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At least 145 records · Page 8

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DOE OSTI2025

Multi-Dimensional Spectroscopy with Intense Entangled Beams: Entanglement-Enabled Phase Matching in a Collinear Beam Geometry

The experimental realization of quantum molecular spectroscopy with entangled photons remains challenging owing to the low signal-to-noise ratio resulting from the use of low-flux entangled photons. High-flux entangled photons via intense entangled beams can be used to improve the signal-to-noise ratio, but the presence of unentangled photons contaminates the quantum signal stemming from entangled photons. Here, we demonstrate how intense entangled beams can be used in multi-dimensional spectroscopy while retaining the advantage of photon entanglement. Our approach is broadly applicable to odd-ordered nonlinear spectroscopies, and it generates purely quantum spectroscopic signals. The proposed approach allows the recording of desired phase-matched signals even in a collinear beam geometry, which lifts the requirement of complicated beam geometry setups for phase matching in multi-dimensional spectroscopies.

Absorption spectroscopy↗

DOE OSTI2020

Suppressing Molecular Charging, Nanochemistry, and Optical Rectification in the Tip-Enhanced Raman Geometry

Classical vs quantum plasmons are operative in tapping vs contact mode tip-enhanced Raman scattering (TERS) and lead to distinct observables. Under otherwise identical experimental conditions, we illustrate the concept through tapping and contact mode TERS mapping of chemically functionalized silver nanocubes. Whereas molecular charging, chemical transformations, and optical rectification are prominent observables in contact mode TERS, the same effects are suppressed using tapping mode feedback. In effect, this work demonstrates that nanoscale physical and chemical processes can be accessed/suppressed on-demand in the TERS geometry. Further, the advantages of tapping mode TERS are otherwise highlighted with the latter in mind.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1994

The Infrared Reflection Nebula Around the Protostellar System in S140

We have studied the protostellar system in S140 at 2.2, 3.1 and 3.45 microns using a 128x128 InSb array at the Lick Observatory 3m telescope. Besides the protostellar sources, the data reveal a bright infrared reflection nebula. We have developed a simple model of this region and derived the physical conditions. IRSI is surrounded by a dense dusty disk viewed almost edge-on. Photons leaking out through the poles illuminate almost directly north and south the inner edge of a surrounding shell of molecular gas, Analysis of the observed colors and intensities of the NIR light, using Mie scattering theory, reveal that the dust grains in the molecular cloud are somewhat larger than in the general diffuse interstellar medium. Moreover, the incident light has a "cool" color temperature, approximately equals 800K, and likely originates from a dust photosphere close to the protostar. Finally, we find little H2O ice associated with the dusty disk around IRSI. Most of the 3.1 micron ice extinction arises instead from cool intervening molecular cloud material. We have compared our infrared dust observations with millimeter and radio observations of molecular gas associated with this region. The large scale structure observable in the molecular gas is indicative of the interaction between the protostellar wind and the surrounding molecular cloud rather than the geometry of the protostellar disk. We conclude that S140 is a young blister formed by this outflow on the side of a molecular cloud and viewed edge-on.

Harker, D.↗

DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2013

Fast Molecular Outflows in Luminous Galaxy Mergers: Evidence for Quasar Feedback from Herschel

We report the results from a systematic search for molecular (OH 119 micron) outflows with Herschel/PACS in a sample of 43 nearby (z < 0.3) galaxy mergers, mostly ultraluminous infrared galaxies (ULIRGs) and QSOs. We find that the character of the OH feature (strength of the absorption relative to the emission) correlates with that of the 9.7 micron silicate feature, a measure of obscuration in ULIRGs. Unambiguous evidence for molecular outflows, based on the detection of OH absorption profiles with median velocities more blueshifted than−50 km/s, is seen in 26 (70%) of the 37 OH-detected targets, suggesting a wide-angle (approx. 145 deg.) outflow geometry. Conversely, unambiguous evidence for molecular inflows, based on the detection of OH absorption profiles with median velocities more redshifted than +50 km/s is seen in only four objects, suggesting a planar or filamentary geometry for the inflowing gas. Terminal outflow velocities of approx. −1000 km/s are measured in several objects, but median outflow velocities are typically approx.−200 km/s−1. While the outflow velocities show no statistically significant dependence on the star formation rate, they are distinctly more blueshifted among systems with large active galactic nucleus (AGN) fractions and luminosities [log (L(sub AGN)/L(sub solar)) => 11.8 +/- 0.3]. The quasars in these systems play a dominant role in driving the molecular outflows. However, the most AGN dominated systems, where OH is seen purely in emission, show relatively modest OH line widths, despite their large AGN luminosities, perhaps indicating that molecular outflows subside once the quasar has cleared a path through the obscuring material.

Outfows↗

DOE OSTI2025

Imaging a light-induced molecular elimination reaction with an X-ray free-electron laser

Tracking the motion of individual atoms during chemical reactions represents a severe experimental challenge, especially if several competing reaction pathways exist or if the reaction is governed by the correlated motion of more than two molecular constituents. Here we demonstrate how ultrashort X-ray pulses combined with coincident ion imaging can be used to trace molecular iodine elimination from laser-irradiated diiodomethane (CH 2 I 2 ), a reaction channel of fundamental importance but small relative yield that involves the breaking of two molecular bonds and the formation of a new one. We map bending vibrations of the bound molecule, disentangle different dissociation pathways, image the correlated motion of the iodine atoms and the methylene group leading to molecular iodine ejection, and trace the vibrational motion of the formed product. Our results provide a quantitative mechanistic picture behind previously suggested reaction mechanisms and prove that a variety of geometries are involved in the molecular bond formation.

Atomic and molecular interactions with photons↗

DOE OSTI2025

Imaging transient molecular configurations in UV-excited diiodomethane

Femtosecond structural dynamics of diiodomethane (CH 2 I 2 ) triggered by ultraviolet (UV) photoabsorption at 290 and 330 nm are studied using time-resolved coincident Coulomb explosion imaging driven by a near-infrared probe pulse. Here, we map the dominant single-photon process, the cleavage of the carbon–iodine bond producing rotationally excited CH 2 I radical, identify the contributions of the three-body (CH 2 + I + I) dissociation and molecular iodine formation channels, which are primarily driven by the absorption of more than one UV photon, and demonstrate the existence of a weak reaction pathway involving the formation of short-lived transient species resembling iso-CH 2 I 2 -like geometries with a slightly shorter I–I separation compared to the ground-state CH 2 I 2 . These transient molecular configurations, which can be separated from the other channels by applying a set of conditions on the correlated momenta of three ionic fragments, are formed within ∼100 fs after the initial photoexcitation and decay within the next 100 fs.

Atomic and molecular processes↗

DOE OSTI2025

Optimizing microfluidic flow cell geometry for in situ resonant soft X-ray characterization of molecular nanostructures

Liquid-phase resonant soft X-ray scattering (LP-RSoXS) is an emerging label-free technique to probe chemically resolved nanostructures of molecular or hybrid materials in liquid environments. Still, quantitative analysis is hindered by the pressure-induced deformation of thin silicon nitride (SiN) membranes used as windows in microfluidic flow cells, which attenuates the signal in nonlinear ways, making experimental optimization difficult. Here, in this work, we directly characterize this deformation under experimental conditions for a variety of cell configurations. We use this to develop a predictive model that combines transmission effects of SiN bowing, incident X-ray beam profiles, and material-dependent resonant scattering cross sections to simulate the effective scattering intensity at the detector across the carbon K-edge. Maps of the total signal across the flow cell window reveal that increasing the window width and polymer concentration shifts the anisotropic intensity distributions from the center toward the edges of the window. It was determined that an optimal SiN thickness of 50 nm, with a window aperture of 104 μm, maximizes the total signal for typical solute concentrations and energies across the carbon K-edge. Our results overturn the assumption that corner regions dominate the scattering signal, offering explicit design guidelines for maximizing LP-RSoXS signals and significantly advancing the quantitative application of this technique to the characterization of molecular and hybrid nanostructured materials in liquids.

Grabner, Devin [Washington State Univ., Pullman, W↗

DOE OSTI2021

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Investigation of the Effect of Framework Flexibility on Adsorption in SIFSIX-3-Cu using a Machine-Learned Force Field

Metal-organic frameworks (MOFs) are a promising class of adsorbents. The performance of MOF sorbents relies on high selectivity and low regeneration energy. This work focuses on the use of machine learned force fields (MLFFs) to model adsorption in a flexible MOF, SIFSIX-3-Cu. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies, forces, and stresses, using an iterative sampling scheme combining sampling based on molecular dynamics, Monte Carlo, and geometry optimization to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included in this model. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations using the MLFF predicted adsorption isotherms in good agreement with experimental data for a range of pressures (40 Pa – 104 Pa) in contrast to rigid models, which overpredict CO2 adsorption at low pressures. The improvement was the result of a description of the variability of fluorine-fluorine diagonal distances at adsorption sites. This detailed description of flexibility afforded by the MLFF resulted in more accurate predictions adsorption isotherms when compared to the experimentally measured values. These results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low pressure applications and provide a robust procedure for training MLFF models for MOFs.

Atomistic Simulation↗

DOE OSTI2023

Guiding Principles for the Rational Design of Hybrid Materials: Use of DFT Methodology for Evaluating Non‐Covalent Interactions in a Uranyl Tetrahalide Model System

Abstract Together with the synthesis and experimental characterization of 14 hybrid materials containing [UO 2 X 4 ] 2− (X=Cl − and Br − ) and organic cations, we report on novel methods for determining correlation trends in their formation enthalpy (ΔH f ) and observed vibrational signatures. Δ H f values were analyzed through isothermal acid calorimetry and a Density Functional Theory+Thermodynamics (DFT+T) approach with results showing good agreement between theory and experiment. Three factors (packing efficiency, cation protonation enthalpy, and hydrogen bonding energy [ ]) were assessed as descriptors for trends in Δ H f . Results demonstrated a strong correlation between and Δ H f , highlighting the importance of hydrogen bonding networks in determining the relative stability of solid‐state hybrid materials. Lastly, we investigate how hydrogen bonding networks affect the vibrational characteristics of uranyl solid‐state materials using experimental Raman and IR spectroscopy and theoretical bond orders and find that hydrogen bonding can red‐shift U≡O stretching modes. Overall, the tightly integrated experimental and theoretical studies presented here bridge the trends in macroscopic thermodynamic energies and spectroscopic features with molecular‐level details of the geometry and electronic structure. This modeling framework forms a basis for exploring 3D hydrogen bonding as a tunable design feature in the pursuit of supramolecular materials by rational design.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Guiding Principles for the Rational Design of Hybrid Materials: Use of DFT Methodology for Evaluating Non‐Covalent Interactions in a Uranyl Tetrahalide Model System

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Modeling Molecules under Pressure with Gaussian Potentials

The computational modeling of molecules under high pressure is a growing research area that augments experimental high-pressure chemistry. Here, a new electronic structure method for modeling atoms and molecules under pressure, Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP) approach, is introduced. In this method, a set of Gaussian potentials is distributed evenly on the van der Waals surface of the investigated chemical system, leading to a compression of the electron density and the atomic scaffold. Since no parameters other than pressure need to be specified, GOSTSHYP allows straightforward geometry optimizations and ab initio molecular dynamics simulations of chemical systems under pressure for nonexpert users. In this work, calculated energies, bond lengths, and dipole moments under pressure fall within the range of established computational methods for high-pressure chemistry. A Diels-Alder reaction and the cyclotrimerization of acetylene showcase the ability of GOSTSHYP to model pressure-induced chemical reactions. The connection to mechanochemistry is pointed out.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Tris(carbene)borates; alternatives to cyclopentadienyls in organolanthanide chemistry

The chemistry of the tris-carbene anion phenyltris(3-alkyl-imidazoline-2-yliden-1-yl)borate, [C3 Me ] - ligand, is initiated for f-block metal cations. Neutral, molecular complexes of the form Ln(C3) 2 I are formed for cerium(III), while a separated ion pair [Ln(C3) 2 ]I forms for ytterbium(III). DFT/QTAIM computational analyses of the complexes and related tridentate tris(pyrazolyl)borate (Tp) – supported analogs demonstrates the anticipated strength of the σ donation and confirms greater covalency in the metal–carbon bonds of the [C3 Me ] - complexes in comparison with those in the Tp Me,Me complexes. The DFT calculations demonstrate the crucial role of THF solvent in accurately reproducing the contrasting molecular and ion-pair geometries observed experimentally for the Ce and Yb complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Reduced scaling formulation of CASPT2 analytical gradients using the supporting subspace method

We present a reduced scaling and exact reformulation of state specific complete active space second-order perturbation (CASPT2) analytical gradients in terms of the MP2 and Fock derivatives using the supporting subspace method. This work follows naturally from the supporting subspace formulation of the CASPT2 energy in terms of the MP2 energy using dressed orbitals and Fock builds. For a given active space configuration, the terms corresponding to the MP2-gradient can be evaluated with O(N5) operations, while the rest of the calculations can be computed with O(N3) operations using Fock builds, Fock gradients, and linear algebra. When tensor-hyper-contraction is applied simultaneously, the computational cost can be further reduced to O(N4) for a fixed active space size. The new formulation enables efficient implementation of CASPT2 analytical gradients by leveraging the existing graphical processing unit (GPU)-based MP2 and Fock routines. We present benchmark results that demonstrate the accuracy and performance of the new method. Example applications of the new method in ab initio molecular dynamics simulation and constrained geometry optimization are given.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1974

Infrared measurements of stratospheric composition

The observational techniques and results of IR measurements of the minor and trace molecular composition of the lower stratosphere are reviewed. Emphasis is given to those theoretical aspects of the formation of emission and absorption spectra which affect the quantitative interpretation of observational data in terms of the vertical distribution of observed molecular species. The principal experimental techniques currently being used are briefly reviewed, followed by a detailed summary of current knowledge of the abundances and spatial variability of the known minor constituents. The question of the determination of the minimum detectable concentration of a constituent molecule and its relationship to the instrumental parameters, the molecular transition intensities, and observation geometry is discussed; upper limit concentrations are given for some additional species of importance in current stratospheric studies.

Farmer, C. B.↗

NASA NTRS1978

2.1 micron H2 emission - High-spectral-resolution observations of the Orion Nebula

High-resolution (45 km/sec) observations of the 2.12 micrometers molecular hydrogen emission line in the Orion Nebula reveal a single feature with delta V (FWHP) not exceeding 30 km/sec at a LSR velocity of + 9.5 + or - 4 km/sec. The results support the suggestion that the H2 emission is collisionally excited in a thin shock-heated layer inside the cool molecular cloud. For a spherical geometry the shock velocity is, therefore, constrained to be at most 15 km/sec.

Joyce, R. R.↗

NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗