Phosphorus-containing Molecules Research Articles

A data-driven exploration of the complexity of the phosphorus-centered pnictogen bonds

Phosphorus-centered pnictogen bonds, similar to well-studied halogen bonds, play a vital role in molecular recognition and assembly. This study aims to explain how pnictogen bonds interact with other noncovalent interactions. A model system, phosphines (PH3), which is also present in phosphorus cycles and reduces planetary atmospheres, is examined. The investigation of the phosphorus trifluoride (PF3) molecule explores its substituent effects. To generate a broad spectrum of molecular configurations, a specially tailored protocol for sampling and optimisation was implemented. The configurations were refined to uncover primary interaction patterns, and a clustering algorithm revealed unique interaction patterns. This report presents the energy stability and distribution of all the clusters. Our findings verify the prevalent presence of pnictogen bonds, identified by their geometric characteristics and co-occurrence with hydrogen bonds, which show an almost linear correlation. Another significant discovery is the correlation between various energy decomposition elements, especially regarding the electrostatic energy and overall binding energy. These results are anticipated to significantly contribute towards our comprehension of non-covalent interactions among phosphorus-containing molecules and the formulation of empirical models having physical interpretations.

Properties of phosphorus-containing polybutylene succinate/polylactic acid composite film material and degradation process effects on physiological indexes of lettuce cultivation

Phosphorus-containing polybutylene succinate (P-PBS) was prepared from the third monomer phenylphosphonic acid to improve the performance of biodegradable materials and endow plants with nutritional functions. The P-PBS/polylactic acid (PLA) composite was produced by blending P-PBS and PLA; its crystallization, thermodynamic, water vapor permeability, degradation, and plant nutrition properties were studied. Introducing phenylphosphoric acid destroyed the regularity of the PBS chain, decreased the crystallinity, and increased the polarity. With PLA, the composite crystallinity was further reduced. A certain intermolecular force combines P-PBS/PLA. When the P-PBS amount was 60%, the two-phase melting point was close, the two-phase compatibility was high, and the crystallinity was the lowest. Additionally, the molecular chain flexibility of the composite was the highest with the optimal thermal and mechanical properties. Furthermore, with 60% P-PBS, the composite material had the highest water vapor transmission rate for possessing the largest two-phase contact surface, which can be used as a mulching film. The composite was degraded in soil supernatant for 6 months, with a 60%–70% degradation rate. LC-MS identification revealed that the degradation products were succinic acid, butanediol, and phenylphosphonic acid oligomers, among which phosphorus-containing small molecules enhanced lettuce growth.

Monitoring of phosphatase and kinase activity using 31P NMR spectroscopy

We provide a new method for the direct identification of enzyme activity based on signal changes of phosphorus-containing small molecules in 31P NMR spectroscopy.

Enhancing toughness, flame retardant, hydrophobic and dielectric properties of epoxy resin by incorporating multifunctional additive containing phosphorus/silicon

Developing epoxy resins with superior toughness, flame retardant and hydrophobic as well as dielectric properties remains a huge challenge. Herein, an epoxy additive (ETP) was prepared by grafting phosphorus-containing molecules into the skeleton of silicone resin through silicon hydrogen addition reaction. Through such a design, the obtained ETP imparted Bisphenol A epoxy resin (DGEBA) with excellent flexibility, fire safety, hydrophobicity and dielectrical property. When only 6 wt% of ETP was introduced into the DGEBA system, the resulting product (ETP-6) passed the V-0 level in the UL-94 test with a high limiting oxygen index of 29.8 %, which could be ascribed to the presence of phosphorus and silicon element. Meanwhile, compared with neat DGEBA, the peak heat releases and smoke emissions of ETP-6 were reduced by 32.7 % and 37.8 % during the combustion. Additionally, ETP also imparted the cured product with excellent hydrophobic and dielectric properties, as well as superior toughness (114.5 % increase in impact strength) due to its “rigid and flexible” silicone skeleton and good dispersion. This work opens up a new strategy for developing high-performance and multifunctional epoxy resin additives with potential versatile applications.

Molecular-micron multiscale toughening and flame retarding for polyurethane foams

Polyurethane foams (PUF), widely used in daily life, has become one of the main triggers of urban fires. The incorporation of flame retardants is the most effective way to reduce the fire risk, but always severely deteriorates the mechanical properties of materials (e.g., fatigue resistance, malleability). Herein, we demonstrate a facile strategy for fabricating phosphorus-containing multiscale energy dissipation networks (PMNs) to engineer PUF with superior toughness and fire safety. By exploiting the polarity/reactivity nature of phosphorus-containing flame-retardant molecules (PMs), the interpenetrating PMNs are fabricated in-situ during foaming, which consist of molecular scale pendants for plasticization and micron-scale particles with compatible interphase/reinforcing mechanisms. Notably, the unique PMNs synergistically facilitate the redistribution and dissipation of external stress, enabling PUF the outstanding capability to sustain large deformation. The corresponding fracture strength, elongation at break (+59%), and toughness (+92%) are simultaneously increased, avoiding the fragility caused by conventional crosslinking networks or rigid fillers. In addition, the flame retardant disparity and mechanism of 3 PMs with tiny chemical differences were investigated. More phosphorus-containing species with radical scavenging abilities, given by hydroxymethyl diphenylphosphine oxide (DPM), endow PUF the ability to rapidly self-extinguish with low addition of 1.8 wt%, which is challenging for the others. The synergistic PMNs, spanning molecular and micron scales, provide new inspiration for solving the contradiction of flame retardancy & mechanical performances and strength & toughness for materials, showing obvious superiority for practical applications.

Sources of Nitrogen-, Sulfur-, and Phosphorus-Containing Feedstocks for Prebiotic Chemistry in the Planetary Environment.

Biochemistry on Earth makes use of the key elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (or CHONPS). Chemically accessible molecules containing these key elements would presumably have been necessary for prebiotic chemistry and the origins of life on Earth. For example, feedstock molecules including fixed nitrogen (e.g., ammonia, nitrite, nitrate), accessible forms of phosphorus (e.g., phosphate, phosphite, etc.), and sources of sulfur (e.g., sulfide, sulfite) may have been necessary for the origins of life, given the biochemistry seen in Earth life today. This review describes potential sources of nitrogen-, sulfur-, and phosphorus-containing molecules in the context of planetary environments. For the early Earth, such considerations may be able to aid in the understanding of our own origins. Additionally, as we learn more about potential environments on other planets (for example, with upcoming next-generation telescope observations or new missions to explore other bodies in our Solar System), evaluating potential sources for elements necessary for life (as we know it) can help constrain the potential habitability of these worlds.

Spectroscopic and Molecular Characterization of Water Soluble Organic Matter from Sediments in the Macrophyte-dominated and Algae-dominated Zones of Taihu Lake

Macrophyte- and algae-dominated lakes (zones) are the two typical states of shallow lakes, where the source and composition of organic matter are distinct. The burial of organic matter (OM) in the sediment supports the role of lakes as carbon sinks. However, organic matter in the sediments could be further processed, influencing the carbon cycle. The post-burial metabolism of the sedimentary OM relates closely to its composition. However, information on the differences in composition remains limited, especially the molecular composition of organic matter from sediments in the macrophyte-dominated and algae-dominated lakes. In this study, sediments were collected from the macrophyte-dominated and algae-dominated zones of Taihu Lake (East Taihu Lake and Meiliang Bay, respectively), and the active pool of sedimentary OM (water soluble organic matter, WSOM) was extracted and purified. The composition of the WSOM was characterized in detail via absorption spectroscopy, fluorescent spectroscopy, infrared spectroscopy, and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The optical index of E2:E3 showed that the molecular size of WSOM in the macrophyte-dominated zone (M-WSOM) was slightly larger than that in the algae-dominated zone (A-WSOM). Consistently, the intensity-weighted molecular weights were identified as 388.9 and 379.9, respectively, via FT-ICR MS analysis. M-WSOM was more humified than A-WSOM, as evidenced by the SUVA254 and HIX values. The FT-ICR MS results showed that the relative abundance of the condensed aromatic substance and the aromatics were 6.3% (intensity-weighted) and 7.7% for M-WSOM and 1.1% and 4.4% for A-WSOM, respectively. The excitation-emission matrix fluorescence-parallel factor analysis (EEM-PARAFAC) suggested that the protein-like component was more in A-WSOM than that in M-WSOM, and the FT-ICR MS results showed that the intensity-weighted relative abundances of peptides were 35.6% and 15.6% for A-WSOM and M-WSOM, respectively. The FT-ICR MS results further showed that the heteroatom-containing molecules were abundant in the sedimentary WSOM, i.e., 82.9% and 91.7% for M-WSOM and A-WSOM, respectively. The nitrogen-containing molecules dominated, contributing to 53.5% and 78.5% of M-WSOM and A-WSOM, respectively. There were 30.4% and 41.4% phosphorus-containing molecules in M-WSOM and A-WSOM, respectively. The phosphorus-containing molecules in M-WSOM were mainly aliphatics and highly unsaturated structures with low oxygen, whereas those in A-WSOM were mainly peptides. This study elucidated the detailed molecular composition of WSOM in the macrophyte-dominated and algae-dominated zones of Taihu Lake, which aids understanding of the carbon, nitrogen, and phosphorus biogeochemical cycles in lakes.

Role of Phosphorus-Containing Molecules on the Formation of Nano-Sized Calcium Phosphate for Bone Therapy.

Calcium phosphate (CaP) is the principal inorganic constituent of bone and teeth in vertebrates and has various applications in biomedical areas. Among various types of CaPs, amorphous calcium phosphate (ACP) is considered to have superior bioactivity and biodegradability. With regard to the instability of ACP, the phosphorus-containing molecules are usually adopted to solve this issue, but the specific roles of the molecules in the formation of nano-sized CaP have not been clearly clarified yet. Herein, alendronate, cyclophosphamide, zoledronate, and foscarnet are selected as the model molecules, and theoretical calculations were performed to elucidate the interaction between calcium ions and different model molecules. Subsequently, CaPs were prepared with the addition of the phosphorus-containing molecules. It is found that cyclophosphamide has limited influence on the generation of CaPs due to their weak interaction. During the co-precipitation process of Ca2+ and PO4 3-, the competitive relation among alendronate, zoledronate, and foscarnet plays critical roles in the produced inorganic-organic complex. Moreover, the biocompatibility of CaPs was also systematically evaluated. The DFT calculation provides a convincing strategy for predicting the structure of CaPs with various additives. This work is promising for designing CaP-based multifunctional drug delivery systems and tissue engineering materials.

Cosmic Dust May Be Key Source of Phosphorus for Life on Earth

When tiny particles enter Earth’s atmosphere, a newly described series of chemical reactions may lead to production of phosphorus-containing molecules that are essential for biological processes.

Staphylococcus aureus Preferentially Liberates Inorganic Phosphate from Organophosphates in Environments where This Nutrient Is Limiting.

Phosphate is an essential nutrient that Staphylococcus aureus and other pathogens must acquire from the host during infection. While inorganic monophosphate (Pi) is the preferred source of this nutrient, bacteria can also obtain it from phosphate-containing organic molecules. The Pi-responsive regulator PhoPR is necessary for S. aureus to cause infection, suggesting that Pi is not freely available during infection and that this nutrient must be obtained from other sources. However, the organophosphates from which S. aureus can obtain phosphate are unknown. We evaluated the ability of 58 phosphorus-containing molecules to serve as phosphate sources for S. aureus Forty-six of these compounds, including phosphorylated amino acids, sugars, and nucleotides, supported growth. Among the organophosphate sources was glycerol-3-phosphate (G3P), which is commonly found in the mammalian host. Differing from the model organism Escherichia coli, S. aureus does not import G3P intact to obtain Pi Instead, S. aureus relies on the phosphatase PhoB to release Pi from G3P, which is subsequently imported by Pi transporters. To determine if this strategy is used by S. aureus to extract phosphate from other phosphate sources, we assessed the ability of PhoB- and Pi transporter-deficient strains to grow on the same library of phosphorus-containing molecules. Sixty percent of the substrates (28/46) relied on the PhoB/Pi transporter pathway, and an additional 10/46 (22%) were PhoB independent but still required Pi transport through the Pi transporters. Cumulatively, these results suggest that in Pi-limited environments, S. aureus preferentially generates Pi from organophosphates and then relies on Pi transporters to import this nutrient.IMPORTANCE For bacteria, the preferred form of the essential nutrient phosphate is inorganic monophosphate (Pi), but phosphate can also be extracted from a variety of phosphocompounds. Pathogens, including Staphylococcus aureus, experience Pi limitation within the host, suggesting that the use of alternative phosphate sources is important during infection. However, the alternative phosphate sources that can be used by S. aureus and others remain largely unexplored. We screened a library of phosphorus-containing compounds for the ability to support growth as a phosphate source. S. aureus could use a variety of phosphocompounds, including nucleotides, phosphosugars, and phosphoamino acids. Subsequent genetic analysis determined that a majority of these alternative phosphate sources are first processed extracellularly to liberate Pi, which is then imported through Pi transporters.

Structure-Activity Relationships of Butyrophilin 3 Ligands.

Phosphoantigens (pAgs) are small phosphorus-containing molecules that stimulate Vγ9Vδ2 T cells with sub-nanomolar cellular potency. Recent work has revealed that these compounds work through binding to the transmembrane immunoglobulin butyrophilin 3A1 (BTN3A1) within its intracellular B30.2 domain. Engagement of BTN3A1 is critical to the formation of an immune synapse between cells that contain pAgs and the Vγ9Vδ2 T cells. This minireview summarizes the structure-activity relationships of pAgs and their implications to the mechanisms of butyrophilin 3 activation leading to Vγ9Vδ2 T cell response.

Flame Retardation of Natural Rubber: Strategy and Recent Progress.

Natural rubber (NR) as a kind of commercial polymer or engineering elastomer is widely used in tires, dampers, suspension elements, etc., because of its unique overall performance. For some NR products, their work environment is extremely harsh, facing a serious fire safety challenge. Accordingly, it is important and necessary to endow NR with flame retardancy via different strategies. Until now, different methods have been used to improve the flame retardancy of NR, mainly including intrinsic flame retardation through the incorporation of some flame-retarding units into polymer chains and additive-type flame retardation via adding some halogen or halogen-free flame retardants into NR matrix. For them, the synergistic flame-retarding action is usually applied to simultaneously enhance flame retardancy and mechanical properties, in which some synergistic flame retardants such as organo-montmorillonite (OMMT), carbon materials, halloysite nanotube (HNT), etc., are utilized to achieve the above-mentioned aim. The used flame-retarding units in polymer chains for intrinsic flame retardation mainly include phosphorus-containing small molecules, an unsaturated chemical bonds-containing structure, a cross-linking structure, etc.; flame retardants in additive-type flame retardation contain organic and inorganic flame retardants, such as magnesium hydroxide, aluminum hydroxide, ammonium polyphosphate, and so on. Concerning the flame retardation of NR, great progress has been made in the past work. To achieve the comprehensive understanding for the strategy and recent progress in the flame retardation of NR, we thoroughly analyze and discuss the past and current flame-retardant strategies and the obtained progress in the flame-retarding NR field in this review, and a brief prospect for the flame retardation of NR is also presented.

Adhesion of lubricant on aluminium through adsorption of additive head-groups on γ-alumina: A DFT study

To improve lubricant formulation, a better understanding of the wettability properties and hence of the interactions between the surface and the lubricant additives is a key parameter. Herein, we use density functional theory calculations to characterize 32 typical head groups, classified into four categories: protic, aprotic, aromatic and phosphorus-containing molecules. By comparing their adsorption energies on γ-alumina, used as a surface model of aluminium sheets, and their solvation energies in a model lubricant base oil, we found that the solvation energy was not a discriminant parameter while the adsorption energy was critical. Phosphates and carboxylic acids are the most strongly adsorbed, and thus more likely to yield to improved wettability properties of the lubricant through film formation.

Globally accurate potential energy surface for PH2 + (11 A′) by using the switching function formalism

As an intermediate product of phosphorus compounds in astrophysical chemistry, has great significance in research on the systems. However, as a basis for studying its reaction mechanisms, lacks an accurate global potential energy surface (PES) and related dynamic reports. In this investigation, based on a multi-reference configuration interaction approach with Davidson correction, an accurate global many-body expansion PES for in its ground state was reported by fitting extensive ab initio energies, as calculated with the correlation-consistent basis set aug-cc-pVQZ. Meanwhile, the switching function formalism was adopted to explain and distinguish the transformation between and in one-body energy terms, which ensured the correct dissociation channel in the reaction process of . The topographical characteristics of the title system PES were meticulously contrasted with those in other literature reports, which were consistent with previous experimental and theoretical values. Subsequently, the time-dependent wave packet approach was adopted to calculate the reaction probability and integral cross-section for the reaction to verify the accuracy of the new PES. This dynamics study may help to further explain the thermochemical reactions of phosphorus-containing molecules in interstellar media.

The Role of the Phosphorus Atom in Drug Design.

Although the phosphorus atom is found in a variety of oxidation states, most of the phosphorus-containing molecules of pharmacological importance possess phosphorus in the form of phosphonate or phosphinate functional groups, or in a major oxidation state as a phosphate group. The most common occurrence of phosphorus in drugs is either in prodrugs or in compounds for which the phosphorus atom plays a role in the biological activity, such as in modified nucleotides, in metabolically stable analogues of metabolites bearing phosphate groups, and as bioisosteric analogues of carboxyl groups.

Ionization of P Atom, P\(_2\) and PX (X = H, C, N, O) Molecules by Electron Impact: Theoretical Studies

Being a biogenic element atomic Phosphorus is one of the significant constituents of the universe [1]. Gulick [2] found a pivotal role of phosphorus in the origin of life. The phosphoruscontaining molecules like PH, PC and PN radicals, have been observed in interstellar gas clouds [3–5] and they are proposed to be present under appropriate conditions. Phosphorous hydrides having numerous applications, are detected in cool stellar atmosphere [6] and circumstellar envelopes. Thus, the present paper addresses the electron impact processes of atomic phosphorus and its diatomic compounds. Ground and metastable states of Atomic P give rise to the probability of presence of metastable state in the atomic beam used for cross section measurement [7]. We have employed the well-known Spherical Complex Optical Potential (SCOP) formalism to calculate total inelastic cross sections. The semi-empirical CSP- ic method is used to extract total ionization cross section \(Q_{ion}\) from total inelastic cross section [8]. A variant CSP- ic approach is also attempted for these targets.

Monolayer doping of germanium by phosphorus-containing molecules

The DPP (diethyl 1-propylphosphonate) and ODPA (octadecylphosphonic acid) molecules are studied as precursors for the monolayer doping (MLD) of germanium. Their adsorption behaviour is investigated, revealing different physicochemical interactions between the phosphorus-containing molecules and the Ge surfaces. It is discovered that DPP adsorption occurs after the oxidation of Ge surface, while the ODPA undergoes chemisorption on –H terminated surfaces. Quantitative phosphorus analysis demonstrates that in the first case more than one monolayer is formed (from 2 to 4), while in the second a single monolayer is formed. Moreover, the analysis of phosphorus diffusion from the surface layers into the Ge matrix reveals that conventional thermal annealing processes are not suitable for Ge injection due to a higher activation energy of the process in comparison with silicon. On the contrary, pulsed laser melting is effective in forming a doped layer, owing to the precursor’s decomposition under UV light.

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.

Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol-1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.

Experimental study of the influence of dimethyl methylphosphonate on methane/air coflow diffusion flames using OH-PLIF

Experiments were conducted to evaluate the inhibition efficiency of dimethyl methylphosphonate (DMMP) on methane/air coflow diffusion flames. An optical diagnostic system (hydroxyl planar laser-induced fluorescence) was used to measure the OH radical distribution in the flames. The minimum extinguishing concentration (MEC) of CO2, as a function of DMMP addition, was measured to characterize the inhibition efficiency of DMMP. Results show that, when the concentration of DMMP is higher than 0.6%, DMMP’s marginal inhibition efficiency reduces to almost zero. It is found that the normalized peak OH concentrations keep unchanged with a value of 0.9 for flames at conditions near extinction limit. This is firstly observed based on experimental measurements. Furthermore, using DMMP alone cannot extinguish the flame even with 4.59% DMMP addition. When the inhibition efficiency of DMMP gets saturated, a large amount of phosphorus-containing molecules agglomerate around the flame. These particles act as sinks for the active phosphorus-containing species with a high inertial force, which are hard to diffuse horizontally into the flame. Therefore, it is concluded that the generation of the particles is a reason for the saturation phenomenon of DMMP in extinguishing the coflow diffusion flames.

Analysis of Staphylococcus aureus wall teichoic acid glycoepitopes by Fourier Transform Infrared Spectroscopy provides novel insights into the staphylococcal glycocode

Surface carbohydrate moieties are essential for bacterial communication, phage-bacteria and host-pathogen interaction. Most Staphylococcus aureus produce polyribitolphosphate type Wall teichoic acids (WTAs) substituted with α- and/or β-O-linked N-acetyl-glucosamine (α-/β-O-GlcNAc) residues. GlcNAc modifications have attracted particular interest, as they were shown to govern staphylococcal adhesion to host cells, to promote phage susceptibility conferring beta-lactam resistance and are an important target for antimicrobial agents and vaccines. However, there is a lack of rapid, reliable, and convenient methods to detect and quantify these sugar residues. Whole cell Fourier transform infrared (FTIR) spectroscopy could meet these demands and was employed to analyse WTAs and WTA glycosylation in S. aureus. Using S. aureus mutants, we found that a complete loss of WTA expression resulted in strong FTIR spectral perturbations mainly related to carbohydrates and phosphorus-containing molecules. We could demonstrate that α- or β-O-GlcNAc WTA substituents can be clearly differentiated by chemometrically assisted FTIR spectroscopy. Our results suggest that whole cell FTIR spectroscopy represents a powerful and reliable method for large scale analysis of WTA glycosylation, thus opening up a complete new range of options for deciphering the staphylococcal pathogenesis related glycocode.