Gauche conformations, hydrogen bonds

With all-atom simulations the locations of the hydrogen atoms are known and so the order parameters can be calculated directly. Another structural property of interest is the ratio of trans conformations to gauche conformations for the CH2—CH2 bonds in the hydrocarbon tail. The trans gauche ratio can be estimated using a variety of experimental techniques such as Raman, infrared and NMR spectroscopy. 

Construct molecular models of the gauche and anti conformations of 1 2 ethanediol and explore the possibility of intramolecular hydrogen bond formation in each one... 

P212121 Z — 8 Dx= 1.57 R = 0.085 for 1,743 intensities. The two independent molecules have similar conformations. The glycosyl dispositions are anti (90.1°, 91.2°), and the D-ribosyl groups are 3T4 (24.0°, 34.1° 15.6°, 35.5°). The exocyclic, C-4 -C-5 bond orientations are gauche+ (63.1°, 53.8°). The orientation of the methyl groups in both molecules is such that it is directed away from the imidazole moiety of the base, that is, the 0-6-C-7 bond is trans to the C-5-C-6 bond this arrangement constitutes an obstacle to formation of Watson-Crick hydrogen-bonds to the complementary base cytosine. In molecule A, 0-6 and C-7 are displaced from the purine plane by 79 and 87 pm, and, in molecule B, by 49 and 16 pm. The bases are stacked. 

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