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At least 775 records · Page 43

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NASA NTRS1999

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Timofeeva, Tatiana V.↗

NASA NTRS2010

The Earliest Ion Channels in Protocellular Membranes

Cellular membranes with their hydrophobic interior are virtually impermeable to ions. Bulk of ion transport through them is enabled through ion channels. Ion channels of contemporary cells are complex protein molecules which span the membrane creating a cylindrical pore filled with water. Protocells, which are widely regarded as precursors to modern cells, had similarly impermeable membranes, but the set of proteins in their disposal was much simpler and more limited. We have been, therefore, exploring an idea that the first ion channels in protocellular membranes were formed by much smaller peptide molecules that could spontaneously selfassemble into short-lived cylindrical bundles in a membrane. Earlier studies have shown that a group of peptides known as peptaibols is capable of forming ion channels in lipid bilayers when they are exposed to an electric field. Peptaibols are small, non-genetically encoded peptides produced by some fungi as a part of their system of defense against bacteria. They are usually only 14-20 residues long, which is just enough to span the membrane. Their sequence is characterized by the presence of non-standard amino acids which, interestingly, are also expected to have existed on the early earth. In particular, the presence of 2-aminoisobutyric acid (AIB) gives peptaibols strong helix forming propensities. Association of the helices inside membranes leads to the formation of cylindrical bundles, typically containing 4 to 10 monomers. Although peptaibols are excellent candidates for models of the earliest ion channels their structures, which are stabilized only by van der Waals forces and occasional hydrogen bonds between neighboring helices, are not very stable. Although it might properly reflect protobiological reality, it is also a major obstacle in studying channel behavior. For this reason we focused on two members of the peptaibol family, trichotoxin and antiamoebin, which are characterized by a single conductance level. This indicates that their structures are unique and stable. In addition, it is also believed that the trichotoxin channel displays some selectivity between potassium and chloride ions. This makes trichotoxin and antiamoebin ideal models of the earliest ion channels that could provide insight into the origins of ion conductance and selectivity. In the absence of crystal structure of the trichotoxin and antiamoebin channels, we propose their molecular models based on experimentally determined number of monomers forming the bundles. We use molecular dynamics simulations to validate the models in terms of their conductance and selectivity. On the basis of our simulations we show that the emergence of channels built of small, alpha-helical peptides was protobiologically plausible and did not require highly specific amino acid sequences, which is a convenient evolutionary trait. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. To this end, we will discuss how the amino acid sequence and structure of primitive channels give rise to the phenomena of ionic conductance and selectivity across the earliest cell walls, which were essential functions for the emergence and early evolution of protocells. Furthermore, we will argue that even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

Mijajlovic, Milan↗

DOE OSTI2022

Ion Transport in 2D Nanostructured $\pi$-Conjugated Thieno[3,2- b ]thiophene-Based Liquid Crystal

Leveraging the self-assembling behavior of liquid crystals designed for controlling ion transport is of both fundamental and technological significance. Here, we have designed and prepared a liquid crystal that contains (2,5-bis(5-(2,5,8,11-tetraoxatridecan-13-yl)thiophen-2yl)thieno[3,2-b]thiophene (BTTT) as mesogenic core and conjugated segment and symmetric tetra(ethylene oxide) (EO4) as polar side chains for ionic conducting regions. Driven by the crystallization of the BTTT cores, BTTT/dEO4 exhibits well-ordered smectic phases below 71.5 °C as confirmed by differential scanning calorimetry, polarized optical microscope, temperature dependent wide-angle X-ray scattering and grazing incidence wide-angle X-ray scattering (GIWAXS). We adopted a combination of experimental GIWAXS and molecular dynamics (MD) simulations to better understand the molecular packing of BTTT/dEO4 films, particularly when loaded with the ion conducting salt, lithium bis(trifluoromethanesulfonyl)imide (LiTFSI). Ionic conduction of BTTT/dEO4 is realized by the addition of LiTFSI, with the material able to maintain smectic phases up to r = [Li + ]/[EO] = 0.1. In this work, The highest ionic conductivity of 8 × 10 -3 S/cm was attained at an intermedium salt concentration of r = 0.05. It was also found that ion conduction in BTTT/dEO4 is enhanced by forming a smectic layered structure with irregular interfaces between the BTTT and EO4 layers and by the lateral film expansion upon salt addition. This can be explained by the enhancement of the misalignment and configurational entropy of the side chains, which increase their local mobility and that of the solvated ions. Our molecular design thus illustrates how, beyond the favorable energetic interactions that drive the assembly and ion solvating domains, modulation of entropic effects can also be favorably harnessed to improve ion conduction.

thin film electrochemical impedance spectroscopy↗

DOE OSTI2023

Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2 O 2 Activation

Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped “His-brace” configuration including the N-terminal histidine and its amine group as ligands. Here, this study explicitly investigates the electronic structure of the d 10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H 2 O 2 O–O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Designing Sequence-Defined Peptoids for Biomimetic Control over Inorganic Crystallization

Crystallization defines what the world is all about, ranging from biomineralization in living organisms to various materials in our lives. During these processes, biomineralization set a superexcellent example of the additive-controlled crystallization. However, the high complexity and low stability of peptides and proteins preclude their wide applications in controlling inorganic crystallization beyond the biological systems. Peptoids are one type of sequence-defined biomimetic polymers with a simple structure, high stability, protein-like molecular recognition, and distinctive self-assembly properties. They provide a promising alternative to mimic peptides and proteins for controlling inorganic crystallization and extend its application to predictive materials synthesis. In this review article, we extract the main concepts of peptoid engineering and highlight the recent advances in peptoid-controlled inorganic crystallization. Our focus is to understand the principles of sequence engineering that lead to the predictable physiochemical properties of these substances, which will give insights into other inorganic systems.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Molecular Structure of Copper and μ-Oxodiiron Octafluorocorrole Derivatives: Insights into Ligand Noninnocence

Single-crystal X-ray structures were obtained for the copper and μ-oxodiiron complexes of 2,3,7,8,12,13,17,18-octafluoro-5,10,15-triphenylcorrole, hereafter denoted as Cu[F 8 TPC] and {Fe[F 8 TPC]} 2 O. A comparison with the crystal structures of other undecasubstituted Cu corroles, including those with H, Ar, Br, I, and CF 3 as β-substituents, showed that the degree of saddling increases in the order: H ≲ F < Ar ≲ Br ≲ I < CF 3 . In other words, Cu[F 8 TPC] is marginally more saddled than β-unsubstituted Cu triarylcorroles, but substantially less saddled than Cu undecaarylcorroles, β-octabromo-meso-triarylcorroles, and β-octaiodo-meso-triarylcorroles, and far less saddled than Cu β-octakis(trifluoromethyl)-meso-triarylcorroles. As for {Fe[F 8 TPC]} 2 O, the moderate quality of the structure did not allow us to draw firm conclusions in regard to bond length alternations in the corrole skeleton and hence also the question of ligand noninnocence. The Fe-O bond distances, 1.712(8) and 1.724(8), however, are essentially identical to those observed for {Fe[TPFPC]} 2 O, where TPFPC 3- is the trianion of 5,10,15-tris(pentafluorophenyl)corrole, suggesting that a partially noninnocent electronic structural description may be applicable for both compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Materials Data on H7AuN4O15 by Materials Project

Au(NO3)4H5O2H2O crystallizes in the monoclinic C2/c space group. The structure is zero-dimensional and consists of four chebi:30328 molecules, four molecular hydrogen;dihydrate molecules, and four water molecules.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Cage Molecules Stabilize Lead Halide Perovskite Thin Films

The environmental stability of hybrid organic-inorganic perovskite (HOIP) materials needs to increase to enable their widespread adoption in thin-film solar and optoelectronic devices. Molecular additives have recently emerged as an effective strategy for regulating HOIP crystal growth and passivating defects. However, to date the choice of additives is largely limited to a dozen or so materials under the design philosophy that high crystallinity is a prerequisite for stable HOIP thin films. Here, in this study, we incorporate porous organic cages (POCs) as functional additives into perovskite thin films for the first time and investigate the HOIP-POC interaction via a combined experimental and computational approach. POCs are significantly larger than the small-molecule additives explored for HOIP synthesis to date but much smaller than polymeric sealants. Partially amorphized composites of MAPbI 3 (methylammonium lead iodide, HOIP) and RCC3 (an amine POC) form a network-like surface topography and lead to an increase in the optical bandgap from 1.60 to 1.63 eV. Further in situ optical imaging suggests that RCC3 can delay the MAPbI 3 film degradation onset up to 50x under heat and humidity stresses, showing promise for improving reliability in HOIP-based solar-cell and light-emitting applications. Furthermore, there is evidence of molecular interactions between RCC3 and MAPbI 3 , as fingerprinted by the suppressed N-H stretching mode in MA + from Fourier transform infrared (FTIR) spectra and density functional theory (DFT) simulations that suggest strong hydrogen bonding between MA + and RCC3. Given the diversity of POCs and HOIPs, our work opens a new avenue to stabilize HOIPs via tailored molecular interactions with functional organic materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Exploring poly-crystallization in semiconductors through assumption-less growth simulations: CdTe/CdS case study

Crystal growth is a complex process with far-reaching implications for high-performance materials across various fields. Recent advancements in structural analysis methods such as polyhedral template matching, which allows semiconductor-specific analysis, coupled with simulation technology, have enabled the comprehensive study of crystallization dynamics in semiconductors. However, the exploration of polycrystalline semiconductors created with minimal external intervention of the crystallization processes is relatively uncharted in comparison with metals. In this study, we employ molecular dynamics to simulate the growth of polycrystalline CdTe/CdS with the assumptions of classical mechanics, a Stillinger–Weber potential, an amorphous substrate, and common vapor growth conditions to allow the polycrystalline structures to evolve naturally. Post-simulation, we identify and analyze impactful structures and events, comparing them to theory and experiment to gain insight into various modes of crystallization dynamics. Two research questions guided the study: (1) How realistic are assumption-less simulated polycrystalline semiconductor structures? (2) To what extent can the approach provide insight into crystallization? The simulations, performed with minimal external control, yield polycrystalline structures mirroring experimental findings. The analysis reveals key crystallization insights, such as the role of amorphous atoms in the transition from nucleation to grain growth and the transformative impact of single events, such as dislocations, on crystallization dynamics. The method paves the way for reproducing and analyzing realistic polycrystalline semiconductor structures with minimal simulation assumptions across various growth modes.

Abdullah, Sharmin↗

DOE OSTI2021

Investigating the magnetic and atomic interface configuration for a model Fe/CrN bilayer system

A bilayer of iron on chromium nitride (Fe/CrN) is an interesting system for exchange biasing and sensing applications as the Néel temperature of CrN is 280 K and the Curie temperature of Fe is 1043 K. In this paper, we study the crystal and magnetic structures of the Fe/CrN interface at the atomic level. High quality epitaxial Fe/CrN bilayers prepared by molecular beam epitaxy grow in 001 orientation on MgO(001) substrates with uniform layer thicknesses and sharp interfaces. Our data reveal the epitaxial correlation between Fe and CrN crystals and their magnetic structures at the interface. The magnetic anisotropy directions of Fe and CrN are found parallel to [110] MgO . We studied the electronic and magnetic properties of the interface by performing the first-principles total-energy calculations. Here, we present a model that combines the crystal and magnetic structures of the Fe/CrN bilayer and fully explains all results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Molecular Mechanisms of Sorbed Ion Effects during Boehmite Particle Aggregation

Classical theories of particle aggregation, such as Derjaguin–Landau–Verwey–Overbeek (DLVO), do not explain recent observations of ion-specific effects or the complex concentration dependence for aggregation. Thus, here, we probe the molecular mechanisms by which selected alkali nitrate ions (Na + , K + , and NO 3 –) influence aggregation of the mineral boehmite (γ-AlOOH) nanoparticles. Nanoparticle aggregation was analyzed using classical molecular dynamics (CMD) simulations coupled with the metadynamics rare event approach for stoichiometric surface terminations of two boehmite crystal faces. Calculated free energy landscapes reveal how electrolyte ions alter aggregation on different crystal faces relative to pure water. Consistent with experimental observations, we find that adding an electrolyte significantly reduces the energy barrier for particle aggregation (~3–4×). However, in this work, we show this is due to the ions disrupting interstitial water networks, and that aggregation between stoichiometric (010) basal–basal surfaces is more favorable than between (001) edge–edge surfaces (~5–6×) due to the higher interfacial water densities on edge surfaces. The interfacial distances in the interlayer between aggregated particles with electrolytes (~5–10 Å) are larger than those in pure water (a few Ångströms). Together, aggregation/disaggregation in salt solutions is predicted to be more reversible due to these lower energy barriers, but there is uncertainty on the magnitudes of the energies that lead to aggregation at the molecular scale. By analyzing the peak water densities of the first monolayer of interstitial water as a proxy for solvent ordering, we find that the extent of solvent ordering likely determines the structures of aggregated states as well as the energy barriers to move between them. Further, the results suggest a path for developing a molecular-level basis to predict the synergies between ions and crystal faces that facilitate aggregation under given solution conditions. Such fundamental understanding could be applied extensively to the aggregation and precipitation utilization in the biological, pharmaceutical, materials design, environmental remediation, and geological regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Synthetic active liquid crystals powered by acoustic waves.

Active nematic materials combine orientational order with activity at the microscopic level. Current experimental realizations of active nematics include vibrating elongated particles, cell layers, suspensions of elongated bacteria, and a mixture of bio-filaments with molecular motors. The majority of active nematics are of biological origin. The realization of a fully synthetic active liquid crystal comprised of a lyotropic chromonic liquid crystal energized by ultrasonic waves, is reported. This synthetic active liquid crystal is free from biological degradation and variability, exhibits phenomenology associated with active nematics, and enables precise and rapid activity control over a significantly extended range. It is demonstrated that the energy of the acoustic field is converted into microscopic extensile stresses disrupting long-range nematic order and giving rise to an undulation instability and proliferation of topological defects. The emergence of unconventional free-standing persistent vortices in the nematic director field at high activity levels is revealed. The results provide a foundation for the design of externally energized active liquid crystals with stable material properties and tunable topological defect dynamics crucial for the realization of reconfigurable microfluidic systems.

active matter↗

NASA NTRS1991

Crystal-field-driven redox reactions: How common minerals split H2O and CO2 into reduced H2 and C plus oxygen

It is difficult to prove the presence of molecular H2 and reduced C in minerals containing dissolved H2 and CO2. A technique was developed which unambiguously shows that minerals grown in viciously reducing environments contain peroxy in their crystal structures. The peroxy represent interstitial oxygen atoms left behind when the solute H2O and/or CO2 split off H2 and C as a result of internal redox reactions, driven by the crystal field. The observation of peroxy affirms the presence of H2 and reduced C. It shows that the solid state is indeed an unusual reaction medium.

Freund, F.↗

DOE OSTI2020

Structural disorder, sublattice melting, and thermo-elastic properties of anti-perovskite Li 3 OBr under high pressure and temperature

Here, in situ synchrotron x-ray diffraction experiments were conducted in the system Li-O-Br at pressures up to 6.5 GPa and temperatures up to the melting points. The thermal equation of state determined from the P–V–T measurements indicates that crystalline anti-perovskite Li 3 OBr exhibits similar thermo-elastic properties to common salts. At temperatures that are 50–75 °C below the crystal melting, a pre-melting behavior was inferred based on weakened Bragg intensity and a substantial increase in the diffuse scattering. Concurrent with the onset of pre-melting, an anomalous increase in the lattice volume was observed and is interpreted as anion sublattice disorder. These findings support previous ab initio molecular dynamics simulations based on a simple anion interchange mechanism, indicating that structural disorder below crystal melting temperature can be a main driving force for Li-sublattice melting and superionic transition in the Li 3 OBr anti-perovskite.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Singlet Fission in Thin Solid Films of Bis(thienyl)diketopyrrolopyrroles

The singlet fission (SF) process discovered in bis(thienyl)diketopyrrolopyrroles (TDPPs) can boost their potential for photovoltaics (PV). The crystal structures of TDPP analogs carrying n-hexyl, n-butyl, or 2-(adamant-1-yl)ethyl substituents are similar, but contain increasingly slipped stacked neighbor molecules. The observed SF rate constants, k SF , (7±4), (9±3) and (5.6±1.9) ns –1 for thin films of the three compounds, respectively, are roughly equal, but the triplet quantum yields vary strongly: (120±40), (160±40) and (70±16), respectively. The recent molecular pair model reproduces the near equality of all three k SF at the crystal geometries and identifies all possible pair arrangements in which SF is predicted to be faster, by up to two orders of magnitude. Furthermore, it is also clear that the presently non-existent ability to predict the rates of processes competing with SF is pivotal for providing a guide for efforts to optimize the materials for PV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2002

Study of Fluid Flow Control In Protein Crystallization Using Strong Magnetic Fields

Ramachandran, N.↗

NASA NTRS2002

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Ramachandran, Narayanan↗

NASA NTRS1991

Rheological properties of ammonia-water liquids and crystal-liquid slurries - Planetological applications

The laboratory-measured viscosities of liquid mixtures representative of the variety of cryovolcanic substances of the icy satellites are presently noted to be much greater than could be expected on the assumption that end-member molecules are noninteractive; this observation is supported by others concerning molar volumes and vapor pressure relations, which indicate the presence of strong molecular-interaction forces that fundamentally affect the mixtures' physical properties. Since the rheological effects of partial crystallization parallel the characteristics of silicate lavas, icy satellite cryovolcanic morphologies are similarly interpretable with allowances for differences in surface gravities and lava densities.

Kargel, J. S.↗