Sensitivity of semiclassical vibrational spectroscopy to potential energy surface accuracy: A test on formaldehyde.

A set of permutationally invariant potential energy surfaces for the electronic ground state of formaldehyde is built at several levels of electronic theory and atomic orbital basis sets starting from a database of more than 34000 ab initio energies. The reliability of the fitted surfaces is determined by comparing the calculated harmonic frequencies with the corresponding ab initio values. Semiclassical estimates of the quantum frequencies of vibration are presented, and their dependence on the employed level of theory, type of atomic orbital basis set, and complexity of the fit is investigated. Comparisons to experimental data show that anharmonic frequencies are influenced by the precision of the fit, while accurate frequency values are obtained also with density functional theory. Results and conclusions support the use of ab initio \u201con-the-fly\u201d semiclassical dynamics as a means of spectroscopic investigation when high level analytical potential energy surfaces are not available

Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields

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 nonpolarizable (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

Parallel Implementation of Semiclassical Transition State Theory

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 (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 pseudocode 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

Deep nuclear resonant tunneling thermal rate constant calculations

A fast and robust time-independent method to calculate thermal rate constants in the deep resonant tunneling regime for scattering reactions is presented. The method is based on the calculation of the cumulative reaction probability which, once integrated, gives the thermal rate constant. We tested our method with both continuous (single and double Eckart barriers) and discontinuous first derivative potentials (single and double rectangular barriers). Our results show that the presented method is robust enough to deal with extreme resonating conditions such as multiple barrier potentials. Finally, the calculation of the thermal rate constant for double Eckart potentials with several quasi-bound states and the comparison with the time-independent log-derivative method are reported. An implementation of the method using the Mathematica Suite is included in the Supporting Information

Vibration-assisted tunneling : a semiclassical instanton approach

A simple method to find the instanton trajectories is developed. This method does not employ any approximation and 'exact' instanton trajectories have been located for several collinear symmetric reactions. Underlying the method is the notion of stability of periodic trajectories and the behaviour of the action derivatives. Applications to thermal rate constants calculations are presented showing that the method is suitable for quantitative rate constant predictions. In the deep tunnelling regime, where a classical rate underestimation is about two orders of magnitude, the semiclassical instanton rate is within a few percent of the exact quantum mechanical value. Then, the consistent amount of tunnelling involved in the heavy particle transfer, as for the collinear H+BrH reaction, shows that 'corner-cutting' is not necessary for tunnelling to occur, even if it is a sufficient condition to detect a significant presence of tunnelling effects

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 3c29 cm-1 with respect to available multiconfiguration time-dependent Hartree calculations and MAE 3c14 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

Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approach

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

A quantum method for thermal rate constant calculations from stationary phase approximation of the thermal flux-flux correlation function integral

This paper presents a quantum mechanical approximation to the calculation of thermal rate constants. The rate is derived from a suitable stationary phase approximation to the time integral of the thermal flux-flux correlation function. The goal is to obtain an expression that barely depends on the position of the flux operators, i.e., of the dividing surfaces, so that it can be applied also to complex systems by arbitrarily locating the dividing surfaces. The approach is tested on one and two dimensional systems where quantum effects are predominant over a wide range of temperatures. The results are quite accurate, i.e., within a few percent of the exact values for a reasonable range of dividing surface positions

Semiclassical vibrational spectroscopy : the importance of quantum anharmonicity in supra-molecular systems

Semiclassical (SC) vibrational spectroscopy has been applied successfully to several molecular systems thanks to the possibility to regain quantum effects accurately starting from short-time classical trajectories.[1-5] Larger molecular and supra-molecular systems represent instead an open challenge in the field of semiclassical spectroscopy mainly due to the necessity to work in very high dimensionality. To start off the talk I will present some recent theoretical advances able to extend the range of applicability of SC vibrational spectroscopy to very high-dimensional systems.[6-7] Then, I will move to applications of semiclassical spectroscopy concerning the vibrational features of water clusters and two supra-molecular systems involving glycine.[8-9] These applications will point out the importance of a multi-reference, dynamical approach able to reproduce quantum anharmonicities without employing any ad-hoc scaling factor. [1] M. F. Herman, E. Kluk, Chem. Phys. 1984, 91, 27. [2] A. L. Kaledin, W. H. Miller, J. Chem. Phys. 2003, 118, 7174. [3] M. Ceotto, S. Atahan, G. F. Tantardini, A. Aspuru-Guzik, J. Chem. Phys. 2009, 130, 234113. [4] R. Conte, A. Aspuru-Guzik, M. Ceotto, J. Phys. Chem. Lett. 2013, 4, 3407. [5] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2017, 13, 2378. [6] M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett. 2017, 119, 010401. [7] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 014307. [8] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 104302. [9] F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, to be submitted