Nonbridging oxygen

Chirahty at the phosphoms is an unavoidable problem in all phosphorothioate syntheses. The phosphoramidite method produces a mixture of both the and the diastereomers having a small excess of the isomer (53). Although some progress has been made in the chiral synthesis of dinucleoside phosphorothioates, low yields have limited the utility of these approaches. The chiral center may be eliminated by replacing the other, nonbridging oxygen with sulfur. Avoidance of the chirahty problem is one reason for the interest in phosphorodithioates. 

Table 5.2 Relationship between the Si/O ratio in a glass, the number of nonbridging oxygens per tetrahedra, and the structure. (Adapted from...

Si/O Molar ratio Number of bridging oxygens per tetrahedron Number of nonbridging oxygens per tetrahedron Pattern of structure... 

The racemization of chiral substrate or the exchange of bridging and nonbridging oxygens during solvolysis (Scheme 8) may occur through an ion-pair reaction... 

The hnal rehned structure showed a 2, 3 -cyclic phosphate product at the Ci7 ribose position and a Cn nucleotide that had moved dramatically and become almost perpendicular to the Watson-Crick faces of conserved nucleotides Gs and Ae in the catalytic pocket. Interactions of functional groups of G5 and Ae with the product and Cn included (1) a hydrogen bond formed between the exocyclic amine (Ne) of Ag and the cyclic phosphate nonbridging oxygen... 

Figure 5.12. Chemical structure of antisense oligodeoxynucleotides (AS-ODN). Phosphorothioate and methylphosphonate AS-ODN have a sulfur atom and a methyl group respectively, substituted for a nonbridging oxygen atom to increase stability to nucleases.

See Positional Isotope Exchange Bridge-to-Nonbridge Oxygen Exchange... 

POSITIONAL ISOTOPE EXCHANGE BRIDGE-TO-NONBRIDGE OXYGEN EXCHANGE... 

Frenkel type reaction, thermally activated A+ leaves the potential minimum near the negatively charged nonbridging oxygen. We may understand this oxygen as a (03/2Si-0 ) unit (silicon tetrahedra to which it adheres included). We formalize this by writing V + R A+ = R V+A,-+. Vj is a cavity in the glass structure which... 

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