Carbon-13 NMR shielding in the twenty common amino acids: comparisons with experimental results in proteins

We have used ab initio quantum chemical techniques to compute the (13)C(alpha) and (13)C(beta) shielding surfaces for the 14 amino acids not previously investigated (R. H. Havlin et al., J. Am. Chem. Soc. 1997, 119, 11951-11958) in their most popular conformations. The spans (Omega = sigma(33) - sigma(11)) of all the tensors reported here are large ( approximately 34 ppm) and there are only very minor differences between helical and sheet residues. This is in contrast to the previous report in which Val, Ile and Thr were reported to have large ( approximately 12 ppm) differences in Omega between helical and sheet geometries. Apparently, only the beta-branched (beta-disubstituted) amino acids have such large CSA span (Omega) differences; however, there are uniformly large differences in the solution-NMR-determined CSA (Deltasigma = sigma(orth) - sigma(par)) between helices and sheets in all amino acids considered. This effect is overwhelmingly due to a change in shielding tensor orientation. With the aid of such shielding tensor orientation information, we computed Deltasigma values for all of the amino acids in calmodulin/M13 and ubiquitin. For ubiquitin, we find only a 2.7 ppm rmsd between theory and experiment for Deltasigma over an approximately 45 ppm range, a 0.96 slope, and an R(2) = 0.94 value when using an average solution NMR structure. We also report C(beta) shielding tensor results for these same amino acids, which reflect the small isotropic chemical shift differences seen experimentally, together with similar C(beta) shielding tensor magnitudes and orientations. In addition, we describe the results of calculations of C(alpha), C(beta), C(gamma)1, C(gamma)2, and C(delta) shifts in the two isoleucine residues in bovine pancreatic trypsin inhibitor and the four isoleucines in a cytochrome c and demonstrate that the side chain chemical shifts are strongly influenced by chi(2) torsion angle effects. There is very good agreement between theory and experiment using either X-ray or average solution NMR structures. Overall, these results show that both C(alpha) backbone chemical shift anisotropy results as well as backbone and side chain (13)C isotropic shifts can now be predicted with good accuracy by using quantum chemical methods, which should facilitate solution structure determination/refinement using such shielding tensor surface information.     

Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections

The main factors affecting the accuracy and computational cost of the calculation of ³¹P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second‐order Møller–Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of ³¹P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS‐2 or larger, and those of Pople, 6‐311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta‐zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of ³¹P NMR chemical shifts within the 1–2‐ppm error. Relativistic corrections to ³¹P NMR absolute shielding constants are of major importance reaching about 20–30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1–2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO‐DFT‐KT2/pcS‐3//pcS‐2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of ³¹P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm. Copyright © 2014 John Wiley & Sons, Ltd.     

MP2 calculation of 77Se NMR chemical shifts taking into account relativistic corrections

The main factors affecting the accuracy and computational cost of the Second‐order Möller‐Plesset perturbation theory (MP2) calculation of ⁷⁷Se NMR chemical shifts (methods and basis sets, relativistic corrections, and solvent effects) are addressed with a special emphasis on relativistic effects. For the latter, paramagnetic contribution (390–466 ppm) dominates over diamagnetic term (192–198 ppm) resulting in a total shielding relativistic correction of about 230–260 ppm (some 15% of the total values of selenium absolute shielding constants). Diamagnetic term is practically constant, while paramagnetic contribution spans over 70–80 ppm. In the ⁷⁷Se NMR chemical shifts scale, relativistic corrections are about 20–30 ppm (some 5% of the total values of selenium chemical shifts). Solvent effects evaluated within the polarizable continuum solvation model are of the same order of magnitude as relativistic corrections (about 5%). For the practical calculations of ⁷⁷Se NMR chemical shifts of the medium‐sized organoselenium compounds, the most efficient computational protocols employing relativistic Dyall's basis sets and taking into account relativistic and solvent corrections are suggested. The best result is characterized by a mean absolute error of 17 ppm for the span of ⁷⁷Se NMR chemical shifts reaching 2500 ppm resulting in a mean absolute percentage error of 0.7%. Copyright © 2015 John Wiley & Sons, Ltd.     

Quantum-chemical calculations of NMR chemical shifts of organic molecules: IV. Effect of intermolecular coordination on <Superscript>31</Superscript>P NMR shielding constants and chemical shifts of molecular complexes of phosphorus pentachloride with azoles

Intermolecular coordination effects on the ³¹P NMR spectra of molecular complexes of N-vinylimidazole and 1-allyl-3,5-dimethylpyrazole with phosphorus pentachloride were studied by theoretical and experimental methods. The formation of intermolecular dative N→P bond was shown to be accompanied by upfield shift of the phosphorus resonance signal by more than 200 ppm. Appreciable contribution of relativistic effects to ³¹P NMR chemical shifts was revealed; the spin-orbital contribution to ³¹P shielding constant was estimated at >210 ppm. Consideration of solvent effect was found to be crucial while studying steric structure of molecular complexes of azoles with phosphorus pentachloride and intermolecular coordination effects on 31P NMR chemical shifts.     

NMR shielding constants in PH3, absolute shielding scale, and the nuclear magnetic moment of 31P

Ab initio values of the absolute shielding constants of phosphorus and hydrogen in PH(3) were determined, and their accuracy is discussed. In particular, we analyzed the relativistic corrections to nuclear magnetic resonance (NMR) shielding constants, comparing the constants computed using the four-component Dirac-Hartree-Fock approach, the four-component density functional theory (DFT), and the Breit-Pauli perturbation theory (BPPT) with nonrelativistic Hartree-Fock or DFT reference functions. For the equilibrium geometry, we obtained σ(P) = 624.309 ppm and σ(H) = 29.761 ppm. Resonance frequencies of both nuclei were measured in gas-phase NMR experiments, and the results were extrapolated to zero density to provide the frequency ratio for an isolated PH(3) molecule. This ratio, together with the computed shielding constants, was used to determine a new value of the nuclear magnetic dipole moment of (31)P: μ(P) = 1.1309246(50) μ(N).     

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.     

The chemical shifts of Xe in the cages of clathrate hydrate Structures I and II

We report, for the first time, a calculation of the isotropic NMR chemical shift of 129Xe in the cages of clathrate hydrates Structures I and II. We generate a shielding surface for Xe in the clathrate cages by quantum mechanical calculations. Subsequently this shielding surface is employed in canonical Monte Carlo simulations to find the average isotropic Xe shielding values in the various cages. For the two types of cages in clathrate hydrate Structure I, we find the intermolecular shielding values [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-214.0 ppm, and [sigma(Xe@5(12)6(2) cage)-sigma(Xe atom)]=-146.9 ppm, in reasonable agreement with the values -242 and -152 ppm, respectively, observed experimentally by Ripmeester and co-workers between 263 and 293 K. For the 5(12) and 5(12)6(4) cages of Structure II we find [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-206.7 ppm, and [sigma(Xe@5(12)6(4) cage)-sigma(Xe atom)]=-104.7 ppm, also in reasonable agreement with the values -225 and -80 ppm, respectively, measured in a Xe-propane type II mixed clathrate hydrate at 77 and 220-240 K by Ripmeester et al.     

(α-Phosphoryl Carbanions. Searching of Course of Wittig-Horner Reaction by 31P Low Temperature NMR

Abstract

Continuing our studies on utilization of the Wittig-Horner reaction in organic synthesis, we have examined reactivity of α-lithium derivatives of several phosphonates towards carbonyl compounds, by ³¹P NMR at low temperature (from -100°C to r.t.). The chemical shifts δ [ppm] of a few representative phosphonates (1), carbanions (2) and betains (3) will be given.     

Solid-State Nuclear Magnetic Resonance Techniques for the Structural Characterization of Geminal Alane-Phosphane Frustrated Lewis Pairs and Secondary Adducts

The first comprehensive solid-state nuclear magnetic resonance (NMR) characterization of geminal alane-phosphane frustrated Lewis pairs (Al/P FLPs) is reported. Their relevant NMR parameters (isotropic chemical shifts, direct and indirect ²⁷Al-³¹P spin-spin coupling constants, and ²⁷Al nuclear electric quadrupole coupling tensor components) have been determined by numerical analysis of the experimental NMR line shapes and compared with values computed from the known crystal structures by using density functional theory (DFT) methods. Our work demonstrates that the ³¹P NMR chemical shifts for the studied Al/P FLPs are very sensitive to slight structural inequivalences. The ²⁷Al NMR central transition signals are spread out over a broad frequency range (>200 kHz), owing to the presence of strong nuclear electric quadrupolar interactions that can be well-reproduced by the static ²⁷Al wideband uniform rate smooth truncation (WURST) Carr-Purcell-Meiboom-Gill (WCPMG) NMR experiment. ²⁷Al chemical shifts and quadrupole tensor components offer a facile and clear distinction between three- and four-coordinate aluminum environments. For measuring internuclear Al⋅⋅⋅P distances a new resonance-echo saturation-pulse double-resonance (RESPDOR) experiment was developed by using efficient saturation via frequency-swept WURST pulses. The successful implementation of this widely applicable technique indicates that internuclear Al⋅⋅⋅P distances in these compounds can be measured within a precision of ±0.1 Å.     

31P Sold-State NMR Investigations on Phosphonic Acids and Phosphonates

Abstract

As known from ³¹P solid-state NMR investigations of inorganic phosphates there is a correlation between chemical shift anisotropy parameters and crystal lattice parameters. For phosphonic acids and phosphonates similar correlations are not known.     

The structure of polymeric dialkyltin oxides [R2SnO] (R  Me,nBu) as probed by high-resolution solid-state 119Sn NMR

Tin-119 CP/MAS high-resolution NMR spectra have been obtained for two solid polymeric dialkyltin oxides. Values for isotropic chemical shifts and shielding tensor components are reported. The data are discussed in terms of postulated chemical structures.     

The isotropic nuclear magnetic shielding constants of acetone in supercritical water: a sequential Monte Carlo/quantum mechanics study including solute polarization

The nuclear isotropic shielding constants sigma((17)O) and sigma((13)C) of the carbonyl bond of acetone in water at supercritical (P=340.2 atm and T=673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Carlo simulations with unpolarized and in-solution polarized solute. The results show that solvent effects on the shielding constants have a significant contribution of the electrostatic interactions and that quantitative estimates for solvent shifts of shielding constants can be obtained modeling the water molecules by point charges (electrostatic embedding). In supercritical water, there is a decrease in the magnitude of sigma((13)C) but a sizable increase in the magnitude of sigma((17)O) when compared with the results obtained in normal water. It is found that the influence of the solute polarization is mild in the supercritical regime but it is particularly important for sigma((17)O) in normal water and its shielding effect reflects the increase in the average number of hydrogen bonds between acetone and water. Changing the solvent environment from normal to supercritical water condition, the B3LYP6-311++G(2d,2p) calculations on the statistically uncorrelated configurations sampled from the Monte Carlo simulation give a (13)C chemical shift of 11.7+/-0.6 ppm for polarized acetone in good agreement with the experimentally inferred result of 9-11 ppm.     

Hydroacridines: part 29. 15N NMR chemical shifts of 9-substituted 1,2,3,4,5,6,7,8-octahydroacridines and their N-oxides-Taft, Swain-Lupton, and other types of linear correlations

The (15)N NMR chemical shifts of 1,2,3,4,5,6,7,8-octahydroacridine, 12 of its 9-substituted derivatives, and of the corresponding N-oxides were measured and examined in terms of the 9-substituent effects and the effects of N-oxidation. For the 9-substituent effects, good linear correlations were found with the Taft and Swain-Lupton substituent constants, for both octahydroacridines and their N-oxides. The (15)N chemical shifts of both octahydroacridines and their N-oxides also correlate well, linearly with the (13)C chemical shifts of the para-carbons in analogously substituted benzene derivatives.Within the studied compounds, the magnitudes of the N-oxidation effects range from - 16.4 to - 27.4 ppm (shielding), and also correlate linearly with the Taft and Swain-Lupton substituent constants, as well as with the bond orders of the N(+)-O(-) bonds in the corresponding N-oxides. Furthermore, a very good linear correlation is found between the (15)N chemical shifts of octahydroacridines and those of the corresponding N-oxides. From the (15)N chemical shifts data, the Taft and Swain-Lupton substituent constants for the diacetylamino group (-NAc(2)) were evaluated in the present paper, as follows: sigma(R) = 0.07 and sigma(I) = 0.15; R = 0.08 and F= 0.20.     

31P chemical shift of adsorbed trialkylphosphine oxides for acidity characterization of solid acids catalysts

A comprehensive study has been made to predict the adsorption structures and (31)P NMR chemical shifts of various trialkylphosphine oxides (R3PO) probe molecules, viz., trimethylphosphine oxide (TMPO), triethylphosphine oxide (TEPO), tributylphosphine oxide (TBPO), and trioctylphosphine oxide (TOPO), by density functional theory (DFT) calculations based on 8T zeolite cluster models with varied Si-H bond lengths. A linear correlation between the (31)P chemical shifts and proton affinity (PA) was observed for each of the homologous R3PO probe molecules examined. It is found that the differences in (31)P chemical shifts of the R3POH(+) adsorption complexes, when referring to the corresponding chemical shifts in their crystalline phase, may be used not only in identifying Br?nsted acid sites with varied acid strengths but also in correlating the (31)P NMR data obtained from various R3PO probes. Such a chemical shift difference therefore can serve as a quantitative measure during acidity characterization of solid acid catalysts when utilizing (31)P NMR of various adsorbed R3PO, as proposed in our earlier report (Zhao; et al. J. Phys. Chem. B 2002, 106, 4462) and also illustrated herein by using a mesoporous H-MCM-41 aluminosilicate (Si/Al = 25) test adsorbent. It is indicative that, with the exception of (TMPO), variations in the alkyl chain length of the R3PO (R = C(n)H(2n+1); n > or = 2) probe molecules have only negligible effect on the (31)P chemical shifts (within experimental error of ca. 1-2 ppm) either in their crystalline bulk or in their corresponding R3POH(+) adsorption complexes. Consequently, an average offset of 8 +/- 2 ppm was observed for (31)P chemical shifts of adsorbed R3PO with n > or = 2 relative to TMPO (n = 1). Moreover, by taking the value of 86 ppm predicted for TMPO adsorbed on 8T cluster models as a threshold for superacidity (Zheng; et al. J. Phys. Chem. B 2008, 112, 4496), a similar threshold (31)P chemical shift of ca. 92-94 ppm was deduced for TEPO, TBPO, and TOPO.     

Theoretical Prediction of 31P NMR Chemical Shifts of Intermediates in Phosphoryl Ester Exchange and N → O Migration Reactions of Dialkyloxyphosphoryl Amino Acid

Based on a detailed ab initio study on the reaction mechanism of phosphoryl ester exchange and N → O migration reactions of dimethyloxyphosphoryl-threonine, ab initio GIAO magnetic shielding calculations have been carried out on the predicted stable intermediate and the corresponding reactant and product. The ³¹P NMR chemical shift of the most stable penta-coordinate phosphorus intermediate has been predicted as about –71 ppm. The theoretical results may lead to a possible way to experimentally examine our predictions and to monitor the most stable intermediate during the reaction process.     

CYCLIC OXYPHOSPHORANES

Abstract

A review on pertinent information on cyclic oxyphosphoranes is presented. Recent X-ray structures and variable temperature ¹H NMR investigations of cyclic pentaoxyphosphoranes reveals a preference for a boat conformation for saturated six-membered rings in apical-equatorial orientations of trigonal bipyramids. These studies include five-, six-, and seven-membered rings and show that the solid state structures are retained in solution. Apical-equatorial ring pseudorotations are more facile for five-membered rings, whereas ligand exchange via diequatorial ring placement is more facile for the larger rings. The importance of the apical-equatorial ring orientation for phosphorinanes appearing as trigonal bipyramidal intermediates in enzymatic reactions of cyclic AMP analogs is emphasized.     

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.     

Quantum capping potentials with point charges: a simple QM/MM approach for the calculation of large-molecule NMR shielding tensors

A simple quantum-mechanics/molecular-mechanics (QM/MM) approach for calculating NMR shielding tensors (sigma) is presented. The method involves capping the QM region with quantum capping potentials (QCPs) and representing the MM region with point charges. Test calculations on simple systems without MM charges show that calculated sigma values improve relative to the full QM results with increasing distance between the capped bond and chromophore. Calculations on the histidine amino acid and cytosine monophosphate (CMP) nucleic acid show that the use of QCPs with point charges result in mean errors in the isotropic component of sigma that are less than 1.6 ppm. The results also reveal that, contrary to previous work, the explicit effect of point charges on sigma through coupling with gauge factors, as in the gauge including atomic orbital approach, is minimal for the CMP molecule. The present QM/MM approach for calculating sigma is easy to apply and requires no code modification.