Hydrogen bond angles flexibility

Both SD and MD simulations of alkanes melts confined by solid surfaces (solid/liquid interfaces) and MD simulations of liquid alkanes at free surfaces (liquid/vapor interfaces) have been performed. The alkane molecules were represented by realistic atomistic force fields with constrained bond lengths. In all cases except Refs 29 and 30, the bond angle flexibility was maintained and in all cases the torsional flexibility was maintained. In most simulations the methyl and methylene groups were represented by single, spherically symmetric Lennard-Jones (LJ) force centers, i.e., the united atom (UA) approximation. Results from simulations which explicitly include the pendant hydrogen atoms as individual force centers, which we refer to as the explicit atom (EA) representation, will also be discussed. 

Hydrogen bonding takes place in three dimensions. Molecules are not planar but have various atoms and groups protruding at various angles. The hard segments tend to form cylindrical clusters with flexible chains in between. 

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