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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

On the performance of composite schemes in determining equilibrium molecular structures

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

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

Molecular structure determination: Equilibrium structure of pyrimidine (m-C 4 H 4 N 2 ) from rotational spectroscopy (reSE) and high-level ab initio calculation (re) agree within the uncertainty of experimental measurement

The pure rotational spectrum of pyrimidine (m-C 4 H 4 N 2 ), the meta-substituted dinitrogen analog of benzene, has been studied in the millimeter-wave region from 235 GHz to 360 GHz. The rotational spectrum of the ground vibrational state has been assigned and fit to yield accurate rotational and distortion constants. Over 1700 distinct transitions were identified for the normal isotopologue in its ground vibrational state and least-squares fit to a partial sextic S-reduced Hamiltonian. Transitions for all four singly substituted 13 C and 15 N isotopologues were observed at natural abundance and were likewise fit. Deuterium-enriched samples of pyrimidine were synthesized, giving access to all eleven possible deuterium-substituted isotopologues, ten of which were previously unreported. Experimental values of rotational constants and computed values of vibration–rotation interaction constants and electron-mass corrections were used to determine semi-experimental equilibrium structures (r e SE ) of pyrimidine. The r e SE structure obtained using coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] corrections shows exceptional agreement with the re structure computed at the CCSD(T)/cc-pCV5Z level (≤0.0002 Å in bond distance and ≤0.03° in bond angle). Of the various computational methods examined, CCSD(T)/cc-pCV5Z is the only method for which the computed value of each geometric parameter lies within the statistical experimental uncertainty (2σ) of the corresponding semi-experimental coordinate. The exceptionally high accuracy and precision of the structure determination is a consequence of the large number of isotopologues measured, the precision and extent of the experimental frequency measurements, and the sophisticated theoretical treatment of the effects of vibration–rotation coupling and electron mass. Taken together, these demanding experimental and computational studies establish the capabilities of modern structural analysis for a prototypical monocyclic aromatic compound.

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

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid “molecular chaperones”, which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Department of Energy Project DE-SC0012198: Probing Electron-Molecule Scattering with HHG: Theory and Experiment (Final Report)

The study of the motion of atoms in molecules is important to understanding many areas of physical and life sciences. Such motion occurs on many different times scales, with electronic motion occurring on a sub-femtosecond time scale, and simple vibrational motion in tens to hundreds of femtoseconds. One way to follow such processes in real time is by the use of shortpulsed lasers, and in particular by studying time-resolved photoionization and the related process of high-harmonic generation (HHG). Thus there has been much effort to develop the tools necessary to probe molecular systems using short pulse lasers and understanding the sensitivity of the different possible probes to the time dependent geometric structure as well as the electronic structure of molecules. Our research has particularly focused on the connection between high-field processes and the more traditional weak field photoionization processes. Strong field and weak field processes can be connected through models that involve the same matrix elements. We have demonstrated in our study of HHG from SF 6 that the spectrum is sensitive to the interplay between the angular dependence of the ionization step and recombination step. In our study of rescattering spectroscopy, we have shown that with a combination of experiment and theory, we can use this high-field spectroscopy to determine molecular structure in molecules such as C 2 H 4 . We have also developed new computational tools based on overset grids to enable studies on larger molecular systems which use much more robust numerical approaches so that the resulting code can be a tool that non-specialists can use to study related systems.

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

Determination of Molecular Structure and Dynamics of Molten Salts by Advanced Neutron and X-ray Scattering Measurements and Computer Modeling

The design and development of fully functional Molten-Salt Reactors (MSR) require detailed knowledge of the molten salt properties in order to understand and predict the salt’s behavior. Fundamental properties of interest include molecular structure, speciation, and dynamics (such as diffusion coefficients) of salt components and dissolved corrosion and fission products. Computer modeling is necessary to predict changes in physical and chemical properties due to irradiation, burning of dissolved fuel, and corrosion. The modeling requires experimental data, and advanced neutron and x-ray scattering and spectroscopy provide the most reliable and direct determination of the structure (Pair-Distribution Functions, PDF), and dynamics of ions in the melt. This project dealt with both fluoride and chloride salts. The PDFs have been measured by a combination of neutron and x-ray diffraction. We utilized the techniques of isotope substitutions, a very powerful tool available for neutron-scattering, to extract the details of the liquid structure. Although similar measurements have been done before, modern advanced neutron and x-ray-scattering techniques allow collecting the data at much higher resolution and in a wider range of temperatures. Importantly, we were among the first to study fluoride salts by neutron scattering. The importance of impurities and their effects on salt properties have become apparent recently and so new methods of salt purification were developed. We took advantage of these developments to produce reliable data, which have been used for computer simulations of both clean salts and those with added fission and corrosion products most relevant for MSRs. Ab initio molecular dynamics simulations have been performed to understand the multi-component liquid solution, in particular solubility of impurities and thermodynamic interactions in relation to the ionic-cluster structure of the fluid. We applied machine learning to regress from the simulation and experimental data in order to develop a fast-acting model that can handle molten salt with an arbitrary (≥ 10) number of chemical elements and be able to predict chemical potential as a function of composition and temperature. This project resulted in a number of experimental and computer-simulation publications, a patent application, and numerous conference presentations (American Physical Society, American Chemical Society, and The Electrochemical Society among others). Multiple students and postdocs participated and collaborated on aspects of this project. This project seeded new collaborations between MIT and other institutions, such as the University of Massachusetts Lowell, the University of Illinois Urbana-Champaign, the University of California Berkeley, and Oak Ridge and Los Alamos National Labs. As such, this project has had a broad and lasting impact beyond its original scientific scope.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2015

In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2025

Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination

High-energy electrons induce sample damage and motion at the nanoscale to fundamentally limit the determination of molecular structures by electron diffraction. Using a fast event-based electron counting (EBEC) detector, we characterize beam-induced, dynamic, molecular crystal lattice reorientations (BIRs). These changes are sufficiently large to bring reciprocal lattice points entirely in or out of intersection with the sphere of reflection, occur as early events in the decay of diffracted signal due to radiolytic damage, and coincide with beam-induced migrations of crystal bend contours within the same fluence regime and at the same illuminated location on a crystal. These effects are observed in crystals of biotin, a series of amino acid metal chelates, and a six-residue peptide, suggesting that incident electrons inevitably warp molecular lattices. The precise orientation changes experienced by a given microcrystal are unpredictable but are measurable by indexing individual diffraction patterns during beam-induced decay. Reorientations can often tilt a crystal lattice several degrees away from its initial position before irradiation, and for an especially beam-sensitive Zn(II)-methionine chelate, are associated with dramatic crystal quakes prior to 1 e − Å −2 electron beam fluence accumulates. Since BIR coincides with the early stages of beam-induced damage, it echoes the beam-induced motion observed in single-particle cryoEM. As with motion correction for cryoEM imaging experiments, accounting for BIR-induced errors during data processing could improve the accuracy of MicroED data.

Vlahakis, Niko (ORCID:0000000250920265)↗
DOE OSTI2022

Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation

Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, the data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Mixed cerium-platinum oxides: Electronic structure of [CeO]Pt{sub n} (n = 1, 2) and [CeO{sub 2}]Pt complex anions and neutrals

The electronic structures of several small Ce–Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt{sub 2} both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt{sub 2} complexes are therefore ionic, with electronic structures described qualitatively as [CeO{sup +2}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −}, respectively. The associated anions are described qualitatively as [CeO{sup +}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −2}, respectively. In both neutrals and anions, the most stable molecular structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt{sub 2} moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO{sub 2}, which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO{sub 2}]Pt{sup −}. The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO{sub 2}]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt–O–Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt{sup −} daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

High current table-top setup for femtosecond gas electron diffraction

Here, we have constructed an experimental setup for gas phase electron diffraction with femtosecond resolution and a high average beam current. While gas electron diffraction has been successful at determining molecular structures, it has been a challenge to reach femtosecond resolution while maintaining sufficient beam current to retrieve structures with high spatial resolution. The main challenges are the Coulomb force that leads to broadening of the electron pulses and the temporal blurring that results from the velocity mismatch between the laser and electron pulses as they traverse the sample. We also present here a device that uses pulse compression to overcome the Coulomb broadening and deliver femtosecond electron pulses on a gas target. The velocity mismatch can be compensated using laser pulses with a tilted intensity front to excite the sample. The temporal resolution of the setup was determined with a streak camera to be better than 400 fs for pulses with up to half a million electrons and a kinetic energy of 90 keV. Finally, the high charge per pulse, combined with a repetition rate of 5 kHz, results in an average beam current that is between one and two orders of magnitude higher than previously demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

On the Structure-Property Relationships of Cation-Exchanged ZK-5 Zeolites for CO 2 Adsorption

The CO 2 adsorption properties of cation-exchanged Li-, Na-, K-, and Mg-ZK-5 zeolites were correlated to the molecular structures determined by Rietveld refinements of synchrotron powder X-ray diffraction patterns. Li-, K-, and Na-ZK-5 all exhibited high isosteric heats of adsorption (Qst) at low CO 2 coverage, with Na-ZK-5 having the highest Qst (ca. 49 kJ mol -1 ). Mg2+ was located at the center of the zeolite hexagonal prism with the cation inaccessible to CO 2 , leading to a much lower Qst (ca. 30 kJ mol-1) and lower overall uptake capacity. Multiple CO 2 adsorption sites were identified at a given CO 2 loading amount for all four cation-exchanged ZK-5 adsorbents. Site A at the flat eight-membered ring windows and site B/B* in the γ-cages were the primary adsorption sites in Li - and Na-ZK-5 zeolites. Relatively strong dual-cation adsorption sites contributed significantly to an enhanced electrostatic interaction for CO 2 in all ZK-5 samples. This interaction gives rise to a migration of Li + and Mg 2+ cations from their original locations at the center of the hexagonal prisms toward the α-cages, in which they interact more strongly with the adsorbed CO 2 .

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

Sterically Encumbered Heteroleptic Copper(I) β-Diketiminate Complexes with Extended Excited-State Lifetimes

One of the main challenges in developing effective copper(I) photosensitizers is their short excited-state lifetimes, usually attributed to structural distortion upon light excitation. We have previously introduced copper(I) charge-transfer chromophores of the general formula Cu(N^N)(ArNacNac), where N^N is a conjugated diimine ligand and ArNacNac is a substituted β-diketiminate ligand. These chromophores were promising regarding their tunable redox potentials and intense visible absorption but were ineffective as photosensitizers, presumably due to short excited-state lifetimes. Here, we introduce sterically crowded analogues of these heteroleptic chromophores with bulky alkyl substituents on the N^N and/or ArNacNac ligand. Structural analysis was combined with electrochemical and photophysical characterization, including ultrafast transient absorption (UFTA) spectroscopy to investigate the effects of the alkyl groups on the excited-state lifetimes of the complexes. The molecular structures determined by single-crystal X-ray diffraction display more distortion in the ground state as alkyl substituents are introduced into the phenanthroline or the NacNac ligand, showing smaller τ 4 values due to the steric hindrance. UFTA measurements were carried out to determine the excited-state dynamics. Sterically encumbered Cu5 and Cu6 display excited-state lifetimes 15–20 times longer than unsubstituted complex Cu1, likely indicating that the incorporation of bulky alkyl substituents inhibits the pseudo-Jahn–Teller (PJT) flattening distortion in the excited state. Furthermore, this work suggests that the steric properties of these heteroleptic copper(I) charge-transfer chromophores can be readily modified and that the excited-state dynamics are strongly responsive to these modifications.

14 SOLAR ENERGY↗
DOE OSTI2018

Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy

In this work, we introduce the so-called “Classical Optimal Control Optimization” (COCO) method for global energy minimization based on the implementation of the diffeomorphic modulation under observable-response-preserving homotopy (DMORPH) gradient algorithm. A probe particle with time-dependent mass $m(t;β)$ and dipole $μ(r,t;β)$ is evolved classically on the potential energy surface $V(r)$ coupled to an electric field $E(t;β)$, as described by the time-dependent density of states represented on a grid, or otherwise as a linear combination of Gaussians generated by the k-means clustering algorithm. Control parameters $β$ defining $m(t;β), μ(r,t;β),$ and $E(t;β)$ are optimized by following the gradients of the energy with respect to $β,$ adapting them to steer the particle toward the global minimum energy configuration. We find that the resulting COCO algorithm is capable of resolving near-degenerate states separated by large energy barriers and successfully locates the global minima of golf potentials on flat and rugged surfaces, previously explored for testing quantum annealing methodologies and the quantum optimal control optimization (QuOCO) method. Preliminary results show successful energy minimization of multidimensional Lennard-Jones clusters. Beyond the analysis of energy minimization in the specific model systems investigated, we anticipate COCO should be valuable for solving minimization problems in general, including optimization of parameters in applications to machine learning and molecular structure determination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Opportunities and Limitations of Nuclear Magnetic Resonance Spectroscopy in Astrobiology

For decades, Nuclear Magnetic Resonance (NMR) spectroscopy has been utilized as a powerful tool in various scientific disciplines, most prominently in chemistry, to determine molecular structures or monitor reactions. While well established in various fields, NMR applications in astrobiology are still unclear. This work aims to explore the potential of NMR in astrobiology, highlighting strengths but also weaknesses. We illustrate capabilities of NMR with two applications: (1) recently developed methods for position-specific carbon isotope analysis of complex organics; and (2) well-established tools for performing quantitative compositional analysis of complex organic mixtures. By utilizing samples relevant to astrobiology, specifically the amino acid valine and analogue mixtures of organics, we showcase that molecules retain a source dependent and distinct intramolecular carbon isotope fingerprint. We demonstrate that compositional sample analysis provides an independent and complementary line of evidence pointing towards the origin of a molecule or mixture. Together, these NMR tools have the potential to support life detection efforts, and aid in distinguishing between biotic and abiotic samples. Finally, we discuss sensitivity, detection limits, the portability of NMR, and propose how integration with mass-spectrometry techniques will be imperative to enable more targeted and comprehensive analyses relevant to astrobiology, including in-situ analysis but also sample return missions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Probing molecular bond-length using molecular-frame photoelectron angular distributions

The molecular-frame photoelectron angular distributions (MFPADs) in O 1s photoemission from CO 2 molecule were measured. Patterns due to photoelectron diffractions were observed in the MFPADs. The polarization-averaged MFPADs were compared with theoretical calculation and were found to be useful in determining the molecular bond-length, which is a component to determine molecular structures.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Volumetric Segmentation via Neural Networks Improves Neutron Crystallography Data Analysis

Crystallography is the powerhouse technique for molecular structure determination, with applications in fields ranging from energy storage to drug design. Accurate structure determination, however, relies partly on determining the precise locations and integrated intensities of Bragg peaks in the resulting data. Here, we describe a method for Bragg peak integration that is accomplished using neural networks. The network is based on a U-Net and identifies peaks in three-dimensional reciprocal space through segmentation, allowing prediction of the full 3D peak shape from noisy data that is commonly difficult to process. The procedure for generating appropriate training sets is detailed. Trained networks achieve Dice coefficients of 0.82 and mean IoUs of 0.69. Carrying out integration over entire datasets, it is demonstrated that integrating neural network-predicted peaks results in improved intensity statistics. Furthermore, using a second dataset, the possibility of transfer learning between datasets is shown. Given the ubiquity and growing complexity of crystallography, we anticipate integration by machine learning to play an increasingly important role across the physical sciences. These early results demonstrate the applicability of deep learning techniques for integrating crystallography data and suggest a possible role in the next generation of crystallography experiments.

Sullivan, Brendan T.↗