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Results for “computational molecular design”

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.

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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗
DOE OSTI2023

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

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

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BP SS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BP SS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BP SS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BP SS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R 0 ) and fluorophore orientation factor (κ 2 ) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Design of Ru-Ni diatomic sites for efficient alkaline hydrogen oxidation

Anion exchange membrane fuel cells are limited by the slow kinetics of alkaline hydrogen oxidation reaction (HOR). Here, we establish HOR catalytic activities of single-atom and diatomic sites as a function of *H and *OH binding energies to screen the optimal active sites for the HOR. As a result, the Ru-Ni diatomic one is identified as the best active center. Guided by the theoretical finding, we subsequently synthesize a catalyst with Ru-Ni diatomic sites supported on N-doped porous carbon, which exhibits excellent catalytic activity, CO tolerance, and stability for alkaline HOR and is also superior to single-site counterparts. In situ scanning electrochemical microscopy study validates the HOR activity resulting from the Ru-Ni diatomic sites. Furthermore, in situ x-ray absorption spectroscopy and computational studies unveil a synergistic interaction between Ru and Ni to promote the molecular H 2 dissociation and strengthen OH adsorption at the diatomic sites, and thus enhance the kinetics of HOR.

25 ENERGY STORAGE↗
DOE OSTI2025

Equilibrium-gated pattern formation: How molecular dissociation thermodynamics drive emergent behavior in dissipative polymeric systems

Emergent patterns in biological systems arise through dissipative processes that balance reaction and transport phenomena, producing highly functional properties from self-regulating mechanisms. Synthetic fabrication, by contrast, often relies on user-controlled, multistep methods that lack the self-organizing capabilities of natural systems. Inspired by nature, we sought chemical systems that integrate strongly coupled reaction and transport phenomena, identifying frontal ring-opening metathesis polymerization (FROMP) as a method capable of creating diverse forms and functions through reactive processing. By employing discrete molecular initiators, FROMP allows precise control of key reaction steps—inhibition, initiation, and propagation. Using an integrated computational and experimental framework, we uncover how near-equilibrium inhibition dynamics, coupled with far-from-equilibrium reaction kinetics, drive pattern formation in frontally polymerized synthetic materials. We propose the concept of equilibrium-gated pattern formation, demonstrating how initiator chemistry can be tuned to achieve programmable macroscale properties. Our study reveals a surprising insight: Emergent behavior in FROMP systems arises from the inhibition-dominated regime of resin composition, expanding prior observations that such behavior is confined to a narrow compositional space near the boundary between front quenching and uniform front propagation. We identify a broader compositional window, far from the quenching regime, where emergent behavior reliably manifests. This expanded design space significantly enhances the operational flexibility of reactive systems and their capacity for self-organization. Furthermore, these insights provide a roadmap for designing bioinspired materials with self-organizing capabilities, unlocking possibilities in synthetic manufacturing.

Architected Polymers↗
DOE OSTI2022

Data-driven design of molecular nanomagnets

Three decades of research in molecular nanomagnets have raised their magnetic memories from liquid helium to liquid nitrogen temperature thanks to a wise choice of the magnetic ion and coordination environment. Still, serendipity and chemical intuition played a main role. In order to establish a powerful framework for statistically driven chemical design, here we collected chemical and physical data for lanthanide-based nanomagnets, catalogued over 1400 published experiments, developed an interactive dashboard (SIMDAVIS) to visualise the dataset, and applied inferential statistical analysis. Our analysis shows that the Arrhenius energy barrier correlates unexpectedly well with the magnetic memory. Furthermore, as both Orbach and Raman processes can be affected by vibronic coupling, chemical design of the coordination scheme may be used to reduce the relaxation rates. Indeed, only bis-phthalocyaninato sandwiches and metallocenes, with rigid ligands, consistently present magnetic memory up to high temperature. Analysing magnetostructural correlations, we offer promising strategies for improvement, in particular for the preparation of pentagonal bipyramids, where even softer complexes are protected against molecular vibrations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.

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

Leveraging Intramolecular π-Stacking to Access an Exceptionally Long-Lived 3 MC Excited State in an Fe(II) Carbene Complex

The ability to manipulate excited-state decay cascades using molecular structure is essential to the application of abundant-metal photosensitizers and chromophores. Ligand design has yielded some spectacular results elongating charge-transfer excited state lifetimes of Fe(II) coordination complexes, but triplet metal-centered ( 3 MC) excited states - recently demonstrated to be critical to the photoactivity of isoelectronic Co(III) polypyridyls - have to date remained elusive, with temporally isolable examples limited to the picosecond regime. Here, with this report, we show how strong-field donors and intramolecular π-stacking can conspire to stabilize a long-lived 3 MC excited state for a remarkable 4.1 ± 0.3 ns in fluid solution at ambient temperature. Analysis of variable-temperature time-resolved absorption data using theoretical models ranging from Arrhenius to semiclassical Marcus theory, combined with computational modeling and X-ray crystallography, reveal a Jahn−Teller stabilized excited state with a high activation barrier for ground-state recovery. The net result is a chromophore with a 3 MC excited-state lifetime that is orders of magnitude longer than anything yet observed for an Fe(II) complex.

carbene compounds↗
DOE OSTI2026

Photocatalytic Ammonia Synthesis using Fe-Based MOFs: The Role of Ligand Functionalization

Photocatalytic ammonia (NH 3 ) synthesis offers a carbon-neutral alternative to the Haber−Bosch process, which generates 42 million metric tons of CO 2 equivalent emissions annually. However, solar-to-ammonia conversion with contemporary photocatalysts remains far from practical requirements, and understanding the limiting factors in systems with well-defined active sites is crucial. Here, we show how the μ 3 -oxo-centered trinuclear Fe cluster in MIL-101(Fe) functions as the catalytic motif for N 2 -to-NH 3 conversion through combined experimental and computational investigations. Comparative studies with a molecular analogue demonstrate that the cluster is stabilized within the MOF framework, sustaining redox cycling and maintaining high catalytic activity. We systematically functionalized the dicarboxylate ligands of MIL-101(Fe) with −NH 2 , −Br, −NO 2 , −F, and −CF 3 to probe how ligand chemistry modulates Fe electron density, N 2 adsorption capacity, and proton availability, correlating these properties with catalytic performance using spectroscopic and surface characterization techniques alongside timeresolved infrared to assess excited-state lifetimes. F-functionalization optimally balances N 2 activation, proton availability at Fe active sites, and excited-state lifetimes, boosting NH 3 production by ∼ 60% relative to unmodified MIL-101(Fe). This study of ligandfunctionalized MIL-101(Fe) MOFs uncovers the underlying structure-activity relationships and advances design principles for solardriven NH 3 synthesis.

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

Inactivation-mimicking block of the epithelial calcium channel TRPV6

Epithelial calcium channel TRPV6 plays vital roles in calcium homeostasis, and its dysregulation is implicated in multifactorial diseases, including cancers. Here, we study the molecular mechanism of selective nanomolar-affinity TRPV6 inhibition by (4-phenylcyclohexyl)piperazine derivatives (PCHPDs). We use x-ray crystallography and cryo–electron microscopy to solve the inhibitor-bound structures of TRPV6 and identify two types of inhibitor binding sites in the transmembrane region: (i) modulatory sites between the S1-S4 and pore domains normally occupied by lipids and (ii) the main site in the ion channel pore. Our structural data combined with mutagenesis, functional and computational approaches suggest that PCHPDs plug the open pore of TRPV6 and convert the channel into a nonconducting state, mimicking the action of calmodulin, which causes inactivation of TRPV6 channels under physiological conditions. This mechanism of inhibition explains the high selectivity and potency of PCHPDs and opens up unexplored avenues for the design of future-generation biomimetic drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

M06-SX screened-exchange density functional for chemistry and solid-state physics

Significance Density functionals with Hartree–Fock exchange have been widely used for a wide range of chemical applications, but the nonlocal character of exchange makes long-range exchange computationally expensive for solid-state calculations with periodic boundary conditions, and full exchange is nonphysical for condensed-phase systems. Here, we present a screened-exchange (SX) density functional, M06-SX, that is especially designed to have good accuracy for both solid-state physics and chemical applications with less computational cost than full Hartree–Fock exchange. The M06-SX functional gives accuracy comparable to functionals with full Hartree–Fock exchange for predicting chemical properties of molecules, while also being practical with good accuracy for plane wave calculations on band gaps and lattice constants of solids.

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

Performance of an atomic mean-field spin–orbit approach within exact two-component theory for perturbative treatment of spin–orbit coupling

The paper reports development of an atomic mean-field (AMF) spin–orbit approach within the spin-free exact two-component theory in its one-electron variant (SFX2C-1e), a new relativistic quantum-chemical method for treating spin-orbit coupling in molecules. The effective one-electron spin–orbit integral matrix in the four-component representation is assembled as a direct sum of one-centre spin–orbit integral matrices with the mean-field two-electron contributions evaluated using atomic SFX2C-1e Hartree–Fock density matrices. It is then transformed into two-component representation using analytic SFX2C-1e energy derivative formulation. The resulting two-component spin–orbit integral matrix is by design suitable for use in perturbative calculations of spin–orbit coupling, treating SFX2C-1e wavefunctions as unperturbed states. The accuracy of the present AMF approach has been demonstrated using benchmark calculations of spin–orbit splittings for representative diatomic radicals at the equation-of-motion coupled-cluster singles and doubles level. In conclusion, to demonstrate the applicability and accuracy of the present perturbative spin–orbit scheme in calculations of challenging heavy-element containing systems, a thorough computational investigation of six low-lying electronic states of ThO+ is reported.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

First High-Throughput Evaluation of Dark Matter Detector Materials

In this work we perform the first high-throughput search and evaluation of materials that can serve as excellent low-mass dark matter detectors. Using properties of close to 1000 materials from the Materials Project database, we project the sensitivity in dark matter parameter space for experiments constructed from each material, including both absorption and scattering processes between dark matter and electrons. Using the anisotropic materials in the dataset, we further compute the level of daily modulation in interaction rates and the resulting directional sensitivities, highlighting materials with prospects to detect the dark matter wind. Our methods provide the basic tools for the data-driven design of dark matter detectors, and our findings lay the groundwork for the next generation of highly optimized direct searches for dark matter as light as the keV scale. This represents a major step in the application of results from condensed matter physics to dark matter search design.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Investigation of Rare Earth Elements Mobility Using Molecular Dynamics

Rare Earth Elements (REE) are critical many applications such as electronics, permanent magnets, agricultural etc. Effective separation of REEs is a challenge due to their similarities in chemical and physical properties. Current separation processes are costly and environmentally detrimental. Therefore, research on REEs mobility in water-based solvents is necessary to design effective separation processes. In this research, the key kinetic and thermodynamic parameters, including diffusion coefficient and hydration shell are determined under the influence of external electric field. The diffusion coefficient of metal ions increases due to electric field in pure water.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Chemical reaction enhanced graph learning for molecule representation

Abstract Motivation Molecular representation learning (MRL) models molecules with low-dimensional vectors to support biological and chemical applications. Current methods primarily rely on intrinsic molecular information to learn molecular representations, but they often overlook effectively integrating domain knowledge into MRL. Results In this article, we develop a reaction-enhanced graph learning (RXGL) framework for MRL, utilizing chemical reactions as domain knowledge. RXGL introduces dual graph learning modules to model molecule representation. One module employs graph convolutions on molecular graphs to capture molecule structures. The other module constructs a reaction-aware graph from chemical reactions and designs a novel graph attention network on this graph to integrate reaction-level relations into molecular modeling. To refine molecule representations, we design a reaction-based relation learning task, which considers the relations between the reactant and product sides in reactions. In addition, we introduce a cross-view contrastive task to strengthen the cooperative associations between molecular and reaction-aware graph learning. Experiment results show that our RXGL achieves strong performance in various downstream tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation The code is publicly available at https://github.com/coder-ACAC/RLM.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Molecules Functionalized with Cycling Centers for Quantum Information Science

The ability for a single molecule to produce enough laser-induced fluorescence to control and detect its quantum state is known as optical cycling. This property has been used to great effect in atoms, where the relatively small number of states promotes their ability to repeatedly fluoresce, for applications such as laser cooling, precision measurement, atomic clocks, and quantum information processing. The extension of this capability to molecular species, however, has been difficult, primarily due to their propensity to become vibrationally excited during illumination. This project brought together experts from atomic physics, physical chemistry, and computational quantum chemistry to develop means to create molecules capable of optical cycling. In particular, this program sought to produce an optical cycling center (OCC), a quantum functional group capable of chemical attachment to a wide variety of molecular hosts while retaining (and thereby furnishing to its host) the ability to optically cycle. Following our team’s theoretical identification of promising species, including alkaline-earth phenoxides, we then created these species and in many cases confirmed their optical cycle closure. We now not only know of the existence of a handful of large, molecular species that can be deployed for applications in quantum technologies and measurement, but have improved our knowledge of the molecular mechanisms leading to this discovery, which will enable generalization in the future. The extension of these ideas for informed chemical design of cycling molecules with bespoke properties is now being pursued by multiple groups.

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

Effects of MOF linker rotation and functionalization on methane uptake and diffusion

The flexible degrees of freedom in metal–organic frameworks (MOFs) can have significant effects on guest molecule behavior. However, in the majority of studies applying molecular simulations to MOFs, the framework is assumed to be rigid in order to minimize computational cost. Here, in this work, we assess the significance of this assumption on a representative example of methane uptake and diffusion in UiO-66. We introduce an open-source code to modify MOFs through functionalization and linker rotation and we perform Grand Canonical Monte Carlo and molecular dynamics simulations of methane in each of the functionalized and linker-rotated derivatives of UiO-66. We find that linker rotation moderately influences methane uptake and significantly influences methane diffusion. Our assessment provides ranges of property values that serve as measures of uncertainty of these two properties associated with linker rotation. We further determine that void volume fraction and minimum pore size are the features that govern methane uptake and diffusion, respectively. These findings illustrate the impact of linker rotation on MOFs and provide design principles to guide future investigations.

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

Solvent-mediated contaminant removal from plastic waste using thermodynamic modeling

Plastics recycling is hindered by the compositional complexity of plastic waste, which can include numerous polymer components as well as low concentrations of additives and non-intentionally added substances. These latter small-molecule species, which we collectively refer to as contaminants, can harm human health and will build up in recycled plastic causing environmental and downstream processing challenges if not removed. In this work, we present molecular modeling approaches using the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) to guide the selection of solvents that are capable of removing targeted contaminants from plastic waste. By considering the thermodynamic partitioning of contaminant species between a solvent phase and polymer phase, we identify guidelines for solvent selection to promote either the low-temperature extraction of contaminants from plastic waste or the removal of contaminants as part of a dissolution-based plastics recycling process. We present four case studies to illustrate the application of the computational approach to the removal of brominated flame retardants, phthalates, and selected perfluoroalkyl substances, and compare to both literature and newly collected experimental data to illustrate model prediction accuracy. Furthermore, the case studies highlight the capability of the modeling approach to help design recycling processes that explicitly account for contaminant removal, thereby increasing product purity during dissolution-based recycling or facilitating chemical recycling of contaminant-free plastics.

Zhou, Panzheng [University of, Wisconsin, Madison,↗