Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular functionalization”

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 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Probing Self-Assembly in Arginine–Oleic Acid Solutions with Terahertz Spectroscopy and X-ray Scattering

A study of the formation of microstructures in the reaction of oleic acid with arginine elucidates dynamical self-assembly processes at the molecular level. Terahertz spectroscopy combined with density functional calculations reveals the initial hydrogen-bonding motifs in the assembly process, leading to the formation of micelles and vesicles. Small-angle X-ray scattering measurements allow for kinetic analysis of the growth processes of these nanostructures, revealing a prenucleation pathway of vesicles and micelles which lead to spongelike structures. This final stage of the assembly into spongelike aggregates is investigated with optical microscopy. The formed structures only occur at pH > 8 and are resistant to extreme acidic and basic conditions. Here, a mechanistic pathway to the formation of the spongelike aggregates is described.

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

Molecular diversity of dissolved organic matter reflects macroecological patterns in river networks

Deciphering dissolved organic matter (DOM) molecular complexity is crucial for understanding ecosystem function. Using the continental-scale Worldwide Hydrobiogeochemistry Observation Network for Dynamic Rivers Systems (WHONDRS) Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) dataset, we reveal fundamental scaling patterns of DOM chemodiversity with watershed characteristics. Analysis of 54 river sites shows local and regional watershed features significantly influence DOM chemodiversity (2500–8718 unique formulae), exhibiting consistent scaling patterns across compound classes and a novel latitudinal gradient (decreasing diversity with increasing latitude). Scaling relationships for DOM composition vary by compound class. Crucially, the scaling parameters (B, baseline chemodiversity; Z, sensitivity) are linearly interrelated. This B–Z relationship is most robust for potentially bio-labile carbohydrates (coefficient of determination R 2 ≈ 0.85), diminishing for recalcitrant, plant-derived molecules (such as lignin), and indicates (potential) biolability-dependent coupling between baseline diversity and environmental responsiveness. These quantitative scaling relationships, with scaling exponents ranging from − 2.1 to 2.2 across compound classes, enable prediction of DOM composition across watersheds, offering a framework to understand ecosystem responses to environmental change. This research bridges biogeochemistry and ecology, providing tools to anticipate molecular transformations across scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Predicting molecular dipole moments by combining atomic partial charges and atomic dipoles

The molecular dipole moment ( μ ) is a central quantity in chemistry. It is essential in predicting infrared and sum-frequency generation spectra as well as induction and long-range electrostatic interactions. Furthermore, it can be extracted directly—via the ground state electron density—from high-level quantum mechanical calculations, making it an ideal target for machine learning (ML). Here, we choose to represent this quantity with a physically inspired ML model that captures two distinct physical effects: local atomic polarization is captured within the symmetry-adapted Gaussian process regression framework which assigns a (vector) dipole moment to each atom, while the movement of charge across the entire molecule is captured by assigning a partial (scalar) charge to each atom. The resulting “MuML” models are fitted together to reproduce molecular μ computed using high-level coupled-cluster theory and density functional theory (DFT) on the QM7b dataset, achieving more accurate results due to the physics-based combination of these complementary terms. The combined model shows excellent transferability when applied to a showcase dataset of larger and more complex molecules, approaching the accuracy of DFT at a small fraction of the computational cost. We also demonstrate that the uncertainty in the predictions can be estimated reliably using a calibrated committee model. The ultimate performance of the models—and the optimal weighting of their combination—depends, however, on the details of the system at hand, with the scalar model being clearly superior when describing large molecules whose dipole is almost entirely generated by charge separation. These observations point to the importance of simultaneously accounting for the local and non-local effects that contribute to μ ; furthermore, they define a challenging task to benchmark future models, particularly those aimed at the description of condensed phases.

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

Leveraging High-resolution Molecular Composition of Soil Organic Matter to Enhance Carbon Cycling Modeling

Soils store more carbon than the atmosphere and vegetation combined, yet Earth system models still struggle to predict how this vast reservoir will respond to environmental change. A central limitation is that most soil biogeochemical models represent organic matter using bulk conceptual pools or chemically homogeneous fractions, preventing direct use of rapidly expanding molecular-scale datasets. Here we develop and test a new soil decomposition framework that explicitly integrates high-resolution information on organic matter composition. First, we construct a molecularly informed litter decomposition module in which plant inputs are partitioned into five functional compound classes—carbohydrates, proteins, lignin-like aromatics, lipids, and carbonyls—using a molecular mixing model calibrated to solid-state 13 C Nuclear Magnetic Resonance (NMR) spectra. Class-specific kinetics, lignin-dependent physical protection, and substrate-driven microbial carbon use efficiency allow the module to capture metabolic tradeoffs associated with enzyme production and nutrient limitation. We then embed this litter module within a microbially explicit whole-soil model that tracks the transformation of these compound classes through particulate organic matter, dissolved organic matter, mineral-associated organic matter, and microbial biomass. High-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS) data are used to link internal pools to measurable soil organic matter fractions and to constrain key process parameters. Applications at soil-core and ecosystem scales demonstrate that the new model reproduces observed soil respiration dynamics while providing mechanistic attribution of CO 2 fluxes to specific chemical classes and pools. Compared to existing frameworks such as the Community Land Model soil biogeochemistry module and the Millennial model, our approach maintains competitive predictive skill while substantially improving interpretability and opportunities for data–model integration. This work illustrates a viable pathway for leveraging molecular-scale observations to reduce structural uncertainty in soil carbon–climate feedback projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Molecular tail chemistry controls thermal transport in fullerene films

Herein we report on the thermal conductivities of alkyl- and indene-group functionalized fullerene derivative thin films as measured via time domain thermoreflectance and steady state thermoreflectance. The thermal conductivities vary from 0.064 ± 0.007 W m – 1 K – 1 for [6,6]-phenyl C 61 -butyric acid methyl ester (PCBM) to 0.15 ± 0.017 W m – 1 K – 1 for indene- C 60 bisadduct at room temperature and do not exhibit significant temperature dependence from 300 to 375 K. In comparison to the thermal conductivity of PCBM, increasing the length of the alkyl chain, as in the case of [6,6]-phenyl C 61 -butyric acid butyl ester, and [6,6]-phenyl C 61 -butyric acid octyl ester leads to higher thermal conductivities. Likewise, increasing the number of alkyl chains attached to the fullerenes as in the case of bisadduct PCBM leads to a higher thermal conductivity compared to that of PCBM. We present atomistic insights into the role of chemical functionalization on the overall heat transfer in these fullerene derivatives by conducting molecular dynamics simulations and lattice dynamics calculations. The thermal conductivities predicted via our atomistic simulations qualitatively agree with the experimental trends for our fullerene derivatives. Lattice dynamics calculations reveal that one of the main factors dictating the ultralow thermal conductivities in fullerene derivatives is the large reduction in modal diffusivities in the molecular crystals as calculated from the Allen-Feldman model, thus providing an explanation for their largely reduced thermal conductivities as compared to that of C 60 crystals. The low diffusivities result from high degrees of localization of Einstein-like vibrations in fullerene derivatives due to the molecular side chains, providing the ability to dial-in the properties of these low thermal conductivity solids via molecular engineering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Molecular Coatings Improve the Selectivity and Durability of CO 2 Reduction Chalcogenide Photocathodes

The quest for solar-driven conversion of carbon dioxide to chemicals and fuels hinges upon the identification of an efficient, durable, and selective photocathode. Chalcogenide p-type semiconductors exemplified by chalcopyrite Cu(In,Ga)Se 2 (CIGS) have been effectively deployed as photocathodes. However, selectivity toward CO 2 reduction and durability of the commonly used CdS adlayer remain primary challenges. Here, we demonstrate that for the wide band gap CuGa 3 Se 5 chalcopyrite absorber these challenges are well addressed by an organic coating generated in situ from an N,N'-(1,4-phenylene)bispyridinium ditriflate salt in the electrolyte. The molecular additive provides a 30-fold increase in selectivity toward CO2R products compared to the unmodified system and lowers Cd corrosion at least 10-fold. This dual functionality highlights the promise of hybrid solid-state-molecular photocathodes for enabling durable and efficient solar fuel systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Computational methods based on density functional theory for reactions and processes involving electronic spin (Final Technical Report)

This award supports one post-doctoral researcher for 1.5 years. Publications that acknowledge this grant: Refs. 1–14. Refs. 3,10,12 assess current methodology for the evaluation of magnetic exchange couplings in transition metal complexes. In particular, Ref. 10 validates the use of an approximate (non-iterative) Green’s function approach for the calculation of magnetic exchange couplings and will be the foundation for Thrust 2 in this proposal. Refs. 3 and 12 focus on widely used density functional approaches based on the standard energy differences methodology for the particular case of oxo-bridged Fe(III) complexes. Refs. 2,4–7,11 apply current methodologies to problems of practical interest in molecular magnetism. Ref. 13 presents a methodology to explicitly simulate the dynamics of open quantum systems within density functional theory (DFT) calculations based on the Liouville-von Neumann equation of motion for quantum systems driven out-of-equilibrium. Ref. 8 uses non-collinear spin DFT to explain the mechanical behavior of magnetic mono-atomic Pt wires produced in break-junction experiments in the presence of a magnetic field.

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

Silicon nitride stress-optic microresonator modulator for optical control applications

Modulation-based control and locking of lasers, filters and other photonic components is a ubiquitous function across many applications that span the visible to infrared (IR), including atomic, molecular and optical (AMO), quantum sciences, fiber communications, metrology, and microwave photonics. Today, modulators used to realize these control functions consist of high-power bulk-optic components for tuning, sideband modulation, and phase and frequency shifting, while providing low optical insertion loss and operation from DC to 10s of MHz. In order to reduce the size, weight and cost of these applications and improve their scalability and reliability, modulation control functions need to be implemented in a low loss, wafer-scale CMOS-compatible photonic integration platform. The silicon nitride integration platform has been successful at realizing extremely low waveguide losses across the visible to infrared and components including high performance lasers, filters, resonators, stabilization cavities, and optical frequency combs. Yet, progress towards implementing low loss, low power modulators in the silicon nitride platform, while maintaining wafer-scale process compatibility has been limited. Here we report a significant advance in integration of a piezo-electric (PZT, lead zirconate titanate) actuated micro-ring modulation in a fully-planar, wafer-scale silicon nitride platform, that maintains low optical loss (0.03 dB/cm in a 625 µm resonator) at 1550 nm, with an order of magnitude increase in bandwidth (DC - 15 MHz 3-dB and DC - 25 MHz 6-dB) and order of magnitude lower power consumption of 20 nW improvement over prior PZT modulators. The modulator provides a >14 dB extinction ratio (ER) and 7.1 million quality-factor (Q) over the entire 4 GHz tuning range, a tuning efficiency of 162 MHz/V, and delivers the linearity required for control applications with 65.1 dB·Hz 2/3 and 73.8 dB·Hz 2/3 third-order intermodulation distortion (IMD3) spurious free dynamic range (SFDR) at 1 MHz and 10 MHz respectively. We demonstrate two control applications, laser stabilization in a Pound-Drever Hall (PDH) lock loop, reducing laser frequency noise by 40 dB, and as a laser carrier tracking filter. This PZT modulator design can be extended to the visible in the ultra-low loss silicon nitride platform with minor waveguide design changes. This integration of PZT modulation in the ultra-low loss silicon nitride waveguide platform enables modulator control functions in a wide range of visible to IR applications such as atomic and molecular transition locking for cooling, trapping and probing, controllable optical frequency combs, low-power external cavity tunable lasers, quantum computers, sensors and communications, atomic clocks, and tunable ultra-low linewidth lasers and ultra-low phase noise microwave synthesizers.

Wang, Jiawei (ORCID:0000000257965220)↗
DOE OSTI2026

Assessing the Limitations of Self-Interaction-Corrected Functionals for Describing the Hydrated Electron

Simulating the hydrated electron using density functional theory is challenging due to the prevalence of self-interaction error in standard functionals. Hybrid functionals like PBEh(40) can reasonably describe the chemistry of an excess electron in water and partially mitigate self-interaction error by incorporating exact Hartree–Fock exchange, but they are computationally expensive making them impractical for large-scale and long-time ab initio molecular dynamics simulations. Explicit self-interaction correction schemes that are applied on an orbital-by-orbital basis offer a potential alternative when the correction is limited to the singly occupied molecular orbital obtained with a generalized gradient approximation functional. Here, we examine whether the Perdew–Zunger self-interaction correction scheme applied to the revPBE functional can provide a computationally efficient and physically sensible alternative to PBEh(40) for the hydrated electron. We find that functionals incorporating a self-interaction correction scheme should be viewed with caution when applied to the hydrated electron and its reactivity. Furthermore, we show that it is critical to consider extensive sampling and diverse chemical environments when validating their performance.

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

Altered Cardiac Energetics and Mitochondrial Dysfunction in Hypertrophic Cardiomyopathy

Background: Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure–function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. Here, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM. Methods: We performed a comprehensive multiomics profile of the molecular (transcripts, metabolites, and complex lipids), ultrastructural, and functional components of HCM energetics using myocardial samples from 27 HCM patients and 13 normal controls (donor hearts). Results: Integrated omics analysis revealed alterations in a wide array of biochemical pathways with major dysregulation in fatty acid metabolism, reduction of acylcarnitines, and accumulation of free fatty acids. HCM hearts showed evidence of global energetic decompensation manifested by a decrease in high energy phosphate metabolites (ATP, ADP, and phosphocreatine) and a reduction in mitochondrial genes involved in creatine kinase and ATP synthesis. Accompanying these metabolic derangements, electron microscopy showed an increased fraction of severely damaged mitochondria with reduced cristae density, coinciding with reduced citrate synthase activity and mitochondrial oxidative respiration. These mitochondrial abnormalities were associated with elevated reactive oxygen species and reduced antioxidant defenses. However, despite significant mitochondrial injury, HCM hearts failed to upregulate mitophagic clearance. Conclusions: Overall, our findings suggest that perturbed metabolic signaling and mitochondrial dysfunction are common pathogenic mechanisms in patients with HCM. These results highlight potential new drug targets for attenuation of the clinical disease through improving metabolic function and reducing mitochondrial injury.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Multilevel Computational Studies Reveal the Importance of Axial Ligand for Oxygen Reduction Reaction on Fe–N–C Materials

The systematic improvement of Fe–N–C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe–N–C materials is the formation of the Fe III –OOH intermediate. They also show that an active site model with a water molecule axially ligated to the iron center throughout the catalytic cycle produces results that are consistent with the experimental measurements. In particular, reliable prediction of the ORR onset potential and the Fe(III/II) redox potential associated with the conversion of Fe III –OH to Fe II and desorbed H 2 O requires an axial H 2 O co-adsorbed to the iron center. The observation of a five-coordinate rather than four-coordinate active site has significant implications for the thermodynamics and mechanism of ORR. Importantly, these findings highlight the importance of solvent–substrate interactions and surface charge effects for understanding the PCET reaction mechanisms and transition-metal redox couples under realistic electrochemical conditions.

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

Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH 2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidal C ≡ C feature in PHTB can be ascribed to its twisted nature. The ability to simulate such subatomic images in nc-AFM reflects the accuracy and efficiency of calculating quantum forces in real space.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Discovery of multi-functional polyimides through high-throughput screening using explainable machine learning

Polyimides have been widely used in modern industries because of their excellent mechanical and thermal properties, e.g., high-temperature fuel cells, displays, and aerospace composites. However, it usually takes decades of experimental efforts to develop a successful product. Aiming to expedite the discovery of high-performance polyimides, we utilize computational methods of machine learning (ML) and molecular dynamics (MD) simulations. Our study provides compelling evidence for the effectiveness of a data-driven approach in discovering novel polyimides. We first build a comprehensive library of more than 8 million hypothetical polyimides based on the polycondensation of existing dianhydride and diamine/diisocyanate molecules. Then we establish multiple ML models for the thermal and mechanical properties of polyimides based on their experimentally reported values, including glass transition temperature, Young’s modulus, and tensile yield strength. The obtained ML models demonstrate excellent predictive performance in identifying the key chemical substructures influencing the thermal and mechanical properties of polyimides. The use of explainable machine learning describes the effect of chemical substructures on individual properties, from which human experts can understand the cause of the ML model decision. Applying the well-trained ML models, we obtain property predictions of the 8 million hypothetical polyimides. Then, we screen the whole hypothetical dataset and identify three (3) best-performing novel polyimides that have better-combined properties than existing ones through Pareto frontier analysis. For an easy query of the discovered high-performing polyimides, we also create an online platform https://polyimide-explorer.herokuapp.com/ that embeds the developed ML model with interactive visualization. Furthermore, we validate the ML predictions through all-atom MD simulations and examine their synthesizability. The MD simulations are in good agreement with the ML predictions and the three novel polyimides are predicted to be easy to synthesize via Schuffenhauer’s synthetic accessibility score. Following the proposed ML guidance, we successfully synthesized a novel polyimide and the experimentally obtained high glass transition/thermal decomposition temperature demonstrated its excellent thermal stability. Here our study demonstrates an efficient way to expedite the discovery of novel polymers using ML prediction and MD validation. The high-throughput screening of a large computational dataset can serve as a general approach for new material discovery in other polymeric material exploration problems, such as organic photovoltaics, polymer membranes, and dielectrics.

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

Molecular and Topographical Organization: Influence on Cicada Wing Wettability and Bactericidal Properties

Numerous natural surfaces have micro/nanostructures that result in extraordinary functionality, such as superhydrophobicity, self-cleaning, antifogging, and antimicrobial properties. One such example is the cicada wing, where differences in nanopillar geometry and composition among species can impact and influence the degree of exhibited properties. To understand the relationships between surface topography and chemical composition with multifunctionality, the wing properties of Neotibicen pruinosus (superhydrophobic) and Magicicada cassinii (hydrophobic) cicadas are investigated at time points after microwave-assisted extraction of surface molecules to characterize the chemical contribution to nanopillar functionality. Electron microscopy of the wings throughout the extraction process illustrates nanoscale topographical changes, while concomitant changes in hydrophobicity, bacterial fouling, and bactericidal properties are also measured. Extract analysis reveals the major components of the nanostructures to be fatty acids and saturated hydrocarbons ranging from C17 to C44. Effects on the antimicrobial character of a wing surface with respect to the extracted chemicals suggest that the molecular composition of the nanopillars plays both a direct and an indirect role in concert with nanopillar geometry. The data presented not only correlates the nanopillar molecular organization to macroscale functional properties, but it also presents design guidelines to consider during the replication of natural nanostructures onto engineered substrates to induce desired properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas–polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.

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

Deciphering the small-angle scattering of polydisperse hard spheres using deep learning

We introduce a deep learning approach for analyzing the scattering function of the polydisperse hard sphere system. We use a variational autoencoder-based neural network to learn the bidirectional mapping between the scattering function and the system parameters, including the volume fraction and polydispersity. Such that the trained model serves both as a generator that produces a scattering function from the system parameters and an inferrer that extracts system parameters from the scattering function. We first generate a scattering dataset by carrying out molecular dynamics simulations of the polydisperse hard spheres modeled by the truncated-shifted Lennard-Jones model, then analyze the scattering function dataset using singular value decomposition to confirm the feasibility of dimensional compression. Then, we split the dataset into training and testing sets and train our neural network on the training set only. Our generator model produces a scattering function with significantly higher accuracy compared to the traditional Percus–Yevick approximation and β correction, and the inferrer model can extract the volume fraction and polydispersity with much higher accuracy than traditional model functions.

Ding, Lijie [ORNL] (ORCID:0000000227454606)↗
DOE OSTI2024

Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study

In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Molecular fingerprint and machine learning to accelerate design of high-performance homochiral metal–organic frameworks

In this report computational screening was employed to calculate the enantioseparation capabilities of 45 functionalized homochiral metal–organic frameworks (FHMOFs), and machine learning (ML) and molecular fingerprint (MF) techniques were used to find new FHMOFs with high performance. With increasing temperature, the enantioselectivities for (R,S)-1,3-dimethyl-1,2-propadiene are improved. The “glove effect” in the chiral pockets was proposed to explain the correlations between the steric effect of functional groups and performance of FHMOFs. Moreover, the neighborhood component analysis and RDKit/MACCS MFs show the highest predictive effect on enantioselectivities among the four ML classification algorithms with nine MFs that were tested. Based on the importance of MF, 85 new FHMOFs were designed, and a newly designed FHMOF, NO 2 -NHOH-FHMOF, with high similarity to the optimal MFs achieved improved chiral separation performance, with enantioselectivities of 85%. The design principles and new chiral pockets obtained by ML and MFs could facilitate the development of new materials for chiral separation.

molecular fingerprint↗