Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds.

This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.

Do Models beyond Hybrid Density Functionals Increase the Agreement with Experiment for Predicted NMR Chemical Shifts or Electric Field Gradient Tensors in Organic Solids?

Ab initio predictions of chemical shifts and electric field gradient (EFG) tensor components are frequently used to help interpret solid-state nuclear magnetic resonance (NMR) experiments. Typically, these predictions employ density functional theory (DFT) with generalized gradient approximation (GGA) functionals, though hybrid functionals have been shown to improve accuracy relative to experiment. Here, the performance of a dozen models beyond the GGA approximation are examined for the prediction of solid-state NMR observables, including meta-GGA, hybrid, and double-hybrid density functionals and second-order Møller-Plesset perturbation theory (MP2). These models are tested on organic molecular crystal data sets containing 169 experimental 13C and 15N chemical shifts and 114 17O and 14N EFG tensor components. To make these calculations affordable, gauge-including projector augmented wave (GIPAW) Perdew-Burke-Ernzerhof (PBE) calculations with periodic boundary conditions are combined with a local intramolecular correction computed at the higher level of theory. Within the context of typical NMR property calculations performed on a static, DFT-optimized crystal structure, the benchmarking finds that the double-hybrid DFT functionals produce errors versus experiment that are no smaller than those of hybrid functionals in the best cases, and they can be larger. MP2 errors versus experiment are even bigger. Overall, no practical advantages are found for using any of the tested double-hybrid functionals or MP2 to predict experimental solid-state NMR chemical shifts and EFG tensor components for routine organic crystals, especially given the higher computational cost of those methods. This finding likely reflects error cancellation benefiting the hybrid functionals. Improving the accuracy of the predicted chemical shifts and EFG tensors relative to experiment would probably require more robust treatments of the crystal structures, their dynamics, and other factors.

The Scientific Method as a Scaffold to Enhance Communication Skills in Chemistry.

Scientific success in the field of chemistry depends upon the mastery of a wide range of soft skills, most notably scientific writing and speaking. However, training for scientific communication is typically limited at the undergraduate level, where students struggle to express themselves in a clear and logical manner. The underlying issue is deeper than basic technical skills; rather, it is a problem of students' unawareness of a fundamental and strategic framework for writing and speaking with a purpose. The methodology has been implemented for individual mentorship and in our regional summer research program to deliver a blueprint of thought and reasoning that endows students with the confidence and skills to become more effective communicators. Our didactic process intertwines undergraduate research with the scientific method and is partitioned into six steps, referred to as "phases", to allow for focused and deep thinking on the essential components of the scientific method. The phases are designed to challenge the student in their zone of proximal development so they learn to extract and ultimately comprehend the elements of the scientific method through focused written and oral assignments. Students then compile their newly acquired knowledge to create a compelling and logical story, using their persuasive written and oral presentations to complete a research proposal, final report, and formal 20 min presentation. We find that such an approach delivers the necessary guidance to promote the logical framework that improves writing and speaking skills. Over the past decade, we have witnessed both qualitative and quantitative gains in the students' confidence in their abilities and skills (developed by this process), preparing them for future careers as young scientists.

Chemical Shift Tensors of Cimetidine Form A Modeled with Density Functional Theory Calculations: Implications for NMR Crystallography.

The principal components of the 13C chemical shift tensors for the ten crystallographically distinct carbon atoms of the active pharmaceutical ingredient cimetidine Form A have been measured using the FIREMAT technique. Density functional theory (DFT) calculations of 13C and 15N magnetic shielding tensors are used to assign the 13C and 15N peaks. DFT calculations were performed on cimetidine and a training set of organic crystals using both plane-wave and cluster-based approaches. The former set of calculations allowed several structural refinement strategies to be employed, including calculations utilizing a dispersion-corrected force field that was parametrized using 13C and 15N magnetic shielding tensors. The latter set of calculations featured the use of resource-intensive hybrid-DFT methods for the calculation of magnetic shielding tensors. Calculations on structures refined using the new force-field correction result in improved values of 15N magnetic shielding tensors (as gauged by agreement with experimental chemical shift tensors), although little improvement is seen in the prediction of 13C shielding tensors. Calculations of 13C and 15N magnetic shielding tensors using hybrid functionals show better agreement with experimental values in comparison to those using GGA functionals, independent of the method of structural refinement; the shielding of carbon atoms bonded to nitrogen are especially improved using hybrid DFT methods.

Moving towards fast characterization of polymorphic drugs by solid-state NMR spectroscopy.

Solid-state nuclear magnetic resonance (SS-NMR) spectroscopy has become a common technique to study polymorphism in pharmaceutical solids at high-resolution. However, high-throughput application of high resolution SS-NMR spectroscopy is severely limited by the long 1H spin-lattice relaxation (T1) that is common to solid phase compounds. Here, we demonstrate the use of paramagnetic relaxation reagents such as chromium (III) acetylacetonate (Cr(acac)3) and nickel (II) acetylacetonate (Ni(acac)2) for fast data acquisition by significantly reducing the T1 value for carbamazepine Forms I, II, III, and dihydrate, cimetidine Forms A and B, nabumetone Form I, and acetaminophen Form I polymorphs. High resolution 13C cross-polarization and magic angle spinning were used to measure T1 values for each polymorph. In order to confirm the absence of polymorphic transitions during SS-NMR experiments, powder x-ray diffraction was implemented. The amount of chromium ions incorporated by the recrystallization process was quantified by using inductively coupled plasma optical emission spectroscopy. Our results suggest that the paramagnetic ions added to the polymorphs do not affect the polymorphic transformation or the quality of NMR spectra. We believe that this successful demonstration of fast data collection will enable high-throughput utilization of SS-NMR techniques to study polymorphic solids and could set the groundwork for NMR crystallography studies.

Study of Perfluorophosphonic Acid Surface Modifications on Zinc Oxide Nanoparticles.

In this study, perfluorinated phosphonic acid modifications were utilized to modify zinc oxide (ZnO) nanoparticles because they create a more stable surface due to the electronegativity of the perfluoro head group. Specifically, 12-pentafluorophenoxydodecylphosphonic acid, 2,3,4,5,6-pentafluorobenzylphosphonic acid, and (1H,1H,2H,2H-perfluorododecyl)phosphonic acid have been used to form thin films on the nanoparticle surfaces. The modified nanoparticles were then characterized using infrared spectroscopy, X-ray photoelectron spectroscopy, and solid-state nuclear magnetic resonance spectroscopy. Dynamic light scattering and scanning electron microscopy-energy dispersive X-ray spectroscopy were utilized to determine the particle size of the nanoparticles before and after modification, and to analyze the film coverage on the ZnO surfaces, respectively. Zeta potential measurements were obtained to determine the stability of the ZnO nanoparticles. It was shown that the surface charge increased as the alkyl chain length increases. This study shows that modifying the ZnO nanoparticles with perfluorinated groups increases the stability of the phosphonic acids adsorbed on the surfaces. Thermogravimetric analysis was used to distinguish between chemically and physically bound films on the modified nanoparticles. The higher weight loss for 12-pentafluorophenoxydodecylphosphonic acid and (1H,1H,2H,2H-perfluorododecyl)phosphonic acid modifications corresponds to a higher surface concentration of the modifications, and, ideally, higher surface coverage. While previous studies have shown how phosphonic acids interact with the surfaces of ZnO, the aim of this study was to understand how the perfluorinated groups can tune the surface properties of the nanoparticles.

Measuring and Modeling Highly Accurate 15 N Chemical Shift Tensors in a Peptide.

NMR studies measuring chemical shift tensors are increasingly being employed to assign structure in difficult-to-crystallize solids. For small organic molecules, such studies usually focus on 13 C sites, but proteins and peptides are more commonly described using 15 N amide sites. An important and often neglected consideration when measuring shift tensors is the evaluation of their accuracy against benchmark standards, where available. Here we measure 15 N tensors in the dipeptide glycylglycine at natural abundance using the slow-spinning FIREMAT method with SPINAL-64 decoupling. The accuracy of these 15 N tensors is evaluated by comparing to benchmark single crystal NMR 15 N measurements and found to be statistically indistinguishable. These FIREMAT experimental results are further used to evaluate the accuracy of theoretical predictions of tensors from four different density functional theory (DFT) methods that include lattice effects. The best theoretical approach provides a root mean square (rms) difference of ±3.9 ppm and is obtained from a fragment-based method and the PBE0 density functional.

Semi-empirical refinements of crystal structures using 17O quadrupolar-coupling tensors.

We demonstrate a modification of Grimme's two-parameter empirical dispersion force field (referred to as the PW91-D2* method), in which the damping function has been optimized to yield geometries that result in predictions of the principal values of 17O quadrupolar-coupling tensors that are systematically in close agreement with experiment. The predictions of 17O quadrupolar-coupling tensors using PW91-D2*-refined structures yield a root-mean-square deviation (RMSD) (0.28 MHz) for twenty-two crystalline systems that is smaller than the RMSD for predictions based on X-ray diffraction structures (0.58 MHz) or on structures refined with PW91 (0.53 MHz). In addition, 13C, 15N, and 17O chemical-shift tensors and 35Cl quadrupolar-coupling tensors determined with PW91-D2*-refined structures are compared to the experiment. Errors in the prediction of chemical-shift tensors and quadrupolar-coupling tensors are, in these cases, substantially lowered, as compared to predictions based on PW91-refined structures. With this PW91-D2*-based method, analysis of 42 17O chemical-shift-tensor principal components gives a RMSD of only 18.3 ppm, whereas calculations on unrefined X-ray structures give a RMSD of 39.6 ppm and calculations of PW91-refined structures give an RMSD of 24.3 ppm. A similar analysis of 35Cl quadrupolar-coupling tensor principal components gives a RMSD of 1.45 MHz for the unrefined X-ray structures, 1.62 MHz for PW91-refined structures, and 0.59 MHz for the PW91-D2*-refined structures.

Calculations of solid-state 43 Ca NMR parameters: A comparison of periodic and cluster approaches and an evaluation of DFT functionals.

We present a computational study of magnetic-shielding and quadrupolar-coupling tensors of 43 Ca sites in crystalline solids. A comparison between periodic and cluster-based approaches for modeling solid-state interactions demonstrates that cluster-based approaches are suitable for predicting 43 Ca NMR parameters. Several model chemistries, including Hartree-Fock theory and 17 DFT approximations (SVWN, CA-PZ, PBE, PBE0, PW91, B3PW91, rPBE, PBEsol, WC, PKZB, BMK, M06-L, M06, M06-2X, M06-HF, TPSS, and TPSSh), are evaluated for the prediction of 43 Ca NMR parameters. Convergence of NMR parameters with respect to basis sets of the form cc-pVXZ (X = D, T, Q) is also evaluated. All DFT methods lead to substantial, and frequently systematic, overestimations of experimental chemical shifts. Hartree-Fock calculations outperform all DFT methods for the prediction of 43 Ca chemical-shift tensors. © 2017 Wiley Periodicals, Inc.

Spin-orbit effects on the (119)Sn magnetic-shielding tensor in solids: a ZORA/DFT investigation.

Periodic-boundary and cluster calculations of the magnetic-shielding tensors of (119)Sn sites in various co-ordination and stereochemical environments are reported. The results indicate a significant difference between the predicted NMR chemical shifts for tin(ii) sites that exhibit stereochemically-active lone pairs and tin(iv) sites that do not have stereochemically-active lone pairs. The predicted magnetic shieldings determined either with the cluster model treated with the ZORA/Scalar Hamiltonian or with the GIPAW formalism are dependent on the oxidation state and the co-ordination geometry of the tin atom. The inclusion of relativistic effects at the spin-orbit level removes systematic differences in computed magnetic-shielding parameters between tin sites of differing stereochemistries, and brings computed NMR shielding parameters into significant agreement with experimentally-determined chemical-shift principal values. Slight improvement in agreement with experiment is noted in calculations using hybrid exchange-correlation functionals.

Analysis of the bond-valence method for calculating (29) Si and (31) P magnetic shielding in covalent network solids.

(29) Si and (31) P magnetic-shielding tensors in covalent network solids have been evaluated using periodic and cluster-based calculations. The cluster-based computational methodology employs pseudoatoms to reduce the net charge (resulting from missing co-ordination on the terminal atoms) through valence modification of terminal atoms using bond-valence theory (VMTA/BV). The magnetic-shielding tensors computed with the VMTA/BV method are compared to magnetic-shielding tensors determined with the periodic GIPAW approach. The cluster-based all-electron calculations agree with experiment better than the GIPAW calculations, particularly for predicting absolute magnetic shielding and for predicting chemical shifts. The performance of the DFT functionals CA-PZ, PW91, PBE, rPBE, PBEsol, WC, and PBE0 are assessed for the prediction of (29) Si and (31) P magnetic-shielding constants. Calculations using the hybrid functional PBE0, in combination with the VMTA/BV approach, result in excellent agreement with experiment. © 2016 Wiley Periodicals, Inc.

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

Density functional investigation of intermolecular effects on 13C NMR chemical-shielding tensors modeled with molecular clusters.

A quantum-chemical method for modeling solid-state nuclear magnetic resonance chemical-shift tensors by calculations on large symmetry-adapted clusters of molecules is demonstrated. Four hundred sixty five principal components of the (13)C chemical-shielding tensors of 24 organic materials are analyzed. The comparison of calculations on isolated molecules with molecules in clusters demonstrates that intermolecular effects can be successfully modeled using a cluster that represents a local portion of the lattice structure, without the need to use periodic-boundary conditions (PBCs). The accuracy of calculations which model the solid state using a cluster rivals the accuracy of calculations which model the solid state using PBCs, provided the cluster preserves the symmetry properties of the crystalline space group. The size and symmetry conditions that the model cluster must satisfy to obtain significant agreement with experimental chemical-shift values are discussed. The symmetry constraints described in the paper provide a systematic approach for incorporating intermolecular effects into chemical-shielding calculations performed at a level of theory that is more advanced than the generalized gradient approximation. Specifically, NMR parameters are calculated using the hybrid exchange-correlation functional B3PW91, which is not available in periodic codes. Calculations on structures of four molecules refined with density plane waves yield chemical-shielding values that are essentially in agreement with calculations on clusters where only the hydrogen sites are optimized and are used to provide insight into the inherent sensitivity of chemical shielding to lattice structure, including the role of rovibrational effects.

13C chemical-shift anisotropy of alkyl-substituted aromatic carbon in anthracene derivatives.

The (13)C chemical-shift anisotropy in anthracene derivatives (9,10-dimethylanthracene, 9,10-dihydroanthracene, dianthracene, and triptycene) has been measured by the 2D FIREMAT timed pulse sequence and the corresponding set of principal values has been determined by the TIGER processing method. These molecules expand the data base of (13)C CSA measurements of fused aromatic rings some bridged by sp(3) carbon resulting in an unusual bonding configuration, which leads to distinctive aromatic (13)C CSA values. Crystal lattice distortions to the CSA were observed to change the isotropic shift by 2.5 to 3.3 ppm and changes as large as 8.3 ppm in principal components. Modeling of the CSA data by GIPAW DFT (GGA-PBE/ultrafine) shielding calculations resulted in an rms chemical-shift distance of 2.8 ppm after lattice including geometry optimization of the diffraction structures by the GIPAW method at GGA-PBE/ultrafine level. Attention is given to the substituted aromatic carbon in the phenyl groups (here forth referred to as the α-carbon) with respect to CSA modeling with electronic methods. The (13)C CSA of this position is accurately determined due to its spectral isolation of the isotropic shift that limits overlap in the FIREMAT spectrum. In cases where the bridging ring is sp(3) carbon, the current density is reduced from extending beyond the peripheral phenyl groups; this plays a significant role in the magnetic shielding of the α-position. Nuclear independent chemical-shift calculations based on GIAO DFT (B3LYP/6-31G(d)) shielding calculations were used to model the intramolecular π-interactions in dianthracene and triptycene. These NICS results estimate the isotropic shift of the α-position in dianthracene to be insignificantly affected by the presence of the neighboring aromatic rings. However, a notable change in isotropic shielding, Δσ(iso)=-2.1 ppm, is predicted for the α- position of triptycene. Experimentally, the δ22 principal component at the α-position for both dianthracene and triptycene increases by at least 12 ppm compared to 9,10-dihydroanthracene. To rationalize this change, shielding calculations in idealized structures are explored. The spatial position of the bicyclic scaffolding of the bridging ring plays a key role in the large increase in δ22 for the α-carbon.

Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves.

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all (13)C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.

Modeling the (13)C chemical-shift tensor in organic single crystals by quantum mechanical methods: finite basis set effects.

The influence of using finite basis sets to calculate (13)C magnetic shieldings were explored using the Hartree-Fock and the B3LYP hybrid density functional methods. The shielding values were compared in a linear least-squares fashion for a test group of 102 (13)C complete chemical-shift tensors determined from 14 organic single crystals. Pople's basis sets allow for the addition of polarization and diffuse functions in a straightforward way, allowing the examination of 81 combinations at the double and triple zeta level. Dunning's correlation-consistent basis sets were explored as well. The errors associated with predicting the shielding values were found to be largely systematic as revealed by the analysis of the determined regression parameters between calculated chemical shieldings and experimental chemical shifts. Expansion of the basis set leads to a convergence of these regression parameters to their ideal values. The random errors, however, do not decrease by employing larger basis sets; therefore, given the appropriate regression parameters, a small basis description such as 3-21G can be adequate in predicting the relative magnetic-shielding values, i.e. the chemical shifts. Furthermore, in certain cases the inclusion of unbalanced diffuse and polarization functions can significantly degrade the predicted shielding rmsd. Unless employed carefully, these functions do not justify their computational expense. The chemical-shift distance is used to evaluate shielding predictions in individual tensor components. The analysis of the chemical-shift's distance between calculated and experimental data indicates an orientational dependence on the magnitude of errors and suggests the use of the shift anisotropy as a useful fiduciary mark to optimize model chemistries for magnetic-shielding calculations.

Modeling NMR chemical shift: A survey of density functional theory approaches for calculating tensor properties.

The NMR chemical shift, a six-parameter tensor property, is highly sensitive to the position of the atoms in a molecule. To extract structural parameters from chemical shifts, one must rely on theoretical models. Therefore, a high quality group of shift tensors that serve as benchmarks to test the validity of these models is warranted and necessary to highlight existing computational limitations. Here, a set of 102 13C chemical-shift tensors measured in single crystals, from a series of aromatic and saccharide molecules for which neutron diffraction data are available, is used to survey models based on the density functional (DFT) and Hartree-Fock (HF) theories. The quality of the models is assessed by their least-squares linear regression parameters. It is observed that in general DFT outperforms restricted HF theory. For instance, Becke's three-parameter exchange method and mpw1pw91 generally provide the best predicted shieldings for this group of tensors. However, this performance is not universal, as none of the DFT functionals can predict the saccharide tensors better than HF theory. Both the orientations of the principal axis system and the magnitude of the shielding were compared using the chemical-shift distance to evaluate the quality of the calculated individual tensor components in units of ppm. Systematic shortcomings in the prediction of the principal components were observed, but the theory predicts the corresponding isotropic value more accurately. This is because these systematic errors cancel, thereby indicating that the theoretical assessment of shielding predictions based on the isotropic shift should be avoided.

Ring-chain tautomerism in solid-phase erythromycin A: evidence by solid-state NMR.

Chemical shift modeling, utilizing the DFT B3LYP/D95** method, provides the spectral assignment of the 35 visible 13C resonances from the solid-phase erythromycin A dihydrate. A new resonance at 110.8ppm is observed in the high-resolution 13C CP/MAS spectrum upon the application of heat or sample desiccation. With the use of the dipolar-dephasing spectral editing technique, this resonance is identified as a hemiketal carbon and the alternative hypothesis, a conformational change to the anomeric carbon of the desosamine sugar, is ruled out. Hence, the formation of a cyclic hemiketal in erythromycin A while in the solid phase is proven by solid-state NMR. The principal components of the 13C chemical-shift tensor corresponding to this hemiketal are reported. This is the first measurement of hemiketal 13C principal values. The delta11 and delta22 components are unique compared to anomeric carbon values reported in the literature.