Periodicity in proton conduction along a H‐bonded chain. Application to biomolecules

Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H⁺)? H₂O? CH₃COO^? model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H‐bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H‐bond lengths and the progression of proton transfer in each link. This “wave” is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The wave nature of the protonic conductivity mechanism in the active site of carboanhydrase

Quantum-chemical calculations were performed for the (NH₃)₃Zn²⁺...(H₂O)_n...NH₃ (n = 3–11) molecular complex to model the proton transfer system of the carboanhydrase enzyme. H-bond proton transfer along the chain connecting the donor and acceptor groups was shown to be concerted vibrational motion of all protons in the chain. A wave of H-bond deformations was related to the moving proton. The displacement of H-bond protons in the transition state of the proton transfer reaction with respect to their equilibrium positions corresponded to a structure that could be defined as a proton wave. The length of this wave found as the distance between H-bond contraction (O-H bond elongation) maxima was ～8 Å. Charge transfer from the donor to the acceptor occurred according to the mechanism of the concerted jump of H-bond protons as the wave reached the chain end. The barrier to transfer was independent of the number of chain links and equaled 10 kcal/mol.     

Conformations of 2-phenylethanol and its singly hydrated complexes: UV–UV and IR–UV ion-dip spectroscopy

The structures of 2-phenylethanol and its 1:1 water complexes have been investigated by UV–UV holeburning and IR–UV ion-dip spectroscopy, coupled with ab initio computation. The most populated molecular conformer is stabilized by an intramolecular π-type H-bond and its rotational band contours suggest the incidence of vibronic coupling involving motion of the side chain. Its 1:1 water complexes are associated with two distinct structures – water binds either as a proton donor or an acceptor. In the latter, the intramolecular H-bond is disrupted and the water molecule inserts between the OH and the aromatic ring. A second, extended anti conformer can also be detected.     

Exploration on regulating factors for proton transfer along hydrogen-bonded water chains.

Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.     

The geometry and electronic structure of the ionic defect in a chain of water molecules between a donor and an acceptor

Quantum chemical calculations of the molecular complexes (NH₃)₃Zn²⁺...(H₂O)_n3...NH₃ (C_n, n=11, 16, 21, and 30) that model the proton donor-aqueous chain-acceptor channel in biological molecules were performed. Periodicity of O-H bond lengths in water chains and charges of the H atoms of H-bonds observed earlier were discussed. In C_n complexes, the geometry and electronic structure of the ionic defect in the aqueous chain with an excess proton were studied. The distributions of O-H bond lengths and charges on H-bond H atoms in the region of the ionic defect obtained in ab initio (B3LYP/6-31+G^**) and semiempirical (PM3) calculations are compared. The influence of aqueous chain extension, the position of the protonated water molecule, and the mobility of water molecules in the chain on the structure of the ionic defect was analyzed.     

The role of the alien proton acceptor on the formation of LC structure in H-bonded monomeric and polymeric derivatives of alkoxybenzoic acids

The formation of the complex between 4-cyanopyridine and 4-(6-acryloyloxy-hexyloxy) benzoic acid and its polymeric analog proceeds due to the proton transfer with the H-bond formation. The presence of two proton acceptor groups within one molecule provides a strong shift of the electron density along the complex molecule due to the conjugation within the proton acceptor molecule. The dielectric relaxation process in a symmetric associate experimentally observed is explained as a kinetic effect related to the formation and destruction of the associate.

Transition from a monomer to a polymer proton donor leads to the formation of the characteristic 1:1 complex with SmC layered structure different from that of a polymer itself.     

Donor-acceptor interaction and intramolecular proton transfer in aminopolyenes

The influence of donor and acceptor substituents at chain termini on the geometry of the chain and charge distribution on atoms was studied for the ground and lower triplet electronically excited state of model ω-dimethylaminopolyene molecules (CH₃)₂N(CH=CH) _n CH=C(CN)₂, n = 1–3. Calculations were performed by the B3LYP/6-31+G** method. The influence of substituents on bond lengths and the amplitude of deviations from the equilibrium carbon-carbon bond length in unsubstituted polyenes increased as the conjugation chain grew longer. The deviations of the effects of both donor and acceptor groups from additivity, however, decreased. In the lower triplet electronically excited state of the molecule, the effect of substituents on changes in C-C bond lengths along the chain was not damped. The section of the potential energy surface for intramolecular proton shift from the donor amino to the acceptor nitrile group in “cyclic” (cis) conformers of the H₂N-CH=CH-CN and H₂N-CH=CH-CH=CH-CN molecules was analyzed. The structure of the reaction transition state and the height of the barrier to proton transfer were calculated.     

Photo Responsive Electron and Proton Conductivity within a Hydrogen-Bonded Organic Framework

Rational design of crystalline porous materials with coupled proton-electron transfer has not yet been reported to date. Herein, we report a donor-acceptor (D-A) π-π stacking hydrogen-bonded organic framework (HOF; HOF-FJU-36 ) with zwitterionic 1,1′-bis(3-carboxybenzyl)-4,4′-bipyridinium (H₂L²⁺) as acceptor and 2,7-naphthalene disulfonate (NDS²⁻) as donor to form a two-dimensional (2D) layer. Three water molecules were situated in the channels to connect with acidic species through hydrogen bonding interactions to give a 3D framework. The continuous π-π interactions along the a axis and the smooth H-bonding chain along the b axis provide the electron and proton transfer pathways, respectively. After 405 nm light irradiation, the photogenerated radicals could simultaneously endow HOF-FJU-36 with photoswitchable electron and proton conductivity due to coupled electron-proton transfer. By single-crystal X-ray diffraction (SCXRD) analyses, X-ray photoelectron spectroscopy (XPS), transient absorption spectra and density functional theory (DFT) calculations, the mechanism of the switchable conductivity upon irradiation has been demonstrated.     

Structure and Mobility Pattern of Proton-Containing Groups in Hydrates of Titanium,Zirconium and Tin Acid Phosphates; Their Conducting and Ion Exchanging Properties

Abstract

Phosphates of tetravalent elements are practically important for ion exchange, catalysis and conductivity. This study deals with a number of hydrates of titanium, tin and zirconium phosphates. PMR data show that the structure of water molecules in hydrates is slightly distorted, and at temperatures higher than 160 K water has high translation mobility. NMR ³¹P proves HPO² ₄ dissociation to be growing with increase of temperature. Energetic parameters of this process are determined. Close values of anion dissociation enthalpy (0, 16/2/Ev) and obtained activation energy of conductivity for di- and monohydrates (0,17/2/Ev) show tunnel pattern of proton transfer along H-bond direction, This type of correlation was not observed in anhydrous compounds. That can be explained by impossibility of anion proton tunneling because of H-bond weakening. Proton conductivity of acid phosphates was studied. Ten-fold decrease of conductivity at room temperature with the loss of each water molecule proves H₂O participation in proton transport. Mechanism of this process is discussed with the use of NMR data. Dependence of water mobility and conductivity level on the degree of crystallinity is also discussed. With the help of NMR-data processes of ion exchange in tin and zirconium acid phosphates, as well as the state of developed salt forms were studied. Presence of lithium with high mobility in Li₂Sn(PO₄)₂ ·nF₂O was established.     

Intermolecular interactions in uracil–nitrous acid complexes: structures,binding energy,topological properties,and nuclear magnetic resonance study

Molecular interactions between uracil and nitrous acid (U–NA) [C₄N₂O₂H₄? NO₂H] have been studied using B3LYP, B3PW91, and MP2 methods with different basis sets. The optimized geometries, harmonic vibrational frequencies, charge transfer, topological properties of electron density, nucleus‐independent chemical shift (NICS), and nuclear magnetic resonance one‐ and two‐bonds spin–spin coupling constants were calculated for U–NA complexes. In interaction between U and NA, eight cyclic complexes were obtained with two intermolecular hydrogen bonds N(C)HU…N(O) and OH_NA…O_U. In these complexes, uracil (U) simultaneously acts as proton acceptor and proton donor. The most stable complexes labeled, UNA1 and UNA2, are formed via NH bond of U with highest acidity and CO group of U with lowest proton affinity. There is a relationship between hydrogen bond distances and the corresponding frequency shifts. The solvent effect on complexes stability was examined using B3LYP method with the aug‐cc‐pVDZ basis set by applying the polarizable continuum model (PCM). The binding energies in the gas phase have also been compared with solvation energies computed using the PCM. Natural bond orbital analysis shows that in all complexes, the charge transfer takes place from U to NA. The results predict that the Lone Pair (LP)(O)_U → σ*(O? H) and LP(N(O)_NA → σ*(N(C)? H)_U donor–acceptor interactions are most important interactions in these complexes. Atom in molecule analysis confirms that hydrogen bond contacts are electrostatic in nature and covalent nature of proton donor groups decreases upon complexation. The relationship between spin–spin coupling constant (^1hJ_H…_Y and ^2hJ_H…_Y) with interaction energy and electronic density at corresponding hydrogen bond critical points and H‐bonds distances are investigated. NICS used for indicating of aromaticity of U ring upon complexation. © 2013 Wiley Periodicals, Inc.     

Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Br?nsted slopes of one and zero, respectively.     

Spectroscopic studies of intermolecular hydrogen bonding and proton transfer complexes of chromotropic acid with some amines in methanol

The proton transfer reactions between chromotropic acid (CTA) and some amines including benzylamine (BA), triethylamine (TEA), pyrrolidine (PY) and 1,8-bis(dimethylamino) naphthalene (DMAN) have been investigated spectrophotometrically in methanol. A long wavelength band at 365 nm has been recorded due to the proton transfer (PT) complex formation. The proton transfer equilibrium constants K_PT were estimated utilizing the minimum–maximum absorbances method. It has been found that K_PT were not depend on the amine pKa values, but strongly depend on the formed structures of the PT complexes. Job^’s method of continuous variations and photometric titrations were applied to identify the compositions of the formed PT complexes where 1:1 complexes (proton donor: proton acceptor) were produced. Due to the rapidity and simplicity of the proton transfer reactions and the stability of the formed complexes, a rapid and accurate spectrophotometric method for the determination of CTA was proposed for the first time.     

Alternating copolymerization of maleic anhydride with allyl chloroacetate

Some regularities of radical alternating copolymerization of maleic anhydride with allyl chloroacetate are studied. The formation of donor–acceptor complexes between comonomers with complexing constant K_c = 0.052 L/mol is found using ¹H NMR spectroscopy. The kinetic parameters for this copolymerization reaction are found and the quantitative contribution of monomer complexes to chain-growth radical reactions is calculated. It is shown that either a “free-monomer” mechanism (dilute solutions) or a “mixed” mechanism (concentrated solutions) prevails for chain growth during radical copolymerization depending on total monomer concentration. It is found that inhibition of degradative chain transfer in the course of the reaction studied takes place owing to the presence of α-chlorine atom in the allyl chloracetate molecule and formation of charge transfer complex.     

Controlling Light-Induced Proton Transfer from the GFP Chromophore

Green Fluorescent Protein (GFP) is known to undergo excited-state proton transfer (ESPT). Formation of a short H-bond favors ultrafast ESPT in GFP-like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light-induced proton transfer from the GFP chromophore in hydrogen-bonded complexes with two anionic proton acceptors, I⁻ and deprotonated trichloroacetic acid (TCA⁻). We address the role of the strong H-bond and the quantum mechanical proton-density distribution in the excited state, which determines the proton-transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton-transfer probability and it can become strongly wavelength dependent. The proton-transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high-level ab initio calculations, we show that light-induced proton transfer takes place in S₁, revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H-bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S₁, depending on the quantum-density distribution upon vibrational excitation. We also show that the S₁ potential-energy surface, and hence excited-state proton transfer, can be controlled by altering the chromophore microenvironment.     

Polarization model representation of hydrogen fluoride for use in gas- and condensed-phase studies

The polarization model, originally developed to describe deformable and ionizable water molecules, has been extended to hydrogen fluoride. Since electronic polarization is explicitly included, the interaction energy in aggregates of molecules (with or without ions) is nonadditive. The model properly describes the structure of (HF)₂, including off-axis bending of the proton acceptor molecule. Calculations are presented to illustrate elementary gas-phase reactions involving proton transfer between HF and F^?, and H₂F⁺ and F^?.     

On the question of hydrogen bond proton transfer

A simple relation is found that connects the proton displacement value along the line of an H-bond X-H…Y at its formation with the proton transfer barrier to the acceptor Y. The fulfillment of the relation is verified by quantum-chemical calculations at the B3LYP/6-31+G(d, p) level of a series of H-bonded molecular complexes at different interatomic distances X…Y. With the aim to analyze the accuracy of this relation, calculations of model complexes were also performed with different basis sets. The effects of the basis set extension and electron correlation on the calculated values of the proton transfer barrier and the length of the X-H covalent bond in the molecular complex are considered. Using the suggested formalism for problems of proton transfer in H-bonded systems is discussed. A criterion of the barrierless transfer is introduced.     

Simulation of proton migration pathways in phenolsulfonic acid-based membranes by B3LYP/6-31G** DFT calculations

Geometrical and energetic characteristics of clusters simulating crystal hydrates of phenolsulfonic acid (PSA) and its complexes with poly(vinyl alcohol) (PVA) and the pathways of proton transport therein were determined using the DFT (B3LYP) theory with the 6-31G** basis set. In the formation of proton-conducting PVA—PSA-based membranes, it is energetically favorable to have at least one water molecule in close proximity of the SO₃H fragment. In water-free media, the proton migration along the SO₃H group is hindered by a barrier of 30–34 kcal mol⁻¹. In the presense of water, the proton conductivity follows the relay mechanism with the activation barrier of 5–8 kcal mol⁻¹, which is close to the experimetally observed barrier of 4–6 kcal mol⁻¹. Thus, the relay mechanism of proton transfer in a sulfonic acid—water complex is energetically the most favorable. The most energetically favorable isomer is the one with the PSA and PVA fragments H-bonded through a water molecule. The deficiency of water causes the PVA OH protons to be involved in hydrogen bonding as well. The role of PVA is to align the acid molecules and participate in the relay proton transfer. Introduction of an aldehyde into the membrane results in significant improvement of its physical properties. The aldehyde reacts with the hydroxyl groups of PVA. At high humidity, one may expect little effect of the degree of cross-linking on the proton mobility.     

Self-assembled liquid crystals by hydrogen bonding between bipyridyl and alkylbenzoic acids: solvent-free synthesis by mechanochemistry

A series of thermotropic hydrogen-bonded liquid crystalline structures based on 4,4′-bipyridyl and aliphatic carboxylic acids was prepared by a mechanosynthesis technique. This series was characterised by polarising optical microscope, differential scanning calorimetry, Fourier transform infrared spectroscopy, X-ray powder diffraction and ¹H NMR relaxometry experimental techniques. In these complexes, the bipyridyl component, a non-mesogenic substance by itself, acts as a double H-bond acceptor, whereas the alkylbenzoic acid acts as a H-bond donor, in a 1:2 proportion. The so-formed complexes exhibit mesophases that are not observed by the single components. A characteristic phase (smectic A) is identified and shown to be affected by the alkyl chain length. The isotropisation temperature is increased by the supramolecular aggregation through the H-bonds.     

Structural Diversity in Multinuclear PdII Assemblies that Show Low‐Humidity Proton Conduction

Systematic investigation on synergetic effects of geometry, length, denticity, and asymmetry of donors was performed through the formation of a series of uncommon Pd^II aggregates by employing the donor in a multicomponent self‐assembly of a cis‐blocked 90° Pd^II acceptor and a tetratopic donor. Some of these assemblies represent the first examples of these types of structures, and their formation is not anticipated by only taking the geometry of the donor and the acceptor building units into account. Analysis of the crystal packing of the X‐ray structure revealed several H bonds between the counteranions (NO₃^?) and water molecules (O?H???O?N). Moreover, H‐bonded 3D‐networks of water are present in the molecular pockets, which show water‐adsorption properties with some variation in water affinity. Interestingly, these complexes exhibit proton conductivity (1.87×10^?5–6.52×10^?4 Scm^?1) at 296 K and low relative humidity (ca. 46 %) with activation energies of 0.29–0.46 eV. Moreover, the conductivities further increase with the enhancement of humidity. The ability of these assemblies to exhibit proton‐conducting properties under low‐humidity conditions makes these materials highly appealing as electrolytes in batteries and in fuel‐cell applications.