GIPAW Method Research Articles

Synthesis, crystal structure and 19F NMR parameters modelling of CaTiF6(H2O)2 yielding to a revision of the bond-valence parameters for the Ti4+/F− ion pair

CaTiF6(H2O)2 was synthetized by a solvothermal method and was found to be isostructural to SrTiF6⋅2H2O. The structure, refined from Powder X-Ray Diffraction (PXRD) data, is built from the connectivity of dimers [Ca2F10(H2O)4] of square antiprisms (SAP) [CaF5(H2O)3] and TiF6 octahedra. To assign the six 19F NMR resonances to the six fluorine crystallographic sites of same multiplicity, 19F magnetic shielding tensors have been calculated using the GIPAW method. Unusually, the plot of the experimental 19F isotropic chemical shift (δiso) values, as a function of the calculated 19F isotropic shielding (σiso) values, shows a much better alignment for the experimental structure than for the DFT-optimized one. Whereas, the dynamics of the structural water molecules under experimental conditions are not captured by the optimized structure, the experimental averaged structure provides a good account of the experimental data and a reliable assignment of the 19F resonances to the F sites. Finally, the previously established bond-valence (BV) parameter Rij for the Ti4+/F− ion pair (1.76 ​Å) leads to overestimated BV sum values for Ti. This trend has been observed for almost all other fluorotitanates. We then undertook to refine its value, using the Ti–F bond lengths from 70 carefully selected structures containing 134 Ti sites forming TiF6 octahedra, and leading to Rij ​= ​1.706 ​Å.

Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments.

Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.

A GIPAW versus GIAO-ZORA-SO study of 13C and 15N CPMAS NMR chemical shifts of aromatic and heterocyclic bromo derivatives

Theoretical simulation of NMR parameters in compounds bearing heavy atoms generally requires the application of relativistic corrections. We report herein the theoretical characterization of 13C and 15N CPMAS NMR of known bromo-derivative crystals by using both the GIPAW and the combined GIAO-ZORA-SO approximation methods. Several statistical analyses were performed to compare both approaches, with non-relativistic GIPAW method being more useful to predict the 13C and 15N chemical shifts. The problem of applying GIPAW to crystal structures showing static or dynamic crystalline disorder of the special class resulting in half-protons will be discussed in detail.

The plane-wave DFT investigations into the structure and the 11B solid-state NMR parameters of lithium fluorooxoborates

The strategy for an application of the first-principles calculations on crystalline systems to predict the 11B solid-state NMR powder-patterns is described, and its efficacy is demonstrated for two novel lithium-containing fluorooxborates, Li2B3O4F3 and Li2B6O9F2. This strategy involves the plane-wave DFT computations of the NMR parameters, whose values are then scaled and used in the spectral simulations, and are supposed to be directly applicable in the NMR crystallography studies of boron-containing systems. In particular, the GIPAW method and the PBE, PW91, and RPBE functionals are applied. Issues specific to the signal-assignment of the two compounds are also discussed.

Theoretical Modeling Of The Structure Of Surface Niobium Sites Based On Solid-State 93nb Nmr

In this work niobium oxide clusters on the surface of Al2O3 are modeled using DFT calculations. 93Nb NMR parameters of modeled clusters were computed with the GIPAW method. The niobia system under consideration represents high niobium loading on the surface of the support. The niobium atoms are highly coordinated and linked to the other niobia polyhedra by one or two bonds. The most of the niobium oxide particles has a coordination number of six. The correlations found between 93Nb NMR parameters and coordination environment are discussed.

Solid State Structure Prediction Through DFT Calculations and 13C NMR Measurements: Case Study of Spiro-2,4-dithiohydantoins

Abstract We present a DFT approach for precise estimation of the intermolecular effects on the experimental and calculated 13C NMR shifts for a series of 5-spiro-2,4-dithiohydantoins (1–5), both in solid state and in solution. It has been found that the used B3LYP/6-31+ G** method gives very good agreement with the experimental structural and the NMR parameters, provided the intermolecular hydrogen bonds are properly considered. For correct description of the experimental NMR shifts in solid state we have initially used the isolated-molecule and the cluster approaches for GIAO calculations of the NMR shifts, followed by periodic boundary condition calculations of the structure and the nuclear magnetic shielding constants by the GIPAW method implemented in the Quantum Espresso code. The best agreement with the experimental solid state data is obtained for the optimized small cluster (a trimer of molecules) in the calculations using the atom-centered orbitals. Excellent agreement between the 13C CPMAS NMR and the GIPAW calculated shift is obtained for fully relaxed bulk structures of compounds 1–5. This has been used as a final verification of the proposed solid state structure of compound 5 whose crystal structure is unknown yet.

Intermolecular Packing in B. mori Silk Fibroin: Multinuclear NMR Study of the Model Peptide (Ala-Gly)15 Defines a Heterogeneous Antiparallel Antipolar Mode of Assembly in the Silk II Form

We have previously suggested that crystalline Bombyx mori silk in silk II form (the silk structure after spinning) is not a simple antiparallel β-sheet but is intrinsically heterogeneous. Using the peptide (AG)15, we have obtained the first fully assigned high resolution solid state 1H NMR spectrum. Distinct heterogeneity was observed, in both 1H and 13C CP/MAS signals. Based on these results, a new model is proposed that contains two different packing arrangements of antiparallel β-sheets. The structures were energetically minimized by CASTEP calculation and used to calculate the solid state 1H, 13C, and 15N NMR chemical shifts using the GIPAW method. This new model was supported by good agreement between the calculated and observed 1H, 13C, and 15N chemical shifts and relative 1H–1H proximities obtained from 2D 1H DQMAS experiments. We conclude that the intermolecular packing of B. mori silk fibroin has been finally resolved.

NbF5 and TaF5: Assignment of 19F NMR resonances and chemical bond analysis from GIPAW calculations

The 19F isotropic chemical shifts (δiso) of two isomorphic compounds, NbF5 and TaF5, which involve six nonequivalent fluorine sites, have been experimentally determined from the reconstruction of 1D 19F MAS NMR spectra. In parallel, the corresponding 19F chemical shielding tensors have been calculated using the GIPAW method for both experimental and DFT-optimized structures. Furthermore, the [M4F20] units of NbF5 and TaF5 being held together by van der Waals interactions, the relevance of Grimme corrections to the DFT optimization processes has been evaluated. However, the semi-empirical dispersion correction term introduced by such a method does not show any significant improvement. Nonetheless, a complete and convincing assignment of the 19F NMR lines of NbF5 and TaF5 is obtained, ensured by the linearity between experimental 19F δiso values and calculated 19F isotropic chemical shielding σiso values. The effects of the geometry optimizations have been carefully analyzed, confirming among other matters, the inaccuracy of the experimental structure of NbF5. The relationships between the fluorine chemical shifts, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the length of the M-F bonds have been established. Additionally, for three of the 19F NMR lines of NbF5, distorted multiplets, arising from 1J-coupling and residual dipolar coupling between the 19F and 93Nb nuclei, were simulated yielding to values of 93Nb-19F 1J-coupling for the corresponding fluorine sites.

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

The 13C 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 13C CSA measurements of fused aromatic rings some bridged by sp3 carbon resulting in an unusual bonding configuration, which leads to distinctive aromatic 13C CSA values. Crystal lattice distortions to the CSA were observed to change the isotropic shift by 2.5 to 3.3ppm and changes as large as 8.3ppm in principal components. Modeling of the CSA data by GIPAW DFT (GGA-PBE/ultrafine) shielding calculations resulted in an rms chemical-shift distance of 2.8ppm 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 13C 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 sp3 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, Δσiso=−2.1ppm, 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 12ppm 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.

NMR crystallography of α-poly(l-lactide)

A complementary approach that combines NMR measurements, analysis of X-ray and neutron powder diffraction data and advanced quantum mechanical calculations was employed to study the α-polymorph of L-polylactide. Such a strategy, which is known as NMR crystallography, to the best of our knowledge, is used here for the first time for the fine refinement of the crystal structure of a synthetic polymer. The GIPAW method was used to compute the NMR shielding parameters for the different models, which included the α-PLLA structure obtained by 2-dimensional wide-angle X-ray diffraction (WAXD) at -150 °C (model M1) and at 25 °C (model M2), neutron diffraction (WAND) measurements (model M3) and the fully optimized geometry of the PLLA chains in the unit cell with defined size (model M4). The influence of changes in the chain conformation on the (13)C σ(ii) NMR shielding parameters is shown. The correlation between the σ(ii) and δ(ii) values for the M1-M4 models revealed that the M4 model provided the best fit. Moreover, a comparison of the experimental (13)C NMR spectra with the spectra calculated using the M1-M4 models strongly supports the data for the M4 model. The GIPAW method, via verification using NMR measurements, was shown to be capable of the fine refinement of the crystal structures of polymers when coarse X-ray diffraction data for powdered samples are available.

Study of the thermal processes in molecular crystals of peptides by means of NMR crystallography

1D and 2D Very Fast Magic Angle Spinning (VF MAS) NMR experiments with sample rotation up to 55 kHz were applied to study both the dihydrate form of Tyr–(D)Ala–Phe–Gly (N-terminal sequence of opioid peptide dermorphin) and the anhydrous form, which was obtained by thermal treatment. Employing both homo-nuclear (1H–1H BABA, 13C–13C SHANGHAI) and hetero-nuclear 2D correlations (1H–13C and 1H–15N) with inverse detection, it was shown that removing water from the crystal lattice of this tetrapeptide does not destroy its subtle pseudo-cyclic structure, and its supramolecular array is preserved. The GIPAW method was employed to compute the geometry of the peptides and calculate the 13C σii principal elements of the NMR shielding tensor parameters and 1H isotropic NMR shifts. The theoretical values of 13C σii were compared with the experimental 13C δii chemical shift tensor values obtained by a 2D PASS experiment. The correlations 13C σii versus δii and 1H σiso versus δiso were used to evaluate the quality of the computational approach. With the new set of coordinates obtained by the GIPAW method, the crystal and molecular structure of the dehydrated Tyr–(D)Ala–Phe–Gly peptide that was obtained by thermal treatment was constructed. Methodology used in this project combining NMR measurements, analysis of X-ray powder diffraction data and advanced quantum mechanical calculations is known as NMR crystallography.

Structural investigation of α-LaZr2F11 by coupling X-ray powder diffraction, 19F solid state NMR and DFT calculations

α-LaZr2F11 has been synthesized by solid state reaction. Its crystal structure has been refined from X-ray powder diffraction data (space group no. 72 Ibam, a=7.785(1) Å, b=10.086(1) Å and c=11.102(1) Å). α-LaZr2F11 contains one La, one Zr and four F inequivalent crystallographic sites. F3 and F4 are shared between one ZrF73− polyhedron and one LaF85− polyhedron, while F1 and F2 bridge two ZrF73− polyhedra. 19F 1D MAS NMR spectra of α-LaZr2F11 are in agreement with the proposed structural model. Assignment of the 19F resonances to the corresponding crystallographic sites has been performed on the basis of both their relative intensities and their correlation patterns in a 19F 2D dipolar-based double-quantum recoupling MAS NMR spectrum. DFT calculations of the 19F chemical shielding tensors have been performed using the GIPAW method implemented in the NMR-CASTEP code, for the experimental structure and two PBE–DFT geometry optimized structures of α-LaZr2F11 (atomic position optimization and full geometry optimization with rescaling of the unit cell volume to the experimental value). Computations were done with and without using a modified La pseudopotential allowing the treatment of the 4f localized empty orbitals of La3+. A relatively nice agreement between the experimental 19F isotropic and anisotropic chemical shifts and the values calculated for the proposed structural model is obtained.

First principles NMR study of fluorapatite under pressure

NMR is the technique of election to probe the local properties of materials. Herein we present the results of density functional theory (DFT) ab initio calculations of the NMR parameters for fluorapatite (FAp), a calcium orthophosphate mineral belonging to the apatite family, by using the GIPAW method (Pickard and Mauri, 2001). Understanding the local effects of pressure on apatites is particularly relevant because of their important role in many solid state and biomedical applications. Apatites are open structures, which can undergo complex anisotropic deformations, and the response of NMR can elucidate the microscopic changes induced by an applied pressure. The computed NMR parameters proved to be in good agreement with the available experimental data. The structural evaluation of the material behavior under hydrostatic pressure (from −5 to +100kbar) indicated a shrinkage of the diameter of the apatitic channel, and a strong correlation between NMR shielding and pressure, proving the sensitivity of this technique to even small changes in the chemical environment around the nuclei. This theoretical approach allows the exploration of all the different nuclei composing the material, thus providing a very useful guidance in the interpretation of experimental results, particularly valuable for the more challenging nuclei such as 43Ca and 17O.

Probing intermolecular interactions and nitrogen protonation in pharmaceuticals by novel 15N-edited and 2D 14N-1H solid-state NMR

We report the applications of two novel magic-angle spinning (MAS) solid-state NMR methods, 1J15N-1H spectral editing and 2D 14N-1H HMQC, to the characterisation of nitrogen functional groups in two pharmaceutical compounds, cimetidine and tenoxicam. The 1J15N-1H spectral editing method can readily differentiate the number of protons directly bonded to a nitrogen site and is not susceptible to motional effects. This enables confirmation of proton transfer, therefore proving or disproving amine salt formation, which is of high significance to the properties of a drug. The recently developed 2D 14N-1H HMQC method can demonstrate the presence of specific hydrogen bonding interactions and thus aid in identifying molecular association. First-principles calculations of NMR chemical shifts and quadrupolar parameters using the GIPAW method were combined with experimental data to assist with spectral assignment and the identification of the hydrogen bonding motifs.

Solution and Solid-State Effects on NMR Chemical Shifts in Sesquiterpene Lactones: NMR, X-ray, and Theoretical Methods

Selected guaianolide type sesquiterpene lactones were studied combining solution and solid-state NMR spectroscopy with theoretical calculations of the chemical shifts in both environments and with the X-ray data. The experimental (1)H and (13)C chemical shifts in solution were successfully reproduced by theoretical calculations (with the GIAO method and DFT B3LYP 6-31++G**) after geometry optimization (DFT B3LYP 6-31 G**) in vacuum. The GIPAW method was used for calculations of solid-state (13)C chemical shifts. The studied cases involved two polymorphs of helenalin, two pseudopolymorphs of 6α-hydroxydihydro-aromaticin and two cases of multiple asymmetric units in crystals: one in which the symmetry-independent molecules were connected by a series of hydrogen bonds (geigerinin) and the other in which the symmetry-independent molecules, deprived of any specific intermolecular interactions, differed in the conformation of the side chain (badkhysin). Geometrically different molecules present in the crystal lattices could be easily distinguished in the solid-state NMR spectra. Moreover, the experimental differences in the (13)C chemical shifts corresponding to nuclei in different polymorphs or in geometrically different molecules were nicely reproduced with the GIPAW calculations.

NMR parameters in alkali, alkaline earth and rare earth fluorides from first principle calculations

(19)F isotropic chemical shifts for alkali, alkaline earth and rare earth of column 3 basic fluorides are measured and the corresponding isotropic chemical shieldings are calculated using the GIPAW method. When using the PBE exchange-correlation functional for the treatment of the cationic localized empty orbitals of Ca(2+), Sc(3+) (3d) and La(3+) (4f), a correction is needed to accurately calculate (19)F chemical shieldings. We show that the correlation between experimental isotropic chemical shifts and calculated isotropic chemical shieldings established for the studied compounds allows us to predict (19)F NMR spectra of crystalline compounds with a relatively good accuracy. In addition, we experimentally determine the quadrupolar parameters of (25)Mg in MgF(2) and calculate the electric field gradients of (25)Mg in MgF(2) and (139)La in LaF(3) using both PAW and LAPW methods. The orientation of the EFG components in the crystallographic frame, provided by DFT calculations, is analysed in terms of electron densities. It is shown that consideration of the quadrupolar charge deformation is essential for the analysis of slightly distorted environments or highly irregular polyhedra.

Ab initio Calculations of NMR Parameters of Highly Coordinated Oxygen Sites in Aluminosilicates.

Ab initio calculations have been carried out for the three polymorphs of SiAl2O5 in order to study the 17O NMR characteristics of tricoordinated O atoms, O[3], and tetracoordinated O atoms, O[4], that are possibly present in the structure of aluminosilicate glasses. We present δiso, CQ, and η calculations using the density functional theory-based GIPAW method for all silicon, aluminum, and oxygen sites and in particular for the 14 O[3] atoms, which are bonded to three Al or Si atoms in the andalusite, sillimanite, and kyanite polymorphs of SiAl2O5. The O[4] parameters calculated in kyanite are also compared with the corresponding site in α-Al2O3. The calculated values for the 29Si and 27Al isotropic chemical shift values as well as 27Al quadrupolar coupling constants (CQ) and asymmetry parameters (η) are in good agreement with experimental data. Apart from in alumina and in grossite CaAl4O7, 17O NMR parameters have not been measured experimentally yet but the CQ and η values obtained for all sites are con...

Ab Initio Calculations of NMR Parameters of Highly Coordinated Oxygen Sites in Aluminosilicates

Ab initio calculations have been carried out for the three polymorphs of SiAl2O5 in order to study the 17O NMR characteristics of tricoordinated O atoms, O[3], and tetracoordinated O atoms, O[4], that are possibly present in the structure of aluminosilicate glasses. We present δiso, CQ, and η calculations using the density functional theory-based GIPAW method for all silicon, aluminum, and oxygen sites and in particular for the 14 O[3] atoms, which are bonded to three Al or Si atoms in the andalusite, sillimanite, and kyanite polymorphs of SiAl2O5. The O[4] parameters calculated in kyanite are also compared with the corresponding site in α-Al2O3. The calculated values for the 29Si and 27Al isotropic chemical shift values as well as 27Al quadrupolar coupling constants (CQ) and asymmetry parameters (η) are in good agreement with experimental data. Apart from in alumina and in grossite CaAl4O7, 17O NMR parameters have not been measured experimentally yet but the CQ and η values obtained for all sites are con...

The effect of radiation damage on local structure in the crystalline fraction of ZrSiO4: Investigating the29Si NMR response to pressure in zircon and reidite

Periodic density functional theory (DFT) was used to calculate the structure of zircon (ZrSiO 4 ) and reidite (scheelite polymorph of ZrSiO 4 ) at pressures from 0-41 GPa. Subsequently, the 29Si nuclear magnetic resonance (NMR) chemical shifts at each pressure were determined using the GIPAW method. The results show that in both zircon and reidite the chemical shifts become more negative with increasing pressure. The chemical shift of reidite is predicted by calculation to be −91.8 ppm and measured as −91.1 ppm. The results are used to interpret the previously observed systematic decrease in 29 Si NMR chemical shifts (increasingly negative) in the crystalline fraction of radiation-damaged zircon with increasing α-dose. The original hypothesis that strain induced by the compression of the crystal by internal regions of damaged, amorphized material at high pressure was the origin of the shifts was disproved. An alternative source of internal pressure in the radiation-damaged crystals linked to “stuffing” of the lattice with interstitial O or He atoms is proposed.