Phosphate distances

Figure 22. The average dimensionless area per molecule (left ordinate) and the phosphate - phosphate distance in lattice units across the bilayer (right ordinate) of phosphatidyl serine bilayers as a function of the square root of the ionic strength...

Fig. 12.7 Relationship between inter-nitrogen distance of a,a>-diaminoalkanes, polyamines, and bisamidines, and binding affinity to lipid A. The inflection point of the sigmoidal curve coincides with the inter-phosphate distance of lipid A (inset)...

Fig. 17A (see color insert) shows a ribbon model of the rhodopsin structure indicating the residues assigned to the interface in each helix by a sphere centered on the corresponding of-carbon. Also shown is a sphere on the a-carbon of residue 314, which is located in the interface (see Section III,F). Clearly, these residues define a unique plane of intersection of the molecule with the membrane-aqueous interface. The shaded band in Fig. 17 represents a phospholipid bilayer with a phosphate-phosphate distance of 40 A, the expected thickness of the bilayer in the disk membrane (Saiz and Klein, 2001). The outer interface of the bilayer is positioned so that the polar head groups coincide with the intersection plane defined by the data in Fig. 16. This procedure then fixes the intersection plane of the molecule on the extracellular surface as well.

Nucleic acids usually bind alkali monovalent metal ions only in an atmospheric manner (in which the M+-phosphate distance is larger than 7 For polyvalent metal ions,... 

The presence of a metal on a phosphoryl transferring-enzyme provides no assurance that the metal is directly involved in phosphoryl transfer. Thus with alkaline phosphatase, no direct interactions of Cl- with enzyme bound Zn2+ (69) or water with enzyme-bound Mn2+ (70) were detected by nuclear relaxation. Similarly no direct interaction of phosphate with enzyme bound Co2+ (71) or Mn2+ (71, 72) was detected by 31P nuclear relaxation. A Mn2+ to phosphate distance of 7.3 A was calculated from NMR data on the inactive Mn2+-enzyme (73) indicative of a second sphere complex. These results are in accord with crystallographic data on the enzyme which at 7.7 A resolution indicate that substrates cannot easily gain direct access to the metal site (74). More recent proton relaxation studies with the Cu2+ enzyme, which retains 5% of the activity, indicate the presence of a rapidly exchanging axial hydroxyl ligand on Cu2+ suggesting that the active metals may promote the nucleophilicity of the water molecule which is to attack the phosphorus (75). 

Figure 17. The variation of the RE-to-phosphate distances is shown as a function of the RE-ion radius for both the monazite- and xenotime-structure orthophosphate compounds. As shown in this figure, the shorter RE-to-phosphorous distances in the monoclinic structure compounds vary linearly with the trivalent RE ion radius with a slope that is close to 1. A similar variation is evident for the RE-P distances in the tetragonal xenotime-structure compounds—a trend that supports the comparison of the [001] polyhedron-P04 tetrahedron chain arrangement in the two structural types (after Ni et al. 1995).

Distance matrix for eight ribose phosphate fragments. 

Multilayers of Diphosphates. One way to find surface reactions that may lead to the formation of SAMs is to look for reactions that result in an insoluble salt. This is the case for phosphate monolayers, based on their highly insoluble salts with tetravalent transition metal ions. In these salts, the phosphates form layer stmctures, one OH group sticking to either side. Thus, replacing the OH with an alkyl chain to form the alkyl phosphonic acid was expected to result in a bilayer stmcture with alkyl chains extending from both sides of the metal phosphate sheet (335). When zirconium (TV) is used the distance between next neighbor alkyl chains is - 0.53 nm, which forces either chain disorder or chain tilt so that VDW attractive interactions can be reestablished. 

Fig. 10. Pharmacophores for angiotension-converting enzyme. Distances in nm. (a) The stmcture of a semirigid inhibitor and distances between essential atoms from which one pharmacophore was derived (79). (b) In another pharmacophore, atom 1 is a potential zinc ligand (sulfhydryl or carboxylate oxygen), atom 2 is a neutral hydrogen bond acceptor, atom 3 is an anion (deprotonated sulfur or charged oxygen), atom 4 indicates the direction of a hydrogen bond to atom two, and atom 5 is the central atom of a carboxylate, sulfate, or phosphate of which atom 3 is an oxygen, or atom 5 is an unsaturated carbon when atom 3 is a deprotonated sulfur. The angle 1- -2- -3- -4 is —135 to —180° or 135 to 180°, and 1- -2- -3- -5 is —90 to 90°.

Fig. 20. Schematic representation of the unrolled major groove of the MPD 7 helix showing the first hydration shell, consisting of all solvent molecules that are directly associated with base edge N and O atoms. Base atoms are labeled N4,04, N6,06 and N7 solvent peaks are numbered. Interatomic distances are given in Aup to 3,5 A represented by unbroken lines, between 3,5-4,1 A by dotted lines. The eight circles connected by double-lines represent the image of a spermine molecule bound to phosphate groups P2 and P22. There are 20 solvent molecules in a first hydration layer associated with N- and O-atoms l58)...

NOTE As the reaction between calcium and orthophosphate is rapid, it is not generally advisable to add phosphate to the feedline at any great distance from the boiler because the precipitation of phosphate sludge may foul the line quickly and eventually cause a complete blockage. 

Figure 8 Possible structures of Sn sites in phosphate-bound [R2Sn(IV)] "-DNA, bond distance r=0.5 1 and [R3Sn(IV)]" -DNA, r=VA (adapted from Ref. (53)).

The use of DNA as a template to fabricate mesoscale structures was also demonstrated in a recent work of Torimoto and coworkers. They used preformed, positively charged 3-nm CdS nanoparticles with a thiocholine-modified surface to be assembled into chains by using the electrostatic interaction between positively charged nanoparticle snr-faces and the phosphate groups of DNA. As determined by TEM analysis, the CdS nanoparticles were arranged in a qnasi-one-dimensional dense packing. This revealed interparticle distances of about 3.5 nm, which is almost equal to the height of one helical tnm of the DNA double strand [98]. 

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