Theoretical pKa Research Articles

Theoretical pKaestimates for solvated P(OH)5from coordination constrained Car–Parrinello molecular dynamics

Car–Parrinello molecular dynamics simulations have been performed on P(OH)5 and its monanionic and dianionic derivatives in liquid water, representing minimal models of the transition complex occurring in the hydrolysis of RNA. P(OH)5 and PO5H4− have been found to be stable in aqueous solution, while PO5H32− is reduced to PO5H4− within femtoseconds by solvent–solute proton transfer. The deprotonated hydroxyl group of the monoanion exhibits pronounced equatoriphilicity. This observation has been underlined by theoretical pKa determination of axial and equatorial hydroxyl groups of P(OH)5, respectively, by means of coordination constrained ab initio molecular dynamics, which has shown the equatorial site to be more acidic by 4.4 units, the absolute values being 14.2 and 9.8.

The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein.

The NMR structure of the 98 residue beta-elicitin, cryptogein, which induces a defence response in tobacco, was determined using 15N and 13C/15N labelled protein samples. In aqueous solution conditions in the millimolar range, the protein forms a discrete homodimer where the N-terminal helices of each monomer form an interface. The structure was calculated with 1047 intrasubunit and 40 intersubunit NOE derived distance constraints and 236 dihedral angle constraints for each subunit using the molecular dynamics program DYANA. The twenty best conformers were energy-minimized in OPAL to give a root-mean-square deviation to the mean structure of 0.82 A for the backbone atoms and 1.03 A for all heavy atoms. The monomeric structure is nearly identical to the recently derived X-ray crystal structure (backbone rmsd 0.86 A for residues 2 to 97) and shows five helices, a two stranded antiparallel beta-sheet and an omega-loop. Using 1H,15N HSQC spectroscopy the pKa of the N- and C-termini, Tyr12, Asp21, Asp30, Asp72, and Tyr85 were determined and support the proposal of several stabilizing ionic interactions including a salt bridge between Asp21 and Lys62. The hydroxyl hydrogens of Tyr33 and Ser78 are clearly observed indicating that these residues are buried and hydrogen bonded. Two other tyrosines, Tyr47 and Tyr87, show pKa's > 12, however, there is no indication that their hydroxyls are hydrogen bonded. Calculations of theoretical pKa's show general agreement with the experimentally determined values and are similar for both the crystal and solution structures.

Peculiar spectroscopic and kinetic properties of Cys-47 in human placental glutathione transferase. Evidence for an atypical thiolate ion pair near the active site.

Cys-47, the most reactive cysteine in the homodimeric glutathione transferase (EC 2.5.1.18) from human placenta (class Pi), displays peculiar acid base and spectroscopic properties. The thiolate form of this residue is characterized by a sharp UV absorption spectrum centered at 229 nm with an epsilon = 7,500 M-1 cm-1. The dependence of the apparent extinction coefficient on pH indicates that the sulfhydryl group of Cys-47 has a pKa value of 4.2. Moreover the dependence of the reactivity of Cys-47 toward bromopyruvate and iodoacetamide with pH resembles that found for the functional sulfhydryls of thiol proteases, which have very low pKa values and exist mainly as a mercaptide-imidazole ion pair. The apparent pKa value for Cys-47, calculated by this kinetic approach, is in good agreement with that determined spectroscopically. X-ray crystallographic data indicate that the protonated amino group of Lys-54, 4.9 A from the sulfur atom, is probably involved in the deprotonation of Cys-47. Calculation of the electrostatic potential on the sulfur atom of Cys-47 gives a theoretical pKa value of 3.5 for the sulfhydryl group. The simulated neutralization of Lys-54 shifts the pKa value of Cys-47 to a normal value of 9.5. These findings suggest that at physiological pH values, Cys-47 exists as the thiolate ion stabilized by an ion pair formation with the protonated amino group of Lys-54, and this probably accounts for its high reactivity.

Prototropic equilibria of electronically excited molecules. Part III. Mono- and bi-cyclic aromatic hydrocarbons

The expectation, based upon π-electron theory or spectroscopic data by use of the Forster cycle, that the acid–base properties of aromatic hydrocarbons in the lowest excited electronic state differ substantially from the corresponding ground state properties has been investigated by measuring the variation in the fluorescence spectrum of mono- and bi-cyclic molecules with changes in the acidity of the solvent and by hydrogen isotope exchange studies. It is found that prototropic equilibrium is not established during the lifetime of the excited state of benzene, toluene, naphthalene, azulene, and indolizine and that theoretical pKa* values for the excited state of these molecules in aqueous solution do not correspond to observable processes. Changes in fluorescence spectrum with acidity follow only ground-state ionic dissociation processes, and the upper limits for the quantum efficiencies of photochemical hydrogen isotope exchange in aqueous 1 M-perchloric acid indicate that the radiative deactivation rate of an electronically excited aromatic hydrocarbon is faster than the rate of protonation by factor > 105.