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At least 541 records · Page 30

Bridging the gap between molecules and materials in quantum chemistry with localized active spaces

The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.

method development↗

Quantum circuit cutting with maximum-likelihood tomography

Abstract We introduce maximum-likelihood fragment tomography (MLFT) as an improved circuit cutting technique for running clustered quantum circuits on quantum devices with a limited number of qubits. In addition to minimizing the classical computing overhead of circuit cutting methods, MLFT finds the most likely probability distribution for the output of a quantum circuit, given the measurement data obtained from the circuit’s fragments. We demonstrate the benefits of MLFT for accurately estimating the output of a fragmented quantum circuit with numerical experiments on random unitary circuits. Finally, we show that circuit cutting can estimate the output of a clustered circuit with higher fidelity than full circuit execution, thereby motivating the use of circuit cutting as a standard tool for running clustered circuits on quantum hardware.

97 MATHEMATICS AND COMPUTING↗

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating the differences in oxidation of high-performance α- and β- diisobutylene biofuels via Synchrotron photoionization mass spectrometry

Abstract Biofuels are a promising ecologically viable and renewable alternative to petroleum fuels, with the potential to reduce net greenhouse gas emissions. However, biomass sourced fuels are often produced as blends of hydrocarbons and their oxygenates. Such blending complicates the implementation of these fuels in combustion applications. Variations in a biofuel’s composition will dictate combustion properties such as auto ignition temperature, reaction delay time, and reaction pathways. A handful of novel drop-in replacement biofuels for conventional transportation fuels have recently been down selected from a list of over 10,000 potential candidates as part of the U.S. Department of Energy’s (DOE) Co-Optimization of Fuels and Engines (Co-Optima) initiative. Diisobutylene (DIB) is one such high-performing hydrocarbon which can readily be produced from the dehydration and dimerization of isobutanol, produced from the fermentation of biomass-derived sugars. The two most common isomers realized, from this process, are 2,4,4-trimethyl-1-pentene (α-DIB) and 2,4,4-trimethyl-2-pentene (β-DIB). Due to a difference in olefinic bond location, the α- and β- isomer exhibit dramatically different ignition temperatures at constant pressure and equivalence ratio. This may be attributed to different fragmentation pathways enabled by allylic versus vinylic carbons. For optimal implementation of these biofuel candidates, explicit identification of the intermediates formed during the combustion of each of the isomers is needed. To investigate the combustion pathways of these molecules, tunable vacuum ultraviolet (VUV) light (in the range 8.1–11.0 eV) available at the Lawrence Berkeley National Laboratory’s Advanced Light Source (ALS) has been used in conjunction with a jet stirred reactor (JSR) and time-of-flight mass spectrometry to probe intermediates formed. Relative intensity curves for intermediate mass fragments produced during this process were obtained. Several important unique intermediates were identified at the lowest observable combustion temperature with static pressure of 93,325 Pa and for 1.5 s residence time. As this relatively short residence time is just after ignition, this study is targeted at the fuels’ ignition events. Ignition characteristics for both isomers were found to be strongly dependent on the kinetics of C 4 and C 7 fragment production and decomposition, with the tert-butyl radical as a key intermediate species. However, the ignition of α-DIB exhibited larger concentrations of C 4 compounds over C 7 , while the reverse was true for β-DIB. These identified species will allow for enhanced engineering modeling of fuel blending and engine design.

09 BIOMASS FUELS↗

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗

In crystallo organometallic chemistry

X-ray crystallography is an invaluable tool in design and development of organometallic catalysis, but application typically requires species to display sufficiently high solution concentrations and lifetimes for single crystalline samples to be obtained. In crystallo organometallic chemistry relies on chemical reactions that proceed within the single-crystal environment to access crystalline samples of reactive organometallic fragments that are unavailable by alternate means. Furthermore, this highlight describes approaches to in crystallo organometallic chemistry including (a) solid–gas reactions between transition metal complexes in molecular crystals and diffusing small molecules, (b) reactions of organometallic complexes within the extended lattices of metal–organic frameworks (MOFs), and (c) intracrystalline photochemical transformations to generate reactive organometallic fragments. Application of these methods has enabled characterization of catalytically important transient species, including σ-alkane adducts of transition metals, metal alkyl intermediates implicated in metal-catalyzed carbonylations, and reactive M–L multiply bonded species involved in C–H functionalization chemistry. Opportunities and challenges for in crystallo organometallic chemistry are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of the structures and heats of formation of MO 2 , MO 3 , and M 2 O 5 for M = V, Nb, Ta, Pa

Structures for the mono-, di-, and tri-bridge isomers of M 2 O 5 as well as those for the MO 2 and MO 3 fragments for M = V, Nb, Ta, and Pa were optimized at the density functional theory (DFT) level. Single point CCSD(T) calculations extrapolated to the complete basis set (CBS) limit at the DFT geometries were used to predict the energetics. Here, the lowest energy dimer isomer was the di-bridge for M = V and Nb and the tri-bridge for M = Ta and Pa. The di-bridge isomers were predicted to be composed of MO 2 + and MO 3 - fragments, whereas the mono- and tri-bridge are two MO 2 + fragments linked by an O 2 - . The heats of formation of M 2 O 5 dimers, as well as MO 2 and MO 3 neutral and ionic species were predicted using the Feller–Peterson–Dixon (FPD) approach. The heats of formation of the MF 5 species were calculated to provide additional benchmarks. Dimerization energies to form the M 2 O 5 dimers are predicted to become more negative going down group 5 and range from -29 to -45 kcal mol -1 . The ionization energies (IEs) for VO 2 and TaO 2 are essentially the same at 8.75 eV whereas the IEs for NbO 2 and PaO 2 are 8.10 and 6.25 eV, respectively. The predicted adiabatic electron affinities (AEAs) range from 3.75 eV to 4.45 eV for the MO 3 species and vertical detachment energies from 4.21 to 4.59 eV for MO 3 - . The calculated M[double bond, length as m-dash]O bond dissociation energies increase from 143 kcal mol -1 for M = V to ~170 kcal mol -1 for M = Nb and Ta to ~200 kcal mol -1 for M = Pa. The M–O bond dissociation energies are all similar ranging from 97 to 107 kcal mol -1 . Natural bond analysis provided insights into the types of chemical bonds in terms of their ionic character. Pa 2 O 5 is predicted to behave like an actinyl species dominated by the interactions of approximately linear PaO 2 + groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast dynamics of fluorene initiated by highly intense laser fields

Here, we present an investigation of the ultrafast dynamics of the polycyclic aromatic hydrocarbon fluorene initiated by an intense femtosecond near-infrared laser pulse (810 nm) and probed by a weak visible pulse (405 nm). Using a multichannel detection scheme (mass spectra, electron and ion velocity-map imaging), we provide a full disentanglement of the complex dynamics of the vibronically excited parent molecule, its excited ionic states, and fragments. We observed various channels resulting from the strong-field ionization regime. In particular, we observed the formation of the unstable tetracation of fluorene, above-threshold ionization features in the photoelectron spectra, and evidence of ubiquitous secondary fragmentation. We produced a global fit of all observed time-dependent photoelectron and photoion channels. This global fit includes four parent ions extracted from the mass spectra, 15 kinetic-energy-resolved ionic fragments extracted from ion velocity map imaging, and five photoelectron channels obtained from electron velocity map imaging. The fit allowed for the extraction of 60 lifetimes of various metastable photoinduced intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GronOR: Massively Parallel and GPU-Accelerated Non-Orthogonal Configuration Interaction for Large Molecular Systems

GronOR is a program package for non-orthogonal configuration interaction calculations for an electronic wave function built in terms of anti-symmetrized products of multi-configuration molecular fragment wave functions. The two-electron integrals that have to be processed may be expressed in terms of atomic orbitals or in terms of an orbital basis determined from the molecular orbitals of the fragments. The code has been specifically designed for execution on distributed memory massively parallel and Graphics Processing Unit (GPU)-accelerated computer architectures, using an MPI+OpenACC/OpenMP programming approach. The task-based execution model used in the implementation allows for linear scaling with the number of nodes on the largest pre-exascale architectures available, provides hardware fault resiliency, and enables effective execution on systems with distinct central processing unit-only and GPU-accelerated partitions. The code interfaces with existing multi-configuration electronic structure codes that provide optimized molecular fragment orbitals, configuration interaction coefficients, and the required integrals. Algorithm and implementation details, parallel and accelerated performance benchmarks, and an analysis of the sensitivity of the accuracy of results and computational performance to thresholds used in the calculations are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mass-selected ion–molecule cluster beam apparatus for ultrafast photofragmentation studies

We describe an apparatus for investigating the excited-state dissociation dynamics of mass-selected ion–molecule clusters by mass-resolving and detecting photofragment-ions and neutrals, in coincidence, using an ultrafast laser operating at high repetition rates. The apparatus comprises a source that generates ion–molecule clusters, a time-of-flight spectrometer, and a mass filter that selects the desired anions, and a linear-plus-quadratic reflectron mass spectrometer that discriminates the fragment anions after the femtosecond laser excites the clusters. The fragment neutrals and anions are then captured by two channeltron detectors. The apparatus performance is tested by measuring the photofragments: I – , CF 3 I – , and neutrals from photoexcitation of the ion–molecule cluster CF 3 I·I – using femtosecond UV laser pulses with a wavelength of 266 nm. Here, the experimental results are compared with our ground state and excited state electronic structure calculations as well as the existing results and calculations, with particular attention to the generation mechanism of the anion fragments and dissociation channels of the ion–molecule cluster CF 3 I·I – in the charge-transfer excited state.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

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↗

Circuit complexity and functionality: A statistical thermodynamics perspective

Circuit complexity, defined as the minimum circuit size required for implementing a particular Boolean computation, is a foundational concept in computer science. Determining circuit complexity is believed to be a hard computational problem. Recently, in the context of black holes, circuit complexity has been promoted to a physical property, wherein the growth of complexity is reflected in the time evolution of the Einstein-Rosen bridge (“wormhole”) connecting the two sides of an anti-de Sitter “eternal” black hole. Here, we are motivated by an independent set of considerations and explore links between complexity and thermodynamics for functionally equivalent circuits, making the physics-inspired approach relevant to real computational problems, for which functionality is the key element of interest. In particular, our thermodynamic framework provides an alternative perspective on the obfuscation of programs of arbitrary length—an important problem in cryptography—as thermalization through recursive mixing of neighboring sections of a circuit, which can be viewed as the mixing of two containers with “gases of gates.” This recursive process equilibrates the average complexity and leads to the saturation of the circuit entropy, while preserving functionality of the overall circuit. The thermodynamic arguments hinge on ergodicity in the space of circuits which we conjecture is limited to disconnected ergodic sectors due to fragmentation. The notion of fragmentation has important implications for the problem of circuit obfuscation as it implies that there are circuits of same size and functionality that cannot be connected via a polynomial number of local moves. Furthermore, we argue that fragmentation is unavoidable unless the complexity classes NP and coNP coincide, a statement that implies the collapse of the polynomial hierarchy of computational complexity theory to its first level.

Science & Technology - Other Topics↗

Energy dependent calculations of fission product, prompt, and delayed neutron yields for neutron induced fission on 235 U, 238 U, and 239 Pu

In this article, we perform energy-dependent calculations of independent and cumulative fission product yields for 235 U, 238 U, and 239 Pu in the first chance fission region. Starting with the primary fission fragment distributions taken from available experimental data and analytical functions based on assumptions for the excitation energy and spin-parity distributions, the Hauser-Feshbach statistical decay treatment for fission fragment de-excitation is applied to more than 1,000 fission fragments for the incident neutron energies up to 5 MeV. The calculated independent yields are then used as an input of β-decay calculations to produce the cumulative yield, and summation calculations are performed. Model parameters in these procedures are adjusted by applying the Bayesian technique at the thermal energy for 235 U and 239 Pu and in the fast energy range for 238 U. The calculated fission observable quantities, such as the energy-dependent cumulative yields, and prompt and delayed neutron yields, are compared with available experimental data. We also study the possible impact of the second chance fission opening on the energy dependence of the delayed neutron yield by on the opening of second chance fission on the energy dependence calculation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Testing of Fusion Machine Components Against Cryogenic Pellet Impacts

Shattered pellet injection (SPI), currently the most effective method of disruption mitigation, is currently implemented on tokamaks worldwide for experimental purposes. Cryogenic pellets are formed and fired into an angled surface before entering the plasma. The impact with the angled surface causes the pellets to fragment into a cloud of particles with the purpose of increasing the surface area for ablation. As pellets traverse guide tubes, depending on design, there is a chance of an off-normal pellet impact. Pellet impacts are also, depending on design, possible in the plasma chamber if not fully ablated and assimilated, or if the fragment plume is not directed in the proper direction. This paper outlines a series of pellet impact tests on various tiles and components relevant to the ITER, JET, and ASDEX Upgrade SPI systems. In conclusion, testing was done to assess the potential damage from pellet and fragment plume impacts through high-speed imaging and the visual inspection of components.

Cryogenic pellets↗

Selective bond scission in formic acid by low-energy electrons

We report recent results of mass-resolved anion fragment momentum imaging experiments to investigate dissociative electron attachment to formic acid, for incident energies between 5 eV and 9 eV. A remarkable site-selectivity is found for a resonance at 8.5 eV by comparing anion fragment yields for two deuterated isotopologues of formic acid. This results in an H – fragment from the O-H bond of the transient anion, with negligible contribution from C-H break. In contrast, a lower-energy resonance at 7.1 eV dissociates by C–H or O–H break to produce H – and the neutral radicals HOCO or HCOO.

74 ATOMIC AND MOLECULAR PHYSICS↗

Shell effects in fission and quasi-fission reactions

Quantum shell effects are responsible for asymmetric fission. They are also expected to affect the formation of fission fragments in quasi-fission reactions occurring in heavy-ion collisions. Systematic time-dependent Hartree-Fock simulations of 40–56 Ca+ 176 Yb collisions show that quasi-fission fragment properties share strong similarities with fragments formed in fission of the compound nuclei. This is an indication that similar shell effects are responsible for the final asymmtery in both mechanisms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Two-body dissociation of formic acid following double ionization by ultrafast laser pulses

We studied the fragmentation of planar formic acid (HCOOH) molecules following their double ionization by intense ultrashort laser pulses. Deuterium tagging (i.e., HCOOD) combined with coincidence momentum imaging measurements of all fragment ions enabled determination of the role of the hydroxyl and carboxyl hydrogen atoms in the breakup. Specifically, we observe a strong preference for the hydroxyl (OD) group to remain intact in a ${\mathrm{HCOOD}}^{2+}{\rightarrow}{\mathrm{OD}}^{+}+{\mathrm{HCO}}^{+}$ fragmentation, which is an order of magnitude more likely than ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$. An even larger preference for breaking the H-C bond over the O-H bond is observed in the ${\mathrm{H}}^{+}+{\mathrm{DCO}}_{2}^{+}$ and ${\mathrm{D}}^{+}+{\mathrm{HCO}}_{2}^{+}$ deprotonation channels. Bond rearrangement, leading to ${\mathrm{H}}_{2}^{+}$ or ${\mathrm{H}}_{2}{\mathrm{O}}^{+}$ formation, exhibits no isotopic preference. The kinetic-energy-release distributions of the ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$ and ${\mathrm{O}}^{+}+{\mathrm{H}}_{2}{\mathrm{CO}}^{+}$ breakup channels suggest that more than one process contributes to these final products, although further theoretical work is needed to identify the specific paths.

74 ATOMIC AND MOLECULAR PHYSICS↗

Transmission spectroscopy of CF 4 molecules in intense x-ray fields

The nonlinear interaction of x rays with matter is at the heart of understanding and controlling ultrafast molecular dynamics from an atom-specific viewpoint, providing new scientific and analytical opportunities to explore the structure and dynamics of small quantum systems. At increasingly high x-ray intensity, the sensitivity of ultrashort x-ray pulses to specific electronic states and emerging short-lived transient intermediates is of particular relevance for our understanding of fundamental multiphoton absorption processes. In this work, intense x-ray free-electron laser (XFEL) pulses at the European XFEL are combined with a gas cell and grating spectrometer for a high-intensity transmission spectroscopy study of multiphoton-induced ultrafast molecular fragmentation dynamics in CF 4 . This approach unlocks the direct intrapulse observation of transient fragments, including neutral atoms, by their characteristic absorption lines in the transmitted broadband x-ray spectrum. The dynamics with and without initially producing fluorine 𝐾-shell holes are studied by tuning the central photon energy. The absorption spectra are measured at different FEL intensities to observe nonlinear effects. Transient isolated fluorine atoms and ions are spectroscopically recorded within the ultrashort pulse duration of a few tens of femtoseconds. An isosbestic point that signifies the correlated transition between intact neutral CF 4 molecules and charged atomic fragments is observed near the fluorine 𝐾 edge. The dissociation dynamics and the multiphoton absorption-induced dynamics encoded in the spectra are theoretically interpreted. Overall, this study demonstrates the potential of high-intensity x-ray transmission spectroscopy to study ultrafast molecular dynamics with sensitivity to specific intermediate species and their electronic structure.

74 ATOMIC AND MOLECULAR PHYSICS↗