Pentacoordinated Phosphorus Compounds Research Articles

Stable Open-Shell Phosphorane Based on a Redox-Active Amidodiphenoxide Scaffold.

The synthesis and redox reactivity of pentacoordinate phosphorus compounds incorporating a redox-active ONO amidodiphenoxide scaffold [ONO = N,N-bis(3,5-di-tert-butyl-2-phenoxide)amide] are described. Dichloro- and diphenylphosphoranes, 2·Cl2 and 2·Ph2, respectively, are synthesized and crystallographically characterized. Cyclic voltammograms of 2·Cl2 show only a single irreversible oxidation (Epa = +0.83 V vs Cp2Fe0/+), while the diphenyl analogue 2·Ph2 is reversibly oxidized at lower applied potential (E1/2 = +0.47 V vs Cp2Fe0/+). Chemical oxidation of 2·Ph2 with AgBF4 produces the corresponding radical cation [2·Ph2]•+, where electron paramagnetic resonance spectroscopy and density functional theory calculations reveal that the unpaired spin density is largely ligand-based and is highly delocalized throughout the ONO framework of the paramagnetic species. The solid-state structures indicate only minor geometrical changes between the neutral 2·Ph2 and oxidized [2·Ph2]•+ species, consistent with fast self-exchange electron transfer, as observed by NMR line-broadening experiments.

Investigation of the C–N bond rotation of spirophosphorane carbamates by dynamic NMR and DFT calculation

Spirophosphorane carbamates are a new type of pentacoordinate phosphorus compounds. In order to explore internal rotation, the dynamic 1H NMR, 31P NMR and molecular theory calculations were employed to investigate the rotation barriers of the N–C(O) bond of symmetrical and asymmetrical spirophosphorane carbamates. The Gibbs free activation, ΔG≠, was calculated by Eyring equation. The results showed that the rotation barriers of spirophosphorane carbamates were about 16–18 kcal/mol, and the rotation isomers coexisted at room temperature. Moreover, it was found that the benzyl group attached to amide nitrogen increased the C–N bond rotation barriers of spirophosphorane carbamates. Furthermore, the preferred conformation of spirophosphorane carbamates was presumed by density functional theory (DFT), and the conformation of solid state were also confirmed by X-ray diffraction analysis.

Progress in the Atherton-Todd reaction and its stereochemical mechanism

In this review, we summarize the literatures in the latest decades on the Atherton-Todd reaction of the tetracoordinated and pentacoordinated phosphorus compounds containing P-H bond. Especially, the review focuses on the development of the stereochemical mechanism of the Atherton-Todd reaction. Although the reaction mechanism has been investigated for decades after the discovery of the reaction, the earlier studies mainly concentrated on the reaction intermediate. Up to the past dozen years, the stereochemical mechanism of the Atherton-Todd reaction was studied in detail. However, up to now, there is few review and introduction to the stereochemical mechanism of the Atherton- Todd reaction. We hope this article could compensate for this limitation, and it not only summarizes the general Atherton-Todd reaction, but also introduces the recent research results on the stereochemical mechanism. It is considered that the further investigation on the stereochemical mechanism of the Atherton-Todd reaction will be helpful to design and synthesize the novel tetracoordinated or pentacoordinated compounds with phosphorus chiral centers.

ChemInform Abstract: Pentacoordinated and Hexacoordinated Compounds

AbstractReview: synthetic routes to pentacoordinated phosphorus compounds by Wittig reactions s well as preparation of hexacoordinated phosphorus compounds by reaction of alk ylenechlorophosphites with hydroxylated bisazomethines; 17 refs.

Reaction pathway for reactivation and aging of paraoxon-inhibited-acetylcholinesterase: A QM/MM study

The organophosphorus pesticide paraoxon is an acetylcholinesterase (AChE) inhibitor which can destroy the function of acetylcholinesterase. In this work, the reactivation and aging mechanism of paraoxon-inhibited AChE complex were studied by using the QM/MM method. Geometries of the stationary points were optimized at the B3LYP/6-31G(d)//CHARMM22 level and the single-point energies were calculated at the B3LYP/6-311++G(d,p)//CHARMM22 level. Studies show that the reactivation process of paraoxon–AChE complex involves the formation, reorganization and dissociation of the trigonal bipyramidal shaped pentacoordinated phosphorus compound, and the formation of this phosphorus compound is the rate determining step with an energy barrier of 29.0kcal/mol. The aging process of paraoxon–AChE complex proceeds via a carbocation shaped transition state with an energy barrier of 26.8kcal/mol. Moreover, the nucleophilic water molecule between residue His447 and Glu202 is more feasible to participate in the reactivation process than aging process, whereas the aging process is promoted by the water molecule on the other side of residue Glu202. Furthermore, Gly122 is the major promoter for both dephosphorylation and dealkylation process, while Gly121 and Tyr133 are the main obstacles for dephosphorylation and dealkylation process, respectively.

Chemistry of pentacoordinated anti-apicophilic phosphorus compounds

Abstract Since the synthesis of the first pentacoordinated organophosphorus compound, Ph5P, by Wittig, the chemistry of pentacoordinated phosphorus compounds has been extensively expanded. Pentacoordinated phosphorus compounds usually take a trigonal bipyramidal structure with two distinctive sites; apical and equatorial positions. In the trigonal bipyramidal structure, electronegative and small substituents prefer the apical positions. Such properties are widely recognized as the apicophilicity rule. However, several examples breaking the apicophilicity rule have been reported in the past few decades and novel properties and reactivities of these new classes of compounds have been found. In this review, the synthesis of novel pentacoordinated phosphoranes with anti-apicophilic arrangement will be introduced, as well as their structures, spectroscopic properties, and reactivities.

New feature in the chiral bisamino acyl pentacoordinate spirophosphoranes

Pentacoordinate phosphorus compounds as intermediates or transition state species are proposed in numerous biological processes.In this thesis,sixteen isomers of chiral bisamino acyl pentacoordinate spirophosphoranes derived from L-or D-amino acids were synthesized and separated,respectively.To investigate the stereochemistry of chiral bisamino acyl pentacoordinate spirophosphoranes systematically,these isomers were characterised by nuclear magnetic resonance(NMR),single crystal X-ray diffraction,circular dichroism(CD),and the theoretical calculation of quantum chemistry.

Determination of the Absolute Configuration of Pentacoordinate Chiral Phosphorus Compounds in Solution by Using Vibrational Circular Dichroism Spectroscopy and Density Functional Theory

Vibrational circular dichroism (VCD) spectroscopic measurements and density functional theory (DFT) calculations have been used to obtain the absolute structural information about four sets of diastereomers of pentacoordinate spirophosphoranes derived separately from l- (or d-) valine and l- (or d-) leucine for the first time. Each compound contains three stereogenic centers: one at the phosphorus center and two at the amino acid ligands. Extensive conformational searches for the compounds have been carried out and their vibrational absorption (VA) and VCD spectra have been simulated at the B3LYP/6-311++G** level. Although both VA and VCD spectra are highly sensitive to the structural variation of the apical axis, that is, the O-P-O or N-P-O arrangement, the rotamers generated by the aliphatic amino side chains show little effect on both. The dominant experimental VCD features in the 1100-1500 cm(-1) region were found to be controlled by the chirality at the phosphorus center, whereas those at the C=O stretching region are determined by the chirality of the amino acid ligands. The good agreement between the experimental VA and VCD spectra in CDCl(3) solution and the simulated ones allows us to assign the absolute configurations of these pentacoordinate phosphorus compounds with high confidence. This study shows that the VCD spectroscopy complemented with DFT calculations is a powerful and reliable method for determining the absolute configurations and dominating conformers of synthetic phosphorus coordination complexes in solution.

ChemInform Abstract: Synthesis and Properties of Pentacoordinated Phosphorus Compounds with Antiapicophilic Arrangement

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Diastereomers of the pentacoordinate chiral phosphorus compounds in solution: absolute configurations and predominant conformations

The absolute structural information about four sets of diastereomers of pentacoordinate spirophosphoranes, derived separately from L (or D)-phenylglycine and L (or D)-phenylalanine, has been obtained by using vibrational circular dichroism (VCD) spectroscopic measurements and density functional theory (DFT) for the first time. Each compound contains a stereogenic centre at the phosphorus center and two at the amino acid ligands. Geometric searches at the B3LYP/6-311++G** level have been performed for all possible low energy conformers whose vibrational absorption (VA) and VCD spectra have also been simulated. The good agreement between the experimental VA and VCD spectra in the dimethyl sulfoxide (DMSO) solution and the simulated ones allows us to assign the absolute configurations and predominant conformations of these pentacoordinate phosphorus compounds with high confidence. Solvent effects have been examined by using both the experimental measurements and theoretical calculations. The implicit continuous polarization model and the explicit solute-solvent intermolecular hydrogen-bonding model have been considered to understand the effects of DMSO on the spectra observed. The influence of basis sets and different functionals on the VA and VCD spectra of this type of coordination compounds has also been investigated.

アピコフィリシティー則に反した５配位リン化合物の合成と性質

Since the synthesis of the first pentacoordinated organophosphorus compound, Ph5P, by Wittig, the chemistry of pentacoordinated phosphorus compounds has been extensively expanded. Pentacoordinated phosphorus compounds usually take a trigonal bipyramidal structure with two distinctive sites; apical and equatorial positions. In the trigonal bipyramidal structure, electronegative and small substituents prefer the apical positions. Such properties are widely recognized as the apicophilicity rule. However, several examples breaking the apicophilicity rule have been reported in the past few decades and novel properties and reactivities of these new classes of compounds have been found. In this review, the synthesis of novel pentacoordinated phosphoranes with anti-apicophilic arrangement will be introduced, as well as their structures, spectroscopic properties, and reactivities.

Synthesis and Properties of Pentacoordinate Phosphorus Compounds Containing a Pentacoordinate Silicon Atom

The first hypervalent compounds bearing both a pentacoordinate silicon atom and a pentacoordinate phosphorus atom were synthesized by the cooperative three-component reaction of a phosphoranide a silane, and THF.

Synthesis, structure and isomerization of arylphosphoranes with anti-apicophilic bonding modes using a novel bidentate ligand with two C2F5 groups

A series of anti-apicophilic pentacoordinate phosphoranes (with one chelating substituent in an O-equatorial, C-apical bonding mode at pentacoordinated phosphorus atom) bearing a para-substituted aryl group (-C(6)H(4)(p-X); X = H, CF(3), F, OMe) or a mesityl (2,4,6-trimethylphenyl) group were isolated using a novel bulky bidentate ligand with two C(2)F(5) groups. These phosphoranes were stable to isomerization at room temperature, and quantitatively converted into the corresponding more stable isomers (O-apical) at elevated temperatures in solution. On the basis of a kinetic study, the free energy of activation (DeltaG(double dagger)) of the stereomutation of the O-equatorial mesitylphosphorane to its O-apical isomer was higher than that of the CF(3) derivative by 2.6 kcal mol(-1), giving rise to a further example of the steric effect of the C(2)F(5) group to freeze the isomerization of the pentacoordinate phosphorus compounds. Kinetic measurements of the isomerization of the O-equatorial ortho-unsubstituted derivatives (-C(6)H(4)(p-X)) to the corresponding O-apical isomers suggested that the O-equatorial isomers were stabilized by the pi --> sigma*(P-O) interaction in the ground state.

Inductive and External Electric Field Effects in Pentacoordinated Phosphorus Compounds.

Pentacoordination at phosphorus is associated with a nucleophilic displacement reaction at tetracoordinated phosphorus compounds and shows a great variability in what respects their geometrical and energetic features. By means of a systematic theoretical study on a series of elementary model compounds, we have analyzed the bonding features. The pentacoordinated phosphorus compounds are held together by dative bonds, and the geometry and stability depends on the inductive effects originated by different substitutes at phosphorus. We show also that an external electric field can modify the geometrical features and the reactivity of the nucleophilic substitution reactions. This issue may have great interest in biological reactions involving pentacoordinated phosphorus where the electric field originated by the folded protein could influence the catalytic process. We report also additional calculations on the geometry and NMR spectra on three triphenyl phosphonium ylide derivatives, and our results compare well with the experimental data.

Penta‐Coordinate Phosphorus Intermediates Analysis on Phospho‐related Proteins

Abstract In this paper, based on known crystal structures of square pyramid (SP) and trigonal bipyramid (TBP) penta coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software for survey the P(5)‐structure of phosphorylated proteins was derived. By this software, it was found that 382 of 398 phosphorus related kinases (96%) from current PDB could go through the penta‐coordinated phosphorus transition state or intermediate.

Addition products of a P(iii)-isothiocyanate to dialkyl acetylenedicarboxylates: a spirocyclic phosphinimine and a triphosphorus heterocycle with tetra- and penta-coordinate phosphorus

Treatment of the P(III) isothiocyanate CH2[6-t-Bu-4-Me-C6H2O]2PNCS (1) with dimethyl acetylenedicarboxylate (DMAD) or diethyl acetylenedicarboxylate (DEAD) yields the spirocyclic phosphinimines CH2[6-t-Bu-4-Me-C6H2O]2P[NC(S)C(CO2R)C(CO2R)][R=Me (2), Et (3)], in a reaction unlike those of organic isocyanates. From the reaction of 1 with DEAD, a second product, the triphosphorus compound 5, with the composition [2x1+3] but with a completely reorganized structure {CH2[6-t-Bu-4-Me-C6H2O]2P=C(CO2Et)C(CO2Et)=CN-}{CH2[6-t-Bu-4-Me-C6H2O]2P(NCS)}-SC=N-P(S)[(OC6H2-6-t-Bu-4-Me)2CH2] with tetra- and penta-coordinate phosphorus, is also isolated. Structure and reactivity of these compounds are discussed. Addition of 2,2,2-trifluoroethanol to 2 or 3 leads to the pentacoordinate phosphorus compounds [CH2(6-t-Bu-4-Me-C6H2O)2P(OCH2CF3){C(CO2R)C(CO2R)-C(S)-NH-}][R=Me (6), Et (7)]. The phosphonate [CH2(6-t-Bu-4-Me-C6H2O)2P(O)C(CO2Et)=C(CO2Et)-C(S)-NH2] (8) is obtained by evaporating a solution of 7 in open air.

Penta-coordinated phosphorus structure analysis on kinases

In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phosphorus-related kinases (96%) from current PDB could go through the penta-coordinated phosphorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 A from the phosphorus atom, and a potential TBP structure consisting GNP2 and N Z could be overlapped with an authentic TBP with an RMSD value of 0.71 A.

Phosphorus heterocycles from 2‐(2‐aminophenyl)‐1H‐benzimidazole

AbstractWe report the syntheses of unsaturated six‐membered heterocycles bearing tri‐, tetra‐, and pentacoordinated phosphorus atoms derived from 2‐(2‐aminophenyl)‐1H‐benzimidazol (1). The presence of three different N–H protons allowed to prepare different compounds by selective substitution. Molecules with two (endo and exocyclic) phosphorus atoms were prepared. The free anilinic proton is the most reactive to substitution reactions, followed by the benzimidazolic, and then the anilinic proton involved in the hydrogen bond. Substitution of the exo‐anilinic proton of 1 by Ph2PCl leads a precursor with a hydrogen bond forming a six‐membered ring, which could be substituted by other groups giving more complex molecules. A pentacoordinated phosphorus compound was obtained after oxidative addition of 3,5‐di‐tert‐butyl‐1,2‐benzoquinone to P(III) heterocycle. © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:321–332, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20022

Ligand Exchange Between Penta‐Coordinated Phosphoryl Serine and Histidine Compounds

AbstractWith the assistance of HPLC‐ESI‐MS/MS, the self‐assembly products of serine and histidine penta‐coordinated phosphorus compound were separated and identified. The expectative product was seryl‐histidine dipeptide, but it was found that there was almost equimolar amount of histidyl‐histidine dipeptide as well as seryl‐histidine dipeptide. The mechanism was speculated that there was ligand exchange between penta‐coordinated phosphoryl serine and histidine in the reaction process. As a result, two types of dipeptide were produced.

Penta-coordinate phosphorous compounds and biochemistry

The relationship between penta-coordinate phosphorus compounds and biochemistry is briefly reviewed. Some interesting phenomena such as peptide formation, ester formation, ester exchange on phosphorus and N to O migration occur at room temperature when the amino group of amino acid is associated with phosphoryl group. Serine or threonine in conjugate of nucleo-side-amino acid could recognize different nucleobases. N-phosphoryl Histine and Ser-His dipeptide could cleavage nucleic acid, protein and ester in neutral medium. It is found that the above phenomena all undergo penta-coordinate intermediate of phosphorus atom, which is proposed as the key factor to determine their activities.