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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
QUANTUM AND SEMICLASSICAL METHODS FOR RATE CONSTANT CALCULATIONS
Full text linkChemical reactions are intrinsically dynamical processes. Reaction rate constants, and thus the understanding of chemical kinetics, can be in principle obtained at a very detailed level if one is able to compute the real time quantum dynamics for the reactive system. Unfortunately, the numerical implementation of real time quantum dynamics is very hard to perform, especially for high dimensional systems, because the computational effort scales exponentially with the number of degrees of freedom.
In this Ph.D. thesis, two open problems in reaction rate theory have been addressed. The first one is to extend to high dimensional systems the inclusion of quantum effects in rate constant computations. The second issue deal with the inclusion of real time dynamics into very accurate rate constants calculations.
The thesis is organized as follows. After a general Introduction, the second chapter is an overview of the state of the art in reaction rate theory. Then, in the third chapter, the derivation of Miller's Semiclassical Transition State Theory (SCTST) is recalled. SCTST is the method employed to obtain accurate and quantum-corrected rate constants for high dimensional reactions. In chapter 4, a novel parallel implementation of this theory (that has also been released as an open source code into J. R. Barker's MultiWell suite of codes) is described together with its application to high dimensional systems. In the following chapters, a new quantum rate approach able to include real time dynamics effects is presented. Derivation and applications of the latter are thoroughly described in chapter 6. The thesis ends with some perspectives about possible future developments
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
Semiclassical investigation of nuclear quantum effects in chemical kinetics and vibrational spectroscopy
Full text linkNuclear Quantum Effects (NQE) manifest in chemistry in both kinetics and spectroscopy fields. Accounting for the Zero Point Energy (ZPE) and tunneling phenomena can explain unexpected experimental observations of reaction rate constants.[1,2] Also, in spectroscopy, some spectral features, such as signal splittings or shifts, are due to tunneling phenomena or quantum delocalization (or localization), which cause the system to sample the potential energy surface in a non-classical way.[3,4] Rigorous but at the same time, affordable methods to include NQE in atomistic simulations must be developed to predict and explain experimental quantum mechanical hallmarks. This talk will describe semiclassical approaches for kinetics and spectroscopic applications. Specifically, the Semiclassical Transition State Theory (SCTST) can include tunneling and ZPE effects at a higher level of theory than widespread tunneling corrections for classical TST rate calculations.[5-7] Then, the Semiclassical Initial Value Representation Molecular Dynamics (SC-IVR-MD) can predict accurate vibrational spectra and even reproduce vibrational quantum eigenfunctions.[9,10] Thus, the SC-IVR-MD technique can reproduce the quantum mechanical sampling of the potential energy surface, fixing purely classical MD vibrational spectroscopy pitfalls.[11]
References
[1]J. Meisner, J. Kästner, Angew. Chem. Int. Ed., 55, 5400-5413 (2016)
[2]P. Schreiner, Trends in Chemistry, 2, 980-989 (2020)
[3]F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci., 9, 7894-7901 (2018)
[4]R. Conte, A. Aspuru-Guzik, M. Ceotto, J. Phys. Chem. Lett., 4, 3407-3412 (2013)
[5]W. Miller, R. Hernandez, N. Handy, D. Jayatilaka, A. Willetts, Chemical Physics Letters, 172, 62-68 (1990)
[6]C. Aieta, F. Gabas, M. Ceotto, J. Phys. Chem. A, 120, 4853-4862 (2016)
[7]C. Aieta, F. Gabas, M. Ceotto, J. Chem. Theory Comput., 15, 2142-2153 (2019)
[8]G. Mandelli, C. Aieta, M. Ceotto, J. Chem. Theory Comput., 18, 623-637 (2022)
[9]C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun., 11, 4348 (2020)
[10]C. Aieta, G. Bertaina, M. Micciarelli, M. Ceotto, The Journal of Chemical Physics, 153, (2020)
[11]R. Conte, C. Aieta, G. Botti, M. Cazzaniga, M. Gandolfi, C. Lanzi, G. Mandelli, D. Moscato, M. Ceotto, Theor. Chem. Acc., 142, 53 (2023
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
An Efficient Computational Approach for the Calculation of the Vibrational Density of States
Full text linkWe present an optimized approach
for the calculation of the density
of fully coupled vibrational states in high-dimensional systems. This
task is of paramount importance, because partition functions and several
thermodynamic properties can be accurately estimated once the density
of states is known. A new code, called paradensum, based on the implementation
of the Wang–Landau Monte Carlo algorithm for parallel architectures
is described and applied to real complex systems. We test the accuracy
of paradensum on several molecular systems, including some benchmarks
for which an exact evaluation of the vibrational density of states
is doable by direct counting. In addition, we find a significant computational
speedup with respect to standard approaches when applying our code
to molecules up to 66 degrees of freedom. The new code can easily
handle 150 degrees of freedom. These features make paradensum a very
promising tool for future calculations of thermodynamic properties
and thermal rate constants of complex systems
The complex vibrational spectrum of proline explained through the adiabatically switched semiclassical initial value representation
Full text linkProline, a 17-atom amino acid with a closed-ring side chain, has a complex potential energy surface characterized by several minima. Its IR experimental spectrum, reported in the literature, is of difficult and controversial assignment. In particular, the experimental signal at 3559 cm −1 associated with the OH stretch is interesting because it is inconsistent with the global minimum, trans-proline conformer. This suggests the possibility that multiple conformers may contribute to the IR spectrum. The same conclusion is obtained by investigating the splitting of the CO stretch at 1766 and 1789 cm−1 and other, more complex spectroscopic features involving CH stretches and COH/CNH bendings. In this work, we perform full-dimensional, on-the-fly adiabatically switched semiclassical initial value representation simulations employing the ab initio dft-d3-B3LYP level of theory with aug-cc-pVDZ basis set.
We reconstruct the experimental spectrum of proline in its main features by studying the vibrational features of trans-proline and cis1 -proline, and provide a new assignment for the OH stretch of trans-proline
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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