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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Anisotropic Coarse-Grained Model for Conjugated Polymers: Investigations into Solution Morphologies

The optoelectronic properties of conjugated polymers are dictated by the interplay of multiscale structural features, including intrachain dihedrals, interchain pi-pi stacking, and the complex mesoscale morphology. While much is known about the structures of polymers with isotropically interacting monomers, little is known about polymers with strongly anisotropic backbone monomers, a class of materials to which conjugated polymers belong. Fundamental understanding is further complicated when the semiflexible and molecularly heterogeneous nature of conjugated polymers is taken into account. We present an anisotropic coarse-grained (CG) model for conjugated polymers that incorporates key molecular features (monomer anisotropy, intermonomer dihedrals, and side chains). Finally, the model is employed to characterize the single-chain conformational properties of conjugated polymers, revealing a rich temperature-dependent conformational landscape. These studies provide a critical link between CG molecular descriptors and conformational ordering in conjugated polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Conjugation in Isomeric Cyclosilane Thioethers

Conjugation in thioether-functionalized cyclosilanes depends on both conformation and connectivity. Borane-catalyzed dehydrocoupling of thiophenols with partially hydrogenated cyclosilanes proceeded with high chemoselectivity for Si–H bonds in the presence of Si–Si bonds. Isomeric 1,3- and 1,4-functionalized cyclosilanes afforded isomeric cyclosilane thioethers that also differed in preference for chair or twist-boat conformations as demonstrated by both X-ray crystal structures and density functional theory (DFT) calculations. Here, the confounding effects of different conformations and connectivity could be distinguished with time-dependent DFT (TD-DFT) calculations and validated with experimentally obtained UV–vis spectra.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

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

Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease

The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. Here, in this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.

SARS-CoV-2↗
DOE OSTI2020

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

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

Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology

Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme’s conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme’s conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cosmological quasiparticles and the cosmological collider

The interplay between cosmology and strongly coupled dynamics can yield transient spectral features that vanish at late times, but which may leave behind phenomenological signatures in the spectrum of primordial fluctuations. Of particular interest are strongly coupled extensions of the standard model featuring approximate conformal invariance. In flat space, the spectral density for a scalar operator in a conformal field theory is characterized by a continuum with scaling law governed by the dimension of the operator, and is otherwise featureless. Anti–de Sitter/conformal field theory arguments suggest that for large 𝑁, in an inflationary background with Hubble rate 𝐻, this continuum is gapped. We demonstrate that there can be additional peak structures that become sharp and particlelike at phenomenologically interesting regions in parameter space, and we estimate their contribution to cosmological observables. We find phenomena that are potentially observable in future experiments that are unique to these models, including displaced oscillatory features in the squeezed limit of the bispectrum. These particles can be either fundamental, and localized to a UV brane, or composite at the Hubble scale, 𝐻, and bound to a horizon in the bulk of the 5D geometry. We comment on how stabilization of conformal symmetry breaking vacua can be correlated with these spectral features and their phenomenology.

conformal field theory↗
DOE OSTI2024

Operando Investigation of the Molecular Origins of Dipole Switching in P(VDF‐TrFE‐CFE) Terpolymer for Large Adiabatic Temperature Change

Abstract Relaxor ferroelectric polymers exhibiting a giant electrocaloric effect (ECE) can potentially be used to create next‐generation solid‐state coolers. Under an electric field, poly(vinylidene fluoride‐trifluoroethylene‐chlorofluoroethylene) terpolymer goes through a large dipolar entropy change producing a high adiabatic temperature change (Δ T ECE ). This work resolves the molecular origins of the large entropy change behind the electric field‐induced dipole switching. A Fourier transform infrared spectroscopy equipped with a high voltage source is used to operandoly observe the characteristic molecular vibrational modes. A short‐range trans (T) conformation of the CF 2 ‐CH 2 dyads interrupted by a gauche (G) conformation, e.g., TTTG in the terpolymer chain, undergoes a dynamic transformation that leads to a corresponding Δ T ECE whenever an electric field is applied. The molecular dynamics simulation also proves that the energy barrier that the transformation from TTTGs into a long T sequence overcomes is smaller than that for all other conformations. A mixed solvent system is used to obtain T3G‐enriched terpolymer films exhibiting a 4.02 K Δ T ECE at 60 MV m −1 and these films are employed to manufacture a 2‐layer‐cascaded cooling device that achieves a 6.7 K temperature lift, the highest reported value for a 2‐layer cascaded device made of fluoropolymers.

Zhu, Yuan↗
DOE OSTI2024

Mechanically Reinforced Pseudosolid Polyelectrolyte Membranes via Layer-by-Layer Assembly for High-Performing Lithium-Metal Batteries

Ionogels are emerging as high-potential pseudosolid electrolytes for lithium-metal batteries (LMBs), leveraging their intrinsic high ionic conductivity from entrapped ionic liquid (IL) electrolytes. However, their practical application is hindered by poor mechanical strength stemming from the confinement of ILs within a polymer matrix. To address this challenge, the formation of conformal polyion coatings with functional groups is reported to be relevant to LMBs’ application on ionogels, utilizing a layer-by-layer (LbL) assembly strategy. Here, this approach significantly enhances the mechanical strength (Young's modulus and tensile strength) and electrochemical performance of ionogels, owing to the tailored interface modifications introduced by functional groups’ specific conformal polyion coatings. The core of this methodology leverages the inherent ionic structure of ionogels to enable facile interface modification through Coulombic interactions between polyanions and polycations. These conformally coated interface functionalized membranes show improved electrochemical performance when integrated with cathode materials such as LiFePO 4 (LFP) and LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811) in an LMB configuration, underscoring their potential for robust, high-conductivity, pseudosolid membranes for LMB applications. These innovative pseudosolid membranes offer improved mechanical and electrochemical properties, leading to higher battery efficiency and safety, making them promising candidates for next-generation LMB technology.

25 ENERGY STORAGE↗
DOE OSTI2025

Manipulating the Assembly and Architecture of Fibrillar Silk

Silk is a unique and exceptionally strong biological material. However, no synthetic method has yet come close to replicating the properties of natural silk. This shortfall is attributed to an insufficient understanding of both silk nanofibril structure and the mechanism of formation. Here in situ atomic force microscopy (AFM) and photo-induced force microscopy (PiFM) is utilized to investigate the formation process and define the basic structural paradigm of individual silk nanofibrils. By visualizing the multistage process of silk nanofibril formation, the importance of conformational transformations along the assembly pathway is revealed. Unfolded silk structures initially accumulate into amorphous clusters, which then evolve into crystal nuclei via conformational transformation into β-crystallites. Nanofibril elongation then occurs through the attachment of silk molecules at a single end of the nanofibril tip; this is facilitated through the formation of a new amorphous cluster that then repeats the aforementioned conformational transformation. However, enzymatic digestion of the amorphous regions leads to direct, rapid elongation of β-crystalline fibers. These findings imply that the energy landscape is characterized by shallow minima associated with intermediate states, which can be eliminated by introducing β-crystallites, and motivate research into the directed modification of the silk assembly pathway to select for features beneficial to specific applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Characterization of a Molecule Partially Confined at the Pore Mouth of a Zeotype

Abstract We investigate the interaction between a molecule and a pore mouth—a critical step in adsorption processes—by characterizing the conformation of a macrocyclic calix[4]arene‐Ti IV complex, which is grafted on the external surface of a zeotype (*‐SVY). X‐ray absorption and 13 C{ 1 H} CPMAS NMR spectroscopies independently detect a unique conformation of this complex when it is grafted at crystallographically equivalent locations that lie at the interface of 7 Å hemispherical microporous cavities and the external surface. Electronic structure calculations support the presence of this unique conformation, and suggest that it is brought about by a specific orientation of the macrocycle that maximizes non‐covalent interactions between calix[4]arene upper‐rim tert ‐butyl substituents and the microporous‐cavity walls. Our comparative study provides a rare “snapshot” of a molecule partially confined at a pore mouth, an essential intermediate for adsorption into micropores, and demonstrates how surrounding environment controls this confinement in a sensitive fashion.

Grosso‐Giordano, Nicolás A.↗
DOE OSTI2022

Rational Control of Off‐State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement**

Abstract Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non‐fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off ‐state conformations, trans1 and trans2 , located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off ‐state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high‐level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue‐ and red‐shifts of the absorption bands associated to trans1 and trans2 , respectively. Thus, due to elimination of trans2 , the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two‐fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2‐V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

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

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

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

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2023

Chain trajectories, domain shapes, and terminal boundaries in block copolymers

The packing geometry of macromolecules in complex mesophases is of key importance to self-organization in synthetic and biological soft materials. While approximate or heuristic models rely on often-untested assumptions about how flexible molecules “fit in” to distinct locations of complex assemblies, physical assemblies derive from ensembles of fluctuating conformations, obscuring the connection between mesophase geometry and the underlying arrangements. Here, we present an approach to extract and analyze features of molecular packing in diblock block copolymer (BCP) melts, a prototypical soft matter system, based on the statistical description of chain conformations in self-consistent field (SCF) theory. We show how average BCP chain trajectories in ordered morphologies can be analyzed from the SCF-derived orientational order parameter of chain segments. We use these extracted trajectories to analyze the features of local packing geometry, including chain bending and tilt, as well as the terminal boundaries that delineate distinct domains in ordered BCP morphologies. In conclusion, we illustrate this analysis by focusing on measurable features of packing frustration in 2D (columnar) and 3D (spherical and bicontinuous) morphologies, notably establishing an explicit link between chain conformations in complex morphologies and their medial geometry.

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

BMS symmetry via AdS/CFT

With a view to understanding extended-BMS symmetries in the framework of the AdS 4 /CFT 3 correspondence, asymptotically AdS geometries are constructed with null impulsive shockwaves involving a discontinuity in superrotation parameters. The holographic dual is proposed to be a two-dimensional Euclidean defect conformal field localized on a particular timeslice in a three-dimensional conformal field theory on de Sitter spacetime. The defect conformal field theory generates a natural action of the Virasoro algebra. The large radius of curvature limit ℓ → ∞ yields spacetimes with nontrivial extended-BMS charges corresponding to a single set of Virasoro charges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Scale-fixed predictions for γ + η c production in electron-positron collisions at NNLO in perturbative QCD

In the paper, we present QCD predictions for γ + η c production at an electron-positron collider up to next-to-next-to-leading order (NNLO) accuracy without renormalization scale ambiguities. The NNLO total cross-section for e + + e – → γ + η c using the conventional scale-setting approach has large renormalization scale ambiguities, usually estimated by choosing the renormalization scale to be the e + e – center-of-mass collision energy $\sqrt{s}$. The Principle of Maximum Conformality (PMC) provides a systematic way to eliminate such renormalization scale ambiguities by summing the nonconformal β contributions into the QCD coupling α s ( Q 2 ). The renormalization group equation then sets the value of α s for the process. The PMC renormalization scale reflects the virtuality of the underlying process, and the resulting predictions satisfy all of the requirements of renormalization group invariance, including renormalization scheme invariance. After applying the PMC, we obtain a renormalization scale-and-scheme independent prediction, σ | NNLO,PMC ≃ 41.18 fb for $\sqrt{s}$=10.6 GeV. The resulting pQCD series matches the series for conformal theory and thus has no divergent renormalon contributions. The large K factor which contributes to this process reinforces the importance of uncalculated NNNLO and higher-order terms. Using the PMC scale-and-scheme independent conformal series and the Padé approximation approach, we predict σ | NNNLO,PMC+Pade ≃ 18.99 fb, which is consistent with the recent BELLE measurement ${\sigma}^{\mathrm{obs}}={16.58}_{-9.93}^{+10.51}$ fb at $\sqrt{s}$ ≃ 10.6 GeV. This procedure also provides a first estimate of the NNNLO contribution.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗