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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Leveraging Natural Language Processing and Generative Models in Molecular Chemistry: Property Prediction and Novel Compound Generation

The accurate prediction of molecular properties is important for the rational design and the advancement of green chemistry and sustainable materials research. However, the predictive power of traditional computational chemistry methods is limited due to computational restrictions. Here, in this study, we examine an alternative approach to the accurate prediction of properties of organic compounds: natural language processing (NLP)-based molecular embedding. Using viscosity, partition coefficient (log P), and enthalpy of vaporization as test properties through a survey of comprehensive datasets comprising 5695 data points for viscosity, 25 870 data points for log P, and 2296 data points for enthalpy of vaporization. These are important properties for the design of greener, safer, and sustainable chemical processes. Models were trained using NLP methods such as Mol2vec and fine-tuned ChemBERTa, and results were compared with traditional input featurization techniques such as Morgan fingerprints and quantum chemistry derived sigma profiles and DFT features. Among the various machine learning models, Mol2vec demonstrated superior predictive capabilities, achieving the highest correlation coefficient (R 2 = 0.945) and lowest RMSE (0.106 mPa s) for viscosity, as well as high accuracy for log P and enthalpy of vaporization predictions. These findings establish the Mol2vec featurization technique, graph-convolutional neural networks (GCNN), and fine-tuned ChemBERTa model as powerful tools for predictive modeling of organic compounds properties, offering a significant improvement over previously used featurization techniques and opening up strategies for very-high-throughput computational screening. Finally, we integrated ML models with hybrid language-model-based generative adversarial networks (LM-GAN) to generate novel molecular sequences with desirable properties for different research applications. The ability to computationally design solvents with lower viscosity, lower log P, and lower enthalpy of vaporization offers a data-driven route to accelerating the discovery of sustainable alternatives to traditionally toxic solvents.

ChemBERTa↗
NASA NTRS2008

Saturn Magnetospheric Impact on Surface Molecular Chemistry and Astrobiological Potential of Enceladus

The active south polar surface of Enceladus is exposed to strong chemical processing by direct interaction with charged plasma and energetic particles in the local magnetospheric environment of this icy moon. Chemical oxidation activity is suggested by detection of H202 at the surface in this region and less directly by substantial presence of C02, CO, and N2 in the plume gases. Molecular composition of the uppermost surface, including ejecta from plume activity, is radiolytically transformed mostly by penetrating energetic electrons with lesser effects from more depleted populations of energetic protons. The main sources of molecular plasma ions and E-ring dust grains in the magnetospheric environment are the cryovolcanic plume emissions from Enceladus. These molecular ions and the dust grains are chemically processed by magnetospheric interactions that further impact surface chemistry on return to Enceladus. For example, H20 neutrals dominating the emitted plume gas return to the surface mostly as H30+ ions after magnetospheric processing. Surface oxidant loading is further increased by return of radiolytically processed ice grains from the E-ring. Plume frost deposition and micrometeoroid gardening protect some fraction of newly produced molecular species from destruction by further irradiation. The evident horizontal and vertical mobility of surface ices in the south polar region drive mixing of these processed materials into the moon interior with potential impacts on deep ice molecular chemistry and plume gas production. Similarly as suggested previously for Europa, the externally driven source of radiolytic oxidants could affect evolution of life in any subsurface liquid water environments of Enceladus.

Cooper, Paul D.↗
NASA NTRS1987

Optical observations related to the molecular chemistry in diffuse interstellar clouds

Observations, which have been published since 1979, of molecular species in diffuse clouds are discussed. Particular attention is given to the ultraviolet measurements of CO with the Copernicus and IUE satellites and to ground-based optical measurements of CH, CH(+), CN, and 02. These data encompass large enough samples to test the chemical schemes expected to occur in diffuse clouds. Upper limits for other species (e.g., H2O, H2O(+), and C3) place restrictions on the pathways for molecular production. Moreover, analysis of the rotational distribution of the C2 molecule results in the determination of the physical conditions of the cloud. These parameters, including density, temperature, and the intensity of the radiation field, are necessary for modeling the chemistry.

Federman, S. R.↗
NASA NTRS2018

Blind to Chemistry: Molecular Contaminant Films We Could Be Missing During Visual Inspections and the Potential Impact to System Performance

Throughout the assembly, integration and test process, molecular contamination levels of space mission hardware are monitored to meet system performance requirements. Qualitatively, reflective surfaces and witness mirrors are continuously inspected for the visible presence of molecular contaminant films. Quantitatively, periodic reflectance measurements of witness mirrors indicate changes of mirror reflectivity over time due to the accumulation of molecular contaminant films. However, both methods only consider the presence of a contaminant film and not the molecular composition. Additionally, there is a risk that hardware may appear to be “visibly clean” even with a molecular contaminant film present on critical surfaces. To address these issues, experiments were performed to quantify the maximum molecular contaminant film that could be missed in visual inspections on witness mirrors with five different contaminants present. The corresponding changes in mirror reflectivity were modeled using the program STACK to determine the impact to space mission hardware performance. The results of this study not only show the criticality in considering the chemical make-up of molecular contaminant films on system performance, but also the need to recognize and understand the limitations of traditional visual inspection techniques on detecting molecular contaminant films.

Seasly, Elaine↗
NASA NTRS1992

A computer model for one-dimensional mass and energy transport in and around chemically reacting particles, including complex gas-phase chemistry, multicomponent molecular diffusion, surface evaporation, and heterogeneous reaction

Various chemically reacting flow problems highlighting chemical and physical fundamentals rather than flow geometry are presently investigated by means of a comprehensive mathematical model that incorporates multicomponent molecular diffusion, complex chemistry, and heterogeneous processes, in the interest of obtaining sensitivity-related information. The sensitivity equations were decoupled from those of the model, and then integrated one time-step behind the integration of the model equations, and analytical Jacobian matrices were applied to improve the accuracy of sensitivity coefficients that are calculated together with model solutions.

Cho, S. Y.↗
NASA NTRS2012

Carbon Isotope Chemistry in Molecular Clouds

Few details of carbon isotope chemistry are known, especially the chemical processes that occur in astronomical environments like molecular clouds. Observational evidence shows that the C-12/C-13 abundance ratios vary due to the location of the C-13 atom within the molecular structure. The different abundances are a result of the diverse formation pathways that can occur. Modeling can be used to explore the production pathways of carbon molecules in an effort to understand and explain the chemical evolution of molecular clouds.

carbon isotopes↗
NASA NTRS2009

Extraterrestrial Radiation Chemistry and Molecular Astronomy

Astronomical observations of both solar system and interstellar regions have revealed a rich chemical inventory that includes most classes of organic molecules and selected inorganics. For example, gas-phase ethylene glycol and SOz have been observed by astronomers, while solidphase detections include OCS, H2O2 , and the cyanate anion.' All of these are found in environments that are, by earthly standards, exceedingly hostile: temperatures of 10 - 100 K, miniscule densities, and near-ubiquitous ionizing-radiation fields. Beyond the simplest chemical species, these conditions have made it difficult-to-impassible to account for the observed molecular abundances using gas-phase chemistry, suggesting solid-phase reactions play an important role. In extraterrestrial environments, cosmic rays, UV photons, and magnetospheric radiation all drive chemical reactions, even at cryogenic temperatures. To study this chemistry, radiation astrochemists conduct experiments on icy materials, frozen under vacuum and exposed to sources such as keV electrons and MeV protons. Compositional changes usually are followed with IR spectroscopy and, in selected cases, more-sensitive mass-spectral techniques. This talk will review some recent results on known and suspected extraterrestrial molecules and ions. Spectra and reaction pathways will be presented, and predictions made for interstellar chemistry and the chemistry of selected solar system objects. Some past radiation-chemical contributions, and future needs, will be explored.

Hudson, Reggie L.↗
NASA NTRS1997

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Jaffe, Richard↗
NASA NTRS1972

Molecular beams in chemistry.

The molecular-beam technique is a means for producing isolated atoms or molecules within a narrow range of speed and solid angle. The phenomena studied with molecular beams can be classified as single-particle interactions, many-particle interactions, and two particle-interactions. The results of scattering experiments fall into two categories including collisions that do not result in atomic rearrangements and collisions that do. Experimental methods are discussed, giving attention to low-energy beams, high-energy beams, and intermediate-energy beams. Examples are presented to illustrate the information that can be obtained from elastic, inelastic, and reactive scattering.

Jordan, J. E.↗
NASA NTRS1997

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗
NASA NTRS1978

Nonequilibrium chemistry in shocked molecular clouds

The gas-phase chemistry is studied behind a 10-km/s shock propagating into a dense molecular cloud. The principal conclusions are that: the concentrations of certain molecules (CO, NH3, HCN, N2) are unperturbed by the shock; other molecules (H2CO, CN, HCO(+)) are greatly decreased in abundance; and substantial amounts of H2O, HCO, and CH4 are produced. Approximately 1 million yr (independent of the density) must elapse after shock passage before chemical equilibrium is attained.

Iglesias, E. R.↗
NASA NTRS1990

Carbon chemistry in dense molecular clouds: Theory and observational constraints

For the most part, gas phase models of the chemistry of dense molecular clouds predict the abundances of simple species rather well. However, for larger molecules and even for small systems rich in carbon these models often fail spectacularly. Researchers present a brief review of the basic assumptions and results of large scale modeling of the carbon chemistry in dense molecular clouds. Particular attention is to the influence of the gas phase C/O ratio in molecular clouds, and the likely role grains play in maintaining this ratio as clouds evolve from initially diffuse objects to denser cores with associated stellar and planetary formation. Recent spectral line surveys at centimeter and millimeter wavelengths along with selected observations in the submillimeter have now produced an accurate inventory of the gas phase carbon budget in several different types of molecular clouds, though gaps in our knowledge clearly remain. The constraints these observations place on theoretical models of interstellar chemistry can be used to gain insights into why the models fail, and show also which neglected processes must be included in more complete analyses. Looking toward the future, larger molecules are especially difficult to study both experimentally and theoretically in such dense, cold regions, and some new methods are therefore outlined which may ultimately push the detectability of small carbon chains and rings to much heavier species.

Blake, Geoffrey A.↗
NASA NTRS1993

The molecular matching problem

Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

Kincaid, Rex K.↗
DOE OSTI2026

Data and scripts associated with “Non-random processes impacting organic matter chemistry are maximized in mid-order streams”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Non-random processes impacting organic matter chemistry are maximized in mid-order streams” submitted to Limnology and Oceanography (L&O) by Danczak et al. (in review). This package contains data and scripts used to investigate dissolved organic matter (DOM) molecular chemistry and diversification processes across 47 surface-water sampling sites in the Yakima River Basin, Washington, USA, during an August 2021 sampling campaign. The package contains analyses of ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), geochemical measurements, geospatial attributes, molecular diversity, and meta-metabolome ecological null models needed to reproduce the main manuscript results. The underlying field data were pulled from exising data packages at https://doi.org/10.15485/1892052 (Fulton et al., 2022) and https://doi.org/10.15485/1898914 (Grieger et al., 2022). For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. We thank the following organizations for providing access to field locations for sample collection: the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, the Confederated Tribes and Bands of the Yakama Nation, and the Cowiche Canyon Conservatory. Research was conducted under Washington State Parks and Recreation Commission Scientific Research Permit #210901. We are grateful to the Yakama Nation Tribal Council and Yakama Nation Fisheries for their collaboration in facilitating sample collection and ensuring data usage aligns with their values and worldview. This data package contains an R-Markdown file for analyses and five folders: (1) Data, (2) Geospatial Data, (3) Supplemental_Files, (5) Figures_pdf, (4) and src. The Data folder contains tabular inputs and derived files used in the manuscript analysis. The Geospatial Data folder contains climate and water-balance, hydrologic, land-cover, population/regional water-use, stream, topographic, and stream-order attribute CSV files. The src folder contains scripts used to process data, run analyses, and generate figures. The Figures_pdf folder contains manuscript figure outputs. The Supplemental_Files folder contains supplemental analysis products. All files are .csv, .pdf, .html, .png, .R, .Rmd, .svg, or .tre. This data package is associated with the rcfsa-RC2-SPS_Null_Modeling repository found at https://github.com/river-corridors-sfa/rcfsa-RC2-SPS_Null_Modeling.

54 ENVIRONMENTAL SCIENCES↗