The salts bis(2-amino-3-methylpyridinium) fumarate dihydrate, 2C6H9N2+·C4H2O22-·2H2O (I), and 2-amino-3-methylpyridinium 5-chlorosalicylate, C6H9N2+·C7H4ClO3- (II), were synthesized from 2-amino-3-methylpyridine with fumaric acid and 5-chlorosalicylic acid, respectively. The crystal structures of these salts were characterized by single-crystal X-ray diffraction, revealing protonation in I and II by the transfer of a H atom from the acid to the pyridine base. In the crystals of both I and II, N-H...O interactions form an R22(8) ring motif. Hirshfeld surface analysis distinguishes the interactions present in the crystal structures of I and II, and the two-dimensional (2D) fingerprint plot analysis shows the percentage contribution of each type of interaction in the crystal packing. The volumes of the crystal voids of I (39.65 Å3) and II (118.10 Å3) have been calculated and reveal that the crystal of I is more mechanically stable than II. Frontier molecular orbital (FMO) analysis predicts that the band gap energy of II (2.6577 eV) is lower compared to I (4.0035 eV). The Quantum Theory of Atoms In Molecules (QTAIM) analysis shows that the pyridinium-carboxylate N-H...O interaction present in I is stronger than the other interactions, whereas in II, the hydroxy-carboxylate O-H...O interaction is stronger than the pyridinium-carboxylate N-H...O interaction; the bond dissociation energies also confirm these results. The positive Laplacian [∇2ρ(r) > 0] of these interactions shows that the interactions are of the closed shell type. An in-silico ADME (Absorption, Distribution, Metabolism and Excretion) study predicts that both salts will exhibit good pharmacokinetic properties and druglikeness.

Addition of trivalent chromium, Cr(III), to solutions undergoing electrospray ionization (ESI) enhances protonation and leads to formation of [M + 2H]2+ for peptides that normally produce [M + H]+. This effect is explored using electronic structure calculations at the density functional theory (DFT) level to predict the energetics of various species that are potentially important to the mechanism. Gas- and solution-phase reaction free energies for glycine and its anion reacting with [Cr(III)(H2O)6]3+ and for dehydration of these species have been predicted, where glycine is used as a simple model for a peptide. For comparison, calculations were also performed with Fe(III), Al(III), Sc(III), Y(III), and La(III). Removal of water from these complexes, as would occur during the ESI desolvation process, results in species that are highly acidic. The calculated pKa of Cr(III) with a single solvation shell is -10.8, making [Cr(III)(H2O)6]3+ a superacid that is more acidic than sulfuric acid (pKa = -8.8). Binding to glycine requires removal of two aqua ligands, which gives [Cr(III)(H2O)4]3+ that has an extremely acidic pKa of -28.8. Removal of additional water further enhances acidity, reaching a pKa of -84.7 for [Cr(III)(H2O)]3+. A mechanism for enhanced protonation is proposed that incorporates computational and experiment results, as well as information on the known chemistry of Cr(III), which is substitutionally inert. The initial step involves binding of [Cr(III)(H2O)4]3+ to the deprotonated C-terminus of a peptide. As the drying process during ESI strips water from the complex, the resulting superacid transfers protons to the bound peptide, eventually leading to formation of [M + 2H]2+.

In this study we have investigated the effects of pH and surfactant on the internal charge transfer (ICT) process in the DSNN derivative, DSNN-NMe+3 (4,4\'-bis(4\'-(N,N-bis(6″-(N,N,N-trimethylammonium)hexyl)amino)-styryl) naphthalene tetraiodide) with the aim to show that environmentally-induced changes in the degree of ICT process determine the spectral response of the DSNN chromophore. Obtained results showed that DSNN chromophore exhibits evident changes in linear optical properties (absorption/emission wavelengths, quantum yield) upon protonation. These changes are a manifestation of the attenuation of the internal charge transfer processes, which accompanies binding of proton to the nitrogen atoms of the dialkylamino groups at the termini of DSNN chromophore. The results obtained in this study clearly demonstrated the sensitivity of the ICT process in DSNN upon protonation, which, together with the affinity of DSNN towards biological and artificial membranes, may open new perspectives for its utility in fluorescence-based sensing. Moreover, the studied compound showed substantial surfactochromic effects in the ionic and non-ionic surfactant solutions, which indicate the formation of various self-organized DSNN-surfactant aggregates. The structure of these aggregates is determined by the type of specific intermolecular interactions between the chromophore and surfactant molecules. The knowledge of the nature of these interactions may be substantial in the future development of DSNN-based sensing platforms with suitable optical properties.

Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.

BACKGROUND: Multidrug and toxic compound extrusion (MATE) family transporters induce multiple-drug resistance (MDR) of bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs. Unfortunately, to date, the details and intrinsic reason about conformational regulation mechanism of MATE transporters remain elusive.
METHODS: In this work, molecular dynamics (MD) simulations were conducted to explore the conformational regulation mechanism of PfMATE transporter from Pyrococcus furiosus based on different protonation state of Asp41. Two (MD) simulation systems were investigated: a system with protonation of Asp41 and a system without protonation of Asp41, which were named by D184(H)D41(H) system and D184(H) system, respectively.
CONCLUSIONS: Firstly, MD simulation results indicate that conformational changes mainly happen in extracellular regions of PfMATE protein. Further analysis reveals that PfMATE protein experiences different motion mode and forms different conformation based on different protonation state of Asp41. In the D184(H)D41(H) system, PfMATE experiences an opening motion and forms a more outward-open conformation. As for the D184(H) system, the protein has an anticlockwise rotational motion with the channel axis of protein and the more outward-open conformation does not appear. It can be inferred that protonation of Asp41 is essential for conformational regulation of PfMATE during transporting substrates.
CONCLUSIONS: These findings provide intrinsic information for understanding the conformational regulation mechanism of PfMATE and will be very meaningful to explore the MDR mechanism of PfMATE further.

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

MR-CISD, MR-CISD+Q, and MR-AQCC calculations have been performed on the minima and transition states (corresponding to intramolecular proton transfer between the protonation sites) of the ground state of protonated nitrosamine and N,N-dimethylnitrosamine. Our highest level results (MR-AQCC/cc-pVTZ) for the smaller system indicate that protonation on the N amino (2a) is practically as favorable as the most favorable protonation on the O atom (1a). They also suggest that protonation on the nitroso N atom (2c) is ∼14.5 kcal/mol less favorable than 1a. Results obtained at the MR-CISD+Q/cc-pVTZ level indicate that the effect of methylation on the relative energies of the tautomers is, in order of importance, 2a > 2c and increases their energies by ∼17.5 and 4.8 kcal/mol, respectively. They also indicate that methylation alters significantly the intramolecular proton transfer barriers. The largest differences between the common geometric parameters of both systems have been found for 2a.

The UV/Vis titration measurements, vibrational and NMR spectroscopy of isomeric dehydrodibenzopyrido[15]annulenes (DBPA) 1 and 2 clearly show that under proper conditions these macrocycles can achieve fast, quantitative and unselective binding of metal ions. The macrocycle 1 is an example of a hindered amine 2,6-bis(R)pyridine and its isomer 2 of a non-hindered amine 3,5-bis(R)pyridine. The protonation stoichiometry for both 1 and 2 was assumed to be DBPA:H(+)=1:1 and the formation constants logK=4.77±0.02 for 1, and logK=6.78±0.08 for 2 were obtained that well agree with those obtained under similar conditions for a macrocycle containing bipyridine units. The protonation of 2 gave the estimated stoichiometry of 2:H(+)=1:1 while the stoichiometric protonation of macrocycle 1 could not be achieved and the lower stability of the ion pair containing 1H(+) is most likely due to the inaccessibility of the nitrogen atom of 1 to the counterions and solvent molecules. The structures and electronic absorption spectra of 1 and 2, as well as the structures and spectra of 1H(+) and 2H(+), i.e. the species formed by protonation of the pyridine nitrogen, were calculated with the time-dependent DFT method with a B3LYP functional and a 6-31+G(d) basis set. The solvent effects were incorporated by means of the polarizable continuum model (PCM). The agreement of the calculated absorption data for the parent and protonated species with the observed spectra is rather satisfactory. Vibrational IR and Raman spectra of 1, 2, 1H(+) and 2H(+) in vacuo were calculated at the B3LYP/cc-pVTZ level of theory. Macrocycles 1 and 2, and their products protonated by trifluoromethanesulfonic acid (1HOTf and 2HOTf) were also characterized by temperature-dependent FTIR technique known as two dimensional IR correlation analysis. Quite large difference in degradation temperature between macrocycle 1 and 2 and their protonated complexes was measured, indicating that inclusion of proton leads to significant thermal stabilization of dehydroannulene ring.

An experimental and theoretical investigation of protonation effects on the UV/Vis absorption spectra of imatinib showed systematic changes of absorption depending on the pH, and a new absorption band appeared below pH 2. These changes in the UV/Vis absorption spectra were interpreted using quantum chemical calculations. The geometry of various imatinib cations in the gas phase and in ethanol solution was optimized with the DFT/B3LYP method. The resultant geometries were compared to the experimentally determined crystal structures of imatinib salts. The semi-empirical ZINDO-CI method was employed to calculate the absorption lines and electronic transitions. Our study suggests that the formation of the extra near-UV absorption band resulted from an increase of imatinib trication concentration in the solution, while the rapid increase of the first absorption maximum could be attributed to both the formation of imatinib trication and tetracation.