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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Ultraviolet H 2 luminescence in molecular clouds induced by cosmic rays

Context. Galactic cosmic rays (CRs) play a crucial role in ionisation, dissociation, and excitation processes within dense cloud regions where UV radiation is absorbed by dust grains and gas species. CRs regulate the abundance of ions and radicals, leading to the formation of more and more complex molecular species, and determine the charge distribution on dust grains. A quantitative analysis of these effects is essential for understanding the dynamical and chemical evolution of star-forming regions. Aims. The CR-induced photon flux has a significant impact on the evolution of the dense molecular medium in its gas and dust components. This study evaluates the flux of UV photons generated by CRs to calculate the photon-induced dissociation and ionisation rates of a vast number of atomic and molecular species, as well as the integrated UV photon flux. Methods. To achieve these goals, we took advantage of recent developments in the determination of the spectra of secondary electrons, in the calculation of state-resolved excitation cross sections of H 2 by electron impact, and of photodissociation and photoionisation cross sections. Results. We calculated the H 2 level population of each rovibrational level of the X, B, C, B′, D, B″, D′, and a states. We then computed the UV photon spectrum of H 2 in its line and continuum components between 72 and 700 nm, with unprecedented accuracy, as a function of the CR spectrum incident on a molecular cloud, the H 2 column density, the isomeric H 2 composition, and the dust properties. The resulting photodissociation and photoionisation rates are, on average, lower than previous determinations by a factor of about 2, with deviations of up to a factor of 5 for the photodissociation of species such as AlH, C 2 H 2 , C 2 H 3 , C 3 H 3 , LiH, N 2 , NaCl, NaH, O 2 + , S2, SiH, l-C 4 , and l-C 5 H. A special focus is given to the photoionisation rates of H 2 , HF, and N 2 , as well as to the photodissociation of H 2 , which we find to be orders of magnitude higher than previous estimates. We give parameterisations for both the photorates and the integrated UV photon flux as a function of the CR ionisation rate, which implicitly depends on the H 2 column density, as well as the dust properties.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Looking at the bigger picture: Identifying the photoproducts of pyruvic acid at 193 nm

Here, photodissociation of pyruvic acid (PA) was studied in the gas-phase at 193 nm using two complementary techniques. The time-sliced velocity map imaging arrangement was used to determine kinetic energy release distributions of fragments and estimate dissociation timescales. The multiplexed photoionization mass spectrometer setup was used to identify and quantify photoproducts, including isomers and free radicals, by their mass-to-charge ratios, photoionization spectra, and kinetic time profiles. Using these two techniques, it is possible to observe the major dissociation products of PA photodissociation: CO 2 , CO, H, OH, HCO, CH 2 CO, CH 3 CO, and CH 3 . Acetaldehyde and vinyl alcohol are minor primary photoproducts at 193 nm, but products that are known to arise from their unimolecular dissociation, such as HCO, H 2 CO, and CH 4 , are identified and quantified. A multivariate analysis that takes into account the yields of the observed products and assumes a set of feasible primary dissociation reactions provides a reasonable description of the photoinitiated chemistry of PA despite the necessary simplifications caused by the complexity of the dissociation. These experiments offer the first comprehensive description of the dissociation pathways of PA initiated on the S 3 excited state. Most of the observed products and yields are rationalized on the basis of three reaction mechanisms: (i) decarboxylation terminating in CO 2 + other primary products (~50%); (ii) Norrish type I dissociation typical of carbonyls (~30%); and (iii) O—H and C—H bond fission reactions generating the H atom (~10%). The analysis shows that most of the dissociation reactions create more than two products. This observation is not surprising considering the high excitation energy (~51 800 cm –1 ) and fairly low energy required for dissociation of PA. We find that two-body fragmentation processes yielding CO 2 are minor, and the expected, unstable primary co-fragment, methylhydroxycarbene, is not observed because it probably undergoes fast secondary dissociation and/or isomerization. Norrish type I dissociation pathways generate OH and only small yields of CH 3 CO and HOCO, which have low dissociation energies and further decompose via three-body fragmentation processes. Experiments with d 1 -PA (CH 3 COCOOD) support the interpretations. The dissociation on S 3 is fast, as indicated by the products’ recoil angular anisotropy, but the roles of internal conversion and intersystem crossing to lower states are yet to be determined.

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

Precise equilibrium structures of 1 H - and 2 H -1,2,3-triazoles (C 2 H 3 N 3 ) by millimeter-wave spectroscopy

The 1H- and 2H-1,2,3-triazoles are isomeric five-membered ring, aromatic heterocycles that may undergo chemical equilibration by virtue of intramolecular hydrogen migration (tautomerization). Using millimeter-wave spectroscopy in the 130–375 GHz frequency range, we measured the spectroscopic constants for thirteen 1H-1,2,3-triazole and sixteen 2H-1,2,3-triazole isotopologues. Herein, we provide highly accurate and highly precise semi-experimental equilibrium (r e SE ) structures for the two tautomers based on the spectroscopic constants of each set of isotopologues, together with vibration–rotation interaction and electron-mass distribution corrections calculated using coupled-cluster singles, doubles, and perturbative triples calculations [CCSD(T)/cc-pCVTZ]. The resultant structures are compared with a “best theoretical estimate” (BTE), which has recently been shown to be in exceptional agreement with the semi-experimental equilibrium structures of other aromatic molecules. Bond distances of the 1H tautomer are determined to <0.0008 Å and bond angles to <0.2°. For the 2H tautomer, bond angles are also determined to <0.2°, but bond distances are less precise (2σ ≤ 0.0015). Finally, agreement between BTE and r e SE values is discussed.

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

Variational deep learning of equilibrium transition path ensembles

Here, we present a time-dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off of the variational path sampling methodology by approximating the time-dependent commitment probability within a neural network ansatz. The reaction mechanisms inferred through this approach are elucidated by a novel decomposition of the rate in terms of the components of a stochastic path action conditioned on a transition. This decomposition affords an ability to resolve the typical contribution of each reactive mode and their couplings to the rare event. The associated rate evaluation is variational and systematically improvable through the development of a cumulant expansion. We demonstrate this method in both over- and under-damped stochastic equations of motion, in low-dimensional model systems, and in the isomerization of a solvated alanine dipeptide. In all examples, we find that we can obtain quantitatively accurate estimates of the rates of the reactive events with minimal trajectory statistics and gain unique insights into transitions through the analysis of their commitment probability.

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

Probing C–I bond fission in the UV photochemistry of 2-iodothiophene with core-to-valence transient absorption spectroscopy

The UV photochemistry of small heteroaromatic molecules serves as a testbed for understanding fundamental photo-induced chemical transformations in moderately complex compounds, including isomerization, ring-opening, and molecular dissociation. Here, a combined experimental-theoretical study of 268 nm UV light-induced dynamics in 2-iodothiophene (C 4 H 3 IS) is performed. The dynamics are experimentally monitored with a femtosecond extreme ultraviolet (XUV) probe that measures iodine N-edge 4d core-to-valence transitions. Experiments are complemented by density functional theory calculations of both the pump-pulse induced valence excitations and the XUV probe-induced core-to-valence transitions. Possible intramolecular relaxation dynamics are investigated by ab initio molecular dynamics simulations. Furthermore, gradual absorption changes up to ~0.5 to 1 ps after excitation are observed for both the parent molecular species and emerging iodine fragments, with the latter appearing with a characteristic rise time of 160 ± 30 fs. Comparison of spectral intensities and energies with the calculations identifies an iodine dissociation pathway initiated by a predominant π → π* excitation. In contrast, initial excitation to a nearby n ⟂ → σ* state appears unlikely based on a significantly smaller oscillator strength and the absence of any corresponding XUV absorption signatures. Excitation to the π → π* state is followed by contraction of the C–I bond, enabling a nonadiabatic transition to a dissociative π→σ C-I * state. For the subsequent fragmentation, a relatively narrow bond-length region along the C–I stretch coordinate between 230 and 280 pm is identified, where the transition between the parent molecule and the thienyl radical + iodine atom products becomes prominent in the XUV spectrum due to rapid localization of two singly occupied molecular orbitals on the two fragments.

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

Matrix-formation dynamics dictate methyl nitrite conformer abundance

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH 3 ONO and trans-CH 3 ONO, with cis being more stable by ∼5 kJ/mol. Here, the barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH 3 ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N 2 , Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH 3 ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N 2 :CH 3 ONO, Ar:CH 3 ONO, or Xe:CH 3 ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH 3 ONO more effectively than trans-CH 3 ONO, likely because cis-CH 3 ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices.

Hockey, Emily K.↗
DOE OSTI2025

The approximate second order coupled-cluster method based on a size-consistent Brillouin–Wigner partitioning

We present a variant of the approximate second order coupled-cluster method (CC2) with a two-parameter size-consistent Brillouin–Wigner (BW-s) partitioning instead of a Møller–Plesset (MP) partitioning for the unperturbed Hamiltonian, which we refer to as BWs-CC2. The computational complexity of this model scales identically to CC2 with molecular size. Conventional CC2 and its regularized BWs-CC2 variants, as well as conventional MP2 and two of its regularized BW-s2 variants, were assessed on a 535 element database spanning thermochemistry, non-covalent interactions, barrier heights, and isomerization energies. To ensure a well-defined model chemistry, the assessment was performed using internally stable spin-polarized Hartree–Fock (HF) orbitals in the finite aug-cc-pVQZ basis without counterpoise corrections. As a result of using stable orbitals, contrary to conventional wisdom, we find that CC2 substantially outperforms MP2 on molecules with significantly spin contaminated reference orbitals without a significant increase in error on systems with a spin-pure reference, showing the value of its single substitutions. While no single choice of regularization parameters can be optimal for all datasets, we find that BWs-CC2 generally outperforms both CC2 and BW-s2 with a single judicious parameter choice. Additional tests on dipole moments and bond lengths of diatomics provide further support for the utility of this choice. Furthermore, the main outliers and poorest performing cases are associated with large amounts of spin-contamination in the HF reference, which is indicative of systems with either strong correlation or extensive artificial symmetry breaking. Overall, these findings argue that the perception of the quality of the CC2 ground state should be reevaluated and that it can be further improved upon by the soundly based BWs-CC2 variant with the recommended parameter choice.

Correlation energy↗
DOE OSTI2020

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇌ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. In this work, we have studied a single-domain bilin-binding photoreceptor All2699g1 ( Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P r ) and far red-absorbing (P fr ) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ~300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens

The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD + ) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.

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

Imaging conical intersection dynamics during azobenzene photoisomerization by ultrafast X-ray diffraction

Significance Vibronic coherences are unique features that emerge in the decisive moments of photochemistry and photophysics. Here we demonstrate how X-ray diffraction can access fundamental information about these coherences. This is enabled by recent developments at free-electron lasers, working toward temporal resolution and single-molecule accessibility of scattering-based measurements. Time-resolved diffraction patterns of the isomerization of azobenzene are simulated. The process is monitored in time via the momentum-space signal, with a special focus on the mixed elastic/inelastic scattering from coherences. We give practical ideas on how this relatively weak contribution to the signal can potentially be retrieved. A direct connection to the real-space movie of the conical intersection dynamics is made, enabling the observation of quantum coherences that direct chemical processes.

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

Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair

Control over transition metal redox state is essential for metalloprotein function and can be achieved via coordination chemistry and/or sequestration from bulk solvent. Human methylmalonyl-Coenzyme A (CoA) mutase (MCM) catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA using 5′-deoxyadenosylcobalamin (AdoCbl) as a metallocofactor. During catalysis, the occasional escape of the 5′-deoxyadenosine (dAdo) moiety leaves the cob(II)alamin intermediate stranded and prone to hyperoxidation to hydroxocobalamin, which is recalcitrant to repair. In this study, we have identified the use of bivalent molecular mimicry by ADP, coopting the 5′-deoxyadenosine and diphosphate moieties in the cofactor and substrate, respectively, to protect against cob(II)alamin overoxidation on MCM. Crystallographic and electron paramagnetic resonance (EPR) data reveal that ADP exerts control over the metal oxidation state by inducing a conformational change that seals off solvent access, rather than by switching five-coordinate cob(II)alamin to the more air stable four-coordinate state. Subsequent binding of methylmalonyl-CoA (or CoA) promotes cob(II)alamin off-loading from MCM to adenosyltransferase for repair. This study identifies an unconventional strategy for controlling metal redox state by an abundant metabolite to plug active site access, which is key to preserving and recycling a rare, but essential, metal cofactor.

Science & Technology - Other Topics↗
DOE OSTI2025

Structural dynamics of laser-ionized cis-stilbene studied by ultrafast electron diffraction

Stilbene has been a model system for studying photoisomerization upon absorption of a UV photon. Although the dynamics of the first excited state have been investigated in great detail, the structural dynamics of cationic states remains largely experimentally unexplored. In this study, the dynamics following ionization via absorption of two UV photons was captured using ultrafast electron diffraction. cis-stilbene (CS) was optically pumped with 267 nm ultraviolet light with two different pump fluences and probed with 3.7 MeV electrons. We compare our experimental results to ab-initio multiple spawning simulations for single-photon excitation and molecular dynamics simulations for ionization in order to separate the contributions from the two channels. We found that with a fluence of 170 mJ cm −2 both the single and two-photon channels are present, while with higher fluence of 280 mJ cm −2 the two-photon channel dominates. We did not observe isomerization of the CS cation and found the main structural motion a to be a vibration of the phenyl rings about the central C–C bond.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Structure of beta-decaying states in the deformed, neutron-rich nucleus 104 Nb

Excited structures in 104 Mo were populated by β decays of the ground and isomeric states in the neutron-rich nucleus 104 Nb. The beams were produced by the CARIBU facility at Argonne National Laboratory, re-accelerated by the ATLAS accelerator and implanted on a moving-tape system in the middle of the GAMMASPHERE array. Separate decay schemes for the two β-decaying states in 104 Nb were constructed for the first time. The structure of the isomers are discussed in the framework of the deformed Nilsson model and systematics of known quasiparticle structures in neighboring nuclei.

Nilsson model↗
DOE OSTI2021

The NUBASE2020 evaluation of nuclear physics properties *

The NUBASE2020 evaluation contains the recommended values of the main nuclear physics properties for all nuclei in their ground and excited, isomeric (T-1/2 >= 100 ns) states. It encompasses all experimental data published in primary (journal articles) and secondary (mainly laboratory reports and conference proceedings) references, together with the corresponding bibliographical information. In cases where no experimental data were available for a particular nuclide, trends in the behavior of specific properties in neighboring nuclei were examined and estimated values are proposed. Evaluation procedures and policies that were used during the development of this evaluated nuclear data library are presented, together with a detailed table of recommended values and their uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Lifetimes of two- and four-neutron-hole states in 204 Pb and 206 Pb

The centroid-shift method was used to determine half-lives of excited levels in 204 Pb and 206 Pb. For the states with 𝐼 𝜋 = 12 + , 17 − , and 19 − in 204 Pb, values of 𝑇 1/2 = 4.9⁢(3), 3.9(3), and 0.9(3) ns, respectively, were determined. The half-life of the 𝐼 𝜋 = 9 − level in 206 Pb was measured to be 1.1(3) ns. In 204 Pb, the 12 + state arises from two neutron holes in the 𝑖 13/2 subshell, while the 17 − and 19 − levels are built on 𝜈⁡(𝑖$^{−3}_{13/2}$, 𝑝$^{−1}_{1/2}$) and 𝜈⁡(𝑖$^{−3}_{13/2}$, 𝑓$^{−1}_{5/2}$) four-neutron-hole configurations, respectively. The 9 − state in 206 Pb results from a 𝜈⁡(𝑖$^{−1}_{13/2}$, 𝑓${−1}_{5/2}$) excitation. As a result, the transition probabilities for the decay of these isomeric levels are reasonably consistent with the expected single-particle values, and these states are described well by shell-model calculations using the kshell code with the KHHE interaction.

190 ≤ A ≤ 219↗
DOE OSTI2026

First Observation of Multiphonon 𝛾-Vibrations in an Odd-Odd Nuclear System

Here, the identification of the first multiphonon 𝛾-vibrational bands in an odd-odd neutron-rich nucleus of the nuclear chart is presented. These high-spin structures of hard to access $^{104}_{41}\textrm{Nb}_{63}$, produced in fission, were studied by combining a spectrometer with isotopic resolution coupled to a 𝛾-ray tracking array and independently from high-fold 𝛾 coincidence measurements. Triaxial projected shell model calculations for the high-spin states are in good agreement with the measured observables for the yrast, one-phonon, and two-phonon 𝛾 bands. The possibility of an oblate shape of an isomeric state and coexistence of triaxial and oblate configurations is investigated from the decay of the 141 keV isomer. The present Letter illustrates the robustness of vibration excitations in the presence of an odd valence proton and neutron as well as the possibly coexisting shapes beyond the 𝑁 = 60 transitional region.

Wang, E. H. [Shandong Univ., Jinan (China); Vander↗