Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions

Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network

Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computational costs of QM methods. In order to overcome these two difficulties, here we developed the residue-based systematic molecular fragmentation method to partition general proteins into only 20 types of amino acid dipeptides and one type of peptide bond at level 1. The total energy of proteins is the combination of the energies of these fragments. Each type of the fragments is then parametrized using neural network (NN) representation of the QM reference. Adopting NN representation can circumvent the limitation of the analytic form of classical molecular mechanics (MM) force fields. Using MM force fields as the baseline, our method adds NN representation of QM corrections at the length scale of amino acid dipeptides. We tested our force fields for both homogeneous and heterogeneous polypeptides. Energy and forces predicted by our force fields compare favorably with full QM calculations from tripeptides to decapeptides. Our development provides an efficient and accurate method of building protein force fields fully from ab initio QM calculations.

Representation of coupled adiabatic potential energy surfaces using neural network based quasi-diabatic Hamiltonians: 1,2 2A′ states of LiFH

A general algorithm for determining diabatic representations from adiabatic energies, energy gradients and derivative couplings using neural networks is introduced.

Vibrational control of selective bond cleavage in dissociative chemisorption of methanol on Cu(111)

Controlling product branching ratios in a chemical reaction represents a desired but difficult achievement in chemistry. In this work, we demonstrate the first example of altering the branching ratios in a multichannel reaction, i.e., methanol dissociative chemisorption on Cu(111), via selectively exciting specific vibrational modes. To this end, we develop a globally accurate full-dimensional potential energy surface for the CH3OH/Cu(111) system and perform extensive vibrational state-selected molecular dynamics simulations. Our results show that O-H/C-H/C-O stretching vibrational excitations substantially enhance the respective bond scission processes, representing extraordinary bond selectivity. At a given total energy, the branching ratio of C-O/C-H dissociation can increase by as large as 100 times by exciting the C-O stretching mode which possesses an unprecedentedly strong vibrational efficacy on reactivity. This vibrational control can be realized by the well-designed experiment using a linearly polarized laser.

Force Field for Water Based on Neural Network

We developed a novel neural network-based force field for water based on training with high-level ab initio theory. The force field was built based on an electrostatically embedded many-body expansion method truncated at binary interactions. The many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: nonpolarizable and polarizable force fields. Simulation results show that the nonpolarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build next-generation force fields at high accuracy and low computational costs, especially for large systems.

Dissociative Chemisorption of O2 on Al(111): Dynamics on a Correlated Wave-Function-Based Potential Energy Surface

Dissociative chemisorption of O₂ on the Al(111) surface represents an extensively studied prototype for understanding the interaction between O₂ and metal surfaces. It is well known that the experimentally observed activation barrier for O₂ dissociation is not captured by conventional density functional theory. The interpretation of this barrier as a result of spin transitions along the reaction path has been challenged by recent embedded correlated wave function (ECW) calculations that naturally yield an adiabatic barrier. However, the ECW calculations have been limited to a static analysis of the reaction pathways and have not yet been tested by dynamics simulations. We present a global six-dimensional potential energy surface (PES) for this system parametrized with ECW data points. This new PES provides a reasonable description of the site-specific and orientation-dependent activation barriers. Quasi-classical trajectory calculations on this PES semiquantitatively reproduce both the observed translational energy dependence of the sticking probability and steric effects with aligned O₂ molecules.

"Divide and conquer" semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

We extensively describe our recently established "divide-and-conquer" semiclassical method [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)] and propose a new implementation of it to increase the accuracy of results. The technique permits us to perform spectroscopic calculations of high-dimensional systems by dividing the full-dimensional problem into a set of smaller dimensional ones. The partition procedure, originally based on a dynamical analysis of the Hessian matrix, is here more rigorously achieved through a hierarchical subspace-separation criterion based on Liouville's theorem. Comparisons of calculated vibrational frequencies to exact quantum ones for a set of molecules including benzene show that the new implementation performs better than the original one and that, on average, the loss in accuracy with respect to full-dimensional semiclassical calculations is reduced to only 10 wavenumbers. Furthermore, by investigating the challenging Zundel cation, we also demonstrate that the "divide-and-conquer" approach allows us to deal with complex strongly anharmonic molecular systems. Overall the method very much helps the assignment and physical interpretation of experimental IR spectra by providing accurate vibrational fundamentals and overtones decomposed into reduced dimensionality spectra.

Tracking the energy flow in the hydrogen exchange reaction OH + H2O → H2O + OH

The prototypical hydrogen exchange reaction OH + H2O → H2O + OH has attracted considerable interest due to its importance in a wide range of chemically active environments. In this work, an accurate global potential energy surface (PES) for the ground electronic state was developed based on ∼44 000 ab initio points at the level of UCCSD(T)-F12a/aug-cc-pVTZ. The PES was fitted using the fundamental invariant-neural network method with a root mean squared error of 4.37 meV. The mode specific dynamics was then studied by the quasi-classical trajectory method on the PES. Furthermore, the normal mode analysis approach was employed to calculate the final vibrational state distribution of the product H2O, in which a new scheme to acquire the Cartesian coordinates and momenta of each atom in the product molecule from the trajectories was proposed. It was found that, on one hand, excitation of either the symmetric stretching mode or the asymmetric stretching mode of the reactant H2O promotes the reaction more than the translational energy, which can be rationalized by the sudden vector projection model. On the other hand, the relatively higher efficacy of exciting the symmetric stretching mode than that of the asymmetric stretching mode is caused by the prevalence of the indirect mechanism at low collision energies and the stripping mechanism at high collision energies. In addition, the initial collision energy turns ineffectively into the vibrational energy of the products H2O and OH while a fraction of the energy transforms into the rotational energy of the product H2O. Fundamental excitation of the stretching modes of H2O results in the product H2O having the highest population in the fundamental state of the asymmetric stretching mode, followed by the ground state and the fundamental state of the symmetric stretching mode.

Dynamics and kinetics of the reaction OH + H2S → H2O + SH on an accurate potential energy surface

Mode specificity and product energy disposal are unveiled in the reaction OH + H₂S → H₂O + SH.

Fitting potential energy surfaces to sum-of-products form with neural networks using exponential neurons

In this paper, the use of the neural network (NN) method with exponential neurons for directly fitting ab initio data to generate potential energy surfaces (PESs) in sum-of-product form will be discussed. The utility of the approach will be highlighted using fits of CS2, HFCO, and HONO ground state PESs based upon high-level ab initio data. Using a generic interface between the neural network PES fitting, which is performed in MATLAB, and the Heidelberg multi-configuration time-dependent Hartree (MCTDH) software package, the PESs have been tested via comparison of vibrational energies to experimental measurements. The review demonstrates the potential of the PES fitting method, combined with MCTDH, to tackle high-dimensional quantum dynamics problems.

Semiclassical "Divide-and-Conquer" Method for Spectroscopic Calculations of High Dimensional Molecular Systems

A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene-three molecules of increasing dimensionality for which benchmark quantum results are available-and then applied to C_{60}, a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken.

Exploring surface landscapes with molecules: rotationally induced diffraction of H2 on LiF(001) under fast grazing incidence conditions

Atomic diffraction by surfaces under fast grazing incidence conditions has been used for almost a decade to characterize surface properties with more accuracy than with more traditional atomic diffraction methods. From six-dimensional solutions of the time-dependent Schrödinger equation, we show that diffraction of H₂ molecules under fast grazing incidence conditions could be even more informative for the characterization of ionic surfaces, due to the large anisotropic electrostatic interaction between the quadrupole moment of the molecule and the electric field created by the ionic crystal. Using the LiF(001) surface as a benchmark, we show that fast grazing incidence diffraction of H₂ strongly depends on the initial rotational state of the molecule, while rotationally inelastic processes are irrelevant. We demonstrate that, as a result of the anisotropy of the impinging projectile, initial rotational excitation leads to an increase in intensity of high-order diffraction peaks at incidence directions that satisfy precise symmetry constraints, thus providing a more detailed information on the surface characteristics than that obtained from low-order atomic diffraction peaks under fast grazing incidence conditions. As quadrupole-ion surface potentials are expected to accurately represent the interaction between H₂ and any surface with a marked ionic character, our analysis should be of general applicability to any of such surfaces. Finally, we show that a density functional theory description of the molecule-ion surface potential catches the main features observed experimentally.

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.

Dynamics of carbon monoxide dissociation on Co(112̄0)

The dissociative chemisorption dynamics of CO on rigid Co(112̄0) is investigated using a quasi-classical trajectory method on a new global six-dimensional potential energy surface.

A global potential energy surface and dynamics study of the Au+ + H2 → H + Au+H reaction

A global potential energy surface (PES) of the ground state of the Au⁺H₂ system was constructed using a neural network method with permutation invariant polynomials.

Dissociative chemisorption of methane on Ni(111) using a chemically accurate fifteen dimensional potential energy surface

A new chemically accurate potential energy surface for the dissociative chemisorption of methane on the rigid Ni(111) surface.

Methane dissociation on Ni(111): A fifteen-dimensional potential energy surface using neural network method

In the present work, we develop a highly accurate, fifteen-dimensional potential energy surface (PES) of CH4 interacting on a rigid flat Ni(111) surface with the methodology of neural network (NN) fit to a database consisted of about 194 208 ab initio density functional theory (DFT) energy points. Some careful tests of the accuracy of the fitting PES are given through the descriptions of the fitting quality, vibrational spectrum of CH4 in vacuum, transition state (TS) geometries as well as the activation barriers. Using a 25-60-60-1 NN structure, we obtain one of the best PESs with the least root mean square errors: 10.11 meV for the entrance region and 17.00 meV for the interaction and product regions. Our PES can reproduce the DFT results very well in particular for the important TS structures. Furthermore, we present the sticking probability S0 of ground state CH4 at the experimental surface temperature using some sudden approximations by Jackson's group. An in-depth explanation is given for the underestimated sticking probability.

Electron-Hole Pair Effects in Polyatomic Dissociative Chemisorption: Water on Ni(111)

The influence of electron-hole pairs in dissociative chemisorption of a polyatomic molecule (water) on metal surfaces is assessed for the first time using a friction approach. The atomic local density dependent friction coefficients computed based on a free electron gas embedding model are employed in classical molecular dynamics simulations of the water dissociation dynamics on rigid Ni(111) using a recently developed nine dimensional interaction potential energy surface for the system. The results indicate that nonadiabatic effects are relatively small and they do not qualitatively alter the mode specificity in the dissociation.

Quantum and classical dynamics of reactive scattering of H2 from metal surfaces

State-of-the-art theoretical models allow nowadays an accurate description of H₂/metal surface systems and phenomena relative to heterogeneous catalysis. Here we review the most relevant ones investigated during the last 10 years.

Quantum dynamics of polyatomic dissociative chemisorption on transition metal surfaces: mode specificity and bond selectivity

Recent advances in quantum dynamical characterization of polyatomic dissociative chemisorption on accurate global potential energy surfaces are critically reviewed.

Towards an accurate specific reaction parameter density functional for water dissociation on Ni(111): RPBE versus PW91

Approximated nine dimensional quantum dynamics on a new potential energy surface for water dissociation on Ni(111) computed using the RPBE functional.

Dynamics of water dissociative chemisorption on Ni(111): effects of impact sites and incident angles

The dissociative chemisorption of water on rigid Ni(111) is investigated using a quasiclassical trajectory method on a nine-dimensional global potential energy surface based on a faithful permutation invariant fit of ∼25 000 density functional theory points. This full-dimensional model not only confirms the validity of our earlier reduced-dimensional model with 6 degrees of freedom, but also allows the examination of the influence of impact sites and incident angles. It is shown that the reactivity depends on the site of impact in a complex fashion controlled by the topography of the potential energy surface rather than the barrier height alone. In addition, the reaction is promoted by momenta both parallel and perpendicular to the surface, as predicted by the recently proposed sudden vector projection model.

Six-dimensional quantum dynamics of dissociative chemisorption of H2 on Co(0001) on an accurate global potential energy surface

Six-dimensional quantum dynamics of hydrogen dissociative chemisorption on Co(0001) is investigated on a DFT based potential energy surface.

Six-dimensional quantum dynamics for dissociative chemisorption of H2 and D2 on Ag(111) on a permutation invariant potential energy surface

Quantum dynamics on a permutation invariant potential energy surface for H₂ dissociation on Ag(111) yield satisfactory agreement with experiment.