Dynamics flexible molecules

Remember that proteins (and other biological macromolecules) are quite dynamic, flexible molecules. Even at equilibrium, and just like all chemical equilibrium processes, this equilibrium is dynamic, since thermal motion never stops. For a two-state process, the exchange kinetics may be described by ... 

The density of states (DOS) of lattice phonons has been calculated by lattice dynamical methods [111]. The vibrational DOS of orthorhombic Ss up to about 500 cm has been determined by neutron scattering [121] and calculated by MD simulations of a flexible molecule model [118,122]. 

The authors believe that electron exchange occurs at every intramolecular collision . Thus, their work should provide the first quantitative measurements of the frequency of intramolecular collision between end-groups attached to flexible chains. According to these authors such frequency reflects an intrinsic property of chain molecules, referred to as the dynamic flexibility, which is a measure of the rate of conformational change. It should be distinguished from the static flexibility, which depends on the multitude of... 

Figure 6.2 Steering of photochemical reactions by coherent control of ultrafast electron dynamics in molecules by shaped femtosecond laser pulses. Ultrafast excitation of electronic target states in molecules launches distinct nuclear dynamics, which eventually lead to specific outcomes of the photochemical reaction. The ability to switch efficiently between different electronic target channels, optimally achieved by turning only a single control knob on the control field, provides an enhanced flexibility in the triggering of photochemical events, such as fragmentation, excited state vibration, and isomerization.

In formalism, many aspects of free-energy simulations lend themselves more to implementation within a Monte Carlo sampling scheme than within a molecular dynamics scheme. Unfortunately, MC schemes applied to large flexible molecules (e.g., proteins) tend to be very inefficient, since most proposed moves of the large molecule are rejected as being too energetically unreasonable, so MD simulations remain the standard. Innovative attempts to combine some of the best features of both have been described, as already noted in Chapter 3. 

Proteins are therefore dynamic, flexible objects whose physical and chemical properties are dominated, not only by their conformation, but also by the continual changes in conformation which are a consequence of their microscopic size22). The marginal stability of most protein conformations suggests that processes at one point in the protein might well have an effect on a portion of the molecule far removed. 

The crystalline state configuration of polymeric selenium is a helix in which all the rotational angles are of the same sign with a value of 78°. This is fairly close to the expected value of 90°.52 The barrier to rotation about the Se-Se bond is thought to be roughly the same as that about S-S bonds. No reliable experimental results are available on the statistical properties of these chains. Some values of the glass-transition temperature of polymeric selenium have been reported15 and these could at least provide a measure of the dynamic flexibility of the chains. However, these results are probably compromised by the presence of cyclic selenium molecules that act as plasticizer. 

As we have seen, the flexible and dynamic behavior of tubulin has consequences at two levels. Tubulin a/p heterodimers are flexible molecules in nature and change conformation in response to a series of stimuli, such as the polymerization status or the binding of ligands. Besides, tubulin heterodimers can self-assemble into MT and a number of other polymer forms like protofilaments, rings or spirals [5], The complexity of this dynamic behavior makes its structural studies both experimentally... 

Molecular modeling using either Monte-Carlo simulations or molecular dynamics is used to apply molecular mechanics energy minimizations to very complex systems [348]. In complex flexible molecules such as proteins or nucleic adds, the number of variable parameters, i.e., bond torsion angles, is such that the global search for energy minima becomes impossible The same problem occurs with theoretical calculations of water structure in aqueous solutions or in heavily hydrated crystals. 

At first glance this definition seems straightforward. What are some of the complications For flexible molecules McCrone would include conformational polymorphs, wherein the molecule can adopt different conformations in the different crystal structures (Corradini 1973 Panagiotopoulis et al. 1974 Bernstein and Hagler 1978 Bernstein 1987). But this is a matter of degree dynamic isomerism or tautomerism... 

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