Conformational degrees of freedom

Note that large density fluctuations are suppressed by construction in a random lattice model. In order to include them, one could simply simulate a mixture of hard disks with internal conformational degrees of freedom. Very simple models of this kind, where the conformational degrees of freedom affect only the size or the shape of the disks, have been studied by Fraser et al. [206]. They are found to exhibit a broad spectrum of possible phase transitions. 

Gharge Transport in Single Au Alkanedithiol Au Junctions Coordination Geometries and Conformational Degrees of Freedom. Journal of the American Chemical Society, 130, 318-326. 

In an early work by Mertz and Pettitt, an open system was devised, in which an extended variable, representing the extent of protonation, was used to couple the system to a chemical potential reservoir [67], This method was demonstrated in the simulation of the acid-base reaction of acetic acid with water [67], Recently, PHMD methods based on continuous protonation states have been developed, in which a set of continuous titration coordinates, A, bound between 0 and 1, is propagated simultaneously with the conformational degrees of freedom in explicit or continuum solvent MD simulations. In the acidostat method developed by Borjesson and Hiinenberger for explicit solvent simulations [13], A. is relaxed towards the equilibrium value via a first-order coupling scheme in analogy to Berendsen s thermostat [10]. However, the theoretical basis for the equilibrium condition used in the derivation seems unclear [3], A test using the pKa calculation for several small amines did not yield HH titration behavior [13],... 

The titration coordinates evolve along with the dynamics of the conformational degrees of freedom, r, in simulations with GB implicit solvent models [37, 57], An extended Hamiltonian formalism, in analogy to the A dynamics technique developed for free energy calculations [50], is used to propagate the titration coordinates. The deprotonated and protonated states are those, for which the A value is approximately 1 or 0 (end-point states), respectively. Thus, in contrast to the acidostat method, where A represents the extent of deprotonation, is estimated from the relative occupancy of the states with A 1 (see later discussions). The extended Hamiltonian in the CPHMD method is a sum of the following terms [42],... 

Furthermore, it is often possible to extract from the structural analysis of solid solvates a significant information on solvation patterns and their relation to induced structural polymorphism. An interesting illustration has been provided by crystal structure determinations of solvated 2,4-dichloro-5-carboxy-benzsulfonimide (5)35). This compound contains a large number of polar functions and potential donors and acceptors of hydrogen bonds and appears to have only a few conformational degrees of freedom associated with soft modes of torsional isomerism. It co-crystallizes with a variety of solvents in different structural forms. The observed modes of crystallization and molecular conformation of the host compound were found to be primarily dependent on the nature of the solvent environment. Thus, from protic media such as water and wet acetic acid layered structures were formed which resemble intercalation type compounds. 

The quantity of primary interest in our thermodynamic construction is the partial molar Gibbs free energy or chemical potential of the solute in solution. This chemical potential reflects the conformational degrees of freedom of the solute and the solution conditions (temperature, pressure, and solvent composition) and provides the driving force for solute conformational transitions in solution. For a simple solute with no internal structure (i.e., no intramolecular degrees of freedom), this chemical potential can be expressed as... 

These groups will reduce the number of conformational degrees of freedom (such as bond rotation) in the reactants and/or intermediates. It is this reduction which is thought to facilitate cyclization relative to polymerization for these systems in essence, the enhancement of cyclization can be considered to be largely a consequence of favourable entropy effects. 

Figure 5.3 (a) Structure-determining factors in SAMs. Chemisorption of molecule onto substrate (1), intermolecular interactions (2) intramolecular conformational degrees of freedom (3) and interactions of SAM with the environment (4). 

The semiempirical valence electron methods have been widely employed for calculating total energies as a function of the conformational degrees of freedom the relative stability of conformers and energy barriers are obtained in the different acyl heterocyclic derivatives. The degree of reliability of the different approaches varies, depending only on the molecular structure ... 

In the present simplified model, we neglect conformational degrees of freedom of the PE and assume a straight polymer consisting of N monomers with a bond length (i.e. distance between dissociable groups) a, located at a distance D from a dielectric interface, as is depicted in Fig. 24. This model is applicable to stiff PEs and for strongly adsorbed PEs, since they are indeed flat. The exact partition function reads... 

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