Dihedral transitions

Figure 24 Probability distributions for the waiting time for 10 dihedral transitions. Time is given in units of the average waiting time 10x. The distributions are peaked around 10 = 1 and are much broader than the Poisson distribution but approach it for high T. For low T, a high probability for short waiting times exists and a long time tail of the distribution develops.

Figure 1. Schematic representation of the free-energy landscape of a polypeptide displaying different kinds of substates and energy barriers, such as cis-trans proline isomerisation, side chain dihedral transition, and to P backbone transition.

OPTICAL ACTIVITY IN DIGONAL DIHEDRAL TRANSITION METAL COMPLEXES. 

A1 OPTICAL ACTIVITY IN DIGONAL DIHEDRAL TRANSITION METAL COMPLEXES, A.D. Liehr... 

The rotational and translational diffusional properties of water were found to be dependent on the relative distance to the interface, slowing down with about a factor of two compared to bulk water behavior. Dihedral transitions in the hydrocarbon chains occurred with a mean time between transitions of 30 ps. This is 2.5 times slower than in the simple model system studied earlier the difference is related to the larger freedom of the headgroups in the direction perpendicular to the membrane surface. This freedom allows the chains to move vertically to accommodate steric hindrance in the chain region, rather than respond with dihedral transitions. The most... 

Readily available properties from simulations are densities. Older parameters of the chains, dihedral distributions, and the dynamics of dihedral transitions. 

You can detect hydroxyl group transitions hy plotting dihedral an gles versn s lime over the course of th e sim n lation. This is the distance history. Grady investigated the distance history of water... 

A powerful and general technique to enhance sampling is the use of umbrella potentials, discussed in Section IV. In the context of alchemical free energy simulations, for example, umbrella potentials have been used both to bias the system toward an experimentally determined conformation [26] and to promote conformational transitions by reducing dihedral and van der Waals energy terms involving atoms near a mutation site [67]. 

Based on the results for propene, we might guess that the transition structure i. halfway between the two minima the structure with a C-C-O-H dihedral angle ul 90°. We would need to verify this with optimization and frequency calculations. 

We can easily identify both structures by the value of the dihedral angle. In the one on the left, the dihedral angle has increased to 118.3°, indicating that this side of the path is leading to the trans form. Indeed, if we look at ail of the points in the reaction path, we see that the dihedral angle steadily increases on this side of the transition structure, and steadily decreases on the opposite side. From the latter, we can conclude that the right structure is tending toward the cis form. Thus, we have confirmed that this transition structure does in fact connect the cis and trans isomers of hydroxycarbene. 

Figure 4-11. INDQ/SCI-caleulalcd evolution of the transition energies (upper pan) and related intensities (bottom pan) of the lowest two optical transitions of a cofacial dimer formed by two stilbenc molecules separated by 4 A as a function of the dihedral angle between the long molecular axes, when rotating one molecule around the stacking axis and keeping the molecular planes parallel (case IV of Figure 4-10). Open squares (dosed circles) correspond to the S(J - S2 (S0 — S, > transition.

In several cases the transitions under tension involve the transformation of gauche-bonds to trans-bonds for instance, for PBT the transition is from a form with dihedral angles, relative to the bonds of the tetramethylene group, of the kind GGTGG toward a form with the same dihedral angles of the kind TTTTT. Analogously for PVDF, under tension, there is a transition from the a form (TGTG chains) toward the 3 form (TTTT chains). 

Among the evidence for the existence of the E2 mechanism are (1) the reaction displays the proper second-order kinetics (2) when the hydrogen is replaced by deuterium in second-order eliminations, there is an isotope effect of from 3 to 8, consistent with breaking of this bond in the rate-determining step. However, neither of these results alone could prove an E2 mechanism, since both are compatible with other mechanisms also (e.g., see ElcB p. 1308). The most compelling evidence for the E2 mechanism is found in stereochemical smdies. As will be illustrated in the examples below, the E2 mechanism is stereospecific the five atoms involved (including the base) in the transition state must be in one plane. There are two ways for this to happen. The H and X may be trans to one another (A) with a dihedral angle... 

There are two possible Cs conformations of the Sy homocycle exo and endo. The exo global minimum (Fig. 2) lies 15 kJ mol below the endo-form. Both conformers undergo facile pseudorotation through C2 transition states, with barriers of less than 4 kJ mol [54]. The exo-conformer possesses the geometry found in the sulfur allotropes y-Sy and 5-Sy [72]. This Cs structure has four bonds near the length of a normal S-S bond and one rather long bond of 215 pm with a dihedral angle of 0°. 

Two reasons may be offered for the enhanced /3-deuterium isotope effect in vinyl cations as compared with carbonium ions (193). As pointed out by Noyce and Schiavelli (21), in the transition state of a vinyl cation, the isotopically substituted C—H bond is ideally suited for overlap with the developing vacant p orbital, as the dihedral angle between the empty p orbital and C—H bonds is zero in the intermediate, as shown in structure 239. Shiner and co-workers (195)... 

The Taft relation Ej 2 = P 2a + x, which was found to hold for organic compounds and some transition metal complexes can also be of use here (37). Phenyl compounds do not fit the relation. This is probably due to a mesomeric effect that depends on the dihedral angle between the phenyl and the NCS2 planes. For bulky substituents deviations are also found which could be caused by widening of the CNC angle, changing the hybridisation of the N. The low values of p indicate that the M.O. s involved in the electron transfer have little ligand contribution. 

Fig. 19. Calculated coupling strength f (in cm-1, thin line) (Torri and Tasumi, 1998) and angle 0 (in degrees, thick line) between the two amide I transition dipoles as a function of the dihedral angles 0 and 0. From Woutersen and Hamm (2001)./. Chem. Phys. 114, 2727-2737, 2001, Reprinted with permission from American Institute of Physics.

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