Absolute NMR Research Articles

Machine learning-based correction for spin-orbit coupling effects in NMR chemical shift calculations.

As one of the most powerful analytical methods for molecular and solid-state structure elucidation, NMR spectroscopy is an integral part of chemical laboratories associated with a great research interest in its computational simulation. Particularly when heavy atoms are present, a relativistic treatment is essential in the calculations as these influence also the nearby light atoms. In this work, we present a Δ-machine learning method that approximates the contribution to 13C and 1H NMR chemical shifts that stems from spin-orbit (SO) coupling effects. It is built on computed reference data at the spin-orbit zeroth-order regular approximation (ZORA) DFT level for a set of 6388 structures with 38 740 13C and 64 436 1H NMR chemical shifts. The scope of the methods covers the 17 most important heavy p-block elements that exhibit heavy atom on the light atom (HALA) effects to covalently bound carbon or hydrogen atoms. Evaluated on the test data set, the approach is able to recover roughly 85% of the SO contribution for 13C and 70% for 1H from a scalar-relativistic PBE0/ZORA-def2-TZVP calculation at virtually no extra computational costs. Moreover, the method is transferable to other baseline DFT methods even without retraining the model and performs well for realistic organotin and -lead compounds. Finally, we show that using a combination of the new approach with our previous Δ-ML method for correlation contributions to NMR chemical shifts, the mean absolute NMR shift deviations from non-relativistic DFT calculations to experimental values can be halved.

A new double-reference correction scheme for accurate and efficient computation of NMR chemical shieldings

Using an extensive set of benchmark geometric data and absolute NMR chemical shieldings for gas phase molecules compiled from the literature, we introduce and test a novel shift-and-scale correction scheme for bringing computed values into closer agreement with experiment. Our approach requires only one additional reference calculation relative to existing methods for computing chemical shifts, and all reference species are small molecules whose absolute nuclear shieldings can be easily obtained, both computationally and experimentally. We demonstrate that our approach is capable of correcting for errors due to choice of electronic structure method and basis set, vibrational averaging effects, and scalar relativistic effects, but cannot account for the influence that heavy atoms have on the chemical shieldings of neighbouring light atoms, via spin-orbit coupling. We particularly recommend using our approach in conjunction with nuclear shieldings computed at DFT optimized geometries, employing hybrid functionals with moderate-to-high quality atomic orbital basis sets, e.g. pc-2.

Single-Laboratory Validation Study of a Proton NMR Method for the Determination of L-Arginine, L-Citrulline, and Taurine Contents in Dietary Supplements.

A quantitative NMR (qNMR) method can provide rapid analysis compared to chromatographic methods. Sample preparation steps are relatively simpler and run time is shorter. Rapid analysis methods for release tests in quality control laboratories are very important for laboratory efficiency. Here, we describe a single-laboratory validation study for a rapid qNMR analysis of L-arginine, L-citrulline, and taurine in powdered and tablet dietary supplement products. This validation work is to provide documented evidence for the qNMR method validity as well as method performance. The method used Bruker 400 MHz high-resolution proton NMR spectroscopy for simultaneous determination of L-arginine, L-citrulline, and taurine contents in dietary supplement product 1 (powder) and dietary supplement product 2 (tablet). The absolute NMR quantitation is based on a principle of universal proton response intensity correlation with the number of protons in each target analyte (amino acids) vs. that of a reference standard (maleic acid). The test method performance was validated with dietary supplement-1 (powder) and dietary supplement-2 (tablet). The linearity of the method was studied from about 360 mg/g to about 675 mg/g of L-arginine; from about 15 mg/g to about 30 mg/g of L-citrulline; and from about 20 mg/g to about 40 mg/g of taurine in dietary supplement-1, and from about 15 mg/g to about 30 mg/g of taurine in dietary supplement-2. The coefficients of determination (R2) are 1.0000 for L-arginine, 0.9967 for L-citrulline, and 0.9995 for taurine in dietary supplement-1 and 0.9903 for taurine in dietary supplement-2. The accuracies measured from the sample matrices are 102%, 101%, and 100% average recoveries for 80%, 100%, and 120% concentration levels of L-arginine, 105%, 105%, and 103% average recoveries for 80%, 100%, and 120% concentration level of L-citrulline, and 101%, 102%, and 100% average recoveries of taurine for 80%, 100%, 120% concentration levels in dietary supplement-1; and 95, 98%, and 93% average recoveries of taurine for 80%, 100%, 120% concentration levels in dietary supplement-2, respectively. The precisions (RSD) are 1% for L-arginine, 5% for L-citrulline, and 2% for taurine in dietary supplement -1, respectively; and 4% for taurine in dietary supplement-2. The ruggedness of the test method is within 2%, 4%, and 2% for L-arginine, L-citrulline, and taurine for dietary supplement -1, respectively, and within 4% for dietary supplement-2. The method is specific for the quantitation of each nutrient with no background interference from the matrix for the proton peaks of L-arginine, L-citrulline, taurine, and maleic acid (standard). The test method is proven to be specific, precise, accurate, rugged, and suitable for intended quantitative analysis of L-arginine, L-citrulline, and taurine in powdered and tablet finished products. The simultaneous determination of all three nutrients of L-arginine, L-citrulline, and taurine using proton NMR provides rapid analysis for quality control release tests that is more efficient versus that of two HPLC methods. Previously, our laboratory was using one HPLC method to analyze L-arginine and L-citrulline while using a second HPLC method to analyze taurine. That approach required two HPLC instruments and two analysts for parallel analysis that takes 2 days using volatile and flammable solvents for extraction and chemical derivatization. This rapid NMR method can analyze the sample "as is" with results obtained in less than 4 h, and is efficient, safe, and environmentally friendly. The initial higher NMR instrument investment versus two HPLC instruments is rewarded with high returns for continued quality control tests.

NMR absolute shielding scales and nuclear magnetic dipole moments of transition metal nuclei.

This work reports new, accurate nuclear magnetic dipole moments for NMR-active transition metal nuclei where the long-standing systematic error due to obsolete diamagnetic correction has been eliminated by ab initio calculations of absolute NMR shielding constants. The error of the diamagnetic correction reaches ≈ -14 000 ppm for rhenium, which results in magnetic dipole moment corrections of about -3 × 10-2μN for the 185Re and 187Re nuclei. Such extreme values are one to two orders of magnitude larger than the corrections reported in the literature so far. These findings may help to resolve discrepancies in hyperfine splitting experiments involving rhenium ions. To obtain the corrected transition metal nuclear magnetic dipole moments, NMR shielding constants for a series of transition metal complexes defined as NMR standards [Harris et al., Pure Appl. Chem., 2001, 73, 1795] were calculated using the non-relativistic coupled cluster method and four-component relativistic density functional theory. To reproduce the experimental conditions of the NMR standards, the solvent effects were incorporated by explicit and implicit solvent models.

1H NMR spectroscopy quantifies visibility of lipoproteins, subclasses, and lipids at varied temperatures and pressures

NMR-based quantification of human lipoprotein (sub)classes is a powerful high-throughput method for medical diagnostics. We evaluated select proton NMR signals of serum lipoproteins for elucidating the physicochemical features and the absolute NMR visibility of their lipids. We separated human lipoproteins of different subclasses by ultracentrifugation and analyzed them by 1H NMR spectroscopy at different temperatures (283-323 K) and pressures (0.1-200 MPa). In parallel, we determined the total lipid content by extraction with chloroform/methanol. The visibility of different lipids in the 1H NMR spectra strongly depends on temperature and pressure: it increases with increasing temperatures but decreases with increasing pressures. Even at 313 K, only part of the lipoprotein is detected quantitatively. In LDL and in HDL subclasses HDL2 and HDL3, only 39%, 62%, and 90% of the total cholesterol and only 73%, 70%, and 87% of the FAs are detected, respectively. The choline head groups show visibilities of 43%, 75%, and 87% for LDL, HDL2, and HDL3, respectively. The description of the NMR visibility of lipid signals requires a minimum model of three different compartments, A, B, and C. The thermodynamic analysis of compartment B leads to melting temperatures between 282 K and 308 K and to enthalpy differences that vary for the different lipoproteins as well as for the reporter groups selected. In summary, we describe differences in NMR visibility of lipoproteins and variations in biophysical responses of functional groups that are crucial for the accuracy of absolute NMR quantification.

Triaminotrinitrobenzene Isomers - A DFT Treatment

1,3,5-triamino-2,4,6-trinitrobenzene known as TATB is an insensitive high energy density material. It has two more constitutional isomers. The present study deals with all these triaminotrinitrobenzene isomers within the constraints of density functional theory at the levels of RB3LYP/6-31G(d,p) and UB3LYP/6-31G(d). Some geometrical and quantum chemical properties have been obtained and compared. The calculated IR and UV-VIS spectra are produced. Additionally the NICS values have been collected by calculating absolute NMR shielding values at the ring centers, NICS(0), and aromaticity of these isomers are compared. UB3LYP/6-31+G(d) level of calculations revealed that monoionic forms of these isomeric compounds are stable.

Correction: Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

[This corrects the article DOI: 10.3762/bjoc.12.188.].

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291.

A new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative, varioloid A (1), was isolated from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291. Its structure was elucidated on the basis of extensive analysis of 1D and 2D NMR data and the absolute configuration was determined by time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations. A similar compound, whose planar structure was previously described but the relative and absolute configurations and 13C NMR data were not reported, was also identified and was tentatively named as varioloid B (2). Both compounds 1 and 2 exhibited cytotoxicity against A549, HCT116, and HepG2 cell lines, with IC50 values ranging from 2.6 to 8.2 µg/mL.

Toward an absolute NMR shielding scale using the spin-rotation tensor within a relativistic framework.

One of the most influential articles showing the best way to get the absolute values of NMR magnetic shieldings, σ (non-measurables) from both accurate measurements and theoretical calculations, was published a long time ago by Flygare. His model was shown to break down when heavy atoms are involved. This fact motivated the development of new theories of nuclear spin-rotation (SR) tensors, which consider electronic relativistic effects. One was published recently by some of us. In this article we take another step further and propose three different models that generalize Flygare's model. All of them are written using four-component relativistic expressions, though the two-component relativistic SO-S term also appears in one. The first clues for these developments were built from the relationship among σ and the SR tensors within the two-component relativistic LRESC model. Besides, we had to introduce a few other well defined assumptions: (i) relativistic corrections must be included in a way to best reproduce the relationship among the (e-e) term (called "paramagnetic" within the non-relativistic domain) of σ and its equivalent part of the SR tensor, (ii) as happens in Flygare's rule, the shielding of free atoms shall be included to improve accuracy. In the highest accurate model, a new term known as Spin-orbit due to spin, SO-S (in this mechanism the spin-Zeeman Hamiltonian replaces the orbital-Zeeman Hamiltonian), is included. We show the results of the application of those models to halogen containing linear molecules.

Hydrophobization of Silica Aerogels: Insights from Quantitative Solid-State NMR Spectroscopy

Silica aerogels have exceptional physical and chemical properties related to their nanoporous structure and high specific surface area. The hydrophobization of the silica surfaces, for example by modification with trimethylsilyl groups (TMS), is of central importance for silica aerogel production by ambient drying methods, particularly on an industrial scale. This study monitored the chemical modification of silica aerogels by quantitative and two-dimensional solid-state NMR spectroscopy. A series of two-step, acid/base-catalyzed silica alcogels were hydrophobized for different times in hexamethyldisiloxane (HMDSO) and subsequently dried at ambient pressure. Two-dimensional 1H–29Si heteronuclear correlation NMR spectroscopy confirms that both ethoxy and TMS groups are chemically bonded to the silica surfaces. For the single-pulse spectra, a procedure to calibrate the absolute 1H, 13C, and 29Si NMR signal intensities with external references was developed. The quantification procedure is validated by the internal consistency between the 1H, 13C, and 29Si results and the agreement between the measured sample mass and that predicted from the NMR data. The quantitative speciation data on the aerogel samples show that the silica surface is covered by a monolayer of ethoxy, TMS, and silanol groups. Silanol groups are progressively replaced by TMS groups with increasing modification time, and the TMS content has a strong effect on the density of the final aerogel.

Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor

A relativistic molecular Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is proposed and transformed from the laboratory to the body-fixed frame of reference. As a first application of the resulting body-fixed relativistic molecular Hamiltonian, the long anticipated relativistic theory of nuclear spin-rotation (NSR) tensor is formulated rigorously. A "relativistic mapping" between experimental NSR and NMR is further proposed, which is of great value in establishing high-precision absolute NMR shielding scales.

Nuclear magnetic resonance shielding constants and chemical shifts in linear 199Hg compounds: A comparison of three relativistic computational methods

We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible.

Structural determination of the O-antigenic polysaccharide from Salmonella Mara (O:39)

The O-antigenic polysaccharide of Salmonella Mara O:39 (formerly Q) was investigated by sugar and methylation analyses, absolute configuration assignment, mass spectrometry and NMR spectroscopy. The experiments revealed an O-polysaccharide chain composed of the following linear tetrasaccharide repeating units with the structure: →2)-α- l-Qui p3NAc-(1→3)-α- d-Man p-(1→3)-α- l-Fuc p-(1→3)-α- d-Gal pNAc-(1→ where α- l-Qui p3NAc is the residue of 3-acetamido-3,6-dideoxy-α- l-glucopyranose. This repeating unit is the first published structure of the O-polysaccharide from 27 serotypes of S almonella bacteria belonging to serogroup O:39 in the Kauffmann–White classification system.

A note on normalization of biofluid 1D 1H-NMR data

One-dimensional 1H nuclear magnetic resonance (1D 1H-NMR) has been used extensively as a metabolic profiling tool for investigating urine and other biological fluids. Under ideal conditions, 1H-NMR peak intensities are directly proportional to metabolite concentrations and thus are useful for class prediction and biomarker discovery. However, many biological, experimental and instrumental variables can affect absolute NMR peak intensities. Normalizing or scaling data to minimize the influence of these variables is a critical step in producing robust, reproducible analyses. Traditionally, analyses of biological fluids have relied on the total spectral area [constant sum (CS)] to normalize individual intensities. This approach can introduce considerable inter-sample variance as changes in any individual metabolite will affect the scaling of all of the observed intensities. To reduce normalization-related variance, we have developed a histogram matching (HM) approach adapted from the field of image processing. We validate our approach using mixtures of synthetic compounds that mimic a biological extract and apply the method to an analysis of urine from rats treated with ethionine. We show that HM is a robust method for normalizing 1H-NMR data and propose it as an alternative to the traditional CS method.

Coupled cluster study of NMR shielding constants and spin-rotation constants in SiH4, PH3 and H2S molecules

Ab initio methods are applied to analyse the NMR shielding constants and spin-rotation constants in SiH4, PH3 and H2S molecules. The electron correlation effects are studied applying the MP2 and coupled cluster perturbation approaches. The basis set convergence is examined at the same time, and the final results for the equilibrium geometries are obtained at the CCSD(T)/cc-pCVQZ level. Zero-point vibrational and temperature contributions are computed at the SCF, MP2 and CCSD level of approximation. In addition, for the shielding constants we also estimate the relativistic effects, to determine total values of the shielding of the third-row nuclei in the studied molecules. Our final results for the shielding constants at 300 K are σ (29Si in SiH4) = 482.35 ppm, σ (31P in PH3) = 611.64 ppm and σ (33S in H2S) = 736.13 ppm. These values, together with estimated corrections and error bars, can be used to determine absolute NMR shielding scales for the heavy nuclei.

The Investigation of Hydration Processes in Horse Chestnut (Aesculus hippocastanum L.) and Pine (Pinus silvestris L.) Bark and Bast Using Proton Magnetic Relaxation

Summary The proton free induction decay (FID) was shown to be effective in monitoring of hydration and the water soluble extractive fraction in horse chestnut (Aesculus hippocastanum, L.) and pine (Pinus silvestris, L.) bark and bast. The signal from the first bound water layers was separated from the whole liquid signal (L) and at low hydration the liquid signal from the stable sealed bark pores was detected. The liquid-to-solid (L/S) signal ratio as a function of relative mass increase (∆m/m0) was proposed as a convenient method to evaluate the relative mass of water, necessary to dissolve the whole soluble proton pool (∆M/m0), the relative mass contribution of solid proton component (p0 in absence of water soluble fraction or pS0 in presence of water soluble fraction), the saturation concentration of the water soluble fraction (cs) and the effective (scaled to water) proton density of solid protons (βs). The measurement of the absolute (in arbitrary units) proton signal versus relative mass increase yielded additionally the effective proton density water soluble proton fraction in solid (βcu) and in liquid (βcd) phase. For the system containing the soluble proton fraction (horse chestnut bast), the values of the parameters obtained from L/S versus ∆m/m0 dependence were compared with the calculated (or fitted) values obtained from the results of the absolute (in arbitrary units) NMR signal measurements. The effective proton densities (βs) were: 0.33 for pine bark, 0.31 for horse chestnut bark and 0.20 for horse chestnut bast, which suggests the presence of paramagnetic impurities in the solid matrix. The presence of various paramagnetic species was further confirmed by ESR spectroscopy. For horse chestnut bast, in which a water soluble extractive fraction is present, the saturation concentration (cs) of the water soluble fraction was 0.64. The contribution of the water soluble fraction was 0.324 of the total dry mass and the relative proton density βcu = 0.55 (in the solid phase). The contribution of non-removable liquid fraction was 0.004 of the total dry mass. The proton relaxation experiment did not directly reveal a percolation threshold, however, the dehydration extended below the removal of the loosely bound mobile water fraction.

Correlation of Empirical δ(TMS) and Absolute NMR Chemical Shifts Predicted by ab Initio Computations

A set of reference linear correlations is presented to convert ab initio quantum mechanically computed absolute chemical shielding tensors into the more common empirical δ(TMS) values. Large deviat...

Calculation of29Si and27Al MAS NMR Chemical Shifts in Zeolite-β Using Density Functional Theory: Correlation with Lattice Structure

29Si and 27Al NMR chemical shifts have been evaluated from the NMR shielding tensors obtained using the SOS-DFPT technique. The 29Si NMR chemical shifts have been calculated for the nine crystallographically distinct Si sites of the zeolite-β lattice. The calculations were carried out on cluster models Si(OSiH3)4 and R3SiOSiR3 (R = OSiH3) representing one (1T) and two (2T) sites in the zeolite lattice, respectively. Using the 1T models, the nine signals of the experimental spectrum have been assigned with a relative error of less than 1 ppm, the absolute error being estimated at about 5 ppm. The use of a “fragment-averaging” technique based on the results obtained with the 2T models leads to calculated absolute NMR shifts with an accuracy of ±1 ppm. The 27Al NMR shifts of AlH(OSiH3)4 models have also been calculated, after relaxation of the local geometry. It was found that the relative positions of the 27Al chemical shifts are in agreement with the experimental spectrum.

Heteronuclear NMR studies of cobalt corrinoids—17. characterization of neopentylcobinamide and neopentyl-13-epicobinamide by 1H and 13C NMR spectroscopy: Inferred corrin ring conformations from chemical shift differentials

While the 1H and 13C NMR spectra of neopentylcobalamin (NpCbl) and its epimer at corrin ring C(13), neopentyl-13-epiCbl (Np-13-epiCbl), are extremely broad, apparently due to chemical exchange between the base-on and base-off species, the cobinamide derivatives, neopentyl cobinamide (NpCbi +) and neopentyl-13-epicobinamide (Np-13-epiCbi +), have sharp, well-resolved NMR spectra. The 1H and 13C NMR spectra of NpCbi + and Np-13-epiCbi + have now been completely assigned by modern two-dimensional NMR methodologies. Comparison of the 13C spectra of these two complexes shows that significant chemical shift differences occur at a variety of corrin ring and peripheral carbon atoms and are not localized near the site of epimerization. Similarly, comparison of the 13C NMR spectra of NpCbi + and 5′-deoxyadenosylcobinamide (AdoCbi +) shows differences at many corrin ring and peripheral carbons. A first attempt at discerning differences in corrin ring conformation from such differences in 13C chemical shift has been made by comparing the X-ray crystal structures and 13C NMR spectra of 5′-deoxyadenosylcobalamin (coenzyme B 12, AdoCbl) and cyanocobalamin (vitamin B 12, CNCbl). After elimination of carbon atoms whose chemical shifts are likely to be significantly affected by differences in the inductive effect of the Ado and CN ligands, and after consideration of differential anisotropic shielding effects in the two complexes due to the presence or absence of the Ado ligand, the difference in magnetic anisotropy of the central cobalt atom, the change in position of the axial nucleotide and differences in the magnetic anisotropy of the corrin ligand, 15 peripheral carbon atoms [C(2), C(18), C(20), C(25), C(26), C(30), C(36), C(37), C(41), C(46), C(47), C(48), C(54), C(55), C(60)] emerge as candidate “reporter” carbons whose 13C chemical shifts may be useful in deducing conformational differences in cobalt corrinoids. Application of this method to adeninylpropylcobalamin (AdePrCbl), for which the X-ray crystal structure and absolute NMR assignments are known, correctly predicts the gross conformational differences between the corrin ring of AdePrCbl and that of CNCbl. Use of these reporter carbon chemical shifts suggests that in NpCbi +, the fold angle, defined as the angle between the “northern” and “southern” planes of the corrin ring, is reduced relative to AdoCbi +. Comparison of the chemical shifts of the reporter carbon atoms in NpCbi + and Np-13-epiCbi + suggests that the fold angle in the former is larger than that for the latter.

Nuclear magnetic relaxation characterization of irradiated Fricke solution

The spin-lattice relaxation rate R1(= T1(-1) of irradiated Fricke solution was studied as a function of the absorbed dose D. The R1 increases linearly with dose up to D approximately 400 Gy after which the response saturates. A model describing the R1 of a solution of either ferrous (Fe2+) or ferric (Fe3+) ions is presented; it is based on the spin relaxation of protons on water molecules in the bulk and protons on water molecules in the coordination shells of the ions with fast exchange occurring between the two water environments. All inherent relaxation parameters of the different proton groups are determined empirically at NMR frequencies of 9 and 25 MHz. An extension of the model is made to describe the spin-lattice relaxation behavior of irradiated Fricke solution. Good agreement between model predictions and experimental results is observed. The model relates the spin-lattice relaxation rate of a Fricke dosimeter to the chemical yield of ferric ion, thus potentially creating an absolute NMR dosimetry technique. Various practical aspects of the NMR-Fricke system, such as the optimal initial ferrous concentration and the NMR frequency dependence of the sensitivity, are described.