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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Vibronic Coupling and Exciton Chirality: Electronic and Structural Rearrangement between Helical to Zero Momentum Molecular Exciton States

Helical porphyrin aggregates are attractive macromolecular nanostructures for biomimetic light-harvesting and energy transfer in solar energy technology due to their large light absorbing cross sections and promising energy conservation benefits from chiral-induced spin selectivity. However, with these soft materials, it is imperative that we understand how the nuclear degrees of freedom impact the excitonic energy landscape and dynamics, particularly pertaining to how it influences the chiral angular momentum of the excitons. To this end, we have measured time-resolved depolarization ratios using femtosecond stimulated Raman spectroscopy to uncover the vibronic coupling guided by molecular vibrations between excitons of different angular momentum in helical tetra(sulfonatophenyl)porphyrin aggregates. We find that while transient absorption anisotropy reveals rapid (1 ps lifetime) exciton rotation from helical to achiral states in the Q-band, time-resolved vibrational depolarization ratios evolve on remarkably faster time scales (<500 fs lifetime) for the totally symmetric 1530 cm –1 vibration and the nontotally symmetric 1540 cm –1 vibration. The time-resolved depolarization ratios of the 1540 cm –1 vibration, in particular, show strong evidence of vibronic coupling and nonadiabatic exciton behavior that mediates the nonradiative transition between chiral and achiral excitons. Furthermore, our study shows that for rational design of helical molecular aggregates for exciton transport, the vibronic coupling between excitons of different angular momenta driven by molecular vibrations must be considered especially in the case where chiral-induced spin selectivity is desired.

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

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Applying the Tremaine–Weinberg Method to Nearby Galaxies: Stellar-mass-based Pattern Speeds and Comparisons with ISM Kinematics

We apply the Tremaine–Weinberg method to 19 nearby galaxies using stellar mass surface densities and velocities derived from the PHANGS-MUSE survey, to calculate (primarily bar) pattern speeds (Ω{sub P}). After quality checks, we find that around half (10) of these stellar-mass-based measurements are reliable. For those galaxies, we find good agreement between our results and previously published pattern speeds, and we use rotation curves to calculate major resonance locations (corotation radii and Lindblad resonances). We also compare these stellar-mass-derived pattern speeds with Hα (from MUSE) and CO(J = 2 − 1) emission from the PHANGS-ALMA survey. We find that in the case of these clumpy interstellar medium (ISM) tracers, this method erroneously gives a signal that is simply the angular frequency at a representative radius set by the distribution of these clumps (Ω{sub clump}), and that this Ω{sub clump} is significantly different from Ω{sub P} (∼20% in the case of Hα, and ∼50% in the case of CO). Thus, we conclude that it is inadvisable to use “pattern speeds” derived from ISM kinematics. Finally, we compare our derived pattern speeds and corotation radii, along with bar properties, to the global parameters of these galaxies. Consistent with previous studies, we find that galaxies with a later Hubble type have a larger ratio of corotation radius to bar length, more molecular-gas-rich galaxies have higher Ω{sub P}, and more bulge-dominated galaxies have lower Ω{sub P}. Unlike earlier works, however, there are no clear trends between the bar strength and Ω{sub P}, nor between the total stellar mass surface density and the pattern speed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

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

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

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

MD Simulation of Water Using a Rigid Body Description Requires a Small Time Step to Ensure Equipartition

In simulations of aqueous systems, it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time step δt for integrating the equations of motion. Thus, δt = 2 fs is often used in simulating rigid models of water. We simulate the SPC/E model of water using δt from 0.5 to 3.0 fs and up to 4 fs using hydrogen mass repartitioning. In these simulations, we find that for all but δt = 0.5 fs, equipartition is not obtained between translational and rotational modes, with the rotational modes exhibiting a lower temperature than the translation modes. To probe the reasons for the lack of equipartition, we study the autocorrelation of the translational velocity of the center of mass and the angular velocity of the rigid water molecule, respectively. Here, we find that the rotational relaxation occurs on a timescale comparable to vibrational periods, calling into question the original motivations for freezing the vibrations. Furthermore, a time step with δt ≥ 1 fs is not able to capture accurately the fast rotational relaxation, which reveals its impact as an effective slowing-down of rotational relaxation. The fluctuation–dissipation relation then leads to the conclusion that the rotational temperature should be cooler for δt greater than the reference value of 0.5 fs. Consideration of fluctuation–dissipation in equilibrium molecular dynamics simulations also emphasizes the need to capture the temporal evolution of fluctuations with fidelity and the role of δt in this regard. The time step also influences the solution thermodynamic properties: both the mean system potential energies and the excess entropy of hydration of a soft repulsive cavity are sensitive to δt.

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

Strong-field ionization of the triplet ground state of O 2

Using strong-field ionization as a probe, we observe highly nonperiodic evolution of the spin-rotation wave packet launched by a nonionizing femtosecond pulse in oxygen. The nonperiodicity is readily apparent only in rotationally cold molecules that are pumped with a weak alignment pulse. We show that this behavior is a consequence of the spin-rotation and the spin-spin couplings in the triplet ground state of the neutral molecule. A model that includes these couplings in the field-free Hamiltonian but in neither the alignment nor the ionization step explains most of the observed dynamics, suggesting that neither process depends explicitly on the electronic spin. We also show that the angle dependence of strong-field ionization can be retrieved from the delay-dependent signal even when coupling to spin complicates the rotational dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture

Abstract Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li 7 P 3 S 11 , a superionic conductor, and show that resulting Li diffusion coefficient is within 14% of that obtained directly from AIMD. The high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.

Chemistry↗
DOE OSTI2020

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗
DOE OSTI2021

Non-adiabatic quantum interference in the ultracold Li + LiNa → Li 2 + Na reaction

Electronically non-adiabatic effects play an important role in many chemical reactions. However, how these effects manifest in cold and ultracold chemistry remains largely unexplored. Here for the first time we present from first principles the non-adiabatic quantum dynamics of the reactive scattering between ultracold alkali-metal LiNa molecules and Li atoms. We show that non-adiabatic dynamics induces quantum interference effects that dramatically alter the ultracold rotationally resolved reaction rate coefficients. The interference effect arises from the conical intersection between the ground and an excited electronic state that is energetically accessible even for ultracold collisions. These unique interference effects might be exploited for quantum control applications such as a quantum molecular switch. The non-adiabatic dynamics are based on full-dimensional ab initio potential energy surfaces for the two electronic states that includes the non-adiabatic couplings and an accurate treatment of the long-range interactions. A statistical analysis of rotational populations of the Li2 product reveals a Poisson distribution implying the underlying classical dynamics are chaotic. The Poisson distribution is robust and amenable to experimental verification and appears to be a universal property of ultracold reactions involving alkali metal dimers.

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

Diagonalizing the Born–Oppenheimer Hamiltonian via Moyal perturbation theory, nonadiabatic corrections, and translational degrees of freedom

This article describes a method for calculating higher order or nonadiabatic corrections in Born–Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner–Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ 2 , where κ = (m/M)1/4 is the usual Born–Oppenheimer parameter. The lowest order term is the usual Born–Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born–Oppenheimer theory. Here, we show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born–Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom.

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

Electrostatic control of photoisomerization pathways in proteins

Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

ancestral sequence reconstruction↗
DOE OSTI2023

Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair

G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B 12 -dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B 12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Porous Nanographenes, Graphene Nanoribbons, and Nanoporous Graphene Selectively Synthesized from the Same Molecular Precursor

In this study, we demonstrate a family of molecular precursors based on 7,10-dibromo-triphenylenes that can selectively produce different varieties of atomically precise porous graphene nanomaterials through the use of different synthetic environments. Upon Yamamoto polymerization of these molecules in solution, the free rotations of the triphenylene units around the C–C bonds result in the formation of cyclotrimers in high yields. In contrast, in on-surface polymerization of the same molecules on Au(111) these rotations are impeded, and the coupling proceeds toward the formation of long polymer chains. These chains can then be converted to porous graphene nanoribbons (pGNRs) by annealing. Correspondingly, the solution-synthesized cyclotrimers can also be deposited onto Au(111) and converted into porous nanographenes (pNGs) via thermal treatment. Thus, both processes start with the same molecular precursor and end with a porous graphene nanomaterial on Au(111), but the type of product, pNG or pGNR, depends on the specific coupling approach. We also produced extended nanoporous graphenes (NPGs) through the lateral fusion of highly aligned pGNRs on Au(111) that were grown at high coverage. The pNGs can also be synthesized directly in solution by Scholl oxidative cyclodehydrogenation of cyclotrimers. We demonstrate the generality of this approach by synthesizing two varieties of 7,10-dibromo-triphenylenes that selectively produced six nanoporous products with different dimensionalities. The basic 7,10-dibromo-triphenylene monomer is amenable to structural modifications, potentially providing access to many new porous graphene nanomaterials. We show that by constructing different porous structures from the same building blocks, it is possible to tune the energy band gap in a wide range.

25 ENERGY STORAGE↗
DOE OSTI2024

Linear response of molecular polaritons

In this article, we show that the collective light–matter strong coupling regime where N molecular emitters couple to the photon mode of an optical cavity can be mapped to a quantum impurity model where the photon is the impurity that is coupled to a bath of anharmonic transitions. In the thermodynamic limit where N ≫ 1, we argue that the bath can be replaced with an effective harmonic bath, leading to a dramatic simplification of the problem into one of the coupled harmonic oscillators. We derive simple analytical expressions for linear optical spectra (transmission, reflection, and absorption) where the only molecular input required is the molecular linear susceptibility. This formalism is applied to a series of illustrative examples, showing the role of temperature, disorder, vibronic coupling, and optical saturation of the molecular ensemble, explaining that it is useful even when describing an important class of nonlinear optical experiments. For completeness, we provide Appendixes A–C that include a self-contained derivation of the relevant spectroscopic observables for arbitrary anharmonic systems (for both large and small N) within the rotating-wave approximation. While some of the presented results herein have already been reported in the literature, we provide a unified presentation of the results as well as new interpretations that connect powerful concepts in open quantum systems and linear response theory with molecular polaritonics.

Chemistry↗
DOE OSTI2021

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy

We experimentally investigated several intra-molecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). Here, we developed a high-throughput single-molecule spectroscopy technique to analyze more than 5,000 single-molecule emission spectra from each of nine commonly used fluorophores with different structural rigidities deposited on substrates with different polarities. We observed an unexpected high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye - Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system’s noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N, N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intra-molecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.

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

Quantized Grain Boundary States Promote Nanoparticle Alignment During Imperfect Oriented Attachment

Oriented attachment (OA) has become a well-recognized mechanism for the growth of metal, ceramic, and biomineral crystals. While many computational and experimental studies of OA have shown that particles can attach with some misorientation then rotate to remove adjoining grain boundaries, the underlying atomistic pathways for this “Imperfect OA” process remain the subject of debate. In this paper, molecular dynamics and in situ TEM were used to probe the crystallographic evolution of up to 30 gold and copper nanoparticles during aggregation. It was found that Imperfect OA occurs because (1) grain boundaries become quantized when their size is comparable to the separation between constituent dislocations and (2) kinetic barriers associated with the glide of grain boundary dislocations are small. In support of these findings, TEM experiments show the formation of a single crystal aggregate after annealing 9 initially misoriented, agglomerated particles with evidence of dislocation slip and twin formation during particle/grain alignment. These observations motivate future work on assembled nanocrystals with tailored defects and call for a revision of Read-Shockley models for grain boundary energies in nanocrystalline materials.

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

NMR relaxometry characterization of water adsorption in corn stover anatomical fractions

Nuclear magnetic resonance (NMR) relaxometry is applied to provide direct measurement of water adsorption in anatomical fractions of corn stover. NMR transverse T 2 relaxation time distribution measurements indicate multiple water populations, which vary with anatomical fraction and water adsorption. Measured T 2 data are used to calculate thermodynamic properties of Brunauer-Emmet-Teller adsorption theory using a model to estimate mono and bilayer relaxation. T 2 data are used directly to determine rotational diffusion correlation times indicating adsorption interaction strength. T 1 -T 2 longitudinal-transverse relaxation time correlation measurements quantify differences in the molecular level structural order of the adsorbate surface water as a function of water activity, i.e. relative humidity or water vapor partial pressure. The T 1 /T 2 ratio provides a measure of the surface energy related to the adsorption strength and surface diffusive mobility of the water adsorbate and differentiates the anatomical fractions. Furthermore, the results indicate that direct measurement of NMR relaxation times can be used to characterize corn stover biomass water adsorption, data relevant to processing and handling considerations.

09 BIOMASS FUELS↗