1,721,146 research outputs found
A General Purpose Implementations of Semiclassical Molecular Dynamics for CPU and GPU hardware
No full textThe calculation of the semiclassical propagator is a Monte Carlo integration over classical trajectories. This can be accelerated either by importance sampling or by parallelization of the phase space integration. In the first case, a multiple coherent states time-averaging [1] semiclassical initial value representation (MC-TA-SC-IVR) method for spectra calculations is presented.[2, 3] The method is implemented for ab initio semiclassical simulations, i.e. a direct dynamics approach, and it is shown to faithfully reproduce all kind of quantum effects, including ZPEs, anharmonicities, tunneling splittings,[4] resonances [5] and vibrational eigenfunctions.[6] This on-the-fly approach is useful in particular for complex systems,[7, 8] where the elaboration of a pre-computed potential energy surface can turn into a formidable task. In the second case, SC-IVR is implemented for GPUs hardware. [9] An almost constant scaling for GPU calculations versus a linear scaling for CPU ones is found respect to the number of trajectories. Issues and limitations related to the GPU implementation will be discussed.
[1] A. L. Kaledin and W. H. Miller, J. Chem. Phys. 118, 7174 (2003)
[2] M. Ceotto, S. Atahan, S. Shim, G. F. Tantardini, and A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 11, 3861 (2009)
[3] M. Ceotto, S. Atahan, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem. Phys. 130, 234113 (2009)
[4] R. Conte, A. Aspuru-Guzik, and M. Ceotto, J. Phys. Chem. Lett. 4, 3407-3412 (2013)
[5] M. Ceotto, D. Dell'Angelo, and G. F. Tantardini, J. Chem. Phys. 133, 054701 (2010)
[6] M. Ceotto, S. Valleau, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem Phys. 134, 234103 (2011)
[7] M. Ceotto, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem. Phys. 135, 214108 (2011)
[8] M. Ceotto, Y. Zhuang, and W.L. Hase, J. Chem. Phys. 138, 054116 (2013)
[9] D. Tamascelli, F. D'Ambrosio, R. Conte, and M. Ceotto, in progres
Ab initio direct semiclassical molecular dynamics
No full textA multiple coherent states time-averaging [1] semiclassical initial value representation (MC-TA-SC-IVR) method for spectra calculations is presented.[2, 3] The method is implemented for ab initio semiclassical simulations, i.e. a direct dynamics approach, and it is shown to faithfully reproduce all kind of quantum effects, including ZPEs, anharmonicities, tunneling splittings, resonances [4] and vibrational eigenfunctions.[5] This on-the-fly approach is useful in particular for complex systems,[5, 6] where the elaboration of a pre-computed potential energy surface can turn into a formidable task. I will show that the method can deal with molecules with multiple wells and as complex as glycine.
[1] A. L. Kaledin and W. H. Miller, J. Chem. Phys. 118, 7174 (2003)
[2] M. Ceotto, S. Atahan, S. Shim, G. F. Tantardini, and A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 11, 3861 (2009)
[3] M. Ceotto, S. Atahan, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem. Phys. 130, 234113 (2009)
[4] M. Ceotto, D. Dell'Angelo, and G. F. Tantardini, J. Chem. Phys. 133, 054701 (2010)
[5] M. Ceotto, S. Valleau, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem Phys. 134, 234103 (2011)
[6] M. Ceotto, G. F. Tantardini, and A. Aspuru-Guzik, J. Chem. Phys. 135, 214108 (2011)
[7] M. Ceotto, Y. Zhuang, and W.L. Hase, J. Chem. Phys. 138, 054116 (2013
Accurate and efficient pre-exponential factor approximations for the semiclassical initial value representation propagator
Full text linkThe semiclassical (SC) theory[1,2] is a very powerful tool to describe molecular reactivity, electronic transitions and molecular vibrations.[3-9] In semiclassical methods quantum informations are obtained by evolving classical trajectories. This is computationally less intense than grid methods. Unfortunately, when the system is complex, the calculation of the SC Herman-Kluk (HK) prefactor[10] is prohibitive, due to the trajectories' instability.[11] For this reason, it is not possible to employ the basic SC-HK approach for large systems. In the past years, several approximations to the HK prefactor have been proposed[12,13] to solve this issue, but they have never been thoroughly assessed.
In this work, first we test some of the most common prefactor approximations on small systems. Then, we put forward a new one starting from the Log-Derivative[13] formulation, and that is potentially suitable for bigger systems. This approximation depends only on the Hessian matrix and does not require the calculation of the monodromy matrix elements, which are often unstable. As a consequence, even chaotic trajectories can be employed for vibrational spectra simulations. The results show that our approximation is very reliable for molecules like H2, H2O, CO2, CH2O, CH4 and CH2D2. Future applications of our new prefactor will concern the evaluation of power spectra of large systems, for which quantum calculations are currently out of reach.
References
[1] W.H. Miller J. Phys. Chem. A 105, 2942 (2001).
[2] W.H. Miller Proc. Natl. Acad. Sci. USA 102, 6660 (2005).
[3] M. Ceotto, S. Atahan, S. Shim, G.F. Tantardini, and A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 11, 3861 (2009).
[4] M. Ceotto, S. Atahan, G.F Tantardini, A. Aspuru-Guzik., J. Chem. Phys. 130, 234113 (2009).
[5] M. Ceotto, D. Dell'Angelo, G.F Tantardini, J. Chem. Phys. 133 (5), 054701 (2010).
[6] M. Ceotto, G.F. Tantardini, and A. Aspuru-Guzik, J. Chem. Phys. 135, 214108 (2011).
[7] R. Conte, A. Aspuru-Guzik, M. Ceotto J. Phys. Chem. Lett., 4, 3407 (2013).
[8] D. Tamascelli, F.S. Dambrosio, R. Conte, M. Ceotto J. Chem Phys., 140, 174109 (2014).
[9] M.L. Brewer, J.S. Hulme, and D.E. Manolopoulos J. Chem. Phys. 106, 4832 (1997).
[10] M.F. Herman, E. Kluk Chem. Phys. 91, 27 (1984).
[11] K.G. Kay J. Chem. Phys. 101, 2250 (1994).
[12] V. Guallar, V.S. Batista, and W.H. Miller J. Chem. Phys. 110, 9922 (1999).
[13] R. Gelabert, X. Gimenez, M. Thoss, H. Wang, and W.H. Miller J. Phys. Chem. A, 104, 10321 (2000)
Quantum nuclear densities from semiclassical on-the-fly molecular dynamics
No full textSemiclassical molecular dynamics is a rigorous approximation to quantum dynamics obtained from the exact quantum propagator expressed as Feynman’s path integral.[1] Recently, our group has introduced the Multiple Coherent Semiclassical Initial Value Representation (MC SCIVR) technique to reduce the number of classical trajectories required to converge vibrational spectra calculations from thousands to just a handful.[2-4] MC SCIVR has been applied successfully to several medium- and large-size molecular systems,[4-10] including fluxional and condensed phase ones.[11-13] In addition to the accurate anharmonic vibrational eigenvalue calculations, MC SCIVR yields vibrational eigenfunctions for both the ground and excited vibrational states.[14] In this talk, I will survey how we obtain the quantum anharmonic vibrational eigenfunctions from ab-initio on-the-fly trajectory simulations and how we extract the quantum nuclear densities and the geometry parameters probability distributions.[15,16] This information allows us to assign each peak in vibrational spectra, going beyond the usual harmonic normal-mode analysis. Our technique quantitatively determines how normal modes involving different functional groups cooperate to originate the spectroscopic signal. Furthermore, it allows for the visualization of the nuclear vibrations in a purely quantum picture, letting us both directly observe and quantify the effects of the full potential energy surface anharmonicity on the molecular structure. In particular, I will illustrate applications to the protonated glycine to reveal quantum mechanical and anharmonic vibrational features. The method will allow for a better rationalization of experimental spectroscopy.
[1] W.H. Miller, J. Phys. Chem. A 2001, 105, 2942.
[2] M. Ceotto, S. Atahan, S. Shim, G.F. Tantardini, A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 2009, 11, 3861.
[3] M. Ceotto, S. Atahan, G.F. Tantardini, A. Aspuru-Guzik J. Chem. Phys. 2009, 130, 234113.
[4] R. Conte, M. Ceotto, In Quantum Chemistry and Dynamics of Excited States: Methods and Applications (eds L. González and R. Lindh) 2020.
[5] M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett. 2017, 119, 010401.
[6] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2017, 13, 2378.
[7] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 014307.
[8] F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci. 2018, 9, 7894.
[9] F. Gabas, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 150, 224107.
[10] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2020, 16, 3476.
[11] G. Bertaina, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 151, 114307.
[12] A. Rognoni, R. Conte, M. Ceotto, Chem. Sci., 2021, 12, 2060.
[13] M. Cazzaniga, M. Micciarelli, F. Moriggi, A. Mahmoud, F. Gabas, and M. Ceotto, J. Chem. Phys. 2020, 152, 104104.
[14] M. Micciarelli, R. Conte, J. Suarez, M. Ceotto, J. Chem. Phys. 2018 149, 064115.
[15] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun 2020, 11, 1.
[16] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, J. Chem. Phys., 2020, 153, 214117
Quantum nuclear densities from semiclassical on-the-fly molecular dynamics
No full textSemiclassical molecular dynamics is a rigorous approximation to quantum dynamics obtained from the exact quantum propagator expressed as Feynman’s path integral.[1] Recently, our group has introduced the Multiple Coherent Semiclassical Initial Value Representation (MC SCIVR) technique to reduce the number of classical trajectories required to converge vibrational spectra calculations from thousands to just a handful.[2-4] MC SCIVR has been applied successfully to several medium and large-size molecular systems,[4-10] including fluxional and condensed phase ones.[11-13] In addition to the accurate anharmonic vibrational eigenvalue calculations, MC SCIVR yields vibrational eigenfunctions for both the ground and excited vibrational states.[14] In this talk, I will survey how we obtain the quantum anharmonic vibrational eigenfunctions from ab-initio on-the-fly trajectory simulations and how we extract the quantum nuclear densities and the geometry parameters probability distributions.[15,16] This information allows us to assign each peak in vibrational spectra, going beyond the usual harmonic normal-mode analysis. Our technique quantitatively determines how normal modes involving different functional groups cooperate to originate the spectroscopic
signal. Furthermore, it allows for the visualization of the nuclear vibrations in a purely quantum picture, letting us both directly observe and quantify the effects of the full potential energy surface anharmonicity on the molecular structure. In particular, I will illustrate applications to the protonated glycine to reveal quantum mechanical and anharmonic vibrational features. The method will allow for a better rationalization of experimental spectroscopy.
[1] W.H. Miller, J. Phys. Chem. A 2001, 105, 2942.
[2] M. Ceotto, S. Atahan, S. Shim, G.F. Tantardini, A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 2009, 11, 3861.
[3] M. Ceotto, S. Atahan, G.F. Tantardini, A. Aspuru-Guzik J. Chem. Phys. 2009, 130, 234113.
[4] R. Conte, M. Ceotto, In Quantum Chemistry and Dynamics of Excited States: Methods and Applications (eds L. González and R. Lindh) 2020.
[5] M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett. 2017, 119, 010401.
[6] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2017, 13, 2378.
[7] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 014307.
[8] F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci. 2018, 9, 7894.
[9] F. Gabas, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 150, 224107.
[10] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2020, 16, 3476.
[11] G. Bertaina, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 151, 114307.
[12] A. Rognoni, R. Conte, M. Ceotto, Chem. Sci., 2021, 12, 2060.
[13] M. Cazzaniga, M. Micciarelli, F. Moriggi, A. Mahmoud, F. Gabas, and M. Ceotto, J. Chem. Phys. 2020, 152, 104104.
[14] M. Micciarelli, R. Conte, J. Suarez, M. Ceotto, J. Chem. Phys. 2018 149, 064115.
[15] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun 2020, 11, 1.
[16] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, J. Chem. Phys., 2020, 153, 214117
Semiclassical vibrational spectroscopy : the importance of quantum anharmonicity in supra-molecular systems
Full text linkSemiclassical (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
A quantum approximate method for the calculation of thermal reaction rate constants
No full textThe calculation of thermal reaction rate constants is a central problem in theoretical chemistry, and exact classical and quantum expressions have been formulated [1]. However, approximate approaches are necessary when dealing with complex reactions, and several techniques have been developed in recent years. They include the inclusion of quantum corrections to the classical transition state theory (TST) [2], semiclassical theories [3], and ring polymer molecular dynamics (RPMD) TST [4].
In this work, we have developed a new quantum mechanical method to compute reaction rate constants, which is related to Miller's quantum instanton [5]. Starting from the exact definition of the thermal rate constant as the time integral of the quantum flux-flux correlation function, upon introduction of a stationary phase approximation, we have derived an expression which has the same structure of the original quantum instanton but includes a contribution from real-time dynamics. This new method has been tested on the one-dimensional Eckart barrier problem, and on the two-dimensional H+H2 collinear reaction. Results over a wide range of temperatures have been found to be in agreement within 10% with exact quantum mechanical estimates.
[1] W.H. Miller, S.D. Schwartz, J.W. Tromp, J. Chem. Phys. 79, 4889 (1983); W.H. Miller, J. Phys. Chem. A 102 (5), 793, (1998)
[2] H. Eyring J. Chem. Phys. 3 (1935), p. 107; E. Wigner J. Chem. Phys, 5 (1937), p. 720
[3] W.H. Miller, J. Chem. Phys, 62, 1899 (1975); R. Hernandez, W.H. Miller Chem. Phys. Lett., 214 (1993), p. 129; T. L. Nguyen, J. F. Stanton, and J. R. Barker, Chem. Phys. Lett. 499, 9 (2010).
[4] J. O. Richardson and S. C. Althorpe, J. Chem. Phys. 131, 214106 (2009); T. J. H. Hele and S. C. Althorpe J. Chem. Phys. 138, 084108 (2013)
[5] W.H. Miller, Y. Zhao, M. Ceotto, S. Yang J. Chem. Phys. 119, 1329 (2003); M. Ceotto, S. Yang, and W.H. Miller J. Chem. Phys. 122, 044109 (2005
A quantum approximate method for the calculation of thermal reaction rate constants
No full textThe calculation of thermal reaction rate constants is a central problem in theoretical chemistry, and exact classical and quantum expressions have been formulated [1]. However, approximate approaches are necessary when dealing with complex reactions, and several techniques have been developed in recent years. They include the inclusion of quantum corrections to the classical transition state theory (TST) [2], semiclassical theories [3], and ring polymer molecular dynamics (RPMD) TST [4].
In this work, we have developed a new quantum mechanical method to compute reaction rate constants, which is related to Miller's quantum instanton [5]. Starting from the exact definition of the thermal rate constant as the time integral of the quantum flux-flux correlation function, upon introduction of a stationary phase approximation, we have derived an expression which has the same structure of the original quantum instanton but includes a contribution from real-time dynamics. This new method has been tested on the one-dimensional Eckart barrier problem, and on the two-dimensional H+H2 collinear reaction. Results over a wide range of temperatures have been found to be in agreement within 10% with exact quantum mechanical estimates.
References
[1] W.H. Miller, S.D. Schwartz, J.W. Tromp, J. Chem. Phys. 79 4889 (1983); W.H. Miller, J. Phys. Chem. A 102 793 (1998)
[2] H. Eyring J. Chem. Phys. 3 107 (1935); E. Wigner J. Chem. Phys, 5 720 (1937)
[3] W.H. Miller, J. Chem. Phys, 62 1899 (1975); R. Hernandez, W.H. Miller Chem. Phys. Lett., 214 129 (1993); T.L. Nguyen, J.F. Stanton, and J.R. Barker, Chem. Phys. Lett. 499 9 (2010).
[4] J.O. Richardson and S.C. Althorpe, J. Chem. Phys. 131 214106 (2009); T.J.H. Hele and S.C. Althorpe J. Chem. Phys. 138 084108 (2013)
[5] W.H. Miller, Y. Zhao, M. Ceotto, S. Yang J. Chem. Phys. 119 1329 (2003); M. Ceotto, S. Yang, and W.H. Miller J. Chem. Phys. 122 044109 (2005
A Time Averaged Semiclassical Approach to IR Spectroscopy
Full text linkSemiclassical vibrational spectroscopy is based on the evolution of classical trajectories and is able to reproduce quantum effects with good accuracy at the cost of a reasonable computational effort. [1-5] Nevertheless, semiclassical vibrational power spectra do not simulate all the features of the experimental IR spectra, since intensities in power spectra are not directly related to IR absorptions. Therefore, we
developed a new semiclassical approach to the calculation of molecular IR spectra by employing the time average technique upon symmetrization of the quantum dipole-dipole autocorrelation function. [6,7] We tested the accuracy of this new method on a few simple analytical systems and small molecules in the gas phase. In particular, spectra in the limit of infinite or zero temperature were investigated. Overall the method features excellent accuracy in calculating absorption intensities and provides estimates for the frequencies of vibrations in agreement with the corresponding power spectra.
[1] R. Conte, A. Aspuru-Guzik, and M. Ceotto, J. Phys. Chem. Lett. 4, 3407 (2013).
[2] G. Bertaina, G. Di Liberto, and M. Ceotto, J. Chem. Phys. 151, 114307 (2019).
[3] C. Aieta, M. Micciarelli, G. Bertaina, and M. Ceotto, Nat. Comm. 11, 4384 (2020).
[4] A. Rognoni, R. Conte, and M. Ceotto, Chem. Sci. 12, 2060 (2021).
[5] R. Conte, C. Aieta, G. Botti, M. Cazzaniga, M. Gandolfi, C. Lanzi, G. Mandelli, D. Moscato, and M. Ceotto, Theor. Chem. Acc. 142, 53 (2023).
[6] A. L. Kaledin and W. H. Miller, J. Chem. Phys. 118, 7174 (2003).
[7] A. L. Kaledin and W. H. Miller, J. Chem. Phys. 119, 3078 (2003)
Semiclassical reaction rate constant calculations: investigation of anharmonicity and quantum effects
Full text linkSemiclassical transition state theory (SCTST) is a relatively simple method for the computation from first principles of reactive rate constants, including quantum effects while accounting for anharmonicity and the coupling between reactive and bound modes.[1-3] In this talk, I will illustrate how we have developed this technique for practical applications[4-7] involving the study of phenomena like kinetic isotope effects, heavy atom tunneling, and elusive conformer lifetimes.[5,6,8]
While many approximate reaction rate theories reduce to the parabolic barrier estimate for the tunneling correction at high temperatures, SCTST, which is based on vibrational perturbation theory (VPT2), gives the exact limit when one considers the leading order term in an expansion of powers of ħ2 of the tunneling transmission coefficient.[9-11] Our investigation of molecular reactive systems assesses the importance of the non-linear corrections to the parabolic barrier estimate of the transmission coefficient. When the reaction barrier is significantly anharmonic, it is mandatory to account for non-linear corrections; otherwise, the transmission coefficient overlooks a high-temperature regime which may be dominated by quantum reflection.[12] These results highlight the importance of having a theory such as SCTST that includes the correct high-temperature limit.
[1] W.H. Miller Faraday Discuss. Chem. Soc. 62, 40 (1977).
[2] W.H. Miller J. Chem. Phys. 62, 1899 (1975)
[3] R. Hernandez et al., Chem. Phys. Lett. 214, 129 (1993).
[4] C. Aieta, F. Gabas, M. Ceotto, J. Phys. Chem. A 120, 4853 (2016).
[5] C. Aieta F. Gabas, M. Ceotto, J. Chem. Theory Comput. 15, 2142 (2019).
[6] G. Mandelli, C. Aieta, M. Ceotto J. Chem. Theory Comput. 18, 623 (2022).
[7] J.R. Barker, MultiWell-2023 software suite; University of Michigan: Ann Arbor, Michigan, USA, 2023; http://clasp-research.engin.umich.edu/multiwell/
[8] G. Mandelli, L. Corneo, C. Aieta J. Phys. Chem. Lett. 14, 9996 (2023).
[9] E. Pollak, J. Cao, Phys. Rev. A, 107, 022203 (2023).
[10] E. Pollak, S Upadhyayula J. Chem. Phys. 160, (2024).
[11] E. Pollak J. Chem. Phys. 160, 150902 (2024).
[12] C. Aieta, M. Ceotto, E. Pollak, in preparation
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