Monte Carlo methods interactions

Sometimes the theoretical or computational approach to description of molecular structure, properties, and reactivity cannot be based on deterministic equations that can be solved by analytical or computational methods. The properties of a molecule or assembly of molecules may be known or describable only in a statistical sense. Molecules and assemblies of molecules exist in distributions of configuration, composition, momentum, and energy. Sometimes, this statistical character is best captured and studied by computer experiments molecular dynamics, Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. Interaction potentials based on quantum mechanics, classical particle mechanics, continuum mechanics, or empiricism are specified and the evolution of the system is then followed in time by simulation of motions resulting from these direct... 

Specific solute-solvent interactions involving the first solvation shell only can be treated in detail by discrete solvent models. The various approaches like point charge models, siipennoleciilar calculations, quantum theories of reactions in solution, and their implementations in Monte Carlo methods and molecular dynamics simulations like the Car-Parrinello method are discussed elsewhere in this encyclopedia. Here only some points will be briefly mentioned that seem of relevance for later sections. 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

Molecular mechanics methods have been used particularly for simulating surface-liquid interactions. Molecular mechanics calculations are called effective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force held is parameterized correctly. 

Some physical problems, such as those involving interaction of molecules, are usually formulated as integral equations. Monte Carlo methods are especially well-suited to their solution. This section cannot give a comprehensive treatment of such methods, but their use in... 

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

Kristof, T. Liszi, J., Application of a new Gibbs ensemble Monte Carlo method to site-site interaction model fluids, Mol. Phys. 1997, 90, 1031-1034... 

Monte Carlo calculations have been carried out to simulate the spin transition behaviour in both mono- and dinuclear systems [197]. The stepwise transition in [Fe(2-pic)3]Cl2-EtOH as well as its modification by metal dilution and application of pressure have been similarly modelled by considering short- and long-range interactions [52, 198, 199]. An additional study of the effect of metal dilution was successfully simulated with the Monte Carlo treatment considering direct and indirect inter-molecular interactions [200]. A very recent report deals with the application of the Monte Carlo method to mimic short- and long-range interactions in cooperative photo-induced LS—>HS conversion phenomena in two- and three-dimensional systems [201],... 

Enantiomers with a particular orientation were randomly generated by the Monte Carlo method on the surface of 23a and 23x defined by the particular van der Waals radius using the reported technique of blowing up the atomic radii.212 Molecular-mechanics calculations between the molecules were then performed step by step. The results of these calculations were evaluated with the averaged interaction energy. 

The main drawback with the application of Monte Carlo method in this ensemble lies in the fact that, due to the perturbation [34] that must be applied to the volume, it takes approximately 15% more of computing time than in the canonical (N,V,T) ensemble. Another possible problem is that some interaction potentials may lead to unreasonable densities in the calculation. 

Monte Carlo method, 210, 21 propagation, 210, 28] Gauss-Newton method, 210, 11 Marquardt method, 210, 16 Nelder-Mead simplex method, 210, 18 performance methods, 210, 9 sample analysis, 210, 29 steepest descent method, 210, 15) simultaneous [free energy of site-specific DNA-protein interactions, 210, 471 for model testing, 210, 463 for parameter estimation, 210, 463 separate analysis of individual experiments, 210, 475 for testing linear extrapolation model for protein unfolding, 210, 465. 

Figure 7.9. Variation of (a) the Gibbs energy, (b) ttie enthalpy and (c) the entropy with temperature (scaled to the nearest-nei bour interaction energy J ) for the complex structure A15. Comparison between BWG CVM in the tetrahedron approximation ( ) and the Monte Carlo method (—) (Turchi and Finel 1992).

Figure 3.2. Equilibrium linear susceptibility in reduced units X = x Hi[/m) versus temperature for three different ellipsoidal systems with equation x ja +y lb + jc < I, resulting in a system of N dipoles arranged on a simple cubic lattice. The points shown are the projection of the spins to the xz plane. The probing field is applied along the anisotropy axes, which are parallel to the z axis. The thick lines indicate the equilibrium susceptibility of the corresponding noninteracting system (which does not depend on the shape of the system and is the same in the three panels) thin lines show the susceptibility including the corrections due to the dipolar interaction obtained by thermodynamic perturbation theory [Eq. (3.22)] the symbols represent the susceptibility obtained with a Monte Carlo method. The dipolar interaction strength is itj = d/ 2o = 0.02.

Schrodinger equation. When the molecule is too large and difficult for quantum mechanical calculations, or the molecule interacts with many other molecules or an external field, we turn to the methods of molecular mechanics with empirical force fields. We compute and obtain numerical values of the partition functions, instead of precise formulas. The computation of thermodynamic properties proceeds by using a number of techniques, of which the most prominent are the molecular dynamics and the Monte Carlo methods. 

Response of the mean square dipole moment, < J2>, to excluded volume is evaluated for several chains via Monte-Carlo methods. The chains differ in the manner in which dipolar moment vectors are attached to the local coordinate systems for the skeletal bonds. In the unperturbed state, configurational statistics are those specified by the usual RIS model for linear PE chains. Excluded volume is introduced by requiring chain atoms participating in long-range interactions to behave as hard spheres. 

The end-to-end distribution of short polymer molecules (represented by a RIS model that includes long-range interactions through a hard-sphere potential is calculated by means of a Monte-Carlo method. The model predictions are contrasted with experimental data of the equilibrium cyclization constants. 

Cyclization of an acyclic polythioethylene chain to form (CHjCHjS)), is studied by Monte-Carlo methods for even x ranging from 4 to 24. Unperturbed acyclic chains are assumed to behave in accord with a RIS treatment which incorporates first- and second-order interactions. The most readily formed macrocycle is that with x = 6, in harmony with results obtained in the POE series. However, cyclization at all x considered is found to be more difficult for polythioethylene than for the equivalent polyoxyethylene. 

Allowing for rotation about the Ca—C bond (/.e., variation of ijr) and for some degree of freedom about the peptide bond [i.e., small variation of ro), the characteristic ratios of the form / (crs) and form II [trans) poly(L-proline) chain are calculated by a Monte Carlo method in which the conformational energies are used as weighting factors. The Monte Carlo method enabled short-range interactions (beyond those involved in a single residue) to be taken into account. 

---