Calculation of NMR chemical shifts for extended systems using ultrasoft pseudopotentials

Yates, Jonathan R.; Pickard, Chris J.; Mauri, Francesco

doi:10.1103/physrevb.76.024401

Cited by 873 publications

(1,116 citation statements)

References 35 publications

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“…Ten possible models were geometry-optimized using first principles electronic structure calculations as implemented in CASTEP (28,36,37), and the NMR parameters and powder XRD patterns associated with the resulting structures were calculated; Table S1 details the eight geometry-optimized structures that give NMR parameters that are, in some way, comparable with experiment, while bearing in mind that the calculated NMR chemical shifts are those for 0 K, whereas experimental values are determined at room temperature. In addition, we took into account that the accuracy of the 13 C chemical shifts in these calculations is ∼1-2% of the chemical shift range of 13 C [i.e., ±(2-4) ppm] (28).…”

Section: Resultsmentioning

confidence: 99%

Citrate bridges between mineral platelets in bone

Davies

Müller

Wong

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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256

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We provide evidence that citrate anions bridge between mineral platelets in bone and hypothesize that their presence acts to maintain separate platelets with disordered regions between them rather than gradual transformations into larger, more ordered blocks of mineral. To assess this hypothesis, we take as a model for a citrate bridging between layers of calcium phosphate mineral a double salt octacalcium phosphate citrate (OCPcitrate). We use a combination of multinuclear solid-state NMR spectroscopy, powder X-ray diffraction, and first principles electronic structure calculations to propose a quantitative structure for this material, in which citrate anions reside in a hydrated layer, bridging between apatitic layers. To assess the relevance of such a structure in native bone mineral, we present for the first time, to our knowledge, 17 O NMR data on bone and compare them with 17 O NMR data for OCP-citrate and other calcium phosphate minerals relevant to bone. The proposed structural model that we deduce from this work for bone mineral is a layered structure with thin apatitic platelets sandwiched between OCP-citrate-like hydrated layers. Such a structure can explain a number of known structural features of bone mineral: the thin, plate-like morphology of mature bone mineral crystals, the presence of significant quantities of strongly bound water molecules, and the relatively high concentration of hydrogen phosphate as well as the maintenance of a disordered region between mineral platelets.NMR crystallography | biomineralization B one is a complex organic-inorganic composite material (1), in which calcium phosphate nanoparticles are held within a primarily collagen protein matrix. The mineral component is a poorly crystalline phase, closely related to hydroxyapatite. The currently accepted model of bone mineral is ∼50-to 150-nmthick stacks of very closely packed apatitic platelets, each of order 2.5-4 nm in thickness (1-4), arranged so that their large (100) faces are parallel to each other and their c axes are strongly ordered (parallel to collagen fibrils) (5). NMR studies show that, in addition to the largely ordered but nonstoichiometric apatitic phase, there is a substantial, highly hydrated, disordered phase containing up to 55% of the bone mineral phosphatic ions (6, 7) but in the form of hydrogen phosphate or phosphate strongly hydrogen-bonded to water rather than apatitic orthophosphate (8). This phase has been assigned as a surface phase, but whether the surface in question is that of individual mineral platelets or the surface of the overall structure formed by a stack of such platelets is not yet clear. There is, however, significant experimental evidence that is not explained by this model as it stands. First, there has never been any observation of an isolated mineral platelet in mature bone, even in preparations in which there have been attempts to disperse the mineral structures (9). This feature suggests that the mineral platelets are not independent structures-indeed, their ordered aggregati...

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Section: Resultsmentioning

confidence: 99%

Citrate bridges between mineral platelets in bone

Davies

Müller

Wong

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

256

246

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“…The GIPAW method 58 , used with ultrasoft Vanderbilt-type pseudo-potentials 59,60 , provides an efficient method to calculate chemical shifts in crystalline solids 61 .…”

Section: D Dft Calculationsmentioning

confidence: 99%

Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy

Baias

Widdifield

Dumez

et al. 2013

Phys. Chem. Chem. Phys.

164

251

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A protocol for the ab initio crystal structure determination of powdered solids at natural isotopic abundance by combining solid-state NMR spectroscopy, crystal structure prediction, and DFT chemical shift calculations was evaluated to determine the crystal structures of four small drug molecules: cocaine, flutamide, flufenamic acid, and theophylline. For cocaine, flutamide and flufenamic acid, we find that the assigned 1 H isotropic chemical shifts provide sufficient discrimination to determine the correct structures from a set of predicted structures using the root-mean-square deviation (rmsd) between experimentally determined and calculated chemical shifts. In most cases unassigned shifts could not be used to determine the structures. This method requires no prior knowledge of the crystal structure, and was used to determine the correct crystal structure to within an atomic rmsd of less than 0.12 Å with respect to the known reference structure. For theophylline, the NMR spectra are too simple to allow for unambiguous structure selection.

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“…Magnetic resonance parameters were calculated using the GIPAW [73][74][75][76] approach which enables the calculation 70 of chemical shifts, electric field gradients and J couplings. Calculations were performed using the experimental X-ray diffraction crystal structure of lithium diborate (ICSD reference code: 65930), as well as geometry optimised (CASTEP) structures (both at X-ray diffraction and optimised 75 lattice parameters).…”

Section: First-principles Calculation Of 2 J Bb Couplingsmentioning

confidence: 99%

Towards homonuclear J solid-state NMR correlation experiments for half-integer quadrupolar nuclei: experimental and simulated 11B MAS spin-echo dephasing and calculated 2JBB coupling constants for lithium diborate

Barrow

Yates

Feller

et al. 2011

Phys. Chem. Chem. Phys.

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is observed: the B3 (larger C Q ) site dephases more slowly than the B4 site at all investigated MAS frequencies (5 to 20 kHz) at 14.1 T. Increasing the MAS frequency leads to markedly slower dephasing for the B3 site, while there is a much less evident effect for the B4 site. Considering samples at 5, 25, 80 (natural abundance) and 100 % 11 B isotopic 15 abundance, dephasing becomes faster for both sites as the 11 B isotopic abundance increases. The experimental behaviour is rationalised using density matrix simulations for two and three dipolarcoupled 11 B nuclei. The experimentally observed slower dephasing for the larger C Q (B3) site is reproduced in all simulations and is explained by the reintroduction of the dipolar coupling by the so-called "spontaneous quadrupolar-driven recoupling mechanism" having a different dependence 20 on the MAS frequency for different quadrupolar frequencies. Specifically, isolated spin-pair simulations show that the spontaneous quadrupolar-driven recoupling mechanism is most efficient when the quadrupolar frequency is equal to twice the MAS frequency. While for isolated spin-pair simulations, increasing the MAS frequency leads to faster dephasing, agreement with experiment is observed for three-spin simulations which additionally include the homogeneous nature of the 25 homonuclear dipolar coupling network. First-principles calculations, using the GIPAW approach, of the 2 J 11B-11B couplings in lithium diborate, metaborate and triborate are presented: a clear trend is revealed whereby the 2 J 11B-11B couplings increase with increasing B-O-B bond angle and B-B distance. However, the calculated 2 J 11B-11B couplings are small (0.95, 1.20 and 2.65 Hz in lithium diborate), thus explaining why no zero crossing due to J modulation is observed experimentally, 30 even for the sample at 25 % 11 B where significant spin-echo intensity remains out to durations of 200 ms.

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Calculation of NMR chemical shifts for extended systems using ultrasoft pseudopotentials

Cited by 873 publications

References 35 publications

Citrate bridges between mineral platelets in bone

Citrate bridges between mineral platelets in bone

Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy

Towards homonuclear J solid-state NMR correlation experiments for half-integer quadrupolar nuclei: experimental and simulated 11B MAS spin-echo dephasing and calculated 2JBB coupling constants for lithium diborate

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