Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.     

Understanding the acid-base properties of adenosine: the intrinsic basicities of N1, N3 and N7

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.     

Spectrophotometric determination of the dissociation constants of methyl yellow in mixed protic solvents

The concentration dissociation constants (pK(a)) of methyl yellow, MY (H(+)In) in mixed aqueous solvents of methanol, ethanol, iso-propanol, tert-butanol have been accurately determined from spectrophotometric measurements at 25 degrees C and a constant ionic strength of 0.1 mol l(-1). It has been shown that in these solvents, the pK(a) values decrease with increasing composition of the organic co-solvent. A linear relationship between pK(a) and the mole fraction (x(2)) of the co-solvent was observed in a limited range of the compositions for each of the solvent systems. The results have been discussed in the light of transfer thermodynamic properties of the species existing in the dissociation equilibrium, solvent basicity and solute-solvent interactions. Furthermore, it was also observed that with the change of the solvents, the absorption spectra of MY shifted apparently and the color transition changed accordingly. The solvent effect on the spectra has been attributed to the isomerization equilibria of MY. A simple application of MY was also shown to the sodium acetate-hydrochloric acid titrations in the mixed solvents.     

Photophysical investigation of neutral and diprotonated free-base bis(arylethynyl)porphyrins

The photophysical properties for a series of free-base arylethynyl porphyrins and the corresponding trans-disubstituted tetraphenylporphyrin (H(2)TPP) derivatives lacking arylethynyl functionalities have been studied via electronic absorption and emission spectroscopy in both neutral and diacid forms. Enhanced substituent effects on porphyrin absorption spectra are observed in the arylethynyl porphyrins relative to the H(2)TPP derivatives, owing to the presence of the ethynyl spacer that allows for a coplanar geometry between the porphyrin macrocycle and the appended phenyl substituents. Upon protonation, both series of porphyrins exhibit substantially red shifted absorption and emission spectra and enhanced oscillator strengths, with the magnitude of the spectral shifts being more substantial in the presence of the ethynyl functionalities. Spectral features of the arylethynyl porphyrin bearing p-dimethylamino substituents closely resemble those previously classified as "hyperporphyrin spectra" and are indicative of excited-state charge-transfer character. Protonation of both series of porphyrins results in reduced fluorescence lifetimes and enhanced nonradiative decay rates, and the impact of protonation on these parameters is attenuated in the presence of the arylethynyl functionalities. Our results coupled with previous structural data showing that arylethynyl porphyrins exhibit less structural distortion upon diacid formation relative to H(2)TPP further substantiate the proposal that significant alteration of porphyrin photophysical properties upon diacid formation can be attributed to nonplanar structural distortions induced by protonation.     

紫外-可见分光光度法测定溴代卟啉的质子化反应常数

采用紫外-可见分光光度法研究了溴代卟啉(H2TPPBrx)在N,N-二甲基甲酰胺(DMF)中的吸收光谱性质,并测定了其在非水溶剂DMF中与HClO4反应的质子化常数。结果表明H2TPP,H2TPPBr2在DMF溶剂中与高氯酸反应得到两个质子生成[H4TPP]2 和[H4TPPBrx]2 ,而H2TPPBr3,H2TPPBr4只能得到一个质子生成[H4TPPBrx] 和[H4TPPBrx] ,其质子化常数分别为:lgK1=3.28,lgK2=2.86,lgK3=2.16,lgK4=1.93。     

A theoretical study of the protonation of methylindole derivatives

Ab initio calculations on indole and all its mono-substituted methyl derivatives, using an STO-3G minimal basis set, show that the most basic site is C3. Protonation at the nitrogen atom cannot compete with protonation at C3; and C2 is the less basic site in all cases. The basicity increases with methyl substitution, with the only exception of 3-methyl indole. A good linear correlation exists between calculated and corresponding thermodynamics pK values. 2-Aminoindole is a much stronger base than methylindoles and its high pK value can be explained by the strong interactions with the solvent through tautomeric forms which accumulate positive charge at the NH₂ group. Intramolecular quenching of the fluorescence of some indole derivatives involves intramolecular proton transfer to C4 rather than C2. Reasons why ring nitrogens can behave as either π-acceptors or π-donors in this series are discussed.     

Equilibrium, kinetic and solvent effect studies on the reactions of [RuIII(Hedta)(H2O)] with thiols

The interaction of [Ru(III)(edta)(H(2)O)](-) with a series of selected thiols having extra functional groups was investigated potentiometrically and kinetically. The pK(a) values of the uncoordinated carboxylic acid group and coordinated water molecule are 3.12 and 7.41, respectively, in aqueous solution at 25 degrees C and 0.1 M ionic strength. The formation constants of the complexes were determined in the pH range 3-9, and the concentration distribution of the various complex species was evaluated as a function of pH. The effect of dioxane on the pK(a) values of [Ru(III)(Hedta)(H(2)O)] and the formation constants of the corresponding thiol complexes is presented. The study also provides mechanistic information on the reaction of [Ru(III)(edta)(H(2)O)](-) with the thiols. The low values of DeltaH(not equal) and negative values of DeltaS(not equal) and DeltaV(not equal) for the substitution reactions of [Ru(III)(edta)(H(2)O)](-) clearly support the associative character of the substitution process.     

H2TPP organocatalysis in mild and highly regioselective ring opening of epoxides to halo alcohols by means of halogen elements

We found that elemental iodine and bromine are converted to trihalide nucleophiles (triiodine and tribromide anion, respectively) in the presence of catalytic amounts of meso-tetraphenylporphyrins (H2TPP). Therefore a highly regioselective method for the synthesis of beta-haloalcohols through direct ring opening of epoxides with elemental iodine and bromine in the presence of H2TPPs as new catalysts is described. At room temperature a series of epoxide derivatives were converted into the corresponding halohydrins resulting from an attack of trihalide species anion atoms at the less substituted carbon atom. This method occurs under neutral and mild conditions with high yields in various aprotic solvents, even when sensitive functional groups are present.     

Protonated benzofuran,anthracene, naphthalene,benzene, ethene,and ethyne: measurements and estimates of pK(a) and pK(R)

Aqueous solvolyses of acyl derivatives of hydrates (water adducts) of anthracene and benzofuran yield carbocations which undergo competitive deprotonation to form the aromatic molecules and nucleophilic reaction with water to give the aromatic hydrates. Trapping experiments with azide ions yield rate constants k(p) for the deprotonation and k(H2O) for the nucleophilic reaction based on the "azide clock". Combining these with rate constants for (a) the H(+)-catalyzed reaction of the hydrate to form the carbocation and (b) hydrogen isotope exchange of the aromatic molecule (from the literature) yields pK(R) = -6.0 and -9.4 and pK(a) = -13.5 and -16.3 for the protonated anthracene and protonated benzofuran, respectively. These pK values may be compared with pK(R) = -6.7 for naphthalene hydrate (1-hydroxy-1,2-dihydronaphthalene), extrapolated to water from measurements by Pirinccioglu and Thibblin for acetonitrile-water mixtures, and pK(a) = -20.4 for the 2-protonated naphthalene from combining k(p) with an exchange rate constant. The differences between pK(R) and pK(a) correspond to pK(H2O), the equilibrium constant for hydration of the aromatic molecule (pK(H2O) = pK(R) - pK(a)). For naphthalene and anthracene values of pK(H2O) = +13.7 and +7.5 compare with independent estimates of +14.2 and +7.4. For benzene, pK(a) = -24.3 is derived from an exchange rate constant and an assigned value for the reverse rate constant close to the limit for solvent relaxation. Combining this pK(a) with calculated values of pK(H2O) gives pK(R) = -2.4 and -2.1 for protonated benzenes forming 1,2- and 1,4-hydrates, respectively. Coincidentally, the rate constant for protonation of benzene is similar to those for protonation of ethylene and acetylene (Lucchini, V.; Modena, G. J. Am. Chem Soc. 1990, 112, 6291). Values of pK(a) for the ethyl and vinyl cations (-24.8) may thus be derived in the same way as that for the benzenonium ion. Combining these with appropriate values of pK(H2O) then yields pK(R) = -39.8 and -29.6 for the vinyl and ethyl cations, respectively.     

Conformational investigation of some macrobicyclic compounds and of their monoprotonated cations through a comparison between X-ray crystal structures and molecular dynamics simulations

Abstract

In preceding works, which have dealt with the synthesis and characterisation of a series of macrobicyclic compounds with five donor atoms, the unusually high basicity constants of these polyaminic cage-like molecules have been ascribed to the inclusion of the proton inside the macrobicyclic cavity which results in a very efficient hydrogen-bond network. The present paper, based on previously reported X-ray crystal structures regarding five-atoms bridging units and on molecular modelling studies shows that the disposition of the five donor atoms in the monoprotonated species is related to the protonation site. Precisely, if the protonation occurs on a bridge-head nitrogen the resulting geometry of the donors is a trigonal bipyramid, whereas it is square pyramidal when the proton is bound to a nitrogen belonging to a macrobicyclic chain. For what concerns the geometrical array of the donor atoms in the free amines, the favoured array seems to be the trigonal bipyramidal.     

Comparison of the acid-base properties of ribose and 2'-deoxyribose nucleotides

The extent to which the replacement of a ribose unit by a 2'-deoxyribose unit influences the acid-base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5'-di- and 5'-triphosphates of 2'-deoxyguanosine [i.e., of H(2)(dGDP)(-) and H(2)(dGTP)(2-)] as well as of the 5'-mono-, 5'-di-, and 5'-triphosphates of 2'-deoxyadenosine [i.e., of H(2)(dAMP)(+/-), H(2)(dADP)(-), and H(2)(dATP)(2-)]. These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2'-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2'-OH group is dependent on the number of 5'-phosphate groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is most significantly enhanced (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or N1H(+) sites is less pronounced but clearly present. In addition, (1)H NMR chemical shift change studies in dependence on pD in D(2)O have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. Overall, our results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact basis for the calculation, determination, and understanding of perturbed pK(a) values in DNAzymes and ribozymes, as needed for the delineation of acid-base mechanisms in catalysis.     

水溶液中新型四氮杂二乙酸基取代大环及其镧系配合物的热力学研究

The protonation constants of the macrocycle H₂L¹ (c-meso-2,4,4,11,13,13-hexamethyl-1,5,10,14-tetraazacyclooctadecane-N,N＂-diacetic acids)were determined potentiometricly and by computer fitting in 0.5 mol·L^-1 KNO₃ solution at 25±0.1℃, 30±0.1℃ and 40±0.1℃. The stability constants of the 1∶1 complexes of H₂L¹ with La³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Dy³⁺, Yb³⁺ were determined by the same method at 40±0.1℃. The ΔH、 ΔS and ΔG of the coodination reaction of H₂L¹ with H⁺ in the aqueous solution were found.     

Photophysics and photochemistry of nalidixic acid

The photophysics and photochemistry of nalidixic acid (NA) were studied as function of pH and solvent properties. The ground state of NA exhibits different protonated forms in the range of pH 1.8-10.0. Fluorescence studies showed that the same species exist at the lowest singlet excited state. Absorption experiments were carried out with NA and with the methylated analog of nalidixic acid (MNE) in different organic solvents and water pH 3, where the main species corresponds to that protonated at the carboxylic group. These studies and the DFT calculation of torsional potential energy profiles suggest that the most stable conformation of the NA in nonprotic solvents corresponds to a closed structure caused by the existence of intramolecular hydrogen bond. Absorption and fluorescence spectra were studied in sulfuric acid solution. The pK value (Ho -1.0) found in these conditions was attributed to the protonation of the 4' keto oxygen atom of the heterocyclic ring. Theoretical calculations (DFT/B3LYP/6-311G*) of the energies of the different monoprotonated forms of the NA and Fukui indexes (f(x)-) showed that the species with the proton attached to 4' keto oxygen atom is the most stable of all the cationic forms. MNE and enoxacin also showed the protonation of the 4' keto oxygen atom with similar pK values. The photodecomposition of NA is dependent on the medium properties. Faster decomposition rates were obtained in strong acid solution. In nonprotic solvents, a very slow decomposition rate was observed.     

Thermodynamic and kinetic behaviour of [Pt(2-methylthiomethylpyridine)(OH2)2]2+

The diaqua complex [Pt(2-methylthiomethylpyridine)(OH(2))(2)](2+), Pt(mtp), was synthesized and investigated thermodynamically as well as kinetically. Spectrophotometric acid-base titrations were performed to determine the pK(a) values of the two coordinated water ligands. A low pK(a1) value of 3.15 was observed for the water molecule trans to the pyridine donor, whereas a pK(a2) value of 6.84 was found for the water molecule trans to the labilising sulphur donor. The substitution of coordinated water by a series of sterically hindered S-containing nucleophiles, viz. thiourea (tu), N,N'-dimethylthiourea (dmtu) and N,N,N',N'-tetramethylthiourea (tmtu), was studied under pseudo first-order conditions as a function of nucleophile concentration, pH (2, 4.75, 7.4), temperature and pressure, using stopped-flow techniques and UV-vis spectroscopy. In general the first substitution reaction takes place trans to the sulphur donor. At pH 2 the nucleophiles react in the order tu (634 ± 10) > dmtu (507 ± 5) ? tmtu (165 ± 3 M(-1) s(-1) at 25 °C), which is caused by steric hindrance. The second observed reaction involves two steps, viz. the displacement of the second water ligand and dechelation of the pyridine ring with the third-order rate constants 73.3 ± 0.8 (tu), 22.1 ± 0.1 (dmtu) and 6.8 ± 0.2 M(-2) s(-1) (tmtu) at 25 °C. At pH 4.75 the reactions are in general slower due to the presence of aqua-hydroxo species. The same order in reactivity was found, viz. tu (106 ± 1) > dmtu (72 ± 1) ? tmtu (14.1 ± 0.5 M(-1) s(-1) at 25 °C). No evidence for ring-dechelation could be observed under these conditions. At pH 7.4 the inert dihydroxo species is predominantly present in solution and consequently no substitution reaction was observed. Quantum chemical calculations were performed to support the interpretation and discussion of the experimental results.     

Protonation of 1, 5-naphthyridine derivatives

The direction of protonation (1-N or 5-N) or 2-, 2,3-, and 2,6-substituted derivatives of 1,5-naphthyridine was determined on the basis of the basicity constants.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 965–968, July, 1977.     

The excited-state chemistry of phycocyanobilin: a semiempirical study.

Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A- into a B- and C-form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pK(B)* of approximately 9.5 units. The acidity is only slightly enhanced with a drop in pK(A)* of only approximately 1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B- and C-forms.     

Spectrophotometric determination of the protolytic dissociation constants of the new chromogenic reagent "PALLADIAZO"-II Study of the protonation processequals, single dot aboves undergone by the azo-groups of the reagent in sulphuric acid media

The protonation of the reagent 1,8-dihydroxynaphthalene-3,6-disulphonic-2,7-bis(azophenyl-p-arsonic) acid ("palladiazo") has been investigated by a spectrophotometric method in 0.25-18M sulphuric acid media. Graphical assessment of the experimental results points to the protonation of only one azo-group, although a two-stage protonation process cannot be conclusively ruled out at very high acidity. The first protonation instability constant is pK(9) = -(2.4 +/- 0.1) and the second is tentatively estimated as -7.4. Most of the current views on the complexation and protonation reactions of bis(azophenyl)chromotropic acid derivatives.with metal cations and protons are reviewed and critically discussed in some detail in order to interpret the experimental findings. It is concluded that the fully protonated palladiazo molecule exists in very concentrated acid media predominantly in the form of a symmetrical positively charged tautomeric quinonehydrazone proton complex species which is responsible for the appearance of a very strong single absorption band with a maximum at 665 run which gives the protonated reagent solutions a characteristic deep-emerald-green colour.     

Photophysics of a series of efficient fluorescent pH probes for dual-emission-wavelength measurements in aqueous solutions

This paper evaluates the 5-aryl-2-pyridyloxazole backbone to engineer donor-acceptor fluorescent pH probes after one- or two-photon absorption. Parent fluorophores, as well as derivatives that can be used to label biomolecules, can be easily obtained in good yields. These molecules exhibit a large one-photon absorption in the near-UV range, and a strong fluorescence emission that covers the whole visible domain. The 5-aryl-2-pyridyloxazole derivatives also possess significant cross sections for two-photon absorption. Upon pyridine protonation, large shifts were observed in the absorption spectra after one- and two-photon excitation, as well as in the emission spectra. This feature was used to measure the pK(a) of the investigated compounds that range between 2 and 8. In most of the investigated derivatives, the pK(a) increased upon light excitation and protonation exchanges took place during the lifetime of the excited state, as shown by phase-modulation fluorometry analysis. Several 5-aryl-2-pyridyloxazole derivatives are suggested as efficient probes to reliably measure the pH of aqueous solutions by means of ratiometric methods that are dependent on fluorescence emission.     

Highly non-planar dendritic porphyrin for pH sensing: observation of porphyrin monocation

Metal-free porphyrin-dendrimers provide a convenient platform for the construction of membrane-impermeable ratiometric probes for pH measurements in compartmentalized biological systems. In all previously reported molecules, electrostatic stabilization (shielding) of the core porphyrin by peripheral negative charges (carboxylates) was required to shift the intrinsically low porphyrin protonation pK(a)'s into the physiological pH range (pH 6-8). However, binding of metal cations (e.g., K(+), Na(+), Ca(2+), Mg(2+)) by the carboxylate groups on the dendrimer could affect the protonation behavior of such probes in biological environments. Here we present a dendritic pH nanoprobe based on a highly non-planar tetraaryltetracyclohexenoporphyrin (Ar(4)TCHP), whose intrinsic protonation pK(a)'s are significantly higher than those of regular tetraarylporphyrins, thereby eliminating the need for electrostatic core shielding. The porphyrin was modified with eight Newkome-type dendrons and PEGylated at the periphery, rendering a neutral water-soluble probe (TCHpH), suitable for measurements in the physiological pH range. The protonation of TCHpH could be followed by absorption (e.g., ε(Soret)(dication)～270,000 M(-1) cm(-1)) or by fluorescence. Unlike most tetraarylporphyrins, TCHpH is protonated in two distinct steps (pK(a)'s 7.8 and 6.0). In the region between the pK(a)'s, an intermediate species with a well-defined spectroscopic signature, presumably a TCHpH monocation, could be observed in the mixture. The performance of TCHpH was evaluated by pH gradient measurements in large unilamellar vesicles. The probe was retained inside the vesicles and did not pass through and/or interact with vesicle membranes, proving useful for quantification of proton transport across phospholipid bilayers. To interpret the protonation behavior of TCHpH we developed a model relating structural changes on the porphyrin macrocycle upon protonation to its basicity. The model was validated by density functional theory (DFT) calculations performed on a planar and non-planar porphyrin, making it possible to rationalize higher protonation pK(a)'s of non-planar porphyrins as well as the easier observation of their monocations.