Concerted rotations

Figure 1.7 (a) Molecular model of coronene (b) hexagonal close packing at the van der Waals diameter parts (c) and (d) illustrate the packing advantage, which can be obtained by a concerted rotation, counterclockwise or clockwise, of all molecules to allow... 

Keywords Monte Carlo simulations polypeptides polynucleotides concerted rotations multicanonical ensemble torsional space... 

On a lattice, so-called crankshaft moves are trivial implementations of concerted rotations [77]. They have been generalized to the off-lattice case [78] for a simplified protein model. For concerted rotation algorithms that allow conformational changes in the entire stretch, a discrete space of solutions arises when the number of constraints is exactly matched to the available degrees of freedom. The much-cited work by Go and Scheraga [79] formulates the loop-closure problem as a set of algebraic equations for six unknowns reducible... 

In summary, the recommended implementation for concerted rotation moves in MC simulations uses ... 

Ulmschneider, J.P., Jorgensen, W.L. Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias. J. Chem. Phys. 2003, 118, 4261-71. 

Dodd, L.R., Boone, T.D., Theodorou, D.N. A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses. Mol. Phys. 1993, 78, 961-96. 

A simpler (in the sense of fewer free parameters) stracture derived from that of perovskite is that of caldte, CCaOa. This may be obtained from the cubic structure by concerted rotations of CaOj octahedra about axes parallel to [111], so that the coordination of C is reduced from O12 to 03 In terms of anion coordination, this corresponds... 

The temperature dependence of AH2 for chloral-PC (Fig. 37) shows that the motions of phenyl rings occur above -80°C. Furthermore, the doublet shape observed for the lH spectrum above room temperature presents a splitting constant of 25 d= 0.2 G, which corresponds to the static interaction between the 2,3 phenyl protons, indicating that the phenyl motions do not affect the dipole-dipole interaction parallel to the 1,4 phenyl axis. A quantitative analysis of the intra- and inter molecular contributions to AH2 leads to the conclusion that the phenyl motions correspond to either isolated or concerted rotations around the 1,4 axis, with little (if any) reorientation of this axis. In addition, it excludes other motions as crankshaft motions, or motion of the phenyl-ethylenic unit as a group. The decrease of AH2 above - 40 °C could be intermolecular in nature. 

The MEP for dissociation of the dimer is defined by the condition that at every intermolecular distance R, 6X and 02 take the values so as to minimize the energy the potential along this MEP is modelec by a Morse potential with De = 4.3-4.5 kcal/mol and a = 1.45-1.55 A. The onedimensional barrier for interconversion and the corresponding correlation between d2 and 0, are presented in Figure 8.11a. The concerted rotation... 

Fig. 9 Schematic representation of the two hydrogen bonding arrangements involved in concerted rotation of the hydroxyl groups about the C-0 bonds in the clathrate of Dianin s compound [176]...

Disrotatory and conrotatory rotation The concerted rotation around two bonds in the same direction, either clockwise or counterclockwise, is described as conrotatory. In the electrocyclic ring opening, the terminal p-orbitals rotate (or twist, roughly 90°) in the same direction known as conrotation (comparable to antarafacial) to form a new ct-bond. In disrotatory cyclization (comparable to suprafacial) the terminal p-orbitals rotate in opposite directions. These two modes of the electrocyclic reaction are shown in Fig. 8.37. 

The orbital symmetry theory rationalizes the result shown above in terms of a disrotatory motion of the orbitals that are involved in the reaction. As shown in Fig. 8.61, the reaction involves simultaneous (concerted) rotation about the C2-C3, C3-C4, C5-C6 and C6-C7 bonds. Rotation about the C2-C3 bond proceeds in a clockwise direction, opposite to that around the C6-C7 bond. This is called a disrotatory motion. 

L. R. Dodd, T. D. Boone, and D. N. Theodorou, Mol. Phys., 78, 961 (1993). A Concerted Rotation Algorithm for Atomistic Monte Carlo Simulation of Polymer Melts and Glasses. 

Fig. 5.4 The r (N1-C1-C2-C3) and q> (Cl-C2-C3-C4) dihedral angles of the green fluorescent protein chromophore. In the protein R, is Gly67 and R2 is Ser65, and in HBDI, an often used model compound, = R2 = CH3. In r one-bond flips (r-OBF) the dihedral rotation occurs around the r torsional angle, in a (p-OBF it is around the (p dihedral angle, in a hula twist (HT) the (p and r dihedral angles concertedly rotate.

Crystallographic resolution of the thyroid receptonthyroxin complex has demonstrated that the active conformation of thyroxin 5 is the transoid form and that the cisoid isomer is not bound and cannot isomerize inside the binding site. Variable temperature m NMR experiments have shown that the CTI process seems to involve a relative motion of the aromatic cycles via a concerted rotation about

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