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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (Φ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, Φ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Magnetism and finite-temperature effects in UZr 2 : A density functional theory analysis

The structure and the thermophysical properties of d-UZr 2 are investigated using 0 K density functional theory and ab initio molecular dynamics (AIMD). Modeling the true paramagnetic state of this intermetallic compound has been challenging using first-principles calculations. For the first time, we find that the generalized gradient approximation method without applying an on-site Coulomb interaction term (Hubbard U) can result in a ground state that is antiferromagnetic (AFM). We believe that this weak AFM ground state is the closest to the real paramagnetic state. We found that structure optimization at finite temperatures using AIMD is necessary to achieve this ground state instead of the non-magnetic and ferromagnetic states previously reported in the literature. Our findings indicate that applying the Hubbard U on uranium f-orbitals in this metallic system is unnecessary and not recommended, as it leads to a large overestimation of the volume and introduces an unphysical strong spin polarization. Finally, our approach results in atomic volume, thermal expansion, and heat capacities that have strong agreement with experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

The effect of ion pairing on speciation and transport in ion exchange membranes at varying hydration levels: A four-state model

Understanding ion pairing in ion exchange membranes (IEMs) is essential for advancing IEM applications in energy and environmental technologies. Here, this study introduces a four-state molecular dynamics model to quantify speciation and transport within Nafion-117, specifically examining the role of ion pairing in monovalent and divalent counterions (NaCl, Na 2 SO 4 , and MgSO 4 ). By analyzing radial distribution functions (RDFs) and molecular snapshots, we distinguish ion pairing modes and classify counterions into four states: condensed counterion, condensed ion pair, free ion pair, and free counterion. A key finding is that while divalent counterions (e. g., Mg 2+ ) maintain stable speciation across hydration levels, monovalent counterions (e.g., Na + ) show notable speciation shifts with hydration. Both monovalent and divalent counterions are not diffusive when condensed onto the polymer (sorbed to membrane functional groups). In contrast, free counterions are diffusive across all hydration levels. To evaluate the overall diffusivity of counterions, four-state fractions and diffusivities are computed, each contributing to counterion transport. The condensed/free ion speciation for multivalent sulfate salts aligns with previous revisions to the Donnan-Manning framework that include ion pairing, thereby validating its relevance to established membrane theories. The four-state model's diffusivity results support several current ion exchange assumptions, including that the condensed counterions are immobile, while uncondensed counterions are mobile. The four-state model offers insights into contact ion pairing within IEMs, highlighting its potential even when undetected in aqueous solution experiments. This work advances the theoretical understanding of counterion speciation in IEMs while identifying model limitations that suggest avenues for refinement, such as distinguishing water-mediated ion pairs between fully hydrated ions.

Ion exchange membranes↗
DOE OSTI2020

Mechanisms of Al3+ dimerization in alkaline solutions

The molecular speciation of aluminum (Al3+) in alkaline solutions is fundamental to its precipitation chemistry within a number of industrial applications that include ore renement and industrial processing of Al wastes. Under these conditions, Al3+ is predominantly Al(OH) {4 , while at high [Al] dimeric species also known to form. To date, the mechanism of dimer formation remains unclear and it is likely infuenced by complex ion ion interactions. In the present work, we investigate the role of ion pairing and a suite of potential dimerization pathways using a three-pronged approach that consists of density functional theory-based molecular dynamics (DFTMD), static DFT calculations (sDFT) and semi-empirical density functional tight binding molecular dynamics (SEMD). Specic cation eects imparted by the background electrolyte cations Na+, Li+ and K+ have been examined. Our simulations predict that when the Al species are ion paired with either cation the formation of the oxo-bridged Al2O(OH) 2{6 is favored with respect to the dihydroxo-bridged Al2(OH) 2{8 , in agreement with previousspectroscopic work. The formation of both dimers rst proceeds by bridging of two monomeric units via one hydroxo ligand, leading to a labile Al2(OH) 2{8 isomer. The eect of contact ion pairing of Li+ and K+ on the dimerization energetics is distinctly more favorable than that of Na+, which may have an impact on further ligomerization.

Pouvreau, Maxime↗
DOE OSTI2022

Machine Learning Models for Binary Molecular Classification using VUV Absorption Spectra

Machine learning methods were combined with differential absorption spectroscopy measurements in the vacuum-ultraviolet region (5.167 – 9.920 eV) in order to develop predictive capabilities for inferring molecular structure from the spectra. Several types of species were analyzed and, for modeling purposes, were defined using a single classification: (1) alkane, (2) conjugation with oxygen (e.g. diacetyl, ethyl vinyl ether), (3) non-conjugated alkene (e.g. 1-butene, 1,4-cyclohexadiene), (4) oxygen-containing (e.g. 1-butanol, tetrahydrofuran), or (5) cyclic (e.g. cyclopentane, cyclohexanone). The latter molecular classification excluded cyclic ethers. Several modeling methods were employed in the analysis of 102 absorption spectra, 24 of which were measured for the first time. The primary objective was to identify suitable methods that enable accurate predictions of molecular structure classifications with minimized statistical uncertainties. Rather than identifying a single, unifying method to reliably predict molecular structure contributions to VUV absorption spectra, coordination is required among a particular method, the type of molecular structure detail (e.g. conjugation), and absorption region of interest. The latter is accomplished using a binning approach, wherein absorption regions of ~0.5 eV were utilized rather than the entire ~4.8 eV range. Photon energy binning enabled analysis of region-specific predictions of accuracy, precision, and recall. The outcome from the binning approach is that, rather than utilizing the entire spectrum, optimal determination of molecular structure using machine learning methods depends on the absorption region. Furthermore, the present work provides separate machine learning models for each molecular classification, which enables the identification of multi-functional species relevant to atmospheric chemistry and combustion chemistry, where isomer-resolved speciation is critical to understanding complex reaction networks.

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

Direct Transformation of SiH 4 to a Molecular L(H) 2 Co=Si=Co(H) 2 L Silicide Complex

The synthesis of bimetallic molecular silicide complexes is reported, based on the use of multiple Si–H bond activations in SiH 4 at the metal centers of 14-electron LCo I fragments (L = Tp", HB(3,5-diisopropylpyrazolyl) 3 – ; [BP 2 tBu Pz], PhB(CH 2 P t Bu 2 ) 2 (pyrazolyl)). Upon exposure of (Tp"Co) 2 (μ-N 2 ) (1) to SiH 4 , a mixture of (Tp"Co) 2 (μ-H) (2) and (Tp"Co) 2 (μ-H) 2 (3) was formed and no evidence for Si–H oxidative addition products was observed. In contrast, [BP 2 tBu Pz]-supported Co complexes led to Si–H oxidative additions with the generation of silylene and silicide complexes as products. Notably, the reaction of ([BP 2 tBu Pz]Co) 2 (μ-N 2 ) (5) with SiH 4 gave the dicobalt silicide complex [BP 2 tBu Pz](H) 2 Co=Si=Co(H) 2 [BP 2 tBu Pz] (8) in high yield, representing the first direct route to a symmetrical bimetallic silicide. Here, the effect of the [BP 2 tBu Pz] ligand on Co–Si bonding in 7 and 8 was explored by analysis of solid-state molecular structures and density functional theory (DFT) investigations. Upon exposure to CO or DMAP (DMAP = 4-dimethylaminopyridine), 8 converted to the corresponding [BP 2 tBu Pz]Co(L) x adducts (L = CO, x = 2; L = DMAP, x = 1) with concomitant loss of SiH 4 , despite the lack of significant Si–H interactions in the starting complex. On heating to 60 °C, 8 underwent reaction with MeCl to produce small quantities of Me x SiH 4–x (x = 1–3), demonstrating functionalization of the μ-silicon atom in a molecular silicide to form organosilanes.

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

Atoms to fibers: Identifying novel processing methods in the synthesis of pitch-based carbon fibers

Understanding and optimizing the key mechanisms used in the synthesis of pitch-based carbon fibers (CFs) are challenging, because unlike polyacrylonitrile-based CFs, the feedstock for pitch-based CFs is chemically hetero- geneous, resulting in complex fabrication leading to inconsistency in the final properties. In this work, we use molecular dynamics simulations to explore the processing and chemical phase space through a framework of CF models to identify their effects on elastic performance. The results are in excellent agreement with experiments. We find that density, followed by alignment, and functionality of the molecular constituents dictate the CF mechanical properties more strongly than their size and shape. Last, we propose a previously unexplored fabrication route for high-modulus CFs. Unlike graphitization, this results in increased sp 3 fraction, achieved via generating high-density CFs. In addition, the high sp 3 fraction leads to the fabrication of CFs with isometric compressive and tensile moduli, enabling their potential applications for compressive loading.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Bridging the Void: Halogen Bonding and Aromatic Interactions to Program Luminescence and Electronic Properties of π -Conjugated Materials in the Solid State

π-Conjugated materials are promising candidates for emerging organic optoelectronic devices empowered by molecular design. The unsolved challenges of predicting and controlling their packing as solids, central to their properties and performance, currently limits their practical application. As noncovalent interactions drive packing, control over such interactions are critical to bridging from chemical structure to functional properties. In molecular crystals, halogen bonding and interactions of aromatic rings have emerged as versatile tools for noncovalent control with tailored luminescence and electronic properties. Here, we describe how the interplay of these directional and tunable interactions can engineer properties, including stimuli-responsive behavior. Specifically, halogen bonding can provide robust designs for directing 2D molecular assembly, whereas the intentional interactions of aromatic rings can yield metastable, switchable packing modes, as well as programmed stacking between layers of chromophores. Examples, herein, demonstrate clear relationships between assembly by design and resulting solid-state properties, and strategies presented offer guidance for future designs of π-conjugated molecular materials using specific aromatic interactions and halogen bonding.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Prediction of hydration energies of adsorbates at Pt(111) and liquid water interfaces using machine learning

Aqueous phase heterogeneous catalysis is important to various industrial processes, including biomass conversion, Fischer–Tropsch synthesis, and electrocatalysis. Accurate calculation of solvation thermodynamic properties is essential for modeling the performance of catalysts for these processes. Explicit solvation methods employing multiscale modeling, e.g., involving density functional theory and molecular dynamics have emerged for this purpose. Although accurate, these methods are computationally intensive. This study introduces machine learning (ML) models to predict solvation thermodynamics for adsorbates on a Pt(111) surface, aiming to enhance computational efficiency without compromising accuracy. In particular, ML models are developed using a combination of molecular descriptors and fingerprints and trained on previously published water–adsorbate interaction energies, energies of solvation, and free energies of solvation of adsorbates bound to Pt(111). These models achieve root mean square error values of 0.09 eV for interaction energies, 0.04 eV for energies of solvation, and 0.06 eV for free energies of solvation, demonstrating accuracy within the standard error of multiscale modeling. Feature importance analysis reveals that hydrogen bonding, van der Waals interactions, and solvent density, together with the properties of the adsorbate, are critical factors influencing solvation thermodynamics. Furthermore, these findings suggest that ML models can provide rapid and reliable predictions of solvation properties. This approach not only reduces computational costs but also offers insights into the solvation characteristics of adsorbates at Pt(111)–water interfaces.

Adsorption↗
DOE OSTI2020

A 3D nm-thin biomimetic membrane for ultimate molecular separation

Multi-functional membranes with high permeance and selectivity that can mimic nature's designs have tremendous industrial and bio-medical applications. In this paper, we report a novel concept of a 3D nanometer (nm)-thin membrane that can overcome the shortcomings of conventional membrane structures. Our 3D membrane is composed of two three-dimensionally interwoven channels that are separated by a continuous nm-thin amorphous TiO 2 layer. This 3D architecture dramatically increases the surface area by 6000 times, coupled with an ultra-short diffusion distance through the 2–4 nm-thin selective layer that allows for ultrafast gas and water transport, ~900 l m –2 h –1 bar –1 . The 3D membrane also exhibits a very high ion rejection (R ~ 100% for potassium ferricyanide) due to the combined size- and charge-based exclusion mechanisms. The combination of high ion rejection and ultrafast permeation makes our 3DM superior to the state-of-the-art high-flux membranes whose performances are limited by the flux-rejection tradeoff. Furthermore, its ultimate Li+ selectivity over polysulfide or gas can potentially solve major technical challenges in energy storage applications, such as lithium–sulfur or lithium–O 2 batteries.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular mechanisms of metabotropic GABA B receptor function

Metabotropic γ-aminobutyric acid G protein–coupled receptors (GABA B ) represent one of the two main types of inhibitory neurotransmitter receptors in the brain. These receptors act both pre- and postsynaptically by modulating the transmission of neuronal signals and are involved in a range of neurological diseases, from alcohol addiction to epilepsy. A series of recent cryo-EM studies revealed critical details of the activation mechanism of GABA B . Structures are now available for the receptor bound to ligands with different modes of action, including antagonists, agonists, and positive allosteric modulators, and captured in different conformational states from the inactive apo to the fully active state bound to a G protein. These discoveries provide comprehensive insights into the activation of the GABA B receptor, which not only broaden our understanding of its structure, pharmacology, and physiological effects but also will ultimately facilitate the discovery of new therapeutic drugs and neuromodulators.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1979

Finite-field Calculations of Molecular Polarizabilities Using Field-Induced Polarization Functions: Second- and Third-order Perturbation Correlation Corrections to the Coupled Hartree-Fock Polarizability of H2O

Ordinary Rayleigh-Schroudinger perturbation theory with Moller-Plesset (RSMP) partitioning is used to calculate second- and third-order correlation corrections to the CHF polarizability and dipole moment of the water molecule by a finite-field procedure. Pade approximants are found to be useful in accelerating the convergence of the property perturbation expansions. Field-induced polarization functions suitable for polarizability calculations are determined. The average polarizability calculated, neglecting vibrational averaging, with Dunning's (9s5p/4s-4s2p/2s) contracted GTO basis set augmented by field-induced lslp2d/lp polarization functions is within 3 per cent of the experimental result. Correlation corrections to the dipole moment and polarizability of the water molecule calculated by the finite-field RSMP and single + double excitation CI(SDCI) methods for the same basis set are found to be in close agreement. The RSMP approach has the advantages of being size-consistent and of being capable of greater efficiency than the SCDI method. Comparative calculations carried out using Epstein-Nesbet partitioning show that through third order RSEN correlation perturbation expansions for the dipole moment and polarizability are less rapidly convergent than RSMP expansions. However, reasonable accord with RSMP results can be achieved by using Pade approximants to accelerate the convergence of RSEN energy perturbation expansions. The convergence of RSMP property correlation expansions based on the zeroth-order uncoupled-Hartree-Fock (UCHF) and coupled-Hartree-Fock (CHF) approximations are compared through third order. Whereas the CHF + RSMP expansions are for practical purposes fully converged, the UCHF + RSMP expansions are not adequately converged.

Langhoff, S. R.↗