Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MOLECULAR INTERACTION”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Effect of tert -Butyl Substitution on the Interactions of Cobalt Phthalocyanine with a Carbon Monoxide-Functionalized Tip

Supported cobalt phthalocyanines (CoPc) are promising catalysts for CO 2 reduction, a critical process for mitigating greenhouse gas emissions. Enhancing the catalytic performance of CoPc involves modifying the interaction between the cobalt center and intermediate species. This study focuses on the effects of tert-butyl substitution on CoPc using (tert-butyl) 4 CoPc, where the substitution can both directly alter the molecule’s intramolecular electronic structure and indirectly alter it by the bulky group weakening the interaction with the support. Toward this end, we investigated the structural and chemical properties of (tert-butyl) 4 CoPc on a Ag(111) surface at the single-molecule level using three-dimensional atomic force microscopy (AFM) with a CO-terminated tip and discussed them in comparison with data for unmodified CoPc and amino-substituted CoPc. Notably, distance-dependent force measurements revealed anomalies in the tert-butyl groups’ force curves, attributed to their rotational flexibility. The tert-butyl (t-butyl) groups were also observed to increase the attraction of the central Co atom to CO, but this effect was attributed largely to enhanced interactions of the back of the tip with the peripheral t-butyl groups. In conclusion, while this longer-range interaction would not be expected to impact the interaction of small molecules with the catalytic center, the results reveal the ability of AFM to characterize longer range environmental interactions that can enhance adsorption and subsequent reactions of larger molecules, as well as the role side chains that offer configurational adaptability may play in these interactions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Post-Modification of Crystalline Peptoid Nanomembranes with Active Nanoparticles for Efficient Photooxidation of a Mustard Gas Simulant

Peptoids (or poly-N-substituted glycines) hold immense potential for assembling into hierarchically structured functional materials via controlled molecular interactions. To create self-assembled materials with tailored functionalities, peptoid sequences are often conjugated with reactive or recognition motifs to enable applications including specific binding, biomimetic catalysis, and fluorescence imaging. However, the direct integration of bulky functional motifs into peptoid sequences can disrupt assembly processes and structural outcomes. Herein, we present a post-modification strategy for functionalizing pre-formed 2D crystalline assemblies. Through introducing clickable active sites, such as azide, alkyne, or thiol groups into a peptoid sequence, site-specific conjugation is achieved post-assembly via efficient “click”-type reactions. This strategy enables the ordered alignment of functional groups and gold nanoparticles (Au NPs) on the surface of 2D peptoid nanomaterials with controlled density, while preserving their high crystallinity and structural integrity. Furthermore, we demonstrated that nanomembranes functionalized with both Au NPs and porphyrins enhance the efficiency and selectivity of the photooxidation of 2-chloroethyl ethyl sulfide, a simulant of sulfur mustard. This innovative strategy lays the groundwork for advancing peptoid-based functional materials across diverse applications, from catalysis to biomedicine.

Chemistry↗
DOE OSTI2024

Tailoring Interface Energies via Phosphonic Acids to Grow and Stabilize Cubic FAPbI 3 Deposited by Thermal Evaporation

Coevaporation of formamidinium lead iodide (FAPbI 3 ) is a promising route for the fabrication of highly efficient and scalable optoelectronic devices, such as perovskite solar cells. However, it poses experimental challenges in achieving stoichiometric FAPbI 3 films with a cubic structure (α-FAPbI 3 ). In this work, we show that undesired hexagonal phases of both PbI 2 and FAPbI 3 form during thermal evaporation, including the well-known 2H-FAPbI 3 , which are detrimental for optoelectronic performance. We demonstrate the growth of α-FAPbI 3 at room temperature via thermal evaporation by depositing phosphonic acids (PAc) on substrates and subsequently coevaporating PbI 2 and formamidinium iodide. We use density-functional theory to develop a theoretical model to understand the relative growth energetics of the α and 2H phases of FAPbI 3 for different molecular interactions. Experiments and theory show that the presence of PAc molecules stabilizes the formation of α-FAPbI 3 in thin films when excess molecules are available to migrate during growth. This migration of molecules facilitates the continued presence of adsorbed organic precursors at the free surface throughout the evaporation, which lowers the growth energy of the α-FAPbI 3 phase. Our theoretical analyses of PAc molecule–molecule interactions show that ligands can form hydrogen bonding to reduce the migration rate of the molecules through the deposited film, limiting the effects on the crystal structure stabilization. Our results also show that the phase stabilization with molecules that migrate is long-lasting and resistant to moist air. These findings enable reliable formation and processing of α-FAPbI 3 films via vapor deposition.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Long-Range Interaction between Molecules with Electronic Degeneracy: Beyond the Born–Oppenheimer Approximation

Long-range intermolecular interaction plays an essential role in (ultra)cold collisions. For monomers with degenerate electronic states, an accurate description of the long-range interaction can be challenging due to the potential breakdown of the Born–Oppenheimer approximation. In this work, we developed a general method to construct long-range interaction potential energy surfaces (IPESs) between arbitrary molecules using the degenerate perturbation theory of Schrödinger. To further simplify the application of this method, a group-theoretical method is introduced to identify nonzero components of electrostatic properties of monomers, especially for the nonlinear molecules. To demonstrate this approach, we report the long-range IPESs of the O( 3 P)–OH( 2 Π) and OH( 2 Π)–OH( 2 Π) systems. The excellent agreement with ab initio calculations in large separations, even near electronic degeneracies, confirms the accuracy of our approach. The method is expected to lay the groundwork for the accurate investigation of (ultra)cold collisional dynamics involving open-shell species.

ab initio calculations↗
DOE OSTI2025

Photoinduced twist and untwist of moiré superlattices

This paper directly observes femtosecond photoinduced twist–untwist motion of WSe₂/MoSe₂ moiré superlattices using ultrafast electron diffraction, showing that optical excitation can dynamically reconfigure moiré lattice structure and interlayer coupling. It supports the proposal by establishing the team’s ability to probe ultrafast interfacial and moiré dynamics, which is relevant to using moiré TMDs as reconfigurable platforms for controlling spin, charge, and molecular interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Bio-inspired multiscale design for perovskite solar cells

Metal halide perovskite semiconductors have attractive light-harvesting and charge-carrier transport properties for photovoltaics. Perovskite solar cells (PSCs) and modules have demonstrated their commercial promise with high power conversion efficiencies, but still face stability challenges. In this Review, we explore how biomaterials offer design inspiration for the development of durable and efficient PSCs at three different scales. At the molecular level, bio-inspired molecular interactions are harnessed towards crystallization control and degradation prevention, which offers an enhancement in long-term maximum-power-point tracking stability. At the microstructural level, self-healing and strength-enhancing strategies, utilizing dynamic bonds and interfacial reinforcement, can help PSCs to recover from physical damage and maintain high performance. At the device level, macroscopic functionalities, such as moth-eye-inspired structures tailored to different layers, can collectively enable antireflection, radiative cooling and self-cleaning to optimize light management, heat dissipation and encapsulation in PSCs. Bio-inspired PSC research can combine improved efficiency and lifetime, with abundant, biocompatible alternatives to conventional stabilizers. Future efforts should focus on screening bioinspired molecules to optimize film crystallization and stability, developing self-healing mechanisms triggered by operational stress, designing cost-efficient biomicrostructures, and integrating multifunctional encapsulation to enhance the efficiency and lifespan of PSCs.

Duan, Tianwei↗
DOE OSTI2024

Molecular structures of residual solvent in polyacrylonitrile based electrolytes: Implications for conductivity and stability

Lithium-ion batteries increasingly play significant roles in modern technologies; however, increased energy density also raises concerns about electrolyte safety. Traditional electrolytes that use volatile organic solvents face risks of thermal runaways and fires from electrode shorting. In response, polymer-based solid electrolytes have been developed for replacement. Polyacrylonitrile (PAN) is a promising fire-resistant component for electrolyte fabrication, but its limited solubility necessitates using low-volatility solvents, which are notoriously difficult to remove in subsequent drying processes. Here, we use femtosecond two-dimensional infrared spectroscopy to provide an in-depth understanding of how residual solvent from processing affects the molecular structures and dynamics within a polymer electrolyte. To this end, linear and nonlinear infrared spectroscopies are employed to interrogate the molecular interactions in PAN-based electrolytes containing various contents of N,N-dimethylformamide (DMF). We show that the amount of DMF within the PAN electrolyte affects the Li+ structure. Further, the coordination can proceed through the carbonyl group and/or the amide nitrogen to form antiparallel structures with the nitrile groups of PAN through dipole–dipole interactions. The free motion of DMF is drastically inhibited upon interaction with Li+ and PAN, which decreases the ionic conductivity and potentially affects the stability (resistance toward removal and chemical decomposition). These findings have implications for the design and processing of solid polymer electrolytes.

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

Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning

Prediction of peptide secondary structure is challenging because of complex molecular interactions, sequence-specific behavior, and environmental factors. Traditional design strategies, based on hydrophobicity and structural propensity, can be biased and could indeed prevent discovery of interesting, diverse, and unconventional peptides with desired nanostructure assembly. Using β sheet formation in pentapeptides as a case study, we used an integrated high-throughput experimental workflow and an artificial intelligence–driven active learning framework to improve prediction accuracy of self-assembly. By focusing on sequences where machine learning (ML) predictions deviate from conventional design strategies, we synthesized and tested 268 pentapeptides, successfully finding 96 forming β sheet assemblies, including unconventional sequences (e.g., ILFSM, LMISI, MITIY, MISIW, and WKIYI) not predicted by traditional methods. Our ML models outperformed conventional β sheet propensity tables, revealing useful chemical design rules. A web interface is provided to facilitate community access to these models. This work highlights the value of ML-driven approaches in overcoming the limitations of current peptide design strategies.

Talluri, Y. Nissi [Indian Inst. of Technology (IIT↗
DOE OSTI2025

Microbes display broad diversity in cobamide preferences

ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.

Mok, Kenny C. (ORCID:0000000252276987)↗
DOE OSTI2025

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

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

Interactions between molecular-scale biogeochemical processes and hyporheic exchange for understanding coupled Fe-S-C cycling in iron-rich riparian wetlands (Final Technical Report)

Riparian wetlands are dynamic interfaces that exert strong control over water quality, contaminant mobility, and greenhouse gas emissions. These systems are characterized by hyporheic exchange between oxic surface water and anoxic groundwater, which generates steep redox gradients and promotes spatially and temporally variable microbial activity. Despite growing recognition of tightly coupled iron (Fe), sulfur (S), and carbon (C) cycling in these environments, the mechanisms governing these interactions—particularly under low-sulfate freshwater conditions—remain poorly constrained. This project developed a mechanistic understanding of how hydrologic variability and microbial processes interact to control Fe–S–C cycling in iron-rich riparian wetlands. Using a multi-scale and multi-method approach integrating field observations, geochemical and spectroscopic analyses, metagenomics, and reactive transport modeling, we demonstrate that “cryptic” sulfur cycling—rapid sulfur transformations involving intermediate-valence species—plays a dominant and previously underrecognized role in freshwater wetlands. These processes persist despite low sulfate concentrations and significantly influence iron reduction, carbon mineralization, and methane dynamics. The results show that cryptic sulfur cycling enhances dissolved Fe 2+ production, regulates methane concentrations, and is strongly controlled by climate-driven hydrologic fluxes. By linking hydroclimate, subsurface flow, and biogeochemical reactions, this work provides a predictive framework for understanding how wetland systems respond to environmental change, with direct implications for water quality and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Influence of Polymer and Support Interactions on the Electrocatalytic Properties of Heterogenized Molecular Complexes

Heterogenized molecular catalysts have been the subject of increasing interest in the context of electrochemical small molecule activation due to the possibility of active site homogeneity and tunability, which can surpass many nanostructured materials. When molecular catalysts strongly interact with carbon supports through π–π interactions, they tend to show higher selectivity and activity during heterogeneous electrochemical reactions. Indeed, ligand modifications in the secondary sphere that allow for more π–π overlap between catalyst and carbon support often show improved performance. Interactions between catalyst and polymer binder are also a possible modulus of control in these reactions, either through coordinating moieties that interact with active sites or through control over substrate or product transport. Finally, the covalent linking of molecular complexes onto carbon materials has also been shown to result in high activity and stability. Recent advances in the use of carbon supports, both through covalent and non-covalent interactions, and polymers to alter small molecule activation by heterogenized molecular catalysts are summarized in this Perspective.

Johnson, Elizabeth K. [University of Virginia, Cha↗
DOE OSTI2025

Molecular axis distribution moments in ultrafast transient absorption spectroscopy: A path toward ultrafast quantum state tomography

In ultrafast time-resolved experiments with gas phase molecules, the alignment of the molecular axis relative to the polarization of the interacting laser pulses plays a crucial role in determining the dynamics following this light–matter interaction. The molecular axis distribution is influenced by the interacting pulses and is intrinsically linked to the electronic coherences of the excited molecules. However, in typical theoretical calculations of such interactions, the signal is either calculated for a single molecule in the molecular frame or averaged over all possible molecular orientations to compare with the experiment. Such averaging removes information about anisotropy in the molecular-axis distribution, even though anisotropic contributions can play a significant role in the measured experimental signal. Here, we calculate the laboratory frame transient electronic first-order polarization [P (1) ] spectra in terms of separated molecular frame and laboratory frame quantities. The laboratory frame polarizations are compared with orientation-averaged quantum master equation calculations, demonstrating that orientation-averaging captures only the isotropic contributions. We show that our formalism also allows us to evaluate the anisotropic contributions to the spectrum. Lastly, we discuss the application of this approach to achieve ultrafast quantum state tomography using transient absorption spectroscopy and field observables in nonlinear spectroscopy.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Molecular Modeling of Surfactant Interaction on Phospholipid Bilayers Mimicking Corneal Epithelium

Surfactants found in consumer products can compromise eye corneal membrane integrity upon accidental exposure. Traditional in vitro and in vivo approaches to evaluate membrane–surfactant interaction pose experimental limitations such as species variability, reproducibility, and most often do not provide the overall picture. These limitations motivate the use of in silico models to study phenomena like cellular disruption assays caused by surfactants at the molecular scale. In this work, coarse-grained molecular dynamics simulations have been employed to investigate how nonionic alcohol ethoxylate (AE) and anionic surfactant alcohol ethoxy sulfate (AES) interact with lipid bilayer liposomes that mimic corneal epithelial cell membranes. The spherical liposome is composed of 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phospho-l-serine (DOPS), and cholesterol, resembling the composition of the corneal epithelial cells’ membrane bilayer. The simulation consisted of varying degrees of representative surfactant compositions and two initial types of surfactant configurations within or outside the liposome. Our results reveal that both surfactants induce outer leaflet bulging, agreeing with membrane solubilization models. The more highly ethoxylated surfactant, AE, caused more consistent inner leaflet disruption than AES, resulting in significantly more water permeation and membrane thinning. In addition, both surfactants increase the lateral diffusion of lipids within the membrane layers, with higher ethoxylated AE showing a stronger effect than AES. This study demonstrates how surfactant structure and localization influence bilayer membrane integrity, offering mechanistic insights into the irritation potential, thus guiding the rational design of effective surfactant-based formulations.

Lipids↗
DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗
DOE OSTI2025

Attosecond control and measurement of chiral photoionization dynamics

Many chirality-sensitive light–matter interactions are governed by chiral electron dynamics. Therefore, the development of advanced technologies making use of chiral phenomena would critically benefit from measuring and controlling chiral electron dynamics on their natural attosecond timescales. Such endeavours have so far been hampered by the lack of characterized circularly polarized attosecond pulses, an obstacle that has recently been overcome. Here we introduce chiroptical spectroscopy with attosecond pulses and demonstrate attosecond coherent control over photoelectron circular dichroism (PECD), as well as the measurement of chiral asymmetries in the forward–backward and angle-resolved photoionization delays of chiral molecules. We show that co-rotating attosecond and near-infrared (IR) pulses can nearly double the PECD and even change its sign compared with single-photon ionization. We demonstrate that chiral photoionization delays depend on both polar and azimuthal angles of photoemission in the light-propagation frame, requiring 3D momentum resolution. We measure forward–backward chiral-sensitive delays of up to 60 as and polar-angle-resolved photoionization delays of up to 240 as, which include an asymmetry of about 60 as originating from chirality in the continuum–continuum transitions. Attosecond chiroptical spectroscopy opens the door to quantitatively understanding and controlling the dynamics of chiral molecules on the electronic timescale.

Atomic and molecular interactions with photons↗
DOE OSTI2025

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗