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Koziol L, Essiz SG, Wong SE, et al. Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics. J Chem Theory Comput. 2013;9(3):1320-7doi: 10.1021/ct3008793.
Koziol, L., Essiz, S. G., Wong, S. E., Lau, E. Y., Valdez, C. A., Satcher, J. H., Aines, R. D., & Lightstone, F. C. (2013). Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics. Journal of chemical theory and computation, 9(3), 1320-7. https://doi.org/10.1021/ct3008793
Koziol, Lucas, et al. "Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics." Journal of chemical theory and computation vol. 9,3 (2013): 1320-7. doi: https://doi.org/10.1021/ct3008793
Koziol L, Essiz SG, Wong SE, Lau EY, Valdez CA, Satcher JH, Aines RD, Lightstone FC. Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics. J Chem Theory Comput. 2013 Mar 12;9(3):1320-7. doi: 10.1021/ct3008793. Epub 2013 Feb 20. PMID: 26587594.
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J Chem Theory Comput. 2013 Mar 12;9(3):1320-7. doi: 10.1021/ct3008793. Epub 2013 Feb 20.

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.

Journal of chemical theory and computation

Lucas Koziol, Sebnem G Essiz, Sergio E Wong, Edmond Y Lau, Carlos A Valdez, Joe H Satcher, Roger D Aines, Felice C Lightstone

Affiliations

  1. Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States.
  2. Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University , 34083 Fatih, Istanbul, Turkey.

PMID: 26587594 DOI: 10.1021/ct3008793

Abstract

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn(2+) aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H(+) + HCO3(-). On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

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