Proton Transfer Mode Research Articles

The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer?

The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. In this article I present the hypothesis on a proton-transport route through the ester groups of bacterial phospholipids as an explanation for the evolutionary divergence seen between bacteria and archaea.ReviewersThis article was reviewed by Uri Gophna (Editorial Board member) and Víctor Sojo.

Hydrated Excess Protons in Acetonitrile/Water Mixtures: Solvation Species and Ultrafast Proton Motions

The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We use two-dimensional infrared (2D-IR) spectroscopy to follow proton dynamics in acetonitrile/water mixtures with the Zundel cation H5O2+ prepared in neat acetonitrile as a benchmark. The 2D-IR spectra of the proton transfer mode of H5O2+ demonstrate stochastic large-amplitude motions in the double-minimum proton potential, driven by fluctuating electric fields. In all cases, the excess proton is embedded in a water dimer, forming an H5O2+ complex as the major solvation species. This observation is rationalized by quantum mechanics/molecular mechanics molecular dynamics simulations including up to four water molecules embedded in acetonitrile. The Zundel motif interacts with its closest water neighbor in an H7O3+ unit without persistent proton localization.

Ultrafast vibrational relaxation and energy dissipation of hydrated excess protons in polar solvents

Vibrational relaxation and energy redistribution of Zundel cations H5O2+ in acetonitrile and neat water are studied by femtosecond infrared pump-probe spectroscopy with resonant excitation of the 1200 cm−1 proton transfer mode. Transient spectra in a range from 1000 to 2200 cm−1 reveal intermode anharmonic couplings and a sub-100 fs decay of the proton transfer mode, followed by femtosecond vibrational redistribution within the cations’ vibrational manifold and picosecond energy transfer to the solvent. Energy transfer to an aqueous environment occurs on the same time scale as within neat water, demonstrating the strong coupling of cations and water solvation shell.

The protonated water trimer and its giant Fermi resonances

The protonated water trimer is a prototype “proton wire” that can transport two protons nearly concertedly. This “proton transfer mode” (PTM) is an important contributor to the infrared spectrum of the isolated gas-phase cluster. We have simulated its infrared spectrum for both the hydrated and deuterated isotopologues, using vibrational 2nd order perturbation theory (VPT2) and ab initio molecular dynamics (AIMD) trajectories. VPT2 calculations explain quantitatively the experimental spectra at both high and low frequencies, provided that high-level quantum chemistry is utilized. In the D2-tagged hydrated cluster, the PTM undergoes giant Fermi resonances (FR’s) with two combination bands. In the deuterated analogue, one observes a single FR of “normal” intensity, manifested as the doublet recently reported experimentally. We provide band assignment for both isotopologues, with and without the D2 tag applied in experiment. We discuss possible manifestations of the giant resonance on proton transfer through water wires.

Two-Dimensional Metal-Free Organic Multiferroic Material for Design of Multifunctional Integrated Circuits.

Coexistence of ferromagnetism and ferroelectricity in a single 2D material is highly desirable for integration of multifunctional units in 2D material-based circuits. We report theoretical evidence of C6N8H organic network as being the first 2D organic multiferroic material with coexisting ferromagnetic and ferroelectric properties. The ferroelectricity stems from multimode proton-transfer within the 2D C6N8H network, in which a long-range proton-transfer mode is enabled by the facilitation of oxygen molecule when the network is exposed to the air. Such oxygen-assisted ferroelectricity also leads to a high Curie temperature and coupling between ferroelectricity and ferromagnetism. We also find that hydrogenation and carbon doping can transform the 2D g-C3N4 network from an insulator to an n-type/p-type magnetic semiconductor with modest bandgap. Akin to the dopant induced n/p channels in silicon wafer, a variety of dopant created functional units can be integrated into the g-C3N4 wafer by design for nanoelectronic applications.

Complete Assignment of the Infrared Spectrum of the Gas-Phase Protonated Ammonia Dimer.

The infrared (IR) spectrum of the ammoniated ammonium dimer is more complex than those of the larger protonated ammonia clusters due to close-lying fundamental and combination bands and possible Fermi resonances (FR). To date, the only theoretical analysis involved partial dimensionality quantum nuclear dynamic simulations, assuming a symmetric structure (D3d) with the proton midway between the two nitrogen atoms. Here we report an extensive study of the less symmetric (C3v) dimer, utilizing both second order vibrational perturbation theory (VPT2) and ab initio molecular dynamics (AIMD), from which we calculated the Fourier transform (FT) of the dipole-moment autocorrelation function (DACF). The resultant IR spectrum was assigned using FTed velocity autocorrelation functions (VACFs) of several interatomic distances and angles. At 50 K, we have been able to assign all 21 AIMD fundamentals, in reasonable agreement with MP2-based VPT2, about 30 AIMD combination bands, and a difference band. The combinations involve a wag or the NN stretch as one of the components, and appear to follow symmetry selection rules. On this basis, we suggest possible assignments of the experimental spectrum. The VACF-analysis revealed two possible FR bands, one of which is the strongest peak in the computed spectrum. Raising the temperature to 180 K eliminated the "proton transfer mode" (PTM) fundamental, and reduced the number of observed combination bands and FRs. With increasing temperature, fundamentals red-shift, and the doubly degenerate wags exhibit larger anharmonic splittings in their VACF bending spectra. We have repeated the analysis for the H3ND(+)NH3 isotopologue, finding that it has a simplified spectrum, with all the strong peaks being fundamentals. Experimental study of this isotopologue may thus provide a good starting point for disentangling the N2H7(+) spectrum.

Infrared and Near-Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone.

The infrared and near-infrared spectra of acetylacetone, acetylacetone-d8, and hexafluoroacetylacetone are characterized from experiment and computations at different levels. In the fundamental region, the intramolecular hydrogen bonded OH-stretching transition is clearly observed as a very broad band with substantial structure and located at significantly lower frequency compared to common OH-stretching frequencies. There is no clear evidence for OH-stretching overtone transitions in the near-infrared region, which is dominated by the CH-stretching overtones of the methine and methyl CH bonds. From molecular dynamics (MD) simulations, with a potential energy surface previously validated for tunneling splittings, the infrared spectra are determined and used in assigning the experimentally measured ones. It is found that the simulated spectrum in the region associated with the proton transfer mode is exquisitely sensitive to the height of the barrier for proton transfer. Comparison of the experimental and the MD simulated spectra establishes that the barrier height is around 2.5 kcal/mol, which favorably compares with 3.2 kcal/mol obtained from high-level electronic structure calculations.

Computational Study of the One‐ and Two‐Dimensional Infrared Spectra of a Proton‐Transfer Mode in a Hydrogen‐Bonded Complex Dissolved in a Polar Nanocluster

The signatures of nanosolvation on the one- and two-dimensional (1D and 2D) IR spectra of a proton-transfer mode in a hydrogen-bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum-classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk-like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time-resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster-to-bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off-diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off-diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk-like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off-diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.

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H5+ is a weakly bound molecular ion, which is formed from the reaction of H3+ and H2 and that has a very rich vibrational spectrum. In this work, diffusion Monte Carlo (DMC) approaches are used to explore the nature of vibrationally excited states of the proton-transfer mode in H5+. On the basis of these calculations, alternative assignments of the recently reported infrared multiphoton dissociation spectra of H5+ and D5+ [J. Phys. Chem. Lett. 2012, 3, 3160−3166] are suggested. In the proposed assignments, progressions of transitions in the proton-transfer mode with up to nine quanta of excitation are invoked. Reduced dimensional calculations of the spectra of H5+ and D5+ are used to provide an understanding of why such high overtones should be observable through absorption spectroscopy. Implications of how excitations of this mode can provide insights into the H3+ + H2 reaction are also discussed.

A ‘clusters-in-liquid’ method for calculating infrared spectra identifies the proton-transfer mode in acidic aqueous solutions

In liquid water the transfer of an excess proton between two water molecules occurs through the Zundel cation, H(2)O···H(+)···OH(2). The proton-transfer mode is the asymmetric stretch of the central O···H(+)···O moiety, but there is no consensus on its identification in the infrared spectra of acidic aqueous solutions. Also, in experiments with protonated gas-phase water clusters, its position shifts with cluster size, which makes its relationship with solution spectra unclear. Here we introduce a 'clusters-in-liquid' approach for calculating the infrared spectrum from any set of charges, even single protons. We apply this procedure to multistate empirical valence-bond trajectories of protonated liquid water and to ab initio molecular dynamics of the protonated water dimer and hexamer in the gas phase. The calculated proton-transfer mode is manifested in both systems as a peak near 1,740 cm(-1), in quantitative agreement with a band of similar frequency in the experimental infrared spectrum of protonated water clusters.

A computational study towards understanding the mechanism of phosphodiester cleavage by two mononuclear Zn(ii) complexes

In this study, the hydrolytic reaction mechanism of HPNP by two effective mononuclear Zn(II) catalysts was explored by using density functional calculations. With the assumption that the active catalyst is in Zn-aqua form, the water-assisted proton transfer mode was found to be energetically the most favorable one for both the catalysts among three possible reaction pathways. The rate-limiting step on this pathway is a concerted double-proton transfer, concomitant with the nucleophilic addition of the deprotonated hydroxyl group to form a five-coordinated phosphorus intermediate. A comparison of potential energy surfaces for both catalysts shows that the three amino groups in the second coordination sphere of one catalyst play an important role in stabilizing the proton transfer (or nucleophilic addition) transition state. The two coordination spheres are found to have almost the same contributions in catalyzing the phosphate ester cleavage reaction. Also, present calculations show that the water-assisted proton transfer mechanism with the catalyst L-Zn-OH(2) is more favorable in energy than the general base pathway with the active catalyst L-Zn-OH suggested previously.

Theoretical Study on Hydrogen-Bond Effects in IR Spectra of High- and Low-Temperature Phases of Nitric Acid Dihydrate

The low- and high-temperature phases (alpha and beta, respectively) of solid nitric acid dihydrate (NAD) are studied in depth by DFT methods. Each phase contains two types of complex structures (H(3)O(+)) x (H(2)O), designated A and B, with different hydrogen-bonding (HB) characteristics. The theoretical study reveals that type A complexes are weakly bound and could be described as (H(3)O)(+) and H(2)O aggregates, with decoupled vibrational modes, whereas in type B structures the proton is situated close to the centre of the O...O bond and induces strong vibrational coupling. The proton-transfer mode is predicted at quite different wavenumbers in each complex, which provides an important differentiating spectral feature, together with splitting of some bands in beta-NAD. Theoretical spectra are estimated by using two GGA parameterizations, namely, PBE and BLYP. The potential-energy surface for each type of HB in NAD is also studied, as is the spectral influence of displacement of the shared H atom along the O-O bond. The results are compared to literature infrared spectra recorded by different techniques, namely, transmission and reflection-absorption, with both normal and tilted incident radiation. This work provides a thorough assignment of the observed spectra, and predictions for some spectra not yet available. The usefulness of high-level theoretical calculations as performed herein to discriminate between two phases of a solid crystal is thus evidenced.

Dynamics and Infrared Spectroscopy of the Protonated Water Dimer

We discuss the spectral signatures in terms of the underlying couplings and dynamics of the different degrees of freedom and compare our results to recent, accurate experiments on this system. For the first time the doublet signal at about 1000 cm � 1 is fully reproduced, analyzed, and assigned. The doublet is found to arise from the coupling between the proton-transfer mode and low-frequency, large-amplitude displacements of both water molecules. Predictions are also made for the lowest-frequency part of the spectrum, which has not yet experimentally been accessed. Several important features of the system are analyzed for the first time, namely

Investigating the Relationship between Infrared Spectra of Shared Protons in Different Chemical Environments: A Comparison of Protonated Diglyme and Protonated Water Dimer

The energetics, dynamics, and infrared spectroscopy of the shared proton in different chemical environments is investigated using molecular dynamics simulations. A three-dimensional potential energy surface (PES) suitable for describing proton transfer between an acceptor and a donor oxygen atom is combined with an all-atom force field to carry out reactive molecular dynamics simulations. The construction of the fully dimensional PES is inspired from the established mixed quantum mechanics/molecular mechanics treatment of larger systems. The "morphing potential" method is used to transform the generic PES for proton transfer along an O...H+...O motif into a three-dimensional PES for proton transfer in protonated diglyme. Using molecular dynamics simulations at finite temperature, the gas phase infrared spectra are calculated for both species from the Fourier transform of the dipole moment autocorrelation function. For protonated diglyme the modes involving the H+ motion are strongly mixed with other degrees of freedom. At low temperature, the O...H+...O asymmetric stretching vibration is found at 870 cm-1, whereas for H5O2+ this band is at 724 cm-1. As expected, the vibrational bands of protonated diglyme show no temperature dependence whereas for H5O2+ at T = 100 K the proton transfer mode is found at 830 cm-1, in good agreement with 861 cm-1 from very recent molecular dynamics simulations.

Microscopic Models for Proton Transfer in Water and Strongly Hydrogen-Bonded Complexes with a Single-Well Proton Potential

A new mechanism and formalism for proton transfer in donor-acceptor complexes with long hydrogen bonds introduced recently [1], is applied to a proton transfer in liquid water. “Structural diffusion” of hydroxonium ions is regarded as totally adiabatic process, with synchronous hindered translation of two closest water molecules to and from the reaction complex as crucial steps. The water molecules induce a “gated” shift of the proton from the donor to the acceptor in the double-well potential with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor and acceptor. The short-range and long-range proton transfer as “structural diffusion” of Zundel complexes is also considered. The theoretical formalism is illustrated with the use of Morse, exponential, and harmonic molecular potentials. This approach is extended to proton transfer in strongly hydrogen-bonded donor-acceptor complexes. In contrast to the above model [1], the short hydrogen bond between the donor and acceptor moieties, however, completely erodes the barrier along the proton transfer mode. This introduces some physical pattern differences from proton transfer reactions in truly double-well potentials with a finite proton transfer barrier at the transition configuration with respect to the environmental nuclear coordinates. The differences apply particularly to the origin of the kinetic isotope effect. We discuss explicitly details of the excess proton conductivity in aqueous solution, but the concepts and formalism apply broadly to acid-base reactions, proton conduction channels, and other strongly hydrogen-bonded O- and N-proton donor-acceptor systems.

On the influence of semirigid environments on proton transfer along molecular chains.

The dynamics of proton transfer along ammonia chains (chemical composition N(x)H(+)(3x+1), x=2, 4, and 6) in a constraining environment is investigated by ab initio molecular dynamics simulations. A carbon nanotube of defined length and diameter is used as an idealized constraining environment such that the ammonia chain is forced to maintain its quasilinear geometry. It is found that, although the energetics of proton transport shows considerable energetic barriers, proton translocation along the wire is possible at finite temperature for all chain lengths studied. The proton transport involves rotational reorientation of the proton-carrying ammonia molecule. High level ab initio calculations (MP2/aug-cc-pVTZ) yield barriers for internal rotation of 9.1 kcal/mol for NH(4) (+)-NH(3) and 11.7 kcal/mol for OH(3) (+)-OH(2), respectively. The infrared spectrum calculated from the dipole-dipole autocorrelation function shows distinct spectral features in the regions (2000-3000 cm(-1)) where the NHN proton transfer mode is expected to absorb. Assigning moderate opposite total charges between 0.002 and 0.2e to the carbon atoms at the end caps of the nanotube leads to a considerable speedup of the proton transfer.

Dynamics of low-barrier proton transfer in polar solvents and protein media

Abstract Proton transfer in chemical, physical, and biological systems frequently involves low and shallow barriers. This is caused by strong donor-acceptor interaction which also imposes fully adiabatic character on the process. Low or shallow barriers are not covered straightforwardly by tunnel views otherwise central in proton transfer theory. We introduce a formalism focused on a shallow enough proton transfer mode that the proton dynamics is indistinguishable from classical behaviour, strongly coupled to stochastic environmental nuclear motion. We derive rate constants for three cases, namely fast solvent relaxation, fast proton equilibration, and proton transfer followed by fast decay of the donor-acceptor complex. These cases may constitute useful descriptions of several kinds of processes including fast intramolecular proton transfer, hydrolytic and redox enzyme catalysis, and physical or biological proton conductivity.

Proton and oxygen diffusion in BaCeO 3 based compounds: A combined thermal gravimetric analysis and conductivity study

Ceramics of composition BaO·0.9 CeO 2·0.05 Gd 2O 3 have been prepared with a density of 98–99%. The material consists of two phases, a perovskite of approximate composition (Ba 0.965Gd 0.035)(Ce 0.935Gd 0.065)O 2.985+δ and an amorphous proton-conducting BaO-rich grain-boundary phase. For the perovskite phase, the proton diffusivity is obtained directly from water-concentration-dependent conductivities and the oxygen diffusion coefficient from 18O-tracer experiments. The results are analyzed consistently in terms of the concentrations and diffusivities of elementary defects. In return, the ionic transference numbers and the chemical diffusion coefficient of water are determined and compared with the experimentally observed kinetics of water uptake. The data suggest structure diffusion as the operating proton conduction mechanism with the proton transfer mode in the configuration OH −/O 2− as the rate-limiting step. It is proposed that the mechanism is heavily assisted by extended vibrations of OH −/ O 2− about their equilibrium position.