a new anhydrous form designated Form X, have been found in mixtures of polymorphs and their (13)C NMR chemical shifts obtained. The results demonstrate that the crystallographic asymmetric units contain three molecules and one molecule, respectively. Attempts to reproduce "Form H1", as described in a patent, resulted in a new IPA solvate hydrate. The previously-reported acetic acid, dioxane, and ethyl acetate solvates have been further characterised, and new THF and diethyl ether solvates prepared and characterised. The crystal structures of the dioxane, IPA, and THF solvates have been determined by single-crystal X-ray diffraction. All the solvates (except the acetic acid case) are found to be hemihydrates, to have a finasteride: solvent molar ratio of 2:1 and to have a common structure. The solvate molecules are highly disordered and sited in channels in the structure. The powder XRD patterns are characteristic of the common structure. These solvates may be distinguished by the characteristic CPMAS (13)C signals from the solvent molecules, but the resonances of the host finasteride structures differ only marginally, and powder XRD patterns are almost indistinguishable. Magic-angle spinning (MAS) proton spectra give sharp lines for the solvent peaks, confirming their high degree of mobility. This is further shown in one case by direct polarisation (13)C spectra. Mobility of the tert-butyl group is also implied. Thermal characteristics have been studied and TGA used (in conjunction with solution-state proton NMR) to estimate molar ratios.

Assigning powders to crystal structures by high-resolution (1)H-(1)H double quantum and (1)H-(13)C J-INEPT solid-state NMR spectroscopy and first principles computation. A case study of penicillin G

We show how powder samples at natural isotopic abundance can be assigned to crystal structures by using high-resolution proton and carbon-13 solid-state NMR spectra in combination with first principles calculations. Homonuclear proton double-quantum spectra in combination with through-bond proton-carbon HSQC spectra are used to assign the NMR spectra. We then show that the proton chemical shifts can be included in the process of assigning the spectra to a crystal structure using first principles calculations. The method is demonstrated on the K salt of penicillin G.