Torsion angle, definition

The bases are in syn or anti orientation. The orientation of the base relative to the sugar moiety is defined by torsion angle x which is constrained by steric interactions, and by the anomeric effect. The main conformations are referred to as syn and anti (see Fig. 17.5). In syn, j X is close to 0° (sp for torsion angle definition, see Box 13.3 Fig. 13.12), and the base is I oriented "above the ribose ring causing steric interactions which in the anti conformation with x close to 180° (ap) are avoided. The anti conformation is therefore preferred and is the j only form observed in double-helical DNA and RNA. An exception is the left-handed Z-DNA with alternating purine/pyrimidine nucleotide sequence where the purines are in the syn conformation. 

Note The formal lUPAC-IUB Commission on Biochemical Nomenclature convention for the definition of the torsion angles polypeptide chain (Biochemistry 9 3471-3479, 1970) is different from that used here, where the atom serves as the point of reference for both rotations, but the result is the same. (Irving Gas)... 

The definitions of the torsional angles are illustrated in Figure 2.7. To emphasize the symmetry (Cs) of the above conformation, the Z-matrix may also be given in terms of symbolic variables, where variables which aie equivalent by symmetry have identical names. 

Like many other chemical concepts the concept of strain is only semi-quantitative and lacks precise definition. Molecules are considered strained if they contain internal coordinates (interatomic distances (bond lengths, distances between non-bonded atoms), bond angles, torsion angles) which deviate from values regarded as normal and strain-free . For instance, the normal bond angle at the tetra-coordinated carbon atom is close to the tetrahedral value of 109.47°. In the course of force field calculations these normal values are defined more satisfactorily, though in a somewhat different way, as force field parameters. 

Fig. 1. A definition of a torsion angle B positive torsion angle C negative torsion angle... 

Definition of torsion angles about thoC -E y bond looking in the direction Cy Q. 

Data for some 90 compounds with the general structure [9] were analysed in terms of the twist-torsion angle r and the out-of-plane bending, x- which measures the extent of pyramidalization at the carbon and nitrogen centres. [Scheme 1. For full details see the definitions in the original paper (Kaftory et al., 1990).] In all cases is small (<5-6°), so pyramidalization at carbon... 

The role of the potential energy is taken by the Dyana target function [8, 28] that is defined such that it is zero if and only if all experimental distance constraints and torsion angle constraints are fulfilled and all nonbonded atom pairs satisfy a check for the absence of steric overlap. A conformation that satisfies the constraints more closely than another one will lead to a lower target function value. The exact definition of the Dyana target function is ... 

Scheme 2. Rotation possibilities for the diphenylguanidinium cation and definition of torsion angles (pi, (p2, X 2--...

A helical unit is inherently chiral. Its chirality sense or helicity can assume two values that correspond to the sign of the torsional angle. Although the definition of the sign is arbitrary (sec Section 1.1.1.). a universal scientific convention2 is followed (Klyne Prelog convention) ... 

Polypeptide(s) 56 - 59. See also Proteins antibiotics 66 chemical synthesis 85 conformation of 59 - 61, 78 definition of 51 torsion angles 59-62 Polypeptides. See also Peptides Polyphosphates 302, 303 Polyprenyl compounds... 

Prokaryotic cells, definition of 2 Proline (Pro, P) 52s in helices 69 reductases 753, 755 Proline rings, torsion angles 62 Prontosil 473s Proofreading... 

T4 lysozyme 33,497 helix stability of 528, 529 hydrophobic core stability of 533, 544 Tanford j8 value 544, 555, 578, 582-Temperature jump 137, 138, 541 protein folding 593 Terminal transferase 408,410 Ternary complex 120 Tertiary structure 22 Theorell-Chance mechanism 120 Thermodynamic cycles 125-131 acid denaturation 516,517 alchemical steps 129 double mutant cycles 129-131, 594 mutant cycles 129 specificity 381, 383 Thermolysin 22, 30,483-486 Thiamine pyrophosphate 62, 83 - 84 Thionesters 478 Thiol proteases 473,482 TNfn3 domain O-value analysis 594 folding kinetics 552 Torsion angle 16-18 Tbs-L-phenylalanine chloromethyl ketone (TPCK) 278, 475 Transaldolase 79 Tyransducin-o 315-317 Transit time 123-125 Transition state 47-49 definition 55... 

Figure 1.10 Definitions of the torsional angles fa ip, and w. These are all equal to 180° for a fully extended polypeptide chain (top left). to, defines rotation about the C,—Nl+1 bond. The normal tram planar peptide bond has = i/r = 180°, bottom) left, fa viewed along N —C bond (N >C) right, fa viewed along the C —C(C , — C j).

Fig. 10.9. Left-hand side Rotational excitation functions Ja and Jb for the dissociation of H2O2 through the lowest two excited states, A and B, as functions of the initial torsional angle tpo- IFa and Wb represent the corresponding weighting functions. For definitions see Section 6.3. Right-hand side The resulting final rotational state distributions of the OH products. Reproduced from Schinke and Staemmler (1988).

Despite recent progress in the study of the stereochemistry of tetraalkyl or aryl diphosphanes O. 2.. ) there is much uncertainty in the definition of the preferred torsional angle, 0 between the lone pairs on phosphorus atoms and there is little experimental evidence to assert the presence or absence of the tAani conformation in the liquid phase (4,5). We present here N.M.R. results obtained from two particular classes of diphosphanes, 1,2-disubstituted diphosphanes (RPH)2 (R = CH3, CH3CH2, c-CgHj1, C6H5, CF3) and CF3 substituted diphosphanes (CF3PX)2 (X = CH3, CN, Br,... 

SCHEME 6. Definition of two characteristic parameters describing the conformation of ditetrenes. k is the tilt angle of the R2E plane towards the E-E bond r is the twist angle, defined as arithmetic mean of the (signed) torsion angles x and r2, thus giving the distortion from an ideal trans-bent conformation (x = — r2)... 

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