Deprotonation Site Research Articles

Hydrogen bonding ability and acid–base behavior of formylphosphinous acid: an isostere of formohydroxamic acid

The conformational isomerism, relative stabilities of isomeric forms, acid–base behavior, and hydrogen bonding of formylphosphinous acid (FPA), an isostere of formohydroxamic acid (FHA) and its tautomer formylphosphine oxide have been analyzed in the present study. Molecular orbital and density functional theory methods in conjunction with 6-31+G* basis set have been employed. The protonation, deprotonation, and hydrogen bonding abilities of FHA and FPA have been compared. FPA has P as preferred site of deprotonation like N in FHA, but they differ in their preferred site of protonation. With similar nature and orientation of H-bond donor and acceptor atoms, stabilization energy of most stable aggregate of FHA with water is 0.99 kcal/mol higher than that of similar aggregate of FPA with water. In addition, FPA is more stable than its corresponding oxide form in gas phase as well as on H-bonding interaction with single water molecule.

Chemical Transformations Drive Complex Self-Assembly of Uracil on Close-Packed Coinage Metal Surfaces

We address the interplay of adsorption, chemical nature, and self-assembly of uracil on the Ag(111) and Cu(111) surfaces as a function of molecular coverage (0.3 to 1 monolayer) and temperature. We find that both metal surfaces act as templates and the Cu(111) surface acts additionally as a catalyst for the resulting self-assembled structures. With a combination of STM, synchrotron XPS, and NEXAFS studies, we unravel a distinct polymorphism on Cu(111), in stark contrast to what is observed for the case of uracil on the more inert Ag(111) surface. On Ag(111) uracil adsorbs flat and intact and forms close-packed two-dimensional islands. The self-assembly is driven by stable hydrogen-bonded dimers with poor two-dimensional order. On Cu(111) complex structures are observed exhibiting, in addition, a strong annealing temperature dependence. We determine the corresponding structural transformations to be driven by gradual deprotonation of the uracil molecules. Our XPS study reveals unambiguously the tautomeric signature of uracil in the contact layer and on Cu(111) the molecule's deprotonation sites. The metal-mediated deprotonation of uracil and the subsequent electron localization in the molecule determine important biological reactions. Our data show a dependence between molecular coverage and molecule-metal interaction on Cu(111), as the molecules tilt at higher coverages in order to accommodate a higher packing density. After deprotonation of both uracil N atoms, we observe an adsorption geometry that can be understood as coordinative anchoring with a significant charge redistribution in the molecule. DFT calculations are employed to analyze the surface bonding and accurately describe the pertaining electronic structure.

Structure of anionic c-type peptide fragments elucidated by IRMPD spectroscopy

In contrast to protonated peptides, collision-induced dissociation of deprotonated peptides is known to yield abundant c- and z-type fragments, in addition to typical a-, b- and y-type ions. Here we investigate the isomeric structures of short anionic c-type peptide fragments using IR photodissociation spectroscopy. As for all N-terminal fragments of deprotonated peptides, an important structural question concerns the site of deprotonation, as no C-terminal COOH group is present in these products. Comparison of the experimental action spectra with spectra computed for several candidate structures suggests that the c1 and c2 ions investigated have linear peptide structures with a C-terminal C(O)NH2 amide group. Competition between deprotonation on the peptide bond nitrogen atom, forming an amidate anion, and on the residue side chain, depending on its gas-phase acidity, is observed.

Effects of protonation and deprotonation on the reactivity of quinolone: A theoretical study

Quinolones are the subject of much research as antibacterial compounds and as a new class of antitumor agents. The protonation (P) and deprotonation (D) sites and conformations of quinolone were investigated. The proton affinity (PA) on each of the possible sites in 4-oxo-1,4-dihydroquinoline has been calculated by the restricted Hartree-Fock (HF) and density functional theory (DFT) methods with the basis set 6–311G**. The O-site of protonation was found to be strongly favored over the N-site for the studied compound in the gas phase. Deprotonation takes place in quinolone by detachment of the N-H and COOH protons. The PA of the simple quinolone molecule was used to characterize quinolone reactivity with DNA binding sites. The relative stabilities of the syn and anti conformations were investigated at the B3LYP/6-311G** level of theory; the syn form was shown to be slightly more stable. Its conformation seems to be intrastabilized by hydrogen-bonds consisting of a hydroxyl proton with the O10 atom as the acceptor. We computed and discussed the charge-density distribution and electrostatic potential to explain the reactivity of quinolone.

Influence of metal complexation on acidity of cytosine nucleosides: Part I, Li+, Na+ and K+ cation

Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M+-L (where L represents cytosine nucleosides and M+ is an alkali metal ion, including Li+, Na+ and K+) complexes have been investigated theoretically, employing B3LY P/6−311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been investigated. The shifted ΔHacidity values are a consequence of a combination of metal ion coordination to OH and NH groups and efficient stabilization of the deprotonated species. For instance, after complexation with Li+, Na+, and K+, the ΔHacidity of O2′H of the cytidine molecule shifts from 346.2 to 251.6, 258.0, and 275.7 kcal mol−1, respectively. Moreover, for a given coordination site, the metal ion changes the gap between the most and least acidic groups, with respect to that in neutral nucleosides. Such dependence of acidities on the coordination region of the metal ion suggests that acidities of active groups could be controlled by modulating the metal ion coordination site and the type of metal ion.

A single amino acid determines the site of deprotonation in the active center of sesquiterpene synthases SbTPS1 and SbTPS2 from Sorghum bicolor

The multitude of terpene carbon skeletons found in nature is formed by enzymes known as terpene synthases (TPSs). These proteins are often multiproduct enzymes converting a single prenyl diphosphate substrate into a mixture of terpene products. The recently identified sesquiterpene synthases SbTPS1 and SbTPS2 from Sorghum bicolor produce terpene blends containing the same products, but in different proportions. A single amino acid in the active site was reported to determine the different product specificities of SbTPS1 and SbTPS2. In this study we examined the reaction mechanism of the Sorghum TPSs. Feeding experiments with deuterium-labeled substrates and chiral analysis of the enzyme products zingiberene, β-sesquiphellandrene and β-bisabolene revealed that the reactions catalyzed by both enzymes proceeded via (S)-nerolidyl diphosphate and the cyclic (6S)-bisabol-7-yl and (6R)-bisabol-1-yl cation intermediates. The site of deprotonation of the final cation was shown to be the only catalytic difference between SbTPS1 and SbTPS2. Docking of the (6R)-bisabol-1-yl cation into structural models of SbTPS1 and SbTPS2 indicated a potential role of initially cleaved pyrophosphate group as a proton acceptor.

Metastable fragmentation of a thymidine-nucleotide and its components

In aqueous biological environment DNA is typically deprotonated. The metastable deprotonated DNA nucleobases are important reaction intermediates in low-energy electron induced damage to DNA. By comparing the metastable decay of small deprotonated DNA building blocks (thymine, thymidine, d-ribose, d-ribose 5-monophosphate) with the metastable decay of thymidine 5′-monophosphate and the hexameric oligonucleotide dT6 we show that the most intense fragmentation pathways of the individual components are inherited to their next larger compositions of one step further in complexity, i.e., from thymine and ribose to thymidine, from thymidine and 2-deoxyribose 5-monophosphate to thymidine 5′-monophosphate, and from thymidine 5′-monophosphate to thymine oligonucleotides. However, fragmentation channels that are dominant in the smaller, principle building blocks such as d-ribose and thymidine do not necessarily prevail beyond their composition, i.e., in thymidine 5′-monophosphate and thymine oligonucleotides. The comparison of the metastable decay mass spectra of molecules of increasing complexity reveals detailed fragmentation mechanisms and shows that the individual fragmentation pathways are determined by the initial deprotonation sites.

Infrared Multiple Photon Dissociation Action Spectroscopy and Computational Studies of Mass-Selected Gas-Phase Fluorescein and 2′,7′-Dichlorofluorescein Ions

Fluorescein (FL) and its derivative 2',7'-dichlorofluoroescein (DCF) are well-known fluorescent dyes used in many biological and biochemical applications. Although extensive studies have been carried out to investigate their chemical and photophysical properties in different solvent media, little is known about their intrinsic behaviors in the gas phase. Here, infrared multiple photon dissociation (IRMPD) action spectra are reported for the three charged prototropic forms of FL and DCF and compared with computed IR spectra from electronic structure calculations. In each case, the measured spectra show good agreement with the calculated spectra of the lowest energy computed conformer. Moreover, the major bands of the monoanion IRMPD spectra show striking similarities to those of the dianions and are quite different from those of the cations. These experimental results clearly indicate that the gaseous monoanions are predominantly deprotonated on the xanthene chromophore, rather than the benzoate deprotonation site favored in solution. Investigations such as this, which provide a better understanding of intrinsic properties of ionic dyes, forms a baseline from which to elucidate solvent effects and will aid the rational design of dyes possessing desirable fluorescence properties.

Fast and metastable fragmentation of deprotonated d-fructose – A combined experimental and computational study

Metastable and prompt fragmentation of the deprotonated monosaccharide d-fructose was studied. By using the isotope labelled molecules 1- 13C- d-fructose, 2- 13C- d-fructose and 6- 13C- d-fructose the origin of the observed fragments could unambiguously be identified. It was found that prompt fragmentation (<200 ns) is characterized by pronounced site selectivity, i.e. the neutral fragments contain C6 and the negative charge remains on the fragment containing the anomeric centre (C2). The selectivity is preserved in metastable dissociation (≈8 μs) only for the generation of the fragment ion C 4H 4O 3 − ( m/ z 100). For all other metastable decay channels fragments with charge retention on the C6 containing fragment contribute appreciably. Density functional theory (DFT) and classical dynamics simulations are applied to predict the formation of fragment ions. Most of the experimentally detected fragment ions were also observed in the simulations thereby revealing detailed information about the fragmentation pathways. We found that the deprotonation site strongly influences the pathway of the dissociation reactions.

The dissociation constants of diprotonated chalcogenobispyridines: Transmission of electronic effects across chalcogen bridges

The dissociation constants of the diprotonated chalcogenobispyridines have been determined using potentiometric titrations to establish a method for the measurement of the ability of a bridging ligand to relay electronic effects. The relationship between pKa and structure of the chalcogenobispyridines results from a balance between inductive, mesomeric, and steric effects. Delocalization of cationic charge onto the bridgehead increases the apparent electronegativity of the bridging atom, thereby relaying a strong base-weakening effect to the site of first deprotonation. Such delocalization was found to be a function of both the substitution site (4-X > 2-X ≫ 3-X) and orbital overlap requirements (S > O ≈ Se > Te). J. Heterocyclic Chem., (2011).

Metastable Atom-Activated Dissociation Mass Spectrometry of Phosphorylated and Sulfonated Peptides in Negative Ion Mode

The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were C(α) - C peptide backbone cleavages and neutral losses of CO(2), H(2)O, and [CO(2) + H(2)O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

Gas phase acidity of substituted benzenes

Deprotonation thermochemistry of benzene derivatives C 6H 5X (X = H, F, Cl, OH, NH 2, CN, CHO, NO 2, CH 3, C 2H 5, CHCH 2, CCH) has been examined at the G3B3 level of theory. For X = F, Cl, CN, CHO and NO 2, the most favorable deprotonation site is the ortho position of the phenyl ring. This regio-specificity is directly related to the field/inductive effect of the substituent. G3B3 gas phase acidities, Δ acidH° and Δ acidG°, compare within less than 4 kJ mol −1 with experimental data. A noticeable exception is nitrobenzene for which tabulated acidity appear to be underestimated by ca. 120 kJ mol −1.

Experimental and theoretical study of the metastable decay of negatively charged nucleosides in the gas phase

Fragmentation of metastable anions of all deoxynucleosides and nucleosides constituting DNA and RNA has been studied experimentally and by computer simulations. The ions were formed through deprotonation in matrix assisted laser desorption/ionisation (MALDI). Clear difference in fragmentation patterns was obtained for nucleosides containing purine vs. pyrimidine bases. To elucidate the role of various potential deprotonation sites, systematic blocking by chemical modification was performed and this gave unambiguous correlation between deprotonation sites and fragments observed. Classical dynamics simulations of the fragmentation process, using density functional theory to describe the electronic degrees of freedom, were performed for the various deprotonation sites. These were found to reproduce the observed fragmentation patterns remarkably well.

Reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam fac-[Ru(NO)Cl2(κ3N4,N8,N11(1-carboxypropyl)cyclam)]Cl·H2O

Chemical reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam, fac-[Ru(NO)Cl(2)(κ(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl·H(2)O ((1-carboxypropyl)cyclam = 3-(1,4,8,11-tetraazacyclotetradecan-1-yl)propionic acid)), (I) are described. Chloride ligands do not undergo aquation reactions (at 25 °C, pH 3). The rate of nitric oxide (NO) dissociation (k(obs-NO)) upon reduction of I is 2.8 s(-1) at 25 ± 1 °C (in 0.5 mol L(-1) HCl), which is close to the highest value found for related complexes. The uncoordinated carboxyl of I has a pK(a) of ∼3.3, which is close to that of the carboxyl of the non coordinated (1-carboxypropyl)cyclam (pK(a) = 3.4). Two additional pK(a) values were found for I at ∼8.0 and ∼11.5. Upon electrochemical reduction or under irradiation with light (λ(irr) = 350 or 520 nm; pH 7.4), I releases NO in aqueous solution. The cyclam ring N bound to the carboxypropyl group is not coordinated, resulting in a fac configuration that affects the properties and chemical reactivities of I, especially as NO donor, compared with analogous trans complexes. Among the computational models tested, the B3LYP/ECP28MDF, cc-pVDZ resulted in smaller errors for the geometry of I. The computational data helped clarify the experimental acid-base equilibria and indicated the most favourable site for the second deprotonation, which follows that of the carboxyl group. Furthermore, it showed that by changing the pH it is possible to modulate the electron density of I with deprotonation. The calculated NO bond length and the Ru/NO charge ratio indicated that the predominant canonical structure is [Ru(III)NO], but the Ru-NO bond angles and bond index (b.i.) values were less clear; the angles suggested that [Ru(II)NO(+)] could contribute to the electronic structure of I and b.i. values indicated a contribution from [Ru(IV)NO(-)]. Considering that some experimental data are consistent with a [Ru(II)NO(+)] description, while others are in agreement with [Ru(III)NO], the best description for I would be a linear combination of the three canonical forms, with a higher weight for [Ru(II)NO(+)] and [Ru(III)NO].

Reaction of soil water repellency to artificially induced changes in soil pH

Soil water repellency (SWR) is widely thought to be influenced by soil pH, however, few studies have systematically investigated the relationship between these variables. Specifically the hypothesis that the pH may control repellency via changes in the variable surface charge of soil material has not yet been tested. In previous work, methods for changing soil pH have also involved changes in soil moisture, but it has been argued that the potential influence of soil moisture changes needs to be eliminated before the actual relationship between pH and SWR can be isolated. The paper addresses this research gap using a new method, which enables adjustment of the pH of soils with low moisture content via the gas phase and thus involves minimal change in moisture content, allowing the response of SWR to pH changes to be evaluated. The method was applied to 14 soil samples from Germany, The Netherlands, the UK, and Australia, using the water drop penetration time ( WDPT) as the indicator of SWR. Additionally, sessile drop contact angles (Θ sess ) were measured on the four samples from Germany and the titratable surface charge of these four soils was measured at selected pH values using a particle charge detector (PCD). Changes in SWR with soil pH were found to be influenced by the density and type of sites able to interact with protons at the available surfaces of organic and mineral materials in soil. The maximum SWR occurred for soil at natural pH and where the charge density was minimal. As pH increased, negative surface charge increased due to deprotonation of sites and WDPT decreased. Two types of behaviour were observed: i) a decrease in repellency with decreasing pH, probably because of a sufficient number of proton accepting surface sites with a significant amount of positive surface charge, ii) no decrease in repellency with decreasing pH in soils with insufficient proton accepting surface sites to develop significant positive surface charge. The data suggest that the availability and relative abundance of proton active sites at mineral surfaces, and those at organic functional groups influence the response of the soil samples to changes in pH. The variety of geographic origins and histories of the soils examined provides a distinction between site specific and more widely applicable soil characteristics of pH dependent SWR.

The effect of ionic strength on the electrophoretic mobility and protonation constants of an EPS-producing bacterial strain

The production of extracellular polymeric substances (EPS) by bacteria significantly alters the physical structure of the cell wall-solution interface, potentially affecting cell surface reactivity and colloidal (transport) properties of the cells. This study investigated the effect of the EPS layer on the electrostatic properties of the cell surface by conducting electrophoretic mobility (EM) analysis and potentiometric titrations at ionic strengths of 0.001 M, 0.01 M and 0.1 M, using both native cells, with the EPS-layer intact, and EPS-free cells of the gram-positive thermophile, Bacillus licheniformis S-86. Electrophoretic mobility measurements indicated that the isoelectric point for both cell types was below pH 2. At low ionic strength (0.001 M), expansion of the EPS layer causes the EM of the native cells to have a smaller magnitude than that of the EPS-free cells. As ionic strength increases, this effect diminishes and at 0.1 M the native cells have a higher EM than the EPS-free cells, which indicates that there is a relatively high charge density in the EPS layer. Higher total site concentrations obtained using potentiometric titration data modelling for the native cells are in agreement with the electrophoretic mobility data, and indicate a higher proton-active site density in the EPS layer compared to the EPS-free cell wall. The results of data modelling for titrations conducted at all three ionic strength values showed that there are no systematic changes in deprotonation constants or site concentrations as a function of ionic strength, indicating that the use of a non-electrostatic model is justified for this EPS-producing bacterial strain.

A density functional study towards substituent effects on anion sensing with urea receptors

Effects of substituents on anion binding in different urea based receptors have been examined using density functional (B3LYP/6-311+G**) level of theory. The complexes formed by a variety of substituted urea with a halide anion (fluoride) and an oxy-anion (acetate) have been calculated. The stronger complexes were predicted for receptors with fluoride ion than that of acetate ion, however, in water the preference was found to be reversed. The pK ( a ) calculations showed the preferred sites of deprotonation for positional isomers, while interacting with anions. The position of the substituent in the receptor, however, could change the preferred sites of deprotonation compared to the site predicted with pK ( a ) values. Figure The substituent effects on anion binding towards different urea receptors have been examined by DFT with B3LYP/6-311+G** level of theory.

DFT calculations on the deprotonation site of the one-electron oxidised guanine–cytosine base pair

As calculated by the density functional theory (DFT), the acidity of cytosine's exocyclic amine group (C-N(4)H2) in the base pair G-C is considerably increased upon its one-electron oxidation. The proton affinity (PA) of the amine moiety is lowered by ionisation of G-C (which yields G(*+)-C) from -348.1 to -269.1 kcal mol(-1). The PA is further decreased by 7.6 kcal mol(-1) as a result of the ensuing proton transfer from G(*+) to C to yield the spin-charge separated base pair G(-H)(*)-C(+H)(+). Under these conditions and taking the hydration energy of H(+) into account, the overall proton transfer from the C-N(4)H2 group to the aqueous phase in the major groove is exothermic by -2.4 kcal mol(-1). This proton transfer to water from the initially present DNA radical cation constitutes separation of charge from spin and thus reduces positive charge transfer in double stranded DNA.

Estimation of Gas-Phase Acidities of Deoxyribonucleosides: An Experimental and Theoretical Study

We determined the gas-phase acidities (DeltaH(acid)) of four deoxyribonucleosides, i.e., 2'-deoxyadenosine (dA), 2'-deoxyguanosine (dG), 2'-deoxycytidine (dC), and 2'-deoxythymidine (dT) by applying the extended kinetic method. The negatively charged proton-bound hetero-dimeric anions, [A - H - B](-) of the deoxyribonucleosides (A) and reference compounds (B) were generated under electrospray ionization conditions. Collision-induced dissociation spectra of [A - H - B](-) were recorded at four different collision energies using a triple quadrupole mass spectrometer. The abundance ratios of the individual monomeric product ions were used to determine the DeltaH(acid) of the deoxyribonucleosides. The obtained DeltaH(acid) value follows the order dA > dC > dT > dG. The DeltaG(acid) (298 K) values were determined by using DeltaG(acid) = DeltaH(acid) - TDeltaS(acid) where the DeltaH(acid) and DeltaS(acid) values were determined directly from the kinetic method plots. The DeltaH(acid) values were also predicted for the deoxyribonucleosides at the B3LYP/6-311+G**//B3LYP/6-311G** level of theory. The acidity trend obtained from the computational investigation shows good agreement with that obtained experimentally by the extended kinetic method. Theoretical calculations provided the most preferred deprotonation site as C5'-OH from sugar moiety in case of dA, and as -NH(2) (dC and dG) or -NH- (dT) from nitrogenous base moiety in the case of other deoxyribonucleosides.

Multiple Protonation States of Vesicular Acetylcholine Transporter Detected by Binding of [3H]Vesamicol

Vesicular acetylcholine transporter (VAChT) is inhibited by (-)-vesamicol [(-)-trans-2-(4-phenylpiperidino)cyclohexanol], which binds tightly to an allosteric site. The tertiary alkylamine center in (-)-vesamicol is protonated and positively charged at acidic and neutral pH and unprotonated and uncharged at alkaline pH. Deprotonation of the amine has been taken to explain loss of (-)-vesamicol binding at alkaline pH. However, binding data deviate from a stereotypical bell shape, and more binding occurs than expected at alkaline pH. The current study characterizes the binding of (-)-vesamicol from pH 5 to pH 10 using filter assays, (-)-[3H]vesamicol (hereafter called [3H]vesamicol), and human VAChT expressed in PC12(A123.7) cells. At acidic pH, protons and [3H]vesamicol compete for binding to VAChT. Preexposure or long-term exposure of VAChT to high pH does not affect binding, thus eliminating potential denaturation of VAChT and failure of the filter assay. The dissociation constant for the complex between protonated [3H]vesamicol and VAChT decreases from 12 nM at neutral pH to 2.1 nM at pH 10. The simplest model of VAChT that explains the behavior requires a proton at site 1 to dissociate with pK1 = 6.5 +/- 0.1, a proton at site A to dissociate with pKA = 7.6 +/- 0.2, and a proton at site B to dissociate with pKB = 10.0 +/- 0.1. Deprotonation of the site 1 proton is obligatory for [3H]vesamicol binding. Deprotonation of site A decreases affinity (2.2 +/- 0.5)-fold, and deprotonation of site B increases affinity (18 +/- 4)-fold. Time-dependent dissociation of bound [3H]vesamicol is biphasic, but equilibrium saturation curves are not. The contrasting phasicity suggests that the pathway to and from the [3H]vesamicol binding site exists in open and at least partially closed states. The potential significance of the findings to development of PET and SPECT ligands based on (-)-vesamicol for human diagnostics also is discussed.