Potential fields intramolecular

Entropy production during chemical change has been interpreted [7] as the result of resistance, experienced by electrons, accelerated in the vacuum. The concept is illustrated by the initiation of chemical interaction in a sample of identical atoms subject to uniform compression. Reaction commences when the atoms, compacted into a symmetrical array, are further activated into the valence state as each atom releases an electron. The quantum potentials of individual atoms coalesce spontaneously into a common potential field of non-local intramolecular interaction. The redistribution of valence electrons from an atomic to a metallic stationary state lowers the potential energy, apparently without loss. However, the release of excess energy, amounting to Au = fivai — fimet per atom, into the environment, requires the acceleration of electronic charge from a state of rest, and is subject to radiation damping [99],... 

Exploration of intramolecular non-local effects could be the beginning of more far-reaching studies. Neural receptors with the ability to exchange information via the quantum-potential field in the vacuum interface, could be another level of quantum object that might eventually explain para-psychic phenomena. 

It is well known that intermolecular forces modify slightly the intramolecular potential field so that molecules have slightly different frequencies in the condensed and gaseous state. 

A very useful application of the formula above of the energy of the quantum oscillator resides in calculation of the energy of the weak intramolecular van der Walls interaction, specific of the biatomic molecules of noble gases (with the typical case of the molecule). Assuming a unidimensional model, or two atoms of Helium, each of them with the two valence electrons (say nos. 1 2), oscillating in the nuclei positive potential field. Then, the potential energy exerted by a system over the other (the nuclei are considered as fixed and separated at the R distance) will be (Putz, 2006) ... 

Neglecting on the first step the correlations between adsorbed molecules we shall describe the relaxation processes by one-pm ticle distribution function fc(E,r,t) of molecules of chemical sort c with energy E at point r. The adsorbed molecule is deemed to be in the static potential field (r, C) (where is the vector of intramolecular coordinates), that includes both static surface potential and the self-consistent potential of interaction between molecules. Each molecule interacts with the phonon and electron subsystems of solid body (inelastic and non-adiabatic interactions respectively) uid collides with other adsorbed molecules. Thus from the... 

The systematic study of piezochromism is a relatively new field. It is clear that, even within the restricted definition used here, many more systems win be found which exhibit piezochromic behavior. It is quite possible to find a variety of potential appUcations of this phenomenon. Many of them center around the estimation of the pressure or stress in some kind of restricted or localized geometry, eg, under a localized impact or shock in a crystal or polymer film, in such a film under tension or compression, or at the interface between bearings. More generally it conveys some basic information about inter- and intramolecular interactions that is useful in understanding processes at atmospheric pressure as well as under compression. 

Potential functions such as MM+ discussed in Chapter 1 are fine for intramolecular interactions. MD was developed long before such sophisticated force fields became available, and in any case the aims of MM and MD simulations tend to be quite different. MM studies tend to be concerned with the identification of equihbrium geometries of individual molecules whilst MD calculations tend to be concerned with the simulation of bulk properties. Inspection of Figure 2.2 suggests that the intramolecular details ought to be less important than the intermolecular ones, and early MD studies concentrated on the intermolecular potential rather than the intramolecular one. 

The rapid rise in computer power over the last ten years has opened up new possibilities for modelling complex chemical systems. One of the most important areas of chemical modelling has involved the use of classical force fields which represent molecules by atomistic potentials. Typically, a molecule is represented by a series of simple potential functions situated on each atom that can describe the non-bonded interaction energy between separate atomic sites. A further set of atom-based potentials can then be used to describe the intramolecular interactions within the molecule. Together, the potential functions comprise a force field for the molecule of interest. 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

The actual calculation consists of minimizing the intramolecular potential energy, or steric energy, as a function of the nuclear coordinates. The potential-energy expressions derive from the force-field concept that features in vibrational spectroscopic analysis according to the G-F-matrix formalism [111]. The G-matrix contains as elements atomic masses suitably reduced to match the internal displacement coordinates (matrix D) in defining the vibrational kinetic energy T of a molecule ... 

The resonance-mediated coupling mechanisms described above involve subtle quantal intramolecular/intermolecular donor-acceptor effects that tend to be inadequately described by current-generation empirical potentials. Simulations based on these potentials are therefore likely to be inherently defective for describing realistic folding processes in proteins. However, approximations such as those illustrated in Example 5.8 may ultimately make it feasible to incorporate additional resonance-mediated effects into empirical force fields of tractable form. 

A key to both methods is the force field that is used,65 or more precisely, the inter- and possibly intramolecular potentials, from which can be obtained the forces acting upon the particles and the total energy of the system. An elementary level is to take only solute-solvent intermolecular interactions into account. These are typically viewed as being electrostatic and dispersion/exchange-repulsion (sometimes denoted van der Waals) they are represented by Coulombic and (frequently) Lennard-Jones expressions ... 

The inter/intramolecular potentials that have been described may be viewed as classical in nature. An alternative is a hybrid quantum-mechanical/classical approach, in which the solute molecule is treated quantum-mechanically, but interactions involving the solvent are handled classically. Such methods are often labeled QM/MM, the MM reflecting the fact that classical force fields are utilized in molecular mechanics. An effective Hamiltonian Hefl is written for the entire solute/solvent system ... 

---