Infrared spectroscopy of small protonated water clusters at room temperature: An effective modes analysis

Influence of the environment on the infrared spectrum of alanine: An effective mode analysis

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm^-1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.

Proton-transfer spectroscopy beyond the normal-mode scenario

A stochastic theory is developed to predict the spectral signature of proton-transfer processes and is applied to infrared spectra computed from ab initio molecular-dynamics simulations of a single [Formula: see text] cation. By constraining the oxygen atoms to a fixed distance, this system serves as a tunable model for general proton-transfer processes with variable barrier height. Three spectral contributions at distinct frequencies are identified and analytically predicted: the quasi-harmonic motion around the most probable configuration, amenable to normal-mode analysis, the contribution due to transfer paths when the proton moves over the barrier, and a shoulder for low frequencies stemming from the stochastic transfer-waiting-time distribution; the latter two contributions are not captured by normal-mode analysis but exclusively reported on the proton-transfer kinetics. In accordance with reaction rate theory, the transfer-waiting-contribution frequency depends inversely exponentially on the barrier height, whereas the transfer-path-contribution frequency is rather insensitive to the barrier height.

Reduced rovibrational coupling Cartesian dynamics for semiclassical calculations: Application to the spectrum of the Zundel cation

We study the vibrational spectrum of the protonated water dimer, by means of a divide-and-conquer semiclassical initial value representation of the quantum propagator, as a first step in the study of larger protonated water clusters. We use the potential energy surface from the work of Huang et al. [J. Chem. Phys. 122, 044308 (2005)]. To tackle such an anharmonic and floppy molecule, we employ fully Cartesian dynamics and carefully reduce the coupling to global rotations in the definition of normal modes. We apply the time-averaging filter and obtain clean power spectra relative to suitable reference states that highlight the spectral peaks corresponding to the fundamental excitations of the system. Our trajectory-based approach allows for the physical interpretation of the very challenging proton transfer modes. We find that it is important, for such a floppy molecule, to selectively avoid initially exciting lower energy modes, in order to obtain cleaner spectra. The estimated vibrational energies display a mean absolute error (MAE) of ∼29 cm^-1 with respect to available multiconfiguration time-dependent Hartree calculations and MAE ∼ 14 cm^-1 when compared to the optically active experimental excitations of the Ne-tagged Zundel cation. The reasonable scaling in the number of trajectories for Monte Carlo convergence is promising for applications to higher dimensional protonated cluster systems.

IR spectral assignments for the hydrated excess proton in liquid water

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm^-1 for every local proton configuration, with the region 2000-2600 cm^-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H⁺⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H₅O2+moiety.

MP4 Study of the Anharmonic Coupling of the Shared Proton Stretching Vibration of the Protonated Water Dimer in Equilibrium and Transition States

The structure and harmonic and anharmonic IR spectra of the protonated water dimer (PWD) were calculated in C₁, C₂, and C_s symmetry at the MP4/acc-pVTZ level of theory. We found that structure and IR spectra are practically identical in C₂ and C₁ symmetry, demonstrating that an equilibrium C₁ configuration of the PWD is not realized. Anharmonic coupling of the shared proton stretching vibration with all other modes in the PWD in C₂ and C_s symmetry was the focus of this investigation. For this purpose, 28 two-dimensional potential energy surfaces (2D PES) were built at the MP4/acc-pVTZ level of theory and the corresponding vibrational Schrödinger equations were solved using the DVR method. Differences in the coupling of the investigated mode with other modes in the C₂ and C_s configurations, along with some factors that determine the red- or blue-shift of the stretching vibration frequency, were analyzed. We obtained a rather reasonable value of the stretching frequency of the bridging proton (1058.4 cm^-1) unperturbed by Fermi resonance. The Fermi resonance between the fundamental vibration ν₇ and the combined vibration ν₂ + ν₆ of the same symmetry was analyzed through anharmonic second-order perturbation theory calculations, as well as by 3D PES constructed using Q₂, Q₆, and Q₇ as normal coordinates. A significant (up to 50%) transfer of intensity from the fundamental vibration to the combined one was found. We have estimated the frequency of the bridging proton stretching vibration in the C_s configuration of the PWD based on calculations of the intrinsic anharmonicity and anharmonic double modes interactions at the MP4/acc-pVTZ level of theory (1261 cm^-1).

Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen-Zundel cation

Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.

Isomer-selective detection of hydrogen-bond vibrations in the protonated water hexamer

The properties of hydrogen ions in aqueous solution are governed by the ability of water to incorporate ions in a dynamical hydrogen bond network, characterized by a structural variability that has complicated the development of a consistent molecular level description of H(+)(aq). Isolated protonated water clusters, H(+)(H2O)n, serve as finite model systems for H(+)(aq), which are amenable to highly sensitive and selective gas phase spectroscopic techniques. Here, we isolate and assign the infrared (IR) signatures of the Zundel-type and Eigen-type isomers of H(+)(H2O)6, the smallest protonated water cluster for which both of these characteristic binding motifs coexist, down into the terahertz spectral region. We use isomer-selective double-resonance population labeling spectroscopy on messenger-tagged H(+)(H2O)6·H2 complexes from 260 to 3900 cm(-1). Ab initio molecular dynamics calculations qualitatively recover the IR spectra of the two isomers and allow attributing the increased width of IR bands associated with H-bonded moieties to anharmonicities rather than excited state lifetime broadening. Characteristic hydrogen-bond stretching bands are observed below 400 cm(-1).