Fabio Gabas

The interaction of water molecules and hydroxyl groups with titanium dioxide (TiO₂) surfaces is ubiquitous and very important in anatase nanoparticle photocatalytic processes. Infrared spectroscopy, assisted by ab initio calculations of vibrational frequencies, can be a powerful tool to elucidate the mechanisms behind water adsorption. However, a straightforward comparison between measurements and calculations remains a challenging task because of the complexity of the physical phenomena occurring on nanoparticle surfaces. Consequently, severe computational approximations, such as harmonic vibrational ones, are usually employed. In the present work we partially address this complexity issue by overcoming some of the standard approximations used in theoretical simulations and employ the Divide and Conquer Semiclassical Initial Value Representation (DC-SCIVR) molecular dynamics. This method allows to perform simulations of vibrational spectra of large dimensional systems accounting not only for anharmonicities, but also for nuclear quantum effects. We apply this computational method to water and deuterated water adsorbed on the ideal TiO₂ anatase(101) surface, contemplating both the molecular and the dissociated adsorption processes. The results highlight not only the presence of an anharmonic shift of the frequencies in agreement with the experiments, but also complex quantum mechanical spectral signatures induced by the coupling of molecular vibrational modes with the surface ones, which are different in the hydrogenated case from the deuterated one. These couplings are further analyzed by exploiting the mode subdivision performed during the divide and conquer procedure.

In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.

Semiclassical spectroscopy is a practical way to get an accurately approximate quantum description of spectral features starting from ab initio molecular dynamics simulations. The computational bottleneck for the method is represented by the cost of ab initio potential, gradient, and Hessian matrix estimates. This drawback is particularly severe for biological systems due to their unique complexity and large dimensionality. The main goal of this manuscript is to demonstrate that quantum dynamics and spectroscopy, at the level of semiclassical approximation, are doable even for sizable biological systems. To this end, we investigate the possibility of performing semiclassical spectroscopy simulations when ab initio calculations are replaced by computationally cheaper force field evaluations. Both polarizable (AMOEBABIO18) and non-polarizable (AMBER14SB) force fields are tested. Calculations of some particular vibrational frequencies of four nucleosides, i.e. uridine, thymidine, deoxyguanosine, and adenosine, show that ab initio simulations are accurate and widely applicable. Conversely, simulations based on AMBER14SB are limited to harmonic approximations, but those relying on AMOEBABIO18 yield acceptable semiclassical values if the investigated conformation has been included in the force field parametrization. The main conclusion is that AMOEBABIO18 may provide a viable route to assist semiclassical spectroscopy in the study of large biological molecules for which an ab initio approach is not computationally affordable.

The vibrational spectroscopy of adsorbates is becoming an important investigation tool for catalysis and material science. This paper presents a semiclassical molecular dynamics method able to reproduce the vibrational energy levels of systems composed by molecules adsorbed on solid surfaces. Specifically, we extend our divide-and-conquer semiclassical method for power spectra calculations to gas-surface systems and interface it with plane-wave electronic structure codes. The Born–Oppenheimer classical dynamics underlying the semiclassical calculation is full dimensional, and our method includes not only the motion of the adsorbate but also those of the surface and the bulk. The vibrational spectroscopic peaks related to the adsorbate are accounted together with the most coupled phonon modes to obtain spectra amenable to physical interpretations. We apply the method to the adsorption of CO, NO, and H₂O on the anatase-TiO₂ (101) surface. We compare our semiclassical results with the single-point harmonic estimates and the classical power spectra obtained from the same trajectory employed in the semiclassical calculation. We find that CO and NO anharmonic effects of fundamental vibrations are similarly reproduced by the classical and semiclassical dynamics and that H₂O adsorption is fully and properly described in its overtone and combination band relevant components only by the semiclassical approach.

We report on a new approach to ease the computational overhead of ab initio “on-the-fly” semiclassical dynamics simulations for vibrational spectroscopy. The well known bottleneck of such computations lies in the necessity to estimate the Hessian matrix for propagating the semiclassical pre-exponential factor at each step along the dynamics. The procedure proposed here is based on the creation of a dynamical database of Hessians and associated molecular geometries able to speed up calculations while preserving the accuracy of results at a satisfactory level. This new approach can be interfaced to both analytical potential energy surfaces and on-the-fly dynamics, allowing one to study even large systems previously not achievable. We present results obtained for semiclassical vibrational power spectra of methane, glycine, and N-acetyl-L-phenylalaninyl-L-methionine-amide, a molecule of biological interest made of 46 atoms.

In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.

We present a novel approach to calculate molecular infrared (IR) spectra based on semiclassical (SC) molecular dynamics. The main advance from a previous SC method [M. Micciarelli et al. J. Chem. Phys. 149, 064115 (2018)] consists of the possibility to avoid state-to-state calculations making applications to systems characterized by sizable densities of vibrational states feasible. Furthermore, this new method accounts not only for positions and intensities of the several absorption bands which make up the IR spectrum but also for their shapes. We show that accurate SC IR spectra including quantum effects and anharmonicities for both frequencies and intensities can be obtained starting from SC power spectra. The approach is first tested against the water molecule and then applied to the 10-atom glycine amino acid.

This paper presents the parsctst code, an efficient parallel implementation of the Semiclassical Transition State Theory (SCTST) for reaction rate constant calculations. Parsctst is developed starting from a previously presented approach for the computation of the vibrational density of states of fully coupled anharmonic molecules (T. L. Nguyen et al. Chem. Phys. Lett. 2010, 499, 915). The parallel implementation makes it practical to tackle reactions involving more than 100 fully coupled anharmonic vibrational degrees of freedom and also includes multidimensional tunneling effects. After describing the pseudo-code and demonstrating its computational efficiency, we apply the new code for estimating the rate constant of the proton transfer isomerization reaction of the 2,4,6-tri-tert-butylphenyl to 3,5-di-tert-butylneophyl. Comparison with both theoretical and experimental results is presented. Parsctst code is user-friendly and provides a significant computational time saving compared to serial calculations. We believe that parsctst can boost the application of SCTST as an alternative to the basic Transition State Theory for accurate kinetics modeling not only in combustion or atmospheric chemistry, but also in organic synthesis, where bigger reactive systems are encountered.

IR spectroscopy is one of the most commonly employed techniques to study molecular vibrations and interactions. However, characterization of experimental IR spectra is not always straightforward. This is the case of protonated glycine supramolecular systems like Gly₂H⁺ and (GlyH + nH₂), whose IR spectra raise questions which have still to find definitive answers even after theoretical spectroscopy investigations. Specifically, the assignment of the conformer responsible for the spectrum of the protonated glycine dimer (Gly₂H⁺) has led to much controversy and it is still debated, while structural hypotheses formulated to explain the main experimental spectral features of (GlyH + nH₂) systems have not been theoretically confirmed. We demonstrate that simulations must account for quantum dynamical effects in order to resolve these open issues. This is achieved by means of our divide-and-conquer semiclassical initial value representation technique, which approximates the quantum dynamics of high dimensional systems with remarkable accuracy and outperforms not only the commonly employed but unfit scaled-harmonic approaches, but also pure classical dynamics simulations. Besides the specific insights concerning the two particular cases presented here, the general conclusion is that, due to the widespread presence of protonated systems in chemistry, quantum dynamics may play a prominent role and should not be totally overlooked even when dealing with large systems including biological structures.

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.