MP2//DFT calculations of interaction energies between acetaminophen and acetaminophen analogues and the aryl sulfotransferase active site

Investigating Paracetamol’s Role as a Potential Treatment for Parkinson’s Disease: Ab Initio Analysis of Dopamine, l-DOPA, Paracetamol, and NAPQI Interactions with Enzymes Involved in Dopamine Metabolism

“…Previous work in our group studied the accuracy of M06, M062X, and M06L for the types of systems studied here, and while the M06-L functional was found to be preferable for modeling systems that contain a transition metal, in this work, only three of the eight systems modeled included a metal, and therefore, M062X was used for all systems studied for consistency. The choice of basis sets used here was based on benchmark studies in our previous work . In this work, we are concerned with relative energies for various molecules in a single active site, and previous work has shown that for these relative comparisons, EBEs follow the same trends as Gibbs free energies of binding .…”

“…The choice of basis sets used here was based on benchmark studies in our previous work. 31 In this work, we are concerned with relative energies for various molecules in a single active site, and previous work has shown that for these relative comparisons, EBEs follow the same trends as Gibbs free energies of binding. 19 Thus, in this work, we use the EBEs to save computational expense.…”

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

“…Padgett left the consortium, Gao ( Central State ) rejoined, and Kelly Anderson ( Roanoke College , physical), Aimée Tomlinson ( North Georgia College , physical), and Sudeep Bhattacharyay and Jim Phillips ( University of Wisconsin‐Eau Claire , biophysical and physical) joined, bringing the total to 17 MERCURY investigators. We published 79 peer‐reviewed papers, [ 159–237 ] or 1.5 papers/faculty/year, which is three times the rate for physical science faculty at undergraduate institutions. [ 46 ] The Shields group's collaboration with Brooks Pate resulted in a Science paper on the structures and energetics of the gas‐phase water hexamer, [ 160 ] which has been cited over 250 times.…”

“…Mauricio Cafieros' research: The Cafiero group studies the binding of small molecules to proteins and the conformations of small peptides. They investigate acetaminophen metabolism by a sulfotransferase enzyme (SULT1A3), [ 197 ] using an active site model from a crystal structure [ 382 ] using DFT and MP2 methods. Working with an experimental collaborator, they expanded this study to how a suite of catecholaminic and catecholic molecules interacts with SULT1A3, [ 228,229 ] SULT1A1, catechol‐ o ‐methyltransferase, [ 260 ] phenylalanine hydroxylase, [ 354 ] tyrosine hydroxylase, [ 308 ] and other enzymes/receptors.…”

DFT and MP2 study of the effects of mutations on the binding of ligands within the SULT1A3 active site

“…After optimization, all ligand/amino acid pairs were isolated (capping amino acid residues with -OH or -H to maintain the charge and polarity found in the protein) and counterpoise-corrected interaction energies for all ligand/amino acid pairs were calculated with two methods, MP2 and M062X, both with a basis set of 6-311+G*. 8 The total interaction energy for each ligand was calculated as a sum of the pairwise interaction energies of the ligand with each amino acid. For the second mutant (E146A), the E146 residue was changed to alanine and the above calculations were repeated.…”