Structural Investigation of Protonated Azidothymidine and Protonated Dimer

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

Protonated p-Benzoquinone

The structure and energetics of protonated p-benzoquinone (pBQ) have been investigated using high-pressure mass spectrometry and ab initio calculations. The experimental proton affinity of pBQ is 801.4 +/- 8.9 kJ/mol (191.5 +/- 2.1 kcal/mol) (1sigma) from bracketing measurements and hydration thermochemistry. This value is supported by theory and by analogies with related compounds. In its protonation chemistry, pBQ behaves as an aliphatic ketone, both structurally and energetically. The dissociation of the hydrate (pBQH(+)).(H(2)O) is characterized by DeltaH degrees (D) = 90.0 +/- 2.3 kJ/mol and DeltaS degrees (D) = 123.4 +/- 4.9 J/mol.K (95% confidence).     

Protonated forms of N-vinylpyrroles

The reaction of N-vinylpyrroles with hydrogen chloride at low temperatures has been studied. At –80C the -position of the heterocycle is protonated while at higher temperatures products of HCl addition to the double bond and protonation of the ring are formed. The C-Cl bond of the chloroethyl radical of the product of HCl addition to the vinyl group is readily dissociated resulting in reversible interconversion of the enantiomers of the racemic mixture which is formed. By introducing a diastereotopic marker (i-Pr) this interconversion can be monitored by dynamic NMR. It has been found that the energy of this process varies with HCl concentration and with the substituents on the ring.Translated from Khimiya Geterotsiklicheskikh Soedinenii, Vol. 24, No. 3, pp. 334–338, March, 1988.     

Surface-Induced Dissociation of Multiply Protonated Peptides

We report here surface-induced dissociation spectra of three multiply charged peptides: doubly protonated angiotensin I, doubly protonated renin substrate, and triply protonated melittin. For comparison, the collision-activated dissociation spectra of renin substrate and melittin are also presented. The spectra show that surface-induced dissociation provides structural information on multiply charged peptides at the picomole per microliter sample concentrations compatible with electrospray ionization. For multiply protonated angiotensin I, renin substrate, and melittin, surface collisions (100–165 eV) favor a limited number of fragmentation pathways, which are the same as those favored in collision-activated dissociation experiments.     

Protonated ethanol and its neutral counterparts

Collisionally activated dissociation and neutralization-reionization experiments reveal that protonation of ethanol leads to two distinct isomers, the classical ion CH₃CH₂OH⁺₂ and the proton-bound complex C₂H₄…H⁺…OH₂. The neutral counterpart of the latter is unstable, whereas that of the former can be produced in a bound state if the CH₃CH₂OH⁺₂ precursor ion is formed under low ion source pressure conditions and, thus, with higher internal energies. This suggests that there are substantial differences in the geometries of CH₃CH₂OH⁺₂ and the hypervalent CH₃CH₂OH₂ ·. This provides only a partial explanation for unusual isotope effects; C₂H₅OD₂ ·, CH₃CD₂OD₂ ·, and CD₃CH₂OD₂ · are substantially more stable than C₂D₅OD₂ · and C₂H₅OH₂ ·.     

Protonated Sodium 1-Hydroxyethane-1,1-diphosphonates

Powder X-ray diffraction study of sodium salts of 1-hydroxyethane-1'1-diphosphonic acid (H₄L)of the compositions NaH₃L·H₂O, Na₂H₂L·4H₂O, Na₃HL·5.5H₂O showed that these compounds aresingle-phase. Some of their properties were determined. The possibility of preparing salts of other compositionswas examined.     

Martini Force Field for Protonated Polyethyleneimine

Polyethyleneimine (PEI), one of the most widely used nonviral gene carriers, was investigated in the presented work at coarse-grained (CG) level. The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA–PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and nonpolarizable water by applying Boltzmann inversion techniques to all-atom (AA) probability distributions for distances, angles, and dihedrals of entire monomers. The fine-tuning of the FFs was achieved by fitting simulated CG gyration radii and end-to-end distances to their AA counterparts. The developed Martini FF models are shown to be well suited for realistic large-scale simulations of size/protonation-dependent behavior of solvated PEI chains, either individually or as part of DNA–PEI systems. © 2019 Wiley Periodicals, Inc.     

Hydration Energies of Protonated and Sodiated Thiouracils

Hydration reactions of protonated and sodiated thiouracils (2-thiouracil, 6-methyl-2-thiouracil, and 4-thiouracil) generated by electrospray ionization have been studied in a gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH ^o n, ΔS ^o n, and ΔG ^o n, for the hydrated systems were obtained by equilibrium measurements. The water binding energies of protonated thiouracils, [2SU]H⁺ and [6Me2SU]H⁺, were found to be of the order of 51 kJ/mol for the first, and 46 kJ/mol for the second water molecule. For [4SU]H⁺, these values are 3–4 kJ/mol lower. For sodiated complexes, these energies are similar for all studied systems, and varied between 62 and 68 kJ/mol for the first and between 48 and 51 kJ/mol for the second water molecule. The structural aspects of the precursors for hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract

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Preparation and Characterization of Protonated Fumaric Acid

Fumaric acid was reacted with the binary superacidic systems HF/SbF₅ and HF/AsF₅. The O,O'-diprotonated [C₄H₆O₄]²⁺([MF₆]^–)₂ (M = As, Sb) and the O-monoprotonated [C₄H₅O₄]⁺[MF₆]^– (M = As, Sb) species are formed depending on the stoichiometric ratio of the Lewis acid to fumaric acid. The colorless salts were characterized by low-temperature vibrational spectroscopy. In case of the hexafluoridoantimonates single-crystal X-ray structure analyses were carried out. The [C₄H₆O₄]²⁺([SbF₆]^–)₂ crystallizes in the monoclinic space group C2/c with four formula units per unit cell and [C₄H₅O₄]⁺[SbF₆]^– crystallizes in the triclinic space group P1 with one formula unit per unit cell. The protonation of fumaric acid does not cause a notable change of the C=C bond length. The experimental data are discussed together with quantum chemical calculations of the cations [C₄H₆O₄ · 4 HF]²⁺ and [C₄H₆O₄ · 2 H₂CO · 2 HF]²⁺.     

Protonated canthaxanthins as models for blue carotenoproteins

It has been suggested that astaxanthin (3,3'-dihydroxy-beta,beta-carotene-4,4'-dione) in the carotenoprotein alpha-crustacyanin occurs in the diprotonated form. As a model system for protonated astaxanthin in [small alpha]-crustacyanin the reactions of canthaxanthin ([small beta],[small beta]-carotene-4,4[prime or minute]-dione) with Bronsted acids (CF(3)COOH and CF(3)SO(3)H) and the Lewis acid BF(3)-etherate have been investigated. Structures of C-5 protonated, C-7 protonated, enolised O-4 protonated and O-4,4[prime or minute], C-7 triprotonated canthaxanthin have been established by VIS-NIR and NMR spectroscopy. The charge distribution in the cations has been considered by comparison of the (13)C chemical shift difference relative to neutral relevant carotenoid models. The experimental evidence for protonated canthaxanthins differs significantly from previous AM1 calculations. Experimental data for O-4,4[prime or minute], C-7 triprotonated canthaxanthin relative to C-7 protonated canthaxanthin is considered a relevant model for O-4,4[prime or minute] diprotonated canthaxanthin, in comparison with neutral canthaxanthin. The positive charge was mainly located at C-6/6[prime or minute][dbl greater-than] C-8/8[prime or minute] > C-10/10[prime or minute] > C-12/12[prime or minute] > C-14/14[prime or minute][similar] C-15/15[prime or minute] in the polyene chain. Moreover, it was inferred that only 14% of the positive charge is delocalised to the polyene chain, the remaining charge must therefore be located at the protonated carbonyl moiety. The results are discussed in relation to previous solid state NMR studies of (13)C labelled astaxanthin in [small alpha]-crustacyanin and recent X-ray analysis of [small beta]-crustacyanin.     

Hydrogen-bond Networks Involving Protonated Bicapped-Keggin Tetradecavanadophosphate Anions

Tetraphenylphosphonium salts of protonated tetradecavanadophosphate (PV₁₄) anions, [(C₆H₅)₄P]₄H₅PV₁₄O₄₂·5H₂O (1) and [(C₆H₅)₄P]₂H₇PV₁₄O₄₂·6H₂O (2), have been synthesized and their crystal structures have been determined. Compound 1 crystallizes in triclinic, P1 with a=12.7866(1), b=15.5261(2), c=16.0730(3) ?, α=109.358(1), β=98.411(1), γ=110.040(1)°. Synchrotron radiation X-ray diffraction revealed that compound 2 crystallizes in monoclinic, P2₁/c with a=16.821(1), b=25.163(2), c=18.817(1) ?, β=109.992(2)°. In compound 1, the PV₁₄ anions are linked into a one-dimensional chain structure by water molecules of crystallization. In compound 2, hydrogen bonds directly link PV₁₄ anions into a zigzag chain, which are then woven into a three-dimensional network by hydrogen bonds bridged by water molecules.Dedicated to Professor Michael T. Pope on the occasion of his retirement, in recognition of his outstanding contributions to the polyoxometalate chemistry.     

Blackbody Infrared Radiative Dissociation of Protonated Oligosaccharides

The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel₆), which is composed of β-(1 → 4)-linked glucopyranose rings, and five malto-oligosaccharides (Mal_x, where x = 4–8), which are composed of α-(1 → 4)-linked glucopyranose units. At the temperatures investigated (85–160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B₁ and B₂) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (E_a and A) were determined. The E_a and A-factors measured for protonated Mal_x (x > 4) are indistinguishable within error (~19 kcal mol⁻¹, 10¹⁰ s⁻¹), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel₆ (24 kcal mol⁻¹, 10¹² s⁻¹) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage.     

IRMPD Spectroscopy of a Protonated,Phosphorylated Dipeptide

The protonated, phosphorylated dipeptide [GpY+H]⁺ is characterized by mid‐infrared multiple‐photon dissociation (IRMPD) spectroscopy and quantum‐chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free‐electron laser. The IRMPD spectra are recorded in the 900–1730 cm^?1 range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP‐D and coupled cluster, is carried out to obtain reliable relative energies of the low‐energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P?O group in all low‐energy structures. This leads to a P?O stretching frequency for [GpY+H]⁺ that is closer to that of [pS+H]⁺ than to that of [pY+H]⁺ and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.