PAP and iron oxide nanoparticles

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Phosphorus ester hydrolysis is one of the key chemical processes ..... Two different iron salt (FeCl3, Fe(NO3)3, J.T. Baker, and Riedel-de Haen) with different ...

天然纳米氧化铁 磷生物地球化学 Iron oxide nanoparticles & Phosphorus biogeochemistry

黄晓澜

Eutrophication 水体富营养化 P fertilizer Red tide in Xiamen, in China's Fujian Province, April 21, 2007. Red tides are nutrient-fueled blooms of phytoplankton that discolor water with their pigments.

A series of phytoplankton blooms. A cyanobacterial (blue-green algae) in the Baltic Sea (upper left). Red tide bloom (dinoflagellate) in the Sea of Japan (upper right). Cyanobacterial bloom in the St John's River Estuary, Florida (lower left). Cyanobacteriachlorophyte bloom in New Zealand (lower right)

This divided body of water shows the remarkable difference between mesotrophic (moderately enriched) (upper basin) and eutrophic water (lower basin).

Redfield ratio: C/N/P ratio (Ecological stoichiometry) Redfield stoichiometry is the atomic ratio of Carbon, nitrogen, and phosphorus found in phytoplankton and throughout the deep oceans. This empirically developed stoichiometric ratio was originally found to be C:N:P = 106:16:1

The global ocean balance between N2 fixation and the loss of fixed N through anammox and denitrification Kevin R. Arrigo Nature 437, 349-355 (15 September 2005) doi:10.1038/nature04159

Martiny, A. C., Vrugt, J. A., & Lomas, M. W. (2014). Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean. Scientific Data, 1., http://www.nature.com/articles/sdata201448

Ocean Fe Fertilization “Give me half a tanker of iron, and I’ll give you an ice age” 

Iron deficiency was limiting ocean productivity and offered an approach to mitigating climate change as well.



Iron fertilization is the intentional introduction of Fe fines to iron-poor areas of the ocean surface to stimulate phytoplankton production.



This is intended to enhance biological productivity and/or accelerate carbon dioxide (CO2) sequestration from the atmosphere

A schematic representation of the first view of the processes governing the ocean iron cycle

Gerringa, L. J. A., H. J. W. de Baar, and K. R. Timmermans (2000), Mar. Chem., 68, 335–346

The complexities of iron chemistry. Components include inorganic chemistry, redox speciation, organic complexation, and the dissolved, colloidal, and particulate phases

John Martin

A revised representation of the major processes in the ocean iron cycle, with emphasis on the Atlantic Ocean A Tagliabue et al. Nature 543, 51–59 (2017) doi:10.1038/nature21058

Knowledge of Iron Chemistry Nature Iron Oxyhydroxide nanoparticle

Iron oxide in soil

Acicular morphology of goethite nanorods with illustration of enclosing facets in the inset.

Iron oxide nanoparticles in iceberghosted sediments

Goethite in soils.

Magnetite from loess

SEM of Green Rust (FOUGERITE) Hematite (highlighted as Hm) nanocrystals at the edge of goethite (Gt) as the weathering dehydration product of goethite under dry conditions.

Gao H B, A S Barnard, 2013, J. Mater. Chem A,1, 27-42

Hematite nanoparticles found in alkaline soils

Knowledge of Iron Chemistry

Nature Iron Oxyhydroxide nanoparticle

X-ray diffraction patterns (Mo Ka radiation) of ferrihydrite.

SEM image of mineralized bacteria from the caldera of Axial Vocno resembling the sheath of Leptothrix orchracae (L), Gallionella ferruginea (G) and PV-1 (P). The inset TEM image is a cross-section of a bacterial structure encrusted with nanoparticulate ferrihydrite.

Eh-pH stability diagram for iron oxides and hydroxides (Scheffer et al., 1989)

Fe Effects of size and morphology on the structure of water around hematite nanoparticles

Cross section of water density around a 2.7 nm (012) faceted and spherical particle. The blue color indicates an iron site, pink color indicates the area with low water density and red color indicates the area with high water density. (b) Partial radial distribution function of an iron site on a planar surface (black line) and corner/edge surface site (red line) of a 2.7 nm (012) particle, an iron site on a spherical surface (blue line) and an iron site on a 1.6 nm disordered particle (green line) with the oxygen of the water molecules Gao H B, A S Barnard, 2013, J. Mater. Chem A,1, 27-42

Knowledge of Iron Chemistry A observation of 0.1M Fe(NO3)3 hydrolysis The hydrolysis of ferric nitrate salts is a more chaotic process than that for ferric chloride. The samples at each hydrolysis ratio evolve differently with time. At the same aging time t, the number of iron atoms in the atomic environment of the central atom 3D model used for the multiple-scattering approach: (a)3Dstructure; (b) several possible multipleFe radial distribution functions increases with n, but the growth scattering paths.  The characteristic distances between two iron octahedra sharing one face or sharing one edge are in the 2.85-2.94 Å or 2.95-3.10 does not follow a defined pathway. Å R-range . Only N3 has a monotonous  The second Fe-Fe (Fe-Fe2, at 3.06 and 3.20 Å ) is associated to an edge sharing between two iron octahedra. evolution with time. It seems that  The third contribution (Fe-Fe3) at 3.40-3.52 Å is attributed to a double-corner sharing.  The fourth Fe-Fe (3.9-4.0 Å) corresponds to a bond between two iron octahedra sharing one corner. the growth of nuclei is associated with the increase of the amount of double corner sharing (Fe-Fe3, 3.5 Å). Edge-sharing linkages between Fe octahedra are associated with the early steps of the nucleation, and for all samples single-corner linkages exist. Rose et al., 1997, Langmuir , 13, 3240-3246

Knowledge of Iron Chemistry Iron (oxyhydr)oxide formation from aqueous solution  Concentration dependent phase formation of iron oxides and oxyhydroxides.  In-situ formation of g-Fe2O3 with hydrazine addition at room temperature  Low concentration gives rise to iron oxyhydroxides and higher concentration gives rise to gamma iron oxide Maiti D, P. Sujatha Devi ,2015, Materials Chemistry and Physics 154:144-151

Fu D et al., 2011, Phys. Chem. Chem. Phys., 13, 18523–18529

Knowledge of Iron Chemistry Iron Oxyhydroxide Nanoparticles in Aqueous Solutions

Structures of iron monomers (a, b) and dimers (c, d, e) sampled at the ends of MD simulations (see Table 1). a−e correspond to the MD systems 1−5 in Table 1: red, O; green, Fe; gray, H; blue, Cl.

Zhang H et al., 2015, J. Phys. Chem. B 119 (33), 10630-10642

Knowledge of Iron Chemistry Precipitation pathways for ferrihydrite formation in acidic solutions  Ferric speciation over time were studied during ferric oxyhydroxide formation in partially-neutralized ferric nitrate solutions ([Fe3+] = 0.2 M, 1.8 < pH < 3).  Fe(H2O)63+, μ-oxo aquo dimers and ferrihydrite are the main Fe species, and that with time, the μ-oxo dimer decreases while the other two species increase in their concentrations.

Reactions that are probably involved in ferrihydrite formation.

A schematic representation of Gibbs free energy versus an arbitrary reaction coordinate during ferrihydrite nucleation

Potential pathways for further condensation. The pathway involving steps 4, 6 and 7 leads to formation of ferrihydrite nuclei.

Zhu MQ et al., 2016, Geochimica et Cosmochimica Acta,172:247-272

Knowledge of Iron Chemistry The structure of Ferrihydrite, a nanocrystalline Material

The basic structural motif of the model, which is closely related to the BakerFiggis d-Keggin cluster, consists of 13 iron atoms and 40 oxygens (Fig. 3). The central tetrahedrally coordinated Fe is connected by m4-oxo bridges to 12 peripheral octahedrally coordinated Fe atoms arranged in edge-sharing groups of three. The 2- to 6-nm ferrihydrite nanoparticles can then be described as a threedimensional packing of these clusters with adjacent clusters connected by a common pair of edge-shared octahedra, forming m4-oxo bridges from the three m2-OH groups cis to each of the m4-oxo centers in the bare cluster. This arrangement creates a cubane-like moiety corresponding to four edgeshared Fe octahedra (Fig. 1).

The structure of Ferrihydrite contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis d-Keggin cluster. Michel et al, 2007, Science, 316:1726-1729

Phosphate Ester 磷酸酯 Glycerol -phosphate

Ribose 5phosphate

Fructose 1phosphate

Chemical structure of RNA ATP, ADP, AMP

PPi; Pyrophosphate

ATP → AMP + PPi Free energy 自由能(焓)

Chemical structure of DNA



ATP is a type of phosphate esters, as the energy supply for all life.



Enzyme is need for the ATP transfer or the processing of hydrolysis

Phosphorus ester hydrolysis is one of the key chemical processes in biological systems, including signaling, free-energy transaction, protein synthesis, and maintaining the integrity of genetic material.

Glucose, Glucose phosphate and Glycolysis 葡萄糖,葡萄糖-6-磷酸, 糖酵解

Phosphatase 磷酸酶

 Glycolysis is common to all organisms, suggesting it evolved early in life.  Hydrolysis of phosphate ester (Dephosphorylation) is the reversible processing of phosphorylation, the first step of glycolysis. The general reaction catalyzed by a phosphatase enzyme

 Phosphatases catalyze the hydrolysis of a phosphomonoester, removing a phosphate moiety from the substrate.  Water is split in the reaction, with the -OH group attaching to the phosphate ion, and the H+ protonating the hydroxyl group of the other product.  The net result of the reaction is the destruction of a phosphomonoester and the creation of both a phosphate ion and a molecule with a free hydroxyl group.

Stages of Glycolysis 糖酵解的第一步是葡萄糖磷酸化为6-磷酸葡萄糖。

 Acid phosphatase,EC 3.1.3.2 酸性磷酸酶  Alkaline phosphatase EC 3.1.3.1碱性磷酸酶

Purple acid phosphatase (PAP) 磷酸水解酶  Dephosphorylation reaction is the process catalyzed by phosphatases, e.g. Purple acid phosphatase (PAP). RCH2OPO32- + H2O

RCH2OH + HPO42-

 Purple acid phosphatases (PAPs) are metalloenzymes that hydrolyze phosphate esters and anhydrides under acidic condition.  The biological roles of PAPs are diverse, including bone resorption, microbial killing and possibly iron transport in animals, and phosphate acquisition in plants.  PAPs have a dinuclear iron center to which a tyrosine residue is connected via a charge transfer. This metallic center is composed of Fe3+ and M with a 3.3 Å distance by the oxo ligand, where M is Fe3+, Zn2+, Mg2+ or Mn2+ .  A minimal homology for amino acid sequence (

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