Browsing by Author "Ayers, Paul W."
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- ItemComputational Study of the Binding Modes of Caffeine to the Adenosine A2A Receptor(2011) Liu, Yuli; Burger, Steven K.; Ayers, Paul W.; Voehringer-Martinez, EstebanUsing the recently solved crystal structure of the human adenosine A(2A) receptor, we applied MM/PBSA to compare the binding modes of caffeine with those of the high-affinity selective antagonist ZM241385. MD simulations were performed in the environment of the lipid membrane bilayer. Four low-energy binding modes of caffeine-A(2A) were found, all of which had similar energies. Assuming an equal contribution of each binding mode of caffeine, the computed binding free energy difference between caffeine and ZM241385 is -2.4 kcal/mol, which compares favorably with the experimental value, -3.6 kcal/mol. The configurational entropy contribution of -0.9 kcal/mol from multiple binding modes of caffeine helps explain how a small molecule like caffeine can compete with a significantly larger molecule, ZM241385, which can form many more interactions with the receptor. We also performed residue-wise energy decomposition and found that Phe168, Leu249, and Ile274 contribute most significantly to the binding modes of caffeine and ZM241385.
- ItemForeword for the Festschrift on the occasion of the 65th birthday of Professor Pratim Kumar Chattaraj(Springer-Verlag GmbH Germany, 2024) Proft, Frank de; Ayers, Paul W.; Liu, Shubin; Toro Labbé, Alejandro Miguel; Sarkar, Utpal
- ItemIn pursuit of negative Fukui functions : molecules with very small band gaps(2014) Echegaray Zipper, Eleonora Ana Luisa; Rabi, S.; Cardenas, C.; Heidar Zadeh, Farnaz; Rabi, Nataly; Lee, Sungmin; Anderson, James S.M.; Toro Labbé, Alejandro; Ayers, Paul W.
- ItemInsights into the Mechanism of an S(N)2 Reaction from the Reaction Force and the Reaction Electronic Flux(2012) Giri, Santanab; Echegaray Zipper, Eleonora Ana Luisa; Ayers, Paul W.; Nuñez, Alvaro S.; Lund, Fernando; Toro Labbé, Alejandro
- ItemPointing the way to the products? Comparison of the stress tensor and the second-derivative tensor of the electron density(2011) Guevara García, Alfredo; Echegaray Zipper, Eleonora Ana Luisa; Toro Labbé, Alejandro; Jenkins, Samantha; Kirk, Steven Robert; Ayers, Paul W.
- ItemRationalization of Diels-Alder reactions through the use of the dual reactivity descriptor Delta f(r)(2008) Morell, Christophe; Ayers, Paul W.; Grand, André; Gutiérrez Oliva, Soledad; Toro Labbé, Alejandro
- ItemRelationships between the third-order reactivity indicators in chemical density-functional theory(AMER INST PHYSICS, 2009) Cardenas, Carlos; Echegaray, Eleonora; Chakraborty, Debajit; Anderson, James S. M.; Ayers, Paul W.Relationships between third-order reactivity indicators in the closed system [N, v(r)], open system [mu, v(r)], and density [rho(r)] pictures are derived. Our method of derivation unifies and extends known results. Among the relationships is a link between the third-order response of the energy to changes in the density and the quadratic response of the density to changes in external potential. This provides a link between hyperpolarizability and the system's sensitivity to changes in electron density. The dual descriptor is a unifying feature of many of the formulas we derive.
- ItemThe mechanics of charge-shift bonds : A perspective from the electronic stress tensor(2011) Jenkins, Samantha; Kirk, Steven R.; Guevara García, Alfredo; Ayers, Paul W.; Echegaray Zipper, Eleonora Ana Luisa; Toro Labbé, Alejandro
- ItemThe Woodward-Hoffmann Rules Reinterpreted by Conceptual Density Functional Theory(2012) Geerlings, Paul; Ayers, Paul W.; Toro Labbé, Alejandro; Chattaraj, Pratim K.; De Proft, Frank
- ItemUnderstanding chemical binding using the Berlin function and the reaction force(ELSEVIER, 2012) Chakraborty, Debajit; Cardenas, Carlos; Echegaray, Eleonora; Toro Labbe, Alejandro; Ayers, Paul W.We use the derivative of the electron density with respect to the reaction coordinate, interpreted through the Berlin binding function, to identify portions of the reaction path where chemical bonds are breaking and forming. The results agree with the conventional description for S(N)2 reactions, but they are much more general and can be used to elucidate other types of reactions also. Our analysis offers support for, and detailed information about, the use of the reaction force profile to separate the reaction coordinates into intervals, each with characteristic extents of geometry change and electronic rearrangement. (C) 2012 Elsevier B.V. All rights reserved.