Abstract
The fullerene-82 cavity is selected as a model system in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecular surface, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and cubic lattice approach to the molecular volume. Accurate measures of the molecular volume and surface area have been performed with the pseudorandom Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the rest of the methods. The SURMO2 method does not recognize the cavity and may not be convenient for intercalation compounds. The programs that detect the cavities never exceed 1% deviation relative to the reference value for molecular volume and 5% for surface area. The GEPOL algorithm, alone or combined with TOPO, shows results in good agreement with those of the UMCVS reference. The uniform random number generator provides the fastest convergence for UMCVS and a correct estimate of the standard deviations. The effect of the internal cavity on the solvent-accessible surfaces has been calculated. Fullerene-82 is compared with fullerene-60 and -70.
Highlights
Analyses of molecular packing in liquids and crystals [1] have shown that cavities may occur as a result of local packing defects
When comparing the molecular volume and surface (MCVS) results with the UMCVS references a bias of 2.5Å3 can be seen for the molecular volume [5 times greater than E(V)] and 2.9Å2 for the molecular surface area [4 times greater than E(S)]. This feature is a consequence of the nonuniform random number generator (RNG) used in MCVS, which results in an underestimation of standard deviations and errors
C82 has been selected as a model cavity in order to test eight different methods for characterizing inclusion molecules
Summary
Analyses of molecular packing in liquids and crystals [1] have shown that cavities may occur as a result of local packing defects. Molecular models are commonly represented as systems of fused hard spheres with unequal radii, and there has been an important body of work on the computation of surface area and volume of such systems [21] and on the topological description of their surfaces [22,23]. In large molecules such as proteins, where most of the van der Waals surface is buried in the interior, other, more suitable definitions such as the solvent-accessible surface [24,25] and solvent-excluding surface have been used.
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