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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Potentials of mean force fail to describe chemical bond-breaking in solution

Many liquid phase studies assume that the potential energy surfaces of reacting molecules are the same as in the gas phase, neglecting complex solvent dynamics that can completely alter the nature of chemical reactivity. Even studies that include solvent effects typically only consider them in an average, equilibrium way as part of a potential of mean force (PMF). In this work, we use mixed quantum/classical simulations to compare how equilibrium and non-equilibrium solvent motions affect the photodissociation of a simple diatomic molecule, NaK + , in liquid tetrahydrofuran. A PMF analysis shows that as the excited-state molecule dissociates with the solvent at equilibrium, the bonding electron remains associated with K + at short bond distances but eventually localizes on Na + at the end of dissociation. When we examine non-equilibrium dynamical photodissociation trajectories, however, we find that they fall into three distinct categories: about a quarter of them have the bonding electron mainly associated with Na + , another quarter stay mainly associated with K + , and about half have the bonding electron shared roughly equally between the two ions. The results show that equilibrium PMFs cannot accurately describe the dynamics of bond-breaking chemical reactions in solution because there is insufficient time for the solvent to reach equilibrium on the time scale over which bond dissociation occurs. Furthermore, our analysis shows that the solvent coupling between the electronic energy surfaces is similar at and away from equilibrium, suggesting that other factors, such as solute velocity-driven solvent memory effects, play a more important role in explaining the failure of the equilibrium PMF to predict the non-equilibrium dynamics.

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

Patchy nanoparticles by atomic stencilling

Stencilling, in which patterns are created by painting over masks, has ubiquitous applications in art, architecture and manufacturing. Modern, top-down microfabrication methods have succeeded in reducing mask sizes to under 10 nm, enabling ever smaller microdevices as today’s fastest computer chips. Meanwhile, bottom-up masking using chemical bonds or physical interactions has remained largely unexplored, despite its advantages of low cost, solution-processability, scalability and high compatibility with complex, curved and three-dimensional (3D) surfaces. Here we report atomic stencilling to make patchy nanoparticles (NPs), using surface-adsorbed iodide submonolayers to create the mask and ligand-mediated grafted polymers onto unmasked regions as ‘paint’. We use this approach to synthesize more than 20 different types of NP coated with polymer patches in high yield. Polymer scaling theory and molecular dynamics (MD) simulation show that stencilling, along with the interplay of enthalpic and entropic effects of polymers, generates patchy particle morphologies not reported previously. These polymer-patched NPs self-assemble into extended crystals owing to highly uniform patches, including different non-closely packed superlattices. We propose that atomic stencilling opens new avenues in patterning NPs and other substrates at the nanometre length scale, leading to precise control of their chemistry, reactivity and interactions for a wide range of applications, such as targeted delivery, catalysis, microelectronics, integrated metamaterials and tissue engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Capturing electronic decoherence in quantum-classical dynamics using the ring-polymer-surface-hopping–density-matrix approach

Simulations of coupled electronic and nuclear dynamics in molecules can be quite challenging due to the involved interplay of the many degrees of freedom. Because a full quantum treatment of both electrons and nuclei is computationally very demanding, it is generally restricted to model systems or rather small molecules and short timescales. Mixed quantum-classical dynamics methods such as Tully's fewest switches surface hopping (FSSH) can be used to overcome this limitation. However, FSSH is known to poorly describe electronic coherences and decoherence phenomena. Here, we present an approach that combines FSSH with ring-polymer molecular dynamics (RPMD) in a specific way that aims to alleviate the coherence problem. Termed the ring-polymer-surface-hopping–density-matrix approach, this method uses an electronic density-matrix formulation to calculate surface hopping rates. Additionally, this incorporates decoherence effects into FSSH in a natural way by taking into account the spatial spreading of the ring polymer that mimics the width of a nuclear wave packet in each RPMD trajectory. By applying our method to Tully's one-dimensional model system, we demonstrate that this method captures a crucial decoherence mechanism that is missing in FSSH. Furthermore, our method turns out to be superior at describing electronic coherences compared with earlier attempts at combining RPMD and FSSH.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Analyzing the effect of pressure on the properties of point defects in $\gamma\mathrm{U–Mo}$ through atomistic simulations

Uranium–molybdenum (U–Mo) alloys in monolithic fuel foil are the primary candidate for the conversion of high-performance research reactors in the USA. Monolithic fuel is utilized in a plate-type design with a zirconium diffusion barrier and aluminum cladding. These fuel types are unique in that they contain no plenum for the release of fission gases, which, in conjunction with the aluminum cladding, can lead to large stress states within the fuel. The nature of how fundamental processes of radiation damage, including the evolution of point defects, under such stresses occur is unknown. In this work, we present molecular dynamics simulations of the formation energy of point defects under applied stress. We report this work will allow for the implementation of stress-dependent microstructural evolution models of nuclear fuels, including those for both fission gas bubble growth and creep, which are critical to ensure the stable and predictable behavior of research reactor fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Impact of Hydrogen Bonds on CO 2 Binding in Eutectic Solvents: An Experimental and Computational Study toward Sorbent Design for CO 2 Capture

Choline-based amino acid ionic liquids with anions glycinate, β-alaninate, phenylalaninate, and prolinate were synthesized and mixed with ethylene glycol to form lower-viscosity benign eutectic solvents for CO 2 capture. The highest capacity measured was 0.7 moles of CO 2 per mole of ionic liquid (2 moles CO 2 per kg solvent) for a 1 to 2 mole ratio mixture of choline prolinate to ethylene glycol at 1 bar of CO 2 and 25 °C. Under 5000 ppm of CO 2 , half of this capacity was realized. Here, through a combined study of quantitative 13 C NMR spectroscopy, molecular dynamics simulations and density functional theory calculations, we show that hydrogen bonding in the eutectic solvent prevents proton-transfer between prolinate anions upon CO 2 absorption, which occurs in the absence of ethylene glycol and deactivates binding sites. Blocking this proton transfer leads to a higher binding capacity compared to neat choline prolinate. This work demonstrates the impact of hydrogen bonding on the CO 2 binding mechanism and energetics, as well as physical and thermal properties in eutectic solvents, thus addressing an unmet need and informing future studies on the development of benign sorbents for capturing CO 2 from dilute streams.

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

Generative Thermodynamic Computing

Here, we introduce a generative modeling framework for thermodynamic computing, in which structured data are synthesized from noise by the natural time evolution of a physical system governed by Langevin dynamics. While conventional diffusion models use neural networks to perform denoising, here the information needed to generate structure from noise is encoded by the dynamics of a thermodynamic system. Training proceeds by maximizing the probability with which the computer generates the reverse of a noising trajectory, which ensures that the computer generates data with minimal heat emission. We demonstrate this framework within a digital simulation of a thermodynamic computer. If realized in analog hardware, such a system would function as a generative model that produces structured samples without the need for artificially injected noise or active control of denoising.

Whitelam, Stephen [Lawrence Berkeley National Labo↗
DOE OSTI2022

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Unveiling the Structure and Dynamics of Water Confined in Colloidal Boehmite Suspensions

Thin fluid layers confined between nanoparticles play an important role in several natural and industrial systems, including radioactive wastes stored in tanks at the U.S. Department of Energy’s Hanford site. Multimodal neutron and computational approaches have been integrated to examine the properties of one, two, and four layers of water (H 2 O or D 2 O) on nanoparticulate, hydrous, or deuterated boehmite (γ-AlOOH or γ-AlOOD). Exposure of deuterated boehmite to H 2 O at 90 °C yielded rapid H/D isotopic exchange likely driven by a Grotthus-like proton-hopping mechanism. The in-plane and out-of-plane vibrations of the structural hydroxyls involved in this exchange were observed for both the hydrated and deuterated boehmite. These observations were confirmed by molecular dynamics simulations that also showed that single water molecules on the (010) surface bond to the structure via four bonds: two from hydrogens (deuteriums) on the water to surrounding oxygens and two from the water’s oxygen to surrounding OD/OH. Bulk water-like properties began to appear once four monolayers of water had been added, but steric crowding limited water diffusion rates once two monolayers had been added. The super-Arrhenius temperature dependence observed at four monolayers indicated glass-like behavior in a well-formed hydrogen-bonding network. Such a network is not sufficiently developed, however, when the surface water coverage is less than four layers. In conclusion, the unique nature of these layers can provide critical information for understanding forces between particles in proximity, and resultant effects on suspension rheology.

Anovitz, Lawrence M. [Oak Ridge National Laborator↗
DOE OSTI2023

Melting curves of ice polymorphs in the vicinity of the liquid–liquid critical point

The possible existence of a liquid–liquid critical point in deeply supercooled water has been a subject of debate due to the challenges associated with providing definitive experimental evidence. The pioneering work by Mishima and Stanley [Nature 392, 164–168 (1998)] sought to shed light on this problem by studying the melting curves of different ice polymorphs and their metastable continuation in the vicinity of the expected liquid–liquid transition and its associated critical point. Based on the continuous or discontinuous changes in the slope of the melting curves, Mishima [Phys. Rev. Lett. 85, 334 (2000)] suggested that the liquid–liquid critical point lies between the melting curves of ice III and ice V. Herein we explore this conjecture using molecular dynamics simulations with a machine learning model based on ab initio quantum-mechanical calculations. We study the melting curves of ices III, IV, V, VI, and XIII and find that all of them are supercritical and do not intersect the liquid–liquid transition locus. We also find a pronounced, yet continuous, change in the slope of the melting lines upon crossing of the liquid locus of maximum compressibility. Finally, we analyze the literature in light of our findings and conclude that the scenario in which the melting curves are supercritical is favored by the most recent computational and experimental evidence. Although the preponderance of evidence is consistent with the existence of a second critical point in water, the behavior of ice polymorph melting lines does not provide strong evidence in support of this viewpoint, according to our calculations.

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

Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.

Wigner distribution↗
DOE OSTI2020

Mechanistic understanding of catalytic conversion of ethanol to 1-butene over 2D-pillared MFI zeolite

Ethanol is an important C2 platform molecule for producing value-added chemicals and distillate hydrocarbon fuels (e.g., jet and diesel). Among these, catalytic upgrading of ethanol to butenes can generate valuable commodity chemicals (e.g., 1-butene) and provide C4 olefin intermediates that can be further upgraded to jet/diesel fuels. 2D zeolites offer hierarchical mesoporous structures, leading to improved mass transport and reduced diffusion length, which can help to address the coking challenges faced by ethanol conversion to hydrocarbons over 3D zeolites. In this study, we investigate the acid-catalyzed conversion of ethanol to 1-butene over the Brønsted acid sites (BAS) in 2D-pillared MFI zeolite (2D-PMFI) using ab initio molecular dynamics (AIMD) simulations, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and calorimetric measurements. A detailed thermodynamic analysis, using quasi-harmonic approximation (QHA), on the Gibbs free energy pathway of ethanol conversion shows that the consideration of entropy is critical to accurately capture the detailed thermodynamic profiles. The formation of bulky ethoxy-ethene complex is found to be a potential rate-determining step (RDS), proceeding via stepwise mechanism. The reactivity of 2D-PMFI can be further tuned by manipulating RDS through a careful control of number of BAS and operating temperatures. The accuracy of computational model is confirmed through the comparison of calculated vibrational density of states (VDOS) against the experimental DRIFTS measurements. Overall, our study provides mechanistic insights into ethanol upgrading over the 2D-PMFI and shows the importance of evaluating entropic effects in such confined system.

Ethanol conversion, 2D-pillared zeolite, MFI, Anha↗
DOE OSTI2021

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

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

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

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

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Thermal transport in defective and disordered materials

With significant recent advancements in thermal sciences—such as the development of new theoretical and experimental techniques, and the discovery of new transport mechanisms—it is helpful to revisit the fundamentals of vibrational heat conduction to formulate an updated and informed physical understanding. The increasing maturity of simulation and modeling methods sparks the desire to leverage these techniques to rapidly improve and develop technology through digital engineering and multi-scale, electro-thermal models. With that vision in mind, this review attempts to build a holistic understanding of thermal transport by focusing on the often unaddressed relationships between subfields, which can be critical for multi-scale modeling approaches. For example, we outline the relationship between mode-specific (computational) and spectral (analytical) models. We relate thermal boundary resistance models based on perturbation approaches and classic transmissivity based models. We discuss the relationship between lattice dynamics and molecular dynamics approaches along with two-channel transport frameworks that have emerged recently and that connect crystal-like and amorphous-like heat conduction. Throughout, we discuss best practices for modeling experimental data and outline how these models can guide material-level and system-level design.

42 ENGINEERING↗
DOE OSTI2022

Understanding Proton Movement in [Fe-Fe] Hydrogenases

Nature uses specialized metalloenzymes to carry out small molecule activation reactions, including CO 2 fixation, O 2 activation, and proton reduction, with unparalleled efficiency, rates, and selectivity. The latter reactions are performed by hydrogenases, protein metallo-complexes that interconverts H 2 to protons and electrons (H 2 oxidation) and the reverse reaction (H 2 production) with incredibly low energy input and amazingly fast kinetics. Reproducing both the activity and efficiency of metalloenzymes in sustainable anthropogenic systems remains one of the “holy grails” of inorganic chemistry. However, identifying the precise molecular components responsible for these desirable properties has been challenging in the natural metalloenzymes, hindering efforts to develop analogous processes in synthetic compounds. Considering the inherent complexity of a metalloenzyme and the many interactions, both strong and weak, that contribute to the function of an enzyme, we have elected to model natural metalloenzymes on a biochemical platform. Towards this end, we have a developed structural, functional, and mechanistic mimic of the [Ni-Fe] hydrogenases within a robust protein scaffold, rubredoxin, to understand the influence of the secondary coordination environment on the metal center. This involved preparing a series of three rubredoxin constructs containing a single point mutation at Val positions and making the NMR chemical shift assignments for the paramagnetic (nickel-substituted) and non-paramagnetic (zinc-substituted) form. These physical studies were complemented with in silico molecular dynamic studies on proteins with [Fe-S] clusters to engineer new proton channels to test in vitro . To assist our search for new natural metalloprotein scaffolds within the vast number of sequenced genomes, we created a neural network-based program to identify proteins with specific metal-binding sites. These computational and physical studies with metalloenzymes provide direct insight into the fundamental chemical principles driving the natural systems and offer design principles for developing catalysts that utilize analogous principles.

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

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗