GIAO‐DFT calculation of 15N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects

¹⁵N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated ¹⁵N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach.     

Excited-state intermolecular proton transfer of firefly luciferin V. Direct proton transfer to fluoride and other mild bases

We studied the direct proton transfer (PT) from electronically excited D-luciferin to several mild bases. The fluorescence up-conversion technique is used to measure the rise and decay of the fluorescence signals of the protonated and deprotonated species of D-luciferin. From a base concentration of 0.25 M or higher the proton transfer rates to the fluoride, dihdyrogen phosphate or acetate bases are fast and comparable. The fluorescence signals are nonexponential and complex. We suggest that the fastest decay component arises from a direct proton transfer process from the hydroxyl group of D-luciferin to the mild base. The proton donor and acceptor molecules form an ion pair prior to photoexcitation. Upon photoexcitation solvent rearrangement occurs on a 1 ps time-scale. The PT reaction time constant is ～2 ps for all three bases. A second decay component of about 10 ps is attributed to the proton transfer in a contact pair bridged by one water molecule. The longest decay component is due to both the excited-state proton transfer (ESPT) to the solvent and the diffusion-assisted PT process between a photoacid and a base pair positioned remotely from each other prior to photoexcitation.     

Collisionally activated dissociation of protonated 2′-deoxycytidine, 2′-deoxyuridine, and their oxidatively damaged derivatives

We examined the collisionally activated dissociation (CAD) pathways of protonated 2'-deoxycytidine (dC), 5-formyl-2'-deoxycytidine (5-FmdC), 5-hydroxy-2'-deoxycytidine (5-OHdC), 5-hydroxymethyl-2'-deoxycytidine (5-HmdC), and their corresponding stable isotope-labeled compounds to gain insights into the effects of modifications on the fragmentation pathways of the pyrimidine bases. Multi-stage MS (MSn) results showed that protonated cytosine, its 5-hydroxyl- and 5-hydroxymethyl-substituted derivatives, but not its 5-formyl-substituted analog, could undergo Dimroth-like rearrangement in the gas-phase. The elimination of HNCO was one of the major fragmentation pathways observed for the protonated ions of all dC derivatives except for 5-hydroxymethylcytosine, which underwent this loss only after a H2O molecule had been eliminated. In addition, the protonated cytosine and 5-hydroxycytosine can undergo a facile elimination of NH3 molecule. This loss, however, was not observed for protonated 5-hydroxymethylcytosine, 5-formylcytosine, and their uracil analogs. Taken together, our study demonstrated that modifications could alter markedly the CAD patterns of the protonated pyrimidine bases. The results from this study provided a basis for the identifications of other modified pyrimidine bases/nucleosides by tandem mass spectrometry.     

PICOSECOND AND NANOSECOND TSOMERIZATION KINETICS OF PROTONATED 11-CIS RETINYLIDENE SCHIFF BASES

Abstract— Picosecond and nonosecond spectroscopy has been used to study the isomerization mechanism of protonated 11- cis retinylidene Schiff bases. The formation and bleaching of absorption bands within 10 ps and corresponding decay and recovery within 11 ns indicate that the isomerization mechanism of the protonated Schiff bases is not identical to rhodopsin in which the primary photophysical event is probably due to electron transfer or partial isomerization of the chromophore to a nonplanar conformation.     

Retention characteristics of protonated mobile phases injected into deuterated mobile phases in capillary liquid chromatography (LC) using on-line nuclear magnetic resonance (NMR) detection

The behavior of protonated binary solvents injected into deuterated binary mobile phases in capillary LC is studied with NMR. Specifically, the solvent elution is followed on-flow with a capillary LC coupled to a 900 nL volume microcoil NMR probe. A range of identical composition 5% protonated (and 95% deuterated) solvents is injected into composition-matched deuterated mobile phases of CD(3)CN/D(2)O and CD(3)OD/D(2)O. The protonated components separate for all solvent combinations except at 80% CD(3)CN/20% D(2)O and similar to 72% CD(3)OD/28% D(2)O where only a single retention time is observed. The more hydrophilic protonated component, HOD, elutes first with higher percentages of hydrophilic solvent, D(2)O, in the mobile phase whereas retention is reversed with the higher percentage of the more hydrophobic solvent (CD(3)CN and CD(3)OD) in the mobile phase. The hydrophilic/hydrophobic nature of the chromatographic system as a function of mobile phase composition is characterized by following the retention times of protonated solvents.     

Proton-block strategy for the synthesis of oligodeoxynucleotides without base protection,capping reaction,and P-N bond cleavage reaction

A new N-unprotected phosphoramidite method called the "proton-block" approach was developed for the chemical synthesis of oligodeoxynucleotides based on the hitherto simplest and rational principle of acid-base reactions. This concept involves protection of the nucleobases of deoxycytidine and deoxyadenosine with "protons" to convert them to unreactive protonated bases during condensation by use of promoters having pK(a) values lower than 2.8. This strategy was applied to the synthesis of d[CpT] and d[ApT] to check the side reactions associated with the base residues. In this "proton-block" method, 5-nitrobenzimidazolium triflate (NBT) was found to be the best promoter, and THF was superior to CH(3)CN as the solvent so that the concomitant detritylation due to the inherent acidity of the promoter could be greatly suppressed. Application of this strategy to the solid-phase synthesis gave d[CpT], d[ApT], d[ApA], d[CpC], and d[GpT] as almost single peaks in HPLC analysis. Similarly, d[ApApApT] and d[CpCpCpT] were successfully synthesized without significant side reactions. Finally, d[CpCpCpCpCpCpT] and d[ApApApApApApT] were obtained as the main products. In the case of a longer oligomer, d[CpApGpTpCpApGpTpCpApGpT], a mixed solvent of CH(3)CN-N-methylpyrrolidone (1:1, v/v) was superior to THF so that the desired oligodeoxynucleotide could be isolated in a satisfactory yield. These results suggest that DNA synthesis can be carried out simply by using the protonated bases at the oligomer level not only without base protection but also without the capping reaction and the posttreatment of branched chains with MeOH-benzimidazolium triflate that previously was requisite. It is concluded that most of the reactions and solvent effects involved in this strategy can be explained in terms of simple acid-base reactions. Some problems associated with the previous posttreatment are also discussed with our own results.     

Enthalpic and polar effects in the reactions of perfluoroalkyl radicals: New selective synthetic developments with alkenes and heteroaromatic bases

Perfluoroalkyl radicals, generated by iodine abstraction from perfluoroalkyl iodides by phenyl radical, react with low selectivity with protonated heteroaromatic bases, due to their electrophilic character and the prevalent enthalpic effect on the reaction. In the presence of alkenes, perfluoroalkyl radicals add very rapidly to the double bond and the polar character of the radical adduct is reversed, allowing the selective substitution of protonated heteroaromatic bases. The mechanism of the reaction and the key role of enthalpic and polar effects are discussed.     

INVESTIGATION INTO THE SPECTROSCOPY AND PHOTOISOMERIZATION OF A SERIES OF POLY (ETHYLENE GLYCOL) PEPTIDE SCHIFF BASES OF 11-cis RETINAL

Abstract— The 11-cis and all-trans isomers of a series of poly(ethylene glycol)-oligopeptide - Schiff bases as models for rhodopsin were synthesized and studied. Absorption data for certain of the PEG-peptide Schiff bases demonstrated that no intramolecular hydrogen-bonding (or protonation) occurs between the Schiff base and an acidic amino acid residue, as was previously thought. Photoisomerization of the 11-cis protonated and unprotonated Schiff bases were examined using both steady state and laser flash techniques. Also with 355 nm excitation (and additionally 532 nm in one case), an approximate 40% increase in quantum yield of isomerization (φ) occurred for all protonated PEG-peptide Schiff bases compared to the H⁺-n-butylamine counterparts (in methanol). In one case, a > 100% increase in φ was found in dichloromethane. These data show that PEG-oligopeptide Schiff bases are still further improved models for rhodopsin compared to their n-butylamine analogs.     

Importance of gas-phase proton affinities in determining the electrospray ionization response for analytes and solvents

The effect of gas-phase proton transfer reactions on the mass spectral response of solvents and analytes with known gas-phase proton affinities was evaluated. Methanol, ethanol, propanol and water mixtures were employed to probe the effect of gas-phase proton transfer reactions on the abundance of protonated solvent ions. Ion-molecule reactions were carried out either in an atmospheric pressure electrospray ionization source or in the central quadrupole of a triple-quadrupole mass spectrometer. The introduction of solvent vapor with higher gas-phase proton affinity than the solvent being electrosprayed caused protons to transfer to the gas-phase solvent molecules. In mixed solvents, protonated solvent clusters of the solvent with higher gas-phase proton affinity dominated the resulting mass spectra. The effect of solvent gas-phase proton affinity on analyte response was also investigated, and the analyte response was suppressed or eliminated in solvents with gas-phase proton affinities higher than that of the analyte.     

Cyclodextrin assisted nanophase determination of alkaloid salts

The poor water solubility of the free base and the high dissociation constant (K_a) hinder mainly the assay of alkaloid salts. We have elaborated an enviroment friendly method that can be carried out in aqueous media. The stability difference of the cyclodextrin (CD) complexes of free and protonated bases were used for this purpose. The base is included into the hydrophobic cavity of the CD (which serves as an apolar solvent phase on molecular level) and its solubility in water is increased. Since the base forms more stable inclusion complex than its protonated species, the pK_a is decreased and the potentiometric titration is promoted by this way, too. Six different hydrohalide alkaloid salts have been investigated and the most appropriate CDs were chosen (depending on the size of the molecules and/or substituents). The results of the assays agree well with those obtained by the direct nonaqueous titrations. The stability constants of the inclusion complexes have been also computed.     

SPECTROSCOPY OF POLYENES–III. ABSORPTION AND EMISSION SPECTRAL INVESTIGATION OF POLYENE SCHIFF BASES AND PROTONATED SCHIFF BASES RELATED TO VISUAL PIGMENTS

Abstract— A number of n -butylamine Schiff bases of polyenals related to retinals as homologues and analogues, and their protonated forms, have been studied for absorption and emission spectral properties. The polyene Schiff bases exhibit the same general features in their absorption spectra as those of the parallel polyenals except that the ^lB_u←¹A_g and π*← n singlet transitions are at substantially higher energy in the Schiff bases (the shift being larger for the π *← n transition). The Schiff bases with short polyene chainlength ( n = 2, 3 where n is the number of double bonds including C=N) do not fluoresce or phosphoresce in 3-methylpentane in the temperature range 298–77 K. The Schiff bases with intermediate chainlength ( n = 4, 5) show fluorescence at 77 K with intensity strongly dependent on the nature of solvent. The Schiff bases with relatively long chainlength ( n = 5–7) show strong or moderately strong fluorescence at 77 K and very weak fluorescence at 298 K ( n = 7) with intrinsic radiative lifetimes much longer than those estimated from the oscillator strength of the low-energy, strong absorption band (¹B_u←¹ A_g ). A discussion on the possible state order and nature of the fluorescing state of the various polyene Schiff base systems is presented.     

Effects of Gas-Phase Basicity on the Proton Transfer between Organic Bases and Trifluoroacetic Acid in the Gas Phase: Energetics of Charge Solvation and Salt Bridges

The unimolecular dissociation pathways and kinetics of a series of protonated trimer ions consisting of two organic bases and trifluoroacetic acid were investigated using blackbody infrared radiative dissociation. Five bases with gas-phase basicities (GB) ranging from 238.4 to 246.2 kcal/mol were used. Both the dissociation pathways and the threshold dissociation energies depend on the GB of the base. Trimers consisting of the two most basic molecules dissociate to form protonated base monomers with an E(0) ~ 1.4 eV. Trimers consisting of the two least basic molecules dissociate to form protonated base dimers with an E(0) ~ 1.1-1.2 eV. These results indicate that the structures of the trimers change as a function of the GB of the basic molecule. The predominant structure of the protonated trimers consisting of the two most basic molecules is consistent with a salt bridge in which both of the basic molecules are protonated, and the trifluoroacetic acid molecule is deprotonated, whereas the predominant structure of the protonated trimers consisting of the two least basic molecules are consistent with charge-solvated complexes in which the proton is shared. The structure of the trimer consisting of the base of intermediate basicity is less clear; it dissociates to form primarily protonated base dimer, but has an E(0) ~ 1.2 eV. These results are consistent with the structure of this trimer as a salt bridge, but the resulting dissociation A(-). BH(+) product does not appear to be stable as an ion pair in the dissociative transition state.     

The pK(a), values of the conjugate acid of imidazole in water-ethanol mixtures

The pK(a) values of protonated imidazole in 10 different water-ethanol mixtures were determined at 25 degrees by potentiometric titration in a cell without liquid junction (glass and silver-silver bromide electrodes). The pK(a) values can be used in a standardization procedure that allows determination of pK(a) values for protonated organic nitrogen bases in aqueous ethanol.     

Quantitative aspects of and ionization mechanisms in positive-ion atmospheric pressure chemical ionization mass spectrometry

The behavior in atmospheric pressure chemical ionization of selected model polycyclic aromatic compounds, pyrene, dibenzothiophene, carbazole, and fluorenone, was studied in the solvents acetonitrile, methanol, and toluene. Relative ionization efficiency and sensitivity were highest in toluene and lowest in methanol, a mixture of molecular ions and protonated molecules was observed in most instances, and interferences between analytes were detected at higher concentrations. Such interferences were assumed to be caused by a competition among analyte molecules for a limited number of reagent ions in the plasma. The presence of both molecular ions and protonated analyte molecules can be attributed to charge-transfer from solvent radical cations and proton transfer from protonated solvent molecules, respectively. The order of ionization efficiency could be explained by incorporating the effect of solvation in the ionization reactions. Thermodynamic data, both experimental and calculated theoretically, are presented to support the proposed ionization mechanisms. The analytical implications of the results are that using acetonitrile (compared with methanol) as solvent will provide better sensitivity with fewer interferences (at low concentrations), except for analytes having high gas-phase basicities.     

Study on the formation of an amoxicillin adduct with methanol using electrospray ion trap tandem mass spectrometry

The possibility of using the protonated methanol-adduct of antimicrobial amoxicillin for its identification and quantification at residue levels has been investigated, since it is impossible to completely suppress the formation of these adducts when methanol is present in the solvent system. This process has been monitored over time and as a function of concentration. It was determined that adducts were instantly formed and that the abundance of the protonated methanol-adduct at m/z 398 increased at the expense of the protonated molecule m/z 366 with storage time. The effect of several common solvents and mobile-phase additives on the ionization efficiency of amoxicillin and the formation of the methanol adduct has also been investigated. It was shown that the mass spectra of amoxicillin were strongly influenced by the solvent in which the analyte is dissolved and by the analyte concentration, as well as by the composition of mobile phase. Methanol was determined to be the best spray solvent, as it provided spectra with the lowest abundance of dimer ions. It was also determined that acetic acid as the mobile-phase additive provided the highest signal intensities, while ammonium acetate should not be used as an additive for the determination of amoxicillin at residue levels. Using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS), fragmentation of the protonated molecules and the protonated methanol-adduct ions, in both positive and negative ion mode, has been performed. The fragmentation was stable and strong product ion spectra were obtained. The linearity of the MS detector response, and that of the chromatographic method, was tested. Due to the linear behaviour it was concluded that the protonated methanol-adduct ion can be used for analytical purposes, i.e. for identification and quantification of amoxicillin at trace levels.     

Effect of buffer cations and of H3O+ on the charge states of native proteins. Significance to determinations of stability constants of protein complexes

The progressive reduction of charge in charge states of non-denatured proteins (lysozyme, ubiquitin, and cytochrome c), observed with nanospray in the positive ion mode, when the buffer salt ammonium acetate is replaced by ethylammonium acetates (EtNH(3)Ac, Et(2)NH(2)Ac and Et(3)NHAc) is rationalized on the basis of the charge residue model (CRM). The charge states of the multiply protonated protein are shown to be controlled by the increasing gas-phase basicities, GB(B), of the bases(B) NH(3), EtNH(2), Et(2)NH and Et(3)N. Charge states derived from evaluated apparent gas-phase basicities GB(app) of the basic side-chains of the protein and the known GB(B) of the above bases are found to be in agreement with the experimentally observed charge states. This is a requirement of the CRM, because in this model the small positive ions (the buffer cations in the present case) at the surface of the electrospray droplets are the excess ions that provide the charge of the final small droplet that contains the protein molecule and on evaporation of the solvent transfer the charge to the protein. The observed charge states in the absence of buffer salts, i.e. pure water, are attributed to excess H(3)O(+) ions produced by the electrolysis process that attends electrospray. A proposed extended mechanism provides predictions of factors that determine the sensitivity for detection of the multiply protonated proteins. Consideration of restraints imposed by the CRM lead to some simple predictions for conditions that should be present to obtain accurate determinations by electrospray and nanospray of stability constants for the protein-complex equilibrium in aqueous solution.     

Amines That Transport Protons across Bilayer Membranes: Synthesis, Lysosomal Neutralization, and Two-Phase pK(a) Values by NMR

It is desirable to be able to control the pH of lysosomes. A collection of lipophilic, nitrogenous bases, designed to act as membrane-active, catalytic proton transfer agents, were prepared and their effective pK(a)s measured in a vigorously stirred, two-phase system. One phase was a phosphate buffer whose pH was varied over the range ca. 1-11. The other was an immiscible, deuterated organic solvent in which the compounds preferentially resided even when protonated. When chemical shift changes versus the pH of the buffer were plotted, clear pK(a) curves were generated that are relevant to transmembrane proton transfer behavior. The two-phase pK(a)s increased with increasing counterion lipophilicity and with increasing organic solvent polarity. The compounds were also tested for their ability to neutralize the acidity of lysosomes, a model for other acidic vesicles involved in drug sorting. The most successful of these, imidazole 6a, has >100 times the neutralizing power of ammonia, a standard lysosomotropic amine, causing a 1.7 unit rise in lysosomal pH of RAW cells at 0.1 mM, compared to a 0.2 and 1.4 unit rise for ammonium chloride at 0.1 and 10 mM, respectively.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Brønsted basicities of diamines in the gas phase, acetonitrile, and tetrahydrofuran

A comprehensive basicity study of alpha,omega-alkanediamines and related bases has been carried out. Basicities in acetonitrile (AN, pK(a) values), tetrahydrofuran (THF, pK(alpha) values), and gas phase (GP, GB values), were measured for 16, 14, and 9 diamine bases and for several related monoamines. In addition the gas-phase basicities and equilibrium geometries were computed for 19 diamino bases and several related monoamines at the DFT B3LYP 6-311+G** level. The effects of the different factors (intrinsic basicity of the amino groups, formation of intramolecular hydrogen bonds, and molecular strain) determining the diamine basicities were estimated by using the method of isodesmic reactions. The results are discussed in terms of molecular structure and solvation effects. The GP basicity is determined by the molecular size and polarizability, the extent of alkylation, and the energy effect of intramolecular hydrogen bond formation in the protonated base. The basicity trends in the solvents differ very much from those in GP: 1) The solvents severely compress the basicity range of the bases studied (3.5 times for the 1,3-propanediamine family in AN, and 7 times in THF), and 2) while stepwise alkylation of the basicity center leads to a steady basicity increase in the gas phase, the picture is complex in the solvents. Significant differences are also evident between THF and AN. The high hydrogen bond acceptor strength of THF leads to this solvent favoring the bases with "naked" protonation centers. In particular, the basicity order of N-methylated 1,3-propanediamines is practically inverse to that in the gas phase. The picture in AN is intermediate between that of GP and THF.