Biomedical subjects

Chris J Pickard

Publications and source records attributed to Chris J Pickard.

17 recordsLinked to original sources

PubMed2006

NMR crystallography of oxybuprocaine hydrochloride, Modification II degrees.

The (13)C CPMAS spectrum is presented for the polymorph of oxybuprocaine hydrochloride which is stable at room temperature, i.e. Mod. II degrees . It shows crystallographic splittings arising from the fact that there are two molecules, with substantially different conformations, in the asymmetric unit. An INADEQUATE two-dimensional experiment was used to link signals for the same independent molecule. The chemical shifts are discussed in relation to the crystal structure. Of the four ethyl groups attached to NH(+) nitrogens, one gives rise to unusually low chemical shifts, very different from those of the other three ethyl groups. This is attributed empirically to gamma-gauche conformational effects, as is confirmed by shielding computations. These considerations allow (13)C signals to be assigned to specific carbons in the two crystallographically inequivalent molecules in the crystal structure. Indeed, information about the conformations is inherent in the NMR spectrum, which thus provides data of crystallographic significance. A (13)C/(1)H HETCOR experiment enabled resolution to be obtained in the (1)H dimension and allowed (1)H and (13)C signals for the same independent molecule to be linked.

Carbon Isotopes↗

PubMed2006

Density functional study of the 13C NMR chemical shifts in small-to-medium-diameter infinite single-walled carbon nanotubes.

NMR chemical shifts were calculated for semiconducting (n,0) single-walled carbon nanotubes (SWNTs) with n ranging from 7 to 17. Infinite isolated SWNTs were calculated using a gauge-including projector-augmented plane-wave (GIPAW) approach with periodic boundary conditions and density functional theory (DFT). In order to minimize intertube interactions in the GIPAW computations, an intertube distance of 8 A was chosen. For the infinite tubes, we found a chemical shift range of over 20 ppm for the systems considered here. The SWNT family with lambda = mod(n, 3) = 0 has much smaller chemical shifts compared to the other two families with lambda = 1 and lambda = 2. For all three families, the chemical shifts decrease roughly inversely proportional to the tube's diameter. The results were compared to calculations of finite capped SWNT fragments using a gauge-including atomic orbital (GIAO) basis. Direct comparison of the two types of calculations could be made if benzene was used as the internal (computational) reference. The NMR chemical shifts of finite SWNTs were found to converge very slowly, if at all, to the infinite limit, indicating that capping has a strong effect (at least for the (9,0) tubes) on the calculated properties. Our results suggest that (13)C NMR has the potential for becoming a useful tool in characterizing SWNT samples.

Carbon Isotopes↗

PubMed2006

High-pressure phases of silane.

High-pressure phases of silane SiH4 are predicted using first-principles electronic structure methods. We search for low-enthalpy structures by relaxing from randomly chosen initial configurations, a strategy which is demonstrated to work well for unit cells containing up to at least ten atoms. We predict that silane will metallize at higher pressures than previously anticipated but might show high-temperature superconductivity at experimentally accessible pressures.

Journal Article↗

PubMed2006

(23)Na multiple-quantum MAS NMR of the perovskites NaNbO(3) and NaTaO(3).

The distorted perovskites NaTaO(3) and NaNbO(3) have been studied using (23)Na multiple-quantum (MQ) MAS NMR. NaTaO(3) was prepared by high temperature solid state synthesis and the NMR spectra are consistent with the expected room temperature structure of the material (space group Pbnm), with a single crystallographic sodium site. Two samples of NaNbO(3) were studied. The first, a commercially available sample which was annealed at 900 degrees C, showed two crystallographic sodium sites, as expected for the room temperature structure of the material (space group Pbcm). The second sample, prepared by a low temperature hydrothermal method, showed the presence of four sodium sites, two of which match the expected room temperature structure and the second pair, another polymorph of the material (space group P21ma). This is consistent with powder X-ray diffraction data which showed weak extra peaks which can be accounted for by the presence of this second polymorph. Density functional theory (DFT) calculations support our conclusions, and aid assignment of the NMR spectra. Finally, we discuss the measured NMR parameters in relation to other studies of sodium in high coordination sites in the solid state.

Calcium Compounds↗

PubMed2006

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.

Algorithms↗

PubMed2006

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

Studies on the solid-state structure of two polymorphs of 4-methyl-2-nitroacetanilide (MNA) were conducted using magic-angle spinning (13)C, (15)N and (1)H NMR spectroscopy, together with first-principles computations of NMR shielding (including use of a program that takes explicit account of the translational symmetry inherent in crystalline structures). The effects on (13)C chemical shifts of side-chain rotations have been explored. Information derived from these studies was then incorporated within a systematic space-search methodology for elucidation of trial crystallographic structures from powder XRD.

Journal Article↗

PubMed2005

Ultrasoft spin-dependent pseudopotentials.

The use of the spin-dependent pseudopotentials has been shown to markedly enhance the transferability of the commonly used spin-neutral pseudopotential method for the study of the structural and magnetic properties of transition-metal-containing materials. Unfortunately, because the method was based on the rather expensive norm-conserving pseudopotential formalism, the method was limited to the study of fairly small systems. Here we present an extension of the spin-dependent pseudopotential method for the far more computationally advantageous ultrasoft formalism and show that it is very easy to add such a feature to any preexisting computer code. We benchmark our new method by comparing to previously published results and then apply it to the study of several relevant test cases: bulk Ni, Fe, and Co, as well as a Pd atomic wire.

Journal Article↗

PubMed2005

Assigning carbon-13 NMR spectra to crystal structures by the INADEQUATE pulse sequence and first principles computation: a case study of two forms of testosterone.

A (13)C CPMAS NMR experiment at high field (11.7 T) has produced significantly improved dispersion for the alpha form of testosterone, allowing revisions and extensions to be made to the assignments. Correlations shown by an INADEQUATE two-dimensional spectrum, recorded at 16.5 T, have allowed the components of most of the doublet signals to be grouped into two sets (for the two crystallographically independent molecules). First-principles computations, employing a fully solid-state approach, have been used to obtain values for the crystallographic splittings, which are discussed in relation to the experimental values. This procedure enables assignments to the two groups to be suggested for all but one of the remaining doublet signals. It also allows the two sets of signals to be identified specifically to the two independent molecules in the crystal structure. Computations were also carried out for the beta form of testosterone (a dihydrate). The shift differences between the alpha and beta forms were compared with the experimental data, with encouraging results. Comparisons were also made between computed and experimental shielding anisotropies and asymmetries for three of the carbons of the alpha form. The methodology has a high potential for future applications, though more examples need to be evaluated before general conclusions can be drawn.

Carbon Isotopes↗

PubMed2005

Combined first-principles computational and experimental multinuclear solid-state NMR investigation of amino acids.

13C, 14N, 15N, 17O, and 35Cl NMR parameters, including chemical shift tensors and quadrupolar tensors for 14N, 17O, and 35Cl, are calculated for the crystalline forms of various amino acids under periodic boundary conditions and complemented by experiment where necessary. The 13C shift tensors and 14N electric field gradient (EFG) tensors are in excellent agreement with experiment. Similarly, static 17O NMR spectra could be precisely simulated using the calculation of the full chemical shift (CS) tensors and their relative orientation with the EFG tensors. This study allows correlations to be found between hydrogen bonding in the crystal structures and the 17O NMR shielding parameters and the 35Cl quadrupolar parameters, respectively. Calculations using the two experimental structures for L-alanine have shown that, while the calculated isotropic chemical shift values of 13C and 15N are relatively insensitive to small differences in the experimental structure, the 17O shift is markedly affected.

Amino Acids↗

PubMed2005

An investigation of weak CH...O hydrogen bonds in maltose anomers by a combination of calculation and experimental solid-state NMR spectroscopy.

Two-dimensional (1)H-(13)C MAS-J-HMQC solid-state NMR spectra of the two anomeric forms of maltose at natural abundance are presented. The experimental (1)H chemical shifts of the CH and CH(2) protons are assigned using first-principles chemical shift calculations that employ a plane-wave pseudopotential approach. Further calculations show that the calculated change in the (1)H chemical shift when comparing the full crystal and an isolated molecule is a quantitative measure of intermolecular C-H...O weak hydrogen bonding. Notably, a clear correlation between a large chemical shift change (up to 2 ppm) and both a short H...O distance (<2.7 A) and a CHO bond angle greater than 130 degrees is observed, thus showing that directionality is important in C-H...O hydrogen bonding.

Carbohydrate Conformation↗

PubMed2005

First-principles calculation of 17O and 25Mg NMR shieldings in MgO at finite temperature: rovibrational effect in solids.

The temperature dependence of (17)O and (25)Mg NMR chemical shifts in solid MgO have been calculated using a first-principles approach. Density functional theory, pseudopotentials, a plane-wave basis set, and periodic boundary conditions were used both to describe the motion of the nuclei and to compute the NMR chemical shifts. The chemical shifts were obtained using the gauge-including projector augmented wave method. In a crystalline solid, the temperature dependence is due to both (i) the variation of the averaged equilibrium structure and (ii) the fluctuation of the atoms around this structure. In MgO, the equilibrium structure at each temperature is uniquely defined by the cubic lattice parameters, which we take from experiment. We evaluate the effect of the fluctuations within a quasiharmonic approximation. In particular, the dynamical matrix, defining the harmonic Hamiltonian, has been computed for each equilibrium volume. This harmonic Hamiltonian was used to generate nuclear configurations that obey quantum statistical mechanics. The chemical shifts were averaged over these nuclear configurations. The results reproduce the previously published experimental NMR data measured on MgO between room temperature and 1000 degrees C. It is shown that the chemical shift behavior with temperature cannot be explained by thermal expansion alone. Vibrational corrections due to the fluctuations of atoms around their equilibrium position are crucial to reproduce the experimental results.

Journal Article↗

PubMed2005

First-principles calculation of the 17O NMR parameters of a calcium aluminosilicate glass.

We have computed the (17)O NMR parameters of an amorphous calcium aluminosilicate (CAS) from first-principles. The atomic coordinates of a CAS glass of composition (CaO)(0.21)(Al(2)O (3))(0.12)(SiO (2))(0.67) were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type. The structure of the glass is found to be overall in good agreement with diffraction experiments. Some excess nonbridging O (NBO) atoms are found and are compensated by tricluster O atoms, i.e., by 3-fold coordinated O atoms to 4-fold coordinated Al or Si atoms. The glass coordinates were used to compute the (17)O NMR parameters using GGA-DFT and a correction of the Ca 3d orbital energy. The chemical shifts and the electric field gradients were obtained with the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods, respectively. The simulated 2D-3QMAS NMR spectrum of the CAS glass is in very good agreement with the available experimental data, notably because it takes into account the disorder present in the glass. This agreement further validates our CAS glass model. We show that the oxygen triclusters are not visible in a 2D-3QMAS NMR (17)O spectrum since their NMR parameters overlap with those of the Al-O-Si, Si-O-Si, or Al-O-Al sites. Finally, correlations between the structural characteristics and the values of the NMR parameters are extracted from the calculation with the aim of helping the interpretation of NMR spectra of glasses of similar compositions.

Journal Article↗

PubMed2004

First-principles calculation of the 17O NMR parameters in Ca oxide and Ca aluminosilicates: the partially covalent nature of the Ca-O bond, a challenge for density functional theory.

We apply density functional theory (DFT) to the calculation of the (17)O NMR parameters in Ca and Mg oxides and aluminosilicates. We study the accuracy of the Perdew, Burke, and Ernzerhof (PBE) generalized-gradient approximation to DFT in the description of these systems and the origin of the experimentally observed large dependence of the (17)O chemical shift on the alkaline earth ion. We find that (i) the partially covalent nature of the Ca-O bond has a huge impact on the O chemical shifts. The Ca-O covalence alone explains why in Ca oxides and aluminosilicates the (17)O chemical shifts are much more deshielded than those of the corresponding Mg compounds. (ii) The Ca-O covalence is overestimated by the PBE functional. Thus PBE-DFT is not able to reproduce the measured (17)O NMR parameters in Ca oxide and Ca aluminosilicates. (iii) It is possible to correct for the PBE-DFT deficiency in a simple and transferable way and to predict very accurate (17)O NMR parameters. Such accuracy allows us to assign the (17)O NMR spectra of two important model systems: the grossite aluminate (CaAl(4)O(7)) and the wollastonite (CaSiO(3)) silicate.

Journal Article↗

PubMed2004

Combined ab initio computational and experimental multinuclear solid-state magnetic resonance study of phenylphosphonic acid.

1H, 13C, 17O and 31P NMR parameters, including chemical shift tensors and quadrupolar parameters for 17O, were calculated for phenylphosphonic acid, C6H5PO(OH)2, under periodic boundary conditions. The results are in very good agreement with experimental data and permit the unambiguous assignment of all the sites present in the structure. In particular, the 17O NMR parameters of the P=O and P-OH environments were precisely determined, which should help in the characterization of the bonding mode of phosphonate molecules in hybrid solids. Moreover, the effect of intermolecular interactions on the NMR parameters were investigated by comparing the results of the calculations in the crystal and in an isolated molecule of phenylphosphonic acid.

Algorithms↗

PubMed2003

Nonlocal pseudopotentials and magnetic fields.

We show how to describe the coupling of electrons to nonuniform magnetic fields in the framework of the widely used norm-conserving pseudopotential approximation for electronic structure calculations. Our derivation applies to magnetic fields that are smooth on the scale of the core region. The method is validated by application to the calculation of the magnetic susceptibility of molecules within density functional theory (DFT) in the local density approximation. Our results are compared with high-quality all-electron DFT results obtained using Gaussian basis sets and another recently proposed pseudopotential formalism.

Journal Article↗

PubMed2003

Accurate first principles prediction of 17O NMR parameters in SiO2: assignment of the zeolite ferrierite spectrum.

17O NMR parameters, both the chemical shifts and the quadrupolar parameters, are calculated for SiO2 polymorphs using density functional theory with the generalized gradient-corrected PBE functional. The gauge including projector augmented wave (GIPAW) method (Pickard, C. J.; Mauri, F. Phys. Rev. B2001, 63, 245101) ensures the reproduction of all electron results while using computationally efficient pseudopotentials. The use of plane-waves permits fully converged calculations to be performed on structures containing 144 atoms in the unit cell, without the need to resort to the cluster approximation. The calculated NMR parameters of cristobalite, quartz, coesite, and faujasite are in excellent agreement with experimental data. This demonstrates that density functional theory is able to reproduce with high accuracy the 17O NMR parameters in SiO2 systems. This precision is used to assign the spectrum of the zeolite ferrierite. The data calculated for SiO2 are used to confirm that no simple correlation between the chemical shift and Cq NMR parameters and Si-O-Si angle exists, emphasizing the importance of predictive theories in this field.

Journal Article↗

PubMed2002

First-principles theory of the EPR g tensor in solids: defects in quartz.

A theory for the reliable prediction of the EPR g tensor for paramagnetic defects in solids is presented. It is based on density functional theory and on the gauge including projector augmented wave approach to the calculation of all-electron magnetic response. The method is validated by comparison with existing quantum chemical and experimental data for a selection of diatomic radicals. We then perform the first prediction of EPR g tensors in the solid state and find the results to be in excellent agreement with experiment for the E(1)(prime) and substitutional phosphorus defect centers in quartz.

Journal Article↗