Explicit-hydrogen model

Attempts were made to include all hydrogen atoms explicitly in the simulations. This computationally demanding explicit-atom model shows (Fig. 1) that the crystal symmetry is orthorhombic, in agreement with the well-known experimental result for polyethylene single crystals, instead of the hexagonal symmetry seen in united-atom model simulations. 

The first three terms, stretch, bend and torsion, are common to most force fields although their explicit form may vary. The nonbonded terms may be further divided into contributions from Van der Waals (VdW), electrostatic and hydrogen-bond interactions. Most force fields include potential functions for the first two interaction types (Lennard-Jones type or Buckingham type functions for VdW interactions and charge-charge or dipole-dipole terms for the electrostatic interactions). Explicit hydrogen-bond functions are less common and such interactions are often modeled by the VdW expression with special parameters for the atoms which participate in the hydrogen bond (see below). 

In other words, since for solvents with H-bonding ability (methanol and water) the aN of the nitroxide radical is shifted to higher values because of the influence of one or more hydrogen bonds between the solute and the solvent, it becomes necessary to build a model in which nonspecific effects are described in terms of continuum polarizable medium with a dielectric constant typical of the protic solvent under study, whereas specific effects are taken into account through an explicit hydrogen-bonded complex between the radical and some solvent molecules. Figure 2.6 reports the aN values for the complexes formed by TEMPO with phenol, methanol, and water measured experimentally at room temperature, and computed in the gas phase and in solution. The values computed in solution fit the experimental data quite well. 

In the Build menu check that Explicit Hydrogens has been selected and then select the Model Build option. 

In the Build menu turn off Explicit Hydrogens and then select the Add H Model Build option. This should generate sensible chelate rings but each nitrogen atom will only have one hydrogen atom attached. 

Calculations at the B3LYP/6-31G level were used to show how hydrogen bond formation influences the chemical reactivity of ketones.70 The effect of the chloroform on the activation energies was modelled by means of discrete-continuum models. Explicit hydrogen bond formation to chloroform lowers the gas-phase activation barrier. A DFT analysis of the global electrophilicity of the reagents provided a sound explanation of the catalytic effects of chloroform (see Table 6 and Chart 3). The electrophilicity of acetone... 

Lynden-Bell and coworkers examined the validity of this approximation by simulating systems with fully explicit methyl groups (i.e. aU hydrogens) as well as united atom models. They found that the united atom approximation leads to a higher density in both the liquid and crystalline states. As a consequence, the dynamics of the united atom system are somewhat slower than for the case of the explicit atom model. 

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