The Existence of an Isolated Hydronium Ion in the Interior of Proteins

Neutron diffraction analysis studies reported an isolated hydronium ion (H₃O⁺) in the interior of d ‐xylose isomerase (XI) and phycocyanobilin‐ferredoxin oxidoreductase (PcyA). H₃O⁺ forms hydrogen bonds (H‐bonds) with two histidine side‐chains and a backbone carbonyl group in PcyA, whereas H₃O⁺ forms H‐bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H₃O⁺ by the protein environment. QM/MM calculations indicated that H₃O⁺ was unstable in the PcyA crystal structure, releasing a proton to an H‐bond partner His88, producing H₂O and protonated His88. On the other hand, H₃O⁺ was stable in the XI crystal structure. H‐bond partners of isolated H₃O⁺ would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.     

The Hydrated Excess Proton in the Zundel Cation H5O2+: The Role of Ultrafast Solvent Fluctuations

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H₅O₂⁺ prepared in room‐temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump‐probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H⁺ transfer vibration and its combination and overtones. Vibrational lifetimes of H₅O₂⁺ are found to be in the sub‐100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low‐frequency modes continuously modify the proton binding site while affecting its motions.     

吡咯和呋喃气相质子化过程的密度泛函理论研究

Density functional theory and ab initio calculations have been used to determine structures and stabilities of the protonated aromatics species AH^＋ and AH2^2＋ （A=pyrrole, furan）. Possible mechanisms and relative energetics for protonation of pyrrole and furan by H3O^＋ and AH^＋ in the gas phase have been explored. Calculations show that the Cα-protonated species was the most stable structure for AH^＋, and the protonated AH^＋ might accommodate the second proton to yield AH2^2＋ if the free proton was available. The gas-phase H3O^＋ could protonate pyrrole and furan with significant exothermiCity and almost without barrier. The proton transfer from AH4^＋ to pyrrole and furan has a barrier ranging from 33.5 to 39.3 kJ/mol in the gas phase.     

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

The formation of the Hg–N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg²⁺ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H₂O)₆]²⁺, (2) T + [Hg(H₂O)₅(OH)]⁺, (3) T + Hg(H₂O)₄(OH)₂, and (4) N3-deprotonated T + Hg(H₂O)₄(OH)₂. The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4–5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg²⁺ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.     

Conformer-selective Photodynamics of TrpH+−H2O

The photodynamics of protonated tryptophan and its mono hydrated complex TrpH⁺−H₂O has been revisited. A combination of steady-state IR and UV cryogenic ion spectroscopies with picosecond pump-probe photodissociation experiments sheds new lights on the deactivation processes of TrpH⁺ and conformer-selected TrpH⁺−H₂O complex, supported by quantum chemistry calculations at the DFT and coupled-cluster levels for the ground and excited states, respectively. TrpH⁺ excited at the band origin exhibits a transient of less than 100 ps, assigned to the lifetime of the excited state proton transfer (ESPT) structure. The two experimentally observed conformers of TrpH⁺−H₂O have been assigned. A striking result arises from the conformer-selective photodynamics of TrpH⁺−H₂O, in which a single water molecule inserted in between the ammonium and the indole ring hinders the barrierless ESPT reaction responsible for the ultra-fast deactivation process observed in the other conformer and in bare TrpH⁺.     

Early Stage Solvation of Protonated Methanol by Carbon Dioxide (cited: 1)

The solvation of protonated methanol by carbon dioxide has been studied via a cluster model. Quantum chemical calculations of the H⁺(CH₃OH)(CO₂)_n⁺(n=1-7) clusters indicate that the rst solvation shell of the OH groups is completed at n=3 or 4. Besides hydrogen-bond interaction, the C_CO2…O_CO2 intermolecular interaction is also responsible for the stabilization of the larger clusters. The transfer of the proton from methanol onto CO₂ with the formation of the OCOH⁺ moiety might be unfavorable in the early stage of solvation process. Simulated IR spectra reveal that vibrational frequencies of free O-H stretching, hydrogen-bonded O-H stretching, and O-C-O stretching of CO₂ unit a ord the sensitive probe for exploring the solvation of protonated methanol by carbon dioxide. IR spectra for the H⁺(CH₃OH)(CO₂)_n⁺(n=1-7) clusters could be readily measured by the infrared photodissociation technique and thus provide useful information for the understanding of solvation processes.     

Proton transfer versus nontransfer in compounds of the diazo‐dye precursor 4‐(phenyldiazenyl)aniline (aniline yellow) with strong organic acids: the 5‐sulfosalicylate and the dichroic benzenesulfonate salts,and the 1:2 adduct with 3,5‐dinitrobenzoic acid

The structures of two 1:1 proton‐transfer red–black dye compounds formed by reaction of aniline yellow [4‐(phenyldiazenyl)aniline] with 5‐sulfosalicylic acid and benzenesulfonic acid, and a 1:2 nontransfer adduct compound with 3,5‐dinitrobenzoic acid have been determined at either 130 or 200 K. The compounds are 2‐(4‐aminophenyl)‐1‐phenylhydrazin‐1‐ium 3‐carboxy‐4‐hydroxybenzenesulfonate methanol solvate, C₁₂H₁₂N₃⁺·C₇H₅O₆S⁻·CH₃OH, (I), 2‐(4‐aminophenyl)‐1‐phenylhydrazin‐1‐ium 4‐(phenyldiazenyl)anilinium bis(benzenesulfonate), 2C₁₂H₁₂N₃⁺·2C₆H₅O₃S⁻, (II), and 4‐(phenyldiazenyl)aniline–3,5‐dinitrobenzoic acid (1/2), C₁₂H₁₁N₃·2C₇H₄N₂O₆, (III). In compound (I), the diazenyl rather than the aniline group of aniline yellow is protonated, and this group subsequently takes part in a primary hydrogen‐bonding interaction with a sulfonate O‐atom acceptor, producing overall a three‐dimensional framework structure. A feature of the hydrogen bonding in (I) is a peripheral edge‐on cation–anion association also involving aromatic C—H...O hydrogen bonds, giving a conjoint R¹₂(6)R¹₂(7)R²₁(4) motif. In the dichroic crystals of (II), one of the two aniline yellow species in the asymmetric unit is diazenyl‐group protonated, while in the other the aniline group is protonated. Both of these groups form hydrogen bonds with sulfonate O‐atom acceptors and these, together with other associations, give a one‐dimensional chain structure. In compound (III), rather than proton transfer, there is preferential formation of a classic R²₂(8) cyclic head‐to‐head hydrogen‐bonded carboxylic acid homodimer between the two 3,5‐dinitrobenzoic acid molecules, which, in association with the aniline yellow molecule that is disordered across a crystallographic inversion centre, results in an overall two‐dimensional ribbon structure. This work has shown the correlation between structure and observed colour in crystalline aniline yellow compounds, illustrated graphically in the dichroic benzenesulfonate compound.     

Mesitylenesulfonic acid dihydrate: structure and proton conductivity

The molecular and crystal structure of single-crystalline mesitylenesulfonic acid dihydrate (1) was determined by X-ray diffraction and IR spectroscopy. According to X-ray diffraction data, water molecules in the crystal structure form H₅O₂ ⁺ cations stabilized by an intracationic hydrogen bond with a length of 2.45(1) Å. The formation of the asymmetric H₅O₂ ⁺ cation was confirmed by IR spectroscopy. The crystallographic nonequivalence of the water molecules results in a shift of the bridging proton from the midpoint of the strong hydrogen bond in the cation toward one of the water molecules. The proton conductivity of compound 1 was measured by impedance spectroscopy. Dihydrate 1 is completely dehydrated upon prolonged storage in a dry argon glove box and undergoes the transition to the dielectric state. Compound 1 is stable in the humidity range of 32–66 rel.%. The conductivity of dihydrate 1 is (2.4±0.3) · 10^?5 Ohm^?1 cm^?1 at 298 K, E _a = 0.21±0.01 eV.     

Ab initio calculations including electron correlation,and mindo/3 calculations on the system C2H+7

Ab initio SCF and CEPA PNO calculations have been performed together with MINDO/3 calculations on the system C₂H⁺₇. In agreement with experimental assignment, but in contradiction to MINDO/3 results, the ab initio methods show the CC protonated structure to be more stable than the CH protonated structure. The energy difference is 8.5 kcal/mol at the SCF level and 6.3 kcal/mol with inclusion of electron correlation. Additionally, ΔH⁰₃₀₀ for the reaction C₂H⁺_s + H₂ = C₂H⁺₇ and the proton affinity of ethane are computed.     

The electric transport of proton-bound water in MF-4SK/PAni nanocomposite membranes

Electrochemical characteristics of MF-4SK/PAni nanocomposite membranes prepared at different times of chemical polymerization of aniline are studied. Electroosmotic permeability and conductivity of membranes in solutions of acids and sodium chloride are determined. It is revealed that the conductivity of nanocomposites in the proton form at 30-day synthesis is approximately 3 times as low as that of the base membrane and composite membrane formed at 5-h synthesis. The transport number of water slightly depends on the structural type of membrane and changes from 3.3 to 2 mol H₂O/mol H⁺ with an increase in the concentration of HCl solution from 0.1 to 3 M. The ratio of transport number to the water content rises about twofold in composites as compared to the initial membrane. It is shown that water is transferred with proton as hydronium structures [H₅O₂]⁺ and [H₉O₄]⁺ by the migration mechanism whose contribution to the total proton transfer in composite membranes increases.     

Experimental Evidence for Unusual Protonation of Tetraethyl p-tert-Butylcalix[4]arene Tetraacetate and the Most Probable Structure of the Resulting Complex

Using ¹H and ¹³C NMR, FT IR spectroscopy together with quantum mechanical DFT calculations, we show that tetraethyl p-tert-butylcalix[4]arene tetraacetate (1) forms a stable equimolecular complex with proton in the form of hydroxonium ion in acetonitrile-d ₃. Protons for this complex were offered by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and converted to hydroxonium ions by traces of water. The complex 1·H₃O⁺ adopts a slightly asymmetric conformation, which is distinctly more cone-like than ligand 1. According to spectral evidence, the hydroxonium ion H₃O⁺ is bound mainly to three of the phenoxy oxygen atoms of 1 by strong hydrogen bonds leaving the ester carbonyl groups, which are the usual coordination site for metal cations, free. Theoretical DFT calculations support the bonding to phenoxy oxygen atoms but slightly prefer a structure with one of the carbonyls being involved in the coordination.     

On the Search for H5O2+centered Water Clusters in the Gas Phase

In searching for H₅O₂⁺-centered water clusters, we employed vibrational predissociation spectroscopy and ab initio calculations. Structures of the clusters were characterized by the free- and hydrogen-bonded-OH stretches of ion cores and solvent molecules. Systematic examination of H⁺(H₂O)_5–7 in a supersonic expansion reveals the presence of both cyclic and noncyclic forms of H₅O₂⁺-centered water clusters. The proton transfer intermediate H₅O₂⁺(H₂O)₄ was identified, for the first time, by its characteristic hydrogen-bonded-OH stretches of the ion core at 3178 cm^?1. Also discovered at n = 7 is the H₅O₂⁺-containing five-membered ring isomer, whose existence is evidenced by the observation of a bonded-OH stretching doublet at 3544 and 3555 cm^?1 of the solvent molecules. The observations are in accord with ab initio calculations which forecast that H₅O₂⁺(H₂O)₄ and H₅O₂⁺(H₂O)₅ are, respectively, the lowest-energy isomers of protonated water hexamers and heptamers.     

Hydrogen bonding in 1:1 proton‐transfer compounds of 5‐sulfosalicylic acid with 4‐X‐substituted anilines (X = F,Cl or Br)

The crystal structures of three proton‐transfer compounds of 5‐sulfosalicylic acid (3‐carboxy‐4‐hydroxy­benzene­sulfonic acid) with 4‐X‐substituted anilines (X = F, Cl and Br), namely 4‐fluoro­anilinium 5‐sulfosalicylate (3‐carboxy‐4‐hydroxybenzenesulfonate) monohydrate, C₆H₇FN⁺·C₇H₅O₆S⁻·H₂O, (I), 4‐chloro­anilinium 5‐sulfosalicylate hemihydrate, C₆H₇ClN⁺·C₇H₅O₆S⁻·0.5H₂O, (II), and 4‐bromo­anilinium 5‐sulfosalicylate monohydrate, C₆H₇BrN⁺·C₇H₅O₆S⁻·H₂O, (III), have been determined. The asymmetric unit in (II) contains two formula units. All three compounds have three‐dimensional hydrogen‐bonded polymeric structures in which both the water molecule and the carboxylic acid group are involved in structure extension. With both (II) and (III), which are structurally similar, the common cyclic (8) dimeric carboxylic acid association is present, whereas in (I), an unusual cyclic (8) association involving all three hetero‐species is found.     

An embedded QM/MM study for different SiO2/Al2O3 ratios of the HZSM‐5 zeolite and for their interaction with n‐heptane

We carried out a theoretical study of the HZSM‐5 zeolite, for different SiO₂/Al₂O₃ ratios, that interacts with the n‐heptane molecule. The study was performed using a QM/MM (quantum mechanics/molecular mechanics) methodology. For the QM part, we have chosen a hybrid Hartree‐Fock density functional theory (DFT). The hybrid ACM/DZP approach, as implemented in Turbomole, was used for the treatment of the QM cluster containing 84 atoms that represents a ring structure model of the zeolite‐n‐heptane interacting system. The MM part was represented by means of an electrostatic forcefield (ESFF), which assesses the electronic embedding. The chosen QM/MM silicalite base model contains 3862 atoms. The studied SiO₂/Al₂O₃ ratios were 2300, 573.5, 287.7, and 189.83, containing 1, 4, 8, and 12 Al atoms, respectively. For the first ratio, the site for the substitution of Al for Si was that of minimum QM total energy value, because this replacement was done in the QM region. For the other SiO₂/Al₂O₃ ratios, the Al atoms were randomly spread through the MM region in accordance with the Lowenstein substitution rule. These results show the importance of the environment on the electronic properties in the QM region, where the active site lies, and their effects on the earlier steps on the activation experienced by the n‐heptane moiety. A minimal content of 12 Al atoms produces significant effects of the environment on the electronic structure of the QM region. Moreover, the carbocationic character of n‐heptane increases with the aluminum content. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Tandem mass spectrometry studies of acetone and acetone/water cluster ions

Ion clusters were formed in a temperature-variable high-pressure ion source from neat acetone and acetone/water mixtures and subjected to tandem mass spectrometry studies-unimolecular and collisionally activated mass-analyzed ion kinetic energy spectroscopy. The predominance of water loss from H⁺(H₂0)(A) _l=3, where A = acetone, suggests that the solvation sphere around H₃O⁺ does not close at l = 3, contrary to the case of acetonitrile or dimethyl ether. The results may be interpreted in terms of suggested ion structures which involve isomerization enroute to dissociation. The virtual absence of H/D scrambling in the collisionally activated dissociation of H₃O⁺(DA)₃, DA =acetone-d ₆, and of D₃O⁺(A)₃ means that if enolization takes place, it is a rate-determining step in an irreversible isomerization. The stability of H⁺(H₂O)(A)₃ is a dominant factor in the observation of acetone loss from H⁺(H₂0)(A)₄.     

4‐Carboxypyridinium perchlorate 18‐crown‐6 dihydrate clathrate and 4‐carboxypyridinium tetrafluoroborate 18‐crown‐6 dihydrate clathrate

Mixtures of 4‐carboxypyridinium perchlorate or 4‐carboxypyridinium tetrafluoroborate and 18‐crown‐6 (1,4,7,10,13,16‐hexaoxacyclooctadecane) in ethanol and water solution yielded the title supramolecular salts, C₆H₆NO₂⁺·ClO₄⁻·C₁₂H₂₄O₆·2H₂O and C₆H₆NO₂⁺·BF₄⁻·C₁₂H₂₄O₆·2H₂O. Based on their similar crystal symmetries, unit cells and supramolecular assemblies, the salts are essentially isostructural. The asymmetric unit in each structure includes one protonated isonicotinic acid cation and one crown ether molecule, which together give a [(C₆H₆NO₂)(18‐crown‐6)]⁺ supramolecular cation. N—H...O hydrogen bonds between the protonated N atoms and a single O atom of each crown ether result in the 4‐carboxypyridinium cations `perching' on the 18‐crown‐6 molecules. Further hydrogen‐bonding interactions involving the supramolecular cation and both water molecules form a one‐dimensional zigzag chain that propagates along the crystallographic c direction. O—H...O or O—H...F hydrogen bonds between one of the water molecules and the anions fix the anion positions as pendant upon this chain, without further increasing the dimensionality of the supramolecular network.     

Multiple hydrogen bonds in cytosinium zoledronate trihydrate

The asymmetric unit of the title compound [systematic name: 4‐amino‐2‐oxo‐2,3‐dihydropyrimidin‐1‐ium 1‐hydroxy‐2‐(1H,3H‐imidazol‐3‐ium‐1‐yl)ethylidenediphosphonate trihydrate], C₄H₆N₃O⁺·C₅H₉N₂O₇P₂⁻·3H₂O, contains one cytosinium cation, one zoledronate anion and three water molecules. The zoledronate anion has a zwitterionic character, in which each phosphonate group is singly deprotonated and an imidazole N atom is protonated. Furthermore, proton transfer takes place from one of the phosphonic acid groups of the zoledronate anion to one of the N atoms of the cytosinium cation. The cytosinium cation forms a C(6) chain, while the zoledronate anion forms a rectangular‐shaped centrosymmetric dimer through N—H...O hydrogen bonds. The cations and anions are held together by N—H...O and O—H...O hydrogen bonds to form a one‐dimensional polymeric tape. The three water molecules play a crucial role in hydrogen bonding, resulting in a three‐dimensional hydrogen‐bonded network.     

Water‐induced pseudo‐quadruple hydrogen‐bonding motifs in xanthine–inorganic acid complexes

In xanthinium nitrate hydrate [systematic name: 2,6‐dioxo‐1,2,3,6‐tetrahydro‐9H‐purin‐7‐ium nitrate monohydrate], C₅H₅N₄O₂⁺·NO₃⁻·H₂O, (I), and xanthinium hydrogen sulfate hydrate [systematic name: 2,6‐dioxo‐1,2,3,6‐tetrahydro‐9H‐purin‐7‐ium hydrogen sulfate monohydrate], C₅H₅N₄O₂⁺·HSO₄⁻·H₂O, (II), the xanthine molecules are protonated at the imine N atom with the transfer of an H atom from the inorganic acid. The asymmetric unit of (I) contains a xanthinium cation, a nitrate anion and one water molecule, while that of (II) contains two crystallographically independent xanthinium cations, two hydrogen sulfate anions and two water molecules. A pseudo‐quadruple hydrogen‐bonding motif is formed between the xanthinium cations and the water molecules via N—H...O and O—H...O hydrogen bonds in both structures, and leads to the formation of one‐dimensional polymeric tapes. These cation–water tapes are further connected by the respective anions and aggregate into two‐dimensional hydrogen‐bonded sheets in (I) and three‐dimensional arrangements in (II).     

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization

Reactions of water dimer cation following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of : ground state (²A″‐like state) and the first excited state (²A′ ‐ like state). All trajectories on the ground‐state PES lead to the proton‐transferred product: H₂O⁺(Wd)‐H₂O(Wa) → OH(Wd)‐H₃O⁺(Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited‐state PES gave two products: an intermediate complex with a face‐to‐face structure (H₂O‐OH₂)⁺ and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited‐state PES: H₂O(Wd)‐H₂O⁺ (Wa) → H₃O⁺(Wd)‐OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc.     

UV laser induced proton-transfer of protein molecule in the gas phase produced by droplet-beam laser ablation

Droplet-beam laser-ablation mass-spectrometry was applied for a study of the UV-laser induced proton-transfer reaction of protonated lysozyme hydrated clusters in the gas phase. Protonated lysozyme hydrated clusters were produced by irradiation of an IR laser onto a droplet-beam of an aqueous solution of lysozyme and were subsequently irradiated by a UV laser. It is found that H⁺ and H₃O⁺ are produced through photodissociation of protonated lysozyme hydrated clusters. The mechanism of the proton-transfer reaction is discussed.