Intramolecular motion consequences

A remark seems here to be appropriate also concerning the comparison of electron diffraction. X-ray diffraction and theoretical results. There are inherent differences between the two diffraction experiments due to the difference in the nature of the physical phenomena involved and also the stmctures may be different indeed due to the difference in molecular environment especially when weak intramolecular interactions are of interest. The theoretical calculations yielding the equilibrium stmc lire are, on the other hand, closer to the unperturbed vapor-phase stmcture, but the relevant experimental data carry the consequences of averaging over the intramolecular motion. This may conceal important stmctural features especially in the case of large-amplitude motion as compared with the equilibrium stmcture. 

It must be remembered, furthermore, that the identification of the H-atom translocation mode is not equivalent to the identification of the reaction coordinate. We have attributed the absence of a deuterium isotope effect on the excited-state H-atom transfer (for the 10-ps component in hypericin and hypo-crellin A) to the zero-point energy in the proton coordinate lying above the barrier, with the H-atom being effectively delocalized between the two oxygen atoms. Consequently, the reaction coordinate for the excited-state H-atom transfer cannot be identified with the proton coordinate, and it must be concluded that other intramolecular motions are in fact responsible for the process. Temperature-dependent measurements indicate that these motions are extremely low amplitude, Ea 0.05 kcal/mol for hypericin [37]. Because the nature of this motion is not yet identified, we refer to it as the skeleton coordinate [48, 71, 82]. We propose that it is the time scale for this latter conformational change... 

Symmetry considerations are fundamental in any description of molecular vibrations, as will be seen later in detail (Chapter 5). First, however, the molecular symmetries will be discussed, ignoring entirely the motion of the molecules. Various molecular symmetries will be illustrated by examples. A simple model will also be discussed to gain some insight into the origins of the various shapes and symmetries in the world of molecules. Our considerations will be restricted, however, to relatively simple, thus rather symmetrical systems. The importance and consequences of intramolecular motion involving relatively large amplitudes, will be commented upon in the final section of this chapter. 

A detailed understanding of the intramolecular motion of highly excited molecules is important for understanding the dissociation dynamics, because the sequences of bound states just below the dissociation threshold continue as resonances to energies above the threshold [52]. Whether the dynamics around the threshold is chaotic or whether the eigenstates show characteristic feamres will have consequences for the lifetime of the excited complex and therefore on the dissociation rate. The same is true, of course, also for the inverse process— that is, the stabilization of complexes in collisions with gas atoms. 

The temperature dependence of proton couplings is probably a consequence of intramolecular motional modes. It also was reported in the early NMR work of Kreilick [36]. 

Numerical simulations have also been instrumental in elucidating the differences between simple and complex solvents in the way they dynamically respond to a newly created charge distribution. The importance of translational motions that change the composition or structure near the solute, the consequent early failure of linear response theory in such systems, and the possible involvement of solvent intramolecular motions in the solvation process were discovered in this way. 

In the interaction of a coherent laser beam with an ensemble of particles (atoms or molecules), one may treat the individual particles as nearly stationary, because even for a fast atomic/molecular beam the particles move only a few micrometres on the time-scale of the photon interaction. Consequently, if the laser photons are absorbed in the interaction, the coherence properties of the laser radiation are transferred to the particle ensemble. It is this coherence transfer that is exploited in experiments such as the orientation of reagents in chemical reactions, or the probing of intramolecular motion in transition states and orientation of products. 

Fortunately, so far at least as the sulphur bond configuration is concerned, the sulphone structures are relatively rigid systems and the various types of interatomic distances are not expected to differ considerably as a consequence of intramolecular motion. Thus eig. calculated K = + C y) >/2r... 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

Investigations on the pure networks (Sect. 7.1.1.3) led to the conclusion that the introduction of a mesh extender allows intramolecular cooperativity to develop. Consequently, it is interesting to determine whether the antiplasticiser prevents these intramolecular cooperative motions from occurring. 

It is worth noting that the cooperativity of p transition motions, observed in PMMA and MGIMx copolymers, is intramolecular, unlike the case of bisphenol A polycarbonate where intra- and intermolecular cooperativi-ties exist. The consequences of such a difference on the mechanical properties (in particular the strain softening) of these two types of polymers are investigated in a second paper [1]. 

In the ft-a crossover region, typically above 50 °C, the intramolecular co-operativity of the ft motions is such that they can be considered as precursors of the a motions. A direct consequence is that yielding and plastic flow can occur under almost identical stresses, as shown in the strain softening amplitude (Fig. 23). 

For micromechanisms of deformation, it clearly appears that the temperature at which SDZs appear is directly related to the high temperature part of the p transition and, consequently, to the occurrence of intramolecular cooperativity of the involved motions. Thus, SDZs appear at very low temperatures (- 120 °C) in BPA-PC, and at around - 100 °C or - 70 °C for xTy 11-y and MTyli-y copolyamides, respectively. For PMMA, SDZs appear at 50 °C, but at 10 °C for MGI-rich copolymers. It is interesting to note that the calculated transition temperatures for CSC-SDZ and SDZ-CDC, obtained by considering one of the compounds in a polymer series as a reference, lead to a satisfactory agreement with the experimentally determined ones. 

The vibrations within a molecular crystal cell are not only a result of molecular motions, but also the relative motions between neighboring molecules. Dominant features of the THz spectra are the sharp absorption peaks caused by phonon modes directly related to the crystalline structure [14], This result originates from the molecular vibrational modes and intramolecular vibrations associated, for example, with RDX [39], Consequently, vibrational modes are unique and distinctive feature of the crystalline explosive materials. The presence of broad features might also be caused by scattering from a structure with dimensions comparable to the THz wavelength. This can occur in materials that contain fibers or grains [37],... 

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