Computational analysis of a Zn-bound tris(imidazolyl) calix[6]arene aqua complex: Toward incorporating second-coordination sphere effects into carbonic anhydrase biomimetics

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn2+ 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 CO 2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

Original languageEnglish (US)
Pages (from-to)1320-1327
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume9
Issue number3
DOIs
StatePublished - Mar 12 2013
Externally publishedYes

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Carbonic anhydrase
carbonic anhydrase
Carbonic Anhydrases
biomimetics
Biomimetics
Conformations
cavities
Molecules
Bicarbonates
Hydration
Free energy
Calixarenes
hydration
molecules
carbonates
free energy
Water
Carbon Monoxide
Scaffolds (biology)
Carbon Dioxide

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Computational analysis of a Zn-bound tris(imidazolyl) calix[6]arene aqua complex : Toward incorporating second-coordination sphere effects into carbonic anhydrase biomimetics. / Koziol, Lucas; Essiz, Sebnem G.; Wong, Sergio E.; Lau, Edmond Y; Valdez, Carlos A.; Satcher, Joe H.; Aines, Roger D.; Lightstone, Felice C.

In: Journal of Chemical Theory and Computation, Vol. 9, No. 3, 12.03.2013, p. 1320-1327.

Research output: Contribution to journalArticle

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abstract = "Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn2+ 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 CO 2 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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T2 - Toward incorporating second-coordination sphere effects into carbonic anhydrase biomimetics

AU - Koziol, Lucas

AU - Essiz, Sebnem G.

AU - Wong, Sergio E.

AU - Lau, Edmond Y

AU - Valdez, Carlos A.

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AU - Aines, Roger D.

AU - Lightstone, Felice C

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