Insertion of a Nontrigonal Phosphorus Ligand into a Transition Metal-Hydride: Direct Access to a Metallohydrophosphorane.

The synthesis and reactivity of an NPN-chelating ligand containing a nontrigonal phosphorous triamide center (L1 = P(N( o-N(2-pyridyl)C6H4)2) is reported. Metalation of L1 with RuCl2(PPh3)3 gives RuCl2(PPh3)(L1) (2). By contrast, metalation of L1 with RuHCl(CO)(PPh3)3 yields RuCl(CO)(PPh3)(L1H) (3), a chelated 10-P-5 ruthenahydridophosphorane, via net insertion into the Ru-H bond. Hydride abstraction from 3 with Ph3CPF6 gives [RuCl(CO)(PPh3)(L1)]PF6 (4); reaction of 4 with NaBH4 returns 3.

Adsorption behavior of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin on pristine and doped black phosphorene: A DFT study.

Polychlorinated dibenzo-p-dioxins (PCDDs) are highly toxic to humans. The search for novel and effective methods and materials for detecting or removing these gas pollutants is becoming more important and urgent. With its high specific surface area, abundance, and variety of potential applications, phosphorene has attracted much research interest. In this study, density functional theory was used to study the interactions between a doped phosphorene sheet and a tetrachlorodibenzo-p-dioxin (TCDD) molecule. The initial configurations of the TCDD and metallic (Ca or Ti) or nonmetallic (S and Se) dopants were investigated during the TCDD-phosphorene interaction study. Adsorption energy, isosurface of electron density difference, and density of states analysis were utilized to explore the interactions between TCDD and phosphorene. The results indicated that Ca dopant effectively improved the interaction between TCDD and phosphorene. Se dopant reduced the interaction between TCDD and phosphorene. Combining interactions between TCDD and the pristine, Ca-doped, and Se-doped phosphorenes, phosphorene could be a promising candidate for TCDD sensing and removal.

Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: implications for the Pro-Tide approach.

Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro-drug approach, Pro-Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6-311+G** level of theory for the plausible mechanisms of action considered. In the five-membered ring case, transition state theory demonstrated how the overall, gas-phase, mechanism of action could be split into two in-line addition-elimination (A-E) steps separated by a penta-coordinate phosphorane intermediate. The difference between five-membered and six-membered ring first A-E was also explored, revealing a single step, unimolecular reaction for the six-membered ring A-E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A-E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro-Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate.

Application of 31P NMR spectroscopy and chemical derivatization for metabolite profiling of lipophilic compounds in human serum.

New methods for obtaining metabolic fingerprints of biological samples with improved resolution and sensitivity are highly sought for early disease detection, studies of human health and pathophysiology, and for better understanding systems biology. Considering the complexity of biological samples, interest in biochemical class selection through the use of chemoselective probes for improved resolution and quantitation is increasing. Considering the role of lipids in the pathogenesis of a number of diseases, in this study fingerprinting of lipid metabolites was achieved by (31)P labeling using the derivatizing agent 2-chloro-4,4,5,5-tetramethyldioxaphospholane. Lipids containing hydroxyl, aldehyde and carboxyl groups were selectively tagged with (31)P and then detected with good resolution using (31)P NMR by exploiting the 100% natural abundance and wide chemical shift range of (31)P. After standardizing the reaction conditions using representative compounds, the derivatization approach was used to profile lipids in human serum. The results show that the (31)P derivatization approach is simple, reproducible and highly quantitative, and has the potential to profile a number of important lipids in complex biological samples.

Biologically relevant phosphoranes: synthesis and structural characterization of glucofuranose-derived phosphoranes with penta- and hexacoordination at phosphorus.

Carbohydrate-based phosphoranes were synthesized by reacting the appropriate diphenol with phosphorus trichloride followed by the addition of chloralose to form 1 and by the addition of isopropylidene-D-glucofuranose to form 2 and 3. Phosphorane 4 was obtained by reacting 1,2-O-isopropylidene-alpha-D-glucofuranosyl-3,5,6-phosphite (13) with a diphenol. For the synthesis of 5-9, the appropriate phosphite was reacted with isopropylidene-glucofuranose. X-ray analyses of 1-9 were carried out successfully. Hexacoordinated structures resulted via oxygen donor action at phosphorus in the cases of phosphoranes 1-3 and via sulfur donor action for phosphoranes 4-6. Trigonal bipyramidal structures formed for 7-9 with the carbohydrate components occupying axial-equatorial sites. The eight-membered ring of the diphenol moiety with weak or no donor groups in 7-9 occupied diequatorial sites of the trigonal bipyramid. Solution NMR data are in agreement with the assigned solid-state structures. Isomerism between penta- and hexacoordination is present in solution for 7. The isomerism observed for 7 and our previous study showing a rapid exchange process that reorients the carbohydrate component of the trigonal bipyramidal phosphorane suggest that these biophosphoranes may serve as models for active sites of phosphoryl-transfer enzymes. At an active site, this type of pseudorotational behavior provides a mechanism that could bring another active site residue into play and account for a means by which some phosphoryl-transfer enzymes express promiscuous behavior.

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction.

Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.

Solid-state nuclear magnetic resonance investigations on chlorocyclophosphazenes.

The present study deals with solid-state nuclear magnetic resonance (NMR) investigations on hexachlorocyclotriphosphazene (N3P3Cl6) and T and K form of octachlorocyclotetraphosphazene (N4P4Cl8). Using 31P NMR we have recorded spectra of different magic-angle spinning (MAS) frequencies and static powder spectra. By means of the analysis of spinning sideband intensities the isotropic chemical shifts and the principal values of the chemical shift tensor could be determined. Because of the interactions between phosphorus and the neighbouring chlorine nuclei in the MAS spectra of N3P3Cl6 and N4P4Cl8 more lines were found to exist than was expected with regard to the isotropic chemical shift values according to the crystallographic phosphorus positions. To support this evidence solid-state spectra of the geminally disubstituted compound 2,2,4,4-tetrachloro-6,6-bisthiophenylcyclotriphosphazene [N3P3Cl4(SPh)2] were used. In addition, by means of the individual gauched localized orbitals (IGLO) method 31P NMR chemical shifts, principal values and the orientation of the principal axes of the shielding tensor were calculated for the chlorocyclophosphazenes.