Phosphate coordination

All preceding programs accept the conventional wisdom of operating within a control box of pH level and phosphate coordinates, despite the vagaries associated with BW sampling, amine contribution to pH and the omnipresent risk of hideout in utility boilers operating at high pressures. 

In weaidy acidic equilibrium systems of 62 and 5 -IMP (21C) or 5 -ITP (21D), two cyclic, presumably trimeric oligomers with respectively N(l) N(7),0(6) (67) and N(l) N(7), O (H2O) (68) binding patterns of adjacently placed nucleobases were present in an approximately 1 1 ratio. The phosphate coordination was absent in the case of this Ir species in the presence of purine nucleoside 5 -triphosphate (2000ICA115). 

The molecular geometry of phospholipid membranes is thus structurally analogous to inorganic phosphate minerals in that corrugated layers of metal ion-phosphate coordination complexes exist in membranes and minerals. In Fig. 5, the structure of a typical phosphate mineral is shown to reveal the type of molecular pattern that is exposed at the ionic surface of phospholipid membranes64,6S. For a recent review on membrane structure see66. ... 

Methyl-p-nitrophenyl phosphate coordinated to the two metal centers in 37 undergoes hydrolysis by a two-step addition-elimination mechanism [73]. The free phosphate hydrolyzes by a concerted mechanism. In both phosphate monoester and diester hydrolysis, the two Co(m) centers in 32 and 37 stabilize the five-coordinate phosphate species (transition state or intermediate) by bringing the phosphate and nucleophile together. This stabilization leads to a change in mechanism from dissociative to concerted for a phosphate monoester hydrolysis [96] and from concerted to stepwise for phosphate diester hydrolysis [73]. 

The L-N3 ligand has also been used to stabilize mononuclear [Mo O] complexes possessing pendant phosphate ester groups (42) and Mo "P distances of 4-8 A (80, 81). The NMR linewidths are strongly dependent upon the Mo—P distance, and reasonable Mo—P distances were derived from longitudinal relaxation times using the Solomon equation 154). Molecular modeling studies of Mo-co indicate that phosphate coordination to the Mo atom is stereochemically feasible, but the P ENDOR studies of the Mo(V) states of xanthine oxidase (67) estimate the Mo—P distance as 7-12 A and seem to rule out such a structure. 

Figure 51 Phosphate coordination geometries and cocrystallized template from the structure-directed preparation of a layered uranyl phosphate (Francis, Drewitt et al. Chem. Commun. 1998, 279-280).

Why do stoichiometrically identical complexes [U02Si04] (XXI) and [U02P04] (XXII) have different structures Indeed, in the structure of XXI, there are uranophane-type sheets with CNu = 7 and Si04" 7/T (Fig. 13a), whereas the structures of uranium micas contain sheets of the XXII type that have CNu = 6 and P04 7/K (Fig. 13b). Taking into account, that, in uranyl compounds the coordination mode of phosphate ions is either or this question can be re-formulated as Why is only the phosphate coordination mode realized in the [U02P04] complexes ... 

Several alternative self-assembly approaches for producing thermally stable, acentric chromophoric multilayers have been reported [142-144]. The most prominent example is that developed by Katz et al. [145,146], which takes advantage of the zirconium phosphonate/phosphate coordinative bonding to fix layers of a dye to one another producing films with a good structural regularity and stability to orientational randomization of up to 150°C. Another example utilizes the electric field-induced LbL assembly technique of ionic species, followed by UV irradiation to convert the ionic bonds between layers into covalent bonds [147],... 

A catalysis through a double Lewis acid activation of the scissile phosphate (coordination of two oxygen atoms of the phosphate onto the copper instead of one oxygen atom for a single Lewis acid assistance) was proposed by Chin (334) to account for the higher reactivity of 8 compared to 6. The mechanism proposed by Bashkin et al. for 6 is totally different and is based on the fact that the optimal rate of phosphate trans-esterification is at a pH value close to the value of the metal-bound water molecule (332, 335). Because monoaqua complexes as in 6 do not form stable four-membered ring phosphate coordinates, they may just behave as acid/base coreactants like histidine residues in ribonuclease A (336) or like imidazole buffer (337). 

Preparations are listed in Table 47. Main interest lies in determining how metal ions catalyze the hydrolysis of ADP and ATP. ATP plays a crucial role in the energy metabolism of all living cells and divalent metal ions (Mg " ", Mn " and Ca ) play an important role in these phosphoryl transfer processes. Divalent metal ions such as Mg ", Ca, Zn " ", Cu and Mn " provide only modest in vitro catalysis and stronger, more specific coordination to phosphate units appears to be required by the enzyme. Co " (and Cr" ) complexes of ADP and ATP have been shown to mimic many of the biological functions of the Mg " " enzyme, and since the cobalt(III)-phosphate coordination remains intact, the specificity of alternative coordination sites, and the stereochemical requirements at phosphorus, have been elucidated in some cases. Often the Co" -enzyme species is biologically active and several enzymic functions of ATP have been examined in this manner. 

Building towards models relevant for polymeric DNA and RNA, nucleotides contain a phosphate attached at the 5 or 3 position. The 5 -nucleotides are most commonly studied, for which the phosphate has a pAa 6 for the first protonation step. Unless otherwise noted, throughout this chapter nucleotide will refer to the 5 -phosphate linkage. In nucleotides, metal-phosphate coordination competes with metal-base interactions. Chelate complexes with both phosphate and base coordination can occur when sterically allowed. Thus, transition metal complexes with purine monophosphates tend to exhibit metal coordination to the base N7 position, with apparent hydrogen bonding of coordinated waters to the phosphate. By contrast, more ionic Mg" binds preferentially to the phosphate groups in nucleotide monophosphates. In di- and tri-phosphate complexes such as metal-ATP compounds, the proximity of multiple phosphates generally favors polyphosphate chelate complexes with metal ions. 

Figure 8. Bidentate (type A, left) and monodentate (type B, right) phosphate coordination to tantalum ions, with the possibility for the formation of intermolecular hydrogen bonding.

David SS, Que Jr L. 1990. Anion binding to uteroferrin evidence for phosphate coordination to the iron(III) ion of the dinuclear acitve site and its interaction with the hy-droxo bridge. JAm Chem Soc 112 6455-6463. 

The second option was that only partial degradation of the complex took place prior to bone uptake, or only partial phosphate coordination takes place in bone mineral. The partial coordination leads to considerable variability in coordination structure and observation of a wide range of P coupling constants in the ESEEM/HYSCORE spectra. Such an explanation was offered by Fukui et al. to explain the broad, unresolved signals below 8 MHz that were thought to be due to diversity in phosphate coordination mode [71]. 

This uncertainty was resolved in a later report of a vanadyl—phosphate model system to investigate die eoordination structure of VO(ema)2 in bone mineral [96], Two, three, and ID 4-pulse, along wifli 2D HYSCORE spectroseopies were used to study the eoordination strueture of the vanadyl-triphosphate system. HYSCORE speetroseopy partnered with eontour Uneshape analysis determined three P hyper-fine eoupling eonstants of 15, 9, and 1 MHz, in exeellent agreement with the in-vivo results. In addition, detailed analysis of the proton matrix peak by ID 4-pulse ESEEM led to assignment of at least one, and probably two, water molecules in the equatorial plane. Thus, the VO-triphosphate model system demonstrated that the vanadyl ions in VO(ema)2-treated rat bone samples were most likely in a facial tris(phosphate) coordination with water moleeules oeeupying the vacant positions in the equatorial plane, as shown in Seheme 3. 

Fourier transformed EXAFS spectra of e purple enzyme reveal three major peaks, assigned as follows first shell, Fe-0(N) second shell, Fe— Fe and Fe-P(C) third shell, Fe—N(C) (imidazole). Due to interference by Fe-0 (tyrosine) bonds at 1.8-1.9 A, an Fe-p-oxo bond could not be detected. The Fe— Fe distance of 3.0 A lies within the range expected for a p-oxo bridged structure. The spectrum of the purple, phosphate bound form also provides direct evidence for phosphate coordination to one of the iron atoms, with an Fe—P distance of 3.0 A. 

In this context also a stability constant study in aqueous solution (25°C I = 0.1 M, NaNOs) of complexes formed with 2 AMP and 3 AMP is of relevance [48]. The complex stability of Cu(2 AMP) is enhanced by 0.25 log unit compared to the stability expected for a sole phosphate coordination the stability of the Cu(3 AMP) complex is only very slightly enhanced, if at all. The different stability enhancements point to different structural properties of the two ligands. In case 7-membered chelates were formed by coordination of the phosphate-bound Cu " with the neighboring hydroxyl group, the situation in 2 AMP and 3 AMP would be equivalent and the same stability enhancement would be expected. Hence, a significant hydroxyl group interaction needs to be ruled out and this leaves as the only explanation of the observed results an interaction of Cu " in Cu(2 AMP) with N3 of the purine residue giving rise to an 8-membered macrochelate. 

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