Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states sim...

To probe the influence of structural variation within dibenzo-16crown-5-oxyacetic acids upon the selectivity of alkali metal cation separations by solvent extraction and liquid membrane transport processes, studies have now been conducted in homogeneous solution by NMR spectroscopy and titration calorimetry and in the solid state. Condensation polymerization of such proton-ionizable lariat ethe...

Ionizable groups play critical roles in biological processes. Computation of pK(a)s is complicated by model approximations and multiple conformations. Calculated and experimental pK(a)s are compared for relatively inflexible active-site side chains, to develop an empirical model for hydration entropy changes upon charge burial. The modification is found to be generally small, but large for cyst...

Novel di-ionizable p-tert-butylcalix[4]arene-1,2-crown-3 ligands in cone and 1,2-alternate conformations were prepared as potential metal ion extractants. Selective bridging of proximal hydroxyl groups of the calix[4]arene platform by a crown-3 polyether unit was achieved under Mitsunobu reaction conditions. In addition to the carboxylic acid group, the acidity tunable N-(X)sulfonyl oxyacetamid...

Metal ion recognition by proton-ionizable calixarenes is often affected by interference from the Na present in many aqueous solutions. To assess the Na-effect on calixarene selectivity towards alkaline earth metal cations (AEMC), competitive solvent extraction of Mg, Ca, Sr, and Ba from aqueous solutions into chloroform by di-ionizable calix[4]arene N(trifluoromethylsulfonyl)carboxamides and co...

This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, protein, and nucleic acid), and distance from the binding region. Standard continuum solvent methodology is used to compute, on an equal footing, pK changes upon ligand bindin...

Abstract The temperature of maximum pyrolysis yield (known as Tmax) can be used to determine the level thermal alteration in sedimentary organic matter; higher Tmax values represent alteration. is commonly measured on petroleum source rocks or similar sediments with high carbon contents. It would desirable measure volcanic because they have complex patterns However, often low total contents and...

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolv...

Polyelectrolytes are polymers carrying either positively or negatively charged ionizable groups. The properties of these polymers in solutions and at charged surfaces depend on the fraction of dissociated ionic groups, solvent quality for polymer backbone, solution dielectric constant, salt concentration, and polymer–substrate interactions. In this review, we summarize the current development o...

The use of macroscopic electrostatic models to calculate the relative energetics of protonation states and the pH-titration properties of ionizable groups in proteins is described. These methods treat the protein as an irregularly-shaped low-dielectric object containing embedded atomic charges immersed in a high-dielectric (solvent) medium. The energetics of altering protonation states then inv...