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At least 613 records · Page 34
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DOE OSTI2024

Deconvolution of dynamic heterogeneity in protein structure

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.

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

Photodissociation dynamics of the tert -butyl perthiyl radical

Here, the photodissociation dynamics of the tert-butyl perthiyl (t-BuSS) radical are investigated by fast-beam coincidence translational spectroscopy. A fast (6 keV-8 keV) beam of neutral t-BuSS radicals is produced via photodetachment of the corresponding anion, followed by photodissociation at 248 nm (5.00 eV) or 193 nm (6.42 eV) and coincident detection of the neutral products. Photofragment mass and translational energy distributions are obtained at both wavelengths. At 248 nm, the dominant product channel (90%) is found to be S loss, with a product translational energy distribution that peaks close to the maximum available energy and an anisotropic photofragment angular distribution, indicating dissociation along a repulsive excited state. A minor channel (10%) leading to the formation of S 2 + t-Bu is also observed. At 193 nm, both two- and three-body dissociation are observed. The formation of S 2 + t-Bu is the dominant two-body product channel, with multiple electronic states of the S 2 molecule produced via excited-state dissociation processes. The formation of S + t-BuS is a minor two-body channel at this dissociation energy. The three-body channels are S 2 + H + isobutene, S 2 + CH 3 + propene, and S + SH + isobutene. The first two of these channels result from a sequential dissociation process in which the loss of S 2 from t-BuSS results in ground-state t-Bu with sufficient internal energy to undergo secondary fragmentation. The third three-body channel, S + SH + isobutene, is attributed to the loss of internally excited HS 2 from t-BuSS, which then rapidly dissociates to form S + SH in an asynchronous concerted dissociation process.

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

Excited state dynamics of cis , cis -1,3-cyclooctadiene: UV pump VUV probe time-resolved photoelectron spectroscopy

We present UV pump, vacuum ultraviolet probe time-resolved photoelectron spectroscopy measurements of the excited state dynamics of cis,cis-1,3-cyclooctadiene. A 4.75 eV deep UV pump pulse launches a vibrational wave packet on the first electronically excited state, and the ensuing dynamics are probed via ionization using a 7.92 eV probe pulse. The experimental results indicate that the wave packet undergoes rapid internal conversion to the ground state in under 100 fs. Comparing the measurements with electronic structure and trajectory surface hopping calculations, we are able to interpret the features in the measured photoelectron spectra in terms of ionization to several states of the molecular cation.

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

How good are polarizable and flexible models for water: Insights from a many-body perspective

We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the Born–Oppenheimer potential energy surface of water from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the accuracy of the polarizable models in reproducing individual many-body contributions to interaction energies and harmonic frequencies of water clusters and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to reproduce the energy landscape of liquid water under ambient conditions. We find that, while correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts fixed atomic charges and demonstrate that the new model retains the same accuracy as the original MB-pol model. Based on the analyses presented in this study, we believe that future developments of both polarizable and explicit many-body models should continue in parallel and would benefit from synergistic efforts aimed at integrating the best aspects of the two theoretical/computational frameworks.

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

Analytical gradients for molecular-orbital-based machine learning

We report molecular-orbital-based machine learning (MOB-ML) enables the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. Here, we present the derivation, implementation, and numerical demonstration of MOB-ML analytical nuclear gradients, which are formulated in a general Lagrangian framework to enforce orthogonality, localization, and Brillouin constraints on the molecular orbitals. The MOB-ML gradient framework is general with respect to the regression technique (e.g., Gaussian process regression or neural networks) and the MOB feature design. We show that MOB-ML gradients are highly accurate compared to other ML methods on the ISO17 dataset while only being trained on energies for hundreds of molecules compared to energies and gradients for hundreds of thousands of molecules for the other ML methods. The MOB-ML gradients are also shown to yield accurate optimized structures at a computational cost for the gradient evaluation that is comparable to a density-corrected density functional theory calculation.

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

57Fe Mössbauer isomer shift of pure iron and iron oxides at high pressure—An experimental and theoretical study

The 57Fe isomer shift (IS) of pure iron has been measured up to 100 GPa using synchrotron Mössbauer spectroscopy in the time domain. Apart from the expected discontinuity due to the α→ε structural and spin transitions, the IS decreases monotonically with increasing pressure. The absolute shifts were reproduced without semi-empirical calibrations by periodic density functional calculations employing extensive localized basis sets with several common density functionals. However, the best numerical agreement is obtained with the B1WC hybrid functional. Extension of the calculations to 350 GPa, a pressure corresponding to the Earth’s inner core, predicted the IS range of 0.00 to -0.85 mm/s, covering the span from Fe(0) to Fe(VI) compounds measured at ambient pressure. The calculations also reproduced the pressure trend from polymorphs of prototypical iron oxide minerals, FeO and Fe2O3. Analysis of the electronic structure shows a strong donation of electrons from oxygen to iron at high pressure. The assignment of formal oxidation to the Fe atom becomes ambiguous under this condition.

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

Beam particle identification and tagging of incompletely stripped heavy beams with HEIST

A challenge preventing successful inverse kinematics measurements with heavy nuclei that are not fully stripped is identifying and tagging the beam particles. For this purpose, the HEavy ISotope Tagger (HEIST) has been developed. HEIST utilizes two micro-channel plate timing detectors to measure the time-of-flight, a multi-sampling ion chamber to measure energy loss, and a high-purity germanium detector to identify isomer decays and calibrate the isotope identification system. HEIST has successfully identified 198 Pb and other nearby nuclei at energies of about 75 MeV/A. In the experiment discussed, a typical cut containing 89% of all 198 Pb 80+ in the beam had a purity of 86%. We examine the issues of charge state contamination. Here, the observed charge state populations of these ions are presented and, using an adjusted beam energy, are well described by the charge state model GLOBAL.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Quantum-classical hybrid algorithm for the simulation of all-electron correlation

While chemical systems containing hundreds to thousands of electrons remain beyond the reach of quantum devices, hybrid quantum-classical algorithms present a promising pathway toward a quantum advantage. Hybrid algorithms treat the exponentially scaling part of the calculation-the static correlation-on the quantum computer and the non-exponentially scaling part-the dynamic correlation-on the classical computer. While a variety of algorithms have been proposed, the dependence of many methods on the total wave function limits the development of easy-to-use classical post-processing implementations. Here, we present a novel combination of quantum and classical algorithms, which computes the all-electron energy of a strongly correlated molecular system on the classical computer from the 2-electron reduced density matrix (2-RDM) evaluated on the quantum device. Significantly, we circumvent the wave function in the all-electron calculations by using density matrix methods that only require input of the statically correlated 2-RDM. Although the algorithm is completely general, we test it with two classical density matrix methods, the anti-Hermitian contracted Schrödinger equation (ACSE) and multiconfiguration pair-density functional theories, using the recently developed quantum ACSE method for simulating the statically correlated 2-RDM. Furthermore, we obtain experimental accuracy for the relative energies of all three benzyne isomers and thereby demonstrate the ability of the developed algorithm to achieve chemically relevant and accurate results on noisy intermediate-scale quantum devices.

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

Infrared spectroscopic signature of a hydroperoxyalkyl radical (•QOOH)

Infrared (IR) action spectroscopy is utilized to characterize a prototypical carbon-centered hydroperoxyalkyl radical (•QOOH) transiently formed in the oxidation of volatile organic compounds. The •QOOH radical formed in isobutane oxidation, 2-hydroperoxy-2-methylprop-1-yl, •CH 2 (CH 3 ) 2 COOH, is generated in the laboratory by H-atom abstraction from tert-butyl hydroperoxide (TBHP). IR spectral features of jet-cooled and stabilized •QOOH radicals are observed from 2950 to 7050 cm –1 at energies that lie below and above the transition state barrier leading to OH radical and cyclic ether products. The observed •QOOH features include overtone OH and CH stretch transitions, combination bands involving OH or CH stretch and a lower frequency mode, and fundamental OH and CH stretch transitions. Most features arise from a single vibrational transition with band contours well simulated at a rotational temperature of 10 K. In each case, the OH products resulting from unimolecular decay of vibrationally activated •QOOH are detected by UV laser-induced fluorescence. Assignments of observed •QOOH IR transitions are guided by anharmonic frequencies computed using second order vibrational perturbation theory, a 2 + 1 model that focuses on the coupling of the OH stretch with two low-frequency torsions, as well as recently predicted statistical •QOOH unimolecular decay rates that include heavy-atom tunneling. Most of the observed vibrational transitions of •QOOH are readily distinguished from those of the TBHP precursor. Furthermore, the distinctive IR transitions of •QOOH, including the strong fundamental OH stretch, provide a general means for detection of •QOOH under controlled laboratory and real-world conditions.

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

Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO 2 -linkage photoisomerization

A family of coordination complexes of the type [Ru(SO 2 )(NH 3 ) 4 X] m+ Y n – (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO 2 -linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.

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

The many-body expansion for metals. I. The alkaline earth metals Be, Mg, and Ca

We examine the many-body expansion (MBE) for alkaline earth metal clusters, Be n , Mg n , Ca n ( n = 4, 5, 6), at the Møller–Plesset second order perturbation theory, coupled-cluster singles and doubles with perturbative triples, multi-reference perturbation theory, and multi-reference configuration interaction levels of theory. The magnitude of each term in the MBE is evaluated for several geometrical configurations. We find that the behavior of the MBE for these clusters depends strongly on the geometrical arrangement and, to a lesser extent, on the level of theory used. Another factor that affects the MBE is the in situ (ground or excited) electronic state of the individual atoms in the cluster. For most geometries, the three-body term is the largest, followed by a steady decrease in absolute energy for subsequent terms. Though these systems exhibit non-negligible multi-reference effects, there was little qualitative difference in the MBE when employing single vs multi-reference methods. Useful insights into the connectivity and stability of these clusters have been drawn from the respective potential energy surfaces and quasi-atomic orbitals for the various dimers, trimers, and tetramers. Through these analyses, we investigate the similarities and differences in the binding energies of different-sized clusters for these metals.

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

Hydrogen bond arrangements in (H 2 O) 20, 24, 28 clathrate hydrate cages: Optimization and many-body analysis

Here we provide a detailed study of hydrogen bonding arrangements, relative stability, residual entropy, and an analysis of the many-body effects in the (H 2 O) 20 (D-cage), (H 2 O) 24 (T-cage), and (H 2 O) 28 (H-cage) hollow cages making up structures I (sI) and II (sII) of clathrate hydrate lattices. Based on the enumeration of the possible hydrogen bonding networks for a fixed oxygen atom scaffold, the residual entropy (S 0 ) of these three gas phase cages was estimated at 0.754 82, 0.754 44, and 0.754 17 · Nk b , where N is the number of molecules and k b is Boltzmann’s constant. A previously identified descriptor of enhanced stability based on the relative arrangement and connectivity of nearest-neighbor fragments on the polyhedral water cluster [strong-weak-effective-bond model] also applies to the larger hollow cages. The three cages contain a maximum of 7, 9, and 11 such preferable arrangements of trans nearest dimer pairs with one “free” OH bond on the donor molecule (t1d dimers). The Many-Body Expansion (MBE) up to the 4-body suggests that the many-body terms vary nearly linearly with the cluster binding energy. Using a hierarchical approach of screening the relative stability of networks starting from optimizations with the TIP4P, TTM2.1-F, and MB-pol classical potentials, subsequently refining at more accurate levels of electronic structure theory (DFT and MP2), and finally correcting for zero-point energy, we were able to identify a group of four low-lying isomers of the (H 2 O) 24 T-cage, two of which are antisymmetric and the other two form a pair of antipode configurations.

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

Computational studies of structural, energetic, and electronic properties of pure Pt and Mo and mixed Pt/Mo clusters: Comparative analysis of characteristics and trends

The added technological potential of bimetallic clusters and nanoparticles, as compared to their pure (i.e., one-component) counterparts, stems from the ability to further fine-tune their properties and, consequently, functionalities through a simultaneous use of the “knobs” of size and composition. The practical realization of this potential can be greatly advanced by the knowledge of the correlations and relationships between the various characteristics of bimetallic nanosystems on the one hand and those of their pure counterparts as well as pure constituent components on the other hand. Here, in this study, we present results of a density functional theory based study of pure Pt n and Mo n clusters aimed at revisiting and exploring further their structural, electronic, and energetic properties. These are then used as a basis for analysis and characterization of the results of calculations on two-component Pt n-m Mo m clusters. The analysis also includes establishing relationships between the properties of the Pt n-m Mo m clusters and those of their Pt n-m and Mo m components. One of the particularly intriguing findings suggested by the calculated data is a linear dependence of the average binding energy per atom in sets of Pt n-m Mo m clusters that have the same fixed number m of Mo atoms and different number n-m of Pt atoms on the fractional content (n-m)/n of Pt atoms. We derive an analytical model that establishes the fundamental basis for this linearity and expresses its parameters—the m-dependent slope and intercept—in terms of characteristic properties of the constituent components, such as the average binding energy per atom of Mo m and the average per-atom adsorption energy of the Pt atoms on Mo m . The conditions of validity and degree of robustness of this model and of the linear relationship predicted by it are discussed.

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

Formation of the C 4 H n + ( n = 2–5) ions upon ionization of acetylene clusters in helium droplets

Infrared (IR) spectroscopy using ultracold helium nanodroplet matrices has proven to be a powerful method to interrogate encapsulated ions, molecules, and clusters. Due to the helium droplets’ high ionization potential, optical transparency, and ability to pick up dopant molecules, the droplets offer a unique modality to probe transient chemical species produced via photo- or electron impact ionization. Here, in this work, helium droplets were doped with acetylene molecules and ionized via electron impact. Ion-molecule reactions within the droplet volume yield larger carbo-cations that were studied via IR laser spectroscopy. This work is focused on cations containing four carbon atoms. The spectra of C 4 H 2 + , C 4 H 3 + , and C 4 H 5 + are dominated by diacetylene, vinylacetylene, and methylcyclopropene cations, respectively, which are the lowest energy isomers. On the other hand, the spectrum of C 4 H 4 + ions hints at the presence of several co-existing isomers, the identity of which remains to be elucidated.

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

Assessment of DFT functionals for a minimal nitrogenase [Fe(SH) 4 H]- model employing state-of-the-art ab initio methods

We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ΔE estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree–Fock included (0%–54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ΔE is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn–Sham orbitals gives results within 4–11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ~5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.

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

Descriptors of water aggregation

For this work, we rely on a total of 23 (cluster size, 8 structural, and 14 connectivity) descriptors to investigate structural patterns and connectivity motifs associated with water cluster aggregation. In addition to the cluster size n (number of molecules), the 8 structural descriptors can be further categorized into (i) one-body (intramolecular): covalent OH bond length (r OH ) and HOH bond angle (θ HOH ), (ii) two-body: OO distance (r OO ), OHO angle (θ OHO ), and HOOX dihedral angle ($\phi$ HOOX ), where X lies on the bisector of the HOH angle, (iii) three-body: OOO angle (θ OOO ), and (iv) many-body: modified tetrahedral order parameter (q) to account for two-, three-, four-, five-coordinated molecules (q m , m = 2, 3, 4, 5) and radius of gyration (R g ). The 14 connectivity descriptors are all many-body in nature and consist of the AD, AAD, ADD, AADD, AAAD, AAADD adjacencies [number of hydrogen bonds accepted (A) and donated (D) by each water molecule], Wiener index, Average Shortest Path Length, hydrogen bond saturation (% HB), and number of non-short-circuited three-membered cycles, four-membered cycles, five-membered cycles, six-membered cycles, and seven-membered cycles. We mined a previously reported database of 4 948 959 water cluster minima for (H 2 O) n , n = 3–25 to analyze the evolution and correlation of these descriptors for the clusters within 5 kcal/mol of the putative minima. It was found that r OH and % HB correlated strongly with cluster size n, which was identified as the strongest predictor of energetic stability. Marked changes in the adjacencies and cycle count were observed, lending insight into changes in the hydrogen bond network upon aggregation. A Principal Component Analysis (PCA) was employed to identify descriptor dependencies and group clusters into specific structural patterns across different cluster sizes. The results of this study inform our understanding of how water clusters evolve in size and what appropriate descriptors of their structural and connectivity patterns are with respect to system size, stability, and similarity. The approach described in this study is general and can be easily extended to other hydrogen-bonded systems.

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

Deprotonated sulfamic acid and its homodimers: Does sulfamic acid adopt zwitterion during cluster growth?

Here we present a joint experimental and computational study on the geometric and electronic structures of deprotonated sulfamic acid (SA) clusters [(SA) n –H] – (n = 1, 2) employing negative ion photoelectron spectroscopy and high-level ab initio calculations. The photoelectron spectra provide the vertical/adiabatic detachment energy (VDE/ADE) of the sulfamate anion (SM – ) H 2 N•SO 3 – at 4.85 ± 0.05 and 4.58 ± 0.08 eV, respectively, and the VDE and ADE of the SM – •SA dimer at 6.41 ± 0.05 and 5.87 ± 0.08 eV, respectively. The significantly increased electron binding energies of the dimer confirm the enhanced electronic stability upon the addition of one SA molecule. The CCSD(T)-predicted VDEs/ADEs agree excellently with the experimental data, confirming the identified structures as the most stable ones. Two types of dimer isomers possessing different hydrogen bonding (HB) motifs are identified, corresponding to SM – binding to a zwitterionic SA (SM – •SA z ) and a canonical SA (SM – •SA c ), respectively. Two N–H$\cdots$O HBs and one superior O–H$\cdots$O HB are formed in the lowest-lying SM – •SA c , while SM – •SA z has three moderate N–H$\cdots$O HBs, with the former being 4.71 kcal/mol more stable. Further theoretical analyses reveal that the binding strength advantage of SM – •SA c over SM – •SA z arises from its significant contributions of orbital interactions between fragments, illustrating that sulfamate strongly interacts with its parent SA acid and preferably chooses the canonical SA in the subsequent cluster formations. Given the prominent presence of SA, this study provides the first evidence that the canonical dimer model of sulfamic acid should exist as a superior configuration during cluster growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗