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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Ab initio metadynamics calculations reveal complex interfacial effects in acetic acid deprotonation dynamics

Acid-base reactions play a central role in solution chemistry, with carboxylic acids being particularly important in atmospheric chemical processes. In this work, we harness metadynamics calculations with Born-Oppenheimer molecular dynamics (BOMD) simulations to understand deprotonation dynamics of acetic acid (CH 3 COOH) in both bulk and air-water interfacial environments. Collective variables are carefully chosen in our well-tempered metadynamics simulations to capture the deprotonation process in various aqueous configurations. Herein, our findings show that the free energy barrier for deprotonation of acetic acid at the air-water interface is lower than in the bulk, in accordance with the available experimental data. Furthermore, our well-tempered metadynamics calculations suggest that the variations in free energy are primarily due to intricate solvation shell effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Leptodermic corrections to the TOV equations and nuclear astrophysics within the effective surface approximation

The macroscopic model for a neutron star (NS) as a liquid drop at the equilibrium is used to extend the Tolman-Oppenheimer-Volkoff (TOV) equations taking into account the gradient terms responsible for the system surface. The parameters of the Schwarzschild metric in the spherical case are found with these surface corrections to the known leading (zero) order of the leptodermic approximation a/R << 1, where a is the NS effective-surface (ES) thickness, and R is the effective NS radius. The energy density $\mathscr{E}$ is considered in a general form including the functions of the particle number density and of its gradient terms. The macroscopic gravitational component $Φ$(ρ) of the energy density is taken into account in the simplest form as expansion in powers of $ρ$ – $\overline{ρ}$, where $\overline{ρ}$ is the saturation density, up to second order, in terms of its contributions to the separation particle energy and incompressibility. Density distributions ρ across the NS ES in the normal direction to the ES, which are derived in the simple analytical form at the same leading approximation, was used for the derivation of the modified TOV (MTOV) equations by accounting for their NS surface corrections. As a result, the MTOV equations are analytically solved at first order and the results are compared with the standard TOV approach of the zero order.

Magner, A. G. [Institute for Nuclear Research, Kyi↗
DOE OSTI2021

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem

Computational simulation of non-adiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons, to name a few. Here, we report an implementation of the fewest-switches surface hopping algorithm in the NWChem computational chemistry program. Here the surface hopping method is combined with linear-response time-dependent density functional theory calculations of adiabatic excited state potential energy surfaces. To treat quantum transitions between arbitrary electronic Born{Oppenheimer states, we have implemented both numerical and analytical differentiation schemes for derivative non-adiabatic couplings. A numerical approach for the time-derivative non-adiabatic couplings together with an analytical method for calculating non-adiabatic coupling vectors is an efficient combination for surface hopping approaches. Additionally, electronic decoherence schemes and a state reassigned unavoided crossings algorithm are also implemented to improve the accuracy of the simulated dynamics and to handle trivial unavoided crossings. We apply our code to study the ultrafast decay of photoexcited benzene, including a detailed analysis of the potential energy surface, population decay time scales, and vibrational coordinates coupled to the excitation dynamics. The development presented in this work is a baseline for future implementations of more sophisticated frameworks for simulating of non-adiabatic molecular dynamics in NWChem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation

Here, extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) in its most recent shadow potential energy version has been implemented in the semiempirical PyTorch-based software PySeQM. The implementation includes finite electronic temperatures, canonical density matrix perturbation theory, and an adaptive Krylov subspace approximation for the integration of the electronic equations of motion within the XL-BOMB approach (KSA-XL-BOMD). The PyTorch implementation leverages the use of GPU and machine learning hardware accelerators for the simulations. The new XL-BOMD formulation allows studying more challenging chemical systems with charge instabilities and low electronic energy gaps. The current public release of PySeQM continues our development of modular architecture for large-scale simulations employing semi-empirical quantum-mechanical treatment. Applied to molecular dynamics, simulation of 840 carbon atoms, one integration time step executes in 4 s on a single Nvidia RTX A6000 GPU.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

SchrödingerNet: A Universal Neural Network Solver for the Schrödinger Equation

Recent advances in machine learning have facilitated numerically accurate solution of the electronic Schrödinger equation (SE) by integrating various neural network (NN)-based wave function ansatzes with variational Monte Carlo methods. Nevertheless, such NN-based methods are all based on the Born–Oppenheimer approximation (BOA) and require computationally expensive training for each nuclear configuration. In this work, we propose a novel NN architecture, SchrödingerNet, to solve the full electronic-nuclear SE by defining a loss function designed to equalize local energies across the system. This approach is based on a translationally, rotationally and permutationally symmetry-adapted total wave function ansatz that includes both nuclear and electronic coordinates. Furthermore, this strategy not only allows for an efficient and accurate generation of a continuous potential energy surface at any geometry within the well-sampled nuclear configuration space, but also incorporates non-BOA corrections, through a single training process. Comparison with benchmarks of atomic and small molecular systems demonstrates its accuracy and efficiency.

Chemical calculations↗
DOE OSTI2025

A Theory of Ultrafast Charge Transfer Relaxation with Non-Innocent Solvent Molecules

In this work we revisit the photodynamics of tetracyanoethylene-hexamethylbenzene (TCNE- HMB), the molecular complex studied by Hochstrasser et al. [J. Chem. Phys. 100, 4797–4810, 1994] that has long challenged the applicability of Marcus’s theory of elec- tron transfer for predicting photochemical reactions. Using a novel black-box electronic structure algorithm (time-dependent density functional theory with one double, TD- DFT-1D) to efficiently run molecular dynamics that can treat charge recombination, we run ab initio surface hopping molecular dynamics and confirm that, for a polar solvent, charge recombination rates can be incredibly fast (indeed faster than the sol- vent relaxation time); for non-polar solvents, the rate is much slower. We demonstrate that, although Marcus theory cannot be directly applied, these nonequilibrium (and sometimes incredibly fast) photoexcited dynamics can be effectively explained within a two-state model without any evidence of a transition through a conical intersection. Most importantly, for this paradigmatic model system, we are able to identify two nuclear coordinates of interest (rather than the single coordinate predicted by Marcus or a full set of internal quantum modes studied by Bixon and Jortner): the solvent relaxation in the first shell (that strongly modulates the energies of the charge trans- fer state and differentiates time scales for relaxation) and a nuclear displacement in the TCNE-HMB complex arising from a handful of vibrations that induces non-Born Oppenheimer motion and eventually facilitates an abrupt electronic transition to the ground state. Altogether, these findings suggest a tractable generalization of Marcus theory for future simulations of photochemistry with non-innocent solvent environ- ments in the spirit of a Hamiltonian suggested by Stuchebrukhov (J. Chem. Phys. 107, 3821, 1997).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF–Water Miscibility Gap

Deuteration is a common chemical modification used in conjunction with experiments such as neutron scattering, NMR, and Fourier-transform infrared for the study of molecular systems. Under the Born–Oppenheimer (BO) approximation, while the underlying potential energy surface remains unchanged by isotopic substitutions, isotopic substitution still alters intramolecular vibrations, which in turn may alter intermolecular interactions. Molecular mechanics (MM) force fields used in classical molecular dynamics simulations are assumed to represent local approximations of the BO potential energy surfaces, and hence, MD simulations using simple isotopic mass substitutions should capture BO-compatible isotope effects. However, standard MM force-field parameterizations do not directly fit to the local harmonic quantum mechanical (QM) Hessian that describes the BO surface, but rather to QM normal-modes and/or mass-dependent internal-coordinate derived distortion energies. In this study, using tetrahydrofuran (THF)–water mixtures as our model system, we show that not only does a simple mass-substitution approach fail to capture an experimentally characterized deuteration effect (the loss of the closed-loop miscibility gap associated with the complete deuteration of THF) but also it is necessary to generate new MM force-field parameters that correctly describe isotopic dependent vibrations to capture the experimental deuteration effect. We show that the origin of this failure is a result of using mass-dependent features to fit the THF MM force field, which unintentionally biases the bonded terms of the force field to represent only the isotopologue used during the original force-field parameterization. In addition, we make use of our isotopologue-corrected force field for D 8 THF to examine the molecular origins of the isotope-dependent loss of the THF–water miscibility gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Simultaneous Optimization of Nuclear–Electronic Orbitals

Accurate modeling of important nuclear quantum effects, such as nuclear delocalization, zero-point energy, and tunneling, as well as non-Born-Oppenheimer effects, requires treatment of both nuclei and electrons quantum mechanically. The nuclear–electronic orbital (NEO) method provides an elegant framework to treat specified nuclei, typically protons, on the same level as the electrons. In conventional electronic structure theory, finding a converged ground state can be a computationally demanding task; converging NEO wavefunctions, due to their coupled electronic and nuclear nature, is even more demanding. Herein, we present an efficient simultaneous optimization method that uses the direct inversion in the iterative subspace method to simultaneously converge wavefunctions for both the electrons and quantum nuclei. In conclusion, benchmark studies show that the simultaneous optimization method can significantly reduce the computational cost compared to the conventional stepwise method for optimizing NEO wavefunctions for multicomponent systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Proton Transfer Dynamics in the Aprotic Proton Accepting Solvent 1-Methylimidazole

The dynamics of proton transfer to the aprotic solvent 1-methylimidazole (MeIm, proton acceptor) from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) were investigated using fast fluorescence measurements. The closely related molecule, 8- methoxypyrene-1,3,6-trisulfonic acid trisodium salt (MPTS), which is not a photoacid, was also studied for comparison. Following optical excitation, the wavelength-dependent population dynamics of HPTS in MeIm resulting from the deprotonation process were collected over the entire fluorescence emission window. Analysis of the time-dependent fluorescence spectra revealed four distinct fluorescence bands that appear and decay on different time scales. We label these four states as: protonated (P), associated I (A I ), associated II (A II ), and deprotonated (D). We find that the simple kinetic scheme of P → A I → A II → D is not consistent with the data. Instead, the kinetic scheme that describes the data has P decaying into A I , which mainly goes on to deprotonation (D), but AI can also feed into A II . A II can return to A I or decay to the ground state, but does not deprotonate within experimental error. Finally, quantum chemistry and excitedstate QM/MM Born-Oppenheimer molecular dynamics simulations indicate that A I and A II are two H-bonding conformations of MeIm to the HPTS hydroxyl, axial and equatorial, respectively.

14 SOLAR ENERGY↗
DOE OSTI2023

Wetting of a Hydrophobic Surface: Far-IR Action Spectroscopy and Dynamics of Microhydrated Naphthalene

The interaction of water and polycyclic aromatic hydrocarbons is of fundamental importance in areas as diverse as materials science and atmospheric and interstellar chemistry. The interplay between hydrogen bonding and dipole–π interactions results in subtle dynamics that are challenging to describe from first principles. Here, we employ far-IR action vibrational spectroscopy with the infrared free-electron laser FELIX to investigate naphthalene with one to three water molecules. We observe diffuse bands associated with intermolecular vibrational modes that serve as direct probes of the loose binding of water to the naphthalene surface. These signatures are poorly reproduced by static DFT or Møller–Plesset computations. Instead, a rationalization is achieved through Born–Oppenheimer Molecular Dynamics simulations, revealing the active mobility of water over the surface, even at low temperatures. Therefore, our work provides direct insights into the wetting interactions associated with shallow potential energy surfaces while simultaneously demonstrating a solid experimental–computational framework for their investigation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Direct Observation of the ππ* to nπ* Transition in 2-Thiouracil via Time-Resolved NEXAFS Spectroscopy

The photophysics of nucleobases has been the subject of both theoretical and experimental studies over the past decades due to the challenges posed by resolving the steps of their radiationless relaxation dynamics, which cannot be described in the framework of the Born–Oppenheimer approximation (BOA). In this context, the ultrafast dynamics of 2-thiouracil has been investigated with a time-resolved NEXAFS study at the Free Electron Laser FLASH. Near Edge X-ray Absorption Fine Structure spectroscopy (NEXAFS) can be used to observe electronic transitions in ultrafast molecular relaxation. We performed time-resolved UV-pump/X-ray probe absorption measurements at the sulfur 2s (L1) and 2p (L2/3) edges. We are able to identify absorption features corresponding to the S2 (ππ*) and S1 (nπ*) electronic states. We observe a delay of 102 ± 11 fs in the population of the nπ* state with respect to the initial optical excitation and interpret the delay as the time scale for the S2 → S1 internal conversion. We furthermore identify oscillations in the absorption signal that match a similar observation in our previous X-ray photoelectron spectroscopy study on the same molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Yttrium Contenting Compositionally Complex Medium-Entropy Li-Garnet Electrolyte with Improved Ionic Conductivity

The compositionally complex medium/high-entropy design concept can greatly expand the categories and affect the properties of the materials. With such a designing concept, a medium-entropy Li-garnet electrolyte with appropriate yttrium content (formula Li 6.6 La 3 ZrNb 0.3 Ta 0.3 Hf 0.3 Y 0.1 O 12 ) shows a record-high ionic conductivity of ∼5.7 × 10 –4 S/cm, the highest reported for any single-site substituted high/medium-entropy Li-garnet. The assembled Li metal symmetric cells also show stable long-term cycling (0.1 mA/cm 2 for over 200 h). Neutron powder diffraction and Rietveld refinement results indicate that a competing conduction mechanism between (1) occupancy on high mobility of 96h sites and (2) the associated site vacancies and the bond length requires an appropriate content of Y for enhanced ionic conductivity. Li-ion hopping through the bottleneck can also contribute to the conductivity. Finally, density functional theory and Born–Oppenheimer molecular dynamics simulations also indicate the high mobility and number of hopping transitions of Li ions, contributing to the high ionic conductivity.

Li-garnet↗
DOE OSTI2025

Highly Active Hydrogen Evolution Reaction (HER) Catalysts Formed by Energetic Pt n Cluster Deposition: Deposition Dynamics and the HER Mechanism

Mass-selected Pt n + (n ≤ 7) were deposited at variable energies on highly oriented pyrolytic graphite (HOPG), creating highly active hydrogen evolution reaction (HER) electrocatalysts. HER mass activities were ~2 to >10 times higher than those for the surface atoms in bulk Pt and for Pt n deposited on several other supports. Thus, high activity reflects the Pt-C structures formed by energetic Pt n -HOPG impacts, in addition to high Pt surface availability. The Pt n /HOPG electrodes were probed by X-ray photoelectron spectroscopy, low energy ion scattering, and electron microscopy. Born-Oppenheimer molecular dynamics (BOMD) was used to simulate Pt n - HOPG impacts, revealing the types of structures formed at different energies, then DFT was used to probe their most important HER pathways. For low deposition energies, the Pt n deposit onto the HOPG surface with sub-unit sticking probability, aggregating at defects. With increasing deposition energy, the sticking probability initially decreases, then rises to unity as subplantation and defect creation allow formation of strongly bonded platinum-carbon structures. Barriers for HER on these structures were found to be low and weakly dependent on Pt n size, consistent with experiment. The activities were highest for small covalently-bonded Pt-C structures created at high deposition energies. The larger aggregated structures formed at low energies were less active, but still substantially better than the bulk Pt surface monolayer. The catalysts were stable in repeated potential cycling at reducing potentials, but electrodes containing subplanted Pt became more active when scanned to oxidizing potentials, due to emergence of subplanted Pt onto the surface.

08 HYDROGEN↗
DOE OSTI2021

Time-resolved relaxation and fragmentation of polycyclic aromatic hydrocarbons investigated in the ultrafast $\mathrm{XUV}$-$\mathrm{IR}$ regime

Polycyclic aromatic hydrocarbons (PAHs) play an important role in interstellar chemistry and are subject to high energy photons that can induce excitation, ionization, and fragmentation. Previous studies have demonstrated electronic relaxation of parent PAH monocations over 10–100 femtoseconds as a result of beyond-Born-Oppenheimer coupling between the electronic and nuclear dynamics. Here, we investigate three PAH molecules: fluorene, phenanthrene, and pyrene, using ultrafast XUV and IR laser pulses. Simultaneous measurements of the ion yields, ion momenta, and electron momenta as a function of laser pulse delay allow a detailed insight into the various molecular processes. We report relaxation times for the electronically excited PAH * , PAH +* and PAH 2+* states, and show the time-dependent conversion between fragmentation pathways. Additionally, using recoil-frame covariance analysis between ion images, we demonstrate that the dissociation of the PAH 2+ ions favors reaction pathways involving two-body breakup and/or loss of neutral fragments totaling an even number of carbon atoms.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Ultrafast lattice disordering can be accelerated by electronic collisional forces

In the prevalent picture of ultrafast structural phase transitions, the atomic motion occurs in a slowly varying potential energy surface determined adiabatically by the fast electrons. However, this ignores non-conservative forces caused by electron-lattice collisions, which can significantly influence atomic motion. Most ultrafast techniques only probe the average structure and are less sensitive to random displacements, and therefore do not detect the role played by non-conservative forces in phase transitions. Here we show that the lattice dynamics of the prototypical insulator-to-metal transition of VO 2 cannot be described by a potential energy alone. We use the sample temperature to control the preexisting lattice disorder before ultrafast photoexcitation across the phase transition and our ultrafast diffuse scattering experiments show that the fluctuations characteristic of the rutile metal develop equally fast (120 fs) at initial temperatures of 100 K and 300 K. This indicates that additional non-conservative forces are responsible for the increased lattice disorder. In conclusion, these results highlight the need for more sophisticated descriptions of ultrafast phenomena beyond the Born-Oppenheimer approximation as well as ultrafast probes of spatial fluctuations beyond the average unit cell measured by diffraction.

36 MATERIALS SCIENCE↗