Molecular modelling general methods

In this chapter we shall discuss some of the general principles involved in the two most common simulation techniques used in molecular modelling the molecular dynamics and the Monte Carlo methods. We shall also discuss several concepts that are common to both of these methods. A more detailed discussion of the two simulation methods can be found in Chapters 7 and 8. 

The operational model allows simulation of cellular response from receptor activation. In some cases, there may be cooperative effects in the stimulus-response cascades translating activation of receptor to tissue response. This can cause the resulting concentration-response curve to have a Hill coefficient different from unity. In general, there is a standard method for doing this namely, reexpressing the receptor occupancy and/or activation expression (defined by the particular molecular model of receptor function) in terms of the operational model with Hill coefficient not equal to unity. The operational model utilizes the concentration of response-producing receptor as the substrate for a Michaelis-Menten type of reaction, given as... 

Most liquid phase molecular simulations with explicit atomic polarizabilities are performed with MD rather than MC techniques. This is due to the fact that, despite its general computational simplicity, MC with explicit polarization [173, 174] requires that Eq. (9-21) be solved every MC step, when even one molecule in the system is moved, and the number of configurations in an average Monte Carlo computation is orders of magnitude greater than in a MD simulation. For nonpolarizable, pairwise-additive models, MC methods can be efficient because only the... 

Molecular mechanics is a useful and reliable computational method for structure, energy, and other molecular properties. The mathematical basis for molecular models in MM3 has been described, along with the limitations of the method. One of the major difficulties associated with molecular mechanics, in general, and MM3 in particular is the lack of accurately parameterized diverse functional groups. This lack of diverse functional groups has severely limited the use of MM3 in pharmaceutical applications. 

The reaction cycle discussed is generally accepted for unmodified cobalt and unmodified rhodium catalysts. But it has to be stressed here that to date no one has been able to prove the single steps conclusively it is still a subject of research, with modern techniques like in situ spectroscopic methods and molecular modeling in conjunction with kinetic investigations. 

Simulation methods have been proved to be useful in the study of many different molecular systems, in particular in the case of flexible polymers chains [ 14]. According to the variety of structures and the theoretical difficulties inherent to branched structures, simulation work is a very powerful tool in the study of this type of polymer, and can be applied to the general problems outHned above. Sometimes, this utility is manifested even for behaviors which can be explained with simple theoretical treatments in the case of linear chains. Thus, the description of the theta state of a star chain cannot be performed through the use of the simple Gaussian model. The adequate simulation model and method depend strongly on the particular problem investigated. Some cases require a realistic representation of the atoms in the molecular models [10]. Other cases, however, only require simplified coarse-grained models, where some real mon-... 

Some authors have described the time evolution of the system by more general methods than time-dependent perturbation theory. For example, War-shel and co-workers have attempted to calculate the evolution of the function /(r, Q, t) defined by Eq. (3) by a semi-classical method [44, 96] the probability for the system to occupy state v]/, is obtained by considering the fluctuations of the energy gap between and 11, which are induced by the trajectories of all the atoms of the system. These trajectories are generated through molecular dynamics models based on classical equations of motion. This method was in particular applied to simulate the kinetics of the primary electron transfer process in the bacterial reaction center [97]. Mikkelsen and Ratner have recently proposed a very different approach to the electron transfer problem, in which the time evolution of the system is described by a time-dependent statistical density operator [98, 99]. 

In principle, quantum mechanics permits the calculation of molecular energies and therefore thermodynamic properties. In practice, analytic solutions of the equations of wave mechanics are not generally accessible, especially for molecules with many atoms. However, with the advances in computer technology and programming, and the development of new computational methods, it is becoming feasible to calculate energies of molecules by ab initio quantum mechanics [11]. Furthermore, molecular modeling with substantial complexity and molecular mechanics treatments for... 

Williams analysis points the way, but still falls short of being a general method to calculate binding energy when the geometry of a complex is known directly from an X-ray determination, or can be surmised from molecular modelling. The approach suffers from two drawbacks. 

In the realni of classical thermodynamics, equations of state arc assumed given. They can be derived from first principles only by the methods of statistical mechanics and quantum mechanics These rely on the adoption of suitable molecular models for substances, and so far no universal, generally applicable model has heen discovered even for narrow classes of subslunces such as gases. 

It is often possible to obtain similar or identical results from statistical mechanics and from thermodynamics, and the assumption that a system will be in a state of maximal probability in equilibrium is equivalent to the law of entropy. The major difference between the two approaches is that thermodynamics starts with macroscopic laws of great generality and its results are independent of any particular molecular model of the system, while statistical methods always depend on some such model. 

It would be important to find analogous mechanism also for description of the main (librational) absorption band in water. After that it would be interesting to calculate for such molecular structures the spectral junction complex dielectric permittivity in terms of the ACF method. If this attempt will be successful, a new level of a nonheuristic molecular modeling of water and, generally, of aqueous media could be accomplished. We hope to convincingly demonstrate in the future that even a drastically simplified local-order structure of water could constitute a basis for a satisfactory description of the wideband spectra of water in terms of an analytical theory. 

---