Gas-Phase Infrared Spectrum of the Protonated Water Dimer: Molecular Dynamics Simulation and Accuracy of the Potential Energy Surface

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.

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.

Prediction of the terahertz absorption features with a straightforward molecular dynamics method

In this paper, we provide a straightforward method to predict the terahertz absorption spectrum based on a fixed charge model with classic molecular dynamics calculations. The absorption features in the frequency range between 1 and 3.4 THz of stearic acid B-form and between 1 and 2.7 THz of C-form were successfully calculated. Most of the absorption peaks from the simulation correspond well with those from the measurements. By calculating the spatial and time-dependent energy accumulation in the molecular system, the core idea of our calculation method is further validated. Compared with the ab initio calculations, our method provides a computationally inexpensive way to accurately predict the locations of absorption features. With regard to the traditional molecular dynamic simulations, our method is able to extract the spatial distribution of the energy accumulation as well as the local motions in the molecular system.

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).

A closer examination of the coupling between ionic hydrogen bond (IHB) stretching and flanking group motions in (CH3OH)2H+: the strong isotope effects

The intermode coupling between shared proton (O–H⁺–O) fundamental stretching and flanking modes in (CH₃OH)₂H⁺ was revisited in the following contexts: (1) evaluation of Hamiltonian matrix elements represented in a “pure state” (PS) basis and (2) tuning of coupling strengths using H/D isotopic substitution.

“On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer

“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.

Probing Small Protonated Water Clusters in Acetonitrile Solutions by 1H NMR

In a previous publication by Kalish et al. (J. Phys. Chem. A 115 (2011) 4063) the existence of well defined small protonated water clusters in acetonitrile has been established by IR spectroscopy. Here we report on a 1H NMR study of triflic acid, CF3SO3H, in acetonitrile-water solutions. Using NMR we are able to corroborate the general solvation scheme we have proposed for the hydrated proton in acetonitrile as a function of the molar ratio between the strong mineral acid and water, n = [H2O]/[acid]. According to this scheme, backed now by both IR absorption spectroscopy and NMR measurements, the very strong triflic acid completely dissociates in acetonitrile/water solutions to yield the aqueous proton and the triflate anion when n > 1. Furthermore, increasing n results in the proton solvated in increasingly larger water clusters formed within the acetonitrile solution.

Clearly distinguishable by NMR are the smallest protonated water clusters, the protonated water monomer, H3 +O, and the protonated water dimer, H5 +O2, which dominate the solution for n = 1,2,3. For larger n the NMR study indicates the gradual increase of the average protonated water cluster size as a function of n while the proton inner solvation core more closely retaining the characteristics of a deformed protonated water dimer, (H2O-H+⋯OH2) s than that of the protonated water monomer (H3 +O) s .

Application of multipolar charge models and molecular dynamics simulations to study stark shifts in inhomogeneous electric fields

Atomic multipole moments are used to investigate vibrational frequency shifts of CO and H(2) in uniform and inhomogeneous electric fields using ab initio calculations and Molecular Dynamics (MD) simulations. The importance of using atomic multipole moments that can accurately represent both molecular electrostatics and the vibrational response of the molecule to changes in the local electric field is highlighted. The vibrational response of CO to applied uniform and inhomogeneous electric fields is examined using Density Functional Theory calculations for a range of test fields, and the results are used to assess the performance of different atomic multipole models. In uniform fields, the calculated Stark tuning rates of Deltamu = 0.52 cm(-1)/(MV/cm) (DFT), Deltamu = 0.55 cm(-1)/(MV/cm) (fluctuating three-point charge model), and Deltamu = 0.64 cm(-1)/(MV/cm) (Multipole model up to octupole), compare favorably with the experimentally measured value of 0.67 cm(-1)/(MV/cm). For H(2), which has no permanent dipole moment, CCSD(T) calculations demonstrate the importance of bond-weakening effects in force fields in response to the applied inhomogeneous electric field. Finally, CO in hexagonal ice is considered as a test system to highlight the performance of selected multipolar models in MD simulations. The approach discussed here can be applied to calibrate a range of multipolar charge models for diatomic probes, with applications to interpret Stark spectroscopy measurements in protein active sites.

Pseudo-Jahn-Teller origin of the low barrier hydrogen bond in N(2)H(7) (+)

The microscopic origin and quantum effects of the low barrier hydrogen bond (LBHB) in the proton-bound ammonia dimer cation N(2)H(7) (+) were studied by means of ab initio and density-functional theory (DFT) methods. These results were analyzed in the framework of vibronic theory and compared to those obtained for the Zundel cation H(5)O(2) (+). All geometry optimizations carried out using wavefunction-based methods [Hartree-Fock, second and fourth order Moller-Plesset theory (MP2 and MP4), and quadratic configuration interaction with singles and doubles excitations (QCISD)] lead to an asymmetrical H(3)N-H(+)cdots, three dots, centeredNH(3) conformation (C(3v) symmetry) with a small energy barrier (1.26 kcalmol in MP4 and QCISD calculations) between both equivalent minima. The value of this barrier is underestimated in DFT calculations particularly at the local density approximation level where geometry optimization leads to a symmetric H(3)Ncdots, three dots, centeredH(+)cdots, three dots, centeredNH(3) structure (D(3d) point group). The instability of the symmetric D(3d) structure is shown to originate from the pseudo-Jahn-Teller mixing of the electronic (1)A(1g) ground state with five low lying excited states of A(2u) symmetry through the asymmetric alpha(2u) vibrational mode. A molecular orbital study of the pseudo-Jahn-Teller coupling has allowed us to discuss the origin of the proton displacement and the LBHB formation in terms of the polarization of the NH(3) molecules and the transfer of electronic charge between the proton and the NH(3) units (rebonding). The parallel study of the H(5)O(2) (+) cation, which presents a symmetric single-well structure, allows us to analyze why these similar molecules behave differently with respect to proton transfer. From the vibronic analysis, a unified view of the Rudle-Pimentel three-center four-electron and charge transfer models of LBHBs is given. Finally, the large difference in the N-N distance in the D(3d) and C(3v) configurations of N(2)H(7) (+) indicates a large anharmonic coupling between alpha(2u)-alpha(1g) modes along the proton-transfer dynamics. This issue was explored by solving numerically the vibrational Schrodinger equation corresponding to the bidimensional E[Q(alpha(2u)),Q(alpha(1g))] energy surface calculated at the MP46-311++G(**) level of theory.

Reactive force fields for proton transfer dynamics

A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I.

Eigen and Zundel Forms of Small Protonated Water Clusters: Structures and Infrared Spectra

The spectral properties of protonated water clusters, especially the difference between Eigen (H3O+) and Zundel (H5O2+) conformers and the difference between their unhydrated and dominant hydrated forms are investigated with the first principles molecular dynamics simulations as well as with the high level ab initio calculations. The vibrational modes of the excess proton in H3O+ are sensitive to the hydration, while those in H5O2+ are sensitive to the messenger atom such as Ar (which was assumed to be weakly bound to the water cluster during acquisitions of experimental spectra). The spectral feature around approximately 2700 cm-1 (experimental value: 2665 cm-1) for the Eigen moiety appears when H3O+ is hydrated. This feature corresponds to the hydrating water interacting with H3O+, so it cannot appear in the Eigen core. Thus, H3O+ alone would be somewhat different from the Eigen forms in water. For the Zundel form (in particular, H5O2+), there have been some differences in spectral features among different experiments as well as between experiments and theory. When an Ar messenger atom is introduced at a specific temperature corresponding to the experimental condition, the calculated vibrational spectra for H5O2+.Ar are in good agreement with the experimental infrared spectra showing the characteristic Zundel frequency at approximately 1770 cm-1. Thus, the effect of hydration, messenger atom Ar, and temperature are crucial to elucidating the nature of vibrational spectra of Eigen and Zundel forms and to assigning the vibrational modes of small protonated water clusters.

Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: application to a Mannich base in solid state and in vacuum

Car-Parrinello molecular dynamics (CPMD) study was performed for an anharmonic system-an intramolecularly hydrogen bonded Mannich-base-type compound, 4,5-dimethyl-2(N,N-dimethylaminemethyl)phenol, to investigate the vibrational spectrum associated with the O-H stretching. Calculations were carried out for the solid state and for an isolated molecule. The classical CPMD simulation was performed and then the proton potential snapshots were extracted from the trajectory. The vibrational Schrodinger equation for the snapshots was solved numerically, and the (O-H) envelope was calculated as a superposition of the 0-->1 transitions. The potential of mean force for the proton stretching mode was calculated from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling, nuclear quantum effects, and effects of the environment. Perspectives for application of the presented methodology in the computational support of biocatalysis are given in the study.