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Results for “intermolecular potentials”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Investigating intermolecular interactions among CO 2 , water and PEEK-ionene membrane using cryo ToF-SIMS and isotopic labeling

Cryogenic time-of-flight secondary ion mass spectrometry (cryo ToF-SIMS) has emerged as a powerful tool for investigating molecular interactions, speciation, and dynamics in materials for CO 2 capture. In this study, we apply cryo ToF-SIMS to probe interactions between CO 2 , water, and PEEK-ionene membranes—a promising material for direct CO 2 capture due to its selectivity, durability, and efficiency. Despite this potential, the mechanisms governing CO 2 diffusion and the influence of water vapor on CO 2 behavior remain unclear. To address this, we loaded PEEK-ionene membranes with 13 CO 2 and D 2 O and employed cryo ToF-SIMS to visualize the 3D distribution of CO 2 and water within the membrane. While prior studies suggest that 13 CO 2 is absorbed under ambient conditions, our cryo ToF-SIMS analysis revealed no enhancement of the 13 C/ 12 C ratio, suggesting weak CO 2 -membrane interactions. As a result, CO 2 vaporizes even at low temperatures (−140°C) under vacuum conditions. In contrast, D 2 O displayed a relatively homogeneous distribution in the membrane, suggesting stronger water-membrane interactions via hydrogen bonding (18–20 kJ/mol). Interestingly, CO 2 was not detected in D 2 O-loaded membranes, indicating minimal interference from water vapor on CO 2 diffusion. As a comparison, the cryo ToF-SIMS data show that 13 CO 2 can readily react with a basic Na 2 CO 3 aqueous solution to form NaH 13 CO 3 . These findings demonstrate cryo ToF-SIMS as a critical technique for understanding gas-water-membrane interactions, offering insights for membrane functionalization to improve CO 2 capture efficiency.

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

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond

Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

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

Local structure analysis of low-temperature neutron pair distribution function coupled with molecular dynamics simulations of CH 4 and CO 2 hydrates from 2 to 210 K

CH 4 hydrates occur naturally and are an abundant potential fuel source with a corresponding risk of potent greenhouse gas release, due to their stability conditions at low temperature and high pressure. Byproduct CO 2 can be exchanged with CH 4 in these natural deposits and can potentially stabilize the hydrates at higher temperatures. CH 4 , CO 2 , and mixed CH 4 -CO 2 hydrates are studied with in situ neutron pair distribution function experiments from 2 to 210 K to investigate the impact of varying the CH 4 -CO 2 guest composition in the gas hydrate structure. These experiments combined with Reverse Monte Carlo analysis allow for the characterization of intermolecular CH 4 and CO 2 interactions with the water molecules which form the hydrate lattice and how they impact the local structure of the lattice itself. Results indicate that when CH 4 and CO 2 co-occupy the hydrate, the host is more strongly distorted than in the pure CH 4 and CO 2 hydrates, but this becomes less defined with increasing temperature. The presence of CO 2 in mixed hydrate increases the stability range and creates a barrier for CH 4 to completely leave the structure.

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

Highly Emissive Semi-Ladder-Type Copolymers, Aggregation State, and Solution-Processed Organic Light-Emitting Transistor

An organic light-emitting transistor (OLET) integrates the logic function of a field-effect transistor (FET) with electroluminescence of a light-emitting diode (LED) into a single device. This has the potential to play an important role in smart displays, electrically pumped organic laser, and other flexible electronic devices. For achieving high-performance solution-processed OLET, three semiladder copolymers—TPTI-CC, TPTI-C, and TPTI-F—were developed in this study. It was found that variation in the chemical structure lead to significant differences in energy level, emission color, and intermolecular aggregation. High photoluminescence quantum yields (PLQY) was obtained in these three polymers. Solution-processed trilayered OLET devices were fabricated, which exhibited strong electroluminescence, balanced charge mobility, and external quantum efficiency (EQE) of 2.8%.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Wetting of a Hydrophobic Surface: Far-IR Action Spectroscopy and Dynamics of Microhydrated Naphthalene

The interaction of water and polycyclic aromatic hydrocarbons is of fundamental importance in areas as diverse as materials science and atmospheric and interstellar chemistry. The interplay between hydrogen bonding and dipole–π interactions results in subtle dynamics that are challenging to describe from first principles. Here, we employ far-IR action vibrational spectroscopy with the infrared free-electron laser FELIX to investigate naphthalene with one to three water molecules. We observe diffuse bands associated with intermolecular vibrational modes that serve as direct probes of the loose binding of water to the naphthalene surface. These signatures are poorly reproduced by static DFT or Møller–Plesset computations. Instead, a rationalization is achieved through Born–Oppenheimer Molecular Dynamics simulations, revealing the active mobility of water over the surface, even at low temperatures. Therefore, our work provides direct insights into the wetting interactions associated with shallow potential energy surfaces while simultaneously demonstrating a solid experimental–computational framework for their investigation.

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

Quantum embedding for material chemistry based on domain separation and open subsystems

Our perspective considers two theories we recently proposed to perform quantum embedding calculations for chemical systems: domain-separated density functional theory (DSDFT) and locally coupled open subsystems (LCOS). The development includes both the fundamentals of each theory as well as potential applications, some technical aspects, and related challenges. DS-DFT is suited to study intramolecular effects, where one can apply a high level of theory (based on DFT or wave function theory) to a region of interest inside a molecule or solid, and lower level theory elsewhere, with smooth switching between the regions. LCOS, in contrast, is a fragment-based embedding which offers computational advantages to study intermolecular behavior such as electron hopping, spin-environment interaction, and charge transfer excitations. Yet, both theories can exchange roles when appropriate. In addition, these theories allow for control of computational scaling of their algorithms. We investigate paths to determine the charge-transfer operator used in LCOS, and suggest an auxiliary energy minimization that can provide a practical estimate to this operator. We also briefly discuss how to implement density fitting techniques in domain separation, and how domain separation can be used for pure wavefunction-based embedding.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Raman spectrum and polarizability of liquid water from deep neural networks

We introduce a scheme based on machine learning and deep neural networks to model the environmental dependence of the electronic polarizability in insulating materials. Application to liquid water shows that training the network with a relatively small number of molecular configurations is sufficient to predict the polarizability of arbitrary liquid configurations in close agreement with ab initio density functional theory calculations. In combination with a neural network representation of the interatomic potential energy surface, the scheme allows us to calculate the Raman spectra along 2-nanosecond classical trajectories at different temperatures for H 2 O and D 2 O. The vast gains in efficiency provided by the machine learning approach enable longer trajectories and larger system sizes relative to ab initio methods, reducing the statistical error and improving the resolution of the low-frequency Raman spectra. Decomposing the spectra into intramolecular and intermolecular contributions elucidates the mechanisms behind the temperature dependence of the low-frequency and stretch modes.

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

Observation of a super-tetrahedral cluster of acetonitrile-solvated dodecaborate dianion via dihydrogen bonding

We launched a combined negative ion photoelectron spectroscopy and multiscale theoretical investigation on the geometric and electronic structures of a series of acetonitrile-solvated dodecaborate clusters, i.e., B 12 H 12 2- ·nCH 3 CN (n = 1–4). The electron binding energies of B 12 H 12 2- ·nCH 3 CN are observed to increase with cluster size, suggesting their enhanced electronic stability. B3LYP-D3(BJ)/ma-def2-TZVP geometry optimizations indicate each acetonitrile molecule binds to B 12 H 12 2- via a threefold dihydrogen bond (DHB) B3–H3 ⋮⋮⋮ H3C–CN unit, in which three adjacent nucleophilic H atoms in B 12 H 12 2- interact with the three methyl hydrogens of acetonitrile. The structural evolution from n = 1 to 4 can be rationalized by the surface charge redistributions through the restrained electrostatic potential analysis. Notably, a super-tetrahedral cluster of B 12 H 12 2- solvated by four acetonitrile molecules with 12 DHBs is observed. The post-Hartree–Fock domain-based local pair natural orbital- coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)] calculated vertical detachment energies agree well with the experimental measurements, confirming the identified isomers as the most stable ones. Furthermore, the nature and strength of the intermolecular interactions between B 12 H 12 2- and CH 3 CN are revealed by the quantum theory of atoms-in-molecules and the energy decomposition analysis. Ab initio molecular dynamics simulations are conducted at various temperatures to reveal the great kinetic and thermodynamic stabilities of the selected B 12 H 12 2- ·CH 3 CN cluster. The binding motif in B 12 H 12 2- ·CH 3 CN is largely retained for the whole halogenated series B 12 X 12 2- ·CH 3 CN (X = F–I). This study provides a molecular-level understanding of structural evolution for acetonitrile-solvated dodecaborate clusters and a fresh view by examining acetonitrile as a real hydrogen bond (HB) donor to form strong HB interactions.

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

Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling

Biological nitrogen fixation is the process by which certain bacteria and archaea use the enzyme nitrogenase to reduce atmospheric nitrogen into bioavailable ammonium. Engineering non‐nitrogen‐fixing organisms, like plants, to use nitrogenase could reduce dependency on synthetic fertilizer and mitigate the environmental impacts of industrial fertilizer production. However, nitrogenase activity requires delivery of reducing power by small electron carrying proteins known as ferredoxins and flavodoxins, and successfully engineering nitrogenase into new systems will require a mechanistic understanding of electron delivery by these proteins. Most organisms often have multiple ferredoxins, raising the question of which ferredoxin can support nitrogenase activity. The purpose of this study is to gain insight into how we can predict which ferredoxin is compatible with the Fe protein, the component of nitrogenase that interacts with ferredoxin or flavodoxin. Our in silico protein–protein docking simulations reveal that most ferredoxins and flavodoxins involved in nitrogen fixation have the shortest distance (≤10 Å) between their redox cofactor and the [4Fe‐4S] cluster of the Fe protein. We found shorter cofactor distance contributes to faster intermolecular electron tunneling rates. Bacterial ferredoxins that play a role in nitrogen fixation also exhibit more complementary interactions with the Fe protein than bacterial and plant ferredoxins not involved in this process. Heterologous expression of a set of ferredoxins from both nitrogen‐fixing and non‐nitrogen‐fixing bacteria in the diazotroph Rhodopseudomonas palustris supports our model‐derived prediction that shorter distances between the electron‐carrying cofactors favor nitrogenase compatibility. These findings offer a framework to predict and potentially enhance ferredoxin–nitrogenase compatibility, which will help to improve our ability to engineer nitrogen fixation into non‐nitrogen‐fixing organisms like plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of Hydrogen Bonding on Nuclear Data Development of Liquid Anhydrous HF

Anhydrous Hydrogen Fluoride (HF) at high temperatures and pressures is used to process and manufacture nuclear fuel. As HF is often used directly with uranium, correct neutron thermal scattering cross sections are crucial to criticality safety applications. Classical molecular dynamics (CMD) simulation of the flexible HF system was used to create the thermal scattering law (TSL) and cross sections. The initial 2-site model is used in LAMMPS, and it can not capture the H-bond. To correctly represent the H-bond effects, a second, 3-site model was constructed in GROMACS. The 3-site model handled H-bonds by connecting a massless charge to the molecule. Key model parameters were compared to experimental data to verify the approach and models. To get the normalized VACF, the model was compared using hydrogen and fluorine bond length, density, potential energy, and diffusion coefficient. The phonon DOSs for both models were derived from the normalized VACF. DOSs were used to estimate the TSL ( S ( α, β )) and neutron thermal scattering cross sections for hydrogen in HF. The TSLs were evaluated using the FLASSH code with the Schofield diffusion model. It was observed that the representation of the hydrogen bonding changes the TSL's diffusional contributions. This is represented in the low energy scattering cross section, where intermolecular binding effects shift the cross section.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Cosolvent-tuned interactions in ionic liquids: A vibrational and quantum-chemical study of ethylene glycol ratio effects

Ionic liquids (ILs) are attractive media for CO 2 capture but remain limited by viscosity and cost. Blending ILs with ethylene glycol (EG) is a practical route to mitigate these constraints, yet the molecular origins of cosolvent effects and their dependence on composition are not well resolved. We combine Fourier-transform infrared (FT-IR) spectroscopy with quantum-chemical (DFT) analysis to elucidate how the IL:EG molar ratio modulates intermolecular interactions and electronic structure. Computed vibrational frequencies enable mode assignment and deconvolution of overlapping bands, revealing systematic, ratio-dependent shifts and broadenings in (i) EG O–H stretching, (ii) cation and EG C–H stretchings (imidazolium C2–H, C4–H, C5–H, methyl and ethyl groups, -CH2 of EG), (iii) anion signature modes (e.g., CN motifs), and (iv) EG C–O and C–C stretchings, consistent with the redistribution of hydrogen-bonding networks. Molecular electrostatic potential (MESP) maps quantify attenuation of extreme potential regions with increasing EG, indicating progressive screening of cation–anion electrostatic interactions. Quantum Theory of Atoms in Molecules (QTAIM) identifies emergent bond critical points between EG and the IL ions, while Reduced Density Gradient–Noncovalent Interaction (RDG–NCI) analysis differentiates strong directional hydrogen bonds from dispersive contacts across compositions. Together, these results show that EG fraction controls a switch from predominantly ion–ion to mixed ion–EG coordination, altering local polarity and polarizability that underlie the observed FT-IR trends. The framework provides composition–structure–spectrum relationships that can guide rational selection of IL:EG ratios to balance favorable molecular interactions with practical performance targets in scalable CO 2 capture systems.

DAC↗
DOE OSTI2022

Density functional theory of water with the machine-learned DM21 functional

The delicate interplay between functional-driven and density-driven errors in density functional theory (DFT) has hindered traditional density functional approximations (DFAs) from providing an accurate description of water for over 30 years. Recently, the deep-learned DeepMind 21 (DM21) functional has been shown to overcome the limitations of traditional DFAs as it is free of delocalization error. To determine if DM21 can enable a molecular-level description of the physical properties of aqueous systems within Kohn–Sham DFT, we assess the accuracy of the DM21 functional for neutral, protonated, and deprotonated water clusters. Furthermore, we find that the ability of DM21 to accurately predict the energetics of aqueous clusters varies significantly with cluster size. Additionally, we introduce the many-body MB-DM21 potential derived from DM21 data within the many-body expansion of the energy and use it in simulations of liquid water as a function of temperature at ambient pressure. We find that size-dependent functional-driven errors identified in the analysis of the energetics of small clusters calculated with the DM21 functional result in the MB-DM21 potential systematically overestimating the hydrogen-bond strength and, consequently, predicting a more ice-like local structure of water at room temperature.

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

Quaternary Charge-Transfer Complex Enables Photoenzymatic Intermolecular Hydroalkylation of Olefins

Intermolecular C–C bond-forming reactions are underdeveloped transformations in the field of biocatalysis. Here we report a photoenzymatic intermolecular hydroalkylation of olefins catalyzed by flavin-dependent ‘ene’-reductases. Radical initiation occurs via photoexcitation of a rare high-order enzyme-templated charge-transfer complex that forms between an alkene, α-chloroamide, and flavin hydroquinone. This unique mechanism ensures that radical formation only occurs when both substrates are present within the protein active site. Here, this active site can control the radical terminating hydrogen atom transfer, enabling the synthesis of enantioenriched γ-stereogenic amides. This work highlights the potential for photoenzymatic catalysis to enable new biocatalytic transformations via previously unknown electron transfer mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Inter-cofactor protein remodeling rewires short-circuited transmembrane electron transfer

Intraprotein electron transfer (ET) requires explicit local control of the environment of cofactors to influence their intermolecular distances, relative orientations, and redox properties. Efficient, longer-range ET often utilizes molecular orbitals of aromatic residues present in the intervening space. Here, revitalization of a vestigial ET pathway in the bacterial photosynthetic reaction center is achieved by scanning with tryptophans to uncover markedly improved routes of electron conduction in a key stabilizing step spanning 15 Å between tetrapyrrole and quinone cofactors. This ET event is maximally enhanced by pairing one or more tryptophans with a threonine to influence quinone binding and/or redox potential. Synergistic effects of these substitutions increase the yield of that ET step to ~95%. Joining these substitutions with mutant residues that improve initial ET steps dramatically enhances transmembrane charge separation via this redesigned version of a pathway that is quantitatively inactive in the native protein-cofactor complex.

Biophysical chemistry↗
DOE OSTI2020

Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies

We report the novel crystal structure and characterization of symmetrical, homodimeric humanized heavy-chain-only antibodies or dimers (HC2s). HC2s were found to be significantly coexpressed and secreted along with mAbs from transient CHO HC/LC cotransfection, resulting in an unacceptable mAb developability attribute. Expression of full-length HC2s in the absence of LC followed by purification resulted in HC2s with high purity and thermal stability similar to conventional mAbs. The V H and C H 1 portion of the heavy chain (or Fd) was also efficiently expressed and yielded a stable, covalent, and reducible dimer (Fd2). Mutagenesis of all heavy chain cysteines involved in disulfide bond formation revealed that Fd2 intermolecular disulfide formation was similar to Fabs and elucidated requirements for Fd2 folding and expression. For one HC2, we solved the crystal structure of the Fd2 domain to 2.9 Å, revealing a highly symmetrical homodimer that is structurally similar to Fabs and is mediated by conserved (C H 1) and variable (V H ) contacts with all CDRs positioned outward for target binding. Interfacial dimer contacts revealed by the crystal structure were mutated for two HC2s and were found to dramatically affect HC2 formation while maintaining mAb bioactivity, offering a potential means to modulate novel HC2 formation through engineering. These findings indicate that human heavy-chain dimers can be secreted efficiently in the absence of light chains, may show good physicochemical properties and stability, are structurally similar to Fabs, offer insights into their mechanism of formation, and may be amenable as a novel therapeutic modality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Exploring NaCl-PuCl 3 molten salts with machine learning interatomic potentials and graph theory

Actinide molten salts are the basis of the liquid fuels used in molten salt reactors. Due to the inherent difficulties associated with high temperature and hazardous conditions, experimental investigations of fundamental properties of these materials are usually challenging. In this work, we describe the structure and transport of NaCl-PuCl 3 mixtures using computational techniques. Three compositions were considered (16, 25, and 36 mol% PuCl 3 ) over a temperature range (730 – 1257K) using ab initio molecular dynamics, which provided the necessary data sets for training machine learned interatomic potentials. Further, molecular dynamics simulations based on these potentials were then used to determine structure and transport properties. A substantial change was noted in the structure factor when increasing the PuCl 3 content from 25 to 36 mol%. This change is linked to the aggregation of larger Pu 3+ clusters. In addition, the similarity of the atomic environments of metal cations in molten salt systems to their solid states counterparts was investigated using an unsupervised learning technique. Finally, graph theory was employed to explore the structure and size of actinide networks. Consistent with the structure factor, a dense Pu 3+ intermolecular structure is observed within the 36 mol% PuCl 3 mixture. The structure of cation-cation inter-junctions is also discussed. In all cases, the diffusion of Pu 3+ is significantly lower than that of Na + and Cl - .

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ultrafast solvent-to-solute proton transfer mediated by intermolecular coherent vibrations

Ultrafast photoinduced excited-state proton transfer (ESPT) plays a crucial role in protecting biomolecules and functional materials from photodamage. However, the influence of solute-solvent interactions on ESPT dynamics remains under active investigation. Here, we present an ultrafast spectroscopic study of ESPT in the photobase 2-(2´-pyridyl)benzimidazole (PBI) in methanol. Ultrafast absorption spectroscopy, supported by quantum chemical calculations, reveals three distinct kinetic steps: (1) a 2.2 ps solvent-to-solute proton transfer, (2) subsequent nonradiative relaxation to the ground state within 31 ps, producing a vibrationally hot ensemble with substantial excess kinetic energy, and (3) equilibration as this energy dissipates into the surrounding solvent bath over 186 ps. Femtosecond-resolved dynamics exhibit oscillatory signals indicative of coherent wavepacket motion on the S 1 potential energy surface. A phase flip in the excited-state absorption maximum confirms this assignment. Fourier analysis resolves two dominant periods (∼117 fs and ∼340 fs), corresponding to in-plane and out-of-plane vibrational modes coupled between PBI and the hydrogen-bonded methanol molecule. The rapid dephasing ( < 300 fs) suggests that the nuclear wavefunction evolves on an anharmonic potential energy surface while traversing the ESPT reaction coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗