Dynamic cavity model

Identical olfactory neurons are located in different places in the cavity, and therefore occupy different positions in the flow path. By using a nasal cavity model, we investigated the influence of the dynamic flow on the sensors response14. The responses from identical fiber optic sensors located... 

The study of solvatochromic shifts is of great importance and has received enormous theoretical attention in recent years. Progress has been achieved in the use of the self-consistent reaction field and cavity models. These advances have also shown several limitations. It is thus of great interest to have alternative procedures to calculate solvent effects. In this respect the use of Monte Carlo/Molecular Dynamics simulations has been growing. In this paper we suggest a procedure to allow a full quantum mechanical calculation of the solute-solvent system. The basic idea is to treat the solute, the solvent and its interaction by quantum mechanics. First a Monte Carlo simulation is performed to characterize the liquid structure. These structures are then used in the quantum mechanical calculation. As a liquid has not one but a great number of structures equally possible within a... 

Figure 9.5 Model for a dipole in a dielectric. The two opposite charges form a dipole that can change its magnitude as a result of their connection by a spring. Inside the cavity, we assume the presence of electronic polarization that adjusts instantaneously to a change in dipole moment but outside the cavity there is polarizable solvent with its own dynamic properties, modeled by the dielectric constant e(o>). The dipole inside...

The noble gases are mostly unreactive. In some instances, they act mostly as a place holder to fill a cavity. For dynamical studies of the bulk gas phase or liquid-phase noble gases, hard-sphere or soft-sphere models work rather well. 

Recently, many experiments have been performed on the structure and dynamics of liquids in porous glasses [175-190]. These studies are difficult to interpret because of the inhomogeneity of the sample. Simulations of water in a cylindrical cavity inside a block of hydrophilic Vycor glass have recently been performed [24,191,192] to facilitate the analysis of experimental results. Water molecules interact with Vycor atoms, using an empirical potential model which consists of (12-6) Lennard-Jones and Coulomb interactions. All atoms in the Vycor block are immobile. For details see Ref. 191. We have simulated samples at room temperature, which are filled with water to between 19 and 96 percent of the maximum possible amount. Because of the hydrophilicity of the glass, water molecules cover the surface already in nearly empty pores no molecules are found in the pore center in this case, although the density distribution is rather wide. When the amount of water increases, the center of the pore fills. Only in the case of 96 percent filling, a continuous aqueous phase without a cavity in the center of the pore is observed. 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

Tatake PA, Pandit AB (2002) Modeling and experimental investigation into cavity dynamics and cavitational yield Influences of dual frequency ultrasound sources. Chem Eng Sci 57 4987 1995... 

Continuum models remove the difficulties associated with the statistical sampling of phase space, but they do so at the cost of losing molecular-level detail. In most continuum models, dynamical properties associated with the solvent and with solute-solvent interactions are replaced by equilibrium averages. Furthermore, the choice of where the primary subsystem ends and the dielectric continuum begins , i.e., the boundary and the shape of the cavity containing the primary subsystem, is ambiguous (since such a boundary is intrinsically nonphysical). Typically this boundary is placed on some sort of van der Waals envelope of either the solute or the solute plus a few key solvent molecules. 

Parchment et al. [271] have provided more recent calculations on the 3-hydroxypyrazole equilibrium at the ab initio level. They noted that tautomer 9, which was not considered by Karelson et al. [268], is the lowest-energy tautomer in the gas phase at levels of theory (including AMI) up to MP4/6-31G //HF/3-21G [271], Although 8 is the dominant tautomer observed experimentally in aqueous solution, in the gas phase 8 is predicted to be nearly 9 kcal/mol less stable than 9 at the MP4 level [271], Using a DO model with an unphysically small cavity radius of 2.5 A, Parchment et al. [271] were able to reproduce at the ab initio level the AMI-DO prediction of Karelson et al. [268], namely that 8 is the most stable tautomer in aqueous solution. With this cavity, though, 8 is predicted to be better solvated than 9 by -22.2 kcal/mol [271], This result is inconsistent with molecular dynamics simulations with explicit aqueous solvation [271], and with PCM and SCME calculations with more reasonable cavities [271] these predict that 8 is only about 3 kcal/mol better solvated than 9. In summary, the most complete models used by Parchment et al. do not lead to agreement with experiment... 

The dynamics of carbon-halogen bond reductive cleavage in alkyl halides was studied by MP3 ab initio calculations, using pseudopotentials for the halogens and semidiffuse functions for the heavy atoms [104], The effect of solvent was treated by means of the ellipsoidal cavity dielectric continuum model. Both a concerted (i.e., a one-step) and a stepwise mechanism (in which an anion radical is formed at first) were... 

Quantitative models of solute-solvent systems are often divided into two broad classes, depending upon whether the solvent is treated as being composed of discrete molecules or as a continuum. Molecular dynamics and Monte Carlo simulations are examples of the former 8"11 the interaction of a solute molecule with each of hundreds or sometimes even thousands of solvent molecules is explicitly taken into account, over a lengthy series of steps. This clearly puts a considerable demand upon computer resources. The different continuum models,11"16 which have evolved from the work of Bom,17 Bell,18 Kirkwood,19 and Onsager20 in the pre-computer era, view the solvent as a continuous, polarizable isotropic medium in which the solute molecule is contained within a cavity. The division into discrete and continuum models is of course not a rigorous one there are many variants that combine elements of both. For example, the solute molecule might be surrounded by a first solvation shell with the constituents of which it interacts explicitly, while beyond this is the continuum solvent.16... 

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