Assigning the correct protonation state to the catalytic residues is essential for a realistic modelling of an enzyme's active site. Plasmepsins are pharmaceutically relevant aspartic proteases involved in haemoglobin degradation by Plasmodium spp. In aspartic proteases, one of the two catalytic aspartates is protonated, while the other is negatively charged. Here, multiple explicit-water molec...

The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its "active-site" residues--glutamate 14 (Glu14) from each subunit--must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations ...

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We ...

A systematic study has been performed of the proton affinity of a large family of agonists and antagonists of the α1-adrenoceptor at the B3LYP/6-31G* level of theory. After a conformational search, all the N atoms were considered as protonation sites and protonation energy values were determined. The inclusion of solvation by means of the Onsager model yielded stabilization in the proton affini...

The protonation constants of L-Aspartic acid have been studied pH-metrically in various concentrations (0-60% v/v) of acetonitrile- and ethylene glycol-water mixtures maintaining an ionic strength of 0.16 mol L-1 at 303K. The protonation constants have been calculated with the computer program MINIQUAD75 and are selected based on statistical parameters. Linear variation of step-wise protonation...

Protonation of the reactive intermediates generated in the raction between dalkyl acetylenedicarboxylates and triphenylphosphine by isonitrosoacetophenone leads to vinyltriphenylphosphonium salts, which undergo intramolecular Wittig reaction to produce dalkyl 4-phenyl-N-hydroxypyrrole-2,3-dicarboxylates in moderate yields.

The site of protonation in a molecule can greatly affect the fragments observed in product ion MS/MS spectra. In electrospray positive ionization mass spectra, protonation usually occurs predominantly on the most basic site on the molecule to produce the thermodynamically favored protonated species. However, the literature is unclear whether liquid phase or gas phase thermodynamics has the grea...

The pH dependent behavior of two flavin cofactors, flavin-adenine dinucleotide (FAD) and flavin mononucleotide (FMN), has been characterized using femtosecond transient absorption spectroscopy for the first time. The flavin excited state was characterized in three states of protonation (Fl(-), Fl, and FlH(+)). We found that Fl and Fl(-) exhibit the same excited state absorption but that the lif...

We provide the first detailed time-resolved mechanistic information on the protonation of a model of the subsite of [FeFe]-hydrogenase, [Fe2(mu-pdt)(CO)4(PMe3)2]; the deceptively simple stoichiometric reaction is shown to be limited by the rate of protonation of the basal-apical isomer followed by its rearrangement to the transoid basal form.

Diiron complexes containing pyridyl-phosphine ligands, that is, (mu-pdt)[Fe(2)(CO)(5)L] (pdt = S(CH(2))(3)S, L = Ph(2)PCH(2)Py, Ph(2)PPy, ) and (micro-pdt)[Fe(CO)(2)(PMe(3))][Fe(CO)(2)L] (L = Ph(2)PCH(2)Py, Ph(2)PPy, ) were prepared as model complexes of the [FeFe]-hydrogenase active site. Protonation of and by HOTf afforded the pyridyl-nitrogen protonated products [H(N)][OTf] and [H(N)][OTf], ...