Theoretical modeling of the formic acid dimer infrared spectrum: Shaping the O–H stretch band

Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials

In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.

Concerted Pair Motion Due to Double Hydrogen Bonding: The Formic Acid Dimer Case

Formic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.

UV absorption spectra of DNA bases in the 350-190 nm range: assignment and state specific analysis of solvation effects

The theoretical assignment of electronic spectra of polyatomic molecules is a challenging problem that requires the specification of the character of a large number of electronic states. We propose a procedure for automatically determining the character of electronic transitions and apply it to the study of UV spectra of DNA bases in the gas phase and in the aqueous environment. The procedure is based on the computation of electronic wave function overlaps and accounts for an extensive sampling of nuclear geometries. Novelties of this work are the theoretical assignment of the electronic spectra of DNA bases up to 190 nm and a state specific analysis of solvation effects. By accounting for different effects contributing to the total solvent shift we obtained a good agreement between the computed and experimental spectra. Effects of vibrational averaging, temperature and solvent-induced structural changes shift excitation energies to lower values. Solvent-solute electrostatic interactions are state specific and strongly destabilize nRyd states, and to lesser extent nπ* and πRyd states. Altogether, this results in the stabilization of ππ* states and destabilization of nπ*, πRyd and nRyd states in solution.

Teaching vibrational spectra to assign themselves

A new paradigm for assigning vibrational spectra is described. Instead of proceeding from potential to Hamiltonian to eigenvalues/eigenvectors/intensities to spectrum, the new method goes "backwards" directly from spectrum to eigenvectors. The eigenvectors then "assign" the spectrum, in that they identify the basis states that contribute to each eigenvalue. To start, we demonstrate an algorithm that can obtain useful estimates of the eigenvectors connecting a real, symmetric Hamiltonian to its eigenvalues even if the only available information about the Hamiltonian is its diagonal elements. When this algorithm is augmented with information about transition intensities, it can be used to assign a complex vibrational spectrum using only information about (1) eigenvalues (the peak centers of the spectrum) and (2) a harmonic basis set (taken to be the diagonal elements of the Hamiltonian). Examples will be discussed, including application to the vibrationally complex spectral region of the formic acid dimer.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH)₂ and (DCOOH)₂, using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm^-1. Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm^-1. In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Quantum and classical IR spectra of (HCOOH)2, (DCOOH)2 and (DCOOD)2 using ab initio potential energy and dipole moment surfaces

Full-dimensional (24 modes) quantum calculation of the IR spectrum of (DCOOD)₂, and comparison with classical MD one.

Adsorbate-induced lifting of substrate relaxation is a general mechanism governing titania surface chemistry

Under ambient conditions, almost all metals are coated by an oxide. These coatings, the result of a chemical reaction, are not passive. Many of them bind, activate and modify adsorbed molecules, processes that are exploited, for example, in heterogeneous catalysis and photochemistry. Here we report an effect of general importance that governs the bonding, structure formation and dissociation of molecules on oxidic substrates. For a specific example, methanol adsorbed on the rutile TiO₂(110) single crystal surface, we demonstrate by using a combination of experimental and theoretical techniques that strongly bonding adsorbates can lift surface relaxations beyond their adsorption site, which leads to a significant substrate-mediated interaction between adsorbates. The result is a complex superstructure consisting of pairs of methanol molecules and unoccupied adsorption sites. Infrared spectroscopy reveals that the paired methanol molecules remain intact and do not deprotonate on the defect-free terraces of the rutile TiO₂(110) surface.

Molecules on a metal surface may be modified by the presence of oxide layers, but further mechanistic understanding is still required. Here the authors show for methanol on rutile TiO₂(110) that strongly bonded adsorbates lift surface relaxations, leading to substrate-mediated interaction between adsorbates.

Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

An extended quantum theoretical approach of the nu(X-H) IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H...Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.