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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme‐binding fold

The opportunistic pathogen Pseudomonas aeruginosa can utilize polyamines (including putrescine, cadaverine, 4‐aminobutyrate, spermidine, and spermine) as its sole source of carbon and nitrogen. Spermidine dehydrogenase (SpdH) is a component of one of the two polyamine utilization pathways identified in P . aeruginosa , but little is known about its structure and function. Here, we report the first crystal structure of SpdH from P . aeruginosa to 1.85 Å resolution. The resulting core structure confirms that SpdH belongs to the polyamine oxidase (PAO) family with flavin‐binding and substrate‐binding domains. A unique N‐terminal extension wraps around the flavin‐binding domain of SpdH and is required for heme binding, placing a heme cofactor in close proximity to the FAD cofactor. Structural and mutational analysis reveals that residues in the putative active site at the re side of the FAD isoalloxazine ring form part of the catalytic machinery. PaSpdH features an unusual active site and lacks the conserved lysine that forms part of a lysine–water–flavin N5 atom interaction in other PAO enzymes characterized to date. Mutational analysis further confirms that heme is required for catalytic activity. This work provides an important starting point for understanding the role of SpdH, which occurs universally in P . aeruginosa strains, in polyamine metabolism.

Che, Shiyou↗
DOE OSTI2025

Ring Pull Strain Analysis Version 1.1

This report details an analysis package, Ring Pull Strain Analysis (RPSA), that can be used to present and quantify digital image correlation (DIC) data as it relates to a gaugeless ring pull test. Gaugeless ring pull is a testing technique for mechanical testing of small annular samples, usually cut from a thin-walled tube. DIC data is often necessary for this kind of test because bending moments present on the ring cause a non-uniform strain distribution and localized measurements are necessary. In addition, the annular geometry of a ring lends itself to a polar representation, which is not present with typical DIC analysis methods. RPSA was made to calculate and plot the polar representation of strain from standard pre-processed DIC data of a gaugeless ring pull test. Further analysis can be done on ring pull including a quasi-uniaxial tensile analysis and coating analysis, which are also performed by RPSA. In addition, due to the universality of DIC plotting and ring pull test analysis, RPSA can accommodate a wide variety of tests, though it is tailored for ring pull testing. This report details how RPSA works, including the theory, assumptions, and logic behind the calculations and the structure of the program.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Solution Structure and Scaling Laws of Cylindrical and Tapered Bottlebrush Polymers

Bottlebrush polymers are a unique class of macromolecular architectures with a plethora of potential industrial and pharmaceutical applications that critically depend on the bottlebrush shape and dimensions. Here, a systematic series of 12 cylindrical and 12 cone-shaped (tapered) bottlebrush polymers with poly(tert-butyl acrylate) (PtBA) or polystyrene (PS) side chains were synthesized using the sequential addition of macromonomers ring-opening metathesis polymerization (SAM-ROMP) grafting-through method. Small-angle neutron scattering (SANS) studies on dilute solutions of the two types of bottlebrush polymers provided noninvasive characterization of their structural dimensions and chain conformations. Simulated SANS traces, generated using coarse-grained molecular dynamics simulations, reproduced the distinctive features observed in the experimental SANS signals and provided necessary validation for data modeling. The combined analysis of experimental and simulated SANS signals yielded key structural and conformational parameters, including the bottlebrush radius, length, and Kuhn length as well as the excluded volume parameter and the correlation length of the polymer side chains. Importantly, the obtained structural parameters followed well-defined scaling laws as a function of the backbone and side chain degrees of polymerization, as predicted by mean field theories. In conclusion, these findings provide clear experimental and computational evidence of the interdependence of structural and conformational properties in an important class of polymer architectures.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro -1,2-diguaiacylpropane-1,3-diol ( erythro -DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C 1 reaction product, and we further demonstrated that both enantiomers of erythro -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

09 BIOMASS FUELS↗
DOE OSTI2023

Employing Long-Range Inductive Effects to Modulate Metal-to-Ligand Charge Transfer Photoluminescence in Homoleptic Cu(I) Complexes

Four Cu(I) bis(phenanthroline) photosensitizers formulated from a new ligand structural motif (Cu1-Cu4) coded according to their 2,9-substituents, were synthesized, structurally characterized, and fully evaluated using steady-state and time-resolved absorption and photoluminescence (PL) measurements as well as electrochemistry. The 2,9-disubstituted-3,4,7,8-tetramethyl-1,10-phenanthroline ligands feature the following six-membered ring systems prepared through photochemical synthesis: 4,4-dimethylcyclohexyl (1), tetrahydro-2H-pyran-4-yl (2), tetrahydro-2H-thiopyran-4-yl (3), and 4,4-difluorocyclohexyl (4). Universally, these Cu(I) metal-to-ligand charge transfer (MLCT) chromophores display excited state lifetimes on the microseconds time scale at room temperature, including the three longest-lived homoleptic cuprous phenanthroline excited states measured to date in deaerated CH 2 Cl 2 , τ = 2.5 to 4.3 μs. This series of molecules also feature high PL quantum efficiencies (ΦPL = 5.3 to 12% in CH 2 Cl 2 ). Temperature-dependent PL lifetime experiments confirmed that all these molecules exhibit reverse intersystem crossing and display thermally activated delayed PL from a 1 MLCT excited state lying slightly above the 3 MLCT state, 1050 – 1490 cm -1 . Ultrafast and conventional transient absorption measurements confirmed that the PL originates from the MLCT excited state, which remains sterically arrested, preventing an excessive flattening distortion even when dissolved in Lewis basic CH 3 CN. Combined PL and electrochemical data provided evidence that Cu1-Cu4 are highly potent photoreductants (E ox * = -1.73 to -1.62 V vs. Fc +/o in CH 3 CN), whose potentials are altered solely based on which heteroatoms or substituents are resident on the 2,9-appended ring derivatives. It is proposed that long-range electronic inductive effects are responsible for the systematic modulation observed in the PL spectra, excited state lifetimes, as well as the ground state absorption spectra and redox potentials. Cu1-Cu4 quantitatively follow the energy gap law, correlating well with structurally related cuprous phenanthrolines and are also shown to triplet photosensitize the excited states of 9,10-diphenylanthracene with bimolecular rate constants ranging from 1.61 to 2.82 × 10 8 M –1 s –1 . Furthermore, the ability to tailor both photophysical and electrochemical properties using long-range inductive effects imposed by the 2,9-ring platforms advocates new directions for future MLCT chromophore discovery.

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

Ultrafast Events in Electrocyclic Ring-Opening Reactions

Electrocyclic reactions are characterized by the concerted formation and cleavage of multiple σ and π bonds in a molecular system and have been extensively studied since they were introduced by Robert Burns Woodward and Roald Hoffmann in 1965. Recent advances and the integration of time-resolved experiments and nonadiabatic quantum molecular dynamics simulations have transformed the traditional understanding of electrocyclic reactions beyond the Woodward–Hoffmann rules. In this review, we focus on recent studies of 1,3-cyclohexadiene and two of its derivatives, α-phellandrene and α-terpinene, to shed light on the underlying mechanisms of electrocyclic photochemical reactions. We highlight recent progress in ultrafast electron diffraction techniques and the simulation approach of ab initio multiple spawning. Together, these approaches can elucidate molecular structure dynamics from femtosecond to picosecond timescales as well as nuclear and electronic responses at conical intersections.

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

A classical molecular dynamics simulation method for the formation of “dry” gels from boro-aluminosilicate glass structures

In contact with water, glass transforms into amorphous and porous structures called gels. A simulation method based on classical molecular dynamics is proposed here to mimic “dry” gels forming from initial oxide glass structures. Six glass compositions were investigated. Two behaviours were evidenced depending on the initial glass composition, and in particular on the quantity of elements removed. If a large quantity of soluble elements (B, Na) was removed, it induced an increase in the average pore size within the gels, and the time needed to stabilise the gel structure increased because more local atomic rearrangements occurred. The gel network displayed a higher proportion of Si-Q4 at the expense of Si-Q3 and a lower average ring size compared to the glass network, irrespective of the glass composition. Surface effects were also highlighted in the dry gels, such as the presence of 3-coordinated Al and a decrease in the average angle Si-O-Si and Al-O-Al. Our findings will be compared to both wet gels and experimental data in further studies, to help find the best procedure to simulate such structures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Toward Rational Design of Supported Vanadia Catalysts of Lignin Conversion to Phenol

In sustainable chemical engineering, catalytic upgrading of lignocellulosic biomass has recently gained attention for producing renewable platform chemicals. To achieve maximal biomass utilization, upgrading the underutilized lignin components is essential. Among various catalysts for lignin upgrading, supported vanadia (V2O5) catalysts are promising because of their cost-effectiveness and tunability of either dopant metals or catalyst supports. Here, computational studies are conducted to derive rational design guidelines of supported V2O5 catalysts for accomplishing the high catalytic activity of lignin upgrading to phenol, a key compound for producing bioplastics and biofuel blendstocks. Guaiacol was used as the model compound since it comprises the highest portion of depolymerized lignin. Computational mechanistic studies for the catalytic guaiacol conversion to phenol were performed for the V2O5 catalysts on Titania (TiO2) and silica (SiO2) to explain higher experimental phenol yields on V2O5/SiO2 than V2O5/TiO2. The hydrogen migration from the methoxy group to the aryl ring was identified as a rate-determining step, and the overall activation energies on the two catalysts were compared. A structural analysis was carried out for the catalysts and rate-determining transition states to gain further insights from mechanistic studies. It was concluded that the tilt angle of the aryl group in the hydrogen migration transition state is a key descriptor determining the catalytic activity of phenol formation. These features correlate well with activation energies and experimental phenol yields, indicating that they provide design guidelines for supported metal catalysts for lignin upgrading before experiments.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2023

Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281

The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking compounds with a pyridine ring appended to the C12 site of metabolism were designed as inhibitors, synthesized, and evaluated in terms of their functional and structural interactions with CYP8B1. While the pyridine nitrogen was intended to coordinate the CYP8B1 active site heme iron, none of these compounds elicited shifts in the CYP8B1 Soret absorbance consistent with this type of interaction. However, when CYP8B1 was cocrystallized with the pyridine-containing compound with the 3-keto-Δ4 steroid backbone most similar to the endogenous substrate, it was apparent that this ligand was bound in a channel leading to the active site, instead of near the heme iron. Inspection of this structure suggested that tryptophan 281 directly above the heme might restrict active site binding of potential inhibitors with this design. This hypothesis was supported when a CYP8B1 W281F mutation did allow all three compounds to coordinate the heme iron as designed. These results indicated that the design of next-generation CYP8B1 inhibitors should be compatible with the low-ceiling tryptophan immediately above the heme iron.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Glycosidic linkage, N -acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β- D -glucopyranosyl-(1→4)-β- D -mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C 15 H 27 NO 11 ·H 2 O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N -acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N -acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis – trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O -glycosidic linkages on linkage torsion angles φ and ψ. Hypersurfaces correlating φ and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.

Chemistry↗
DOE OSTI2021

Elucidating the structural properties and reversible regional texture effect of GdB 6 under high pressure

As hard and refractory materials with high chemical resistance and mechanical strength, lanthanide hexaborides (LnB 6 ) have attracted much attention. Among the family of LnB 6 , gadolinium hexaboride (GdB 6 ) occupies a special position due to the half-filled 4f shell of Gd. Here, using in situ synchrotron radiation angle-dispersive X-ray diffraction in a diamond anvil cell at room temperature, the structural stability and compression behavior of GdB 6 are investigated extensively, GdB 6 is observed to be structurally stable up to 73 GPa, and the bulk modulus of 177 GPa is obtained under hydrostatic compression. In this paper, an interesting observation of pressure-induced spotty diffraction rings of GdB6 is reported, its formation mechanism can be well described by the reversible regional texture effect, which highlights the rearrangement of crystal grains under high pressure. The rearrangement mechanism has been well explained by investigating the pressure dependence of full width at half maximum, macro-differential stress and grain size. Collective grain rotation behavior motivated by stress difference is critical for the rearrangement process, the strong isotropy and strong stability of GdB 6 structure also provide necessary conditions for high-pressure grain rotation behavior. These results will help to promote the understanding of high-pressure structural properties of GdB 6 , and provide novel insights on the high-pressure grain behavior in hard materials with strong isotropy and three-dimensional skeleton constituted of strong covalent bonds.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal engineering of heterocyclic arylene(ethynylene) oligomers through programmed aromatic stacking

Conjugated oligomers and polymers consisting of aromatic heterocycles are examples of next-generation organic electronic materials. However, control and optimization of the self-assembly of these materials in the solid-state, which is a crucial parameter for high efficiency performance, remains an unsolved challenge in materials development. In this work, we provide valuable insight into aromatic stacking interactions between fluorinated arene rings (ArF) and heterocycles with different electronic character (Het), and elaborate on the prospect of using these interactions to control the solid-state configurations of three-ring phenyleneethynylene oligomers (PEs). Oligomers possessing heterocycles typically thought of as electron-rich (ER) show blue-shifted optical spectra in the solid-state, while those incorporating heterocycles typically thought of us electron deficient (ED) show red-shifted solid-state optical spectra. Crystal structures show ArF-Het stacking interactions between the fluorinated side-chains and ER units, which twist the backbone out of planarity and prevent chromophore aggregation. Further, the interactions are absent in ED oligomers, highlighting cofacial incompatibility between ArF rings and ED units. A combination of TD-DFT computations and novel heterocycle descriptors reinforce our assignment of the oligomers as ED or ER, while exhaustive conformer analysis shows ArF-Het stacking interactions are a significant contributor to compound stability. Overall, this work describes the importance of heterocycle electronics in conformational control in the solid state, understanding of which can be a valuable asset in the development of novel optoelectronic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O 2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The ß-sheet–rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE 3 F 3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Furthermore, comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

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

Over 15% Efficiency Polymer Solar Cells Enabled by Conformation Tuning of Newly Designed Asymmetric Small‐Molecule Acceptors

Abstract The prosperous period of polymer solar cells (PSCs) has witnessed great progress in molecule design methods to promote power conversion efficiency (PCE). Designing asymmetric structures has been proved effective in tuning energy level and morphology, which has drawn strong attention from the PSC community. Two hepta‐ring and octa‐ring asymmetric small molecular acceptors (SMAs) (IDTP‐4F and IDTTP‐4F) with S‐shape and C‐shape confirmations are developed to study the relationship between conformation shapes and PSC efficiencies. The similarity of absorption and energy levels between two SMAs makes the conformation a single variable. Additionally, three wide‐bandgap polymer donors (PM6, S1, and PM7) are chosen to prove the universality of the relationship between conformation and photovoltaic performance. Consequently, the champion PCE afforded by PM7: IDTP‐4F is as high as 15.2% while that of PM7: IDTTP‐4F is 13.8%. Moreover, the S‐shape IDTP‐4F performs obviously better than their IDTTP‐4F counterparts in PSCs regardless of the polymer donors, which confirms that S‐shape conformation performs better than the C‐shape one. This work provides an insight into how conformations of asymmetric SMAs affect PCEs, specific functions of utilizing different polymer donors to finely tune the active‐layer morphology and another possibility to reach an excellent PCE over 15%.

Guo, Qing↗
DOE OSTI2020

Revealing Molecular Mechanisms in Hierarchical Nanoporous Carbon via Nuclear Magnetic Resonance

Hierarchical nanoporous carbons (HNC) have been proven to be an effective adsorbent for the adsorption of volatile organic compounds (VOCs) and CO 2 . However, questions remain regarding the hierarchical structure regulation, the adsorption mechanisms of adsorbate uptake, and interactions within the HNC. Here, we synthesize HNC from wood, using a microwave-induced heating method incorporating K 2 CO 3 activation. Our HNC exhibit Murray's law multiscale structures, prompting a molecular-scale study of adsorbate adsorption via nuclear magnetic resonance (NMR). NMR chemical shifts are consistent with ring-current effects from the adsorbent. Our NMR technique provides a convenient way to quantitate adsorption of adsorbate in HNC. VOC vapor adsorption results show NMR chemical-shift changes with time, suggesting initial adsorption into mesopores, followed by diffusion into micropores. Schroeder's paradox is demonstrated by differences in observed shifts for adsorbed liquid vis-à-vis vapor phase in these HNC. These HNC show high CO 2 adsorption capacity, portending applications to carbon capture.

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

Snapshots of Ce 70 Toroid Assembly from Solids and Solution

Crystallization at the solid–liquid interface is difficult to spectroscopically observe and therefore challenging to understand and ultimately control at the molecular level. The Ce70-torroid formulated [Ce IV 70 (OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4– , part of a larger emerging family of M IV 70 -materials (M = Zr, U, Ce), presents such an opportunity. We elucidated assembly mechanisms by the X-ray scattering (small-angle scattering and total scattering) of solutions and solids as well as crystallizing and identifying fragments of Ce 70 by single-crystal X-ray diffraction. Fragments show evidence for templated growth (Ce 5 , [Ce 5 (O) 3 (SO 4 ) 12 ] 10- ) and modular assembly from hexamer (Ce 6 ) building units (Ce 13 , [Ce 13 (OH) 6 (O) 12 (SO 4 ) 14 (H 2 O) 14 ] 6– and Ce 62 , [Ce 62 (OH) 30 (O) 58 (SO 4 ) 58 ] 14- ). Ce 62 , an almost complete ring, precipitates instantaneously in the presence of ammonium cations as two torqued arcs that interlock by hydrogen boding through NH 4 + , a structural motif not observed before in inorganic systems. The room temperature rapid assemblies of both Ce 70 and Ce 62 , respectively, by the addition of Li + and NH 4 + , along with ion-exchange and redox behavior, invite exploitation of this emerging material family in environmental and energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Filling the gap with a bulky diaryl boron group: fluorinated and non-fluorinated copper pyrazolates fitted with a dimesityl boron moiety on the backbone

Successful synthesis has been reported of 4-Mes 2 B-3,5-(CF 3 ) 2 PzH and 4-Mes 2 B-3,5-(CF 3 ) 2 PzH bearing sterically demanding diarylboron moieties at the pyrazole ring 4-position, and their corresponding copper(I) pyrazolate complexes. They show visible blue photoluminescence in solution. The X-ray crystal structures revealed that the fluorinated {[4-BMes 2 -3,5-(CF 3 ) 2 Pz]Cu} 3 crystallizes as discrete trinuclear molecules whereas as the non-fluorinated {[4-BMes 2 -3,5-(CH 3 ) 2 Pz]Cu} 3 forms dimers of trimers with two close inter-trimer Cu···Cu separations. The solid {[4-BMes 2 -3,5-(CF 3 ) 2 Pz]Cu} 3 featuring a sterically confined Cu 3 N 6 core displays bright blue phosphorescence while {[4-BMes 2 -3,5-(CH 3 ) 2 Pz]Cu} 3 , which is a dimer of a trimer, is a red phosphor at room temperature. Here, this work illustrates the modulation of photo-physical properties of metal pyrazolates by adjusting the supporting ligand steric features and introducing secondary diarylboron luminophores. Computational analysis of the structures and photophysical properties of copper complexes are also presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

59 BASIC BIOLOGICAL SCIENCES↗