Multiple Protonation Research Articles

Flash-induced H + binding by bacterial photosynthetic reaction centers: Comparison of spectrophotometric and conductimetric methods

H + binding following flash excitation of isolated reaction centers from Rhodobacter sphaeroides was measured using a conductimetric method. A procedure is described for calibrating the H + change and the method is compared to the more widely used spectrophotometric assay of pH-indicator dyes. The two methods agree extremely well and confirm a severe paradox in the pH dependence of the H + binding stoichiometry - that reaction centers in the light-activated, charge-separation state, P +(Q AQ B) −, fail to bind net protons at pH values near neutral or lower, although proton binding is seen at higher pH. This is in contrast to expectations arising from the equilibrium redox behavior of the acceptor quinones, Q A and Q B, and with the pH dependence of the one-electron equilibrium between Q − AQ B and Q AQ − B. The observed proton binding is discussed in terms of multiple protonation equilibria linked to the redox states of the acceptor quinones and of the primary donor.

Calculated proton affinities for some molecules containing group VIA atoms

The proton affinities and structures of a series of small molecules containing group VIA atoms are calculated via ab initio electronic structure techniques. The series under study included CX, OCX, XCX, and H2CX, where X=O, S, Se, and Te. In those cases where multiple protonation sites are available, a definitive assignment of the most stable site is reported. Excellent agreement with the experimentally known proton affinities is found in almost all cases. The results indicate that the general trend which one would expect upon moving down a column of the periodic table is born out, with a particularly large change on going from the first to the second row. Calculations were performed at both the SCF and correlated levels with compact effective potentials used to replace the core electrons. Complete structural optimizations via analytic gradients were performed utilizing basis sets of at least double zeta plus polarization quality.

Use of polylysine-coated slides in preparation of cell samples for diagnostic cytology with special reference to urine sample.

<h3>Abstract</h3> The prediction of acid dissociation constants (p<i>K</i>_a) is a prerequisite for predicting many other properties of a small molecule, such as its protein-ligand binding affinity, distribution coefficient (log <i>D</i>), membrane permeability, and solubility. The prediction of each of these properties requires knowledge of the relevant protonation states and solution free energy penalties of each state. The SAMPL6 p<i>K</i>_a Challenge was the first time that a separate challenge was conducted for evaluating p<i>K</i>_a predictions as part of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) exercises. This challenge was motivated by significant inaccuracies observed in prior physical property prediction challenges, such as the SAMPL5 log <i>D</i> Challenge, caused by protonation state and p<i>K</i>_a prediction issues. The goal of the p<i>K</i>_a challenge was to assess the performance of contemporary p<i>K</i>_a prediction methods for drug-like molecules. The challenge set was composed of 24 small molecules that resembled fragments of kinase inhibitors, a number of which were multiprotic. Eleven research groups contributed blind predictions for a total of 37 p<i>K</i>_a distinct prediction methods. In addition to blinded submissions, four widely used p<i>K</i>_a prediction methods were included in the analysis as reference methods. Collecting both microscopic and macroscopic p<i>K</i>_a predictions allowed in-depth evaluation of p<i>K</i>_a prediction performance. This article highlights deficiencies of typical p<i>K</i>_a prediction evaluation approaches when the distinction between microscopic and macroscopic p<i>K</i>_as is ignored; in particular, we suggest more stringent evaluation criteria for microscopic and macroscopic p<i>K</i>_a predictions guided by the available experimental data. Top-performing submissions for macroscopic p<i>K</i>_a predictions achieved RMSE of 0.7-1.0 p<i>K</i>_a units and included both quantum chemical and empirical approaches, where the total number of extra or missing macroscopic p<i>K</i>_as predicted by these submissions were fewer than 8 for 24 molecules. A large number of submissions had RMSE spanning 1-3 p<i>K</i>_a units. Molecules with sulfur-containing heterocycles or iodo and bromo groups were less accurately predicted on average considering all methods evaluated. For a subset of molecules, we utilized experimentally-determined microstates based on NMR to evaluate the dominant tautomer predictions for each macroscopic state. Prediction of dominant tautomers was a major source of error for microscopic p<i>K</i>_a predictions, especially errors in charged tautomers. The degree of inaccuracy in p<i>K</i>_a predictions observed in this challenge is detrimental to the protein-ligand binding affinity predictions due to errors in dominant protonation state predictions and the calculation of free energy corrections for multiple protonation states. Underestimation of ligand p<i>K</i>_a by 1 unit can lead to errors in binding free energy errors up to 1.2 kcal/mol. The SAMPL6 p<i>K</i>_a Challenge demonstrated the need for improving p<i>K</i>_a prediction methods for drug-like molecules, especially for challenging moieties and multiprotic molecules.

Protonization of purine, adenine, and guanine. NMR spectra and structure of mono, di, and tri cations

AbstractProton NMR. spectra of purine, adenine, guanine and methylsubstituted guanines have been measured in CF3COOH, FSO3H and FSO3HSbF5SO2 at 27° and low temperatures. These conditions permit to study multiple protonation of purines, using chemical shifts of CH, NH and OH protons. The spectra of mono‐, di‐ and tri‐cations are described and fully assigned.