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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Barrier Heights for Diels–Alder Transition States Leading to Pentacyclic Adducts: A Benchmark Study of Crowded, Strained Transition States of Large Molecules

Theoretical characterization of reactions of complex molecules depends on providing consistent accuracy for the relative energies of intermediates and transition states. Here we employ the DLPNO-CCSD(T) method with core–valence correlation, large basis sets, and extrapolation to the CBS limit to provide benchmark values for Diels–Alder transition states leading to competitive strained pentacyclic adducts. We then used those benchmarks to test a diverse set of wave function and density functional methods for the absolute and relative barrier heights of these transition states. Our results show that only a few of the tested density functionals can predict the absolute barrier heights satisfactorily, although relative barrier heights are more accurate. The most accurate functionals tested are ωB97M-V, M11plus, ωB97X-V, PBE-D3(0), M11, and MN15 with MUDs from best estimates less than 3.0 kcal. Furthermore, these findings can guide selection of density functionals for future studies of crowded, strained transition states of large molecules.

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

Analytical ab initio hessian from a deep learning potential for transition state optimization

Identifying transition states—saddle points on the potential energy surface connecting reactant and product minima—is central to predicting kinetic barriers and understanding chemical reaction mechanisms. In this work, we train a fully differentiable equivariant neural network potential, NewtonNet, on thousands of organic reactions and derive the analytical Hessians. By reducing the computational cost by several orders of magnitude relative to the density functional theory (DFT) ab initio source, we can afford to use the learned Hessians at every step for the saddle point optimizations. We show that the full machine learned (ML) Hessian robustly finds the transition states of 240 unseen organic reactions, even when the quality of the initial guess structures are degraded, while reducing the number of optimization steps to convergence by 2–3× compared to the quasi-Newton DFT and ML methods. All data generation, NewtonNet model, and ML transition state finding methods are available in an automated workflow.

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

Cysteine residues contribute to the regulation of Arabidopsis state transition 7 kinase

State transitions are an acclimatory response by which plants, algae, and cyanobacteria counteract photosynthetic inefficiency caused by changes in incident light quality. In plants and green algae, state transition 7 (STN7/STT7) kinase promotes state 2 transition. Conserved cysteine residues are implicated in STN7/STT7 regulation, but the precise nature of their involvement remains unclear. Here, an analysis of the STN7 thiols in vitro and a determination of their midpoint redox potential indicate that the lumenal disulfide linkage is unlikely to be redox regulated while the stromal cysteines form a regulatory intramolecular disulfide. We further show that thioredoxin f 1 (Trx‐ f 1) reduces the STN7 stromal disulfide linkage as consistent with a Trx‐ f 1‐mediated inhibition of the kinase under high light.

Ibrahim, Iskander M.↗
DOE OSTI2022

Influence of Long-Range Forces on the Transition States and Dynamics of NaCl Ion-Pair Dissociation in Water

We study NaCl ion-pair dissociation in a dilute aqueous solution using computer simulations both for the full system with long-range Coulomb interactions and for a well-chosen reference system with short-range intermolecular interactions. Analyzing results using concepts from Local Molecular Field (LMF) theory and the recently proposed AI-based analysis tool “State predictive information bottleneck” (SPIB), we show that the system with short-range interactions can accurately reproduce the transition rate for the dissociation process, the dynamics for moving between the underlying metastable states, and the transition state ensemble. Contributions from long-range interactions can be largely neglected for these processes because long-range forces from the direct interionic Coulomb interactions are almost completely canceled (>90%) by those from solvent interactions over the length scale where the transition takes place. Thus, for this important monovalent ion-pair system, short-range forces alone are able to capture detailed consequences of the collective solvent motion, allowing the use of physically suggestive and computationally efficient short-range models for the dissociation event. Here, we believe that the framework here should be applicable to disentangling mechanisms for more complex processes such as multivalent ion disassociation, where previous work has suggested that long-range contributions may be more important.

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

Microscopic Derivation of Transition-state Theory for Complex Quantum Systems

The decay of quantum complex systems through a potential barrier is often described with transition-state theory, also known as RRKM theory in chemistry. Here we derive the basic formula for transition-state theory based on a generic Hamiltonian as might be constructed in a configuration-interaction basis. Two reservoirs of random Hamiltonians from Gaussian orthogonal ensembles are coupled to intermediate states representing the transition states at a barrier. Under the condition that the decay of the reservoirs to open channels is large, an analytic formula for reaction rates is derived. Here, the transition states act as independent Breit–Wigner resonances which contribute additively to the total transition probability, as is well known for electronic conductance through resonant tunneling states. It is also found that the transition probability is independent of the decay properties of the states in the second reservoir over a wide range of decay widths.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues

Clostridium difficile causes life-threatening diarrhea and is the leading cause of healthcare-associated bacterial infections in the United States. TcdA and TcdB bacterial toxins are primary determinants of disease pathogenesis and are attractive therapeutic targets. TcdA and TcdB contain domains that use UDP-glucose to glucosylate and inactivate host Rho GTPases, resulting in cytoskeletal changes causing cell rounding and loss of intestinal integrity. Transition state analysis revealed glucocationic character for the TcdA and TcdB transition states. We identified transition state analogue inhibitors and characterized them by kinetic, thermodynamic and structural analysis. Iminosugars, isofagomine and noeuromycin mimic the transition state and inhibit both TcdA and TcdB by forming ternary complexes with Tcd and UDP, a product of the TcdA- and TcdB-catalyzed reactions. Both iminosugars prevent TcdA- and TcdB-induced cytotoxicity in cultured mammalian cells by preventing glucosylation of Rho GTPases. Iminosugar transition state analogues of the Tcd toxins show potential as therapeutics for C. difficile pathology.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS1980

A study of the effects of state transition matrix approximations

The effects of using an approximate state transition matrix in orbit estimation are investigated. The approximate state transition matrix results when higher order geopotential terms in the equations of motion are ignored in the formation of the variational equations. Two methods of orbit estimation are considered: the differential correction procedure (DC) and the extended Kalman filter (EKF). The system used for the study is the Research & Development version of the Goddard Trajectory Determination System. The effects of the approximation are analyzed on a number of orbits. These orbits of various inclinations and semimajor axes. Other parameters studied include geopotential models and DC arc length.

May, J. A.↗
DOE OSTI2023

Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology

Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme’s conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme’s conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

The structure and energetics of the HCN-HNC transition state

The optimum geometries and quadratic force constants of HCN, HNC and the transition state connecting them have been determined at the single- and double-excitation coupled-cluster (CCSD) and CCSD(T) levels of theory. Energy differences were evaluated using the CCSD and CCSD(T) methods in conjunction with large atomic natural orbital basis sets containing g-type basis functions on the heavy atoms and f-type functions on hydrogen. The most reliable structure obtained for the transition state has bond distances of 1.194, 1.188, and 1.389 A for r(CN), r(CH), and r(NH), respectively. Including a correction for zero-point vibrational energies, the transition state is predicted to be 44.6 + or - 1.0 kcal/mol above the HCN isomer, while HNC is predicted to be 14.4 + or - 1.0 kcal/mol above HCN. The latter value is in excellent agreement with the most recent experimental determination (14.8 + or - 2.0 kcal/mol).

Lee, Timothy J.↗
NASA NTRS2006

The Galactic Black Hole Transient H1743-322 During Outburst Decay Connections Between Timing Noise, State Transitions, And Radio Emission

Multiwavelength observations of Galactic black hole transients during outburst decay are instrumental for our understanding of the accretion geometry and the formation of outflows around black hole systems. H1743-322, a black hole transient observed intensely in X-rays and also covered in the radio band during its 2003 decay, provides clues about the changes in accretion geometry during state transitions and also the general properties of X-ray emission during the intermediate and low-hard states. In this work, we report on the evolution of spectral and temporal properties in X-rays and the flux in the radio band, with the goal of understanding the nature of state transitions observed in this source. We concentrate on the transition from the thermal dominant state to the intermediate state that occurs on a timescale of 1 day. We show that the state transition is associated with a sudden increase in power-law flux. We determine that the ratio of the power-law flux to the overall flux in the 3-25 keV band must exceed 0.6 for us to observe strong timing noise. Even after the state transition, once this ratio was below 0.6, the system transited back to the thermal dominant state for 1 day. We show that the emission from the compact radio core does not turn on during the transition from the thermal dominant state to the intermediate state but does turn on when the source reaches the low-hard state, as seen in 4U 1543-47 and GX 339-4. We find that the photon index correlates strongly with the QPO frequency and anticorrelates with the rms amplitude of variability. We also show that the variability is more likely to be associated with the power-law emission than the disk emission.

Kalemci, E.↗
DOE OSTI2026

How state transitions balance photosynthetic electron transport in plants – a quantitative study

In plants, the process of state transition regulates the allocation of sunlight energy between Photosystem II (PSII) and PSI. However, the implications of state transitions for harmonizing electron transport rates between photosystems, and a full quantitative picture of this process, remain underexplored. We integrated quantitative biology (biochemical and biophysical approaches) with in vivo spectroscopy on wild-type Arabidopsis and protein phosphorylation mutants. This combination facilitated monitoring of Chl redistribution and its functional implications for light harvesting and electron transport. Our findings demonstrate the reallocation of 12% of highly phosphorylated ‘extra’ light-harvesting complex II under state 2 from stacked to unstacked thylakoids. This reduces the number of Chls per PSII from 216 to 182, while increasing the number in PSI from 187 to 223. Such Chl redistribution compensates for differences in photosystem stoichiometry and photochemical quantum efficiencies, thereby precisely synchronizing electron transport rates in both photosystems. Mutant analyses corroborate that this regulatory mechanism involves reversible phosphorylation. We inferred that state transitions optimize linear electron transport, leaving no additional capacity for cyclic electron transport. Furthermore, the results suggest that the controversies about long-range migration of LHCII from stacked to unstacked thylakoid domains arise from differences in phosphorylation levels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Sound speed measurements in silver shock compressed to 300 GPa: Solid-state transition, melting, and liquid-state response

To gain insight into the thermodynamic response of shock compressed Ag states corresponding to the face-centered-cubic (fcc) to body-centered-cubic (bcc) transformation and melting observed using in-situ x-ray diffraction (XRD) measurements, we present longitudinal sound speed results and their analysis in Ag at peak stresses ranging from 60 to 300 GPa. The measured sound speeds increased linearly with density compression to 171 GPa, showing that the sound speeds (and longitudinal moduli) in the fcc and bcc phases are very similar. Between 171 and 218 GPa, the sound speed dropped significantly, consistent with the melting reported using XRD measurements in shock compressed Ag. From 218 to 300 GPa, the increasing sound speeds and Hugoniot states provide a determination of the liquid phase Ag response. In particular, determination of the Grüneisen parameter (Γ) showed that the density – Grüneisen parameter product (ρΓ) for liquid Ag is constant, but differs significantly from that for solid Ag at ambient conditions. Furthermore, the Mie- Grüneisen equation of state can be used to describe the Hugoniot and off-Hugoniot response of liquid Ag.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Semiclassical transition state theory through the lens of the restricted partition function

The wide adoption of transition state theory in resolving the rates of molecular processes relies on the simplification from reducing the formal and numerical expense of dynamics by a geometric constraint. Such a reduction is at odds with the uncertainty in localization that the uncertainty principle requires. While many forms of semiclassical transition state theory (SCTST) have been aimed at addressing this challenge, a popular approach has relied on resolving the underlying phase space structure of the exact rate formula to leverage Bohr–Sommerfeld quantization. Here, the Hernandez–Miller SCTST reframed the thermal rate formula into an integral of the so-called restricted partition function (RPF) over the action associated with the reaction. The density-of-state SCTST has reframed the rate formula in terms of the instanton’s density of states (DoS). Here, we show the relationship between the RPF-SCTST and the DoS-SCTST and derive the latter from the former. In this way, we help unify these branches of SCTST and provide a clearer formalism for future advances.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1977

An Analytical State Transition Matrix for Orbits Perturbed by an Oblate Spheroid

An analytical state transition matrix and its inverse, which include the short period and secular effects of the second zonal harmonic, were developed from the nonsingular PS satellite theory. The fact that the independent variable in the PS theory is not time is in no respect disadvantageous, since any explicit analytical solution must be expressed in the true or eccentric anomaly. This is shown to be the case for the simple conic matrix. The PS theory allows for a concise, accurate, and algorithmically simple state transition matrix. The improvement over the conic matrix ranges from 2 to 4 digits accuracy.

Mueller, A. C.↗
DOE OSTI2022

Temperature-induced valence-state transition in double perovskite Ba 2 - x Sr x TbIrO 6

In this paper, a temperature-induced valence-state transition is studied in a narrow composition range 0.2 ≤ x ≤ 0.375 of Ba 2 - x Sr x TbIrO 6 by means of x-ray and neutron powder diffraction, resonant inelastic x-ray scattering, magnetic susceptibility, electrical resistivity, and specific heat measurements. The valence-state transition involves an electron transfer between Tb and Ir leading to the valence-state change between Tb 3 + / Ir 5 + and Tb 4 + / Ir 4 + phases. This first-order transition has a dramatic effect on the lattice, transport properties, and the long-range magnetic order at low temperatures for both Tb and Ir ions. Ir 5 + ion has an electronic configuration of 5 d 4 ( J eff = 0 ), which is expected to be nonmagnetic. In contrast, Ir 4 + ion with a configuration of 5 d 5 ( J eff = 1/2) favors a long-range magnetic order. For x = 0.1 with Tb 3 + / Ir 5 + configuration to the lowest temperature (2 K) investigated in this paper, a spin-glass behavior is observed around 5 K indicating Ir 5 + ( J eff = 0 ) ions act as a spacer reducing the magnetic interactions between Tb 3 + ions. For x = 0.5 with Tb 4 + / Ir 4 + configuration below the highest temperature 400 K of this paper, a long-range antiferromagnetic order at T N = 40 K is observed highlighting the importance of Ir 4 + ( J eff = 1/2) ions in promoting the long-range magnetic order of both Tb and Ir ions. For 0.2 ≤ x ≤ 0.375, a temperature-induced valence-state transition from high-temperature Tb 3 + / Ir 5 + phase to low-temperature Tb 4 + / Ir 4 + phase occurs in the temperature range 180 K ≤ T ≤ 325 K and the transition temperature increases with x . The compositional dependence demonstrates the ability to tune the the valence state for a critical region of x that leads to a concurrent change in magnetism and structure. Furthermore, this tuning ability could be employed with suitable strain in thin films to act as a switch as the magnetism is manipulated.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Rate coefficients for rotational state-to-state transitions in H 2 O + H 2 O collisions for cometary and planetary applications, as predicted by mixed quantum-classical theory

We present new calculations of collision cross sections for state-to-state transitions between the rotational states in an H 2 O + H 2 O system, which are used to generate a new database of collisional rate coefficients for cometary and planetary applications. Calculations were carried out using a mixed quantum-classical theory approach that is implemented in the code MQCT. The large basis set of rotational states used in these calculations permits us to predict thermally averaged cross sections for 441 transitions in para- and ortho-H 2 O in a broad range of temperatures. It is found that all state-to-state transitions in the H 2 O + H 2 O system split into two well-defined groups, one with higher cross-section values and lower energy transfer, which corresponds to the dipole-dipole driven processes. The other group has smaller cross sections and higher energy transfer, driven by higher-order interaction terms. We present a detailed analysis of the theoretical error bars, and we symmetrized the state-to-state transition matrixes to ensure that excitation and quenching processes for each transition satisfy the principle of microscopic reversibility. We also compare our results with other data available from the literature for H 2 O + H 2 O collisions.

79 ASTRONOMY AND ASTROPHYSICS↗