Rotational molecular dynamics

Whichever is the mechanism of reorientation, the rotational molecular dynamics in condensed matter is a random process and usually can be... 

Because of limitations of space, this section concentrates very little on rotational motion and its interaction with the vibrations of a molecule. However, this is an extremely important aspect of molecular dynamics of long-standing interest, and with development of new methods it is the focus of mtense investigation [18, 19, 20. 21. 22 and 23]. One very interesting aspect of rotation-vibration dynamics involving geometric phases is addressed in section A1.2.20. 

The direct dissociation of diatomic molecules is the most well studied process in gas-surface dynamics, the one for which the combination of surface science and molecular beam teclmiques allied to the computation of total energies and detailed and painstaking solution of the molecular dynamics has been most successful. The result is a substantial body of knowledge concerning the importance of the various degrees of freedom (e.g. molecular rotation) to the reaction dynamics, the details of which are contained in a number of review articles [2, 36, 37, 38, 39, 40 and 41]. 

The interaction of a molecular species with electromagnetic fields can cause transitions to occur among the available molecular energy levels (electronic, vibrational, rotational, and nuclear spin). Collisions among molecular species likewise can cause transitions to occur. Time-dependent perturbation theory and the methods of molecular dynamics can be employed to treat such transitions. 

Run a molecular dynamics simulation, then rotate the molecular system in the Molecular Coordinate System. This changes the coordinates of all atoms, but not the velocity vectors present at the end of the last molecular dynamics simulation. 

Coordinates of atoms can be set by normal translation or rotation of HyperChem molecules. To set initial velocities, however, it is necessary to edit the HIN file explicitly. The unit of velocity in the HIN file is Angstroms/picosecond. Areact.hin file and a script react.scr are included with HyperChem to illustrate one simple reacting trajectory. In order to have these initial velocities used in a trajectory the Restart check box of the Molecular Dynamics Options dialog box must be checked. If it is not, the initial velocities in the HIN file will be ignored and a re-equilibration to the temperature T of the Molecular Dynamics Options dialog box will occur. This destroys any imposed initial conditions on the molecular dynamics trajectory. 

The relaxed structures of the various (rotational) symmetric toroidal forms were obtained by steepest decent molecular-dynamics simulations[15]. For the elongated tori derived from torus C240, the seven-fold rotational symmetry is found to be the most stable. Either five-fold or six-fold rotational symmetry is the most stable for the toroidal forms derived from tori Cjyo and C540, respectively (see Fig. 5). 

To make evaluations more definite, we use optical and microwave experimental data, as well as calculations of molecular dynamics of certain simple liquids which usually fit the experiment. Rotation is everywhere considered as classical, and the objects are two-atomic and spherical molecules, as well as hard ellipsoids. 

It was demonstrated in Chapter 6 that impact theory is able to describe qualitatively the main features of the drastic transformations of gas-phase spectra into liquid ones for the case of a linear molecule. The corresponding NMR projection of spectral collapse is also reproduced qualitatively. Does this reflect any pronounced physical mechanism of molecular dynamics In particular, can molecular rotation in dense media be thought of as free during short time intervals, interrupted by much shorter collisions ... 

The measurement of these angles for a series of [PdClj(NHC) P(OR)3 ] complexes permitted to evidence the remarkable flexibility of NHCs due to rotations aronnd the iV-substituent bonds [82]. This flexibility, captured by the allows NHCs to respond actively to the steric requirements of co-ligands. This is further confirmed by ab initio molecular dynamics simulations aimed at understanding the variability of ( )j and in a series of NHCs containing Ru-complexes relevant to olefin metathesis [83]. 

The set of rotations used in MPC dynamics can be chosen in various ways and the specific choice will determine the values of the transport properties of the system, just as the choice of the intermolecular potential will determine the transport properties in a system evolving by full molecular dynamics through Newton s equations of motion. It is often convenient to use rotations about a randomly chosen direction, n, by an angle a chosen from a set of angles. The... 

Vol. 9 Vibration-Rotational Spectroscopy and Molecular Dynamics ed. D. Papousek... 

---