Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular modelling”

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

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Efficient Intermolecular Charge Transport in π-Stacked Pyridinium Dimers Using Cucurbit[8]uril Supramolecular Complexes

Intermolecular charge transport through π-conjugated molecules plays an essential role in biochemical redox processes and energy storage applications. In this work, we observe highly efficient intermolecular charge transport upon dimerization of pyridinium molecules in the cavity of a synthetic host (cucurbit[8]uril, CB[8]). Stable, homoternary complexes are formed between pyridinium molecules and CB[8] with high binding affinity, resulting in an offset stacked geometry of two pyridiniums inside the host cavity. The charge transport properties of free and dimerized pyridiniums are characterized using a scanning tunneling microscope-break junction (STM-BJ) technique. Our results show that π-stacked pyridinium dimers exhibit comparable molecular conductance to isolated, single pyridinium molecules, despite a longer transport pathway and a switch from intra- to intermolecular charge transport. Control experiments using a CB[8] homologue (cucurbit[7]uril, CB[7]) show that the synthetic host primarily serves to facilitate dimer formation and plays a minimal role on molecular conductance. Molecular modeling using density functional theory (DFT) reveals that pyridinium molecules are planarized upon dimerization inside the host cavity, which facilitates charge transport. In addition, the π-stacked pyridinium dimers possess large intermolecular LUMO–LUMO couplings, leading to enhanced intermolecular charge transport. Altogether, this work demonstrates that supramolecular assembly can be used to control intermolecular charge transport in π-stacked molecules.

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

Splitting the Ring: Impact of Ortho and Meta Pi Conjugation Pathways through Disjointed [8]Cycloparaphenylene Electronic Materials

In this report, we describe the synthesis and electronic properties of small-molecule and polymeric [8]cycloparaphenylenes ([8]CPPs) with disjointed pi conjugated substituents. Arylene-ethynylene linkers were installed on opposite sides of the [8]CPP nanohoop as separated by three phenyl units on either side such that the monomer systems have syn (C2 symmetry) and anti (C1 symmetry) conformers with a small energy gap (0.1-0.6 kcal/mol). This disjoined substitution pattern necessarily forces delocalization through and around the CPP radial structure. We demonstrate new electronic states from this radial/linear mixing in both the small molecules and the pi extended polymers. Quantum chemical calculations reveal these electronic processes to arise from multiple operative radial/linear conjugation pathways, as the disjoint pattern results in both ortho and meta connections to the CPP ring. Furthermore, these results affirm the unique nature of hybrid radial and linear pi electron delocalization operative in these new conjugation pathways.

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

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

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

Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics

Recombinant T cell receptors (TCRs) can be used to redirect naïve T cells to eliminate virally infected or cancerous cells; however, they are plagued by low stability and uneven expression. Here, we use molecular modeling to identify mutations in the TCR constant domains (Cα/Cβ) that increase the unfolding temperature of Cα/Cβ by 20 °C, improve the expression of four separate α/β TCRs by 3- to 10-fold, and improve the assembly and stability of TCRs with poor intrinsic stability. The stabilizing mutations rescue the expression of TCRs destabilized through variable domain mutation. The improved stability and folding of the TCRs reduces glycosylation, perhaps through conformational stabilization that restricts access to N-linked glycosylation enzymes. The Cα/Cβ mutations enables antibody-like expression and assembly of well-behaved bispecific molecules that combine an anti-CD3 antibody with the stabilized TCR. These TCR/CD3 bispecifics can redirect T cells to kill tumor cells with target HLA/peptide on their surfaces in vitro.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Toward a mechanistic understanding of electrocatalytic nanocarbon

Electrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microbial production of megadalton titin yields fibers with advantageous mechanical properties

Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy — outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Abstract Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN + ) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN + -based reducing power. This is based on an orthogonal, NMN + -dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN + . With a throughput of >10 6 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering

Abstract IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Science & Technology - Other Topics↗
DOE OSTI2023

Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection

Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Au 3 -to-Ag 3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength

An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(m-Pz-(i-C 3 H7) 2 )] 3 ∙[Ag(m-Tz-(n-C 3 F 7 ) 2 )] 3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1st crystallographically-verified M 3 @M' 3 stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M' (Au / Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol -1 between the two trimer moieties – a large value for intermolecular interactions between adjacent d 10 centres (nearly doubling the value for a recently claimed Au(I) / Cu(I) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol -1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked M 3 @M' 3 product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M–M' bonds in this family of molecules. The Au / Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H 3 N: → Ag in [Ag(NH 3 ) 2 ] + , as demonstrated herein quantitatively. Solidstate and molecular modeling illustrate electron flow from the p-basic gold trimer to the p-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL'CT) and metal-to-ligand (MLCT) charge transfer.

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

Synthesis and exceptional operational durability of polyaniline-inspired conductive ladder polymers

Ladder-type structures can impart exceptional stability to polymeric electronic materials. This article introduces a new class of conductive polymers featuring a fully ladder-type backbone. A judicious molecular design strategy enables the synthesis of a low-defect ladder polymer, which can be efficiently oxidized and acid-doped to achieve its conductive state. The structural elucidation of this polymer and the characterization of its open-shell nature are facilitated with the assistance of studies on small molecular models. An autonomous robotic system is used to optimize the conductivity of the polymer thin film, achieving over 7 mS cm −1 . Impressively, this polymer demonstrates unparalleled stability in strong acid and under harsh UV-irradiation, significantly surpassing commercial benchmarks like PEDOT:PSS and polyaniline. Moreover, it displays superior durability across numerous redox cycles as the active material in an electrochromic device and as the pseudocapacitive material in a supercapacitor device. This work provides structural design guidance for durable conductive polymers for long-term device operation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Ambient mechanosynthesis of flexible two-dimensional covalent organic frameworks

We present the first ambient mechanosynthesis of 16 flexible covalent organic frameworks (COFs) within an hour. Notably, one representative COF exhibited a high iodine uptake capacity of ∼4.3 g g −1 from aqueous solutions and 5.97 g g −1 from vapor. Flexible two-dimensional covalent organic frameworks (2D COFs) constructed from nonplanar building blocks represent an emerging paradigm in COF design. Nevertheless, the prevailing solvothermal synthesis suffers from low time efficiency, environmental unfriendliness, and cumbersome protocols. Here, we address these challenges by developing the first ambient mechanosynthesis of a diverse library of flexible 2D COFs. Sixteen distinct triazine-cored Schiff-base COFs, including five as-yet-unreported ones, were rapidly synthesized via ball milling using 2,4,6-tris(4-aminophenoxy)-1,3,5-triazine (TPT-NH 2 ) and 2,4,6-tris(4-formylphenoxy)-1,3,5-triazine (TPT-CHO) as building blocks. Notably, the representative COF, MC-flexible-COF-1, was synthesized in as little as one hour under mechanosynthesis conditions, whereas it remained unattainable via the traditional solvothermal method, despite prolonged heating and extensive solvent screening. The highly dynamic nature of the imine linkage was unequivocally demonstrated through mechanochemical “scrambling” experiments using molecular model compounds. Furthermore, MC-flexible-COF-1 exhibited a high iodine uptake capacity of ∼4.30 g g −1 from aqueous solutions and 5.97 g g −1 from the vapor phase. This work underscores the immense potential of mechanochemistry as a powerful and sustainable tool for the rapid synthesis of advanced 2D COFs, including those inaccessible via conventional solution-based methods.

Nailwal, Yogendra↗
DOE OSTI2020

Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions

This article reviews recent molecular simulation studies of "collective" properties of aqueous electrolyte solutions, specifically free energies and activity coefficients, solubilities, nucleation rates of crystals, and transport coefficients. These are important fundamental properties for biology and geoscience, but also relevant for many technological applications. Their determination from molecular-scale calculations requires large systems and long sampling times, as well as specialized sampling algorithms. As a result, such properties have not typically been taken into account during optimization of force field parameters; thus, they provide stringent tests for the transferability and range of applicability of proposed molecular models. There has been significant progress on simulation algorithms to enable the determination of these properties with good statistical uncertainties. Comparisons of simulation results to experimental data reveal deficiencies shared by many commonly used models. Moreover, there appear to exist specific tradeoffs within existing modeling frameworks, so that good prediction of some properties is linked to poor prediction for specific other properties. For example, non-polarizable models that utilize full charges on the ions generally fail to predict accurately both activity coefficients and solubilities; the concentration dependence of viscosity and diffusivity for these models is also incorrect. Scaled-charge models improve the dynamic properties and could also perform well for solubilities, but fail in the prediction of nucleation rates. Even models that do well at room temperature for some properties generally fail to capture their experimentally observed temperature dependence. Finally, the main conclusion from the present review is that qualitatively new physics will need to be incorporated in future models of electrolyte solutions to allow description of collective properties for broad ranges of concentrations, temperatures, and solvent conditions.

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

Evaluation of two-particle properties within finite-temperature self-consistent one-particle Green’s function methods: Theory and application to GW and GF2

One-particle Green’s function methods can model molecular and solid spectra at zero or non-zero temperatures. One-particle Green’s functions directly provide electronic energies and one-particle properties, such as dipole moment. However, the evaluation of two-particle properties, such as $\langle$S 2 $\rangle$ and $\langle$N 2 $\rangle$, can be challenging because they require a solution of the computationally expensive Bethe–Salpeter equation to find two-particle Green’s functions. We demonstrate that the solution of the Bethe–Salpeter equation can be completely avoided. Applying the thermodynamic Hellmann–Feynman theorem to self-consistent one-particle Green’s function methods, we derive expressions for two-particle density matrices in a general case and provide explicit expressions for GF2 and GW methods. Such density matrices can be decomposed into an antisymmetrized product of correlated one-electron density matrices and the two-particle electronic cumulant of the density matrix. Cumulant expressions reveal a deviation from ensemble representability for GW, explaining its known deficiencies. We analyze the temperature dependence of $\langle$S 2 $\rangle$ and $\langle$N 2 $\rangle$ for a set of small closed-shell systems. Interestingly, both GF2 and GW show a non-zero spin contamination and a non-zero fluctuation of the number of particles for closed-shell systems at the zero-temperature limit.

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

Experimental and theoretical examination of shock-compressed copper through the fcc to bcc to melt phase transitions

Recent studies show a face-centered cubic (fcc) to body-centered cubic (bcc) transformation along the shock Hugoniot for several metals (i.e., Cu, Au, and Ag). Here, we combine laser-shock compression of Cu foils on nanosecond timescales with in situ x-ray diffraction (XRD) to examine the microstructural changes with stress. We study the fcc phase and the phase transition from fcc to bcc (pressures greater than 180 GPa). Textural analysis of the azimuthal intensities from the XRD images is consistent with transformation into the bcc phase through the Pitsch-distortion mechanism. We use embedded atom model molecular dynamics simulations to determine the stability of the bcc phase in pressure–temperature space. Finally, our results indicate that the bcc phase is stabilized only at high temperatures and remains stable at pressures greater than 500 GPa.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Accelerating the density-functional tight-binding method using graphical processing units

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Herein two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1–6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1–2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.

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

The contribution of Compton ionization to ultrafast x-ray scattering

We investigate the role of Compton ionization in ultrafast non-resonant x-ray scattering using a molecular model system, which includes the ionization continuum via an orthonormalized plane wave ansatz. Elastic and inelastic components of the scattering signal, as well as coherent-mixed scattering that arises from electron dynamics, are calculated. By virtue of a near-quantitative distinction between scattering related to electronic transitions into bound and continuum states, we demonstrate how Compton ionization contributes to the coherent-mixed component. Analogous to inelastic scattering, the contribution to the coherent-mixed signal is significant and particularly manifests at intermediate and high-momentum transfers. Strikingly, for molecules with inversion symmetry, the exclusion of bound or continuum transitions may lead to the prediction of spurious coherent-mixed signals. We conclude that qualitative and quantitative accuracies of predicted scattering signals on detectors without energy resolution require that elements of the two-electron density operator are used. This approach inherently accounts for all accessible electronic transitions, including ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗