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

IMPLEMENTATION OF SEMICLASSICAL THEORIES FOR SPECTROSCOPY

Vibrational spectroscopy is a fundamental tool for detecting and understanding the structure of molecular systems. Alongside the experimental measures, theoretical methods have been always employed to interpret and understand vibrational spectra. The semiclassical approach has demonstrated its reliability in the field, especially by means of the recent \u201cMultiple Coherent\u201d and \u201cDivide and Conquer\u201d formulations. In this PhD thesis the implementation and application of these modern techniques to a variety of molecular systems are presented, ranging from isolated medium size molecules to complex supramolecular systems, up to more than one hundred degrees of freedom. In particular the vibrational features of glycine, deoxyguanosine, a small dipeptide and glycine-based supramolecular systems are illustrated and discussed. A final Section is dedicated to the possibility to employ the Amber94 classical molecular force field, for computationally cheaper semiclassical calculations. This work demonstrates and highlights the validity and accuracy of semiclassical methods as theoretical spectroscopicy tools by successfully detecting quantum effects in medium size systems, whereas other formulations fail

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

Divide-and-Conquer Semiclassical Dynamics: A Viable Method for Vibrational Spectra Calculations of High Dimensional and Anharmonic Molecular Systems

The prediction of accurate vibrational frequencies is often necessary for the interpretation of experimental outcomes, especially when sources of strong anharmonic effects such as hydrogen bonding are present. Unfortunately, the most relevant stumbling block to fill in the gap between theory and experiment is usually represented by dimensionality problems, when quantum mechanical effects like Zero Point Energy, quantum anharmonicities, and overtones cannot be neglected. In this circumstance quantum applications are generally limited to small and medium sized molecules. One possible alternative is represented by Semiclassical theory, which allows to recover accurate spectral densities by taking advantage of quantities arising from classical mechanics simulations. [1-5] In particular, here we present a method, called Semiclassical \u201cDivide-and-Conquer\u201d, able to reproduce spectra of high-dimensional molecular systems accurately. [6,7] The method is first validated by performing spectra of small and medium sized molecules, and then it is used to calculate the spectra of benzene and a C 60 model, which is made of 174 degrees of freedom. Then, we show results of variously sized-water clusters characterized by strong hydrogen-bonding that red shifts the involved OH stretches. [8] Finally, the method is combined with ab-initio molecular dynamics to abandon the necessity to employ pre-fitted Potential Energy Surfaces, and applied to study supramolecular systems like the protonated glycine dimer and hydrogen-tagged protonated glycine. [9] [1] W. H. Miller, J. Chem. Phys. 1970, 53, 3578; [2] E. J. Heller, J. Chem. Phys. 1981, 75, 2923; M. F. Herman and E. Kluk, Chem. Phys. 1984, 91, 27. [3] K. G. Kay, J. Chem. Phys. 1994, 101, 2250; W. H. Miller, J. Phys. Chem. A 2001, 105, 2942. [4] A. L. Kaledin and W. H. Miller, J. Chem. Phys. 2003, 118, 7174. [5] R. Conte, A. Aspuru-Guzik, and M. Ceotto, J. Phys. Chem. Lett. 2013, 4, 3407. [6] M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 2017, 119, 010401. [7] G. Di Liberto, R. Conte, and M. Ceotto, J. Chem. Phys. 2018, 148, 014307. [8] G. Di Liberto, R. Conte, and M. Ceotto, J. Chem. Phys. 2018, 148, 104302. [9] F. Gabas, G. Di Liberto, R. Conte, and M. Ceotto In preparation

Divide-and-Conquer Semiclassical Dynamics: A Viable Route for Spectroscopic Calculations of High Dimensional Molecular Systems

The accurate prediction of vibrational spectra has become a very challenging task for theoretical methods. The most relevant stumbling block is represented by the necessity to employ quantum methods, since very often quantum effects, like zero point energy, quantum anharmonicities, and overtones, are not negligible to gain insights into the physics of a molecular system. Unfortunately, quantum mechanical methods are usually affected by the so-called curse of dimensionality problem, which limits their applicability to small and medium sized molecules. A viable alternative is represented by the Semiclassical theory, which is obtained by stationary-phase approximating to the second order of the Feynman Path-Integral representation of the Quantum time evolution operator, and allows to calculate spectral densities. In particular, the Coherent State Representation was shown to be very valid in molecular applications. However, even in this case the curse of dimensionality occurs and the method runs out of steam when the system dimensionality increases to 25-30 degrees of freedom or more. Here, we present a method, called Divide-and-Conquer, able to overcome this issue, and to reproduce spectra of high-dimensional molecular systems, while retaining the typical semiclassical accuracy (20-30 cm-1). The method is tested on simple molecules. Then, it is used to calculate spectra of a C60 model, which is made by 174 degrees of freedom, and of variously sized-water clusters characterized by strong hydrogen-bonding that red shifts the involved OH stretches. Finally, the method is also combined with ab-initio molecular dynamics to abandon the necessity to employ pre-fitted Potential Energy Surfaces, and applied to study supramolecular systems as the protonated glycine dimer and hydrogen-tagged protonated glycine

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

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

Semiclassical vibrational spectroscopy with Hessian databases

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

Deoxyguanosine and Ac-Phe-Met-NH2 vibrational spectra: a comparison between ab-initio and force field molecular dynamics

The theory of semiclassical dynamics has recently been demonstrated to be an important and powerful method in the field of vibrational spectroscopy. In particular, it has been successfully applied not only to the calculation of small and medium sized isolated molecules spectra but also to the study of complex systems, like water clusters and the Zundel cation. Furthermore, semiclassical dynamics may be efficiently associated to ab-initio molecular dynamics (AIMD) when the focus is on high dimensional systems. This combination showed very good accuracy, but unfortunately it presents high computational costs. In contrast, empiric Force Fields (FF) are known to be fast and computationally cheap. Here we present the vibrational power spectra of two biological systems: the Deoxyguanosine and the Ac-Phe-Met-NH2 dipeptide in their very interesting high frequency region. By employing different approaches (i.e. at harmonic, semiclassical and classical level), we discuss the validity of the Amber94 force field against the performance of DFT-based AIMD. We find that the semiclassical method associated to the FF potential gives the worst results, while better estimates are obtainable through classical formulations and via harmonic frequencies calculations. In particular, Amber94 is accurate for the normal modes associated to simple molecular motions, while it is poor for more complex normal modes. Conversely, AIMD always leads to accurate results. In light of these findings, we conclude that the Amber94 force field should be revised to permit a reliable semiclassical vibrational analysis, at least for in vacuo simulations

Parallel Implementation of Semiclassical Transition State Theory and its application to high-dimensional tunneling reactions

Semiclassical Transition State Theory (SCTST) can incorporate the non-separable coupling between degrees of freedom (DOFs) of reactive systems and include the effects of reaction path curvature and anharmonicity, as well as quantum tunneling contributions in the rate constant. The rate expression is derived by relying on a perturbative expansion for the vibrational energy which makes it possible to express the semiclassical cumulative reaction probability in a convenient way, without any further assumptions about the separability of the DOFs.[1-4] The main goal of the talk is the extension of this semiclassical methodology to systems of increasing dimensionality upon computation of the densities of states for the reactants and the transition state by means of a convenient parallel implementation of the Wang-Landau algorithm.[5-6] The new strategy is implemented into two codes, \u201cparadensum\u201d and \u201cparsctst\u201d, which are currently distributed with the open source MultiWell program suite for chemical kinetics.[7] The needed input information is just the reaction barrier height, the normal mode frequencies, and the anharmonic force constants, which are routinely calculated by suitable electronic structure packages. After describing the codes and demonstrating their computational accuracy and efficiency, the new implementation is applied to estimate the rate constant of the proton transfer isomerization of the 2,4,6-tri-tert-butylphenyl to 3,5-di-tert-butylneophyl, a reaction involving 145 degrees of freedom and showing a clear tunneling regime below 250K.[6] References [1] Miller, W.H. J. Chem. Phys., 1975, 62, 1899 \u2013 1906. [2] Miller, W.H. Faraday Discuss. Chem. Soc. 1977, 62, 40 \u2013 46. [3] Miller, W.H.; Hernandez, R.; Handy, N.C.; Jayatilaka, D.; Willetts, A. Chem. Phys. Letters 1990, 172, 62 \u2013 68. [4] Hernandez, R.; Miller, W. H. Chem. Phys. Lett. 1993, 214 (2), 129 \u2013 136. [5] Aieta, C.; Gabas, F.; Ceotto, M. J. Phys. Chem. A 2016, 120 (27), 4853 \u2013 4862. [6] Aieta, C.; Gabas, F.; Ceotto, M. J. Chem. Theory Comput. 2019, 15, 2142 12 2153. [7] Barker, J.R.; Nguyen, T.L.; Stanton, J.F.; Aieta, C.; Ceotto, M.; Gabas, F.; Kumar, T.J.D.; Li, C.G.L.; Lohr, L.L.; Maranzana, A.; Ortiz, N.F.; Preses, J.M.; Simmie, J.M.; Sonk, J.A.; Stimac, P.J.; MultiWell-2017 Software Suite; J.R. Barker, University of Michigan, Ann Arbor, Michigan, USA, 2019; http://clasp-research.engin.umich.edu/multiwell/