31P Chemical Shift Research Articles

Analysis of UV and vibrational spectra (FT-IR and FT-Raman) of hexachlorocyclotriphosphazene based on normal coordinate analysis, MP2 and DFT calculations

The Raman (1400–100cm−1) and infrared (4000–400cm−1) of solid hexachlorocyclotriphosphazene, P3N3Cl6 (HCCTP) were recorded. The conformational energies were calculated using MP2 and DFT (B3LYP and B3PW91) methods utilizing a variety of basis sets up to 6-311+G(d). On the basis of D3h symmetry, the simulated vibrational spectra of P3N3Cl6 from MP2 and DFT methods were in excellent agreement with those obtained experimentally. Additionally, Frontier Molecular Orbitals and electronic transitions were predicted using steady state and time dependent DFT(B3LYP)/PCM calculations respectively, each employing the 6-311+G(d,p) optimized structural parameters. The predicted wavelengths were in excellent agreement with experimental values when CH2Cl2 was used as solvent. The 14N and 31P chemical shifts were predicted with B3LYP/6-311+G(2d,p) calculations using the GIAO technique with solvent effect modeled using the PCM method. The computed structural parameters of the planar P3N3Cl6 (D3h) agree well with experimental values from both X-ray and electron diffraction data with slight distortions observed due to lattice defects in the solid phase. The experimental/computational results favor a slightly distorted D3h symmetry for the title compound in the gas and solid phases and in solution (τPNPN and τNPNP ranged from 0.018° to 0.90°). Aided by normal coordinate analysis, and the simulated vibrational spectra utilizing MP2, B3LYP and B3PW91 methods at 6-31G(d) basis set, revised and complete vibrational assignments for all fundamentals are provided herein.

Structural disorder and the effects of aging in a phosphate glass: Results from two-dimensional 31P PASS NMR spectroscopy

The nature of the short-range structural disorder and its dependence on the fictive temperature are investigated in a phosphate glass of composition 60ZnO·40P2O5 using 31P two-dimensional phase adjusted spinning sidebands nuclear magnetic resonance (2D PASS NMR) spectroscopy. The 2D PASS experiment is shown to be a robust method for determining the correlations between the 31P isotropic shift and chemical shift tensor parameters and their distributions in this glass that allows for a remarkably detailed quantification of structural disorder. The spectra in the isotropic dimension indicate a Q-species disproportionation reaction in this glass of the type 2Q1=Q2+Q0 that is driven to the right hand side with increasing fictive temperature. Such a reaction can be a source of configurational entropy as well as a mechanism of Q-species exchange associated with viscous flow in the supercooled liquid. In the anisotropic dimension, the 31P chemical shift anisotropy (CSA) parameters and their distributions are quantified for the constituent Q-species and are found to be sensitive to the thermal history of the glass. Specifically, the span and the asymmetry parameter of the 31P chemical shift tensor decrease with lowering of the fictive temperature implying a concomitant increase in the P site symmetry resulting from the structural relaxation of the network.

Linking 31P Magnetic Shielding Tensors to Crystal Structures: Experimental and Theoretical Studies on Metal(II) Aminotris(methylenephosphonates)

The (31)P chemical shift tensor of the phosphonate group [RC-PO(2)(OH)](-) is investigated with respect to its principal axis values and its orientation in a local coordinate system (LCS) defined from the P atom and the directly coordinated atoms. For this purpose, six crystalline metal aminotris(methylenephosphonates), MAMP·xH(2)O with M = Zn, Mg, Ca, Sr, Ba, and (2Na) and x = 3, 3, 4.5, 0, 0, and 1.5, respectively, were synthesized and identified by diffraction methods. The crystal structure of water-free BaAMP is described here for the first time. The principal components of the (31)P shift tensor were determined from powders by magic-angle-spinning NMR. Peak assignments and orientations of the chemical shift tensors were established by quantum-chemical calculations from first principles using the extended embedded ion method. Structure optimizations of the H-atom positions were necessary to obtain the chemical shift tensors reliably. We show that the (31)P tensor orientation can be predicted within certain error limits from a well-chosen LCS, which reflects the pseudosymmetry of the phosphonate environment.

31P NMR study of the stoichiometry and stability of several mercury(II) halides with a phosphorus ylide in different solvents

31P NMR measurements were employed to monitor the stoichiometry and stability of complexes between HgCl2, HgBr2 and HgI2 with 4-methylbenzoylmethylenetriphenylphosphorane (L) in acetonitrile (AN), dimethylsulfoxide (DMSO), dimethylformamide (DMF) and tetrahydrofuran (THF) solvents of varying composition. In all cases studied, the variation of 31P chemical shift with the [M]/[L] mole ratio indicated the formation of 1:1 complexes. The formation constants of the resulting complexes were evaluated from computer fitting of the mole ratio data to an equation that relates the observed chemical shifts to the formation constant. In all solvents used, the stabilities of the resulting 1:1 complexes varied in the order HgCl2>HgBr2>HgI2.

Trans Influence and Steric Effect on the Distortions in Planar NiS4, NiS2PN, and NiS2P2 Chromophores

AbstractThe planar diamagnetic complexes [Ni(achdtc)2] (1),[Ni(achdtc)(PPh3)(NCS)] (2), and [Ni(achdtc)(PPh3)2]ClO4·0.5EtOAc (3) (achdtc = allylcyclohexylcarbodithioate) were prepared, characterized by elemental analysis, electronic, IR, NMR (1H, 13C, and 31P) spectroscopy and the crystal structures were determined by single‐crystal X‐ray crystallography. The characteristic thioureide bands occur at 1478, 1503, and 1507 cm–1 for 1, 2, and 3, respectively and the corresponding 13C chemical shifts are observed at 207.67, 204.16, and 202.31 ppm. 31P chemical shifts are observed at δ = 29.24 and 22.73 ppm for 2 and 3, respectively, indicating a strong interaction. Electronic spectral bands are observed at 480, 483, and 475 nm for 1, 2, and 3, corresponding to d → dxy/d transitions. Ni–S distances are asymmetric. The trans influence of PPh3 elongates the Ni–S bonds. The decrease in the S–Ni–S bite angle in 2 [78.80(16)°] and in 3 [78.36(2)°] compared to that observed in 1 [79.42(3)°] is due to the steric crowding of PPh3 around the central metal atom. A comparison of the bond parameters of compounds 1–3 shows a change in the arrangement from a planar NiS4 chromophore to distorted planar NiS2P2 chromophores. The observed distortion from planar to tetrahedral arrangement is influenced by the bulky triphenylphosphine ligand.

Complexation of the [Rh(NH3)5H2O]3+ ion in aqueous solutions of H3PO4 based on 31P NMR data

The kinetics of the reaction between the [Rh(NH3)5H2O]3+ ion and H3PO4 was studied by 31P NMR at 323–343 K (Ea = 100.9 ± 0.3 kJ/mol, lnA = 35.7 ± 0.1). An empirical dependence of the 31P chemical shift on the equilibrium pH was found. The acid dissociation constants of the coordinated H2PO4− (3.9) and H PO42− ions (9.1) were estimated. The chemical shifts of the [Rh(NH3)5H2PO4]2+, [Rh(NH3)5HPO4]+, and [Rh(NH3)5PO4]0 complex ions were 8.38 ± 0.03, 10.76 ± 0.05, and 13.63 ± 0.05 ppm, respectively.

The Structure of the XPF-ssDNA Complex Underscores the Distinct Roles of the XPF and ERCC1 Helix- Hairpin-Helix Domains in ss/ds DNA Recognition

Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.

NMR Determination of Protein Partitioning into Membrane Domains with Different Curvatures and Application to the Influenza M2 Peptide

The M2 protein of the influenza A virus acts both as a drug-sensitive proton channel and mediates virus budding through membrane scission. The segment responsible for causing membrane curvature is an amphipathic helix in the cytoplasmic domain of the protein. Here, we use 31P and 13C solid-state NMR to examine M2-induced membrane curvature. M2(22–46), which includes only the transmembrane (TM) helix, and M2(21–61), which contains an additional amphipathic helix, are studied. 31P chemical shift lineshapes indicate that M2(21–61) causes a high-curvature isotropic phase to both cholesterol-rich virus-mimetic membranes and 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayers, whereas M2(22–46) has minimal effect. The lamellar and isotropic domains have distinct 31P isotropic chemical shifts, indicating perturbation of the lipid headgroup conformation by the amphipathic helix. 31P- and 13C-detected 1H T2 relaxation and two-dimensional peptide-lipid correlation spectra show that M2(21–61) preferentially binds to the high-curvature domain. 31P linewidths indicate that the isotropic vesicles induced by M2(21–61) are 10–35 nm in diameter, and the virus-mimetic vesicles are smaller than the 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles. A strong correlation is found between high membrane curvature and weak drug-binding ability of the TM helix. Thus, the M2 amphipathic helix causes membrane curvature, which in turn perturbs the TM helix conformation, abolishing drug binding. These NMR experiments are applicable to other curvature-inducing membrane proteins such as fusion proteins and antimicrobial peptides.

Disentanglement of Heterogeneous Solid-State NMR Parameter Measurements in Model Membranes

Solid-state NMR is ideal for studying membranes and membrane-associated proteins and peptides that are difficult or impossible to study by other means. Disorder and heterogeneity that are typical of these types of samples, however, makes analysis of the resulting challenging. Examples include (a) heterogeneous distributions of 31P chemical shift tensor parameters that report on phospholipid headgroup disorder; and (b) distributions of internuclear distances measured by rotational-echo double-resonance (REDOR), for example, of heteronuclear pairs within membrane-associated peptides. A method that uses an adaptation of Boltzmann statistics maximum entropy for a model-free approach to analysis of this type of troublesome data provides the means to characterize the distributions of such heterogeneous systems.In the case of REDOR data, the method can reveal multiple distances with relatively few data points, which is of particular benefit in application to biological systems where signal lifetimes are limited by relaxation. This has been recently extended to include spin systems for which the observe nucleus is dipolar coupled to two or three dephasing nuclei. The method reverses the practice where preconceived internuclear distance models are slowly optimised to better “fit” experimental REDOR data, and instead provides the information necessary to construct models based on unbiased data analysis. Examples include application to membrane-associated Alzheimer's β peptide. In the case of chemical shift tensor analysis, we have applied the method to arbitrarily complex phospholipid mixtures for analysis of subtle perturbations, for example, by association of antimicrobial peptides with model membrane systems.

Quantum-chemical calculation of NMR chemical shifts of organic molecules: III. Intramolecular coordination effects on the 31P NMR chemical shifts of phosphorylated N-vinylazoles

Theoretical and experimental studies on magnetic shielding of the phosphorus nucleus in trichloro-[2-(1H-pyrazol-1-yl)ethenyl]phosphonium hexachlorophosphate(V) and 1,1,1,1-tetrachloro-1H-1λ6-pyrazolo-[1,2-a][1,2,3]diazaphosphol-8-ium-1-ide showed that intramolecular coordination of the phosphorus atom in the chlorophosphonium group to the nitrogen atom in the pyrazole ring leads to upfield shift of the phosphorus signal (to δP 170 ppm) and that the contribution of the spin-orbital contribution to the 31P chemical shift reaches 15%. Relativistic effects and effects of the medium are determining in the theoretical calculation of 31P NMR chemical shifts.

Synthesis, NMR and single crystal X-ray structural studies on planar NiS4 and NiS2PN chromophores: Steric and electronic effects

The planar nickel(II) complexes [Ni(echdtc)2] (1) and [Ni(echdtc)(PPh3)(NCS)] (2), (where echdtc=ethylcyclohexyl dithiocarbamate) have been prepared, characterized by elemental analysis, electronic, IR and NMR (1H, 13C, and 31P) spectra, and their structures have been determined by single crystal X-ray crystallography. Both the complexes are diamagnetic and planar. The characteristic thioureide bands occur at 1485 and 1504cm−1 for (1) and (2), respectively. NMR spectra of the complexes show the (N)13CS2-chemical shifts at 206.29 and 202.68ppm for (1) and (2), respectively. The 31P chemical shift for (2) was observed at 22.51ppm, indicating a strong interaction. Electronic spectra of complexes (1) and (2) show signature bands at 412 and 478nm, corresponding to dz2→dxy/dx2–y2 transitions. Single crystal X-ray structures of [Ni(echdtc)2] (1) and [Ni(echdtc)(PPh3)(NCS)] (2) indicate that the central atom is in a planar environment in the complexes. In both complexes, the Ni–S distances are significantly different due to steric and electronic effects of the donors. Complex (2) is asymmetric with respect to the Ni–S distances, attributed to the trans influence exerted by PPh3 and NCS−. The decrease in the S–Ni–S bite angle [78.63(3)°] for (2) compared to that of (1) [79.19(2)°] is due to steric crowding around the metal center. The P–Ni–S angle, 170.91(3)°, clearly shows the steric influence of the triphenylphosphine, which contrasts well with the much cramped S–Ni–S angle of 78.63(3)°.

Rapid quantitative determination by 13C NMR of the composition of acetylglycerol mixtures as byproduct in biodiesel synthesis

Commercially available partly acetylated glycerols (mono- and diacetin) are mixtures of glycerol, 1- and 2-acetylglycerol, 1,2- and 1,3-diacetylglycerol, and triacetin. Diacetin and monoacetin are by-products of the biodiesel and triacetin production using glycerol esterification with acetic acid or triglyceride interesterification with methyl acetate. Usually, primary analytical methods involve chromatography (HPLC or GC), spectroscopy (MS or NIR), and wet chemical techniques (potentiometric, iodometric titration) which are often time-consuming due to sample preparation, extended analysis time and/or complicated data analysis. Moreover, these methods require pure mono- and diacetin as standard, which are commercially unavailable.In this work, a complete 31P and 13C chemical shift data for glycerol, mono-, di- and triacetin (including isomers) allows for the identification and quantification of these components in the commercial mixtures. This experimental protocol allows for rapid analysis of mixtures that include these six components. Quantitative 31P NMR and 13C NMR results were validated to those obtained with other analytical methods, such as GC and HPLC-ELSD. 13C NMR is preferred due to allows to measure the content of triacetin, which has no free hydroxyl group, and no signal was detected by 31P NMR.

Prediction of 31P-NMR Chemical Shifts Using Empirical Models with Modest Methods and Optimally Selected Basis Sets

The performance of the ab initio and density functional theory (DFT) functional, B3LYP and PBEPBE, in conjunction with selected basis sets for the prediction of 31P shielding constants for small phosphorous-containing molecules is assessed. The effects of applied factors are discussed. By including the electron correlation treatment, B3LYP and PBEPBE are the most accurate methods to compute the chemical shielding for a set of small phosphines that was studied. Also, additional improvements of DFT were obtained by empirical scaling of basis sets in calculation of chemical shifts. For molecules containing only phosphorous and carbon atoms with sp3 hybridization, the PBEPBE/6-311G(d,p) level of theory has been shown to provide reliable 31P chemical shifts. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file. GRAPHICAL ABSTRACT

Crystalline O, O′-di- sec-butyl and O, O′-diethyl dithiophosphate platinum(II) complexes: Synthesis, 13C and 31P CP/MAS NMR, single crystal X-ray diffraction studies and thermal behaviour

Crystalline bis( O, O′-di- sec-butyldithiophosphato)platinum(II) was prepared and studied by means of 13C, 31P CP/MAS NMR spectroscopy and single-crystal X-ray diffraction. The unit cell of the platinum(II) compound is comprised of one centrosymmetric mononuclear molecule [Pt{S 2P(O- sec-C 4H 9) 2} 2], in which the dithiophosphate groups display structural equivalence in both 31P NMR and XRD data. A pair of the dithiophosphate ligands exhibit the same S, S′-bidentate chelating structural function and form two planar four-membered chelate rings, [PtS 2P], in this molecule. The planar configuration of the [PtS 4] chromophore in structure 1 is governed by the dsp 2-hybrid state of platinum(II). The structural states of the dithiophosphate groups in two different samples of complex 1 (one crystallised from ethanol and the other one precipitated from an aqueous solution) are all characterised by almost rhombic 31P chemical shift tensors. The observed essential dispersion of the 31P NMR chemical shift is caused by a coexistence of six optical isomers of molecule 1. The thermal behaviour of this compound was studied by means of simultaneous thermal analysis (a combination of TG and DSC) under an argon atmosphere. The thermal behaviour shows that the mass of 1 is lost in three steps, involving successive thermal decompositions of the organic and inorganic parts of this compound with platinum(II) dithio- meta-phosphate and reduced metallic platinum as the intermediate and the final products, respectively.

Overestimation of the importance of phytate in NaOH–EDTA soil extracts as assessed by 31P NMR analyses

Solution 31P NMR analysis of NaOH–EDTA extracts is the most widely used method for determining the speciation of organic P in soils. In this paper, we bring together results from a number of our recent studies that highlight some of the difficulties in obtaining accurate quantitative results and propose that these difficulties may have resulted in the systematic overestimation of soil phytate concentrations. The first problem is peak identification, which is complicated by variations in chemical shift with pH and ionic strength, and the impracticality of the primary 31P chemical shift reference (85% H 3PO 4). Unambiguous peak assignment can be achieved by spiking suspected compounds directly into soil extracts prepared for NMR analysis; this ensures native and added compounds experience exactly the same chemical environment. The second problem is quantifying NMR signal for individual species in the crowded and overlapping phosphate monoester region. Spectral deconvolution has been employed for this purpose, but very different results are obtained depending on whether or not the fitting procedure includes a broad signal that probably comes from P in large, “humic” compounds. In particular, failing to consider this broad peak in the deconvolution procedure results in overestimation of small organic P compounds, including phytate. The ready decomposition of phytate is demonstrated with an incubation experiment in which phytate added at various concentrations to a calcareous soil is shown to be decomposed to produce orthophosphate. The decomposition follows a first order exponential decay with a half-life of 4–8 weeks.

Spectroscopic characterization and Ab initio calculations of new diazaphosphole and diazaphosphorinane

Phosphoryl chloride is used as a starting material to synthesize new diazaphosphole, Open image in new window (1) and diazaphosphorinane, Open image in new window (2). The products are characterized by 1H, 13C, 31P NMR, and IR spectroscopy. A high value 2J(PNH) = 17.0 Hz, 17.2 Hz is measured for two non-equivalent NH protons of endocyclic nitrogen atoms in compound 1, while it greatly decreases to 4.5 Hz in 2. Also, great amounts are obtained for two 2J(P,C) as well as two 3J(P,C) in the 13C NMR spectrum of 1, but they are zero in 2. Here, the effect of ring strain and ring size on the structural and spectroscopic parameters is observed. The 31P NMR spectra reveal that δ(31P) of compound 1 is far much more downfield (12.63 ppm) relative to that of compound 2 (−10.39 ppm). Furthermore, ab initio quantum chemical calculations are performed to optimize the structures of these molecules by density functional theory (B3LYP) and Hartree-Fock (HF) methods, using the standard 6−31+G** basis set. The stabilization energies are calculated by the equation ΔEstabilization = Emolecule − ΣEi, where i = atom. To obtain the atomic hybridizations, NBO computations are made at the B3LYP/6−31+G** level. Also, by NMR calculations the 1H, 13C, 31P chemical shifts are obtained and compared with the experimental ones.

Disentanglement of Heterogeneous Dynamics in Mixed Lipid Systems

Static phosphorous NMR has been a powerful technique for the study of model supramolecular phospholipid structures. Application to natural lipid bilayers with complex compositions, however, has been severely limited by the difficulty in deconvoluting overlapping broad lineshapes. We demonstrate a solution to this problem, using a global fit to a few slow magic-angle spinning spectra, in combination with an adaptation of Boltzmann statistics maximum entropy. The method provides a model-free means to characterize a heterogeneous mix of lipid dynamics via a distribution of 31P chemical shift anisotropies. It is used here to identify clear changes in membrane dynamics of a phosphatidylethanolamine and phosphatidylglycerol mixture, mimicking an Escherichia coli membrane upon addition of just 2% of the antimicrobial peptide maculatin 1.1. This illustration opens the prospect for investigation of arbitrarily complex natural lipid systems, important in many areas of biophysical chemistry and biomedicine.

Acidic Strengths of Brønsted and Lewis Acid Sites in Solid Acids Scaled by 31P NMR Chemical Shifts of Adsorbed Trimethylphosphine

The validity of using 31P NMR of adsorbed trimethylphosphine (TMP) as a probe molecule for discerning the types (Brønsted vs Lewis) and strengths of acid sites in solid acid catalysts have been studied by density functional theory (DFT) calculations. Brønsted acid sites with varied acidic strengths covering from weak, strong, to superacid, mimicked by 8T zeolite cluster models having different Si−H bond lengths and hence proton affinities, were examined together with Lewis acid systems having different metallic centers, e.g., BClnF3−n (n = 0−3), AlClnF3−n (n = 0−3), and TiClnF4−n (n = 0−4) and their mixed halides. The theoretical 31P chemical shifts predicted for the hydrogen-bonded TMP···H complex and the TMPH+ adducts were −61 ± 1 and −3 ± 1 ppm, respectively, in good agreement with the experimental data. For the TMP−Lewis acid complex, a linear correlation between the calculated 31P chemical shifts and corresponding binding energies was observed for the B-, Al-, and Ti-containing Lewis acids, respectively, indicating the feasibility of using the 31P chemical shift of adsorbed TMP as a scale for Lewis acidic strength.

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-chemical calculations of NMR chemical shifts of organic molecules: II. Influence of medium, relativistic effects, and vibrational corrections on phosphorus magnetic shielding constants in the simplest phosphines and phosphine chalcogenides

The influence of solvent nature, relativistic effects, and vibrational corrections on the accuracy of calculation of 31P chemical shifts of the simplest phosphines, phosphine oxides, phosphine sulfides, and phosphine selenides was studied. Consideration of the above factors at the stage of both geometry optimization and calculation of magnetic shielding constants was found to appreciably improve the accuracy of calculation of 31P NMR chemical shifts in the series of phosphines and phosphine chalcogenides.