scholarly journals Optical Spectra in the Condensed Phase: Capturing Anharmonic and Vibronic Features Using Dynamic and Static Approaches

2019 ◽  
Author(s):  
Tim Zuehlsdorff ◽  
Andres Montoya-Castillo ◽  
Joseph Anthony Napoli ◽  
Thomas E. Markland ◽  
Christine Isborn
Keyword(s):  
Condensed Phase ◽  
Potential Energy Surfaces ◽  
Energy Gap ◽  
Time Correlation ◽  
Optical Spectra ◽  
Ab Initio Molecular Dynamics ◽  
Classical Dynamics ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Franck Condon

<p>Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and their induced asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic timescale separation; the Franck-Condon method, which includes dynamical effects but only at the harmonic level; as well as the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.<br></p>

scholarly journals Optical Spectra in the Condensed Phase: Capturing Anharmonic and Vibronic Features Using Dynamic and Static Approaches

2019 ◽  
Author(s):  
Tim Zuehlsdorff ◽  
Andres Montoya-Castillo ◽  
Joseph Anthony Napoli ◽  
Thomas E. Markland ◽  
Christine Isborn
Keyword(s):  
Condensed Phase ◽  
Potential Energy Surfaces ◽  
Energy Gap ◽  
Time Correlation ◽  
Optical Spectra ◽  
Ab Initio Molecular Dynamics ◽  
Classical Dynamics ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Franck Condon

<p>Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and their induced asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic timescale separation; the Franck-Condon method, which includes dynamical effects but only at the harmonic level; as well as the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.<br></p>

Quantum simulations

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Ab Initio ◽  
Quantum Monte Carlo ◽  
Degrees Of Freedom ◽  
Small Region ◽  
Time Correlation ◽  
Ab Initio Molecular Dynamics ◽  
Classical Dynamics ◽  
Integral Methods ◽  
Quantum Time ◽  
Low Mass

This chapter covers the introduction of quantum mechanics into computer simulation methods. The chapter begins by explaining how electronic degrees of freedom may be handled in an ab initio fashion and how the resulting forces are included in the classical dynamics of the nuclei. The technique for combining the ab initio molecular dynamics of a small region, with classical dynamics or molecular mechanics applied to the surrounding environment, is explained. There is a section on handling quantum degrees of freedom, such as low-mass nuclei, by discretized path integral methods, complete with practical code examples. The problem of calculating quantum time correlation functions is addressed. Ground-state quantum Monte Carlo methods are explained, and the chapter concludes with a forward look to the future development of such techniques particularly to systems that include excited electronic states.

THEORETICAL TRANSITION PROBABILITIES FOR THE $\tilde{A}^{2}A_{1} -\tilde{X}^{2}B_{1}$ SYSTEM OF H2O+ AND D2O+ AND RELATED FRANCK–CONDON FACTORS BASED ON GLOBAL POTENTIAL ENERGY SURFACES

2005 ◽  
Vol 04 (01) ◽  
pp. 225-245 ◽  
Author(s):  
IKUO TOKUE ◽  
KATSUYOSHI YAMASAKI ◽  
SATOSHI MINAMINO ◽  
SHINKOH NANBU
Keyword(s):  
Potential Energy ◽  
Photoelectron Spectroscopy ◽  
Potential Energy Surfaces ◽  
Least Squares Method ◽  
Transition Probabilities ◽  
Three Dimensional ◽  
Equilibrium Geometry ◽  
Condon Factors ◽  
Energy Surfaces ◽  
Franck Condon

To elucidate the ionization dynamics, in particular the vibrational distribution, of H 2 O +(Ã) produced by photoionization and the Penning ionization of H 2 O and D 2 O with He *(2 3S) atoms, Franck–Condon factors (FCFs) were given for the [Formula: see text] ionization, and the transition probabilities were presented for the [Formula: see text] emission. The FCFs were obtained by quantum vibrational calculations using the three-dimensional potential energy surfaces (PESs) of [Formula: see text] and [Formula: see text] electronic states. The global PESs were determined by the multi-reference configuration interaction calculations with the Davidson correction and the interpolant moving least squares method combined with the Shepard interpolation. The obtained FCFs exhibit that the [Formula: see text] state primarily populates the vibrational ground state, as its equilibrium geometry is almost equal to that of [Formula: see text], while the bending mode (ν2) is strongly enhanced for the H 2 O +(Ã) state; the maximums in the population of H 2 O + and D 2 O + are approximately v2 = 11–12 and 15–17, respectively. These results are consistent with the distributions observed by photoelectron spectroscopy. Transition probabilities for the [Formula: see text] system of H 2 O + and D 2 O + show that the bending progressions consist primarily of the [Formula: see text] emission, with combination bands from the (1, v′2 = 4–8, 0) level being next most important.

scholarly journals Energetic Self-Folding Mechanism in α-Helixes

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Reasonable Agreement ◽  
Dihedral Angles ◽  
Native Conformation ◽  
Experimental Values ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Large Peptide

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues towards the α<sub>R </sub>conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation, or zipper models, and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.

Empirical Potential-Energy Surfaces Fitting Using Feed forward Neural Networks

2012 ◽  
Author(s):  
Lionel Raff ◽  
Ranga Komanduri ◽  
Martin Hagan ◽  
Satish Bukkapatnam
Keyword(s):  
Potential Energy ◽  
Ab Initio ◽  
Potential Energy Surfaces ◽  
Force Fields ◽  
Pair Potential ◽  
Potential Surfaces ◽  
Empirical Potential ◽  
Functional Forms ◽  
Dynamics Simulations ◽  
Energy Surfaces

When the system of interest becomes too complex to permit the use of ab initio methods to obtain the system potential-energy surfaces (PES), empirical potential surfaces are frequently employed to represent the force fields present in the system under investigation. In most cases, the functional forms present in these potentials are selected on the basis of chemical and physical intuitions. The parameters of the surface are frequently adjusted to fit a very small set of experimental data that comprise bond energies, equilibrium bond distances and angles, fundamental vibrational frequencies, and perhaps measured barrier heights to reactions of interest. Such potentials generally yield only qualitative or semiquantitative descriptions of the system dynamics. Several research groups have significantly improved the accuracy of the values of the experimental properties computed using empirical potential surfaces by fitting the chosen functional form for the potential to the force fields obtained from trajectories using ab initio Car-Parrinello molecular dynamics simulations. The fitting to the force fields is usually done using a least-squares fitting approach. This method has been employed by Izvekov et al. to obtain effective non-polarizable three-site force fields for liquid water. Carré et al. have employed such a procedure to obtain a new pair potential for silica. In their investigation, the vector of potential parameters was fitted using an iterative Levenberg-Marquardt algorithm. Tangney and Scandolo have also developed an interatomic force field for liquid SiO2 in which the parameters were fitted to the forces, stresses, and energies obtained from ab initio calculations. Ercolessi and Adams have used a quasi-Newtonian procedure to fit an empirical potential for aluminum to data obtained from first-principals computations. Empirical potentials can be improved by making the parameters parameterized functions of the coordinates defining the instantaneous positions of the atoms of the system. This approach has been successfully employed by numerous investigators The difficulty with this procedure is that the number of parameters that must be adjusted increases rapidly. Appropriate fitting of these parameters requires a much more extensive database. Finally, the actual fitting process can often be tedious, difficult, and time-consuming.

scholarly journals Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Aik Rui Tan ◽  
Rafael Gómez-Bombarelli
Keyword(s):  
Potential Energy Surfaces ◽  
Automatic Differentiation ◽  
Ground Truth ◽  
Training Data ◽  
Interatomic Potentials ◽  
Collective Variables ◽  
Molecule Interactions ◽  
Dynamics Simulations ◽  
Fast Prediction ◽  
Energy Surfaces

AbstractNeural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification methods can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined with an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers, collective variables in molecules, and supramolecular chemistry in zeolite-molecule interactions, and can be extended to any NN potential architecture and materials system.

Classical dynamics calculations for the F+H2→HF+H reaction on two recent potential energy surfaces

1994 ◽  
Vol 218 (5-6) ◽  
pp. 422-432 ◽  
Author(s):  
F.J. Aoiz ◽  
L. Ban˜ares ◽  
V.J. Herrero ◽  
V. Sa´ez Ra´banos
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Classical Dynamics ◽  
Energy Surfaces

scholarly journals Nonadiabatic Dynamics in Multidimensional Complex Potential Energy Surfaces

2020 ◽  
Author(s):  
Fábris Kossoski ◽  
Mario Barbatti
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Electron Attachment ◽  
Complex Surface ◽  
Nonadiabatic Dynamics ◽  
Surface Hopping ◽  
Molecular Systems ◽  
Out Of Plane ◽  
Dynamics Simulations ◽  
Energy Surfaces

<p>Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the p*/s* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the p* orbital promotes C=C stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the s* orbital at the C-I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic Coulombic decay, and time-dependent luminescence.</p>

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