Helicity descriptor

The 2,3-dihydro-l //-l, 4-bcnzodiazepin-2-ones exist as an equilibrium mixture of two conformers, designated by the helical descriptors M and P, that reflect chirality associated with the 7 -N(l)-C(7)-C(8) dihedral angle (Scheme 1). The interconversion barrier between the M- and P- atropoisomers is dependent upon the size of the N-l substituent with AG = 12.3, 18.0, 21.1, and >24 kcal mob1 for H, Me, /-propyl, and /-butyl, respectively, a function of increasing... 

In the section on "Helical Descriptors" (part of Section 6.1.2), we showed an allene and two related structures and gave M / P assignments. Show that the same assignments are obtained if you sight down the opposite end of the axis shown. 

Consider the experimental data from native starch. Fiber diffraction patterns indicate the helical symmetry and the pitch, so the main helical descriptors n and h can be worked out. One complication arises from the possibility of multistranded helices. The fiber axis repeat distance is 10.5 A and three-fold symmetry is indicated by diffraction spots on the meridian at the third and sixth layer lines. Those data could result from either a three-fold helix repeating in 10.5 A (n —3, p = 10.5 A), or from a double helix composed of two strands, with n 6 and p = 21.0 A, that are related by rotational symmetry. Modeling studies were important in working out the accepted double helical result. ... 

The first step for a successfid memory of chirality reaction should involve deprotonation of the stereogenic center in the enantiopure reactant (S)-substrate forming a conformationally chiral reactive (Af)-intermediate with high enantioselectivity. The helical descriptors (A/)- and Py are used to describe the chirality of the intermediates (see section 1.3.8). Most importantly, the conformationally chiral (M)-intermediate should not racemize easily on the time scale of the desired subsequent reaction. The final criterion is that the conformationally chiral intermediate must... 

This helicity descriptor should actually read (P,P,P) because in principle (though never observed as yet) one phenyl group could also be rotated in the contrary sense, thus leading to a (P,P,M) diastereomer. 

The author is well aware of the fact that many chemists still advocate use of the traditional RIS symbols also for at least some, if not all, compound types with helical stereogenic units, even if these are not in concordance with the proper helicity descriptors as in the case of axially chiral compounds where A M and A P. For the sake of consistency,... 

The first demand is easily solved by omitting the sign, i.e., disregarding helicity of the torsional angle. In order to solve problem , established descriptors are available ... 

M-), (P-) Stereochemical descriptors (M = minus, P = plus) introduced to describe the chirality of helical molecules. Extension of the CIP system to planar chirality gave an alternative description aR/aS for helical molecules such as helicenes, aR invariably = (M) and aS = (P), but for compounds showing planar chirality the reverse, with pR = (P) and pS = (M). Best avoided. See Section 7.3.2. 

Rigoutsos I, Riek P, Graham RM, Novotny J. Structural details (kinks and nonce conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. Nucleic Acids Res 2003 31 4625-4631. 

The folding patterns of hexapeptide fragments have been determined from the atomic coordinates of the protein structures using the standard procedure of Kabsch and Sander [66]. Every residue is given a secondary structure descriptor. To reduce complexity, residues were classified as helical h (G, H or I in Kabsch-Sander nomenclature), extended strand s (E), P turn t (T) or remained unassigned n. With these four structural classes there are still 4096 possible folding patterns for hexapep-... 

P and M descriptors a helical, propeller or screw-shaped structure (e.g. S has a helical chain) can be right- or left-handed and is termed P ( plus ) or M ( minus ), respectively. This is illustrated with P)- and (M)-hexahelicene ... 

Figure 6 Example of base stacking between base pairs. Main geometric descriptors of twist and rise are shown in relation to helical axis and backbone strand polarity, (a) Duplex DNA and a GC base pair (b) a stacked tetrad consisting exclusively of guanines bases...

Figure 1. Top P2]2i2i-unit cell (a = 9.535(2), b = 9.782(2), c = 16.428(3) A) of 15, left- and right-handed arrangement middle left-handed (A/) and right-handed helix P) of 15 where M and P are descriptors for helicity (M = minus and P = plus) bottom (l/ ,45)-16 and (15,4/f)-16.

Two simple shape descriptors use local properties of special bonds to characterize a macromolecular structure. These are the helical content and the distribution of peptidic dihedral angles (the Ramachandran diagram). 

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