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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Influence of Hyperfine Coupling Strain on Two-Dimensional ESEEM Spectra from I = 1/2 Nuclei

HYSCORE, a variant of two-dimensional ESEEM spectroscopy, is currently one of the most effective tools in high-resolution solid-state EPR spectroscopy. Our systematic studies of hydrogen bonds with semiquinones in 15 N-labeled proteins have previously provided us with an extensive collection of 15 N HYSCORE spectra produced by N–H…O nitrogen donors. Examination of these spectra has indicated in several cases lineshape distortions not described by available theoretical models. We were able to explain all observed artificial phenomena in the 15 N spectra of semiquinones considering a single mechanism—strain of the isotropic hyperfine interaction. In this review article, we introduce the HYSCORE experiment and the theoretical background for spectra of I = 1/2 nuclei in orientation-disordered samples. We then present a description of the observed lineshape distortions and an explanation of the hyperfine strain’s influence on the experimental spectra. In the final part of the article, we discuss (i) similar lineshape distortions found in previously published spectra from 15 N, 29 Si, 31 P, and 57 Fe nuclei that can be explained using the approach applied for the analysis of the 15 N spectra of semiquinones, and (ii) a recently published analysis of 31P spectra with a different type of lineshape distortion based on a more sophisticated method, where the strength of anisotropic coupling is correlated with the sign and value of the isotropic constant in different conformations of a Cu(II) complex.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2023

Functional group effect of chemically modified microcrystalline methyl cellulose on thermoplastic polyurethane composites

Microcrystalline cellulose (MCC) is a promising bio-based filler for lightweight yet mechanically high-performance eco-polymer composites because of its low density and high biocompatibility. However, intermolecular hydrogen bonding among MCC is stronger than the polymer–filler interactions, which deteriorate the mechanical properties of the composites. Herein, we investigated the effects of functional groups on the mechanical properties of composites by scrutinizing chemically modified microcrystalline methyl cellulose (m-MMC) with three different substitution levels of hydroxyl group to hydroxypropyl (HP) group: no-, low-, and high-level substitution (HP-0, HP-low, and HP-high). The degree of HP substitution of m-MMC was quantitatively measured by CP/MAS NMR analysis. The relatively bulky HP groups interrupted the filler–filler intermolecular interactions and reduced the crystallinity and density of m-MMC, as evident from X-ray diffractometer and pycnometer data, respectively. For scalable production of the composites, the m-MMC were compounded with thermoplastic polyurethane (TPU) by a twin-screw extruder at concentrations between 0.5 and 10 wt%. Despite its low filler concentration, the toughness of m-MMC/TPU composites was remarkably enhanced, up to 28% (229.2 to 294.4 MJ/m 3 ) at 0.5 wt% loading of HP-low, owing to the enhanced polymer–filler interactions. In conclusion, the fundamental understanding on structure–property relationships will provide insights for designing of mechanically robust yet eco-friendly polymer composites.

composites↗
DOE OSTI2023

Relaxation dynamics of water in the vicinity of cellulose nanocrystals

Water molecules near cellulose nanocrystals (CNCs; produced via the sulfuric acid-catalyzed hydrolysis of wood pulp) are believed to relax slower than those in the bulk liquid, which may result in unique properties of CNC aqueous dispersions. Herein this study analyzed the polarization behavior of water molecules in CNC aqueous dispersions and other reference samples using a dielectric relaxation spectroscopy (DRS) technique in the microwave frequency range (0.2–20 GHz). As the CNC concentration increases, two slow relaxation components become prominent. The comparison with DRS data of aqueous dispersions of nanoporous silica, polyvinyl alcohol (PVA), and hairy CNC (HCNC) with amorphous chains protruding from both ends suggested that these slow relaxation modes of water near CNC surfaces cannot be attributed to direct hydrogen bonding interactions with the hydroxyl (OH) groups exposed and immobilized at the solid surface. Instead, they are similar to the water molecules interacting with OH groups attached to flexible polymer chains. Molecular dynamics (MD) simulations of the polarization behavior of water near the (110) facet of cellulose Iβ crystals confirmed that the interactions of water molecules with the cellulose crystal surface do not cause slower relaxations in the frequency range studied via the DRS. These results indicated that the CNC surface cannot be depicted with the crystallographic facets of cellulose Iβ; instead, it resembles a polymer-brush surface on which the short glucan residues or fragments of the strong acid-catalyzed hydrolysis process are swollen and extended into the aqueous phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Patterns in interactions of variably acetylated xylans with hydrophobic cellulose surfaces

The recalcitrance of plant cell wall lignocellulosic biomass to deconstruction is a major hurdle to sustainable biofuel/bioproduct economy. A multitude of interactions stabilize lignocellulosic biomass structure. Among these, tight packing of hemicellulose-cellulose is partly responsible for biomass recalcitrance. Here, unrestrained molecular dynamics simulations are employed to understand the influence of the nature and pattern of naturally-occuring acetyl decorations of the xylan backbone on interactions with the (100) hydrophobic cellulose surface. Periodically O2-acetylated xylan (2AcX) assume twofold helical screw conformations that are stabilized by a combination of multiple hydrophobic contacts and hydrogen bonds with the hydrophobic cellulose surface. In contrast, acetylation at the O3 position in xylan obstructs interactions, thereby adopting threefold helical screw conformations that potentially preferably interact with lignin rather than cellulose. Fully acetylated xylan desorbs from the surface implying a minimum number of unsubstituted residues on the xylan backbone is required for interaction with the surface. Here, the substituted residues must form ~ 20% fewer contacts than the unsubstituted residues to sustain stable twofold helical screw xylan conformations on the cellulose surface. Thus, specific roles of macromolecular conformations of cellulose and hemicellulose in influencing the supramolecular interactions and function of plant cell walls have been determined.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Significantly increased Raman enhancement on defect-rich O-incorporated 1T-MoS 2 nanosheets

Improving charge transfer is the key to the performance of non-noble metal semiconductor-based surface enhanced Raman scattering (SERS) substrates. In this work, the O-incorporated 1T-MoS 2 nanosheets with rich sulfur defects (ID-MoS 2 ) are obtained by simple calcination of 1T-MoS 2 nanosheets in air atmosphere. Using rhodamine 6G (R6G) as typical probe molecules, ID-MoS 2 nanosheets show ultrahigh Raman enhancement effects with an enhancement factor of 1.24 × 10 7 due to sulfur defects and O incorporation in the 1T-MoS 2 lattice. First-principle density functional theory calculations suggest that the existence of sulfur defects and O incorporation significantly increase the Fermi energy level (E f ) and electronic density of states of ID-MoS 2 . Furthermore, O incorporation can enhance the interactions between the substrate and the adsorbed molecules through electrostatic and hydrogen bonding. All these improve the charge transfer resonance and result in the remarkable SERS activity of ID-MoS 2 nanosheets. This is the first study on the increasing SERS performance of semiconductor substrates by simultaneously employing defect and dopant incorporation. This study provides an approach to optimize the performance of semiconductor-based SERS substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Group 7 and 8 Catalysts for Electrocatalytic CO 2 Conversion

Group 7 and 8 CO 2 reduction electrocatalysts have seen advances in selective product formation (primarily CO and formate) achieved through structural innovation and fine-tuning of coordination chemistry over the last decade. Furthermore, significant improvements have also been made by involving the secondary ligand coordination sphere in CO 2 reduction. Hydrogen bonding interactions with CO 2 and charged groups in the secondary sphere in particular are shown to lower overpotentials, stabilize intermediates or transition states and improve catalytic rates.

14 SOLAR ENERGY↗
DOE OSTI2026

Fluorinated ionic liquids as gas chromatographic stationary phases for the separation of volatile per- and polyfluoroalkyl substances

Background Here, the production of fluorinated organic compounds in the manufacturing, semiconductor, and pharmaceutical industries has increased exponentially over the past decade. This rapid growth has created an urgent need for efficient chromatographic platforms capable of selectively separating these compounds from complex mixtures, not only to support industrial quality control and waste management practices, but also to enable reliable environmental monitoring of volatile fluorinated contaminants. Conventional GC stationary phases lack the fluorophilic interactions needed for highly fluorinated analytes. Consequently, there is a clear demand for specialized stationary phases designed to improve chromatographic retention and selectivity for these compounds. Results Three stationary phases composed of fluorinated ionic liquids (ILs) with varied extent of fluorination were prepared to study fluorophilic interactions with fluorinated/non-fluorinated probe molecules by gas chromatography (GC). IL stationary phases featuring linear and branched perfluoroalkyl moieties, as well as a branched alkyl moiety, were systematically investigated. Chromatographic performance was examined using fluorinated compounds and their hydrocarbon analogs, including CF 3 -substituted aromatics, aliphatic alcohols, fluorotelomer alcohols (FTOHs), and perfluoroalkenes. Measurements on 5 m and 20 m columns revealed that the IL possessing branched alkyl provided stronger dispersive and hydrogen bonding interactions toward non-fluorinated aromatic and long-chain alcohols, whereas the fluorinated ILs enhanced retention of highly fluorinated FTOHs and perfluorodecene. Comprehensive two-dimensional GC (GC × GC), using a nonpolar primary column coupled with secondary columns featuring cross-bonded poly(trifluoropropylmethyl siloxane) (Rtx-200 ms), the branched fluorinated IL, or the branched non-fluorinated IL, highlighted complementary selectivity with the branched fluorinated IL providing the strongest interactions with fluorinated analytes. Significance These results demonstrate that fluorinated IL stationary phases are promising alternatives to conventional polysiloxane stationary phases for improving the separation of per- and polyfluoroalkyl substances and related fluorinated compounds. By correlating IL structure with fluorophilic interactions, this work establishes design principles for GC stationary phases that enable enhanced selectivity for highly fluorinated analytes while maintaining complementary interactions with non-fluorinated compounds.

Comprehensive two-dimensional GC↗
DOE OSTI2022

Calcium silicate hydrate colloid at different humidities: Microstructure, deformation mechanism, and mechanical properties

Calcium silicate hydrate (C-S-H) is the main hydration product of Portland cement, while fundamental questions persist regarding its colloidal structure and water content. In this work, we developed a full atomistic C-S-H colloid model and investigated the physical and mechanical properties at different gel water concentrations. Water confined in nanometer gel pores degrades the mechanical properties of C-S-H because of its hydrolysis effect. A “ductile to brittle” transition was observed in the C-S-H colloid model with increasing gel water contents, evolving from transgranular failure to intergranular fracture. The gel water confined in nanometer-sized pores displays glassy characteristics, and it acts as a lubricant and facilitates structure distortions during the deformation. We elucidated the topology effect of the hydrogen bond network on the evolution of the viscoelasticity of C-S-H at different humidities. In conclusion, this work sheds light on the role of water in C-S-H colloids from nanostructure perspectives.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Traction-separation response of bilayer graphene interfaces: The role of an intercalated single atomic layer of water molecules and hydroxyl groups

Molecular dynamics simulations of the normal and shear traction-separation response of dry and wet bilayer graphene interfaces were performed. The influence of a single, atomic layer of water molecules sandwiched between graphene layers and hydroxyl functionalization on one or both layers were investigated. Hydroxyl groups provided a shielding effect during normal separation while favoring stick-slip friction under sliding conditions. The single, atomic layer of water molecules confined between hydrophilic and asymmetric hydrophobic/hydrophilic surfaces was found to ease sliding friction. The mechanisms arose from the balance between the attractive and repulsive graphene/water interactions through bridges of single water molecules between the two surfaces and the structure of the water monolayer under confinement for which an out-of-plane water/water hydrogen bond network could not be developed. The single, atomic layer of water molecules reduced the sliding friction the most when both surfaces were hydrophilic and lowered the sliding friction of the asymmetric hydrophobic/hydrophilic interfaces to that when both surfaces were hydrophobic. An optimal hydroxyl surface coverage of less than 10% may exist for efficient water lubrication, with diminishing effect with increasing number of hydroxyl groups. Finally, the findings offer a design strategy for assembling bilayer graphene interfaces with tailored friction and sliding contact properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Facilitating enzymatic hydrolysis with a novel guaiacol-based deep eutectic solvent pretreatment

In this work, we established a novel deep eutectic solvent (DES) using lignin-derived guaiacol as hydrogen bond donor (HBD). The sole ChCl/guaiacol system was found to be inefficient for the fractionation of wheat straw (WS), while the incorporation of trace AlCl 3 significantly facilitated the degradation of hemicellulose and lignin, resulting in a complete enzymatic digestibility of the pretreated WS. Further, this study revealed that the DES-degraded lignin was readily precipitated during the washing process, and thus hindered the enzymatic hydrolysis of poplar and bamboo (with hydrolysis yield of 42.03% and 71.67%, respectively). Alkali washing offers a possible approach to remove the precipitated lignin, after which a near 100% hydrolysis yield was also obtained for poplar and bamboo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Utilization of guaiacol-based deep eutectic solvent for achieving a sustainable biorefinery

This study proposed a renewable deep eutectic solvent (DES) pretreatment using lignin-derived guaiacol as the hydrogen bond donor. The DES showed excellent biomass fractionation efficiency after the incorporation of trace AlCl 3 as the reinforcer, which removed 79.1 % lignin while preserving more than 90 % glucan. The pretreated bamboo exhibited 96.2 % glucan enzymatic hydrolysis yield at only 110 °C. The physicochemical properties of the pretreated solids were comprehensively investigated to explain how the DES fractionation overcame the biomass recalcitrance. The regenerated lignin from the DES pretreatment was also analyzed, which revealed that lignin β-O-4 bond was significantly cleaved. In conclusion, this guaiacol-based DES could greatly contribute to establish a closed-loop biorefinery sequence with high lignin fractionation efficiency and great solvent recyclability.

09 BIOMASS FUELS↗
DOE OSTI2022

Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites

Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA 2 “green” (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA 2 into preformed host–guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA 2 was found to be similar to those reported earlier at the same DNA site for BLMB 2 , the intercalated bithiazole of BLMB 2 is “flipped” 180° relative to DNA-bound BLMA 2 . Further, this finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluation of darunavir-derived HIV-1 protease inhibitors incorporating P2' amide-derivatives: Synthesis, biological evaluation and structural studies

Here, we report here the synthesis and biological evaluation of darunavir derived HIV-1 protease inhibitors and their functional effect on enzyme inhibition and antiviral activity in MT-2 cell lines. The P2' 4-amino functionality was modified to make a number of amide derivatives to interact with residues in the S2' subsite of the HIV-1 protease active site. Several compounds exhibited picomolar enzyme inhibitory and low nanomolar antiviral activity. The X-ray crystal structure of the chloroacetate derivative bound to HIV-1 protease was determined. Interestingly, the active chloroacetate group converted to the acetate functionality during X-ray exposure. The structure revealed that the P2' carboxamide functionality makes enhanced hydrogen bonding interactions with the backbone atoms in the S2'-subsite.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tetrazole-based inhibitors of the bacterial enzyme N -succinyl- L,L -2,6-diaminopimelic acid desuccinylase as potential antibiotics

Based on a hit from a high-throughput screen, a series of phenyltetrazole amides was synthesized and assayed for inhibitory potency against DapE from Haemophilus influenzae (HiDapE). The inhibitory potency was modest but confirmed, with the most potent analog containing an aminothiazole moiety displaying an IC 50 = 50.2 ± 5.0 μM. Finally, docking reveals a potential binding mode wherein the amide carbonyl bridges both zinc atoms in the active site, and the tetrazole forms key hydrogen bonds with Arg330.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

Channelrhodopsins (ChR) are light-sensitive cation channels used in optogenetics, a technique that applies light to control cells (e.g., neurons) that have been modified genetically to express those channels. Although mutations are known to affect pore kinetics, little is known about how mutations induce changes at the molecular scale. To address this issue, we first measured channel opening and closing rates of a ChR chimera (C1C2) and selected variants (N297D, N297V, and V125L). Then, we used atomistic simulations to correlate those rates with changes in pore structure, hydration, and chemical interactions among key gating residues of C1C2 in both closed and open states. Overall, the experimental results show that C1C2 and its mutants do not behave like ChR2 or its analogous variants, except V125L, making C1C2 a unique channel. Furthermore, our atomistic simulations confirmed that opening of the channel and initial hydration of the gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N297 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.

59 BASIC BIOLOGICAL SCIENCES↗