Electric field driven protonation/deprotonation of self-assembled monolayers of acid-terminated thiols

Using electrochemical impedance spectroscopy (EIS), we provide an explanation for the pH dependence of the voltammetric peak height for the electric-field-driven protonation and deprotonation of carboxylic acid-terminated thiol self-assembled monolayers (SAMs). The current flowing through the interface can be divided into a purely capacitive current and a protonation/deprotonation current that is directly related to the rate of change of the SAM's protonation (or deprotonation). We demonstrate that at applied potentials close to those corresponding to half-ionization of the SAM and pHs near the pK(1/2), the equivalent circuit describing the interface consists of a Helmholtz film capacity in parallel with a "protonation/deprotonation" impedance which is further shown to be a series combination of a resistor, Rp, and capacitor Cp. Explicit expressions for Rp and Cp are derived in terms of the rate constants for the forward (protonation) and reverse (deprotonation) reactions. Simulated EIS data demonstrate the agreement between our model of the interface and experimental impedance and voltammetric data.     

Redox induced pH-switch of Tb(III) centered luminescence of Tb(III) complex with p-sulfonatothiacalix[4]arene

The reversible redox switching of Tb(III) centered luminescence resulting from the protonation/deprotonation of the ligand has been realized. The redox couple quinone/hydroquinone serves as a proton pump, leading to the reversible protonation/deprotonation of the phenolate groups of p-sulfonatothiacalix[4]arene and following decomplexation/complexation with Tb(III) ion in aqueous solution.     

Ionization mechanism of oligonucleotides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The ionization of nucleosides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was systematically investigated using adenine (A), thymine (T), guanine (G) and cytosine (C) with several common matrices. Experimental results of the protonation and deprotonation of the bases of A, T, G and C in the matrices 2,5-dihydroxybenzoic acid (2,5-DHB), alpha-cyano-4-hydroxycinnamic acid (alpha-CHCA) and 3-hydroxypicolinic acid (3-HPA) provide an insight into the ionization mechanism of oligonucleotides in MALDI. It was found that the low ion signal from DNA in poly-G in MALDI as reported in earlier work could be attributed to the fact that the base of G is difficult to ionize. Our results suggest that the ionization of DNA in MALDI is dominated by the protonation and deprotonation of bases and it is basically independent of the backbone of DNA. Both the protonation and deprotonation are strongly structure dependent. The protonation is dominated by pre-protonation before laser ablation, while the deprotonation is controlled by the thermal reaction.     

The hydrogen sulfate recognition properties of azo-salicylaldehyde schiff base receptors

Azo-salicylaldehyde Schiff base-typed receptors containing an acidic H-bond donor moiety were syn-thesized and characterized. The UV-Vis data indicate that these receptors could act as selective col-orimetric sensors for basic anions and acidic species hydrogen sulfate by different color changes in a water-containing medium. The experiment of Brφnsted acid-base reaction by adding the sodium hy-droxide or perchloric acid revealed that the mechanism of recognition of anions might be deprotona-tion/protonation of the OH fragments by interacting with different anions and that the deprotona-tion/protonation process is fully reversible. The deprotonation/protonation of the receptors is respon-sible for the dramatic color change.     

A "molecular pivot-hinge" based on the pH-regulated intramolecular switching of Pt-Pt and pi-pi interactions

The binuclear cycloplatinated complex {[Pt(L)]2(mu-dppm)}2+ (1), where HL is a new cyclometalating ligand 2-phenyl-6-(1H-pyrazol-3-yl)pyridine, is found to behave as a molecular pivot-hinge in which the closing and opening of the hinge is effected by the reversible formation and cleavage of the Pt-Pt d8-d8 interaction and the intramolecular pi-pi interaction mediated by the protonation/deprotonation of the 1-pyrazolyl-NH on the cyclometalating ligand L.     

质子化和脱质子化对酞菁光谱的影响

系统地研究四异丙氧基酞菁的子化和脱质子化对吸收和发射光谱的影响，研究表明，三氟乙酸可对酞菁分子连续质子化，分别生成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．Ｈ＾＋）＾和（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．２Ｈ＾＋）＾２＋，而硫酸可使酞菁形成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．４Ｈ＾＋＾４＋此外，ＮａＯＨ／ＥｔＯＨ可使酞菁分子脱质子化生成（Ｐｃ（Ｏ＾ｉＰｒ）４）＾２－反应一步完成，表明分子中的两个吡咯－ＮＨ－同步酸解，质子化可使     

Synthesis of ionisable [2 x 2] grid-type metallo-arrays and reversible protonic modulation of the optical properties of the [Co4(II)L4]8+ species

The new bis-hydrazone based ligands A and B form ionisable [2 x 2] grid-type transition metal complexes whose properties may be modulated by multiple protonation/deprotonation as shown by the reversible change in optical properties of the [Co2(II)L4]8+ complexes depending on their protonation state.     

Protonation and deprotonation of hydroxamic acids. An MO ab initio study

Ab initio molecular orbital calculations with 4-31G//4-31G, 6-31G^*//4-31G and 6-31+G//4-31G basis sets have been used to examine the structure, relative energy, protonation and deprotonation of a series of seven hydroxamic acids in the gas phase. The results show that hydroxamic acids are predominantly in the E-TS form and that the most probable protonation site is the carbonyl oxygen atom, while deprotonation proceeds by loss of NH hydrogen.     

Structures and charging of alpha-alumina (0001)/water interfaces studied by sum-frequency vibrational spectroscopy

Sum-frequency vibrational spectroscopy in the OH stretch region was employed to study structures of water/alpha-Al2O3 (0001) interfaces at different pH values. Observed spectra indicate that protonation and deprotonation of the alumina surface dominate at low and high pH, respectively, with the interface positively and negatively charged accordingly. The point of zero charge (pzc) appears at pH approximately = 6.3, which is close to the values obtained from streaming potential and second-harmonic generation studies. It is significantly lower than the pzc of alumina powder. The result can be understood from the pK values of protonation and deprotonation at the water/alpha-Al2O3 (0001) interface. The pzc of amorphous alumina was found to be similar to that of powder alumina.     

A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization

In this study, classic molecular dynamics (MD) simulations followed by density functional theory (DFT) calculations are employed to calculate the proton transfer reaction enthalpy shifts for native and derivatized peptide ions in the MALDI plume. First, absolute protonation and deprotonation enthalpies are calculated for native peptides (RPPGF and AFLDASR), the corresponding hexyl esters and three common matrices α-cyano-4-hydroxycinnamic acid (4HCCA), 2,5-dihydroxybenzoic acid (DHB), and 6 aza-2-thiothymine (ATT). From the proton exchange reaction calculations, protonation and deprotonation of the neutral peptides are thermodynamically favorable in the gas phase as long as the corresponding protonated/deprotonated matrix ions are present in the plume. Moreover, the gain in proton affinity shown by the ester ions suggests that the increase in ion yield is likely to be related to an easier proton transfer from the matrix to the peptide.     

Electric-Field Effects in 13-Demethyl-11,14-Epoxyretinal-Bacteriorhodopsin Films

Abstract— We report the results of experiments on the application of electric fields across thin, dry Alms of a bacteriorho-dopsin (BR) analog pigment in which the retinal chro-mophore has been replaced with 13-demethyl-11,14-epoxyretinal. As previously observed in other BR variants with low Schiff-base pK values, this pigment exhibits protonation and deprotonation of the Schiff base under an applied electric field, depending on the initial Schiff-base protonation state or effective pH. At low effective pH, a fast (<200 μs) deprotonation reaction dominates. At high pH, an apparently different mechanism leads to Schiff-base protonation on the time scale of seconds. Comparison of our results with a simple model suggests that the external field causes a shift in the pK of the Schiff base by1–2 pH units.     

Study of pH-dependent charges of soils by surface acid-base properties

The pH-dependent charges of Hungarian soils have been studied via surface acid-base properties. The intrinsic stability constants of protonation and deprotonation processes, as well as the concentration of surface sites, have been determined by surface complexation modeling. The protonation and deprotonation constants have been nearly the same for most soils. There is a relation between the concentration of surface sites and composition, expect for the freshly deposited soils with high primary silicate content. The results show that the concentrations of silanol and aluminol sites are different for each soil, the intrinsic stability constants of protonation and deprotonation processes, however, are nearly the same within experimental error. This can only be explained if these stability constants are real thermodynamic equilibrium constants. The fact that these constants are nearly the same supports the conclusion that we succeeded in excluding all processes that would disturb the measurements. The parameters characteristic of the edge sites of the soils are of two types: (a) the parameters depending on the quality and composition of the soils, (i.e.), the concentration of surface sites; (b) the parameters depending on the thermodynamically well-defined acid-base processes, independent of soil composition.     

The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage

The enzyme-substrate contacts that are believed to be involved in depurination by proton transfer have been modelled by protonation and deprotonation of 3-methyl-2'-deoxyadenosine (3-MDA) using quantum mechanical calculations in the gas-phase and solution media. The change in the charge distribution on the sugar ring and nucleobase that is introduced by the protonation and deprotonation strongly affects the N-glycosidic bond length. The unimolecular cleavage and hydrolysis of the N-glycosidic bond, involving D(N)*A(N) and A(N)D(N) pathways, have been considered at several levels of theory. The trend in the energy barriers is A(N)D(N) > cleavage > D(N)*A(N). All probable proton transfer reactions resulting from enzyme-substrate contacts do not facilitate the N-glycosidic bond cleavage of 3-MDA. The deprotonation of 3-MDA that may result from the interaction between H6 and enzyme do not facilitate bond cleavage. The protonation at N7 induces more positive charge on the sugar ring and further facilitates the depurination relative to the protonation at N1. The changes in the charges calculated on the ribose and nucleobase are in good relationship with the C1'-C2', C1'-O4', and N-glycosidic bond lengths along the cleavage. The change in energy barrier ΔE of glycosidic bond cleavage from the gas-phase to solution media strongly depends on the charge of the species.     

Proton-bound homodimers: how are the binding energies related to proton affinities?

High-level quantum chemical calculations [G3(MP2)-RAD//MP2/6-31+G(d,p)] have been employed to investigate the relationship between the binding energy (BE) of a substrate (X) and its protonated form [H-X]+ with the proton affinity (PA) of the substrate (X) in several series of protonated homodimers ([X...H-X]+). We find that for each series of closely related substrates, the binding energy (BE) is correlated with the proton affinity (PA) in an approximately quadratic manner. Thus, for a given series, the BE initially increases in magnitude with increasing PA, reaches a point of maximum binding, and then becomes smaller as the PA increases further. This behavior can be attributed to the competing effects of the exothermic partial protonation of the substrate and the endothermic partial deprotonation of the protonated substrate. As the PA increases, protonation of X contributes to increased binding but the penalty for partial deprotonation of [H-X]+ also increases. Once the PA becomes sufficiently high, the penalty for the partial deprotonation of [H-X]+ dominates, leading to maximum binding occurring at intermediate PA.     

A proton induced conformational change in metal complexes with potential hydrogen bonding triplet motifs

Biguanide-like bidentate ligands in a variety of transition metal complexes of different geometries exhibit conformational changes upon protonation/deprotonation that alter their capacity to recognise complementary hydrogen bonding motifs.     

Contraction/extension molecular motion by protonation/deprotonation induced structural switching of pyridine derived oligoamides

NMR, mass spectrometry and X-ray diffraction studies show reversible structural interconversion between helical and extended forms of pyridine derived oligoamide molecular strands, by simple protonation/deprotonation.     

Off-on-off luminescent switching of a dye containing imidazo[4,5-f][1,10]phenanthroline

A new acid-base fluorescent switch containing both imidazo[4,5-f][1,10]-phenanthroline and triphenylamine groups has been synthesized.Its fluorescence emissions and absorptions can be reversibiy changed through protonation/deprotonation of imidazole and amine moiety by controlling the intramolecular charge transfer(ICT) process,leading to off-on-off fluorescent molecular switching.     

Formation and stability of enolates of acetamide and acetate anion: an Eigen plot for proton transfer at alpha-carbonyl carbon

Second-order rate constants were determined in D(2)O for deprotonation of acetamide, N,N-dimethylacetamide, and acetate anion by deuterioxide ion and for deprotonation of acetamide by quinuclidine. The values of k(B) = 4.8 x 10(-8) M(-1) s(-1) for deprotonation of acetamide by quinuclidine (pK(BH) = 11.5) and k(BH) = 2-5 x 10(9) M(-1) s(-1) for the encounter-limited reverse protonation of the enolate by protonated quinuclidine give pK(a)(C) = 28.4 for ionization of acetamide as a carbon acid. The limiting value of k(HOH) = 1 x 10(11) s(-1) for protonation of the enolate of acetate anion by solvent water and k(HO) = 3.5 x 10(-9) M(-1) s(-1) for deprotonation of acetate anion by HO(-) give pK(a)(C) approximately 33.5 for acetate anion. The change in the rate-limiting step from chemical proton transfer to solvent reorganization results in a downward break in the slope of the plot of log k(HO) against carbon acid pK(a) for deprotonation of a wide range of neutral alpha-carbonyl carbon acids by hydroxide ion, from -0.40 to -1.0. Good estimates are reported for the stabilization of the carbonyl group relative to the enol tautomer by electron donation from alpha-SEt, alpha-OMe, alpha-NH(2), and alpha-O(-) substituents. The alpha-NH(2) and alpha-OMe groups show similar stabilizing interactions with the carbonyl group, while the interaction of alpha-O(-) is only 3.4 kcal/mol more stabilizing than for alpha-OH. We propose that destabilization of the enolate intermediates of enzymatic reactions results in an increasing recruitment of metal ions by the enzyme to provide electrophilic catalysis of enolate formation.     

A theoretical study on NH bond dissociation enthalpies of oxo, thio and seleno carbamates and their N-protonated and N-deprotonated species

The effect of N-protonation and N-deprotonation on structure, NH bond dissociation enthalpies (BDEs) and stabilities of radicals formed on H-abstraction from nitrogen atom of carbamates and their thio- and seleno-analogs have been investigated. For those molecules where experimental results are available for comparison, the ROB3LYP/6-311++G(d,p)//B3LYP/6-31+G* theoretical level is in agreement within the estimated experimental uncertainty. The NH BDE of carbamates H₂NC(=X)YCH₃ [X = O; Y = O, S, Se] are higher but lower when X = S, Se and Y = O, S, Se in comparison to NH BDE of NH₃. DFT calculations indicate that the NH bond dissociation enthalpies are decreased by protonation and deprotonation at nitrogen atom; but the effect of deprotonation is rather smaller than the protonation. The variations are analyzed in terms of stabilities of molecules, their protonated and deprotonated species along with their respective radicals. The electron delocalization from nitrogen, X and Y atoms, electrostatic interactions, conjugative interactions and spin delocalization are the important factors affecting the stability. The spin delocalization and shift of radical center to chalcogen X (X = S, Se) are the main determinants for radical stability.     

pH dependent in-out isomerism of an amino-beta-cyclodextrin derivative

An amino derivative of beta-cyclodextrin [6-(6-aminehexanamide)-6-deoxy)-beta-cyclodextrin (6-betaCD)] was synthesized, and the formation of an intramolecular inclusion complex was studied by NMR techniques. The deprotonation/protonation of the amino group stimulates an in/out movement of the pendant group toward/from the cyclodextrin cavity, the protonated species lying outside the hydrophobic cyclodextrin cavity but the unprotonated one residing inside and outside the cavity. The protonation of the amino group is a fast exchange rate NMR time-scale process, but the chain movement is a slow one. The equilibrium constants of both processes were determined from 1H NMR experiments and the kinetic constants for the slow process were determined from exchange spectroscopy (EXSY) experiments.