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

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

Análise De Metais Pesados No Sistema Aquífero Bauru Em Mato Grosso Do Sul

Heavy metals are contaminants of great concern in the aquifers due to their toxicity at certain concentration and difficult remediation. This study aimed to analyze the concentrations of Cu, Cr, Fe, Mn and Zn present in Bauru Aquifer System in Mato Grosso do Sul State, from 2009 to 2013. The content of Cu, Cr and Zn were within the limits of drinking water from Brazilian legislation, unlike Mn and Fe. The use of vinasse in fertigation of sugar cane cultivation and mineral tanning leather can influence the quality of groundwater in the outcropping area of the aquifer. This study reinforces the importance of monitoring groundwater quality in order to establish a zoning of vulnerability to pollution through control measures, prevention and remediation. © 2017, ABES - Associacao Brasileira de Engenharia Sanitaria e Ambiental. All rights reserved.22115516

Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics

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

In vitro cell cytotoxicity profile and morphological response to polyoxometalate-stabilised gold nanoparticles

The size and redox properties of molecular polyoxometalates (POMs) make them extremely relevant for bioapplications: from disrupting tumour growth and enzyme inhibition, to DNA-intercalating agents and antimicrobial applications. Their unique ability to reversibly dominate and receive electrons, coupled with their high anionic charge, also makes them suitable for the preparation of zero-valent state metal nanoparticles (NPs) from molecular precursors. Polyoxometalate-stabilised nanoparticles (NPs@POM) are therefore an ideal delivery vehicle for bioactive POMs. Here we show how POM-stabilised gold NPs (AuNPs@POM) are massively internalised into Vero (kidney epithelial) and B16 (skin melanoma) cell lines with variable cytotoxic effects. Cell viability assays and quantification of cytoplasmic membrane composition revealed that the Vero cell line was unaltered by the internalisation of these hybrid particles; while their internalisation in B16 tumour cells produced mild cytotoxic effects and an antiproliferative cell cycle arrest in the G0/G1 and G2/M phases. The observed perturbation of the tumour cell line combined with the high degree of internalisation means that these (or similar) NPs@POM could serve as candidates for a range of bioapplications in diagnostics or therapy

Semiclassical Methods for Spectroscopic Calculations of High Dimensional Molecular Systems

I will present some novel semiclassical methods for spectroscopic calculations. These approaches can be employed for spectroscopic calculations of gas-phase molecular and supramolecular systems up to hundreds of degrees of freedom, as well as to condensed phase systems. Some methods are based on a \u201cdivide-and-conquer\u201d approach, where the full dimensional spectra are obtained as a composition of several lower dimensional ones. Others exploit hierarchically the different levels of accuracy of different semiclassical propagators. For instance, in a system-bath problem lower semiclassical accuracy is dedicated to the bath, while the system is treated with higher accuracy and the system spectrum is eventually singled out. All methods are amenable to ab initio molecular dynamics simulations. References 1. M. Micciarelli, R. Conte, J. Suarez, and M. Ceotto, JCP 149, 064115 (2018); 2. M. Buchholz, F. Grossmann, and M. Ceotto, JCP 148, 114107 (2018); 3. G. Di Liberto, R. Conte, and M. Ceotto, JCP 148, 104302 (2018); 4. G. Di Liberto, R. Conte, and M. Ceotto, JCP 148, 014307 (2018); 5. M. Buchholz, F. Grossmann, and M. Ceotto, JCP 147, 164110 (2017); 6. M. Ceotto, G. Di Liberto, and R. Conte, PRL 119, 010401 (2017); 7. F. Gabas, R. Conte, and M. Ceotto, JCTC 13, 2378-2388 (2017); 8. G. Di Liberto, M. Ceotto, JCP 145, 144107 (2016); 9. M. Buchholz, F. Grossmann, M. Ceotto, JCP 144, 094102 (2016)

Semiclassical Dynamics: A Viable Route to Molecular Spectroscopy

Reliable molecular spectroscopy simulations require an accurate quantum description of nuclear motion. Since purely quantum mechanical approaches are not affordable when dealing with high dimensional systems, an alternative path must be followed. Semiclassical methods have been demonstrated to provide a viable route to obtain quantum features starting from classical trajectories. Based on the time-averaged version of Miller\u2019s semiclassical initial value representation, we have developed new semiclassical techniques able to yield accurate vibrational spectra upon classical evolution of just a handful of trajectories. Our techniques can be interfaced to ab initio on-the-fly dynamics and can tackle problems involving hundreds of degrees of freedom by means of a divide-and-conquer strategy. We present some relevant applications that cover a large dimensionality range, going from ammonia (with tunneling splitting detection), to glycine (with a potential energy surface characterized by multiple shallow wells) and C 60 fullerene (a system made of 174 degrees of freedom)

Semiclassical Molecular Dynamics for Spectroscopic Calculations of Complex Systems

I will present some novel semiclassical methods for spectroscopic calculations. These approaches can be employed for spectroscopic calculations of gas-phase molecular and supramolecular systems up to hundreds of degrees of freedom, as well as to condensed phase systems. Some methods are based on a \u201cdivide-and-conquer\u201d approach, where the full dimensional spectra are obtained as a composition of several lower dimensional ones. Others exploit hierarchically the different levels of accuracy of different semiclassical propagators. For instance, in a system-bath problem lower semiclassical accuracy is dedicated to the bath, while the system is treated with higher accuracy and the system spectrum is eventually singled out. All methods are amenable for ab initio molecular dynamics simulations. References 1. F. Gabas, G. Di Liberto, R. Conte, and M. Ceotto, Chemical Science 9 (41), 7885-8026 (2018); 2. X. Ma, G. Di Liberto, R. Conte, W. L. Hase, and M. Ceotto, JCP 149, 164113 (2018) 3. M. Micciarelli, R. Conte, J. Suarez, and M. Ceotto, JCP 149, 064115 (2018); 4. M. Buchholz, F. Grossmann, and M. Ceotto, JCP 148, 114107 (2018); 5. G. Di Liberto, R. Conte, and M. Ceotto, JCP 148, 104302 (2018); 6. G. Di Liberto, R. Conte, and M. Ceotto, JCP 148, 014307 (2018); 7. M. Buchholz, F. Grossmann, and M. Ceotto, JCP 147, 164110 (2017); 8. M. Ceotto, G. Di Liberto, and R. Conte, PRL 119, 010401 (2017); 9. F. Gabas, R. Conte, and M. Ceotto, JCTC 13, 2378-2388 (2017); 10. G. Di Liberto, M. Ceotto, JCP 145, 144107 (2016); 11. M. Buchholz, F. Grossmann, M. Ceotto, JCP 144, 094102 (2016)