Proton molecular modeling approaches

The important impact of these experimental insights for molecular modeling is that the development of structure versus property relations of PEMs does not require multiscale approaches going all the way to the macroscopic scale. Rather, the main job is done if one arrives at the scale of several 10s of nanometers. Notably, operation at low hydration emphasizes even more the importance of (sub)nanoscale phenomena controlled by explicit interactions in the polymer-water-proton system. 

The complications for fhe fheoretical description of proton fransporf in the interfacial region befween polymer and water are caused by the flexibility of fhe side chains, fheir random distributions at polymeric aggregates, and their partial penetration into the bulk of water-filled pores. The importance of an appropriate flexibilify of hydrated side chains has been explored recently in extensive molecular modeling studies. Continuum dielectric approaches and molecular dynamics simulations have been utilized to explore the effects of sfafic inferfacial charge distributions on proton mobility in single-pore environments of Molecular level simulations were employed... 

A series of articles were published by Ennari et al. on MD simulation of transport processes in Poly(Ethylene Oxide) and sulfonic acid-based polymer electrolyte.136,137 The work was started by the determination of the parameters for the ions missing from the PCFF forcefield made by MSI (Molecular Simulations Inc.), to create a new forcefield, NJPCFF. In the models, the proton is represented as a hard ball with a positive charge. Zhou et al. used the similar approach to model Nation.138 The repeating unit of Nafion (Fig. 17) was optimized using ab initio VAMP scheme. The protons were modeled with hydronium ions. Three unit cell or molecular models were used for the MD simulation. The unit cell contains 5000 atoms 20 pendent side chains, and branched Nafion backbone created with the repeating unit. Their water uptakes or water contents were 3, 13, or 22 IEO/SO3, which correspond to the room temperature water uptakes at 50% relative humidity (RH), at 100% RH, and in liquid water respectively.18 The temperature was initially set at a value between 298.15 and 423.15 K under NVE ensemble with constant particle number, constant volume (1 bar), and constant energy. 

In order to approach this problem, we must first identify the structure of the starting compound when the acidic proton is oriented fraws-periplanar to the bromide. The relevant configuration is illustrated below and can be visualized using molecular models. 

The steric effect is shown by the successive decrease in ft31 found for the reaction of hydrosulphide and acetate ions, which reflects the smaller solid angle of the surface of the anion available for reprotonation. Molecular models show that, for example, the proton can only approach the acetate ion over about half its surface, which corresponds to the halving of the recombination rate compared with that for fluoride. 

Whatever the explanation, the effect of acids is less marked than the selectivffy in alkaline solutions, where a attack is largely suppressed. The effect of alkali may depend upon the formation and selective reduction of enolate anions. The A2 4-dienolate anion, which is the major product of kinetically-controlled enolisation by bases (see p. 156) is seen from a molecular model to have a somewhat "folded conformation of the A/B ring system (ii). The convex / -face of the A/B ring system and the absence of an axial 2jS-proton should favour approach to the catalyst from this direction, whereas the a-face of the A -bond is severely hindered by the axial hydrogens at C(7) and C<9>. 

An interesting approach of structure refinement is based on the use of NOEs plus chemical shifts that are caused by intermolecular interactions. Iwadate et performed calculations on the geometry of a melittin tetramer at dilferent temperatures. The structural models rely on a relatively small number of intermolecular chemical shifts caused by the interaction of special groups such as tryptophan rings with protons. There are even a number of examples where aggregation chemical shifts are used to build and refine molecular models.For example, van Rossum et used the shift... 

The initial reaction is a Prins reaction, catalysed by the boron trifluoride complex. In order to achieve maximum overlap of the -orbitals of the olefin and aldehyde groups, the aldehyde must approach the olefin from below, as will easily be seen using molecular models. This means that the resultant alcohol function is located on the downward side of the molecule as shown in Figure S21. A 1,2-carbon shift followed by a transannular bond formation with concomitant loss of a proton, provides the skeletal rearrangement to the product. It may not be too obvious in the figure, but an experiment with molecular models will soon... 

A recently developed approach based inter alia on molecular modelling and on analysis of NMR data including vicinal proton-carbon couplings has been tested by Tanaka et alP They used one of the synthetic chiral dihydrofuro-angelicines, 4-methyl-8(2- -phenylethenyl)-8,9-dihydro-2H-furo[2.3-/i]-l-ben-zopyran-2-one, as a model compound and extended the method to establish the absolute stereochemistry of six new dihydrofuroangelicins bearing C-8 substituted double bonds. 

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