Chemical Shielding Calculations Research Articles

First-principles study on the NMR shielding of transition metal semiconductors

The theoretical calculation of chemical shielding can help us understand the information of nuclear magnetic resonance experiment more deeply. In this work, three different functionals had been used to study the isotropic shielding of various transition metal nuclei. The predicted trend of our theoretical results matched the experimental results well. It was found that the large (more than 2000 ppm) variation of measured 93Nb and 51V chemical shifts were mainly determined by the occupied and empty states of d orbitals. Furthermore, the effect of the energy differences between the occupied and empty states of d orbitals had been discussed as well. This work is helpful to understand the sources and differences of chemical shifts of certain nuclei in transition metal semiconductors.

NMR chemical shielding in cyclosarcosyl

NMR chemical shifts have a role to play when determining the structure of proteins by NMR methods through their dependence on the local conformation. NMR chemical shielding calculations are presented demonstrating that with an appropriate electronic model and basis set the CαH inequivalence in cyclosarcosyls can be rationalised. In the case of cyclotrisarcosyl the inequivalence is best understood in terms of a steric effect. While for cyclotetrasarcosyl, although significant distant, non-bonded, effects of a peptide group are seen, the vast majority of the large, greater than 2 ppm, inequivalence is attributable to the local conformation between adjacent sarcosine.

Improving the accuracy of GIPAW chemical shielding calculations with cluster and fragment corrections

Ab initio methods for predicting NMR parameters in the solid state are an essential tool for assigning experimental spectra and play an increasingly important role in structural characterizations. Recently, a molecular correction (MC) technique has been developed which combines the strengths of plane-wave methods (GIPAW) with single molecule calculations employing Gaussian basis sets. The GIPAW + MC method relies on a periodic calculation performed at a lower level of theory to model the crystalline environment. The GIPAW result is then corrected using a single molecule calculation performed at a higher level of theory. The success of the GIPAW + MC method in predicting a range of NMR parameters is a result of the highly local character of the tensors underlying the NMR observable. However, in applications involving strong intermolecular interactions we find that expanding the region treated at the higher level of theory more accurately captures local many-body contributions to the N15 NMR chemical shielding (CS) tensor. We propose alternative corrections to GIPAW which capture interactions between adjacent molecules at a higher level of theory using either fragment or cluster-based calculations. Benchmark calculations performed on N15 and C13 data sets show that these advanced GIPAW-corrected calculations improve the accuracy of chemical shielding tensor predictions relative to existing methods. Specifically, cluster-based N15 corrections show a 24% and 17% reduction in RMS error relative to GIPAW and GIPAW + MC calculations, respectively. Comparing the benchmark data sets using multiple computational models demonstrates that N15 CS tensor calculations are significantly more sensitive to intermolecular interactions relative to C13. However, fragment and cluster-based corrections that include direct hydrogen bond partners are sufficient for optimizing the accuracy of GIPAW-corrected methods. Finally, GIPAW-corrected methods are applied to the particularly challenging NMR spectral assignment of guanosine dihydrate which contains two guanosine molecules in the asymmetric unit.

Ammonia: The molecule for establishing 14N and 15N absolute shielding scales and a source of information on nuclear magnetic moments.

Multinuclear Nuclear Magnetic Resonance (NMR) studies of the gaseous mixtures 3He/14NH3 and 3He/15NH3 are reported. Precise analysis of the 3He, 14N, 15N, and 1H resonance frequencies show a linear dependence on the gas density. Extrapolation of these results to the zero-pressure limit gives ν0(1H), ν0(14N), and ν0(15N) resonance frequencies of the isolated ammonia molecule at 300K. The analogous value for 3He atoms in gaseous mixtures ν0(3He) was measured as well. The application of a new scheme to introduce the most important electronic effects on NMR shieldings, together with highly accurate quantum chemical shielding calculations, allows the 14/15N and 1H shielding of the isolated ammonia molecule to be obtained with the greatest accuracy and precision. For the first time, these studies were carried out on ammonia within the so-called four-component relativistic framework. The NMR frequency comparison method provides an approach for determining the 14N and 15N nuclear magnetic moments. The new shielding parameters in ammonia were used for re-evaluation of the entire nitrogen absolute shielding scale. Additionally, the absolute shielding values of several gaseous compounds and secondary reference substances in liquids were presented. It was established that 14N and 15N absolute shielding constants in 14NH3 and 15NH3 are very similar and only differ by less than 0.01 ppm, which is not usually measurable in NMR experiments. Precise calculations of 14N and 15N dipole moments were also made from these accurate shielding values.

Probing Nuclear Dipole Moments and Magnetic Shielding Constants through 3-Helium NMR Spectroscopy

Multinuclear NMR studies of the gaseous mixtures that involve volatile compounds and 3He atoms are featured in this review. The precise analyses of 3He and other nuclei resonance frequencies show linear dependencies on gas density. Extrapolation of the gas phase results to the zero-pressure limit gives the ν0(3He) and ν0(nX) resonance frequencies of nuclei in a single 3-helium atom and nuclei in molecules at a given temperature. The NMR frequency comparison method provides an approach for determining different nuclear magnetic moments. The application of quantum chemical shielding calculations, which include a more complete and careful theoretical treatment, allows the shielding of isolated molecules to be achieved with great accuracy and precision. They are used for the evaluation of nuclear moments, without shielding impacts on the bare nuclei, for: 10/11B, 13C, 14N, 17O, 19F, 21Ne, 29Si, 31P, 33S, 35/37Cl, 33S, 83Kr, 129/131Xe, and 183W. On the other hand, new results of nuclear moments were used for the reevaluation of absolute nuclear magnetic shielding in the molecules under study. Additionally, 3He gas in water solutions of lithium and sodium salts was used for measuring 6/7Li and 23Na magnetic moments and reevaluating the shielding parameters of Li+ and Na+ water-solvated cations. In this paper, guest 3He atoms that play a role in probing the electron density in many host macromolecules are also presented.

Delivery of Capecitabine by Single-Walled Carbon Nanotube

Application of the zigzag (24, 0) single-walled carbon nanotube (SWCNT) in delivery of carbamate and imine tautomers of capecitabine is investigated via quantum mechanical geometry optimizations followed by chemical shielding calculations. Torsion angle between ribose and cytosine rings is very close to the experimental value in both tautomers. This suggests that relative orientation of these rings is independent of presence of SWCNT. Their carbon nuclei become closer to the tube’s internal surface by about 1Å, when going from cytosine ring to aliphatic tail. Their cytosine and ribose rings bend so that fluorine atoms and 2[Formula: see text]-OH group form ion-[Formula: see text] interaction with the surface. Calculated binding energies aside from observation of these sorts of interactions in these tautomers can propose SWCNT as their potent delivery tool. Most of the obtained conclusions are manifested in the observed trends for calculated chemical shielding values. They make connections among the reported experimental and computational distributions of chemical shielding values inside SWCNTs.

The detailed electronic structure, spectroscopic features, and reactivity of dimethylanisoles

The spectroscopic features, reactive natures, molecular docking, and electronic properties of anisole and six dimethylanisoles (DMAs) are investigated thoroughly to have insight into the effect of methyl substitution in anisole derivatives. The spectroscopic properties of studied molecules, including FT-IR, FT-Raman, and 1H and 13C NMR spectra were have been obtained by using DFT calculations at B3LYP/6–311++G(d,p) level of theory, and compared with the ones measured experimentally. Reactivity features were determined based on global descriptors, electron density mapping, and Fukui analysis to reveal the electrophilic and nucleophilic nature of them. The methyl position mainly affects the reactivity of the methoxy group and the aromatic nature of the ring. The methyl position dependency of aromaticity and π-stacking ability in DMAs have been explored through the nuclear independent chemical shielding (NICS) calculations, aromaticity indexes, and π orbital overlapping analysis. The static and dynamic polarizability and first and second hyperpolarizability have been carried out to explore the potential of the molecules in optical applications and the effect of methyl position on these characteristics. Bioactive potency and toxicity characteristics have been tested through molecular docking of the molecules to the odorant-binding protein.

Local Structure of Glassy Lithium Phosphorus Oxynitride Thin Films: A Combined Experimental and Ab Initio Approach

AbstractLithium phosphorus oxynitride (LiPON) is an amorphous solid‐state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF‐sputtered LiPON. Information about the short‐range structure results from 1D and 2D solid‐state NMR experiments. These results are compared with first principles chemical shielding calculations of Li‐P‐O/N crystals and ab initio molecular dynamics‐generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON′s stability is a result of its glassy character. Free‐standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.

Local Structure of Glassy Lithium Phosphorus Oxynitride Thin Films: A Combined Experimental and Ab Initio Approach.

Lithium phosphorus oxynitride (LiPON) is an amorphous solid-state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF-sputtered LiPON. Information about the short-range structure results from 1D and 2D solid-state NMR experiments. These results are compared with first principles chemical shielding calculations of Li-P-O/N crystals and ab initio molecular dynamics-generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON's stability is a result of its glassy character. Free-standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.

Identification of Distinct Framework Aluminum Sites in Zeolite ZSM-23: A Combined Computational and Experimental 27Al NMR Study

ZSM-23 (MTT) is a silicon-rich zeolite with one-dimensional, 10-membered ring channels, which has recently attracted interest as a promising catalyst in aromatic-free methanol-to-hydrocarbons conversion. To obtain a better understanding of the catalytic activity and ultimately to design a better catalyst, it is crucial to locate the active sites in the zeolite framework. This work investigates the tetrahedral aluminum framework sites in two zeolite H-ZSM-23 samples by experimental and computational 27Al NMR spectroscopy. 27Al MQMAS NMR experiments at six different magnetic fields (4.7–22.3 T) were utilized to resolve distinct Al sites. The detected tetrahedral framework Al sites were assigned to the specific tetrahedral sites in the crystal structure by DFT calculations of the 27Al chemical shieldings. A comprehensive investigation of the structural model, basis set, and exchange–correlation potential used in the DFT calculations was performed. Two avenues were pursued for calculating the 27Al isotropic c...

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1H and 13C chemical shifts are determined from two-dimensional 1H-13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

Basis Sets and Nuclear Magnetic Resonance Shielding Effects for Mixing of MWBN and CNTs

Density functional theory calculations (DFT), as well as hybrid methods (B3LYP) and HF method for MWCNTs have been carried out to study structural stability. The geometry of the MWCNTs have been optimized at DFT and HF methods within CCPTZ-CCPVZ, EPR-II, EPR-II, 6-31G* and 6-31++G** basis sets. According to GIAO method, NMR parameters have been evaluated. The Gaussian quantum chemical package is used for all calculations. The gauge including atomic orbital (GIAO) approach was applied for chemical shielding calculations of (5, 5)@(10, 10), (3, 3)@(7, 7), (4, 4)@(8, 8) DWCNTs.

Self-Assembled Oligoanilinic Nanosheets: Molecular Structure Revealed by Solid-State NMR Spectroscopy

The products obtained during the early stages of the oxidative polymerization of aniline in the “falling pH” reaction were investigated using multinuclear solid-state magic-angle spinning (MAS) NMR combined with first-principles NMR chemical shielding calculations using the GIPAW (gauge-including projector augmented wave) method. A sample was synthesized starting from a 50:50 mixture of U–13C aniline and 15N-labeled aniline; two-dimensional 13C refocused INADEQUATE, 15N–13C double CP, 15N PDSD, and 1H–13C/15N refocused INEPT MAS NMR spectra revealed the presence of quinoneimine structural units. Structural models that are consistent with the connectivities revealed by the 13C refocused INADEQUATE and 15N–13C Double CP spectra are proposed. GIPAW chemical shift calculations are performed for model structures based on the proposed oligomeric structures; noting that the model structures do not take into account intermolecular hydrogen bonding and CH−π interactions, agreement and discrepancy to experiment are discussed.

Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems

Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.

Quantum Study of Amino Acid Bind to Carbon Nanotube in View of Magnetic Properties

Investigation framework fast quantum conductance of the interaction between carbon nanotubes (CNTs) and biomolecules within a binding approximation is essential to the CNT-based nanotechnology and biotechnology. Nanotubes have also been successfully coated with proteins, nanocrystals, and metalloporphyrin through hydrogen bonding, and these coated tubes have great potentials in the areas of chemical sensors. In this study, the Quantum Mechanics (QM) is used for investigated the basis set effects on amino acids stability and their interaction with single-walled carbon nanotubes (SWCNTs). The geometry of the ALA and ARG have been identified through the HF level of theory using 6-31++G**, 6-31+G**, 6-31G** and 6-31G* basis sets. The HF method for ALA and ARG molecule has been obtained to study structural stability, total energy, and chemical shift nucleus magnetic resonance. The gauge including atomic orbital (GIAO) approach was applied for chemical shielding calculations. According to the GIAO method, NMR parameters have been evaluated. The contact angle between SWCNT and amino acids was changed. In this work, a comparison of the effects of contact angle on the electronic structure of amino acids has been carried out. The Gaussian quantum chemical package is used for all calculations.

An assessment of the intercarbon stretching phenomenon in C-substituted “pseudocloso” {3,1,2-RuC2B9} metalladicarbaboranes

DFT calculation of cluster shapes and their related boron-vertex 11B nuclear shieldings for a range of substituted 12-vertex metalladicarbaborane cluster compounds [3,1,2-R2-3-(η6-C6H6)-3,1,2-RuC2H9H9] confirms that the array of experimentally observed C–C distances in the group of progressively more open closo, ‘semipseudocloso’ and ‘pseudocloso’ clusters results from the inherent propensity of the [(η6-C6H6)RuC2H9H9R2] cluster to occupy, in the absence of steric drivers, either closo-structured or so-called ‘pseudocloso’-structured fundamental local minima on the overall potential energy surface. The shallow profiles of the potential wells, together with the electronic and steric influences of substituents on the cluster carbon vertices, alter the relative energies of the closo and ‘pseudocloso’ minima, and alter the energy profile between them, thereby accounting for the observed variations in the distances in the crystallographically measured C–C separations. We propose that these differ fundamentally due to either the closo or ‘pseudocloso’ configuration being electronically preferred, with some instances of the ‘pseudocloso’ configuration being compressed towards closo by packing forces, or stretched further beyond ‘pseudocloso’ by steric effects of bulky substituents on carbon. This contrasts with one view postulated in the literature which holds that steric repulsion between the C-bound substituents is the sole driver that forces an inherently fundamental closo cluster to open into an anomalous ‘pseudocloso’ configuration. In two reported cases, the cluster flexibility is evident in solution and, in these cases, GIAO calculation of the 11B chemical shieldings explains the measured 11B chemical shifts, which can be interpreted in terms of the dynamic interchange of the closo and ‘pseudocloso’ species. A currently held view is that the ‘weighted average’ of 11B chemical shifts reflects the inherent degree of electronic ‘pseudocloso’ character in a particular cluster can therefore often equally be rationalised in terms of lability between similarly stable fundamentally closo and ‘pseudocloso’ forms.

Finite-field implementation of NMR chemical shieldings for molecules: Direct and converse gauge-including projector-augmented-wave methods

Two finite-field implementations for the calculation of chemical shieldings of molecular systems using a plane-wave basis set and the Gauge-Including Projector-Augmented-Wave method are presented. The direct approach mimics the nuclear magnetic resonance experiment in that it puts the molecule in a uniform magnetic field and obtains shieldings from the current response. The other is based on the recently introduced "converse method" [T. Thonhauser, D. Ceresoli, A. A. Mostofi et al., J. Chem. Phys. 131, 101101 (2009)]. In both methods two-center contributions to the shieldings can be included via a numerically simple augmentation construction. Results obtained with both methods are discussed as well as (dis)similarities in their behaviors.

Probing theoretical level effect on fluorine chemical shielding calculations

The extensive quantum‐chemical calculations are assessed for prediction of the 19F nuclear magnetic shielding constants. The methods within domain of density functional theory (DFT) and ab initio, Hartree–Fock (HF), and second‐order Møller–Plesset perturbation theory (MP2) are employed for calculation of the 19F chemical shielding constants for a series of 30 small fluorine‐containing molecules. The importance of inclusion of four factors, namely, electron correlation treatment, triple‐ξ valence shell, diffuse function, and polarization function on calculating the fluorine NMR chemical shieldings for a variety of Pople's standard basis sets at gauge invariant atomic orbital (GIAO) and continuous set of gauge transformation (CSGT) conditions are discussed by employing the linear regression analysis. The systematic investigation performed here on the influence of the method, level of theory, and basis set size on the accuracy of 19F chemical shielding demonstrates that the presence of a high level of electron correlation factor in level as well as the polarization function in basis set leads to an accurate wave function to compute the reliable fluorine chemical shielding. The results analysis illustrates that the polarization function has a significant effect on the basis sets to minimize the difference between theoretical and experimental values in several fluorine molecules. An additional comparison of the GIAO and CSGT results is used as a supplementary study to confirm the validity of the results. The basis set dependence of fluorine chemical shielding constants verifies that GIAO provides results that are often more accurate than those that are calculated with CSGT approach at the same basis set size, as expected. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 140‐153, 2013.

Aluminum phosphide nanotubes: Density functional calculations of aluminum-27 and phosphorus-31 chemical shielding parameters

Electronic structures of two representative armchair and zigzag models of aluminum phosphide nanotube (AlPNT) were investigated by density functional theory (DFT) calculation of chemical shielding (CS) parameters of Al-27 and P-31 atoms. The optimized Al–P bond length was identical for both models. The diameters of both ends of the armchair model were identical whereas the diameter of P-end was much wider than Al-end of the zigzag model. The isotropic and anisotropic CS parameters were divided into layers based on detecting of similar electronic environments by the atomic sites of each layer. For the armchair model, the strength of Al–P bond at the end of nanotube was weaker than the body of nanotube whereas this trend was observed only for the P-end of the zigzag model.

NMR chemical shift data and ab initio shielding calculations: emerging tools for protein structure determination

In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the accuracy of different computational methods are discussed. It is anticipated that incorporating theoretical information on chemical shifts will increase the accuracy of protein structures, in the solid and liquid state alike, and extend the applicability of NMR spectroscopy to ever larger systems.