Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model

✍ Scribed by Potter, Michael J.; Kirchhoff, Paul D.; Carlson, Heather A.; McCammon, J. Andrew

• Publisher: John Wiley and Sons
• Year: 1999
• Tongue: English
• Weight: 373 KB
• Volume: 20
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19990715)20:9<956::aid-jcc7>3.0.co;2-r

✦ Synopsis

Time scales currently obtainable in explicit᎐solvent molecular dynamics simulations are inadequate for the study of many biologically important processes. This has led to increased interest in the use of continuum solvent models. For such models to be used effectively, it is important that their behavior relative to explicit simulation be clearly understood. Accordingly, 5 ns stochastic dynamics simulations of a derivative of cryptophane-E alone, and complexed with tetramethylammonium and neopentane were carried out. Solvation electrostatics were accounted for via solutions to the Poisson equation. Nonelectrostatic aspects of solvation were incorporated using a surface areadependent energy term. Comparison of the trajectories to those from previously reported 25 ns explicit᎐solvent simulations shows that use of a continuum solvent model results in enhanced sampling. Use of the continuum solvent model also results in a considerable increase in computational efficiency. The continuum solvent model is found to predict qualitative structural characteristics that are similar to those observed in explicit solvent. However, some differences are significant, and optimization of the continuum parameterization will be required for this method to become a efficient alternative to explicit᎐solvent