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Free Energy, Entropy, and Induced Fit in Host−Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm
Abstract
This study applies a novel computational method to study molecular recognition for three sets of synthetic hosts: molecular clips, molecular tweezers, and a synthetic barbiturate receptor. The computed standard free energies of binding for the 12 binding reactions agree closely with experiment and provide insight into the roles of configurational entropy, preorganization, and induced fit in the systems studied. The computed changes in configurational entropy are comparable in magnitude to the changes in mean potential plus solvation energy, and they result primarily from changes in the average width of the energy wells upon binding. A strong correlation is observed between the changes in configurational energy and configurational entropy upon binding, resulting in near-linear compensation analogous to classical entropy-enthalpy compensation.
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Citations
Cited by
Supramolecular Binding Thermodynamics by Dispersion‐Corrected Density Functional Theory
Grimme, S. (2012) · Chemistry – A European Journal · doi:10.1002/chem.201200497 · Cited by 2,111
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
Chodera, J. D., & Mobley, D. L. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130318 · Cited by 531
Moghaddam, S., Yang, C., Rekharsky, M., Ko, Y. H., Kim, K., Inoue, Y., & Gilson, M. K. (2011) · Journal of the American Chemical Society · doi:10.1021/ja109904u · Cited by 344
Self-citationRapid Context-Dependent Ligand Desolvation in Molecular Docking
Mysinger, M. M., & Shoichet, B. K. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100214a · Cited by 317
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery
Valkov, E., Sharpe, T., Marsh, M., Greive, S., & Hyvönen, M. (2011) · Topics in Current Chemistry · doi:10.1007/128_2011_265 · Cited by 107
Metadata
- Authors
- Chang, C.-E., & Gilson, M. K.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2004-09-18
- Volume
- 126
- Issue
- 40
- Pages
- 13156-13164
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2089442765
- Cited by
- 211
- References
- 0
- FWCI
- 3.60
- Type
- journal article
- Language
- en
- Open access
- closed
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