The effect of substitution on protonation sites: evidence for protonation at N(3) in N(7)-substituted adenine

Several experimental and theoretical studies have shown that N(1) is the first site for protonation in adenine and N(9)-substituted adenine derivatives. N(7) is considered the site for the second protonation to yield dipositive cations. Results are reported here which indicate that this protonation pattern is altered in N(7)-substituted adenine derivatives. In particular, an X-ray diffraction analysis of the structure of 7-methyladenine dihydrochloride, [C₆N₅H₇]Cl₂, definitively shows that the sites for protonation are N(3), as opposed to N(1), and N(9). Theoretical calculations of the molecular electrostatic potential in various systems suggest that such changes in preferred protonation sites should be expected, in general, when a modification of the molecular structure creates adjacent sites with similar reactivity, such as the N(3) and N(9) sites in 7-methyladenine.     

Aromatic protonation.—3: 1H NMR parameters of some methyl substituted anthracenium ions. Study on the site of protonation

1-Methylanthracene (1-MeA), 2-MeA, 1,2-Me₂A, 1,3-Me₂A, 1,4 Me₂A, 2,3-Me₂A, 1,4,9-Me₃A and 2,3,6,7-Me₄A have been protonated with FSO₃H in SO₂CIF as cosolvent at ?78°. With all substrates C(10)- and/or C(9)-protonation was observed. The site of protonation of the hydrocarbons was found to depend on (i) the degree of mesomeric stabilisation of the positive charge of the resulting anthracenium ions by the Me substituents, and (ii) the relief of steric strain between H(9) and the peri-Me substituent at position 1 on protonation at C(9).     

Resonance Raman spectroscopy and DFT calculations of the protonation of 4-(2-pyridylazo)-N,N-dimethylaniline in solution and adsorbed on oxide surfaces

The protonation of 4-(2-pyridylazo)-N,N-dimethylaniline (PYAD) in aqueous solution and its adsorption on oxide surfaces has been studied by resonance Raman (RR) spectroscopy. The gas phase structures of neutral, protonated and diprotonated forms of PYAD were modelled by SCF-DFT calculations at the B3-LYP/DZ level, enabling determination of the simulated vibrational spectra of these species, together with vibrational assignments, and providing confirmation that protonation occurs initially at the pyridyl nitrogen atom. Electronic absorption spectra were interpreted using time-dependent DFT calculations. Adsorption of PYAD on SiO₂ or Al₂O₃ surfaces is mainly via the neutral species, hydrogen bonded to surface OH groups, although a small proportion of adsorbed molecules are protonated. By contrast, adsorption on SiO₂–Al₂O₃ results in complete protonation, indicating the presence of Brønsted acidic sites with pK_a values ? 4.5, whereas adsorption on H-mordenite results in diprotonation, indicating the presence of Brønsted acidic sites with pK_a values ? 2.     

A calorimetric and NMR determination of the microscopic protonation constants of some N-methyl-substituted α,ω-thiadiamines

A method has been developed to calculate the microscopic protonation constants for some asymmetric N-methyl-substituted α,ω-thiadiamines, n,m-(R)(R′)NSN (R = H or CH₃: R′= CH₃; n = 2 or 3 and m = 2,3 or 4). The method is based on differences in enthalpies of protonation between the N-methyl substituted diamines n,m-(R)(R′)NSN and their corresponding non-substituted n,m-NSN analogues. A comparison of the calorimetric microscopic constants with those obtained with the ¹H-NMR technique confirms the value of the proposed calorimetric method. The microbasicity of the amino functions follows the sequence: secondary ? primary ? tertiary.     

Protonation of homotroponeiron tricarbonyl and cyclooctatrienoneiron tricarbonyl complexes

2,3-Homotroponeiron tricarbonyl, 8-methyl- and 8,8-dimethyl-2,3-homotroponeiron tricarbonyl complexes have been shown to undergo O-protonation in trifluoroacetic (TFA) and 96% sulfuric acids. In the latter acid the O-protonated cations rearrange to give the thermodynamically more stable C-protonated isomers. Cyclooctatrienoneiron tricarbonyl undergoes protonation H₂SO₄ to give the same cation as was obtained from the protonation of the homotroponeiron tricarbonyl complex in H₂SO₄. On the basis of reaction in D₂SO₄, it is suggested that the kinetically preferred site of protonation of the cyclooctatrienone complex is at C(2) one of the coordinated carbon atoms.     

An ammonium/bis-ammonium switchable molecular shuttle

A pH shuttle has been developed in which the mean position of the macrocycle can be switched between dialkylammonium stations of differing acidities. With only the most basic binding site protonated (dibenzylammonium), the macrocycle resides almost exclusively on the protonated station; when the second ammonium group (diethylammonium) is generated by further protonation, a mixture of translational diastereomers is observed in CD₂Cl₂ at 298 K, with the diethylammonium binding site preferred by the crown ether macrocycle in a ratio of ∼2:1.     

Synthesis of (2S,3R)- and (2S,3S)-[3-H1]-proline via highly stereoselective hydrolysis of a silyl enol ether

A straightforward synthesis of (2S)-[3,3-²H₂]-proline 1c and (2S,3R)- and (2S,3S)-[3-²H₁]-proline, 1b and 1a, respectively, has been devised. The key step of the route to the latter compounds involves highly stereoselective hydrolysis of the silyl enol ethers 3 and 3a, respectively, with protonation (deuteriation) from the re-face of the silyl enol ether.     

Kinetic and Thermodynamic Control of Protonation in Atmospheric Pressure Chemical Ionization

For p-(dimethylamino)chalcone (p-DMAC), the N atom is the most basic site in the liquid phase, whereas the O atom possesses the highest proton affinity in the gas phase. A novel and interesting observation is reported that the N- and O-protonated p-DMAC can be competitively produced in atmospheric pressure chemical ionization (APCI) with the change of solvents and ionization conditions. In neat methanol or acetonitrile, the protonation is always under thermodynamic control to form the O-protonated ion. When methanol/water or acetonitrile/water was used as the solvent, the protonation is kinetically controlled to form the N-protonated ion under conditions of relatively high infusion rate and high concentration of water in the mixed solvent. The regioselectivity of protonation of p-DMAC in APCI is probably attributed to the bulky solvent cluster reagent ions (S_nH⁺) and the analyte having different preferred protonation sites in the liquid phase and gas phase.

Different reaction routes found in acid-catalyzed glycosylation of endo- and exo-glycals: competition between Ferrier rearrangement and protonation

Acid-mediated glycosylations of endo- and exo-glycals have been carried out in good to excellent yields, in which a mixture of two products is often obtained resulting from Ferrier rearrangement and protonation. The former reaction exclusively takes place with the t-butyl carbonate or hydroxyl substituent at the C3 position of endo-glycals, while the latter mainly occurs in the glycosylation of exo-glycals with allyl benzyl ether or acetate. In addition to the substituent effect, protecting groups are critical to determine the activity and favored reaction pathway. Furthermore, the method is applicable to O-, C-, and N-nucleophiles.     

Oxidation process of MoOxCy to MoO3: kinetics and mechanism

A non-isothermal kinetic study of the oxidation of “carbon-modified MoO₃” in the temperature range of 150-550°C by simultaneous TGA-DTA was investigated. During the oxidation process, two thermal events were detected, which are associated with the oxidation of carbon in MoO_xC_y and MoO₂ to MoO₃. The model-free and model-fitting kinetic approaches have been applied to TGA experimental data. The solid state-kinetics of the oxidation of MoO_xC_y to MoO₃ is governed by F1 (unimolecular decay), which suggests that the reaction is of the first order with respect to oxygen concentration. The constant (Ea)_α value (about 115±5 kJ/mol) for this first stage can be related to the nature of the reaction site in the MoO₃ matrix. This indicates that oxidation occurs in well-defined lattice position sites (energetically equivalent). On the other hand, for the second stage of oxidation, MoO₂ to MoO₃, the isoconversional analysis shows a complex (Ea)_α dependence on (α) and reveals a typical behavior for competitive reaction. A D2 (two-dimensional diffusion) mechanism with a variable activation energy value in the range 110-200 kJ/mol was obtained. This can be interpreted as an inter-layer oxygen diffusion in the solid bulk, which does not exclude other simultaneous mechanism reactions.     

X-ray structural and13C NMR spectroscopic investigation of 4,7-diaminocoumarins

An x-ray structural study has been made of 7-diethylaminocoumarin and 4-morpholino-7-diethylaminocoumarin. A study has been made of the¹³C NMR spectra of these compounds and other 4,7-diaminocoumarins, in CDCl₃, and in acidic media. These studies have established that the site of first protonation is the nitrogen atom in position 7, and the site of the second protonation is the lactone oxygen atom. It is concluded that the 4-amino group is effectively conjugated with the carbonyl group in 4,7-diaminocoumarins.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 802–810, April, 1991.     

Anion recognition by d-ribose-based receptors

Anion recognition properties of d-ribose-based receptors α- and β-1 were measured by ¹H NMR in CDCl₃ and MeCN-d₃. Receptor β-1 showed effective binding with anions by cooperative hydrogen bonds of cis-diol. The anomeric isomer α-1 is a less effective anion receptor which has similar cis-diol as a recognition site, indicating that the stereo configuration of the anomeric position is of significant influence on the anion recognition ability.     

Potentiometric and Theoretical Studies of (2Z, 3Z)-2H-benzo[b][1,4]thiazine-2,3(4H)-dionedioxime with Some Divalent Transition Metal Ions

The protonation equilibria of (2Z, 3Z)-2H-benzo[b][1,4]thiazine-2,3(4H)-dionedioxime (BTDH₂) together with the equilibria of its bis- binary complexes of Co(II), Ni(II), Cu(II) and Zn(II) were investigated potentiometrically. The investigation was carried out at 25 ± 0.1 °C, in aqueous solution, with a constant ionic strength of 0.100 mol·dm^?3 NaCl. The protonation constants of the ligand together with the stability constants of a variety of complexes were determined potentiometrically in 10 % ethanol–water mixed solution using the SUPERQUAD computer program. Theoretical calculations were set up to assist in understanding the protonation sequence in the ligand molecule via the semi-empirical molecule orbital method of parameterized model number 3. Results are discussed in connection to the basicity of the donor atoms and structural arrangement of the ligand. Although BTDH₂ has two dissociable protons, four protonation constants can be measured under the experimental conditions presented. These four protonation constants (as log₁₀ βs) are 10.245, 19.397, 22.414 and 25.176.     

Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis

Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. For the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. Here we carry out extensive QM/MM free energy simulations to probe the kinetics of relevant proton transfer steps and analyze the effects of local structure and hydration level. We show that protonation of the proton loading site (PLS, taken to be a propionate of heme a₃) requires a concerted process in which a key glutamic acid (Glu286H) delivers the proton to the PLS while being reprotonated by an excess proton coming from the D-channel. The concerted nature of the mechanism is a crucial feature that enables the loading of the PLS before the cavity containing Glu286 is better hydrated to lower its pK _a to experimentally measured range; the charged rather than dipolar nature of the process also ensures a tight coupling with heme a reduction, as emphasized by Siegbahn and Blomberg. In addition, we find that rotational flexibility of the PLS allows its protonation before that of the binuclear center (the site where oxygen gets reduced to water). Together with our recent study (P. Goyal, et al., Proc. Natl. Acad. Sci. U. S. A., 2013, 110, 18886–18891) that focused on the modulation of Glu286 pK _a, the current work suggests a mechanism that builds in a natural sequence for the protonation of the PLS prior to that of the binuclear center. This provides microscopic support to the kinetic constraints revealed by kinetic network analysis as essential elements that ensure an efficient vectorial proton transport in cytochrome c oxidase.     

A potentiometric and calorimetric study of the protonation and complexation with Cu2+ and Ni2+ of some sulphur-containing α,ω-amino acids

The behaviour in aqueous solution of some aminocarboxylates of the type NH₂(CH₂)_nS(CH₂)_m-1COO^? (abbreviated as n,m-NSO; n and m = 2 or 3) in equilibria with H⁺, Cu²⁺ and Ni²⁺ ions has been investigated potentiometrically and calorimetrically at 25° C in a 0.5 M KNO₃ medium.The protonation of the amino function and especially the carboxylate function is attended by strong desolvation effects, which are characterized by low exothermic enthalpies and strongly positive entropies of protonation.In [Cu(n,m-NSO)]⁺ and [Ni(n,m-NSO)]⁺ the aminocarboxylates act as tridentate ligands, forming complexes with a strong hard—hard character. The biligand species [Ni(n,m-NSO)₂] behave as six-coordinated complexes whereas in [Cu(n,m-NSO)₂] the second ligand is bound only through the N and S donor, forming a five-coordinated species.Finally, the n,m-NSO ligands also form protonated species with the Cu²⁺ ion.     

DFT and NBO theoretical study of protonation of tri-tert-butoxysilanethiol and its anion

Density functional theory (DFT) calculations of geometry optimization at the B3LYP/6-31+G(d) level have been made for the tri-tert-butoxysilanethiolato anion, i.e. (^tBuO)₃SiS⁻ [coded A], and its O- and S-protonated derivatives: (^tBuO)₃SiSH (B), (^tBuO⁺H)(^tBuO)₂SiS⁻ (C), (^tBuO)₃SiSH₂⁺ (D) and (^tBuO⁺H)(^tBuO)₂SiSH (E). Energy balances for the protonation of silanethiol B in vacuum and the aqueous phase (using the polarized continuum IPCM model) were considered. Based on theoretical calculations, it was found that protonation on the oxygen atom causes Si–S bond shortening, while protonation on the sulfur atoms results in elongation of the bond. Changeability of the Si–S and Si–O bond lengths was analyzed in terms of the natural bond orbital (NBO) method. Principal electronic delocalizations caused by anomeric effects of the sulfur and oxygen lone pairs interaction with the anti-bonding Si–O orbitals were confirmed by the correlation between the shortening of the Si–S bond length and the elongation of the Si–O bond within the structures of the species A–E.     

Reliability of protonation constants of vildagliptin dimers by the regression analysis of pH-titration data

Protonation constants of protonated monomers and dimers of the vildagliptin are determined potentiometrically. For the low concentration c _L = 3.3 mmol dm^?3 the monomers L and LH dominate, while for a higher concentration c _L = 6.3 mmol dm^?3 the dimers L₂H₂, L₂H₃, L₂H₄ and L₂H are mainly present. The algorithm used has little influence on the precision of the formation constants in comparison with the reproducibility of the titration. The mixed protonation constants of vildagliptin dimers L _q H _r at various temperatures are determined using FBSTAC4 and HYPERQUAD regression analysis of the potentiometric titration data. The accuracy of the protonation constants log₁₀ β _qr depends on the accuracy of the group parameters. As two group parameters L ₀, H _T are ill conditioned in a model, their determination is therefore uncertain; both can significantly cause a systematic error in the estimated common parameters log₁₀ β _qr . Using various regression diagnostics the goodness-of-fit proves the reliability of all parameter estimates. A rough estimation of thermodynamic enthalpies ΔH ⁰ (kJ mol^?1) and entropies ΔS ⁰ (J K^?1 mol^?1) is determined from the temperature variation of protonation constants. The enthalpy shows the protonation process is exothermic, and the entropy indicates that it is spontaneous.      

Activite optique de polyamines tertiaires du type poly[thio-(N-R1-N-R2 aminomethyl)-1 ethylene]

Ultra-violet, ORD and CD spectra of (?)poly[thio1-(N-N-diethylaminomethyl) ethylene] (Ia) prepared by stereoelective polymerization of racemic N-N-diethyl-N-(thiirane-2-ylmethyl) amine using ZnEt₂-(—) 3-3-dimethyl-1,2 butanediol as initiator system, of (+)poly[thio1-(N-N-diethyl aminomethyl) ethylene] obtained from a partially resolved enantiomer using ZnEt₂-CH₃OH as initiator system, of poly[thio1-(N-methyl-N-sec-butyl aminomethyl) ethylene] and of poly[thio1-(N-methyl-N-(1-phenylethyl) aminomethyl) ethylene] in organic solvents (tertiary amine form) and in water (hydrochloride form) are described. Observed Cotton effects are associated with electronic transitions of chromophores by comparison with model molecules: N-methyl2-aminobutane, ethyl-thio-2-methylbutane and polypropylene sulfide. For polyamine (Ia), their contributions to optical rotatory powers in the visible are evaluated after decomposition of corresponding CD curves in Gaussian partial Cotton effects. The effects of other optically active electronic transitions located below 180 nm are deduced by difference. Influence of positions of chromophores with regard to chiral centers and of the protonation of nitrogen atoms on observed Cotton effects are discussed.     

Acid/base properties of poly(4-vinylpyridine) anchored within microporous membranes

Membranes consisting of poly(4-vinylpyridine) anchored within the pores of microporous polypropylene and polyethylene membranes exhibit a very large, fully reversible change in permeability over a very narrow pH range (pH valve). A detailed examination of the acid/base properties of the incorporated poly(4-vinylpyridine) has been undertaken in order to understand the factors affecting the position (pH) at which this valve operates. It was shown that the position and magnitude of the valve is the same when either HCl, H₃PO₄, or CH₃COOH are used to adjust the acidity of the feed solution, indicating that pH of the aqueous phase is the major determining factor controlling the valve operation with these acids. However, the valve behavior of the membrane with H₂SO₄ was found to be completely different than with the other acids in that the valve both closed at a substantially higher pH than with the other acids and then fully re-opened when the pH was decreased below 3. Potentiometric titrations of membranes containing poly(4-vinylpyridine) and control experiments involving solutions/suspensions of the homopolymer in water were undertaken. It was found that there are substantial differences in the protonation of poly(4-vinylpyridine) both in terms of its environment (membrane bound or in solution) as well as with the acid used. The differences in the pK observed between H₂SO₄ and the other acids are discussed in terms of conformational changes of poly(4-vinylpyridine) which are induced by both protonation and the counter-ion (anion) present. The results of potentiometric titrations parallel the valve behavior of the membranes. The conformational changes underlying the pH valve effects in different acids were visualized by atomic force microscopy and followed by thickness changes in the membranes.     

On the tautomerism of pyrazolones: the geminal J[pyrazole C-4,H-3(5)] spin coupling constant as a diagnostic tool

The tautomerism of pyrazolones unsubstituted at position 3(5) has been investigated by ¹³C- and ¹H NMR spectroscopic methods. Apart from chemical shift considerations and NOE effects the magnitude of the geminal ²J[pyrazole C-4,H3(5)] spin coupling constant permits the unambiguous differentiation between 1H-pyrazol-5-ol (OH) and 1,2-dihydro-3H-pyrazol-3-one (NH) forms. Whereas 1H-pyrazol-5-ols and 2,4-dihydro-3H-pyrazol-3-ones (CH-form) exhibit ²J values of approximately 9-11 Hz, in 1,2-dihydro-3H-pyrazol-3-ones this coupling constant is considerably reduced to 4-5 Hz. This can be mainly attributed to the removal of the lone-pair at pyrazole N−1 in the latter due to protonation or alkylation. According to the data obtained, 2-substituted 4-acyl-1,2-dihydro-3H-pyrazol-3-ones exist predominantly as pyrazol-5-ols in CDCl₃ or benzene-d₆ solution, whereas in DMSO-d₆ also minor amounts of NH tautomer may contribute to the tautomeric composition. 2,4-Dihydro-2-phenyl-3H-pyrazol-3-one (1-phenyl-2-pyrazolin-5-one) exists in benzene-d₆ solely in the CH-form, in CDCl₃ as a mixture of CH and OH-form, whereas in DMSO-d₆ a fast equilibrium between OH and NH isomer (with the former far predominating) is probable. For 11 compounds, including neutral and protonated molecules, we have calculated at the B3LYP/6-311++G** level, the ²J(¹H,¹³C) coupling constants which are in good agreement with those measured experimentally.