13C NMR investigation of tautomeric and acid-base equilibria of pyrazolone T and three analogs

Pyrazolone T and three derivatives have been characterized by ¹³C and, in part, ¹⁵N nmr at several pH values. The ¹³C chemical shifts have been assigned at, or near, the equivalence points and pK_a values of these four compounds. Closely situatued quaternary carbon signals were assigned by means of a heteronuclear chemical shift correlation (FLOCK) experiment which is sensitive to, and was optimized for, 3-bond C-H couplings. The ¹³C chemical shift data indicate the existence of both tautomeric and acid-base equilibria and demonstrate that the four congeners exist in surprisingly different forms at certain common pH values.     

Intrinsic Acid–Base Properties of a Hexa‐2′‐deoxynucleoside Pentaphosphate,d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

The intrinsic acid‐base properties of the hexa‐2′‐deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1?G2?G3?C4?C5?T6)=(HNPP)^5?] have been determined by ¹H NMR shift experiments. The pK_a values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single‐strand conditions (i.e., 10 % D₂O, 47 °C, I=0.1 M , NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G?G), the two (N3)H⁺ (C?C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G?G) and the (N3)H (T) sites. Based on measurements with 2′‐deoxynucleosides at 25 °C and 47 °C, they were transferred to pK_a values valid in water at 25 °C and I=0.1 M . Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pK_a clusters occur, that is those encompassing the pK_a values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five‐fold protonated H₅(HNPP)^±, the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4 %, respectively. Tautomer distributions reveal pathways for proton‐donating as well as for proton‐accepting reactions both being expected to be fast and to occur practically at no “cost”. The eight pK_a values for H₅(HNPP)^± are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1?G2?G3? C4?C5?U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pK_a values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.     

15N NMR studies of amino acids and their reaction products with formaldehyde

Natural abundance ¹⁵N NMR spectroscopy has been used to investigate the effect of pH on the ¹⁵N chemical shifts of lysine and of ε-hydroxymethyllysine. A computer calcualtion which fits the chemical shifts of both α-and ε-nitrogen atoms versus pH has been used to predict the pK_a values. ¹⁵N chemical shifts and some ¹J(¹⁵NH) values of some other amino acids and of their reaction products with formaldehyde are also reported.     

1H NMR spectroscopic identification of protonable sites in cryptolepines with C‐11 substituents containing two amino functionalities

Knowledge of protonable sites and acid dissociation constants of cryptolepine derivatives having C‐11 substituents containing two amino functionalities is of great importance to the understanding of the mechanism of their antimalarial action, which may contribute to their further development as drug candidates. In this work, we applied ¹H NMR titration to investigate the acid–base characteristics of these polyprotic compounds in the pH range 3–13. We identified three acid–base equilibria with most acid dissociation constants (pK_a*) being greater than 10.5, which prevented us from using the potentiometric method. Overall, ¹H NMR titration was sensitive and suitable for the determination of pK_a values for these drug leads. Copyright © 2012 John Wiley & Sons, Ltd.     

NMR investigations on alanyl-[15% 13C, 95% 15N]-proline: 15N chemical shifts and 13C?15N coupling constants

The dipeptide alanylproline has been prepared with the proline residue both ¹³C (15%) and ¹⁵N (95%) enriched. ¹⁵N NMR spectra of alanylproline reveal signals for both possible conformations—cis and trans—of the dipeptide backbone in solution. Different pK values for both conformers are obtained from the pH dependence of the ¹⁵N chemical shifts using a least square programme based on the Henderson–Hasselbach equation. These different values are discussed in terms of interaction between the α-amino group and the carboxylate group and between the carboxylate oxygen and the carbonyl oxygen of the dipeptide via hydrogen bonding. Further evidence for these interactions is obtained from the pH dependence of the ratio of the ¹⁵N NMR signal intensities of the two conformers. One, two or three bonded ¹³C? ¹⁵N coupling constants measured in the ¹³C NMR high resolution spectra have different values in the cis and trans isomers of alanylproline and thus indicate different geometry in the pyrrolidine ring.     

Determination of pKa values of some novel benzimidazole salts by using a new approach with 1H NMR spectroscopy

Benzimidazoles and their derivatives including imidazole are studied widely because they exist in the structure of natural products and different drugs. pK_a values are extremely important for drug discovery and improvement in order to determine pharmacokinetic and pharmacodynamic features such as permeation through biological barriers, interactions with the target area or side effects. Acid–base features (pK_a) have great importance not only for physiological characteristics but also for being used as a ligand or changing physico‐chemical features by turning benzimidazoles into salts. Within the scope of this study, a variety of new benzimidazole salts were synthesized, and their characterizations were made by NMR spectroscopy, FTIR spectroscopy and element analysis techniques. The pK_a values of synthesized benzimidazole salts were determined by inflection point approach using integration values obtained with ¹H NMR spectroscopy and Henderson–Hasselbalch analysis. pK_a values of some benzimidazole salts were also determined by potentiometric methods in order to compare those of NMR spectroscopy results. Copyright © 2015 John Wiley & Sons, Ltd.     

Theoretical Study of Firefly Luciferin pKa Values—Relative Absorption Intensity in Aqueous Solutions

Ground‐state vibrational analyses of firefly luciferin and its conjugate acids and bases are performed. The Gibbs free energies obtained from these analyses are used to estimate pK_a values for phenolic hydroxy and carboxy groups and the N–H⁺ bond in the N‐protonated thiazoline or benzothiazole ring of firefly luciferin. The theoretical pK_a values are corrected using the experimental values. The concentrations of these chemical species in solutions with different pH values are estimated from their corrected pK_a values, and the pH dependence of their relative absorption intensities is elucidated. With the results obtained we assign the experimental spectra unequivocally. Especially, the small peak near 400 nm at pH 1–2 in experimental absorption spectra is clarified to be due to the excitation of carboxylate anion with N‐protonated thiazoline ring of firefly luciferin. Our results show that the pK_a values of chemical species, which are contained in the aqueous solutions, are effective to assign experimental absorption spectra.     

Enantioselective Synthesis and Physicochemical Properties of Libraries of 3‐Amino‐ and 3‐Amidofluoropiperidines

The enantioselective syntheses of 3‐amino‐5‐fluoropiperidines and 3‐amino‐5,5‐difluoropiperidines were developed using the ring enlargement of prolinols to access libraries of 3‐amino‐ and 3‐amidofluoropiperidines. The study of the physicochemical properties revealed that fluorine atom(s) decrease(s) the pK_a and modulate(s) the lipophilicity of 3‐aminopiperidines. The relative stereochemistry of the fluorine atoms with the amino groups at C3 on the piperidine core has a small effect on the pK_a due to conformationnal modifications induced by fluorine atom(s). In the protonated forms, the C?F bond is in an axial position due to a dipole–dipole interaction between the N?H⁺ and C?F bonds. Predictions of the physicochemical properties using common software appeared to be limited to determine correct values of pK_a and/or differences of pK_a between cis‐ and trans‐3‐amino‐5‐fluoropiperidines.     

Investigations on the dissociation behavior of hydrolyzed alternating copolymers of maleic anhydride and alkenes: 13C-NMR spectra and potentiometric titrations

The pK_a values of the succinic acid moieties of hydrolyzed alternating ethene- and isobutene-maleic anhydride copolymers were determined in D₂O. The pD-dependence on the ¹³C chemical shift of selected signals was analyzed for these copolymers. Four different pK_as were determined for the copolymer with ethene due to the existence of both the erythro- and threo-configuration of the succinic acid moiety: pK_01,erythro = 4.2, pK_0.1,threo = 4.1, pK_02,erythro = 6.1, pK_02,threo = 6.8. The isobutene-maleic anhydride copolymer contains only threo-units. Therefore, only two dissociation steps with pK₀₁ = 3.0 and pK₀₂ = 8.7 were observed for the hydrolyzed form. © 1996 John Wiley & Sons, Inc.     

Capillary zone electrophoresis of basic drugs in non-aqueous acetonitrile with buffers based on a conventional pH scale

Summary The pK _a ^* values of 10 nitrogen-containing basic drugs in non-aqueous acetonitrile were determined from the pH^* dependence of their electrophoretic mobilities. The pH^* scale in the organic solvent was established using background electrolytes with known conventional pK _a ^* values, making further calibration with reference pH electrodes unnecessary. In acetonitrile the pK _a ^* values of analytes (or their conjugated cation acids, BH⁺, respectively) were 5.2±8.9 pK units>those in water. The observed change in pK _a ^* values of cationic analytes was, however, much less than the known respective change for neutral acids type HA. From the pK _a ^* values and the actual mobilities, it is possible to predict pH^* conditions to enable separation of analytes, and this was demonstrated for two pairs of common drugs.     

Basicity of some aliphatic amines in mixed H2O?CH3CN solvents

The values of pK_a^ms (K_a^ms represents ionization constant of conjugate acid of amine base in mixed water–acetonitrile solvent) for all amines, except for charged amine bases, show a mild decrease (ca. 0.1–0.4 pK units) with the increase in CH₃CN content from 2 to ∼60% v/v. However, the pK_a^ms values at 70% v/v CH₃CN become nearly equal or slightly larger (by ≤0.7 pK units) than the corresponding pK_a^ms at 2% v/v CH₃CN for all neutral and charged amines. The values of pK_a^ms for phenol increase from 10.17 to 13.38 with the increase in the content of CH₃CN from 2 to 70% v/v in mixed aqueous solvent. Taft reaction constants, ρ*, obtained from the plots of pK_a^ms against ∑σ* for primary and secondary amines decrease by ca. 0.8 ρ* units with the increase in the CH₃CN content from 2 to 70% v/v. The values of pK_a^ms show an empirical linear relationship with the corresponding values of pK_a^w (where pK_a^w represents the pK_a obtained in aqueous solvent containing 2% v/v CH₃CN), which allows the estimation of a pK_a in mixed H₂O CH₃CN solvents from that in water. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 146–152, 2000     

A Mini‐Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class

Nucleolytic ribozymes catalyze site‐specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild‐type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine‐6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pK_a value of 5.1 was determined for a ¹³C2‐labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pK_a of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine‐6 in the catalytic mechanism besides the previously identified invariant guanine‐48 and a Mg²⁺ ion, both of which are directly coordinated to the non‐bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn²⁺ or Cd²⁺ accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X‐ray structure of a 2′‐OCH₃‐U5 modified twister ribozyme.     

Design of Biosolvents Through Hydroxyl Functionalization of Compounds with High Dielectric Constant

We proposed basic principles for biosolvent design on the viewpoint of ionization. Two classes of biosolvents, based on cyclic carbonate moiety and amide moiety, were designed through hydroxyl functionalization of highly dielectric compound. The newly designed compounds, glycerol carbonate (GC) and N-hydroxymethyl formamide (HOF), were synthesized for the development of soluble enzymatic systems and characterized by ¹³C NMR and ¹H NMR. All the characterization data were consistent with the expected structures. Using conductance measurements, the pK _a values of trichloroacetic acid in GC and HOF were determined as 0.80 and 0.85 at 25.0 °C, which was very close to that in water (pK _a = 0.70), suggesting that the ionizing and dissociating abilities of GC and HOF are similar to those of water. The effects of various reaction parameters on activity and stability of Candida antarctica lipase B and lipase from Pseudomonas cepacia were investigated using the transesterification of ethyl butyrate with n-butanol as a model reaction. The activities of lipases in GC and HOF were comparable to those in water, indicating that the newly designed compounds were biocompactible. Biosolvent design is a promising and versatile method for developing new biosolvents.     

NMR determination of pKa values of indoloquinoline alkaloids

Malaria is one of the most serious global health problems. Isolating new therapeutic agents with potential antimalarial activity from natural sources or preparing such agents either semisynthetically or synthetically is one strategy for solving the problem of resistance constantly evolving to the drugs currently in use. For alkaloids, the acid–base dissociation constant, pK_a, is an important characteristic, thought to be associated with biological activity. In this contribution, pK_a values for several indoloquinoline alkaloids were determined by using ¹H NMR spectroscopy in a mixture of solvents. The data were recalculated for water solutions using the correction factors reported previously. The structural dependence of the pK_a values for cryptolepine and its isomers neocryptolepine, isocryptolepine and isoneocryptolepine as well as some substituted neocryptolepine derivatives is discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of hydration equilibrium constants and pKa values of 4-piperidones in buffered water solutions

¹H and ¹³C chemical shift parameters are given for 4-piperidones and their derivatives in buffered aqueous solution. The ¹³C shift increments of methyl substituents on the nitrogen atom are discussed. The pH-shift dependence is studied in detail and pK_a values are given for ketone forms and hydration products. The hydration equilibria are measured as a function of pH and temperature.     

2-Phosphonobutane-1,2,4,-Tricarboxylic Acid (PBTC): pH-Dependent Behavior Studied by Means of Multinuclear NMR Spectroscopy

Although 2-phosphonobutane-1,2,4,-tricarboxylic acid, PBTC, has manifold industrial applications, relevant and reliable data on the protonation of PBTC are poor. However, these data are critical parameters for ascertaining PBTC speciation, especially with regard to a sound structural and thermodynamic characterization of its metal ion complexes. A rigorous evaluation of pH-dependent ¹H, ¹³C, and ³¹P chemical shifts along with accessible scalar spin–spin coupling constants (J) was performed in order to determine the pK_a values of PBTC in 0.5 molal NaCl aqueous solution by means of nuclear magnetic resonance (NMR) spectroscopy. The phosphonate group revealed pK_a values of 0.90 ± 0.02 and 9.79 ± 0.02, and the pK_a values associated with the carboxylic groups are 3.92 ± 0.02, 4.76 ± 0.03, and 6.13 ± 0.03. Supported by DFT-calculated structures revealing strong intramolecular hydrogen bonding, the sequence of deprotonation could be unambiguously determined.     

Synthesis and some transformations of dimethyl anabasylethynephosphonate

A new phosphorylated ynamine, dimethyl anabasylethynephosphonate, was synthesized by reaction of dimethyl chloroacetylenephosphonate with anabasine. Anabasylethynephosphonate obtained was shown to react under mild conditions with primary aromatic amines like p-chloroaniline, p-anisidine, and p-aminoacetophenone, whose pK _b values are in the range of 9–13, to form new asymmetrical phosphorylated acetamidines in high yields. Structure of the compounds obtained was proved by ¹H, ¹³C, and ³¹P NMR spectroscopy.     

Determination of pK a of N-alkyl-N,N-dimethylamine-N-oxides using 1H NMR and 13C NMR spectroscopy

The pK _a values of N-alkyl-N,N-dimethylamine-N-oxides were determined from the pH dependences of chemical shifts in ¹H NMR and ¹³C NMR spectra. The dependences were measured at concentrations below and above the critical micelle concentration of the amine oxides. Above the critical micelle concentration, the plots of the peak positions vs. pH were either sigmoid (the groups close to the nitrogen) or “peak type” (farther groups). The sigmoidal behaviour was a direct result of the acid-base reaction; on the other hand, the “peak type” behaviour was probably an indirect consequence of the pH variation, mediated with the change in micelle size.     

Nitrogen-15 n.m.r. studies of 13C, 15N labeled arginine

¹⁵N n.m.r. spectra of [¹³C-2, 3-¹⁵N₂-guanidino]arginine and [¹³C, ¹⁵N₂] urea were obtained in D₂O and H₂O at a variety of pH values both with and without proton decoupling. The effects of the proton exchange rate are readily observable in the proton coupled ¹⁵N spectra. When the guanidino group is deprotonated (pK = 12.5), the terminal nitrogens give a single resonance 6.6 ppm downfield of the protonated species, indicating a rapid tautomeric exchange. The observed NH and CN couplings are compared with calculated values, and good agreement is found for ¹J(CN) using a Blizzard–Santry type calculation. The ramifications of the proton exchange on ¹⁵N n.m.r. spectra of amino acids and peptides are discussed.     

Polynuclear Branched Tetrazole Systems. 2. New 2-(5-Tetrazolyl)ethylpodands and Their NH-Acidity

Nine new polynuclear 2-(5-tetrazolyl)ethyl podands have been obtained by the azidation of the corresponding nitriles. Using Bjerrum distribution functions, the values of pK _a ¹, pK _a ², pK _a ³, and pK _a ⁴ have been determined by a potentiometric method for 14 polynuclear tetrazoles in aqueous and aqueous methanolic solution. The found values lie in the range from 3.5 to 7.5 pH units. The overall rules and the sequence of the ionization of the spatially separated tetrazole fragments in these podand systems are discussed.