ISSN:
0192-8651
Keywords:
cryptophanes
;
molecular dynamics
;
free energy perturbation
;
preorganization
;
binding selectivity
;
solvent effects
;
molecular recognition
;
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
Quantitative assessment of the “best fit” between neutral molecules and the cavity of a “rigid” neutral receptor is a challenging task in supramolecular chemistry, drug design, and biology. We investigate this question by molecular dynamics and free-energy perturbation simulations performed on the macrocyclic ligand cryptophane-E (L) and its L·S complexes with three tetrahedral guests (S=CH2Cl2, CHCl3, and CCl4) in the gas phase and in chloroform solution. The van der Waals interactions are shown to play a crucial role in the calculated complexation selectivity. Calculations using Lennard-Jones 6-12 potentials and “standard” OPLS R*Cl and εCl parameters for the Cl atoms of S lead to a preference for CCl4, in contrast to the selectivities observed experimentally in solution (CHCl3 〉 CH2Cl2 〉 CCl4). Based on systematic investigations of the relative free energies of binding of CHCl3/S, we derive a set of R*Cl and εCl van der Waals parameters that account for experimental binding data. Although the complexes are of the van der Waals type, their electrostatic representation is also crucial for correct calculation of relative stabilities. Thus, the recognition of the “best guest” stems from a subtle balance of distance and time-dependent, cumulative noncovalent interactions between atoms of S and of L, which require an accurate representation. In addition, even in a weakly polar solvent, like chloroform, solvation effects are shown to modulate the recognition of the neutral substrates. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 820-832, 1998
Additional Material:
12 Ill.
Type of Medium:
Electronic Resource
