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Identification of Isolated Cavity Features Within Molecular Dynamics Simulated Chromatographic Surfaces



Katrice A. Lippa, Lane C. Sander, Raymond D. Mountain


Highly ordered morphological features were characterized for molecular dynamics simulated alkyl-modified silica models that represent chromatographic materials with enhanced shape recognition capability. Deep cavities (8-10 wide) within the alkyl chains were identified for C18 polymeric models corresponding to shape-selective RPLC stationary phases. The all-trans conformational distal-end segments of these isolated cavities averaged over a 100 ps simulation time interval were observed to increase (up to 15 ) in models with an increase in both surface coverage and corresponding shape selectivity. Similar-structure cavities with significant alkyl chain ordered regions (>11 ) were isolated from two independent C18 models (differing in bonding chemistry, density and temperature) that represent highly shape-selective materials. The size and depth of these ordered regions increased (up to 28 ) for the extended-length C30 alkyl phase models. These initial results offer a physical representation of alkyl-modified surfaces that may facilitate the identification of potential molecular features that may be involved in the shape-selective retentive processes, as well as illustrating the potential for such computational techniques to predict the molecular recognition capabilities of novel analyte-specific sorbents.
128 No. 1-2
Conference Dates
June 13-14, 2005
Conference Title
Journal of Chromatography A


alkylsilanes, molecular surface area, monomeric, polymeric, reversed-phase liquid chromatography, RPLC, shape selectivity, trans conformation


Lippa, K. , Sander, L. and Mountain, R. (2006), Identification of Isolated Cavity Features Within Molecular Dynamics Simulated Chromatographic Surfaces, Journal of Chromatography A (Accessed June 12, 2024)


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Created July 1, 2006, Updated February 17, 2017