Proton Transfer Energy Research Articles

Thermodynamic View of Activation Energies of Proton Transfer in Various Gramicidin A Channels

The temperature dependencies (range: 5–45°C) of single-channel proton conductances ( g H) in native gramicidin A (gA) and in two diastereoisomers (SS and RR) of the dioxolane-linked gA channels were measured in glycerylmonooleate/decane (GMO) and diphytanoylphosphatidylcholine/decane (DiPhPC) bilayers. Linear Arrhenius plots (ln ( g H) versus K −1) were obtained for the native gA and RR channels in both types of bilayers, and for the SS channel in GMO bilayers only. The Arrhenius plot for proton transfer in the SS channel in DiPhPC bilayers had a break in linearity around 20°C. This break seems to occur only when protons are the permeating cations in the SS channel. The activation energies ( E a) for proton transfer in various gA channels (∼15 kJ/mol) are consistent with the rate-limiting step being in the channel and/or at the membrane-channel/solution interface, and not in bulk solution. E a values for proton transfer in gA channels are considerably smaller than for the permeation of nonproton currents in gA as well as in various other ion channels. The E a values for proton transfer in native gA channels are nearly the same in both GMO and DiPhPC bilayers. In contrast, for the dioxolane linked gA dimers, E a values were strongly modulated by the lipid environment. The Gibbs activation free energies ( Δ G o # ) for protons in various gA channels are within the range of 27–29 kJ/mol in GMO bilayers and of 20–22 kJ/mol in DiPhPC bilayers. The largest difference between Δ G o # for proton currents occurs between native gA (or SS channels) and the RR channel. In general, the activation entropy ( Δ S o # ) is mostly responsible for the differences between g H values in various gA channels, and also in distinct bilayers. However, significant differences between the activation enthalpies ( Δ H o # ) for proton transfer in the SS and RR channels occur in distinct membranes.

Calculation of the Free Energy of Proton Transfer from an Aqueous Phase to Liquid Acetonitrile

Protons in liquid phases are stabilized by long-range electrostatic interactions, hydrogen bonding, and the formation of covalent bonds between H+ and solvent molecules. Thus, a small proton affinity, a low dielectric constant, or the inability to form hydrogen bonds that characterize many nonaqueous solvents hinders the transfer of protons from an aqueous phase. As a result, the particle that is readily transferred is a hydrated proton, H2n+1On+, rather than the bare proton, H+. Here we present calculations of the free energy of proton transfer from water to liquid acetonitrile, including the dehydrated particle, H+, and two hydrated particles, H3O+ and H9O4+. We use a combination of ab initio density functional theory and a polarizable continuum model within the self-consistent reaction field method. This allows the first and second solvation shells of the proton to be described explicitly from first principles. Vibrational contributions to the enthalpy and entropy have been added in. Values taken from ...

Proton transfer reaction of 4-methyl-2,6-diamidophenol in alcoholic solvents at room temperature and 77 K

Ground and excited state proton transfer reaction of 4-methyl-2,6-diamidophenol (MDOH) has been studied in alcoholic solvents, using steady state and nanosecond spectroscopy, at room temperature (RT) and 77 K both in presence and absence of triethylamine (TEA). Solute–solvent interaction appears to play a major role in determining the nature of the absorbing and fluorescing species. The emission properties of MDOH have been examined in relation to those of 4-methyl-2,6-diformylphenol (MFOH). At 77 K the emission due to the open conformer is markedly suppressed and consists of phosphorescence both in presence and absence of TEA. The fluorescence decay rates are relatively slow in alcoholic solvents compared to those in non-polar solvents and non-radiative decay rates are always found to be dominant over the radiative rates. Generation of the trajectories for the intramolecular proton transfer reaction in the ground (S 0) and the lowest excited singlet (S 1) states using the semiempirical AM1-SCI method demonstrates that the intramolecular proton transfer process is favored in the S 1 state both thermodynamically and kinetically. The activation energy for the excited state intramolecular proton transfer (ESIPT) process has been calculated in various alcoholic solvents differing in polarity assuming Onsager's dielectric continuum model.

Solvent Effect on the Gibbs Energy of Proton Transfer in the 2,6-Dichlorophenol-Triethylamine Complex

Using dipole moment measurements, the Gibbs energy ΔGPT of proton transfer in the complex of 2,6-dichlorophenol with triethylamine was determined in different solvents. The effect of solvent on ΔGPT was quantitatively discussed in terms of reaction field models for homogeneous and heterogeneous dielectric media. The specific complex–solvent interactions which, in addition to electrostatic interaction, stabilize the PT polar form of the complex is discussed as a function of the empirical parameters describing the polar and hydrogen-donating (electron-accepting) properties of the solvent.

Proton diffusion in perovskites: comparison between BaCeO 3, BaZrO 3, SrTiO 3, and CaTiO 3 using quantum molecular dynamics

Quantum molecular dynamics simulations have been carried out to calculate the diffusion coefficients and the activation energies of protonic defects in BaCeO 3, BaZrO 3, SrTiO 3 and CaTiO 3. The calculated activation energies are in agreement with experimental data within statistical uncertainty. The activation energy for proton transfer is found to be significantly affected by the repulsive interaction of the proton with the B-cation (B=Ce, Zr, Ti). A physical interpretation for the measured infra-red spectra can also be obtained from the numerical results.

A Proton Relay Process as the Mechanism of Activation of the Histamine H3-Receptor Determined by1H NMR and ab Initio Quantum Mechanical Calculations

This study proposes a new mechanism of activation of the histamine H3-receptor based on stabilization of the active state of the receptor protein by a proton relay process. A series of histamine H3-receptor agonists and one antagonist, all containing an imidazole and a side chain amino group, were studied using 1H NMR and ab initio quantum mechanical calculations. A significant correlation (r = −0.87) between the formation energy of the active reaction intermediate and the agonistic activity is found. The calculated proton-transfer energies and pKa values of the reaction intermediates (at the MP2/6-31+G*//HF/6-31+G* level in the gas and aqueous phases), as well as, 1H NMR conformational analysis, enable a qualitative and quantitative determination of intramolecular hydrogen bonding and its effect on proton release from the imidazole N(τ)-atom. The results indicate that the histamine H3-receptor is not activated by a proton release from imidazole N(τ)-atom but through adoption of a folded conformation of t...

Theoretical Analysis of Molecular Structure, Hydrogen Bond Strength, and Proton Transfer Energy in O−H··O Aromatic Compounds

Molecular geometries for a set of 2-hydroxybenzoyl compounds were obtained at B3LYP/6-31G** level and analyzed in view of a parametric model of intrinsic substituent effects by Taft and Topsom. The structural study of the non- and hydrogen-bonded species, together with proton transferred forms, resulted as very useful in understanding the different factors determining the intramolecular hydrogen bond strength and the proton transfer process in this family of molecules. In addition, the previous study was extended to a sequence of other related six-membered hydrogen-bonded structures (alkane, naphthalene, and alkene derivatives) with increasing aromaticity. The results clearly showed the influence of the covalent and electrostatic (acid−base) nature of the hydrogen bond system on its commonly related chemical properties, hydrogen bond strength, and proton-transfer energy. A significant finding in this paper is the approach between the oxygens that yields the internal hydrogen bond, which occurs in the midpoint of the proton transfer, depends on the acid−base characteristics of the proton donor and acceptor groups, and it is not substantially affected by the aromaticity of the system.

Ab Initio Study of Energetics of Protonation and Hydrogen Bonding of Pyridine N-Oxide and Its Derivatives

The energetics of protonation and hydrogen-bonded complex formation between the base and its conjugated acid (homoconjugation) of pyridine N-oxide and its selected derivatives was investigated by means of Restricted Hartree-Fock (RHF) and Møller-Plesset (MP2) ab initio calculations. It has been found that introducing the d polarization functions (the 6-31G* basis set) is required to reproduce correctly the geometry of the N−O bond. The proton-transfer energy surface in the homoconjugated cations exhibits a double minimum, with 2.4 kcal/mol energy barrier for the pyridine N-oxide homocomplex; this barrier vanishes when the thermodynamic correction is included. The protonation and homoconjugation Gibbs free energies computed in vacuo correlate well with the acid dissociation and cationic homoconjugation constants determined in acetonitrile.

The Alkane σ-Bond Basicity Scale Revisited

The energy of the n-butonium and isobutonium cations was calculated. At the MP4/6-311++G**//MP2(fu)/6-31G** level, the C-carbonium ions were more stable than the H-carbonium ions. The results are in agreement with gas-phase data of n-butane and isobutane protonation but disagree with results in liquid superacid, where protonation of the tertiary C−H of isobutane is preferred over C−C protonation. Additional calculations, including the superacid moiety, revealed that the activation energy for C−C protonation is higher than the energy for attack at the tertiary C−H. This suggests that the σ bond reactivity in the liquid superacid system is controlled by the activation energy for proton transfer, rather than by the intrinsic basisity of the bond. The higher stability of the C-carbonium relative to the H-carbonium ions was ascribed to a better charge distribution among the atoms and groups of the three center bond.

Gas-phase and solution-phase proton transfer to H 2O analyzed by high-level ab initio quantum chemistry including complete basis set and Gaussian theory schemes

Free energies of the gas-phase proton transfer to H 2O are calculated for H 2O, formic acid, acetic acid, phenol and 3-chlorophenol using high-level quantum chemistry including DFT, CBS and Gaussian theory. The overall best agreement with experimental data within 8 kJ/mol is achieved by MP2//6-311+G(2d,2p) and DFT. For the aromatic compounds, G1 and G2 yield errors of 600–750 kJ/mol, which can be traced back to artefacts of MP4-level basis set corrections. Comparison with solution-phase p K a suggests that protonated water clusters are energetically significant for the dissociation in aqueous solution.

Theoretical evaluation of a model of the catalytic triads of serine and cysteine proteases by ab initio molecular orbital calculation.

Serine and cysteine proteases are structurally distinct families of proteolytic enzymes that exert analogous catalytic reactions. It is known that serine, histidine, and aspartate residues are involved in a putative catalytic triad of serine proteases whereas cysteine, histidine and aspartate (or asparagine) are involved in that of cysteine proteases. Although the overall three-dimensional structures of the two classes of proteases are quite different, a similar feature of the catalytic mechanism can be observed. We carried out a theoretical study in the gas phase on their two catalytic steps using ab initio molecular orbital calculation to evaluate the efficiency of each proteolytic activity. To examine the key aspects of the catalytic processes in their active sites, we employed simple molecular models, in which serine and histidine were substituted for by CH3OH and CH3SH, respectively, and aspartate by CH3CO2-. Molecular geometries of the two models were fully optimized by an energy-gradient method. The activation energies for proton transfer in the proteolytic steps and the total energies of each molecule in the intermediate states were calculated. These results revealed that the activation energy for proton transfer in the CH3SH-His-CH3CO2-system was smaller by 11 kcal mol-1than that of the CH3OH-His-CH3CO2-system. The calculated potential energy surface and the relative magnitudes of all steps in these reaction paths with regard to double proton transfer supported the above results. Taken together, these results indicated that the Cys-His-Asp proteolytic system might work more efficiently than the Ser-His Asp system.

Quantum chemical analysis of the energy of proton transfer from phenol and chlorophenols to H2O in the gas phase and in aqueous solution

Proton transfer energies of phenol and 14 chlorophenols with H2O as a base are analyzed in the gas phase and in solution using quantum chemical methods at the semiempirical and ab initio level of computation. The effect of aqueous solution was accounted for by applying the density functional theory (DFT) implementation of the conductor-like screening model (COSMO) as well as semiempirical continuum-solvation models. The results reveal substantial and systematic overestimations of the free energies of proton transfer as derived from experimental solution-phase pKa data. This can be traced back to both deficiencies in the current model parameterization as well as to limitations of the underlying gas-phase quantum chemical models, which is further illustrated by additional complete-basis-set (CBS) calculations for the proton transfer reaction with phenol. In contrast, the relative pKa trend is reflected well by COSMO-DFT calculations with correlation coefficients (adjusted for degrees of freedom) of 0.96. Decomposition of the dissociation energy in aqueous solution into a gas-phase term and a term summarizing the solvation contributions provides new insights into the effect of solvation on proton transfer energies, and yields mechanistic explanations for the observed differences in the gas-phase and solution-phase acidity orders of various subgroups of the compounds.

Prediction of the pKa of Carboxylic Acids Using the ab Initio Continuum-Solvation Model PCM-UAHF

Experimental pKa data for 16 aliphatic carboxylic acids are compared with calculated proton-transfer energies in the gas phase and in aqueous solution. The calculations are performed at the SCF and MP2 levels with inclusion of SCF-level entropic and thermochemical corrections to yield free energies of dissociation, using the basis sets 6-31G**, 6-31+G**, 6-311G(2d,2p), and 6-311+G(2d,2p) and the recently parametrized continuum−solvation method PCM-UAHF for the solvation contribution. Relative pKa trends are reproduced well with correlation coefficients (adjusted for degrees of freedom) of up to 0.97 and standard errors down to 0.24 log units, while the computational accuracy is not sufficient for predicting absolute proton-transfer energies. The latter is mainly caused by deficiencies of the underlying gas-phase calculations, as is demonstrated by a separate analysis of the gas-phase and solution-phase contributions to pKa.

Protonizable Water Model for Quantum Dynamical Simulations

A new functional form for describing proton transfer and hydrogen bond potential energy functions in condensed phase simulations is presented. Rather than fitting a potential energy function to ab ...

Proton Transfer in the Enzyme Carbonic Anhydrase: An ab Initio Study

Ab initio calculations have been performed to probe possible proton-transfer pathways in carbonic anhydrase. It is found that the proton transfer in the dehydration direction involves an energy barrier of around 8−10 kcal/mol, which agrees well with experiment, while the proton-transfer barrier in the hydration (away from zinc) direction is sensitive to the histidine ligand bonding around the Zn ion. The water ligand dependence of the proton-transfer energy barrier reveals a requirement of certain hydrogen bond formation in the active site. Preliminary studies involving two and three proton transfers through hydrogen-bonded water chains show that the donor−acceptor distance and the water chain motion are crucial to the proton-transfer energetics. On the basis of these results, a picture of the proton-transfer energetics and mechanism is presented and the effect of the His-64 ligand on the process is discussed.

A quantum molecular dynamics study of the cubic phase of BaTiO 3 and BaZrO 3

High proton mobility in perovskite-type oxides of composition ABO 3 strongly depends on the dynamics of the proton environment, especially on the fluctuations of the oxide ion separations. The dynamics of the oxide host lattices of the model materials BaTiO 3, and BaZrO 3 have been studied using quantum molecular dynamics simulations. The simulation method has already been shown to yield numerical results in agreement with experimental findings for the cubic phase of BaCeO 3. At elevated temperatures, rotational diffusion of the protons around the oxygen atoms in the plane perpendicular to the B-O-B axis is found. The free energy of the oxygen lattice vibrations is evaluated and the activation energy for proton transfer is estimated to be 0.45 eV for BaTiO 3, 0.69 eV for BaZrO 3, and 0.64 eV for BaCeO 3.

The peculiarities of hydrogen bonds in raman spectra of solid superionic polyantimonic acids

Raman scattering spectra in hydrated antimonium pentaoxide (APO) were measured on two samples with different crystal structure. Essentially higher ionic conductivity of tetragonal modification is caused by possibility of formation of H5O2 +-complexes which are located mainly on microcrystals surfaces and characterized by lower energy of proton transfer in comparison with H3O+-complexes which occur in bulk of APO with cubic structure. Explanation of the nature of wide band in Raman scattering spectra is proposed. Model calculations and theoretical curves are presented.

Correlation effects in proton transfer reactions in solution

The effects of correlation energy on proton transfer reactions in solution for [H 2OHOH 2] + and [NH 3HH 2O] + systems have been studied. Solvent effects have been represented by means of a continuum model. The proton transfer energy profiles for fixed proton donor-proton acceptor distances have been obtained in the gas phase and in solution, both at the HF/6-311G ∗∗ and MP2/6-311G ∗∗//HF levels of theory. Differences between the correlation energies calculated in the gas phase and in solution are negligible, showing that solvent effects can be correctly described for these proton transfer processes at the HF level.

Reactions of protonated acetic acid clusters (CH3COOH)nH+ (n = 1–3)

AbstractReactions of (CH3COOH)nH+ (n = 1–3) with a series of base molecules B were studied using a selected ion flow tube. All the reactions observed proceed at near gas kinetic collision rates for bases having higher proton affinities than acetic acid. Different reaction channels are observed with increasing proton affinity of the neutral: association and proton transfer for the proton‐bound monomer; association, ligand switching and proton transfer for the dimer; association, ligand switching, switching with solvent evaporation and proton transfer for the trimer. A thermochemical comparison of the appearance enthalpy and free energy for proton transfer from (CH3COOH)3H+ and (C2H5OH)3H+ established that both sets of reactions take place by forming BH+ with evaporation of three monomeric units (of acetic acid or ethanol, respectively) rather than evaporation of neutral dimers. Proton transfer from (CH3COOH)2H+ is fast provided that the reaction is exothermic; proton transfer from (CH3COOH)3H+ is fast even if the reaction is endothermic (but exergonic).

AM1 studies of hydrogen bonded adducts between 2,5-dihydroxy- p-quinone and N-bases

Semiempirical AM1 calculations were used to optimize the geometry of the adducts formed by 2,5-dihydroxy- p quinone (DH pQ) with substituted pyridines or imidazole. Hydrogen bond formation was seen to be responsible for the stability of the adducts. From the study of the total energy function, obtained by imposing fixed positions to the proton, two structures were found to be possible for each adduct, one schematically indicated as -OH … N-base and the proton transfer one, indicated as -O − … HN +base. The proton transfer energy was found to vary linearly with the base p K a value. A study was also carried out on the system formed by DH pQ and a cluster of three water molecules acting as proton acceptors. The implications were discussed relating to possible hydrogen bond formation between trihydroxyphenylalanine quinone, the coenzyme of bovine serum amine oxidase, and some basic residue or water molecule, lying close to the protein active site.