Dihedral angle rotation

Vicinal to each other (a I 4 dihedral angle rotation relation-sh ip)... 

DAD-XYZ and finally these cartesian coordinates arrive in ARTEP which generates the new picture. All these steps are repeated 10 times (for example, if one wants to study a 60° variation of a given dihedral angle, ROTATION adds 6° ten times to this angle and, via ARTEP, calculates the ten corresponding pictures). The 10 pictures are saved on a diskette named IMSTOCK and animated then by the MOUVEMENT (= Movement) program (Fig. 49). 

MM force fields include the use of ab initio quantum chemical results to improve the potential energy surface for peptide backbone dihedral angle rotation.75,76... 

Stochastic dynamics has been found to be particularly useful for introducing simplified descriptions of the internal motions of complex systems. When applied to small systems (e.g., a peptide or an amino acid sidechain) it is possible to do simulations that extend into the microsecond range, where many important phenomena occur. Simulation studies using this method have been carried out, for example, to explore solvent effects on the dynamics of internal soft degrees of freedom in small biopolymers, e.g., the dynamics of dihedral angle rotations in the alanine dipeptide (see Chapt. IX.B.l). 

Vn is often called the barrier of rotation. This is intuitive but misleading, because the exact energetic barrier of a particular rotation is the sum of all V components and other non-bonding interactions with the atoms under consideration. The multiplicity n gives the number of minima of the function during a 360° rotation of the dihedral angle o). The phase y defines the exact position of the minima. 

The functional form for dihedral angle (torsional) rotation is identical to that shown in equation (13) on page 175. The barrier heights are in kcal/mol and are in the file pointed to by the Fouri-erTorsion entry for the parameter set in the Registry or the chem. ini file, usually called tor.txt(dbf). If more than one term is... 

The //NMR spectrum (Fig. 2.19) displays anAB system for the protons adjacent to this bond the coupling constant = 72 Hz. From this can be deduced first that the dihedral angle 9 between the C7/bonds is about 180°, second that conformer 14b with minimised steric repulsion between the substituents predominates and third that there is restricted rotation around this CC bond. 

This table gives the displacements for the normal mode corresponding to the imaginary frequency in terms of redundant internal coordinates (several zero-valued coordinates have been eliminated). The most significant values in this list are for the dihedral angles D1 through D6. When we examine the standard orientation, we realize that such motion corresponds to a rotation of the methyl group. 

Step through the sequence of structures depicting rotation about the C i - C+ bond in 2-methyl-2-butyl cation. Plot energy (vertical axis) vs. CCCC dihedral angle (horizontal axis). What is the preferred conformation, with the ethyl group in plane or perpendicular to the plane ... 

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