![]() ![]() The intrinsic flexibility of the pentoses in RNA allows dynamic transmission of information on the electronic character of the nucleobase to modulate the sugar conformation by an interplay of gauche and anomeric effects. The bonding order for the bridging \(P-O\) bonds in a phosphate diester group is about 1, and for the non-bridging \(P-O\) bonds about 1.5.Official URL: (SICI)1521-3773(19991216)3. In a phosphate diester, for example, the two non-bridging oxygens share a -1 charge, as illustrated by the two major resonance contributors below. In phosphate esters, diesters, and anhydrides the π bonding is delocalized primarily over the non-bridging bonds, while the bridging bonds have mainly single-bond character. This orbital arrangement allows for four s bonds with tetrahedral geometry in addition to a fifth, delocalized \(p\) bond formed by \(p\) overlap between the half-filled \(3d\) orbital on phosphorus and \(2p\) orbitals on the oxygen atoms. In contrast to an amine, however, four of the five valance electrons on phosphorus occupy \(sp^3\) orbitals, and the fifth occupies an unhybridized \(3d\) orbital. In the hybrid orbital picture for phosphate ion, a single \(3s\) and three \(3p\) orbitals also combine to form four \(sp^3\) hybrid orbitals with tetrahedral geometry. Recall from section 2.1 the hybrid bonding picture for the tetrahedral nitrogen in an amine group: a single \(2s\) and three \(2p\) orbitals combine to form four \(sp^3\) hybrid orbitals, three of which form s bonds and one of which holds a lone pair of electrons. The minus 3 charge on a fully deprotonated phosphate ion is spread evenly over the four oxygen atoms, and each phosphorus-oxygen bond can be considered to have 25% double bond character: in other words, the bond order is 1.25. Phosphorus can break the 'octet rule' because it is on the third row of the periodic table, and thus has \(d\) orbitals available for bonding. The four oxygen substituents in phosphate groups are arranged about the central phosphorus atom with tetrahedral geometry, however there are a total of five bonds to phosphorus - four s bonds and one delocalized \(\pi \) bond. However it is in the form of phosphate, rather than phosphine, that phosphorus plays its main role in biology. Indeed, phosphines - phosphorus analogs of amines - are commonly used in the organic laboratory. Looking at the location of phosphorus on the periodic table, you might expect it to bond and react in a fashion similar to nitrogen, which is located just above it in the same column. Notice that the 'P' abbreviation includes the associated oxygen atoms and negative charges. For example, glucose-6-phosphate and isopentenyl diphosphate are often depicted as shown below. Organic phosphates are often abbreviated using '\(OP\)' and '\(OPP\)' for mono- and diphosphates, respectively. ![]() The backbone of DNA is linked by phosphate diesters. An organic diphosphate has two bridging oxygens (one in the phosphate ester linkage and one in the phosphate anhydride linkage) and five non-bridging oxygens:Ī single phosphate is linked to two organic groups is called phosphate diester. ![]() Oxygen atoms in phosphate groups are referred to either as 'bridging' or 'non-bridging', depending on their position. Adenosine monophosphate (AMP) has a single phosphate ester linkage.Īdenosine triphosphate has one phosphate ester linkage and two phosphate anhydride linkages. The chemical linkage between phosphate and a carbon atom is a phosphate ester. When two phosphate groups are linked to each other, the linkage itself is referred to as a 'phosphate anhydride', and the compound is called 'inorganic pyrophosphate' (often abbreviated \(PP_i\)). The fully deprotonated conjugate base of phosphoric acid is called a phosphate ion, or inorganic phosphate (often abbreviated '\(P_i\)'). ![]()
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