Average Chemical Shift Research Articles

Dissociation of HNO3 in water revisited: experiment and theory.

Nitric acid dissociation in water is studied as a function of concentration, employing experimental techniques (1H NMR spectroscopy and calorimetry), quantum chemical methods (B3LYP and PBE functionals for molecular clusters) and molecular dynamics simulations (the PBE-D3 functional for solutions under periodic boundary conditions). The extent of dissociation, via proton transfer to a neighboring water molecule, as a function of concentration is studied computationally for molecular nitric acid clusters HNO3(H2O)x (x = 1-8), as well as periodic liquids (HNO3 mole fractions of 0.19 and 0.5, simulated at T = 300 K and 450 K). Despite the simple nature of these structural models, their computed and simulated average 1H chemical shifts compare well with the experimental measurements in this study. Finally, the measured and calculated chemical shifts have shown reasonable relationships with the enthalpy change upon mixing of this binary complex.

Localizing Oleylamine Ligands on Amine–Halide Copassivated Indium Phosphide Nanocrystals

The surface capping of organic ligands is a full part of a colloidal nanocrystal (NC) that provides colloidal stability, helps passivating electronic trap-states, or governs charge hopping between adjacent NCs. A central aspect to understanding this ligand shell is its inherently heterogeneous nature caused by, for example, site- or facet-dependent adsorption energies. Even so, the identification of ligands bound to different surface sites remains highly challenging. In this work, we propose a case study on oleylamine/chloride copassivated InP NCs, for which we show that the heterogeneous broadening of 1H resonances in the nuclear magnetic resonance spectrum enables ligands adsorbed to facets to be distinguished from edge- or corner-bound ligands. More specifically, we demonstrate by means of the recovery of spectral holes burned in the alkene resonance of surface-bound oleylamine that the ligand shell consists of spatially distinct pools of oleylamine characterized by a different average chemical shift. Combining this observation with classical molecular dynamics simulations, we assign the downfield and upfield side of the alkene resonance to oleylamine bound to facets, or edges and corners, respectively. Importantly, we show that this proposed spectral fingerprint of surface-localization of ligands agrees with the change in shape of the alkene resonance when increasing the NC size and when exchanging part of the oleylamine for hexadecanethiol. Given the general applicability of the methodology introduced here, we believe this work offers a starting point to assess ligand localization for a broad range of colloidal NCs and develop a better understanding of the binding and packing of ligands on NC surfaces.

NMR spectrum prediction for dynamic molecules by machine learning: A case study of trefoil knot molecule.

Nuclear magnetic resonance (NMR) spectroscopy is one of the indispensable techniques in chemistry because it enables us to obtain accurate information on the chemical, electronic, and dynamic properties of molecules. Computational simulation of the NMR spectra requires time-consuming density functional theory (DFT) calculations for an ensemble of molecular conformations. For large flexible molecules, it is considered too high-cost since it requires time-averaging of the instantaneous chemical shifts of each nuclear spin across the conformational space of molecules for NMR timescales. Here, we present a Gaussian process/deep kernel learning-based machine learning (ML) method for enabling us to predict, average in time, and analyze the instantaneous chemical shifts of conformations in the molecular dynamics trajectory. We demonstrate the use of the method by computing the averaged 1H and 13C chemical shifts of each nuclear spin of a trefoil knot molecule consisting of 24 para-connected benzene rings (240 atoms). By training ML model with the chemical shift data obtained from DFT calculations, we predicted chemical shifts for each conformation during dynamics. We were able to observe the merging of the time-averaged chemical shifts of each nuclear spin in a singlet 1H NMR peak and two 13C NMR peaks for the knot molecule, in agreement with experimental measurements. The unique feature of the presented method is the use of the learned low-dimensional deep kernel representation of local spin environments for comparing and analyzing the local chemical environment histories of spins during dynamics. It allowed us to identify two groups of protons in the knot molecule, which implies that the observed singlet 1H NMR peak could be composed of the contributions from protons with two distinct local chemical environments.

Application of 1H-NMR- and LC-MS based Metabolomic analysis for the evaluation of celery preservation methods

In this study, 1H NMR spectroscopy coupled with multivariate analyses was used to evaluate the effectiveness of celery preservation techniques. The extraction parameters were optimised to achieve high recoveries of the majority (9 out of 14) of the quantified metabolites, and to reduce fluctuations in concentrations (within relative standard deviation of 3.5%) and average chemical shifts (0.011 ppm). Subsequently, the optimised method was applied to evaluate metabolite changes caused by different preservation treatments over a 14-day storage period. Nanocellulose treatment (5 g/L) was ascertained to be the most effective from untargeted and targeted principal component analysis (PCA) results, correlating with visual findings, and the significantly reduced metabolite variations (p < 0.05) detected by NMR were identified to be in asparagine, mannitol, malic acid, glucose, and glutamine. LC-MS analysis also revealed significant suppression of phenylpropanoid pathway metabolites (apiin, psoralen, xanthotoxin, and bergapten) by 1.5–25 times. Nanocellulose treatment was an efficient strategy for celery preservation, and NMR- and LC-MS-based metabolomics was an effective approach for establishing reliable metabolomic fingerprints and profiles, enabling the identification and quantitation of metabolite biomarkers for the assessment of storage conditions.

Analysis and information content of quadrupolar NMR in glasses: 25Mg NMR in vitreous MgSiO3 and CaMgSi2O6

The static wideline and high-resolution magic angle spinning (MAS) 25Mg NMR lineshapes measured for isotopically enriched enstatite and diopside glasses indicate a wide distribution of the electric-field gradient (EFG) components at the 25Mg position caused by disorder. The correct characterization of this distribution requires simulations with special attention paid to the experimental parameters. Here, both the static spectra obtained by wideband excitation and the MAS-NMR spectra obtained via rotor-synchronized Hahn spin echo acquisition were successfully simulated with the Czjzek distribution model, using one consistent set of parameters. Average nuclear electric quadrupole coupling constants near 8 MHz and a distribution width around 4 MHz were obtained for both materials, which suggests that earlier results on these glasses need to be re-examined. The results of this study outline a general strategy for characterizing the local environments of strongly coupled quadrupolar nuclei in amorphous and glassy materials. Despite the discrepancies between the interaction parameters extracted from our data and those published in earlier NMR work, the best fit to the data indicate an average isotropic chemical shift near 13 ppm (vs. aqueous MgCl2 solution) for both the enstatite and diopside glasses. Assuming the applicability of the current database relating the 25Mg chemical shifts with coordination numbers in crystalline compounds, this value suggests that the Mg2+ ions are six-coordinated. This conclusion, however, is based on the simplifying assumption that the 25Mg spectrum comprises a Czjzek distribution centered at a single isotropic chemical shift value and stands in contrast to the results of recent isotope-selective neutron diffraction studies which give an average Mg-O coordination number of 4.4–4.5 for both glasses. However, reasonable fits to the MAS-NMR spectra can also be obtained when constraining the average isotropic chemical shift to 50 ppm, a value typical of four-coordinated Mg. We conclude that multiple Mg sites with different coordination numbers may well be present and that, in the present glasses, 25Mg NMR at typically used spinning rates and magnetic field strengths (20 kHz, 14.1 T) is not capable of resolving them due to excessive broadening by quadrupolar interactions.

Structural and dynamic properties of MgO–Al2O3–SiO2 glasses from molecular dynamics simulations and NMR

Magnesium aluminosilicate glasses have a wide range of applications in composite fiber reinforcements, aircraft windshields, due to their excellent chemical stability and mechanical properties. In this work, molecular dynamics simulations were used to obtain the short- and medium-range structural evolution of MgO/Al2O3 in MgO–Al2O3–SiO2 glass. The structural information was verified using a combination of combining Raman and Nuclear Magnetic Resonance (NMR) spectroscopy. The composition-structure-property relationship of the MgO–Al2O3–SiO2 glasses was constructed, using high-temperature viscosity results calculated by the Einstein-Stoke equation. The results showed that with the increase of MgO/Al2O3 ratio, Mg2+ changed from charge compensator to network modifier, which led to the gradual depolymerization of the glass network. Moreover, with the gradual replacement of Si by Al in the glass network, the disorder of the glass system increases, evidenced by the high-frequency Raman bands and the average chemical shifts of [AlOn] (n = 4, 5) shift linearly. In addition, we found that the de-polymerization led to a decrease in viscosity and an increase in fragility. The viscosity is negatively correlated with both the fragility and the atomic diffusion coefficient. It provides a theoretical basis for improving the preparation process of MgO–Al2O3–SiO2 glass and optimizing the glass properties.

Rh(II)‐mediated one‐pot synthesis of dihydrobenzofuran and spiro[2.5]oct‐1‐ene: Experimental and DFT studies

AbstractThis study represents an experimental and computational approach to investigate the rhodium‐catalyzed one‐pot synthesis of dihydrobenzofuran‐4‐one (DBF) and spiro[2.5]oct‐1‐ene (SOE) derivatives. Density functional theory (DFT) calculations were performed at B3LYP and M06‐2X level theory. For mechanistic studies, the calculation employing B3LYP/GenECP/LanL2DZ/6‐311++G(d,p) level of theory demonstrated that a [3 + 2] cycloaddition reaction between diazo compound and phenylacetylene (PhA) proceeds through a two‐step mechanism via a barrierless and highly exergonic process with relative free energy 73.61 kcal/mol to yield the kinetically favored DBF derivatives (50%–62.5%). In contrast, the assemble of SOE derivatives follows [2 + 1] cycloaddition between in situ generated cyclohexane‐1,3‐dione carbene‐2 and PhA, with the potential energy barrier 4.41 kJ/mol. Thermochemistry calculation disclosed that the cycloaddition reactions are spontaneous, and DBF (6a) is thermodynamically more stable than its constitutional isomer SOE (7a) by 42.59 kcal/mol. However, natural bond orbital (NBO), HOMO–LUMO energy gaps (4.62–4.89 eV), dipole moments, polarizability, first‐order hyperpolarizability, and global reactivity descriptors were calculated to understand products' structural features. Additionally, Merck Molecular Force Field (MMFF94), followed by the B3LYP level of theory, was applied to predict the relative stability for the various conformations of 6b and 7b. The Boltzmann weighted average 1H chemical shift computed by GIAO‐B3LYP/6‐311+(2d,p) method and UV‐Vis absorption calculated using time‐dependent density functional theory (TD‐DFT) agree with experimental results. Finally, the synthesis of DBF and SOE derivatives is herein illustrated.

An improved statistical approach for conformational analysis from 13C NMR chemical shifts

In this article we propose an improved statistical approach for the estimation of the mole fraction of each conformer in a given conformational equilibrium from the measured averaged 13C NMR chemical shifts. As each compound has a different number of conformers, an iterative process of fitting (backfitting type) is necessary. In each iteration, two estimates are made, i) fitting to a ridge regression model with equality and inequality constraints and selection of variables for each compound and ii) re-fitting for all compounds. This new procedure leads to consistent results, with low standard error and good p-values, allowing the estimation of the conformational composition for small molecules with a reduced number of conformers.

Structure‐property relations in crack‐resistant alkaline‐earth aluminoborosilicate glasses studied by solid state NMR

AbstractThe effect of the average ionic potential ξ = Ze/r of the network modifier cations on crack initiation resistance (CR) and Young's modulus E has been measured for a series of alkaline‐earth aluminoborosilicate glasses with the compositions 60SiO2–10Al2O3–10B2O3–(20−x)M(2)O–xM’O (0 ≤ x ≤ 20; M, M’ = Mg, Ca, Sr, Ba, Na). Systematic trends indicating an increase of CR with increasing ionic potential, ξ, have been correlated with structural properties deduced from the NMR interaction parameters in 29Si, 27Al, 23Na, and 11B solid state NMR. 27Al NMR spectra indicate that the aluminum atoms in these glasses are essentially all four‐coordinated, however, the average quadrupolar coupling constant &lt;CQ&gt; extracted from lineshape analysis increases linearly with increasing average ion potential computed from the cation composition. A similar linear correlation is observed for the average 29Si chemical shift, whereas the fraction of four‐coordinate boron decreases linearly with increasing ξ. Altogether the results indicate that in pure alkaline‐earth boroaluminosilicate glasses the crack resistance/E‐modulus trade‐off can be tailored by the alkaline‐earth oxide inventory. In contrast, the situation looks more complicated in glasses containing both Na2O and the alkaline‐earth oxides MgO, CaO, SrO, and BaO. For 60SiO2–10Al2O3–10B2O3–10MgO–10Na2O glass, the NMR parameters, interpreted in the context of their correlations with ionic potentials, are consistent with a partial network former role of the MgO component, enhancing crack resistance. Altogether the presence of MgO in aluminoborosilicate glasses helps overcome the trade‐off issue between high crack resistance and high elasticity modulus present in borosilicate glasses, thereby offering additional opportunities for the design of glasses that are both very rigid and very crack resistant.

Predicting Cell Wall Lytic Enzymes Using Combined Features.

Due to the overuse of antibiotics, people are worried that existing antibiotics will become ineffective against pathogens with the rapid rise of antibiotic-resistant strains. The use of cell wall lytic enzymes to destroy bacteria has become a viable alternative to avoid the crisis of antimicrobial resistance. In this paper, an improved method for cell wall lytic enzymes prediction was proposed and the amino acid composition (AAC), the dipeptide composition (DC), the position-specific score matrix auto-covariance (PSSM-AC), and the auto-covariance average chemical shift (acACS) were selected to predict the cell wall lytic enzymes with support vector machine (SVM). In order to overcome the imbalanced data classification problems and remove redundant or irrelevant features, the synthetic minority over-sampling technique (SMOTE) was used to balance the dataset. The F-score was used to select features. The Sn, Sp, MCC, and Acc were 99.35%, 99.02%, 0.98, and 99.19% with jackknife test using the optimized combination feature AAC+DC+acACS+PSSM-AC. The Sn, Sp, MCC, and Acc of cell wall lytic enzymes in our predictive model were higher than those in existing methods. This improved method may be helpful for protein function prediction.

Identification and validation of a novel anti-virulent that binds to pyoverdine and inhibits its function

ABSTRACT Pseudomonas aeruginosa: causes serious infections in patients with compromised immune systems and exhibits resistance to multiple antibiotics. The rising threat of antimicrobial resistance means that new methods are necessary for treating microbial infections. We conducted a high-throughput screen for compounds that can quench the innate fluorescence of the chromophore region of the P. aeruginosa siderophore pyoverdine, a key virulence factor. Several hits were identified that effectively quench pyoverdine fluorescence, and two compounds considerably improved the survival of Caenorhabditis elegans when worms were challenged with P. aeruginosa. Commercially available analogs of the best hit, PQ3, were tested for their ability to rescue C. elegans from P. aeruginosa and to interact with pyoverdine via fluorescence and solution NMR spectroscopy. 1H-15N and 1H-13C HSQC NMR were used to identify the binding site of PQ3c. The structure model of pyoverdine in complex with PQ3c was obtained using molecular docking and molecular dynamics simulations. PQ3c occupied a shallow groove on pyoverdine formed by the chromophore and N-terminal residues of the peptide chain. Electrostatic interactions and π-orbital stacking drove stabilization of this binding. PQ3c may serve as a scaffold for the development of pyoverdine inhibitors with higher potency and specificity. The discovery of a small-molecule binding site on apo-pyoverdine with functional significance provides a new direction in the search of therapeutically effective reagent to treat P. aeruginosa infections. Abbreviations: NMR: nuclear magnetic resonance; SAR: structure–activity relationship; MD: molecular dynamics; RMSF: root-mean-square fluctuation; HSQC: heteronuclear single quantum correlation; DMSO: dimethyl sulfoxide; Δδavg: average amide chemical shift change; DSS: 2,2-dimethyl-2-silapentane-5-sulfonate; RMSD: root-mean-square deviation; LJ-SR: Lennard–Jones short-range; Coul-SR: Coulombic short-range; FRET: fluorescence resonance energy transfer

NMR study of the influence and interplay of water, HCl and LiCl with the extraction agent Aliquat 336 dissolved in toluene

The quaternary amine Aliquat 336 (A336·Cl) was dissolved in toluene and thoroughly mixed with aqueous solutions containing LiCl or HCl. After mixing, the organic phase was separated from the aqueous phase and analysed using NMR and acid–base titration. The different proton species HCl, H2O and H3O+ present in the aqueous phase are normally not distinguishable using NMR due to fast exchange conditions (on the NMR time scale) and therefore they give rise to mainly one single peak in the proton spectrum. The chemical shift of this single ‘composite’ peak is affected by the relative distribution of the various proton species present in the aqueous solution and is made use of in this work. For instance, ratio of molecular hydrochloric acid (HCl) and dissociated acid (H3O+-Cl−) was found to be between 0.966 and 1.005 in a concentrated (37 wt%) HCl solution, assuming a HCl chemical shift of 0.5 ppm. Moreover, by applying 7Li NMR, the number ratio between Li+ and A336 in the organic phase was found to increase from 0.12 to 5.4 as the LiCl concentration increased from 0.2 to 5 mol/kg in the aqueous phase, before extraction. In addition, the average chemical shift of the –N-CH3 protons in A336 was found to increase linearly with the concentration of Li+ and introduces a simple and fast technique to determine the concentration of Li+ in the organic phase. Not surprisingly, the NMR data suggest that most cations in the organic phase are located in spatial proximity to the –N-CH3 group. Finally, the relative number of Cl− ions in the organic phase, after extraction, was estimated from the NMR data by imposing electrical neutrality, on the solution.

Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features.

There are a lot of bacteria in the environment, and Gram-positive bacteria are the most common ones. Some Gram-positive bacteria are very harmful to the human body, so it is significant to predict Gram-positive bacterial protein subcellular location. And identification of Gram-positive bacterial protein subcellular location is important for developing effective drugs. In this paper, a new Gram-positive bacterial protein subcellular location dataset was established. The amino acid composition, the gene ontology annotation information, the hydropathy dipeptide composition information, the amino acid dipeptide composition information, and the autocovariance average chemical shift information were selected as characteristic parameters, then these parameters were combined. The locations of Gram-positive bacterial proteins were predicted by the Support Vector Machine (SVM) algorithm, and the overall accuracy (OA) reached 86.1% under the Jackknife test. The overall accuracy (OA) in our predictive model was higher than those in existing methods. This improved method may be helpful for protein function prediction.

17O NMR as a measure of basicity of alkaline-earth oxide surfaces: A theoretical study.

The surface basicity of the alkaline-earth metal oxides has been investigated by studying the properties of 17O nuclear magnetic resonance (NMR). To this end, we performed density functional theory calculations and determined the 17O chemical shift and the quadrupolar coupling constants of the regular and stepped surfaces of MO (M = Mg, Ca, Sr, and Ba) oxides. The computed average chemical shift (δiso av) for 17O NMR of bulk MgO, CaO, SrO, and BaO is 46, 301, 394, and 636 ppm, respectively, in excellent agreement with the experiment. The 17O NMR chemical shifts correlate linearly with the Madelung potential in the four oxides. Next, we considered the changes in the 17O chemical shift due to the adsorption of BR3 (R = F and OCH3) and pyrrole as probe molecules. We found that the 17O NMR signal of the O ion directly bound to the probe molecule shifts considerably compared to the clean surface. This is due to a change in the polarization of the O charge distribution due to the molecular adsorption. This change is the largest for BaO, with the strongest bond and the shortest surface-adsorbate distance, and the smallest for MgO, thus showing a direct correlation between 17O NMR and surface basicity. The 17O chemical shift of the basic site correlates linearly also with several properties of the adsorbed molecules, providing a direct measure of the surface basicity.

A unified 23Na NMR chemical shift correlation with structural parameters in multicomponent silicate‐based glasses

AbstractFrom a large ensemble of 34 silicate‐based glasses from the borosilicate, phosphosilicate, and borophosphosilicate systems that comprise either Na as a sole glass‐network modifier or when mixed with Ca, we established a good correlation between the 23Na average isotropic chemical shift () and the average coordination number of Na and the mean Na–O distance. The latter parameters were obtained by atomistic molecular dynamics simulations. We also demonstrated that is essentially independent on the precise network forming (Si, B, P) species but depends primarily on the net molar fraction of Na and Ca, thereby offering a straightforward 23Na chemical shift prediction from the glass composition alone.

The structure and thermochemistry of K2CO3–MgCO3 glass

Abstract

Density functional theory, molecular docking and bioassay studies on (S)-2-hydroxy-N-(2S,3S,4R,E)-1,3,4 trihydroxyicos-16-en-2-yl)tricosanamide

A novel indigoferamide-A, earlier isolated from the seeds of Indigofera heterantha Wall was characterized using density functional theory, molecular docking and bioassays studies. Density functional theory calculations were performed at B3LYP/6-31G(d,p) to gain geometric insight of the compound. Conformational analyses have been performed around three important dihedral angles to explore the lowest energy structure and conformer. The simulated vibrational spectrum of the compound at B3LYP/6-31G(d,p) was scaled with two scaling factors, and the scaled harmonic vibrations shows nice correlation with the experimental values. 1H and 13C NMR chemical shifts were calculated using Cramer's re-parameterized function W04 at 6- 31G(d,p) basis set. Several conformers lying within 2 kcal mol−1 of the minimum energy conformer were considered; however, the chemical shifts were not significantly different among these conformers. The Gaussian averaged theoretical 1H and 13C chemical shifts correlate nicely with the experimental data. Electronic properties such as band gap, ionization potential and electron affinities were also simulated for the first time, however, no comparison could be made with the experiment. The compound was also screened for urease, antiglycation activities and the theoretical explanation of the results is provided based on molecular docking simulations.

Cross-term Splittings Due to the Orientational Inequivalence of Proton Magnetic Shielding Tensors: Do Water Molecules Trapped in Crystals Hop or Tunnel?

Water molecules trapped in crystals of barium chlorate monohydrate have been investigated by magic-angle spinning (MAS) proton NMR spectroscopy in the temperature range 110-300 K. At high temperatures, a single spinning sideband pattern is observed. Below 150 K, however, two interleaved spinning sideband manifolds appear, with distinct centerbands that do not coincide with the average isotropic chemical shift seen at high temperatures. This hitherto unknown "cross-term splitting" results from the interplay of the homonuclear dipole-dipole coupling and two anisotropic proton shielding tensors that have identical principal components but nonequivalent orientations. The resulting cross terms cannot be averaged out by rotation about the magic angle. The analysis of the exchange-induced broadening, coalescence, and narrowing of the cross-term splitting in MAS spectra allows one to estimate the rate of exchange of the two protons between 140 and 190 K. The experimental data is compared with 2H and 1H NMR studies of the same sample reported in the literature. Density functional theory methods are utilized to estimate the thermal activation energy for a 2-fold hopping process of proton exchange about the H-O-H bisector. The Bell-Limbach model allows one to take into account contributions due to incoherent quantum tunneling in the low-temperature regime.

Predicting protein structural classes for low-similarity sequences by evaluating different features

Protein structural class could provide important clues for understanding protein fold, evolution and function. However, it is still a challenging problem to accurately predict protein structural classes for low-similarity sequences. This paper was devoted to develop a powerful method to predict protein structural classes for low-similarity sequences. On the basis of a very objective and strict benchmark dataset, we firstly extracted optimal tripeptide compositions (OTC) which was picked out by using feature selection technique to formulate protein samples. And an overall accuracy of 91.1% was achieved in jackknife cross-validation. Subsequently, we investigated the accuracies of three popular features: position-specific scoring matrix (PSSM), predicted secondary structure information (PSSI) and the average chemical shift (ACS) for comparison. Finally, to further improve the prediction performance, we examined all combinations of the four kinds of features and achieved the maximum accuracy of 96.7% in jackknife cross-validation by combining OTC with ACS, demonstrating that the model is efficient and powerful. Our study will provide an important guide to extract valuable information from protein sequences.

Effect of torsional motion on the 13C, 1H and 19F NMR chemical shifts in 2,2′-difluorobiphenyl

Abstract Contribution of inter-ring torsional motion of 2,2′-difluorobiphenyl (DFBPh) to the NMR chemical shifts (CSs) and lineshapes is investigated using B3LYP/aug-cc-PVDZ computations. The anharmonic potential energy curve for this vibrational motion is calculated by a relaxed scan over the whole span of its coordinate, inter-ring dihedral angle D. The NMR CS curves for the most affected 1H, 13C and 19F nuclei are calculated as functions of D for these relaxed structures using IGAIM method. Lineshapes arising from the unaveraged NMR CSs are simulated for each vibrational state, and their corresponding state averages and the thermally averaged values at two temperatures are calculated. Lineshape broadening in slow regime is significant especially for the 19F nuclei. The averaged CSs differ slightly, but detectably, from their corresponding equilibrium values. It is thus concluded that for accurate evaluation of the NMR CSs and experimentally compatible NMR spectra, such vibrational analysis is necessary.