Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular quantum mechanics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Learning together: Towards foundation models for machine learning interatomic potentials with meta-learning

Abstract The development of machine learning models has led to an abundance of datasets containing quantum mechanical (QM) calculations for molecular and material systems. However, traditional training methods for machine learning models are unable to leverage the plethora of data available as they require that each dataset be generated using the same QM method. Taking machine learning interatomic potentials (MLIPs) as an example, we show that meta-learning techniques, a recent advancement from the machine learning community, can be used to fit multiple levels of QM theory in the same training process. Meta-learning changes the training procedure to learn a representation that can be easily re-trained to new tasks with small amounts of data. We then demonstrate that meta-learning enables simultaneously training to multiple large organic molecule datasets. As a proof of concept, we examine the performance of a MLIP refit to a small drug-like molecule and show that pre-training potentials to multiple levels of theory with meta-learning improves performance. This difference in performance can be seen both in the reduced error and in the improved smoothness of the potential energy surface produced. We therefore show that meta-learning can utilize existing datasets with inconsistent QM levels of theory to produce models that are better at specializing to new datasets. This opens new routes for creating pre-trained, foundation models for interatomic potentials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Insights into the Properties of MXenes and MXene Analogs from Atomistic Simulation

We review the properties that have been predicted for MXenes and MXene analogs from computational simulation with a focus on structural and electronic properties, energy storage, and ion transport. Methods considered range from quantum mechanical approaches to classical molecular dynamics. We conclude by reviewing current limitations and outstanding questions for simulation and MXene properties that have been little explored to-date.

Muraleedharan, Murali Gopal↗
DOE OSTI2020

Biased Spin-State Energetics of Fe(II) Molecular Complexes within Density-Functional Theory and the Linear-Response Hubbard U Correction

The spin-state energetics of six Fe(II) molecular complexes are computed using the linear-response Hubbard U approach within DFT. The adiabatic energy differences, ΔE H-L , between the high-spin (S = 2) and the low-spin (S = 0) states are computed and compared with accurate-coupled cluster-corrected CASPT2 results. We show that DFT+U fails in correctly capturing the ground state for strong-field ligands yielding ΔE H-L that are almost constant throughout the molecular series. This bias toward high spin together with the metal/ligand charge transfer upon U correction are here quantified and explained using molecular orbital diagrams involving both σ- and π-bonding interactions. Furthermore, with increasing ligand-field strengths this bias also increases owing to the stronger molecular character of the metal/ligand Kohn–Sham orbitals thus resulting in large deviations from the reference larger than 4 eV. Smaller values of U can be employed to mitigate this effect and recover the right energetics.

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

The Remarkable I 2 O 3 Molecule: A New View from Theory

Atmospheric iodine chemistry has garnered increasing attention as a result of increased iodine emissions. A key subset of this chemistry involves iodine oxides (I 2 O 2–5 ), which serve as precursors to particle formation. Among these, I 2 O 3 is the simplest iodine oxide involved in particle formation, but it has remained undetected in the atmosphere. Previous theoretical studies have characterized this peculiar molecule, primarily using energies to refine geometries obtained at low levels of theory. Due to the reemerging interest in I 2 O 3 , this study presents geometries optimized at the CCSD(T)/aug-cc-pwCVTZ-PP level of theory─marking the first instance, to the best of our knowledge, where this system has been studied exclusively with CCSD(T). Harmonic vibrational frequencies were computed at the same level of theory. Final energetics were obtained using the very high level CCSDT(Q) method with basis sets up to quintuple-zeta cardinality (aug-cc-pwCV5Z-PP) and extrapolated to the CBS limit to yield CCSDT(Q)/CBS//CCSD(T)/aug-cc-pwCVTZ-PP energies. These energies include harmonic zero-point vibrational energy corrections and scalar relativistic energy corrections. Additionally, this study discovers new isomers along the I 2 O 3 potential energy surface, a novel contribution to the field. The performance of different computational methods and DFT functionals commonly used in atmospheric chemistry is also assessed relative to high-level theoretical methods.

basis sets↗
DOE OSTI2026

Exploring Excited State Proton Transfer Dynamics upon Ultraviolet Excitation

Excited state intramolecular proton transfer (ESIPT) has been investigated in two prototypical systems─salicylaldehyde azine (SAA) and 1,5-dihydroxyanthraquinone (DHAQ)─using transient absorption spectroscopy upon ultraviolet excitation into the less studied higher excited (S n ) manifold. Excitation with sub-30 fs pulses and broadband visible probing has allowed for direct measurement of the ESIPT rate. In conjunction with steady-state measurements and TD-DFT calculations, a complete delineation of the ultrafast photophysics has been carried out. In SAA, ESIPT remains ultrafast (∼30 fs), consistent with previous S 1 excitation studies. Coherent vibrational beats maps reveal significant wavelength dependence, however. Theoretical analysis suggests that the observed modes and their intensities in coherent vibrational spectra are modulated by the nature of the electronically excited state. In DHAQ, the first direct observation of ESIPT presents a time-constant of ∼85 fs, and a slower component of 9 ps, akin to previous reports on double-proton transfer systems. Collectively, the results suggest that while the ultrafast ESIPT rate remains largely invariant vis-à-vis the excitation energy, the product yield, as well as accompanying coherent oscillations, may be substantively altered, owing to the existence of alternative decay pathways.

excited states↗
DOE OSTI2023

High-Level Reverse Intersystem Crossing and Molecular Rigidity Improve Spin Statistics for Triplet–Triplet Annihilation Upconversion

The structural factors affecting triplet−triplet annihilation (TTA) at the molecular level are not well-understood. Here, our steady-state photoluminescence and transient absorption results demonstrate that the spin statistical factor, η, decreases from 0.60 to 0.46 and 0.14 going from 9,10-diphenylanthracene (DPA) to the 1,5-DPA and 2,6-DPA isomers, respectively, during photon upconversion with a platinum octaethylporphyrin sensitizer. Density functional theory (DFT) shows that η depends on the energetics of hot triplet states and molecular rigidity. The significantly high conical intersection energy between the S 0 and T 1 states for 9,10-DPA gives its longer triplet lifetime. Time-dependent DFT calculations show that 9,10-DPA and 1,5-DPA can undergo high-level reverse intersystem crossing from their T 2 and T 3 states, respectively, to the bright S 1 state, increasing the limit of the spin statistical factor. Both factors ultimately serve to enhance the TTA efficiency. Furthermore, this work provides insight into designing molecules for efficient light-emitting and photon upconversion applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Design Rules for Open-Shell Molecular Wires: Insights from Correlated Many-Body Transport

Open-shell π-conjugated systems have emerged as promising molecular wires that can sustain unusually high low-bias conductance over tens of nanometers. However, predictive design rules remain limited because near-degeneracy and spin polarization give rise to correlated electronic states that are not reliably captured by standard density functional theory and Landauer transport descriptions. Here, we establish physically transparent design rules for long-range, weakly length-dependent charge transport based on the interplay between bond-length alternation and electron–electron interactions. Using a fully correlated transport framework that combines density matrix renormalization group calculations with nonequilibrium Green’s function embedding, we show that weak dimerization maintains spatially extended edge states, while moderate on-site interaction stabilizes open-shell character without excessively separating transport-relevant resonances. This balance yields zero-bias transmission that is largely insensitive to molecular length, providing a route to connect chemically tunable structure to correlated transport beyond mean-field descriptions.

Charge transport↗
DOE OSTI2026

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗
DOE OSTI2020

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

Abstract Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1966

Long-range /retarded/ intermolecular forces.

Retarded intermolecular forces, discussing Casimir and Polder retarded dipole-dipole energy of interaction between two ground state atoms in terms of trigonometric integrals

ENERGY EXCHANGE↗
NASA NTRS1999

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Timofeeva, Tatiana V.↗
DOE OSTI2022

Exploring far-from-equilibrium ultrafast polarization control in ferroelectric oxides with excited-state neural network quantum molecular dynamics

Ferroelectric materials exhibit a rich range of complex polar topologies, but their study under far-from-equilibrium optical excitation has been largely unexplored because of the difficulty in modeling the multiple spatiotemporal scales involved quantum-mechanically. To study optical excitation at spatiotemporal scales where these topologies emerge, we have performed multiscale excited-state neural network quantum molecular dynamics simulations that integrate quantum-mechanical description of electronic excitation and billion-atom machine learning molecular dynamics to describe ultrafast polarization control in an archetypal ferroelectric oxide, lead titanate. Far-from-equilibrium quantum simulations reveal a marked photo-induced change in the electronic energy landscape and resulting cross-over from ferroelectric to octahedral tilting topological dynamics within picoseconds. The coupling and frustration of these dynamics, in turn, create topological defects in the form of polar strings. The demonstrated nexus of multiscale quantum simulation and machine learning will boost not only the emerging field of ferroelectric topotronics but also broader optoelectronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A deep potential model with long-range electrostatic interactions

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make molecular simulations with the accuracy of quantum mechanical density functional theory possible at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation, we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei + core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the DP long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples: the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Toward witnessing molecular exciton entanglement from spectroscopy

Entanglement is a defining feature of quantum mechanics that can be a resource in engineered and natural systems, but measuring entanglement in experiment remains elusive especially for large chemical systems. Most practical approaches require determining and measuring a suitable entanglement witness which provides some level of information about the entanglement structure of the probed state. A fundamental quantity of quantum metrology is the quantum Fisher information (QFI), which is a rigorous witness of multipartite entanglement that can be evaluated from linear response functions for certain states. Here, in this paper, we explore measuring the QFI of molecular exciton states of the first-excitation subspace from spectroscopy. In particular, we utilize the fact that the linear response of a pure state subject to a weak electric field over all possible driving frequencies encodes the variance of the collective dipole moment in the probed state, which is a valid measure for QFI. The systems that are investigated include the molecular dimer, N-site linear aggregate with nearest-neighbor coupling, and N-site circular aggregate, all modeled as a collection of interacting qubits. Our theoretical analysis shows that the variance of the collective dipole moment in the brightest dipole-allowed eigenstate is the maximum QFI. The optical response of a thermally equilibrated state in the first-excitation subspace is also a valid QFI. Theoretical predictions of the measured QFI for realistic linear dye aggregates as a function of temperature and energetic disorder due to static variations of the host matrix show that two- to three-partite entanglement is realizable. This paper lays some groundwork and inspires measurement of multipartite entanglement of molecular excitons with ultrafast pump-probe experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗