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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Physics-informed machine learning to predict solvatochromic parameters of designer solvents with case studies in CO 2 and lignin dissolution

The polarity of solvents plays a critical role in various research applications, particularly in their solubilities. Polarity is conveniently characterized by the Kamlet-Taft parameters that is, the hydrogen bonding acidity (α), the basicity (β), and the polarizability (π*). Obtaining Kamlet-Taft parameters is very important for designer solvents, namely ionic liquids (ILs) and deep eutectic solvents (DESs). However, given the unlimited theoretical number of combinations of ionic pairs in ILs and hydrogen-bond donor/acceptor pairs in DESs, experimental determination of their Kamlet-Taft parameters is impractical. To address this, the present study developed two different machine learning (ML) algorithms to predict Kamlet-Taft parameters for designer solvents using quantum chemically derived input features. The ML models developed in the present study showed accurate predictions with high R 2 and low RMSE values. Further, in the context of present interest in the circular bioeconomy, the relationship between the basicities and acidities of designer solvents and their ability to dissolve lignin and carbon dioxide (CO 2 ) is discussed. Our method thus guides the design of effective solvents with optimal Kamlet-Taft parameter values dissolving and converting biomass and CO 2 into valuable chemicals.

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

Anion-dependent phase behavior of methylimidazolium-based ionic liquids mixed with water: Correlation between local molecular structure and mesoscale behaviors

The mesoscopic phase behavior of decylmethylimidazolium (C 10 mim) ionic liquids (ILs) bearing three monovalent anions—thiocyanate (SCN − ), nitrate (NO 3 − ), and chloride (Cl − )—mixed with water at relatively high IL contents (50–95 wt%) was investigated. Small-angle and wide-angle X-ray scattering (SAXS/WAXS) were employed to follow the evolution of both local and mesoscale structures across this composition range. In the absence of water, C 10 mimSCN and C 10 mimCl behaved as disordered liquids, whereas C 10 mimNO 3 spontaneously formed a hexagonally ordered cylindrical mesophase and displayed a sticky-solid macroscopic appearance. Upon addition of water, C 10 mimSCN remained a viscous liquid and only weakly ordered lamellar domains were observed. This limited ordering is attributed to the lack of hydrogen bonding and weak interaction energy between SCN − anions and C 10 mim + cations. In contrast, the trigonal-planar NO 3 − and point-like Cl − anions promoted the formation of well-defined hexagonal mesophases up to 35–45 wt% water. The formation of hydrogen bonding of the two anions with imidazolium ring protons likely enabled the creation of compact ion clusters that effectively exclude water molecules from the immediate vicinity of the IL aggregates. These findings demonstrate that the interaction energy between ion pairs dictate IL-water interactions and therefore control the transition from disordered liquids to ordered mesophases in IL/water mixtures with high IL contents. In conclusion, the combined SAXS/WAXS analysis reveals a correlation between local intermolecular structure and the emergence of mesoscopic order, providing a systematic framework for tailoring mesoscale structures in alkylimidazolium-based IL/water systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Molecular Modes Elucidate the Nuclear Magnetic Resonance Relaxation of Viscous Fluids

The Bloembergen, Purcell, and Pound (BPP) theory of nuclear magnetic resonance (NMR) relaxation in fluids dating back to 1948 continues to be the linchpin in interpreting NMR relaxation data in applications ranging from characterizing fluids in porous media to medical imaging (MRI). The BPP theory is founded on assuming molecules are hard spheres with 1 H– 1 H dipole pairs reorienting randomly; assumptions that are severe in light of modern understanding of liquids. Nevertheless, it is intriguing to this day that the BPP theory was consistent with the original experimental data for glycerol, a hydrogen-bonding molecular fluid for which the hard-sphere-rigid-dipole assumption is inapplicable. To better understand this incongruity, atomistic molecular simulations are used to compute 1 H NMR T 1 relaxation dispersion (i.e., frequency dependence) in two contrasting cases: glycerol, and a (non hydrogen-bonding) viscosity standard. At high viscosities, simulations predict distinct functional forms of T 1 for glycerol compared to the viscosity standard, in agreement with modern measurements, yet both in contrast to BPP theory. The cause of these departures from BPP theory is elucidated, without assuming any relaxation models and without any free parameters, by decomposing the simulated T 1 response into dynamic molecular modes for both intramolecular and intermolecular interactions. The decomposition into dynamic molecular modes provides an alternative framework to understand the physics of NMR relaxation for viscous fluids.

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

Phenanthroline-strapped calix[4]pyrroles: anion receptors displaying affinity reversal as a function of solvent polarity

Calix[4]pyrroles 1 and 2, diametrically strapped with a phenanthroline via ester and amide linkages, respectively, have been synthesized as anion receptors. It was revealed by 1 H NMR spectroscopic analysis that receptors 1 and 2 possessing both hydrogen bonding donors and acceptors were able to bind the bicarbonate anion (as its tetraethylammonium (TEA + ) or sodium salt) in CDCl 3 , as well as in 15% aqueous DMSO with high affinity and selectivity over other anions. The amide-based receptor 2 contains additional potential hydrogen bonding donors relative to its ester-based congener 1. Nevertheless, in CDCl 3 receptor 1 was found to display a higher affinity for all test anions than receptor 2. In contrast, in 15% aqueous DMSO solution the affinities of receptor 2 for anions, in particular chloride, bicarbonate, and dihydrogen phosphate, were enhanced, whereas those of receptor 1 were reduced dramatically with no appreciable interaction being seen in the case of most test anions considered in this study. These reversals in selectivity and affinities underscore the importance of solvent in regulating the recognition features of seemingly similiar anion binding agents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1997

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Jaffe, Richard↗
NASA NTRS2003

Structure-Derived Proton-Transfer Mechanism of Action Human Pyruvate Dehydrogenase

The derivative of vitamin B1 thiamin pyrophosphate (TPP) is a cofactor of pyruvate dehydrogenase (E1p) that is involved in decarboxylation of pyruvate followed by reductive acetylation of lipoic acid covalently bound to a lysine residue of dihydrolipoamide acetyltransferase. The structure of E1p recently determined in our laboratory revealed patterns of association of foul subunits and specifics of two TPP binding sites. The mechanism of action in part includes a conserved hydrogen bond between the N1' atom of the aminopyrimidine ring of the cofactor and the carboxylate group of Glu59 from the beta subunits, and a V-conformation of the cofactor that brings the N4' atom of the aminopyrimidine ring to the distance of the intramolecular hydrogen bond formed with the C2-atom of the thiazolium moiety. The carboxylate group of Glu59 is the local proton acceptor that enables proton translocation within the aminopyrimidine ring and stabilization of the rare N4' - iminopyrimidine tautomer. Based on the analysis of E1p structure, we postulate that the protein environment drives N4' - amino/N4' - imino dynamics resulting in a concerted shuttle-like movement of the subunits. We also propose that this movement of the subunits is strictly coordinated with the two enzymatic reactions carried out in E1p by each of the two cofactor sites. It is proposed that these reactions are in alternating phases such that when one active site is involved in decarboxylation, the other is involved in acetylation of lipoyl noiety.

Ciszak, Ewa↗
DOE OSTI2023

De novo design of monomeric helical bundles for pH ‐controlled membrane lysis

Abstract Targeted intracellular delivery via receptor‐mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH‐responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli , 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH‐dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH‐responsiveness and control lysis of model membranes within a very narrow range of pH (6.0–5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure and thermodynamics of water adsorption in NU-1500-Cr

Abstract Metal-organic frameworks (MOFs) are a class of materials with diverse chemical and structural properties, and have been shown to effectively adsorb various types of guest molecules. The mechanism of water adsorption in NU-1500-Cr, a high-performance atmospheric water harvesting MOF, is investigated using a combination of molecular dynamics simulations and infrared spectroscopy. Calculations of thermodynamic and dynamical properties of water as a function of relative humidity allow for following the adsorption process from the initial hydration stage to complete filling of the MOF pores. Initial hydration begins at the water molecules that saturate the open Cr 3+ sites of the framework, which is then followed by the formation of water chains that extend along the channels connecting the hexagonal pores of the framework. Water present in these channels gradually coalesces and fills the hexagonal pores sequentially after the channels are completely hydrated. The development of hydrogen-bond networks inside the MOF pores as a function of relative humidity is characterized at the molecular level using experimental and computational infrared spectroscopy. A detailed analysis of the OH-stretch vibrational band indicates that the low-frequency tail stems from strongly polarized hydrogen-bonded water molecules, suggesting the presence of some structural disorder in the experimental samples. Strategies for designing efficient water harvesting MOFs are also proposed based on the mechanism of water adsorption in NU-1500-Cr.

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

Pressure-induced structural and dielectric changes in liquid water at room temperature

Understanding the pressure-dependent dielectric properties of water is crucial for a wide range of scientific and practical applications. In this study, we employ a deep neural network trained on density functional theory data to investigate the dielectric properties of liquid water at room temperature across a pressure range of 0.1–1000 MPa. We observe a nonlinear increase in the static dielectric constant ɛ 0 with increasing pressure, a trend that is qualitatively consistent with experimental observations. This increase in ɛ 0 is primarily attributed to the increase in water density under compression, which enhances collective dipole fluctuations within the hydrogen-bonding network as well as the dielectric response. Despite the increase in ɛ 0 , our results reveal a decrease in the Kirkwood correlation factor G K with increasing pressure. Furthermore, this decrease in G K is attributed to pressure-induced structural distortions in the hydrogen-bonding network, which weaken dipolar correlations by disrupting the ideal tetrahedral arrangement of water molecules.

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

Spin‐State and Clustering Effects in Fe‐Complex Negolytes for Near‐Neutral Aqueous Redox Flow Batteries

Cost-effective redox-active materials are essential for advancing redox flow batteries (RFBs). Iron, with its abundance and suitability as a redox couple, is a promising candidate; however, achieving stable and fast redox reactions in aqueous RFBs remains a challenge. Here, this study presents an Fe-based negolyte stabilized by a hexadentate ligand, where Fe–ligand bonds are enhanced through intermolecular interactions. The sulfonate-substituted Fe complex exhibits a formal potential of −0.44 V versus Ag/AgCl and an exceptionally high rate constant of 0.69 cm s −1 . Near-neutral RFBs incorporating 0.5 M Fe complex show excellent cycling stability, with no discernible capacity fading over 300 cycles. This performance is attributed to intermolecular hydrogen bonds that reinforce Fe–ligand coordination and promote the formation of stable trimeric clusters. Operando electrochemical Raman spectroscopy and density functional theory reveal that π-backdonation from Fe(II) to the imino-phenolate moiety further stabilizes the complex after reduction. In contrast, the hydroxyl-substituted complex exhibits inferior stability due to weaker hydrogen bonding and less pronounced π-backdonation. These findings underscore the importance of ligand design and intermolecular interactions in developing cost-effective, high-performance redox-active materials for aqueous RFBs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Enhanced active-site electric field accelerates enzyme catalysis

In this study, the design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme’s activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn 2+ with Co 2+ . Based on the electric field enhancement, we make a quantitative prediction of rate acceleration—50-fold faster than the wild-type enzyme—which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity—electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography

Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potential Foldamers Based on an ortho- Terphenyl Amino Acid

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. Here, these oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform. Molecular simulations find no sign of folding as a monomer, and in fact suggest that hydrogen bond patterning is anti-cooperative, inhibiting longer helices.

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

Investigation of a Lignin-Based Deep Eutectic Solvent Using p -Hydroxybenzoic Acid for Efficient Woody Biomass Conversion

Deep eutectic solvents (DESs) are effective solvents for biomass conversion and have been proposed as alternatives to ionic liquids (ILs). In this paper, we first report an effective pretreatment of woody biomass using a novel hardwood lignin-based DES prepared from p -hydroxybenzoic acid (PB) and choline chloride (ChCl), which are used as the hydrogen bond donor and acceptor, respectively. The impacts of the ChCl-PB DES on structural properties and enzymatic hydrolysis of poplar wood were comprehensively evaluated. The performance of ChCl-PB DES was also compared with two other DESs with p -coumaric acid (PCA) and 4-hydroxybenzaldehyde (PHA) as the hydrogen bond donors, which have been successfully applied to herbaceous biomass conversion in previous studies. The results showed that hemicellulose and lignin were effectively fractionated during the proposed ChCl-PB DES pretreatment under a relatively mild temperature. The ChCl-PB DES pretreatment resulted in up to 69% of delignification, and the pretreated poplar residues had over 90% of glucose yield by a 72 h-enzymatic hydrolysis. Transformation of poplar biomass during the DES pretreatment was evaluated by gel permeation chromatography (GPC), two-dimensional heteronuclear single quantum coherence (2D-HSQC), and 31 P nuclear magnetic resonance (NMR) spectroscopies. The recovered lignin showed relatively high purity, narrow molecular weight distribution (PDI < 1.6), and relatively low molecular weight (~1400 g/mol for M w ). A sustainable process was achieved by recycling DES as well as the utilization of PB, which is a producible aromatic compound from hardwood lignin, for the proposed DES formation in the system. This study indicates that the proposed novel DES with a hardwood lignin-based PB compound is a promising pretreatment solvent to achieve an economically feasible biomass conversion process.

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

Choline Fluoride-Ethylene glycol deep eutectic solvent mixture – Synthesis and physicochemical properties

A critical factor in achieving tunability in DESs is varying the type of hydrogen bond acceptors (HBAs) and donors (HBDs). Choline halides (ChX), such as ChCl and ChBr, have been studied to investigate the effect of the choline anion on DESs. However, ChF-based DESs have been underrepresented in scientific research. ChF has excellent potential, such as high electron affinity, ionization potential, and strong hydrogen bond interactions. Moreover, ChF-based DES can lead to a deeper understanding of DESs due to the NMR-active 19F nuclear spin nature. We report the first synthesis and characterization of choline fluoride-EG (1:2, ChF:EG) DES, which we named “EthalineF.” We studied this mixture using various spectroscopic techniques, including NMR, FT-IR, Raman, and UV–vis spectroscopies. Polarity, density, viscosity, and conductivity measurements were collected as well. Transient absorption spectroscopy (TAS) was used to study the solvation dynamics of EthalineF. 19F NMR indicated that some fluoride anions (~15%) are coordinated to the choline cation. In EthalineF, the new type of observed fluoride anions is proposed to be a tight-binding choline-fluoride ion pair. Further, EthalineF has a larger solvodynamic radius than Ethaline. This can explain the lower conductivity for EthalineF compared to Ethaline despite the higher fluidity and solvation dynamics for EthalineF.

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

Microsolvation in V + (H 2 O) n Clusters Studied with Selected-Ion Infrared Spectroscopy

Gas phase ion-molecule clusters of the form V + (H 2 O) n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit red-shifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V + ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of AAD (acceptor-acceptor-donor) coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly-charged or doubly-charged cation-water clusters. Finally, this indicates that cation identity and charge-site location in the cluster can produce discernible spectral differences for clusters in this size range.

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

Rapid water dynamics structures the OH-stretching spectra of solitary water in ionic liquids and dipolar solvents

In a recent study [J. Phys. Chem. B 126, 4584–4598 (2022)], we have used infrared spectroscopy to investigate the solvation and dynamics of solitary water in ionic liquids and dipolar solvents. Complex shapes observed for water OH-stretching bands, common to all high-polarity solvents, were assigned to water in several solvation states. Here, in the present study, classical molecular dynamics simulations of a single water molecule in four ionic liquids and three dipolar solvents were used to test and refine this interpretation. Consistent with past assignments, simulations show solitary water usually donates two hydrogen bonds to distinct solvent molecules. Such symmetrically solvated water produces the primary pair of peaks identified in the OH spectra of water in nearly all solvents. We had further proposed that additional features flanking this main peak are due to asymmetric solvation states, states in which only one OH group makes a hydrogen bond to solvent. Such states were found in significant concentrations in all of the systems simulated. Simulations of the OH stretching spectra using a semiclassical description and the vibrational map developed by Auer and Skinner [J. Chem. Phys. 128, 224511–224512 (2008)] provided semi-quantitative agreement with experiment. Analysis of species-specific spectra confirmed assignment of the additional features in the experimental spectra to asymmetrically solvated water. The simulations also showed that rapid water motions cause a marked motional narrowing compared with the inhomogeneous limit. This narrowing is largely responsible for making the additional features due to minority solvation states manifest in the spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism

Tryptophan indole lyase (TIL; [E.C. 4.1.99.1]) is a bacterial pyridoxal-5′-phosphate (PLP)-dependent enzyme that catalyzes reversible β-elimination of indole from L-tryptophan. The mechanism of elimination of indole from L-tryptophan starts with the formation of an external aldimine of the substrate and PLP, followed by deprotonation of the α-CH of the substrate, forming a resonance-stabilized quinonoid intermediate. Proton transfer to C3 of the indole ring and carbon–carbon bond cleavage of the quinonoid intermediate provide indole and aminoacrylate bound to PLP, which then releases indole, followed by iminopyruvate. We have now determined the X-ray crystal structures of TIL complexes with (3S)-dioxindolyl-l-alanine, an inhibitor, and with substrates L-tryptophan, 7-aza-L-tryptophan, and S-ethyl-l-cysteine (SEC) in the presence of benzimidazole (BZI), an isostere of the product indole. These structures show a mixture of gem-diamine, external aldimine, quinonoid, and aminoacrylate intermediates, in both open and closed active site conformations. In the closed conformations of L-tryptophan, (3S)-dioxindolyl-l-alanine, and 7-aza-L-tryptophan complexes, hydrogen bonds form between Asp-133 with N1 of the ligand heterocyclic ring and NE2 of His-458 in the small domain of TIL. This hydrogen bond also forms in the BZI complex with the aminoacrylate intermediates formed from both L-tryptophan and SEC. The closed quinonoid complex of 7-aza-L-tryptophan shows that the azaindole ring in the closed conformation is bent out of plane of the Cβ–C3 bond by about 40°, putting it in a geometry that leads toward the transition-state geometry. Thus, both conformational dynamics and substrate activation play critical roles in the reaction mechanism of the TIL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗