Hydrogen, explicit

Some force fields replace the Lennard-Jones 6-12 term between hydrogen-bonding atoms by ail explicit hydrogen-bonding term, which is often described using a 10-12 Lennard-Jones potential ... 

United Atom force fields are used often for biological polymers. In these molecules, a reduced number of explicit hydrogens can have a notable effect on the speed of the calculation. Both the BlO-t and OPUS force fields are United Atom force fields. AMBER contains both a United and an All Atom force field. 

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). 

Metal-free organocatalysis through explicit hydrogen-bonding interactions. (P. R. Schreiner, 2003) [la]. 

Scheme 6.139) [293]. Ricci and co-workers explained the outcome of their aza-Michael reaction with the mechanistic picture visualized in Scheme 6.140 C9-epi-QN -derived thiourea 121 displayed a bifunctional mode of catalysis, which simultaneously activated both the chalcone Michael acceptor and the donor O-benzylhydroxylamine through explicit hydrogen bonding. 

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. 

Atom specification Elemental identity is represented by a standard atomic symbol without explicit hydrogen if the number of attached hydrogens... 

Draw six bonds starting at a common point - there is no need to worry about the geometry at this point. Note if the Explicit Hydrogens option in the Build menu is on, this creates six hydrogen atoms and it is therefore easier if this is turned off. If not, clicking on each atom in turn will convert it to a nitrogen atom. 

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. 

Normalization of the structure data set e.g., removal of explicit hydrogen atoms, standard representation of nitro, azido and similar groups, deionization , and removal of duplicate structures). 

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