Deprotonation Site Research Articles

Measurement of the Population of Electrosprayed Deprotomers of Coumaric Acids Using UV-Vis Laser Photodissociation Spectroscopy.

The measurement of deprotonation sites in multifunctional molecules following electrospray ionization is important to better inform a wide range of spectroscopic and photophysical studies that use electrospray to prepare molecular species for study in the gas phase. We demonstrate that low-resolution UV–vis laser photodissociation spectroscopy can be applied in situ to identify the deprotomers of three coumaric acids, trans-para-coumaric acid (CMA), trans-caffeic acid (CA), and trans-ferulic acid (FA), formed via electrospray. Electronic absorption spectra of the deprotonated coumaric acids are recorded via photodepletion and photofragmentation following electrospray from solutions of ethanol and acetonitrile. By comparing the experimental spectra to wave function theory calculations, we are able to confirm the presence of phenoxide and carboxylate deprotomers upon electrospray for all three coumaric acids, when sprayed from both protic and aprotic solvents. Ratios of the phenoxide:carboxylate deprotomers are obtained by generating summed theoretical absorption spectra that reproduce the experimental spectra. We find that choice of electrospray solvent has little effect on the ratio of deprotomers obtained for deprotonated CMA and CA but has a greater impact for FA. Our results are in excellent agreement with previous work conducted on deprotonated CMA using IR spectroscopy and demonstrate that UV photodissociation spectroscopy of electrosprayed ions has potential as a diagnostic tool for identifying deprotomeric species.

Following in Emil Fischer's Footsteps: A Site-Selective Probe of Glucose Acid-Base Chemistry.

Liquid-jet photoelectron spectroscopy was applied to determine the first acid dissociation constant (pKa) of aqueous-phase glucose while simultaneously identifying the spectroscopic signature of the respective deprotonation site. Valence spectra from solutions at pH values below and above the first pKa reveal a change in glucose’s lowest ionization energy upon the deprotonation of neutral glucose and the subsequent emergence of its anionic counterpart. Site-specific insights into the solution-pH-dependent molecular structure changes are also shown to be accessible via C 1s photoelectron spectroscopy. The spectra reveal a considerably lower C 1s binding energy of the carbon site associated with the deprotonated hydroxyl group. The occurrence of photoelectron spectral fingerprints of cyclic and linear glucose prior to and upon deprotonation are also discussed. The experimental data are interpreted with the aid of electronic structure calculations. Our findings highlight the potential of liquid-jet photoelectron spectroscopy to act as a site-selective probe of the molecular structures that underpin the acid–base chemistry of polyprotic systems with relevance to environmental chemistry and biochemistry.

Tracking the deprotonation site of dehydroandrographolide with electrospray ionization mass spectrometry by deuteration.

Dehydroandrographolide (DA) is a diterpene compound of biological interest that contains one α,β-unsaturated lactone group and two hydroxy groups. In the ESI (electrospray ionization) negative ion mode mass spectral analysis of 15-dideuterodehydroandrographolide (15-D2 -DA), the deuterium nucleus at the γ position of the α,β-unsaturated lactone was more easily dedeuterated than deprotonation of the protons from the hydroxy groups. Exploring the rationality of deuteration as a tool for deprotonation position tracking is significant for gas-phase acidity. The mass spectra of DA and 15-D2 -DA in positive and negative ion mode were acquired by liquid chromatography/ion trap time-of-flight mass spectrometry (LC/IT-TOF) systems. The deprotonation and dedeuteration energies at specific sites were calculated by the B3LYP and M06-2X density functional theory (DFT) methods with the program Gaussian 16. The [M + H]+ ion of 15-D2 -DA was 2amu larger than that of DA due to the substitution of two hydrogens with two deuteriums; however, the anion base peak of 15-D2 -DA was only 1amu larger than that of the [M-H]- ion of DA. Dedeuteration at the C15 site was proposed according to the mass spectral data. The deprotonation (dedeuteration) energies calculated by the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31 + G(d) and M06-2X-D3/ma-TZVP methods showed that the C-H and C-D bonds at the C15 site have lower deprotonation (dedeuteration) energies than the energies of the hydroxy groups of DA, making their deprotonation (dedeuteration) more thermodynamically favourable. Deuteration of DA provided direct evidence of the deprotonation site of DA in the ESI source of the mass spectrometer, and the DFT method well predicted the gas-phase deprotonation site of DA.

Action spectroscopy of isomer-selected luciferin anions

Luciferin molecules are common luminophores found throughout the biological kingdoms. Here, electrospray ionization and tandem ion mobility spectrometry coupled with laser spectroscopy are used to demonstrate that D-luciferin and oxyluciferin deprotonated anions can be produced in two isomeric forms, which can be separated by virtue of their different collision cross sections with a buffer gas. The two isomers possess distinguishable but partially overlapping photodepletion action spectra over the visible range, implying distinct intrinsic absorption profiles. The site of deprotonation and tautomeric forms of the electrosprayed isomers are assigned through comparisons between experimental and calculated collision cross sections and electronic excitation energies. The study clearly shows that electrospray ionization of biochromophore molecules can generate multiple isomeric forms with distinct electronic spectra.

Acid-Base Equilibrium of a 6-Methyluracil Derivative with 1,2,3-Triazole Fragment in Aqueous Solutions

The constants and thermodynamic characteristics of the acid-base equilibrium between the first synthesized 6-methyluracil derivative with a 1,2,3-triazole ring at the C(5) atom of the uracil ring—5-(1-pentyl-4-methyl-1,2,3-triazol-4-yl)-6-methyluracil (1)—and its model compound 5,6-dimethyluracil were determined by potentiometric titration in aqueous solutions. It was shown that the 1,2,3-triazole ring does not significantly affect the acid-base properties of the uracil fragment in compound 1. The deprotonation sites of compound 1 in aqueous alkaline and DMSO solutions were suggested. The structure of compound 1 was proved by NMR and IR spectroscopy and elemental analysis.

Antioxidant action of deprotonated flavonoids: Thermodynamics of sequential proton-loss electron-transfer

Despite the intensive research on radical scavenging action of flavonoids, a systematic study of the thermochemistry for their mono-deprotonated species in aqueous solution is still missing. In this work, reaction enthalpies related to Sequential Proton-Loss Electron-Transfer (SPLET) mechanism were theoretically investigated for all mono-deprotonated forms of nine flavonoids: apigenin, luteolin, fisetin, kaempferol, quercetin, taxifolin, tricetin, tricin and cyanidin. Differences in reaction enthalpies of the first and the second deprotonation can be lower than 10 kJ mol−1, when two successive deprotonations occur in different aromatic rings of the molecule. For neutral flavonoids, thermodynamically preferred deprotonation sites are 4′-OH and 7-OH groups. In cyanidin (cation in native form), preferred second deprotonation site is 5-OH group. In the case of the formation of the preferred dianions, reaction enthalpies of the second proton loss are not affected by the structural distinctions between the flavonoids. In aqueous solution, deprotonated flavonoids show higher tendency to enter SPLET mechanism in comparison to Hydrogen Atom Transfer (HAT) or electron transfer.

Deprotonation of Isoxazole: A Photoelectron Imaging Study.

We report a photoelectron imaging study of gas-phase deprotonation of isoxazole in which spectroscopic data are compared to the results of electronic structure calculations for the anion products corresponding to each of three possible deprotonation sites. The observed photoelectron spectra are assigned to a mixture of the anion isomers. Deprotonation at the most acidic (C5) and the least acidic (C4) positions yields the respective C5- and C4-isoxazolide anions, while the reaction at the intermediate-acidity C3 site leads to a cleavage of the O-N bond and an opening of the ring in the anion. Following photodetachment, the ground states of neutral C5- and C4-isoxazolyl are assigned to be σ radicals (X2A'), while the ground-state neutral derived from the ring-open C3-anion is a π radical (X2A″). The relative intensities of the spectral bands exhibit sensitivity to the ion source conditions, giving evidence of competing and varying contributions of the dominant C5 and C3, as well as possible C4, deprotonation pathways.

Computing Surface Acidity Constants of Proton Hopping Groups from Density Functional Theory-Based Molecular Dynamics: Application to the SnO2(110)/H2O Interface.

Proton transfer at metal oxide/water interfaces plays an important role in electrochemistry, geochemistry, and environmental science. The key thermodynamic quantity to characterize this process is the surface acidity constant. An ab initio method that combines density functional theory-based molecular dynamics (DFTMD) and free energy perturbation theory has been established for computing surface acidity constants. However, it involves a reversible proton insertion procedure in which frequent proton hopping, e.g., for strong bases and some oxide surfaces (e.g., SnO2), can cause instability issues in electronic structure calculation. In the original implementation, harmonic restraining potentials are imposed on all O-H bonds (denoted by the VrH scheme) to prevent proton hopping and thus may not be applicable for systems involving spontaneous proton hopping. In this work, we introduce an improved restraining scheme with a repulsive potential Vrep to compute the surface acidities of systems in which proton hopping is spontaneous and fast. In this Vrep scheme, a Buckingham-type repulsive potential Vrep is applied between the deprotonation site and all other protons in DFTMD simulations. We first verify the Vrep scheme by calculating the pKa values of H2O and aqueous HS- solution (i.e., strong conjugate bases) and then apply it to the SnO2(110)/H2O interface. It is found that the Vrep scheme leads to a prediction of the point of zero charge (PZC) of 4.6, which agrees well with experiment. The intrinsic individual pKa values of the terminal five-coordinated Sn site (Sn5cOH2) and bridge oxygen site (Sn2ObrH+) are 4.4 and 4.7, respectively, both being almost the same as the PZC. The similarity of the two pKa values indicates that dissociation of terminal water has almost zero free energy at this proton hopping interface (i.e., partial water dissociation), as expected from the acid-base equilibrium on SnO2.

A Predictive Model Towards Site‐Selective Metalations of Functionalized Heterocycles, Arenes, Olefins, and Alkanes using TMPZnCl⋅LiCl

AbstractThe development of a predictive model towards site‐selective deprotometalation reactions using TMPZnCl⋅LiCl is reported (TMP=2,2,6,6‐tetramethylpiperidinyl). The pKa values of functionalized N‐, S‐, and O‐heterocycles, arenes, alkenes, or alkanes were calculated and compared to the experimental deprotonation sites. Large overlap (>80 %) between the calculated and empirical deprotonation sites was observed, showing that thermodynamic factors strongly govern the metalation regioselectivity. In the case of olefins, calculated frozen state energies of the deprotonated substrates allowed a more accurate prediction. Additionally, various new N‐heterocycles were analyzed and the metalation regioselectivities rationalized using the predictive model.

A Predictive Model Towards Site-Selective Metalations of Functionalized Heterocycles, Arenes, Olefins, and Alkanes using TMPZnCl⋅LiCl.

The development of a predictive model towards site‐selective deprotometalation reactions using TMPZnCl⋅LiCl is reported (TMP=2,2,6,6‐tetramethylpiperidinyl). The pK a values of functionalized N‐, S‐, and O‐heterocycles, arenes, alkenes, or alkanes were calculated and compared to the experimental deprotonation sites. Large overlap (>80 %) between the calculated and empirical deprotonation sites was observed, showing that thermodynamic factors strongly govern the metalation regioselectivity. In the case of olefins, calculated frozen state energies of the deprotonated substrates allowed a more accurate prediction. Additionally, various new N‐heterocycles were analyzed and the metalation regioselectivities rationalized using the predictive model.

Mechanism study on TiO2 inducing [rad]O2- and O[rad]H radicals in O3/H2O2 system for high-efficiency NO oxidation

To achieve high NO oxidation efficiency, excessive O3 must be used, which would lead to the high cost and escape of ozone. Herein, we adopted low cost and environmental-friendly TiO2 as the catalyst of low concentration O3 and H2O2 system for high-efficiency NOx oxidation. The Ti sites on TiO2 were the deprotonation sites of H2O2 and H2O into Ti-OOH and Ti-OH species, respectively. We found that the surface of rutile phase TiO2 had a low concentration Ti-OOH component but a large amount of Ti-OH after contacting with H2O2 solution, thus lots of ·OH and a few O2− radicals formed with introducing O3 molecules. H2O2 solution induced the formation of a large amount of Ti-OOH and Ti-OH species on the anatase phase TiO2 surface, thus lots of O2− generated in the O3/H2O2 system. O2− and OH radicals could efficiently oxidize NO, in which O2− radicals could oxidize NO to NO3− in one step with high selectively. Therefore, anatase TiO2 had better performance in NOx oxidation than rutile phase TiO2. The effect of temperature and SO2 concentration on NO oxidation was also investigated, the results showed that TiO2-A/O3/H2O2 system promoted NO oxidation at a low temperature and a low concentration of SO2.

Predicting Deprotonation Sites Using Alchemical Derivatives.

An alchemical transformation is any process, physical or fictitious, that connects two points in the chemical space. A particularly important transformation is the vanishing of a proton, whose energy can be linked to the proton dissociation enthalpy of acids. In this work we assess the reliability of alchemical derivatives in predicting the proton dissociation enthalpy of a diverse series of mono- and polyprotic molecules. Alchemical derivatives perform remarkably well in ranking the proton affinity of all molecules. Additionally, alchemical derivatives could be use also as a predictive tool because their predictions correlate quite well with calculations based on energy differences and experimental values. Although second-order alchemical derivatives underestimate the dissociation enthalpy, the deviation seems to be almost constant. This makes alchemical derivatives extremely accurate to evaluate the difference in proton affinity between two acid sites of polyprotic molecule. Finally, we show that the reason for the underestimation of the dissociation enthalpy is most likely the contribution of higher-order derivatives.

Negative Charge as a Lens for Concentrating Antiaromaticity: Using a Pentagonal “Defect” and Helicene Strain for Cyclizations

AbstractIncorporation of a five‐membered ring into a helicene framework disrupts aromatic conjugation and provides a site for selective deprotonation. The deprotonation creates an anionic cyclopentadienyl unit, switches on conjugation, leads to a >200 nm red‐shift in the absorbance spectrum and injects a charge into a helical conjugated π‐system without injecting a spin. Structural consequences of deprotonation were revealed via analysis of a monoanionic helicene co‐crystallized with {K+(18‐crown‐6)(THF)} and {Cs+2(18‐crown‐6)3}. UV/Vis‐monitoring of these systems shows a time‐dependent formation of mono‐ and dianionic species, and the latter was isolated and crystallographically characterized. The ability of the twisted helicene frame to delocalize the negative charge was probed as a perturbation of aromaticity using NICS scans. Relief of strain, avoidance of antiaromaticity, and increase in charge delocalization assist in the additional dehydrogenative ring closures that yield a new planarized decacyclic dianion.

Two Different Selective Ways in the Deprotonation of β‐Bromopropionanilides: β‐Lactams or Acrylanilides Formation.

AbstractThe reactivity of 3‐bromo‐N‐(p‐bromophenyl)propanamide with different bases in an ionic liquid (BMImBF4) and in acetonitrile (ACN) was studied. Two possible deprotonation sites are present in this molecule, leading to different products. When the NH group is deprotonated, a β‐lactam is obtained after internal halide displacement; when the CH2 in alpha to the carbonyl is deprotonated, the corresponding acrylanilide is formed. This study allowed determining the experimental conditions to obtain selectively and in high yields both products starting from the same molecule. In particular, to obtain the acrylanilide Et3N in ACN is to be used, while to obtain selectively the β‐lactam ring the base must be generated by cathodic reduction of a DMF or ACN‐Et4NBF4 solution. These reactions were extended to other β‐bromopropionanilides, allowing to easily synthesize both β‐lactams and acrylanilides, molecules having noteworthy biological activities.

Oryza sativa Parkeol Cyclase: Changes in the Substrate-Folding Conformation and the Deprotonation Sites on Mutation at Tyr257: Importance of the Hydroxy Group and Steric Bulk.

Y257 of Oryza sativa parkeol synthase (OsOSC2) corresponds to H234 of Saccharomyces cerevisiae lanosterol cyclase (ScLAS), which is believed to be responsible for the final deprotonation reaction. An Ala mutant afforded nine tetracyclic skeletons as the main products; they consisted of protostadienol scaffolds with both 17R and 17S configurations and both 20R and 20S configurations, as well as a pair of 20R- and 20S-configured parkeols. The production of 20R- and 20S-configured tetracycles (59:40 ratio) through the action of the Y257A mutant indicated that the substrate folding had been altered from a chair-boat-chair-chair (a normal folding pattern) to a chair-boat-chair-boat structure (an unusual folding pattern). Other mutants with different steric bulks also yielded both 20R- and 20S-configured tetracycles. Thus, the primary function of Y257 appears to be to impose a normal chair structure at the D-ring site through having appropriate steric bulk. In contrast, mutations at H234 of ScLAS were reported to cause no conformational changes. The OsOSC2 Phe mutant also yielded 20R- and 20S-configured parkeols (25:33 ratio), thus suggesting that the OH group of Y257 can form hydrogen bonds with other amino acids to force a chair conformation at the D-ring site, and this variant also gave 20R- and 20S-configured parkeols in a high yield (60 %). Y257 is unlikely to act as a base to abstract H-11 and stabilize the transient cation through cation-π interactions. Thus, the catalytic roles of Y257 are significantly different from those of H234 of ScLAS.

5-Fluorouracil-Complete Insight into Its Neutral and Ionised Forms.

5-Fluorouracil (5FU), a common anti-cancer drug, occurs in four tautomeric forms and possesses two potential sites of both protonation and deprotonation. Tautomeric and resonance structures of the ionized forms of 5FU create the systems of connected equilibriums. Since there are contradictory reports on the ionized forms of 5FU in the literature, complex theoretical studies on neutral, protonated and deprotonated forms of 5FU, based on the broad spectrum of DFT methods, are presented. These indicate that the O4 oxygen is more willingly protonated than the O2 oxygen and the N1 nitrogen is more willingly deprotonated than the N3 nitrogen in a gas phase. Such preferences are due to advantageous charge delocalization of the respective ions, which is demonstrated by the NBO and ESP analyses. In an aqueous phase, stability differences between respective protonated and deprotonated forms of 5FU are significantly diminished due to the competition between the mesomeric effect and solvation. The calculated pKa values of the protonated, neutral and singly deprotonated 5FU indicate that 5FU does not exist in the protonated and double-deprotonated forms in the pH range of 0–14. The neutral form dominates below pH 8 and the N1 deprotonated form dominates above pH 8.

Generation of Tautomers Using Micro-p Ka's.

Solutions of organic molecules containing one or more heterocycles with conjugated bonds may exist as a mixture of tautomers, but typically only a few of them are significantly populated even though the potential number grows combinatorially with the number of protonation and deprotonation sites. Generating the most stable tautomers from a given input structure is an important and challenging task, and numerous algorithms to tackle it have been proposed in the literature. This work describes a novel approach for tautomer prediction that involves the combined use of molecular mechanics, semiempirical quantum chemistry, and density functional theory. The key idea in our method is to identify the protonation and deprotonation sites using estimated micro-p Ka's for every atom in the molecule as well as in its nearest protonated and deprotonated forms. To generate tautomers in a systematic way with minimal bias, we then consider the full set of tautomers that arise from the combinatorial distribution of all such mobile protons among all protonatable sites, with efficient postprocessing to screen away high-energy species. To estimate the micro-p Ka's, we present a new method designed for the current task, but we emphasize that any alternative method can be used in conjunction with our basic algorithm. Our approach is therefore grounded in the computational prediction of physical properties in aqueous solution, in contrast to other approaches that may rely on the use of hard-coded rules of proton distribution, previously observed tautomerization patterns from a known chemical space, or human input. We present examples of the application of our algorithm to organic and drug-like molecules, with a focus on novel structures where traditional methods are expected to perform worse.

Photoinitiated Intramolecular Proton Transfer in Deprotonated para-Coumaric Acid.

Deprotonated para-coumaric acid is commonly considered as a model for the chromophore in photoactive yellow protein, which undergoes E → Z isomerization following absorption of blue light. Here, tandem ion mobility mass spectrometry is coupled with laser excitation to study the photochemistry of deprotonated para-coumaric acid, to show that the E isomers of the phenoxide and carboxylate forms have distinct photochemical responses with maxima in their action spectra at 430 and 360 nm, respectively. The E isomer of the phenoxide anion undergoes efficient autodetachment upon excitation of its lowest ππ* transition. For the E isomer of the carboxylate deprotomer, a one-way photoinitiated proton transfer generates the phenoxide deprotomer through a mechanism postulated to involve an excited-state enol-keto tautomerism followed by a series of ground-state rearrangements including a second proton transfer. This mechanism is supported by experiments in which the relevant intermediate keto isomer is prepared and spectroscopically probed and through master equation modeling of possible ground-state isomerization processes. The Z isomer of the carboxylate deprotomer shows a weak Z → E photoisomerization response that occurs in competition with photodestruction (presumably electron detachment), demonstrating that the E and Z isomers undergo different processes in their excited states. The study highlights the utility of isomer-selective spectroscopy for characterizing the photochemistry of isolated anions possessing multiple deprotonation sites.

Study of the Lysine Deprotonation Mechanism in Ubiquitin Conjugating Enzyme Ubc13

Ubiquitin (Ub) is a regulatory protein with the ability to flag proteins to be degraded by the proteosome. Ub is covalently attached to a lysine on the target protein by a series of reactions catalyzed by three types of enzymes: ubiquitin activating enzymes, E1; ubiquitin conjugating enzymes, E2; and ubiquitin ligases, E3. Before Ub is transferred to its target, it is bonded to the E2 via a thioester linkage. In this study, we examine the E2 enzyme, Ubc13, which catalyzes the formation of K63-linked polyubiquitin chains. The chains are formed when a lysine on the target Ub (K63) attacks the thioester bond between Ubc13 and the substrate Ub. To initiate this reaction, K63 on the target Ub must be deprotonated, turning it into an active nucleophile. There are two possible deprotonation sites: a conserved aspartate in Ubc13 (D119) and a conserved glutamate in the target ubiquitin (E64). In order to determine any preference between D119 and E64, we used classical molecular dynamics, Born-Oppenheimer molecular dynamics and single point QM/MM to model K64 deprotonation in several E2∼Ub conjugates.

T1 Population as the Driver of Excited-State Proton-Transfer in 2-Thiopyridone.

Excited‐state proton transfer (ESPT) is a fundamental process in biomolecular photochemistry, but its underlying mediators often evade direct observation. We identify a distinct pathway for ESPT in aqueous 2‐thiopyridone, by employing transient N 1s X‐ray absorption spectroscopy and multi‐configurational spectrum simulations. Photoexcitations to the singlet S2 and S4 states both relax promptly through intersystem crossing to the triplet T1 state. The T1 state, through its rapid population and near nanosecond lifetime, mediates nitrogen site deprotonation by ESPT in a secondary intersystem crossing to the S0 potential energy surface. This conclusively establishes a dominant ESPT pathway for the system in aqueous solution, which is also compatible with previous measurements in acetonitrile. Thereby, the hitherto open questions of the pathway for ESPT in the compound, including its possible dependence on excitation wavelength and choice of solvent, are resolved.