SEARCH · Search NASA

Results for “aromatic side chains”

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.

SourceResearch connectionFrom yearThrough year

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

At least 19 records

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Improving Cooperative Interactions Between Halogenated Aromatic Additives and Aromatic Side Chain Acceptors for Realizing 19.22% Efficiency Polymer Solar Cells

Processing additive plays an important role in the standard operation procedures for fabricating top performing polymer solar cells (PSCs) through efficient interactions with key photovoltaic materials. However, improving interaction study of acceptor materials to high performance halogenated aromatic additives such as diiodobenzene (DIB) is a widely neglected route for molecular engineering toward more efficient device performances. Here, in this work, two novel Y-type acceptor molecules of BTP-TT and BTP-TTS with different aromatic side chains on the outer positions are designed and synthesized. The resulting aromatic side chains significantly enhanced the interactions between the acceptor molecules and DIB through an arene/halogenated arene interaction, which improved the crystallinity of the acceptor molecules and induced a polymorph with better photovoltaic performances. Thus, high power conversion efficiencies (PCEs) of 18.04% and 19.22% are achieved in binary and ternary blend devices using BTP-TTS as acceptor and DIB as additive. Aromatic side chain engineering for improving additive interactions is proved to be an effective strategy for achieving much higher performance photovoltaic materials and devices.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Gas-phase formation of the resonantly stabilized 1-indenyl (C 9 H 7 • ) radical in the interstellar medium

The 1-indenyl (C 9 H 7 • ) radical, a prototype aromatic and resonantly stabilized free radical carrying a six- and a five-membered ring, has emerged as a fundamental molecular building block of nonplanar polycyclic aromatic hydrocarbons (PAHs) and carbonaceous nanostructures in deep space and combustion systems. However, the underlying formation mechanisms have remained elusive. Here, we reveal an unconventional low-temperature gas-phase formation of 1-indenyl via barrierless ring annulation involving reactions of atomic carbon [C( 3 P)] with styrene (C 6 H 5 C 2 H 3 ) and propargyl (C 3 H 3 • ) with phenyl (C 6 H 5 • ). Macroscopic environments like molecular clouds act as natural low-temperature laboratories, where rapid molecular mass growth to 1-indenyl and subsequently complex PAHs involving vinyl side-chained aromatics and aryl radicals can occur. These reactions may account for the formation of PAHs and their derivatives in the interstellar medium and carbonaceous chondrites and could close the gap of timescales of their production and destruction in our carbonaceous universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Regions of hepatitis C virus E2 required for membrane association

Hepatitis C virus (HCV) uses a hybrid entry mechanism. Current structural data suggest that upon exposure to low pH and Cluster of Differentiation 81 (CD81), the amino terminus of envelope glycoprotein E2 becomes ordered and releases an internal loop with two invariant aromatic residues into the host membrane. Here, we present the structure of an amino-terminally truncated E2 with the membrane binding loop in a bent conformation and the aromatic side chains sequestered. Comparison with three previously reported E2 structures with the same Fab indicates that this internal loop is flexible, and that local context influences the exposure of hydrophobic residues. Biochemical assays show that the amino-terminally truncated E2 lacks the baseline membrane-binding capacity of the E2 ectodomain. Thus, the amino terminal region is a critical determinant for both CD81 and membrane interaction. These results provide new insights into the HCV entry mechanism.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

DOE OSTI2023

Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

36 MATERIALS SCIENCE↗

DOE OSTI2026

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗

DOE OSTI2022

Burn Intensity Drives the Alteration of Phenolic Lignin to (Poly) Aromatic Hydrocarbons as Revealed by Pyrolysis Gas Chromatography–Mass Spectrometry (Py-GC/MS)

High-intensity wildfires alter the chemical composition of organic matter, which is expected to be distinctly different from low-intensity prescribed fires. In this study, we used pyrolysis gas chromatography/mass spectrometry (Py-GC/MS), in conjunction with solid-state 13 C nuclear magnetic resonance (NMR) and Fourier transform infrared (FT-IR) spectroscopy, to assess chemical alterations from three wildfires and a long-term frequent prescribed fire site. Our results showed that black ash formed under moderate intensity burns contained less aromatic (ArH), polyaromatic hydrocarbon (PAH), and nitrogen-containing compounds (Ntg) but more lignin (LgC) and phenol compounds (PhC), compared to white ash formed under high intensity burns. Both 13 C NMR and FT-IR confirmed a higher relative percentage of carboxyl carbon in white ash, indicating the potential for higher water solubility and more mobile carbon, relative to black ash. Compared to wildfires, ash from low-intensity prescribed fire contained less ArH, PAH, and Ntg and more LgC and PhC. Controlled laboratory burning trials indicated that organic matter alteration was sensitive to the burn temperature, but not related to the fuel type (pine vs fir) nor oxygen absence/presence at high burn temperatures. This study concludes that higher burn temperatures resulted in higher (poly)aromatic carbon/nitrogen and lower lignin/phenol compounds.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Anion Exchange Ionomers: Impact of Chemistry on Thin-Film Properties

Ionomer thin-films (i.e., 20–100 nm) on supports serve as model systems to understand ionomer-catalyst interfacial behavior as well as the confinement-driven deviation in properties from bulk membranes. While ionomer thin-films have been examined for proton exchange ionomers, the thin-film properties of anion exchange ionomers (AEIs) remain largely unexplored. More importantly, delineating the convoluted impact of chemistry and confinement on thin-film morphology and hydration is of interest to advancing the field on functional ionic interfaces. In this work, these aspects are studied by using AEIs of different backbones (perfluorinated, aliphatic, and aromatic) and side chains (various lengths, and single versus dual functional groups). Quartz-crystal microbalance and spectroscopic ellipsometry are used to analyze density and coupled with calculated free volume fraction of thin-films to provide insights on their gas transport properties. AEI side-chain's chemical character plays a key role in how confinement modulates hydration (in thin-film versus bulk). Overall, the results elucidate the effects of backbone, side-chain chemistry versus anion/cation type in the confinement-driven changes in thin-film morphology and swelling. This study also provides new insights for tuning AEI transport functionalities at interfaces via chemistry, which can benefit the design and development of electrode-ionomers for alkaline membrane-based energy systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Water Dynamics of Superacid Aromatic Proton Exchange Membranes for Fuel Cell Applications

Proton exchange membranes (PEMs) with high conductivity are of critical importance for the development of fuel cells, electrolyzers, and other electrochemical technologies. In this research, poly(1,1,2,2-tetrafluoro-2-phenoxyethane-1-sulfonic acid) (PTPS) with an aromatic polymer main chain and a perfluorinated superacidic polymer side chain was synthesized. The water dynamics of PTPS were characterized across various length scales using a combination of Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR) and compared with Nafion, a standard perfluorinated PEM, and sulfonated poly(ether sulfone) (SPES 40), an aromatic PEM without perfluorinated superacid side chains. The T 1 and T 2 relaxation times of water in the samples probed by NMR increase from SPES 40 to PTPS to Nafion, indicating that the local motion of the water molecules becomes faster. This trend corresponds well with the relative fraction of bulk-like water determined using FTIR. At larger length scales, the diffusion coefficient of water was characterized using pulsed-field gradient NMR (PFG-NMR). At a longer diffusion time (Δ = 100 ms), PTPS has a smaller diffusion coefficient compared with both Nafion and SPES 40, due to restricted diffusion, and this effect is also evident in the proton conductivity of the hydrated membranes. From this comparison, it is apparent that the aromatic backbone and side chain type greatly influence the water dynamics in PEMs at various length scales and the water dynamics significantly impact the bulk proton conductivity. These insights will lead to new designs for aromatic PEMs and help to identify bottlenecks in current materials.

25 ENERGY STORAGE↗

DOE OSTI2022

Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin

Actin histidine N τ -methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3-catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N-nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Polymer Hole Transport Material Functional Group Tuning for Improved Perovskite Solar Cell Performance

As lead halide perovskites (LHPs) continue to achieve success as a light-harvesting material in perovskite solar cells (PSCs), exploring and understanding other materials in the device stack become increasingly important. Particularly, selection of suitable hole transport materials (HTMs) that demonstrate high performance and stability is imperative in the design of P-I-N PSCs. Presented here are a family of 12 structurally related polymers based on either fluorene or carbazole main chains with select aromatic side groups that introduce tunable properties for use in PSCs. How properties such as the highest occupied molecular orbital energy level, conductivity, glass-transition temperature, and wettability of the HTM affect the PSC performance is explored. Devices that incorporate the polymer HTMs perform well relative to PTAA in benchmark P-I-N PSC architectures while exhibiting similar or superior stability under accelerated aging studies. The relative synthetic simplicity and resultant performance of the HTMs in PSCs coupled with the ability to customize properties with different functional groups demonstrates the potential of this family of HTMs for a variety of LHP materials.

14 SOLAR ENERGY↗

DOE OSTI2025

Empirical evidence that glucan-interacting amino acid side chains within the transmembrane channel collectively facilitate cellulose synthase function

The fundamental mechanism of cellulose synthesis is widely conserved across Kingdoms and depends on cellulose synthases, which are processive, dual-function, family 2 glycosyltransferases (GT-2). These enzymes polymerize glucose on the cytoplasmic side of the plasma membrane and export the glucan chain to the cell surface through an integral transmembrane (TM) channel. Structural studies of active plant cellulose synthases (CESAs) have revealed interactions between the nascent glucan chain and the side chains of polar, charged, and aromatic amino acid residues that line the TM channel. However, the functional consequences of modifying these side chains have not been tested in vivo in CESAs or other processive GT-2s. To test this, we used an established in vivo assay based on genetic complementation of CESA5 in the moss, Physcomitrium patens. For accurate prediction of glucan-interacting amino acid residues, we generated a complete homotrimeric molecular model of PpCESA5 using a combination of homology and de novo modeling. All-atom molecular dynamics-based analyses of contact metrics and interaction energy identified 23 amino acid residues with high propensity to interact with the nascent glucan chain within the TM channel or on the apoplastic surface of PpCESA5. Mutating any one of 18 of these amino acid residues to alanine, thereby removing their side chains, abolished or impaired CESA function, with the strongest effects observed upon the loss of charged amino acid side chains. This provides direct evidence to support the hypothesis that multiple amino acid residues collectively maintain a smooth energy landscape within the TM channel to facilitate glucan translocation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Single-Molecule Electron Transport in Peptoids

Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure−function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N−C α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green’s function−density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N−C α position. Overall, this work provides new insights into the structure−function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.

Charge transport↗

DOE OSTI2025

Truncating 2D Framework Materials Down to a Single Pore: Synthetic Approaches and Opportunities

Here, in this Accounts article, we summarize our recent work on truncating conjugated two-dimensional framework materials down to a single pore, or a single macrocycle. Conjugated 2D architectures have emerged as one of the most synthetically adaptable motifs for coupling semiconductivity and porosity in metal–organic frameworks (MOFs) and covalent organic frameworks (COFs). However, despite their prevalence, 2D architectures have several limitations. In particular, the strong interlayer π–π stacking can limit both processability and the accessibility of internal active sites. We have found that simple macrocycles preserve key aspects of 2D framework structure and function, including porosity and out-of-plane electrical conductivity, while providing improved processability, surface tunability, and mass transport properties. In this article, we first describe our synthetic approach and general design considerations. Specifically, we show how ditopic analogues of the tritopic ligands commonly found in the synthesis of 2D MOFs and COFs can be used to achieve a diverse library of conjugated macrocycles that resemble fragments of semiconducting frameworks in both form and function. The length of the peripheral side chains, the size of the aromatic core, and the solubility of intermediates are all key variables in favoring selective macrocycle formation over undesired linear polymers and oligomers. Next, we highlight the unique advantages that macrocycles provide, including improved processability, atomically precise surface tunability, and greater active site accessibility. In particular, the identity of the peripheral side chains dramatically impacts both solubility and colloidal stability as well as crystal size and morphology. We further show how the solution processability and nanoscale dimensions of macrocycles can simplify electronic device fabrication and improve electrochemical performance. Finally, we end with a forward-looking discussion on how macrocycles offer a unique bridge between conjugated molecules and extended frameworks, enabling new application areas and fundamental science.

charge transport↗

DOE OSTI2020

Formation of phenanthrene via H–assisted isomerization of 2–ethynylbiphenyl produced in the reaction of phenyl with phenylacetylene

Model chemistry G3(MP2,CC)//B3LYP/6–311G(d,p) calculations of the potential energy surface for the reaction of phenyl radical (C 6 H 5 ) with phenylacetylene (C 8 H 6 ) have been carried out and combined with Rice–Ramsperger–Kassel–Marcus/Master Equation calculations of temperature– and pressure–dependent rate constants. The results showed that the reaction can serve as a viable source for the formation of phenanthrene via an indirect route involving a primary reaction of phenyl addition to the ortho carbon in the ring of phenylacetylene and H elimination producing 2–ethynylbiphenyl followed by secondary H–assisted isomerization of 2–ethynylbiphenyl to phenanthrene. In the secondary reaction, the H atom adds to the α carbon of the ethynyl side chain, then a six–member ring closure takes place followed by aromatization via an H loss. The channel of H addition to the side chain of 2–ethynylbiphenyl appears to be much faster than H addition to the ortho carbon in the ethynyl–substituted ring leading back to the initial C 6 H 5 + C 8 H 6 reactants. Rate constants for the primary C 6 H 5 + C 8 H 6 ⇌2–ethynylbiphenyl (p1) + H and secondary p1 + H⇌phenanthrene (p2) + H reactions have been computed in the temperature range of 500–2500 K at pressures of 30 Torr, 1, 10, and 100 atm and fitted to modified Arrhenius expressions. Here, the suggested kinetic scheme and rate constants are proposed as a prototype for the modeling of the growth of polycyclic aromatic hydrocarbons via the phenyl addition–dehydrocyclization (PAC) mechanism involving an addition of a PAH radical to an ethynyl–substituted PAH molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds

Biological deconstruction of lignocellulose for sustainable chemical production offers an opportunity to harness evolutionarily specialized enzymes and organisms for industrial bioprocessing. While hydrolysis of cellulose and hemicellulose by CAZymes yields fermentable sugars, ligninolysis releases a heterogeneous mix of aromatic compounds that likely play a crucial role in shaping microbial communities and microbial metabolism. Here, we interrogated the metabolomic and transcriptomic response of a lignocellulolytic anaerobic fungus, Neocallimastix californiae, to a heterogeneous mixture of aromatic compounds derived from lignin. Through exposing the fungus to both a concentration it might experience in its native environment and an elevated concentration of alkaline lignin, we observe that N. californiae transforms vanillin and that supplying alkaline lignin at 0.125 g/L, alongside cellulose, enhances the growth and polysaccharide-degrading activity of N. californiae. Altogether, our results further suggest that vanillin consumption, increased polymer-degrading activity, increased metabolic activity, and transcriptomic remodeling of amino acid synthesis genes all coincide with increased melanin production by fungal cells. These observations challenge previous notions that aromatics from lignocellulose only inhibit the growth and polymer deconstruction capabilities of the biomass-degrading anaerobic fungi (Neocallimastigomycetes). This study demonstrates that anaerobic fungi have a complex relationship with aromatic chemicals derived from lignin and hemicellulose and shift their metabolism in response to the addition of lignocellulose-derived aromatics to their growth medium. Further, as no known pathways for the biochemical transformation of aromatics were detected in these organisms despite observed transcriptome remodeling in the presence of aromatics, we suggest they might encode novel biochemical routes for scavenging amino acid building blocks from aromatic monomers derived from hemicellulose side chains and lignin.

Anaerobic fungi↗

DOE OSTI2025

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗