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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.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Advancing molecular machine learning representations with stereoelectronics-infused molecular graphs

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have used strings, fingerprints, global features and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a new approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects, enhancing expressivity and interpretability. Learning to predict the stereoelectronics-infused representation with a tailored double graph neural network workflow enables its application to any downstream molecular machine learning task without expensive quantum-chemical calculations. We show that the explicit addition of stereoelectronic information substantially improves the performance of message-passing two-dimensional machine learning models for molecular property prediction. We show that the learned representations trained on small molecules can accurately extrapolate to much larger molecular structures, yielding chemical insight into orbital interactions for previously intractable systems, such as entire proteins, opening new avenues of molecular design. Finally, we have developed a web application (simg.cheme.cmu.edu) where users can rapidly explore stereoelectronic information for their own molecular systems.

Boiko, Daniil A↗
DOE OSTI2022

Inference of molecular divertor density from filtered camera analysis of molecularly induced Balmer line emission during detachment in JET L-mode plasmas

Here a previously presented Monte Carlo method for estimating local plasma conditions in 2D based on intensity ratios of deuterium Balmer D α , D γ and D ε lines was amended to consider also the D α and D γ emission contributions arising from molecular processes. The obtained estimates were used to infer the molecular divertor density with the help of the molecular databases of EIRENE. The method was benchmarked against EDGE2D-EIRENE simulations and observed to reproduce the molecularly induced emission fractions and the molecular divertor densities primarily within 25% of the references. Experimental analysis of a JET L-mode density scan suggested molecularly induced D α and D γ contributions of up to 60–70% and 20%, respectively, during the process of detachment. The independent estimates of the molecular divertor density inferred from the obtained molecularly induced D α and D γ intensities agree within uncertainties with each other. Both estimates show the molecular density increasing up to approximately 1.0–2.0 x 10 20 m -3 at the outer strike point in deep detachment with its ratio to the local electron density agreeing with EDGE2D-EIRENE predictions within the scatter of the experimental data.

interferometry↗
DOE OSTI2022

Experimental distinction of the molecularly induced Balmer emission contribution and its application for inferring molecular divertor density with 2D filtered camera measurements during detachment in JET L-mode plasmas

A previously presented model for generating 2D estimates of the divertor plasma conditions at JET from deuterium Balmer line intensity ratios, obtained from tomographic reconstructions of divertor camera images, was amended to consider also the Balmer emission arising from molecular processes. Utilizing the AMJUEL and H2VIBR atomic and molecular databases of EIRENE enabled also inference of the molecular divertor density from the distinguished molecularly induced emission. Analysis of a JET L-mode density scan suggests the molecularly induced emission accounting for up to 60%–70% and 10%–20% of the Balmer Dα and Dγ intensities, respectively, at the onset of detachment, while electron-ion recombination becomes increasingly dominant with deepening detachment. Similar observations were made by post-processing EDGE2D-EIRENE simulations, which indicated significant roles of molecular D$^{+}_{2}$ ions and vibrational excitation of the D 2 molecules as precursors for the molecularly induced emission. The experimentally inferred molecular density at the outer strike point was found to increase monotonously with decreasing strike point temperature, reaching approximately 30%–50% of the local electron density at n mol, osp = 1–2 X 10 20 m -3 at T e,osp ≈ 0.7 eV. A further steep increase by a factor of 3–5 was observed with decrease of T e,osp to 0.5 eV. The observations are in qualitative and reasonable quantitative agreement with EDGE2D-EIRENE predictions of n mol, osp within the uncertainties of the experimental data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods like the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite like GAMESS is maintained and developed is considered. Future developments are briefly summarized.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Molecular coupling competing with defects within insulator of the magnetic tunnel junction-based molecular spintronics devices

Nearly 70 years old dream of incorporating molecule as the device element is still challenged by competing defects in almost every experimentally tested molecular device approach. This paper focuses on the magnetic tunnel junction (MTJ) based molecular spintronics device (MTJMSD) method. An MTJMSD utilizes a tunnel barrier to ensure a robust and mass-producible physical gap between two ferromagnetic electrodes. MTJMSD approach may benefit from MTJ's industrial practices; however, the MTJMSD approach still needs to overcome additional challenges arising from the inclusion of magnetic molecules in conjunction with competing defects. Molecular device channels are covalently bonded between two ferromagnets across the insulating barrier. An insulating barrier may possess a variety of potential defects arising during the fabrication or operational phase. This paper describes an experimental and theoretical study of molecular coupling between ferromagnets in the presence of the competing coupling via an insulating tunnel barrier. We discuss the experimental observations of hillocks and pinhole-type defects producing inter-layer coupling that compete with molecular device elements. We performed theoretical simulations to encompass a wide range of competition between molecules and defects. Monte Carlo Simulation (MCS) was used for investigating the defect-induced inter-layer coupling on MTJMSD. Our research may help understand and design molecular spintronics devices utilizing various insulating spacers such as aluminum oxide (AlOx) and magnesium oxide (MgO) on a wide range of metal electrodes. This paper intends to provide practical insights for researchers intending to investigate the molecular device properties via the MTJMSD approach and do not have a background in magnetic tunnel junction fabrication.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations

MRI is an indispensable diagnostic tool in modern medicine; however, understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge, hindering the molecular-guided development of more effective contrast agents. By using quantum-based polarizable force fields, the first-of-its-kind molecular dynamics (MD) simulations of Gadobutrol are reported where the 1 H NMR longitudinal relaxivity r 1 of the aqueous phase is determined without any adjustable parameters. The MD simulations of r 1 dispersion (i.e., frequency dependence) show good agreement with measurements at frequencies of interest in clinical MRI. Importantly, the simulations reveal key insights into the molecular level processes leading to r 1 dispersion by decomposing the NMR dipole–dipole autocorrelation function G(t) into a discrete set of molecular modes, analogous to the eigenmodes of a quantum harmonic oscillator. The molecular modes reveal important aspects of the underlying mechanisms governing r 1 , such as its multiexponential nature and the importance of the second eigenmodal decay. By simply analyzing the MD trajectories on a parameter-free approach, the Gadobutrol simulations show that the outer-shell water contributes ∼50% of the total relaxivity r 1 compared to the inner-shell water, in contrast to simulations of (nonchelated) gadolinium-aqua where the outer shell contributes only ∼15% of r 1 . The deviation between simulations and measurements of r 1 below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol, in good agreement with independent studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗
DOE OSTI2020

Developing Scaling Relationships for Molecular Electrocatalysis through Studies of Fe-Porphyrin-Catalyzed O 2 Reduction

The oxygen reduction reaction (ORR) is a multiproton/multielectron transformation in which dioxygen (O 2 ) is reduced to water or hydrogen peroxide and serves as the cathode reaction in most fuel cells. The ORR (O 2 + 4e – + 4H + → 2H 2 O) involves up to nine substrates and thus requires navigating a complicated reaction landscape, typically with several high-energy intermediates. Many catalysts can perform this reaction, though few operate with fast rates and at low overpotentials (close to the thermodynamic potential). Attempts to optimize these parameters, both in homogeneous and heterogeneous electrocatalytic systems, have focused on modifying catalyst design and understanding kinetic/thermodynamic relationships between catalytic intermediates. One such method for analyzing and predicting catalyst reactivity and efficiency has been the development of “molecular scaling relationships”. In this work, we share our experience deriving and utilizing molecular scaling relationships for soluble, iron-porphyrin-catalyzed O 2 reduction in organic solvents. These relationships correlate turnover frequencies (TOF max ) and effective overpotentials (η eff ), properties uniquely defined for homogeneous catalysts. Following a general introduction of scaling relationships for both homogeneous and heterogeneous electrocatalysis, we describe the components of such scaling relationships: (i) the overall thermochemistry of the reaction and (ii) the rate and rate law of the catalyzed reaction. We then show how connecting these thermodynamic and kinetic parameters reveals multiple molecular scaling relationships for iron-porphyrin-catalyzed O 2 reduction. For example, the log(TOF max ) responds steeply to changes in ηeff that result from different catalyst reduction potentials (18.5 decades in TOF max /V in η eff ) but much less dramatically to changes in η eff that arise from varying the pKa of the acid buffer (5.1 decades in TOF max /V in η eff ). Thus, a single scaling relationship is not always sufficient for describing molecular electrocatalysis. This is particularly evident when the catalyst identity and reaction conditions are coupled. Using these multiple scaling relationships, we demonstrate that the metrics of turnover frequency and effective overpotential can be predictably tuned to achieve faster rates at lowered overpotentials. This Account uses a collection of related stories describing our research on soluble iron-porphyrin-catalyzed ORR to show how molecular scaling relationships can be derived and used for any electrocatalytic reaction. Such scaling relationships are powerful tools that connect the thermochemistry, mechanism, and rate law for a catalytic system. We hope that this collection shows the utility and simplicity of the molecular scaling approach for understanding catalysis, for enabling direct comparisons between catalyst systems, and for optimizing catalytic processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification

We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.

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

Molecular Engineering of Emissive Molecular Qubits Based on Spin-Correlated Radical Pairs

Spin chemistry of photogenerated spin-correlated radical pairs (SCRPs) offers a practical approach to control chemical reactions and molecular emissions by using weak magnetic fields. This capability to harness magnetic field effects (MFEs) paves the way for developing SCRPs-based molecular qubits. Here, in this work, we introduce a new series of donor–chiral bridge–acceptor (D–χ–A) molecules that demonstrate significant MFEs on fluorescence intensity and lifetime in solution at room temperature—critical for quantum sensing. By precisely tuning the donor site through torsional locking, distance extension, and planarization, we achieved remarkable control over key quantum properties, including field-response range and line width. In the most responsive systems, emission lifetimes increased by over 200%, and the total emission intensity was modulated by up to 30%. This level of tunability shows the power of synthetic spin chemistry. The rational design principle of optically addressable SCRP-based molecular systems, presented in this work, represents a major leap toward functional synthetic molecular qubits, advancing the field of molecular quantum technologies.

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

Dipole-Phonon Quantum Logic with Trapped Polar Molecular Ions

The interaction between the electric dipole moment of a trapped molecular ion and the phonon modes of the confined Coulomb crystal couples the orientation of the molecule to its motion. We consider the practical feasibility of harnessing this interaction to initialize, process, and read out quantum information encoded in molecular ion qubits without ever optically illuminating the molecules. We present two schemes wherein a molecular ion can be entangled with a cotrapped atomic ion qubit, providing, among other things, a means for molecular state preparation and measurement. Here, we also show that virtual phonon exchange can significantly boost the range of the intermolecular dipole-dipole interaction, allowing strong coupling between widely separated molecular ion qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Intra-molecular coupling within double-segmented molecules impacting magnetic tunnel junction-based molecular spintronics devices

The intra-molecular coupling within multiple units of paramagnetic molecules can produce various effects on molecular spintronics devices (MSD). Here, this paper focuses on double-segmented molecules as the device element to advance understanding of the Impact of internal molecular structure on magnetic tunnel junction-based MSD (MTJMSD). We performed Monte Carlo simulations (MCS) to fill the knowledge gap about the intramolecular coupling role in the magnetic properties of the MTJMSD. This study explored a double-segmented molecule containing two atomic sections, each with a net spin state interacting via Heisenberg exchange coupling within molecules and with ferromagnetic electrodes at different thermal energies, magnetic fields, and coupling strengths. This study also investigated the effect of magnetic field on the double-segmented molecule-based cross-junction-shaped MTJMSD. We also compared the effect of the magnetic field on the mono and double-segmented molecules when connected to two ferromagnetic electrodes. In the strong coupling regime, the intramolecular coupling and molecule coupling with the two ferromagnetic electrodes dominated the MTJMSD response near the molecular junction area. This study provides insight for evaluating the impact of molecular nanostructure internal connectedness on the integrated MSD.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Atomic Diffusion, Segregation, and Grain Boundary Migration in Nickel-Based Alloys from Molecular Dynamics Simulations

Grain boundary diffusion and metal mobility in alloys control material performance in many applications and yet remain poorly understood at a mechanistic level. With advances in accessible time and length scales for computational molecular simulations, and recent force field developments, we now possess tools to help unravel those mechanisms. Using large-scale molecular dynamics simulations, here we examined vacancy-mediated diffusion processes in Ni-5Cr alloy with low and high-energy grain boundaries. We show that atomic diffusion inside the grain boundary plane is about four times higher than bulk diffusion, at any temperature, and exhibits a typical Arrhenius behavior with a very small energy barrier (0~.8 eV for Cr and 0.7 eV for Ni within 1300-1600 K). Additionally, the fastest diffusing species inverts; Cr diffusion was faster than Ni in the bulk but slower in the grain boundaries. This is attributed to the creation of high cohesive energy clusters of Cr at the grain boundary. Grain boundary migration was also observed to be temperature dependent and appears to be two times higher in the 5% Cr alloy than in pure Ni, highlighting the important role of the alloying element on grain boundary motion.

Simonnin, Pauline GN↗
DOE OSTI2021

Cavity molecular dynamics simulations of vibrational polariton-enhanced molecular nonlinear absorption

We report recent experiments have observed that the chemical and photophysical properties of molecules can be modified inside an optical Fabry– Pérot microcavity under collective vibrational strong coupling (VSC) conditions, and such modification is currently not well understood by theory. In an effort to understand the origin of such cavity-induced phenomena, some recent studies have focused on the effect of the cavity environment on the nonlinear optical response of the molecular subsystem. Here, we use a recently proposed protocol for classical cavity molecular dynamics simulations to numerically investigate the linear and the nonlinear response of liquid carbon dioxide under such VSC conditions following an optical pulse excitation. We find that applying a strong pulse of excitation to the lower hybrid light–matter state, i.e., the lower polariton (LP), can lead to an overall molecular nonlinear absorption that is enhanced by up to two orders of magnitude relative to the excitation outside the cavity. This polariton-enhanced multiphoton absorption also causes an ultrashort LP lifetime (0.2 ps) under strong illumination. Unlike usual polariton relaxation processes—whereby polaritonic energy transfers directly to the manifold of singly excited vibrational dark states—under the present mechanism, the LP transfers energy directly to the manifold of higher vibrationally excited dark states; these highly excited dark states subsequently relax to the manifold of singly excited states with a lifetime of tens of ps. Because the present mechanism is generic in nature, we expect these numerical predictions to be experimentally observed in different molecular systems and in cavities with different volumes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Monte Carlo simulation to study the effect of molecular spin state on the spatio-temporal evolution of equilibrium magnetic properties of magnetic tunnel junction based molecular spintronics devices

With a variable spin state, paramagnetic molecules can affect the impact of magnetic exchange coupling strength between two ferromagnetic electrodes. Our magnetic tunnel junction based molecular spintronics devices (MTJMSD) were successful in connecting paramagnetic single molecular magnet (SMM) between two ferromagnetic electrodes. Isolated SMM exhibited a wide range of spin states. However, it was extremely challenging to identify the SMM spin state when connected to the ferromagnetic electrodes. Our prior experimental and Monte Carlo Simulations (MCS) studies showed that paramagnetic molecules produced unprecedented strong antiferromagnetic coupling between two ferromagnets at room temperature. The overall antiferromagnetic coupling occurred when a paramagnetic SMM made antiferromagnetic coupling to the first electrode and ferromagnetic coupling to the second ferromagnetic electrode. This paper studies the impact of variable molecular spin states of the SMMs, producing strong antiferromagnetic coupling between the ferromagnetic electrodes of MTJMSD. The MTJMSD used in this study was represented by an 11 x 50 x 50 Ising model, with 11 being the thickness of the MTJMSD and 5 x 10 x 50 being each electrode’s size. We employed a continuous MCS algorithm to investigate SMM’s spin state’s impact as a function of molecular exchange coupling strength and thermal energy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Relative molecular orientation can impact the onset of plasticity in molecular crystals

Abstract Creating or moving dislocations is the first step to dissipating mechanical energy via plastic deformation under contact loading. In molecular crystals there is both a lattice that defines crystal orientation and a relative orientation of the basis of the molecules. We define a normalization parameter which relates strain at yield, the hardness of the bulk crystal, and a distance parameter analogous to a Burgers vector that nominally predicts the relative ease of initiating plasticity in this broad class of materials. Analyzing the yield behavior of 10 different molecular crystals of varying space groups shows the inter-molecular orientation predicts the experimentally observed applied stress needed to nucleate dislocations. When molecules are oriented ‘parallel’ relative to one another the normalized maximum shear stress at the onset of plasticity is on the order of 3–5 times lower than when molecules within the crystal are ‘anti-parallel’, and molecules with a more equiaxed shape fall in between these bounds. This provides an initial indication of a structural feature which predicts the relative ease of initiating plasticity during contact loading in molecular crystals.

36 MATERIALS SCIENCE↗