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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

botulinum neurotoxin↗
DOE OSTI2018

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be C $O\atop{P}$=192.2 and 193.8 J mol -1 K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Reduced partition function ratios of iron and oxygen in goethite

First-principles calculations based on the density functional theory (DFT) with or without the addition of a Hubbard U correction, are performed on goethite in order to determine the iron and oxygen reduced partition function ratios (beta-factors). The calculated iron phonon density of states (pDOS), force constant and beta-factor are compared with reevaluated experimental beta-factors obtained from Nuclear Resonant Inelastic X-ray Scattering (NRIXS) measurements. The reappraisal of old experimental data is motivated by the erroneous previous interpretation of the low- and high-energy ends of the NRIXS spectrum of goethite and jarosite samples (Dauphas et al., 2012). Here the NRIXS data are analyzed using the SciPhon software that corrects for non-constant baseline. New NRIXS measurements also demonstrate the reproducibility of the results. Unlike for hematite and pyrite, a significant discrepancy remains between DFT, NRIXS and the existing Mossbauer-derived data. Calculations suggest a slight overestimation of the NRIXS signal possibly related to the baseline definition. The intrinsic features of the samples studied by NRIXS and Mossbauer spectroscopy may also contribute to the discrepancy (e. g., internal structural and/or chemical defects, microstructure, surface contribution). As for oxygen, DFT results indicate that goethite and hematite have similar beta-factors, which suggests almost no fractionation between the two minerals at equilibrium.

58 GEOSCIENCES↗
DOE OSTI2015

Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-Chaperone Sis1

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at heir C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways, Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activity with Hsp70ΔEEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interactions between the J-domain and glycine-rich region control co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. However, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively.

Yu, Hyun Young↗
DOE OSTI2016

Anion exchange membranes composed of a poly(2,6-dimethyl-1,4-phenylene oxide) random copolymer functionalized with a bulky phosphonium cation

A random copolymer, tris(2,4,6-trimethoxyphenyl) phosphonium functionalized poly(2,6-dimethyl-1,4-phenylene oxide) (PPO-TPQP) was cast from three different solvents: dimethyl sulfoxide (DMSO), ethyl lactate, or a 41:59 vol% mixture of DMSO and ethyl lactate. Solvents were selected via analysis of the Hansen solubility parameters to vary the phase separation of the polymer in the films. An optimized mixture of DMSO and ethyl lactate chosen for film fabrication and this film was contrasted with films cast from the neat constituent solvents. Atomic force microscopy identified domains from nanometer to tens of nanometer sizes, while the light microscopy showed features on the order of micron. SAXS revealed a cation scattering peak with a d-spacing from 7 to 15 A. Trends in conductivity and water diffusion for the membranes vary depending on the solvent from which they are cast. The mixed solvent cast membrane shows a linear Arrhenius behavior indicating fully dissociated cationic/anionic groups, and has the highest bromide conductivity of 3 mS/cm at 95% RH, 90 degrees C. The ethyl lactate cast membrane shows a linear Arrhenius relation in conductivity, but a Vogel-Tamman-Fulcher behavior in its water self-diffusion. While water increases bromide dissociation, water and bromide transport in these films seems to be decoupled. This is particularly true for the film cast from ethyl lactate.

Liu, Ye↗
DOE OSTI2012

The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1

Proper formation of protein phosphatase 2A (PP2A) holoenzymes is essential for the fitness of all eukaryotic cells. Carboxyl methylation of the PP2A catalytic subunit plays a critical role in regulating holoenzyme assembly; methylation is catalyzed by PP2A-specific methyltransferase LCMT-1, an enzyme required for cell survival. We determined crystal structures of human LCMT-1 in isolation and in complex with PP2A stabilized by a cofactor mimic. The structures show that the LCMT-1 active-site pocket recognizes the carboxyl terminus of PP2A, and, interestingly, the PP2A active site makes extensive contacts to LCMT-1. We demonstrated that activation of the PP2A active site stimulates methylation, suggesting a mechanism for efficient conversion of activated PP2A into substrate-specific holoenzymes, thus minimizing unregulated phosphatase activity or formation of inactive holoenzymes. A dominant-negative LCMT-1 mutant attenuates the cell cycle without causing cell death, likely by inhibiting uncontrolled phosphatase activity. Our studies suggested mechanisms of LCMT-1 in tight control of PP2A function, important for the cell cycle and cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Functionality-Directed Screening of Pb-Free Hybrid Organic–Inorganic Perovskites with Desired Intrinsic Photovoltaic Functionalities

The material class of hybrid organic–inorganic perovskites has risen rapidly from a virtually unknown material in photovoltaic applications a short 7 years ago into an ~20% efficient thin-film solar cell material. Although this class of materials is promising, there are limitations associated with its poor long-term stability, nonoptimal band gap, presence of environmentally toxic Pb element, etc. We herein apply a functionality-directed theoretical materials selection approach as a filter for initial screening of the compounds that satisfy the desired intrinsic photovoltaic functionalities and might overcome the above limitations. First-principles calculations are employed to systemically study thermodynamic stability and photovoltaic-related properties of hundreds of candidate hybrid perovskites. We have observed in this materials selection process 14 Ge- and Sn-based materials with potential superior bulk-material-intrinsic photovoltaic performance. A distinct class of compounds containing NH 3 COH + with the organic molecule derived states intriguingly emerging at band-edges is found. Comparison of various candidate materials offers insights on how composition variation and microscopic structural changes affect key photovoltaic relevant properties in this family of materials.

14 SOLAR ENERGY↗
DOE OSTI2017

Investigation of Structural Evolution of Li 1.1 V 3 O 8 by In Situ X-ray Diffraction and Density Functional Theory Calculations

Li 1.1 V 3 O 8 is a promising cathode material for Li-ion batteries, because of its high theoretical capacity (362 mAh g-1) and good rate performance. In this study, the structural evolution of Li 1.1 V 3 O 8 material during electrochemical dis(charge) processes was investigated using a combination of theoretical calculations and experimental data. Density functional theory (DFT) was used to predict the intermediate structures at various lithiation states, as well as the stability of major phases. In order to validate these predictions, in situ X-ray diffraction (XRD) data was collected operando, allowing for the phase transformations to be monitored under current load and eliminating the possibilities of structural relaxation processes and environmental oxidation. Rietveld refinement was performed to fit the diffraction data with the DFT-derived structures and to analyze the fractions of major phases as a function of dis(charge). The DFT calculations identified three stable states that were validated by the in situ XRD result: a Li-poor α-phase (Li1), a Li-rich α-phase (Li2.5), and a β-phase (Li4). The DFT-predicted particle shape based on the surface energy of the (100), (001), and (010) planes rationalized the preferential orientation of Li 1.1 V 3 O 8 particles along the [010] direction in the electrode. Furthermore, the onset and offset of the α → β transition, as well as the phase fractions of α and β determined via in situ XRD, related well with the DFT-derived relative stability of each phase. Thus, by integrating DFT calculations with experimental work, this work provides a thorough understanding of the structural transformations in Li 1.1 V 3 O 8 during electrochemical dis(charge).

25 ENERGY STORAGE↗
DOE OSTI2018

Rational Design of Pore Size and Functionality in a Series of Isoreticular Zwitterionic Metal–Organic Frameworks

The isoreticular expansion and functionalization of charged-polarized porosity has been systematically explored by the rational design of 11 isostructural zwitterionic metal-organic frameworks (ZW-MOFs). This extended series of general structural composition {[M 3 F(L1) 3 (L2) 1.5 ]·guests} n was prepared by employing the solvothermal reaction of Co and Ni tetrafluoroborates with a binary ligand system composed of zwitterionic pyridinium derivatives and traditional functionalized ditopic carboxylate auxiliary ligands (HL1·Cl = 1-(4-carboxyphenyl)-4,4'-bipyridinium chloride, Hcpb·Cl; or 1-(4-carboxyphenyl-3-hydroxyphenyl)-4,4'-bipyridinium chloride, Hchpb·Cl; and H 2 L2 = benzene-1,4-dicarboxylic acid, H 2 bdc; 2-aminobenzene-1,4-dicarboxylic acid, H 2 abdc; 2,5-dihydroxy-1,4-benzenedicarboxylic acid, H 2 dhbdc; biphenyl-4,4'-dicarboxylic acid, H 2 bpdc; or stilbene-4,4'-dicarboxylic acid, H 2 sdc). Single-crystal structure analyses revealed cubic crystal symmetry ( I -43 m , a = 31-36 Å) with a 3D pore system of significant void space (73-81%). The pore system features three types of pores being systematically tunable in size ranging from 17.4 to 18.8 Å (pore I), 8.2 to 12.8 Å (pore II), and 4.8 to 10.4 Å (pore III) by the choice of auxiliary ligands. All members of this series have noninterpenetrating structures and exhibit robust architectures, as evidenced by their permanent porosity and high thermal stability (up to 300 °C). The structural integrity and specific surface areas could be systematically optimized using supercritical CO 2 exchange methods for framework activation resulting in BET surface areas ranging from 1250 to 2250 m 2 /g. Most interestingly, as a structural landmark, we found the pore surfaces lined with charge gradients employed by the pyridinium ligands. This key feature results in significant adsorption of carbon dioxide and methane which is attributed to polarization effects. With this contribution we pioneer the reticulation of pyridinium building blocks into extended zwitterionic networks in which specific properties can be targeted.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Defining the Specificity of Carbohydrate–Protein Interactions by Quantifying Functional Group Contributions

Protein–carbohydrate interactions are significant in a wide range of biological processes, disruption of which has been implicated in many different diseases. The capability of glycan-binding proteins (GBPs) to specifically bind to the corresponding glycans allows GBPs to be utilized in glycan biomarker detection or conversely to serve as targets for therapeutic intervention. However, understanding the structural origins of GBP specificity has proven to be challenging due to their typically low binding affinities (mM) and their potential to display broad or complex specificities. Here we perform molecular dynamics (MD) simulations and post-MD energy analyses with the Poisson–Boltzmann and generalized Born solvent models (MM-PB/GBSA) of the Erythrina cristagalli lectin (ECL) with its known ligands, and with new cocrystal structures reported herein. While each MM-PB/GBSA parametrization resulted in different estimates of the desolvation free energy, general trends emerged that permit us to define GBP binding preferences in terms of ligand substructure specificity. Additionally, we have further decomposed the theoretical interaction energies into contributions made between chemically relevant functional groups. Based on these contributions, the functional groups in each ligand can be assembled into a pharmacophore comprised of groups that are either critical for binding, or enhance binding, or are noninteracting. It is revealed that the pharmacophore for ECL consists of the galactopyranose (Gal) ring atoms along with C6 and the O3 and O4 hydroxyl groups. This approach provides a convenient method for identifying and quantifying the glycan pharmacophore and provides a novel method for interpreting glycan specificity that is independent of residue-level glycan nomenclature. As a result, a pharmacophore approach to defining specificity is readily transferable to molecular design software and, therefore, may be particularly useful in designing therapeutics (glycomimetics) that target GBPs.

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

Natural Charge-Transfer Analysis: Eliminating Spurious Charge-Transfer States in Time-Dependent Density Functional Theory via Diabatization, with Application to Projection-Based Embedding

For many types of vertical excitation energies, linear-response time-dependent density functional theory (LR-TDDFT) offers a useful degree of accuracy combined with unrivaled computational efficiency, although charge-transfer excitation energies are often systematically and dramatically underestimated, especially for large systems and those that contain explicit solvent. As a result, low energy electronic spectra of solution-phase chromophores often contain tens to hundreds of spurious charge-transfer states, making LR-TDDFT needlessly expensive in bulk solution. More nefariously, intensity borrowing by the low-energy charge-transfer states can affect intensities of the valence excitations even if those excitation energies are accurate. At higher excitation energies, it is difficult to distinguish spurious CT states from genuine charge-transfer-to-solvent (CTTS) excitations. In this work, we introduce an automated diabatization scheme that enables fast and effective screening of the CTTS acceptor space in bulk solution. Our procedure introduces the concept of “natural charge-transfer orbitals”, which provide a means to isolate characteristic pairs of orbitals that are most likely to participate in a CTTS excitation. The projection of these orbitals onto solvent-centered virtual orbitals provides a criterion for defining the most important solvent molecules in a given excitation. We apply this method to analyze an ab initio molecular dynamics (MD) trajectory of I-(aq) and report the lowest-energy CTTS band in the absorption spectrum. Our results are in excellent agreement with experimental measurements for bulk I-(aq), and only one-third of the water molecules in the I-(H2O)96 simulation cell need to be described with LR-TDDFT in order to obtain excitation energies that are converged to < 0.1 eV. The tools introduced herein will improve the accuracy, efficiency, and usability of LR-TDDFT in solution-phase environments

Carter-Fenk, Kevin D.↗
DOE OSTI2018

Projection-Based Correlated Wave Function in Density Functional Theory Embedding for Periodic Systems

In this report we present a level shift projection operator-based embedding method for systems with periodic boundary conditions—where the “active” subsystem can be described using either density functional theory (DFT) or correlated wave function (WF) methods and the “environment” is described using DFT. Our method allows for k-point sampling, is shown to be exactly equal to the canonical DFT solution of the full system under the limit that we use the full system basis to describe each subsystem, and can treat the active subsystem either with periodic boundary conditions—in what we term “periodic-in-periodic” embedding—or as a molecular cluster—in “cluster-in-periodic” embedding. We explore each of these methods and show that cluster WF-in-periodic DFT embedding can accurately calculate the absorption energy of CO on to a Si(100)-2×1 surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding [Development of a Many-Body Density Functional Tight Binding Model for Plutonium Surface Hydriding]

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. Here, we find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H 2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Lastly, our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗