Intra-molecular dynamics

It is possible to encode an enormous amount of amplitude and phase information into a short pulse of electromagnetic radiation. The pulse can be designed to direct the intra-molecular dynamics toward an a priori specified target state, the pulse can be modified empirically based on some sort of learning algorithm to maximize a desired dynamical outcome (e.g., a specified photofragment) (Judson and Rabitz, 1992 Bardeen, et al., 1997 Feurer, et al., 2001 Rice and Zhao, 2000 Levis, et al., 2001 Weinacht, et al., 2001 Levis and Rabitz, 2002), or the pulse can be tailored to create a F(t) in which the amplitudes and phases of individual electronic or rotation-vibration eigenstates could be used as a multibit memory element in a quantum computer (Ahn, et al., 2000 Ballard, et al., 2002). 

Fig. 5.16 Intra-molecular dynamics model for the interchange H and C atoms of TMM+ between three equivalently distorted Civ structures with the ground A2 state rj...

The Colonel taught chemists to think about (a) three-center bonds and fractional bonds, (b) intra-molecular dynamics, (c) boron hydrides, and (d) the... 

Wiewior, P. P. Shirota, H. Castner, E. W., Jr. (2002). Aqueous dimethyl sulfoxide solutions Inter- and intra-molecular dynamics. Journal of Chemical Physics, 116, 4643-4654... 

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

Reaction dynamics deals with the intra- and intermolecular motions that characterize the elementary act of a chemical reaction. It also deals with the quantum states of the reactants and product. Since the dynamic study is concerned with the microscopic level and dynamic behaviour of reacting molecules, therefore, the term molecular dynamics is employed. 

The diverse nature of chemical bonding arrangements exhibited by humus enables the formation of associations both with non-humic materials and with other humic materials to create a dynamic structure. Such a structure is capable of undergoing inter- and intra-molecular bonding to add or lose constituents or change configuration in response to ambient conditions. The chemically diverse and highly reactive nature of the humic matrix imparts the ability of humus both to lose and to acquire molecular moieties in a dynamic manner. 

Exploiting the principles of statistical mechanics, atomistic simulations allow for the calculation of macroscopically measurable properties from microscopic interactions. Structural quantities (such as intra- and intermolecular distances) as well as thermodynamic quantities (such as heat capacities) can be obtained. If the statistical sampling is carried out using the technique of molecular dynamics, then dynamic quantities (such as transport coefficients) can be calculated. Since electronic properties are beyond the scope of the method, the atomistic simulation approach is primarily applicable to the thermodynamics half of the standard physical chemistry curriculum. 

Molecular dynamics in organometallic compounds is a potentially important area, as it can influence the course of solid-state reactions, and there are many such reactions known for organometallic compounds. Studying molecular dynamics can also give useful information on both intra- and intermolecular interactions, which between them govern molecular dynamics. This subject has been reviewed extensively elsewhere.126... 

Architecture of Hydrates and Local Structure of Acetic Acid Aqueous Solution Ab Initio Calculations and Car-Parrinello Molecular Dynamics (CPMD) Simulations on Hydrogen-Bonding Rings, Network, and Intra-Hydrate Protonation in Multi-Hydrates of Acetic Acid Monomer... 

Similiar problems are known in classical MD simulations, where intramolecular and intermolecular dynamics evolve on different time scales. One possible solution to this problem is the method of multiple time scale propagators which is describede in section 5. Berne and co-workers [21] first used different time steps to integrate the intra- and intermolecular degrees of freedom in order to reduce the computational effort drastically. The method is based on a Trotter-factorization of the classical Liouville-operator for the time evolution of the classical system, resulting in a time reversible propagation scheme. The multiple time scale approach has also been used to speed up Car-Parrinello simulations [20] and ab initio molecular dynamics algorithms [21]. 

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