Reaction cavity definition

M. J. Frisch, in Abstracts of Papers, 205th National Meeting of the American Chemical Society, Denver, CO, American Chemical Society, Washington, DC, 1993. Paper COMP 3 A Reaction Field Model Which Includes an Ab Initio Definition of the Reaction Cavity and a Comparison of All Current Reaction Field Models. 

Batch synthesis in single-mode reactors is definitely limited in scale as the size of the utilized microwave cavities is restricted to being monomodal. However, the Biotage Initiator EXP series allows a 100-fold linear scale-up when employing the different available vessel sizes, going from 0.2 mL to 20 mL operation volume (Fig. 1). Repetitive reaction cycles using the au-... 

Over the last years, the basic concepts embedded within the SCRF formalism have undergone some significant improvements, and there are several commonly used variants on this idea. To exemplify the different methods and how their results differ, one recent work from this group [52] considered the sensitivity of results to the particular variant chosen. Due to its dependence upon only the dipole moment of the solute, the older approach is referred to herein as the dipole variant. The dipole method is also crude in the sense that the solute is placed in a spherical cavity within the solute medium, not a very realistic shape in most cases. The polarizable continuum method (PCM) [53,54,55] embeds the solute in a cavity that more accurately mimics the shape of the molecule, created by a series of overlapping spheres. The reaction field is represented by an apparent surface charge approach. The standard PCM approach utilizes an integral equation formulation (IEF) [56,57], A variant of this method is the conductor-polarized continuum model (CPCM) [58] wherein the apparent charges distributed on the cavity surface are such that the total electrostatic potential cancels on the surface. The self-consistent isodensity PCM procedure [59] determines the cavity self-consistently from an isodensity surface. The UAHF (United Atom model for Hartree-Fock/6-31 G ) definition [60] was used for the construction of the solute cavity. 

Enzymatic reactions will be considered in another chapter of this book. We shall only remark that continuum ASC models, and in particular the PCM, may be of some help in studying reactions involving large molecules. In the set of approximations we have considered no additional changes in the PCM formalism were introduced. In particular, the same definition of cavity in terms of interlocking spheres, its partition in tesserae resulting from the inscription of a pentakisdodecahedron in each sphere, and the self-polarization of apparent charges, have been used. 

The expansion of the electrostatic potential into spherical harmonics is at the basis of the first quantum-continuum solvation methods (Rinaldi and Rivail, 1973 Tapia and Goschinski, 1975 Hylton McCreery et al., 1976). The starting points are the seminal Kirkwood s and Onsager s papers (Kirkwood 1934 Onsager 1936) the first one introducing the concept of cavity in the dielectric, and of the multipole expansion of the electrostatic potential in that spherical cavity, the second one the definition of the solvent reaction field and of its effect on a point dipole in a spherical cavity. The choice of this specific geometrical shape is not accidental, since multipole expansions work at their best for spherical cavities (and, with a little additional effort, for other regular shapes, such as ellipsoids or cylinders). 

The hole-size relationship between cations and crown ethers has been a part of the lore in the cation binding area for nearly two decades. Although, to our knowledge, no formal definition of this principle has ever been offered, the general concept seems to be that cation binding will be optimized when the cation diameter and macrocycle cavity size are identical. A simple consequence of this concept is the notion that 15-crown-5 is selective (binds more strongly) for Na+ over K+. We have measured the homogeneous (equilibrium) stability constants for the reaction... 

Enzymes are comprised of proteins which have definitive primary structures that can organize into secondary, tertiary and even quaternary structures. The enzyme consists of a peptide framework that contains cavities in which the catalytically reactive centers are incorporated. The enzyme protein is typically about 20-40 nm in size. The catalytically reactive centers can be part of the peptide that builds the enzyme framework such as carboxylic acid groups, or consist of cationic centers such as the porphyrins or nonreducible cations as Zn " " or Mg " " directly attached to the protein cavity. As mentioned earlier, the external part of the enzyme is hydrophilic and the internal microcavity is hydrophobic, with the possible exception of the often polar reaction center. In enzymatic reactions, the match between shape and size of reactant or product and catalytic center cavity is important. 

The NR changes activation parameters (ie, AG nr AG buik) and reduces the reaction activation energy barrier (ie, AG nr < AG buit) through stabilization of transition states (AG (Fig. 1.2a). Stabilization can stem from non-covalent interactions between the transition state and the functional groups in NR microenvironment, enthalpic stabilization (A/f ), and/or entropic factors [7], As mentioned before, encapsulation of substrate within the confined cavity of NR with definite size and shape can result in snbstrate preorganization toward the transition state and decrease the potential negative entropy of a reaction. 

Deep-cavity cavitands that dimerize into capsules via the hydrophobic effect, in the presence of a suitable guest molecule and in aqueous solution, have been developed by the Gibb group [110,111], Such complexes possess hydrophilic outer coats, hydrophobic rims that favor self-assembly, and deep hydrophobic pockets (up to 1 nm wide to 2 nm long). They have been used to drive the formation of high-definition assemblies with a number of guest molecules, including steroid and hydrocarbon molecules [112]. Reactions within the capsule (eg, selective oxidation of substrates) and potential applications in hydrocarbon gas separation [111] have been also achieved or demonstrated [113]. 

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