Phosphorus-oxygen Bond Research Articles

Research new type of cation-exchange resin for waste water treatment

This article presents the studies obtaining and research new polycondensation type phosphoric cation-exchange resin. The conditions for the phosphorylation of this polymer were selected from the experiments accumulated in relation to the phosphorylation reactions of low- and high-molecular compounds. The resulting polymer had an exchange capacity for a 0.1 N NaOH solution – 5,5-5,6 mEq/g and contained 16,5% phosphorus. Based on the studies carried out, the optimal conditions for the synthesis of the styrene-furfural polymer are assumed to be: the reaction temperature is 90°C, the concentration of the ZnCl2 catalyst is 0.07 mol per mole of furfural, and the molar ratio of styrene to furfural is 1:1. There was studied an interaction of the cation exchanger in Na- and H-forms with solutions of salts of copper sulfate, nickel, cobalt, sodium chloride, calcium and uranyl nitrate. In order to elucidate the mechanism of sorption of the cations of these metals, were taken the IR-spectra of the cation exchanger in the H- and Na- form, saturated with copper ions. The less dissociated phosphoric acid groups, the stronger hydrogen bond forms phosphoryl oxygen with OH-groups. Therefore, it can be expected that as the cation exchanger is saturated with sodium, the maximum of the band corresponding to the phosphorus-oxygen bond vibrations will slightly shift to longer wavelengths as a result of the destruction of the weaker hydrogen bond.

In-situ surface patch-passivation via phosphorus oxygen bond for efficient PbS colloidal quantum dot infrared solar cells

PbS colloidal quantum dots (CQDs) have been widely applied in infrared (IR) solar cells, as they can broaden the photon conversion region beyond 1100 nm, which can help promote an extra 6% of power conversion efficiency (PCE) as bottom subcells for silicon solar cell. Although halide liquid exchange is the dominant passivation strategy for CQDs, it is difficult to passivate all the surface defects, especially for IR CQD, which leaves the main limitation for improving PCE. Here, a facile in-situ solution-processed patch-passivation strategy was first proposed for developing efficient PbS CQD IR solar cells. A typical Lewis base triphenylphosphine oxide (TPPO) was added to I − /Br − capped PbS CQDs, aiming at passivation with uncoordinated Pb 2+ as a “patch-ligand”. As a result, the phosphorus oxygen bond coordination could help suppress the non-radiative recombination in CQD films. The TPPO-passivated devices delivered an IR PCE as high as 1.36% under silicon-filtered AM 1.5G, along with a promising open-circuit voltage ( V OC ) of 0.44 V, both of which are the highest among other single-junction solar cells with a band gap of ∼0.95 eV. The significant VOC and fill factor (FF) enhancement can be attributed to the decrease in defect density and faster charge transport in TPPO-passivated devices. • Triphenylphosphine oxide (TPPO) is proposed and used as a “patch-ligand” in I − /Br − capped PbS CQD solar cells. • A high IR-PCE (1100 nm cut) of 1.36% with a V OC of 0.44 V have been realized after TPPO passivation. • The effects of TPPO on defect state density and charge carrier transport are disscussed.

Theoretical consideration on phosphorus–oxygen bond formation of sterically crowded triarylphosphines and their radical cations

The phosphorus–oxygen bond formation reactions often observed for the sterically crowded triarylphosphines and their radical cations were studied by DFT calculation. The oxidations of the trimethyl-, triphenyl-, and trimesityl-phosphines to the corresponding phosphine oxides with peroxides are shown to proceed through the SN2 like transition states and the overall influence of the steric hindrance on the activation energy is limited. The reaction of the radical cation of tris(2,4,6-triisopropylphenyl)phosphine with oxygen to give the heterocyclic phosphonium cation is modeled by employing (2,6-diisopropylphenyl)diphenylphosphine and the comparison of the intermediates suggests highly exergonic nature of the reaction.

A Click Reaction Enabled by Phosphorus‐Oxygen Bond for Synthesis of Triazoles

AbstractSynthesis of various N−H triazoles via azidyl radical was achieved using diphenyl phosphoryl azide (DPPA) and internal alkynes containing carbonyl group in wet‐DMSO at 90 °C in excellent yield. Mechanistic investigations revealed that an azidyl radical was generated in the reaction medium. The driving force was probably due to the presence of the C=O group of ester or ketone in conjugation with the triple bond of the substrate. This resulted in cleavage of the phosphorus nitrogen (P−N) bond of DPPA by forming an allenic intermediate. The C=O group of the ester or ketone is a determinant factor that results in triazole as the outcome. The formation of the phosphorus oxygen bond resulted in cleavage of a strong P−N bond (617.1±20.9 kJ mol−1) of phosphoryl azidate in an additive free Click reaction of internal alkynes. Overall, good to excellent yield of N1‐H triazole scaffolds were synthesized following the protocol.

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials.

We report the results of calculations of the Gibbs energy profiles of the guanosine triphosphate (GTP) hydrolysis by the Arl3-RP2 protein complex using molecular dynamics (MD) simulations with ab initio type QM/MM potentials. The chemical reaction of GTP hydrolysis to guanosine diphosphate (GDP) and inorganic phosphate (Pi) is catalyzed by GTPases, the enzymes, which are responsible for signal transduction in live cells. A small GTPase Arl3, catalyzing the GTP → GDP reaction in complex with the activating protein RP2, constitute an essential part of the human vision cycle. To simulate the reaction mechanism, a model system is constructed by motifs of the crystal structure of the Arl3-RP2 complexed with a substrate analog. After selection of reaction coordinates, energy profiles for elementary steps along the reaction pathway GTP + H2O → GDP + Pi are computed using the umbrella sampling and umbrella integration procedures. QM/MM MD calculations are carried out, interfacing the molecular dynamics program NAMD and the quantum chemistry program TeraChem. Ab initio type QM(DFT)/MM potentials are computed with atom-centered basis sets 6-31G** and two hybrid functionals (PBE0-D3 and ωB97x-D3) of the density functional theory, describing a large QM subsystem. Results of these simulations of the reaction mechanism are compared to those obtained with QM/MM calculations on the potential energy surface using a similar description of the QM part. We find that both approaches, QM/MM and QM/MM MD, support the mechanism of GTP hydrolysis by GTPases, according to which the catalytic glutamine side chain (Gln71, in this system) actively participates in the reaction. Both approaches distinguish two parts of the reaction: the cleavage of the phosphorus-oxygen bond in GTP coupled with the formation of Pi, and the enzyme regeneration. Newly performed QM/MM MD simulations confirmed the profile predicted in the QM/MM minimum energy calculations, called here the pathway-I, and corrected its relief at the first elementary step from the enzyme–substrate complex. The QM/MM MD simulations also revealed another mechanism at the part of enzyme regeneration leading to pathway-II. Pathway-II is more consistent with the experimental kinetic data of the wild-type complex Arl3-RP2, whereas pathway-I explains the role of the mutation Glu138Gly in RP2 slowing down the hydrolysis rate.

Nonclassical Abramov Products Formed on Orifices of Cage-Opened C60 Derivatives.

By nucleophilic addition of phosphite P(OMe)3 to a cage-opened C60 derivative, α-hydrophosphate and enol phosphate were obtained as kinetic and thermodynamic products, respectively. Different from classical Abramov products bearing a phosphorus-carbon bond, these products have a phosphorus-oxygen bond. The observed anomaly originates from the fully conjugated π system, which significantly stabilizes zwitterionic intermediates bearing a phosphorus-oxygen bond. The thus formed enol phosphate was found to exhibit an intense absorption band that extended to 730 nm, reflecting the intramolecular charge-transfer transitions. We also report domino phosphorylation reactions, which gave a cage-opened C60 derivative bearing a direct P-C bond.

DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects

Here, we present the theoretical–computational modelling of the free energy barrier of the phosphodiester bond cleavage as occurring in the mesophilic variant of endonuclease I-DmoI bound to DNA. Our data, obtained by means of hybrid quantum mechanics/molecular mechanics approach, indicate that the influence of the environment, exerted by the enzyme, the solvent and the DNA, shifts the mechanism towards a more dissociative reaction pathway, compared to the unperturbed reaction. The perturbation of the environment results in an earlier transition state of hydrolysis, i.e. more similar to reagents. By such an approach, we estimate that the enzyme lowers the phosphorus–oxygen bond break free energy barrier of about 7.9 kcal/mol compared to the gas phase, which turns out to be consistent with experimental data. Such an approach points out the importance of an extended and accurate treatment of the environmental effects in the modelling of chemical reactions and confirms the reliability of our procedure in the modelling of important biochemical processes at a limited computational cost.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Adducts of Mn and Re vinylidenes with P–OR nucleophiles: Hydrolysis rather than the intramolecular Michaelis–Arbuzov rearrangement

The reactions of vinylidene complexes Ср(CO)2Mn = C=C(H)Ph (Mn1) and Cp(CO)2Re = C=C(H)Ph (Re1) with P–OR nucleophiles P(OR)R'R" (OR = R' = R" = OMe, OEt, OPri, OPh; OR = OEt, R' = R" = Ph; OR = R' = OEt, R" = Ph) proceed as nucleophilic addition to the Cα vinylidene atom to initially afford zwitter-ionic complexes Z-Ср(CO)2M¯−C[+P(OR)R'R"] = C(H)Ph which were identified by spectroscopic methods and, in some cases, their molecular structures were confirmed by X-ray diffraction. These adducts are extremely sensitive to water and hydrolyzed by water traces to afford the corresponding η2-phosphorylalkene complexes Cp(CO)2M{η2-E-HC[P(O)R'R"] = C(H)Ph}. The isotopic label experiments with D2O and H218O showed the hydrolysis to proceed with the phosphorus–oxygen bond cleavage and binding of the water hydrogen to the carbon atom bearing the > P=O group.

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.

Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates.

Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate.

Cancer-associated point mutations in Ras, in particular, at glycine 12 and glycine 13, affect the normal cycle between inactive GDP-bound and active GTP-bound states. In this work, the role of G12V and G13V replacements in the GAP-stimulated intrinsic GTP hydrolysis reaction in Ras is studied using molecular dynamics (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. A model molecular system was constructed by motifs of the relevant crystal structure (Protein Data Bank entry 1WQ1 ). QM/MM optimization of geometry parameters in the Ras-GAP-GTP complex and QM/MM-MD simulations were performed with a quantum subsystem comprising a large fraction of the enzyme active site. For the system with wild-type Ras, the conformations fluctuated near the structure ready to be involved in the efficient chemical reaction leading to the cleavage of the phosphorus-oxygen bond in GTP upon approach of the properly aligned catalytic water molecule. Dynamics of the system with the G13V mutant is characterized by an enhanced flexibility in the area occupied by the γ-phosphate group of GTP, catalytic water, and the side chains of Arg789 and Gln61, which should somewhat hinder fast chemical steps. Conformational dynamics of the system with the G12V mutant shows considerable displacement of the Gln61 side chain and catalytic water from their favorable arrangement in the active site that may lead to a marked reduction in the reaction rate. The obtained computational results correlate well with the recent kinetic measurements of the Ras-GAP-catalyzed hydrolysis of GTP.

Phosphinate Chemistry in the 21st Century: A Viable Alternative to the Use of Phosphorus Trichloride in Organophosphorus Synthesis.

Organophosphorus compounds are important in everyday applications ranging from agriculture to medicine and are used in flame retardants and other materials. Although organophosphorus chemistry is known as a mature and specialized area, researchers would like to develop new methods for synthesizing organophosphorus compounds to improve the safety and sustainability of these chemical processes. The vast majority of compounds that contain a phosphorus-carbon bond are manufactured using phosphorus trichloride (PCl3) as an intermediate. However, these reactions require chlorine, and researchers would like to avoid the use of PCl3 and develop safer chemistry that also decreases energy consumption and minimizes waste. Researchers have already proposed and discussed two primary strategies based on elemental phosphorus (P4 or Pred) or on phosphine (PH3) as alternatives to PCl3. However, phosphinates, an important class of phosphorus compounds defined as any compound with a phosphorus atom attached to two oxygens, R(1)R(2)P(O)(OR) (R(1)/R(2) = hydrogen/carbon), offer another option. This Account discusses the previously neglected potential of these phosphinates as replacements of PCl3 for the preparation of organophosphorus compounds. Because of their strong reductive properties, industry currently uses the simplest members of this class of compounds, hypophosphites, for one major application: electroless plating. In comparison with other proposed PCl3 surrogates, hypophosphorous derivatives can offer improved stability, lower toxicity, higher solubility, and increased atom economy. When their reducing power is harnessed to form phosphorus-carbon or phosphorus-oxygen bonds, these compounds are also rich and versatile precursors to organophosphorus compounds. This Account examines the use of transition metal-catalyzed reactions such as cross-coupling and hydrophosphinylation for phosphorus-carbon bond formation. Because the most important industrial organophosphorus compounds include compounds triply or quadruply bound to oxygen, I also discuss controlled transfer hydrogenation for phosphorus-oxygen bond formation. I hope that this Account will further promote research in this novel and exciting yet much underdeveloped area of phosphinate activation.

Synthesis of diterpenoid steviol derivative containing a posphorus-carbon bond on the basis of Pudovik reaction

Organophosphorus compounds involving P–C bond (phosphonolipids, phosphonopyruvic acid, phosphinothricin and its analog, etc.) are regarded usually as formal analogs of phosphates, with the difference that their biological properties (for example, anti-microbial, antiviral, anticancer activity, enzyme inhibition, etc.) are much higher and more varied due to certain difficulties of enzymatic degradation of the phosphorus–carbon bond compared with the phosphorus–oxygen bond [1, 2]. Despite this circumstance, there is a significant number of natural metabolites of high biological activity with the phosphorus–carbon bond [3]. Various methods for their preparation including the Arbuzov, Michaelis–Becker, Pudovik, and Abramov reactions have been reported [1, 2]. Isoprenoid phosphorus-containing derivatives with a P–C bond have not been found in natural sources, but the synthesis of these compounds was performed on the basis of secondary metabolites of monoterpenoid (citral, menthane, carane, pinane, bornane derivatives [4–13]), diterpenoid (abietane derivatives [14, 15]) and steroid (cholestane derivatives [16]) series. They were obtained by the Pudovik reaction of unsaturated isoprenoids (limonene, carvomenthone, camphene, αand β-pinenes) with diethyl phosphite [5, 6]; the reaction of alkali metals arylphosphides with menthyl chloride [7, 8], hydroxy derivatives of maleopimaric and fumaropimaric acids [14, 15] and cholestan-3-one [16]; the reaction of some α,β-unsaturated isoprenoid oxocompounds (citral, carvone, pinocarvone, 3-caren4-one) and nitriles of monoterpenoid series with threeand dialkylphosphites [4], dibenzylphosphine oxide [9–11] and sodium diethylphosphide [12]; the Diels– Alder reaction of α-phellandrene with trans-vinylenebis(diphenylphosphine sulfide) [13].

One-pot synthesis of phosphate diesters and phosphonate monoesters via a combination of microwave-CCl3CN–pyridine coupling conditions

Simple and convenient one-pot synthesis of a phosphorus–oxygen bond in phosphate diesters and phosphonate monoesters using trichloroacetonitrile as an activating agent and pyridine as a solvent under microwave irradiation conditions was described. This method is useful for the preparation of various biologically interesting glycophospholipids and also phosphate diesters or phosphonate monoesters containing diverse moieties such as alkyl, prenyl, and benzyl substituents.

ChemInform Abstract: Stereospecific Reduction of Menthyloxyphosphine-Boranes with One- Electron Reducing Agents.

Abstract The phosphorus-oxygen bond of diastereomerically pure menthyloxyphosphine-boranes was reductively cleaved at −78 °C by lithium naphthalenide or Li-NH 3 in excellent yields wilh almost complete retention of configuration at phosphorus.

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary (18)O kinetic isotope effects (KIEs) and solvent D(2)O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed (18)O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ((18)k(LG) = 1.034 +/- 0.004) and phosphorus-nucleophile bond formation ((18)k(NUC) = 0.984 +/- 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK(a) of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ((18)k(NUC) = 0.995 +/- 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (ca. 1.02) on deprotonation of the 2'-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary (18)O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.

ChemInform Abstract: Formation and Rearrangement of Dithioxo- and Diselenoxophosphoranes Carrying Bulky 4-t-Butyl-2,6-bis(methoxyalkyl)phenyl Groups.

Abstract [4-t-Butyl-2,6-bis(1-methoxy-1-methylethyl)phenyl]phosphine, [4-t-butyl-2,6-bis(2-methoxy-1,1-dimethylethyl)phenyl]phosphine, and [4-t-butyl-2,6-bis(3-methoxy-1,1-dimethylpropyl)phenyl]phosphine were prepared and allowed to react with sulfur or selenium, to give heterocyclic compounds containing phosphorus–oxygen bond, via rearrangement of the methyl moiety of the methoxy group.

Altered Transition State for the Reaction of an RNA Model Catalyzed by a Dinuclear Zinc(II) Catalyst

The cyclization of 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group ((18)k(lg) = 1.0064 +/- 0.0009 and (15)k = 1.0002 +/- 0.0002) and that nucleophilic bond formation occurs in the rate-determining step ((18)k(nuc) = 1.0326 +/- 0.0008). In the catalyzed reaction, larger leaving group isotope effects ((18)k(lg) = 1.0113 +/- 0.0005 and (15)k = 1.0015 +/- 0.0005) and a smaller nucleophile isotope effect ((18)k(nuc) = 1.0116 +/- 0.0010) indicate a later TS with greater leaving group bond fission and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2'-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.

New access to H-phosphonates via metal-catalyzed phosphorus–oxygen bond formation

A novel approach to H-phosphonates from hypophosphorous acid using a transfer hydrogenation process was developed. This method is atom-economical, environmentally friendly, catalytic, and efficient, leading easily to H-phosphonate monoesters or ammonium salt in moderate to good yields.

A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase

Sequence profile and fold recognition methods identified mammalian purple acid phosphatase (PAP), a member of a dimetal-containing phosphoesterase (DMP) family, as a remote homolog of human acid sphingomyelinase (ASM). A model of the phosphoesterase domain of ASM was built based on its predicted secondary structure and the metal-coordinating residues of PAP. Due to the low sequence identity between ASM and PAP (approximately 15%), the highest degree of confidence in the model resides in the metal-binding motifs. The ASM model predicts residues Asp 206, Asp 278, Asn 318, His 425, and His 457 to be dimetal coordinating. A putative orientation for the phosphorylcholine head group of the ASM substrate, sphingomyelin (SM), was made based on the predicted catalysis of the phosphorus-oxygen bond in the active site of ASM and on a structural comparison of the PAP-phosphate complex to the C-reactive protein-phosphorylcholine complex. These complexes revealed similar spatial interactions between the metal-coordinating residues, the metals, and the phosphate groups, suggesting a putative orientation for the head group in ASM consistent with the mechanism considerations. A conserved sequence motif in ASM, NX3CX3N, was identified (Asn 381 to Asn 389) and is predicted to interact with the choline amine moiety in SM. The resulting ASM model suggests that the enzyme uses an SN2-type catalytic mechanism to hydrolyze SM, similar to other DMPs. His 319 in ASM is predicted to protonate the ceramide-leaving group in the catalysis of SM. The putative functional roles of several ASM Niemann-Pick missense mutations, located in the predicted phosphoesterase domain, are discussed in context to the model.