Furanoses pseudorotation

The furanose rings of the deoxyribose units of DNA are conformationally labile. All flexible forms of cyclopentane and related rings are of nearly constant strain and pseudorotations take place by a fast wave-like motion around the ring The flexibility of the furanose rings (M, Levitt, 1978) is presumably responsible for the partial unraveling of the DNA double helix in biological processes. 

Ab initio molecular orbital calculations (using the Gaussian 80 computer program) on the barrier to pseudorotation (for the furanose ring) of two model compounds, 2-deoxy-/ -D- /) cero-tetrofuranosylamine (781) and 2-deoxy-2-fluoro-)3-D-erythrofuranosylamine (782) were reported. Al-... 

The conformational dynamics of furanose rings may be described by the mechanisms of pseudorotation and inversion. The former mechanism describes a continuous pathway of interconversion between twenty idealized non-planar (envelope, twist) conformers (Figures 1 and 2) that does not involve the planar form (e.g., - E4 — ... 

Figure 1. The pseudorotational itinerary 2-14 describing the interconversion of non-planar furanose conformers. Regions of the itinerary are denoted as north, south, east and west as indicated. Envelope and twist conformers are denoted by E and T, respectively.

Energy profiles in Figure 14 also reveal that planar furanose forms are often of lower energy than puckered conformers. For example, relative conformational energies determined for 7 with the 3-21G basis set indicate that the planar conformer is more stable than the Eq conformer in 8, the planar conformer is calculated to be more stable than. These observations suggest that the conformational dynamics of some furanose rings may not be completely described by pseudorotation in these cases,conformer interconversion may occur by both inversion and pseudorotational pathways, with the latter being the more preferred route. 

Figure 11.3. The pseudorotation cycle showing the relation between the pseudorotation angle P (0-360°) calculated from the five torsional angles of the furanose.

Furanose flve-membered rings are never planar. They adopt a puckered form for which a family of pseudorotational conformers [541] are possible. The main conformations are the envelope and twist forms denoted by atom names, Le., C(2 ) and C(3 ), and descriptors endo and exo. They refer to the displacement of these atoms from the mean plane through the other atoms of the five-membered ring, with reference to the exocyclic C(4 )-C(5 ) bond (Fig. 17.4). 

ROder O, LUdemann HD, von Goldammer E (1975) Determination of the activation energy for pseudorotation of the furanose ring in nucleosides by 13C nuclear-magnetic resonance relaxation. Eur J Biochem 53 517-524... 

A module for unsubstituted 2-deoxy-cryt/iro-jS-pentofuranose permits the calculation from the pseudorotation angle of all the /ch, 2./ci i, and 3/CH couplings around the furanose ring, except that, in some cases, the relative proportions of the two... 

Roder, 0., Ludemann, H. D., and Von Goldammer, E. (1975). Eur. J. Biochem. 53, 517. Determination of the Activation Energy for Pseudorotation of the Furanose Ring in Nucleosides by 13C Nuclear Magnetic Resonance Relaxation. 

The pseudorotation concept was introduced to describe the continuous interconversion of puckered forms of the cyclopentane ring [104]. The same concept is applied to the furanose geometry where the Cl, 04, and C4 atoms lie in one plane and the C2 and C3 atoms lie above and below that plane. A statistical analysis of X-ray crystal structures of nucleosides and nucleotides has shown that North (N) 130 and South (S) 131 conformations are the most dominant forms, which has been the basis of the assumption of the two-state N — S pseudorotational equilibrium in solution (Fig. 2.44). 

The pseudorotation concept has been introduced by K. S. Pitzer [49] to describe the continuous interconversions between an infinite number of indefinite puckered conformations of the cyclopentane ring. PseudorotatiOTi [50] allows cyclopentane to relieve the ring strain, which would be induced by a 120° bond angle and the torsional strain by an eclipsed methylene group, if it were to adopt a planar conformation. A barrier to the planarity of cyclopentane of 22 kJ/mol has been reported [51]. The concept of pseudorotation has been applied for the first time to sugar furanoses by Hall et al. [52] studying the conformational analysis of pentofuranosyl fluorides. 

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