Chemical Shielding Anisotropy Research Articles

Genetic algorithms and solid state NMR pulse sequences

The use of genetic algorithms for the optimisation of magic angle spinning NMR pulse sequences is discussed. The discussion uses as an example the optimisation of the C721 dipolar recoupling pulse sequence, aiming to achieve improved efficiency for spin systems characterised by large chemical shielding anisotropies and/or small dipolar coupling interactions. The optimised pulse sequence is found to be robust over a wide range of parameters, requires only minimal a priori knowledge of the spin system for experimental implementations with buildup rates being solely determined by the magnitude of the dipolar coupling interaction, but is found to be less broadbanded than the original C721 pulse sequence. The optimised pulse sequence breaks the synchronicity between r.f. pulses and sample spinning.

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic (15)N chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures. Our results indicate that the amidic (15)N CSA tensor has sensitive responses to the introduction of the phosphate group and the phosphorylation-promoted rearrangement of solvent molecules and hydrogen bonding networks in the vicinity of the phosphorylated site. Yet, the calculated (15)N CSA tensors in phosphorylated model peptides were in range of values experimentally observed for non-phosphorylated proteins. The extent of the phosphorylation induced changes suggests that the amidic (15)N CSA tensor in phosphorylated proteins could be reasonably well approximated with averaged CSA tensor values experimentally determined for non-phosphorylated amino acids in practical NMR applications, where chemical surrounding of the phosphorylated site is not known a priori in majority of cases. Our calculations provide estimates of relative errors to be associated with the averaged CSA tensor values in interpretations of NMR data from phosphorylated proteins.

MRC special issue on NMR of small molecules in anisotropic media

It was a great pleasure to edit and even a greater one to present this special issue to the readers of Magnetic Resonance in Chemistry. The relatively recent developments of weak alignment media compatible with organic solvents have opened new avenues on the structural analysis of complex natural and synthetic small organic molecules by NMR spectroscopy.1 The first NMR experiment of a small molecule in anisotropic media was performed by Saupe and Englert in 1963, in which benzene was partially aligned in the nematic phase of p-azoxyanisole.2 This experiment led to the later development of the theory of alignment3 and also permitted the empirical determination of the chemical shielding anisotropy of the benzene ring. The strong degree of alignment induced by nematic liquid crystal prevented their practical application to the structural analysis of complex small organic molecules. However, NMR spectroscopy of liquid crystals developed itself into a strong field of research and applications. This topic is outside the scope of this special issue. Weak alignment was first introduced by Tjandra and Bax in 1997 as a new and powerful tool for the study of the structure and dynamics of proteins.4 Its application quickly extended to the analysis of nucleic acids, and several alignment media compatible with water were developed since then. However, small organic molecules had to wait nearly 40 years to be analyzed by NMR in weak alignment media compatible with organic solvents. The deuterium quadrupolar coupling and the dipolar coupling are anisotropic NMR parameters not observable in conventional liquid state NMR experiments, but save for relaxation effects, they can be revealed when molecules are exposed to orienting media. Residual dipolar couplings (RDCs) have proven to be very powerful for the constitutional, configurational, and conformational analysis of small molecules,1 as a complementary tool to existing NMR parameters used for the same purpose, e.g. NOE and the J-based analysis. For certain compounds, the use of only these two existing NMR parameters leads to more than one solution structure, and this ambiguity can be lifted if RDCs are added to the analysis. The residual deuterium quadrupolar coupling has been extensively used as a tool for enantio-discrimination when small molecules are aligned in chiral non-racemic lyotropic liquid crystalline phases, e.g. different types of helical polymers dissolved in organic solvents.5 On the other side, a third anisotropic NMR parameter, the residual chemical shift anisotropy, has been explored as a complementary tool to the application of RDCs to the structural analysis of small molecules.6 This special issue is focused on new NMR methodologies for the analysis of small organic molecules oriented in weak alignment media. This is an emerging field with plenty of room for new discoveries and development of necessary tools such as software and methodologies for data analysis, pulse sequences, and alignment media. However, its application is not yet widespread in the small molecules community. In this special issue, the readers will have the opportunity to enjoy a diverse set of research articles contributed by the experts in the field. I hope that the scientific community finds this special issue particularly inspiring to bring these new methodologies into their everyday work. I want to thank the Editor In Chief, Prof. James Keeler, for the invitation to edit this special issue. I also want to thank the members of the Editorial Board, Prof. Helmut H. Duddeck, Prof. Bozhana P. Mikhova, and Prof. Angela M. Gronenborn for their encouragement and support. Finally, my thanks to all my colleagues who gave me the honor of editing their contributions.

Nuclear Magnetic Resonance Parameters of Pure and Diborinin‐Doped (6,0) Single‐Walled Zigzag BNNT: DFT Study

A computational study on the basis of density functional theory (DFT) calculations has been performed to investigate the properties of the electronic structure of (6,0) zigzag boron nitride nanotubes and two models ((a) and (b)) of diborinin‐doped boron nitride nanotubes (DBD‐BNNTs). The calculated structural energies yield similar values for two models of DBD‐BNNTs. Isotropic (CSI) and anisotropic (CSA) chemical shielding parameters of the optimized BNNT and DBD‐BNNTs are calculated. The results illustrate that the changes in chemical shielding tensors of 11B and 15N nuclei are more significant in the nearest neighborhood of the diborinin ring due to doping process. The changes of the electronic sites of the N atoms are also more significant than those of the B atoms. The dipole moments of the diborinin‐doped BNNT structures show changes with respect to the pristine model. It is clear that the doping of diborinin ring decreases the energy gaps of the pure BNNT. For the pure model, the HOMO is located on the nitrogen atoms, and the LUMO is uniformly distributed throughout the B–N bonds. In contrast, for the diborinin‐doped models, the majority of the HOMO and LUMO are located at the diborinin‐doped regions.

Robust and efficient 19F heteronuclear dipolar decoupling using refocused continuous-wave rf irradiation

Refocused continuous wave (rCW) decoupling is presented as an efficient and robust means to obtain well-resolved magic-angle-spinning solid-state NMR spectra of low-γ spins, such as 13C dipolar coupled to fluorine. The rCW decoupling sequences, recently introduced for 1H decoupling, are very robust towards large isotropic and anisotropic shift ranges as often encountered for 19F spins. In rCW decoupling, the so-called refocusing pulses inserted into the CW irradiation eliminate critical residual second- and third-order dipolar coupling and dipolar-coupling against chemical shielding anisotropy cross-terms in the effective Hamiltonian through time-reversal (i.e. refocusing). As important additional assets, the rCW decoupling sequences are robust towards variations in rf amplitudes, operational at low to high spinning speeds, and easy to set-up for optimal performance experimentally. These aspects are demonstrated analytically/numerically and experimentally in comparison to state-of-the-art decoupling sequences such as TPPM, SPINAL-64, and frequency-swept variants of these.

Influence of NO2 attachment on the nuclear magnetic shielding tensors of N and B nuclei in C30B15N15 heterofullerene: a DFT study

Adsorption of nitrogen dioxide in three different configurations on the exterior surface of C30B15N15 is studied using density functional theory calculations. To this end, we optimized the structures of raw C30B15N15 and nine NO2–C30B15N15 complexes at the B3LYP/6-31G* level of theory and then calculated chemical shielding (CS) tensors at the GIAO-B3LYP/6-311G** level for the optimized structures. The calculated chemical shielding isotropy (CSI), chemical shielding anisotropy (CSA), and orientation of CS tensors (Euler angles) reveal that the adsorption configurations (nitro, trans-nitrite, and cis-nitrite) have different effects on the electronic structure of C30B15N15. Natural atomic charges based on natural population analysis (NPA) were used to justify the changes in CSI values after gas sorption.

The Al-Doped Carbon Nanotubes: A DFT Study

NMR parameters consisting of isotropic and anisotropic chemical shielding parameters have been calculated based on density functional theory (DFT) to investigate the properties of the electronic structures of the aluminum doped (Al-doped) carbon nanotubes (CNTs). The structures are allowed to relax by performing all atomic optimization. Then the chemical shielding (CS) tensors are calculated for 13C and 27Al nuclei in the Al-doped forms and also pristine models of the (4,4) armchair and (6,0) zigzag CNTs. The calculated CS tensors in the optimized structures are converted to chemical-shielding isotropic (CSI) and chemical-shielding anisotropic (CSA) parameters. In comparison to the pristine model, the CSI parameters of the C atoms around the Al-doped are significantly influenced by the doping process. Density functional theory (DFT) calculations are performed using Gaussian 98 suite of programs.

A DFT study on carbon-doping at different sites of (8, 0) boron nitride nanotube

A density functional theory study is carried out to investigate the geometries and electronic structure of pristine and carbon-doped (8, 0) single-walled boron nitride nanotubes (BNNTs). In order to understand the effect of impurities or doping on (8, 0) single-walled BNNT, we simulated C-doping in six different ways. Geometry optimizations reveal that in the considered models, B–N bond lengths are not significantly influenced by C-doping. Based on the quantum theory of atoms in molecules analysis, charge density accumulation for axial B–N bond critical points (BCPs) of pristine BNNT is slightly larger than zigzag ones. However, due to C-doping at the B- or N-tips, the evaluated electron density tends to decrease slightly at both axial and zigzag B–N BCPs. Besides, results indicate that influence of C-doping on properties of the (8, 0) BNNT could be also detected by values of chemical shielding isotropy (σ iso) and anisotropy (Δσ).

Effect of Gallium Doping on Electronic and Structural Properties (6,0) Zigzag Silicon Carbide Nanotube as a p-Semiconductor

Density functional theory (DFT) calculations were performed to investigate the electronic and structural properties of pristine and Ga-doped (6,0) zigzag silicon carbide nanotubes (SiCNTs) as a p-semiconductor at the B3LYP/6-31G* level of theory in order to evaluate the influence of Ga doping on (6,0) zigzag SiCNTs. We extended the DFT calculation to predict the electronic structure properties of Ga-doped silicon carbide nanotubes, which are very important for production of solid-state devices and other applications. To this aim, pristine and Ga-doped SiCNT structures in two models (GaSi and GaC) were optimized and structural properties, the isotropic (CSI) and anisotropic (CSA) chemical shielding parameters for the sites of various 29Si and 13C atoms, and quantum molecular descriptors were calculated in the optimized structures. The optimized structures, NMR parameters, and the electronic energies for the GaSi and GaC of the (6,0) zigzag SiCNT models show that the GaSi model is a better p-semiconductor from GaC model in production of solid-state devices.

Gallium doped in armchair and zigzag models of boron phosphide nanotubes (BPNTs): A NMR study

Abstract The electrical properties and NMR parameters of the pristine and Ga-doped structures of two representative (8, 0) zigzag and (4, 4) armchair of boron phosphide nanotubes (BPNTs) have been investigated. The structural geometries of above nanotubes have been allowed to relax by optimization and then the isotropic and anisotropic chemical shielding parameters (CSI and CSA) of 11B and 31P have been calculated based on DFT theory. The results reveal that the influence of Ga-doping was more significant on the geometries of the zigzag model than the armchair one. The difference of band gap energies between the pristine and Ga-doped armchair BPNTs was larger than the zigzag model. Significant differences of NMR parameters of those nuclei directly contributed to the Ga-doping atoms have been observed.

BN-Substituted fullerenes C60−2x (BN) x : a computational 11B and 15N NMR study

Density functional theory has been used to investigate the 15N and 11B NMR parameters of heterofullerenes C60−2x(BN)x (x = 1, 2, 3, 6, 9, 12, 15, 18, 21, and 24). Geometry structures of all the BN-substituted fullerenes have been optimized at the B3LYP/6-31+G* level of theory. Afterward, 11B and 15N chemical shielding isotropy and anisotropy (CSI, CSA) parameters have been calculated at the same level. The obtained results illustrate the electrostatic environment divisions of the nuclei into few layers, which have been then confirmed by calculating natural charges at B and N sites. A good correlation has been seen between the layers of CSI and CSA values and three local structures around boron and nitrogen atoms. The effects of curvature of fullerene structure on chemical shielding (CS) parameters of heterofullerenes have also been investigated by computing CS tensors for curved and relaxed structures of a set of small fragments separated from the heterofullerenes, suggesting high sensitivity of CS parameters to the curvature of fullerene structure.

A Computational NICS and 13C NMR Characterization of C60−n Si n Heterofullerenes (n = 1, 2, 6, 12, 20, 24, 30)

Density functional theory (DFT) calculations are performed for a representative set of low-energy structures of C60-nSin heterofullerenes (n = 1, 2, 6, 12, 20, 24, 30) to investigate the effect of silicon doping on the electron structure of fullerene. The results show that chemical shielding (CS) parameters are so sensitive to the structural distortion made by outwardly relaxing silicon doped atoms from the fullerene surface which results in puckered Si-doped rings. As a result, the chemical shifts of the nearest carbon sites of silicon atoms considerably shift to downfield. Our survey shows that those first neighbors of silicon atoms which have minor 13C chemical shift belong to normal (un-puckered) rings. Meanwhile, the chemical shielding anisotropy (Δσ) parameter detects the effects of dopant so that Δσ values of the carbon atoms which are contributed to the Si–C bond are mainly larger than the others. Compensation between diatropic and paratropic ring currents lead to less negative NICS values at cage centers of Si-doped fullerenes than that of C60 except C58Si2-b and C54Si6-b in which more negative NICS values may be attributed to more spherical geometries of their carbon cages.

Exploiting the Chemical Shielding Anisotropy to Probe Structure and Disorder in Ceramics: 89Y MAS NMR and First-Principles Calculations

The local structure and cation disorder in Y2(Sn,Ti)2O7 pyrochlores, materials proposed for the encapsulation of lanthanide- and actinide-bearing radioactive waste, is investigated using 89Y (I = 1/2) NMR spectroscopy and, in particular, measurement of the 89Y anisotropic shielding. Although known to be a good probe of the local environment, information on the anisotropy of the shielding interaction is removed under magic angle spinning (MAS). Here, we consider the feasibility of experimental measurement of the 89Y anisotropic shielding interaction using two-dimensional CSA-amplified PASS experiments, implemented for 89Y for the first time. Despite the challenges associated with the study of low-γ nuclei, and those resulting from long T1 relaxation times, the successful implementation of these experiments is demonstrated for the end member pyrochlores, Y2Sn2O7 and Y2Ti2O7. The accuracy and robustness of the measurement to various experimental parameters is also considered, before the approach is then applied to the disordered materials in the solid solution. The anisotropies extracted for each of the sideband manifolds are compared to those obtained using periodic first-principles calculations, and provide strong support for the assignment of the spectral resonances. The value of the span, Ω, is shown to be a sensitive probe of the next nearest neighbor (NNN) environment, i.e., the number of Sn and Ti on the six surrounding “B” (i.e., six-coordinate) sites, and also provides information on the local geometry directly, through a correlation with the average Y–O8b distance (where 8b indicates the Wyckoff position of the oxygen).

The effects of SiC-doped on the NMR parameters of the armchair and zigzag models of aluminum phosphide nanotubes: A DFT study

In this work the density functional theory (DFT) calculations are used to investigate the electrical properties of three SiC atoms doped on the representative (4, 4) armchair and (8, 0) zigzag aluminum phosphide nanotubes (AlPNTs). The mouths of nanotubes are capped by hydrogen atoms in order to saturate the dangling bonds of the boundaries and to simulate a longer tube and to decrease calculation time. The structures of all nanotubes were allowed to relax and the chemical shielding (CS) parameters were calculated for the atoms of optimized structures. The results indicated that the band gap energies and NMR parameters detect the effects of doping. The CS parameters also indicated that in both models of (4, 4) armchair and (8, 0) zigzag among all the P and Al atoms, which are directly connected to the Si and C atoms, have the smallest isotropic and anisotropic chemical shielding.

Ge-doped (4,4) armchair single-walled boron phosphide nanotube as a semiconductor: a computational study

Density functional theory (DFT) calculations were performed to investigate the electronic structure properties of Ge-doped boron phosphide nanotubes (BPNTs) as a semiconductor at the B3LYP/6-31G* level of theory in order to evaluate the influence of Ge doping on (4,4) armchair BPNTs. We extended the DFT calculations to predict the electronic structure properties of Ge-doped boron phosphide nanotubes, which are very important for production of solid-state devices and other applications. The isotropic (CSI) and anisotropic (CSA) chemical shielding parameters for the sites of various 11B and 31P atoms, and the quadrupole coupling constant (C Q) and asymmetry parameter (η Q) at the sites of various 11B nuclei, were calculated in pristine and Ge-doped (4,4) armchair BPNT models. The calculations indicated that, in these two forms of Ge-doped BPNTs, the binding energies are not attractive and do not characterize a chemisorption process. In comparison with the pristine model, the band gap of the two forms of Ge-doped BPNTs is reduced and increases their electrical conductance. The dipole moments of the Ge-doped BPNT structures show notable changes with respect to the pristine model. The nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR) results show that the GeB model is a more reactive material than the pristine or GeP model.

Intra- and inter-molecular interactions in salicylic acid — Theoretical calculations of17O and1H chemical shielding tensors and QTAIM analysis

A density functional theory (DFT) study was performed to examine intra- and inter-molecular hydrogen bond (HB) properties in crystalline salicylic acid (SA). BLYP, B3LYP, and M06 functionals with 6–311++G** basis set were employed to calculate NMR chemical shielding isotropy (σiso) and anisotropy (Δσ) at the sites of the17O and1H nuclei of SA. From this study, it appears that the intra- and inter-molecular O–H···O as well as C–H···O HBs around the SA molecule in the crystal lattice have a major influence on the chemical shielding tensors and more specifically on the carbonyl17O isotropy value. The quantum theory of atoms in molecules (QTAIM) analysis was also employed to elucidate the interaction characteristics in SA H-bonded network. Based on QTAIM results, a partial covalent character is attributed to the intra- and inter-molecular O–H···O HBs in SA.

The effect of doping three Al and N atoms on the chemical shielding tensor parameters of the boron phosphide nanotubes: A DFT study

In this work, an armchair model of the (4,4) boron phosphide nanotubes (BPNTs) with a 1-nm length and consisting of 32 B and 32 P atoms is considered to study the influence of doping three atoms of aluminum in sites of boron (B 3AlPNTs) and three atoms of nitrogen in sites of phosphors (BP 3NNTs) on the electrostatic structure properties. The mouths of nanotubes are capped by hydrogen atoms in order to saturate the dangling bonds of the boundaries and to decrease the calculation time. The structures of BPNTs, B 3AlPNTs and BP 3NNTs are optimized by performing the level of density functional theory (DFT) using 6-31G ⁎ basis set. The optimized structures are used for calculating the chemical shielding (CS) tensors and nuclear magnetic resonance parameters such as isotropic chemical shielding (CS I) and anisotropic chemical shielding (CS A). The results reveal that in both models of B 3AlPNTs and BP 3NNTs by doping N atoms the chemical shielding parameters of P and B atoms, which are directly connected to the Al and N atoms decreased and the other sites significantly changed.

Thermal Phase Behavior of DMPG Bilayers in Aqueous Dispersions as Revealed by 2H- and 31P-NMR

The synthetic lipid 1,2-dimyristoyl-sn-3-phosphoglycerol (DMPG), when dispersed in water/NaCl exhibits a complex phase behavior caused by its almost unlimited swelling in excess water. Using deuterium ((2)H)- and phosphorus ((31)P)-NMR we have studied the molecular properties of DMPG/water/NaCl dispersions as a function of lipid and NaCl concentration. We have measured the order profile of the hydrophobic part of the lipid bilayer with deuterated DMPG while the orientation of the phosphoglycerol headgroup was deduced from the (31)P NMR chemical shielding anisotropy. At temperatures >30 °C we observe well-resolved (2)H- and (31)P NMR spectra not much different from other liquid crystalline bilayers. From the order profiles it is possible to deduce the average length of the flexible fatty acyl chain. Unusual spectra are obtained in the temperature interval of 20-25 °C, indicating one or several phase transitions. The most dramatic changes are seen at low lipid concentration and low ionic strength. Under these conditions and at 25 °C, the phosphoglycerol headgroup rotates into the hydrocarbon layer and the hydrocarbon chains show larger flexing motions than at higher temperatures. The orientation of the phosphoglycerol headgroup depends on the bilayer surface charge and correlates with the degree of dissociation of DMPG-Na(+). The larger the negative surface charge, the more the headgroup rotates toward the nonpolar region.

The Ge-doped (6,0) zigzag single-walled boron phosphide nanotubes: A computational study

Electronic structure properties including bond lengths, bond angles, tip diameters, dipole moments ( μ), energies, band gaps, NMR, and NQR parameters were calculated using density functional theory for Ge-doped boron phosphide nanotubes (BPNTs). Geometry optimizations were carried out at the B3LYP/6-31G ∗ level of theory the Gaussian 03 program suites. The isotropic (CS I) and anisotropic (CS A) chemical shielding parameters for the sites of various 11B and 31P atoms, and quadrupole coupling constant ( C Q ) and asymmetry parameter ( η Q ) at the sites of various 11B nuclei were calculated for Ge-doped (6,0) zigzag BPNT models. The calculations indicated that average B–P bond lengths of the Ge B model are larger than average B–P bond lengths of pristine and the Ge P models. For the Ge B and Ge P models, the diameters values changes were almost negligible. The dipole moments of the two Ge-doped BPNT structures show slightly changes due to the Ge-doping with respect to the pristine model. In comparison with the pristine model, band gaps of the two Ge-doped models are reduced and increase their electrical conductance. The changes in the NMR and NQR parameters due to the Ge-doping are more significant for the Ge B model than for the Ge P model with respect to the pristine model.

Calculating the Response of NMR Shielding Tensor σ(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation

Dependence of NMR (31)P shielding tensor and (2)J(P,C) coupling constants on solvation of nucleic acid phosphate by Mg(2+) and water was studied using methods of bioinformatic structural analyses of crystallographic data and DFT B3LYP calculations of NMR parameters. The effect of solvent dynamics on NMR parameters was calculated using molecular dynamic. The NMR calculations for representative solvation patterns determined in crystals of B-DNA and A-RNA molecules pointed out the crucial importance of local Mg(2+) coordination geometry, including hydration by explicit water molecules and necessity of dynamical averaging over the solvent reorientation. The dynamically averaged (31)P chemical shift decreased by 2-9.5 ppm upon Mg(2+) coordination, the chemical shielding anisotropy increased by 0-20 ppm, and the (2)J(P,C5') coupling magnitude decreased by 0.2-1.8 Hz upon Mg(2+) coordination. The calculated decrease of the (31)P chemical shift is in excellent agreement with the 1.5-10 ppm decrease of the phosphorothioate (31)P chemical shift upon Cd(2+) coordination probed experimentally in hammerhead ribozyme (Suzumura; et al. J. Am. Chem. Soc. 2002, 124, 8230-8236; Osborne; et al., Biochemistry 2009, 48, 10654-10664). None of the dynamically averaged NMR parameters unequivocally distinguishes the site-specific Mg(2+) coordination to one of the two nonesterified phosphate oxygen atoms of the phosphate determined by bioinformatic analyses. By comparing the limit cases of static and dynamically averaged solvation, we propose that mobility of the solvent has a dramatic impact on NMR parameters of nucleic acid phosphate and must be taken into account for their accurate modeling.