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Results for “molecular functionalization”

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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electric field sensitivity of molecular color centers

Molecular color centers with S=1 ground states are promising candidates for quantum sensing of electric fields. These molecules have an electronic structure similar to solid state color centers, but they allow for processing modalities that permit direct interfacing with an analyte. Currently, it is unknown how sensitive these molecules are to electric fields and what molecular properties affect their sensitivity. We perform density functional theory calculations to understand the impact of electric fields on the electronic structure of five nominally tetrahedral molecular color centers exhibiting variable transition metal chemistry and ligand densities. We then extract the Stark parameters from each of these molecules and compare them to molecular properties such as the dipole moment and inner shell stiffness and find that the dipole moment of the molecule largely governs sensitivity. We predict that polar heteroleptic molecules may have electric field sensitivities comparable to solid state color centers such as nitrogen-vacancy centers in diamond.

Physics↗
DOE OSTI2020

Accelerated epigenetic aging as a risk factor for chronic obstructive pulmonary disease and decreased lung function in two prospective cohort studies

Chronic obstructive pulmonary disease (COPD) is a frequent diagnosis in older individuals and contributor to global morbidity and mortality. Given the link between lung disease and aging, we need to understand how molecular indicators of aging relate to lung function and disease. Using data from the population-based KORA (Cooperative Health Research in the Region of Augsburg) surveys, we associated baseline epigenetic (DNA methylation) age acceleration with incident COPD and lung function. Models were adjusted for age, sex, smoking, height, weight, and baseline lung disease as appropriate. Associations were replicated in the Normative Aging Study. Of 770 KORA participants, 131 developed incident COPD over 7 years. Baseline accelerated epigenetic aging was significantly associated with incident COPD. The change in age acceleration (follow-up – baseline) was more strongly associated with COPD than baseline aging alone. The association between the change in age acceleration between baseline and follow-up and incident COPD replicated in the Normative Aging Study. Associations with spirometric lung function parameters were weaker than those with COPD, but a meta-analysis of both cohorts provide suggestive evidence of associations. Accelerated epigenetic aging, both baseline measures and changes over time, may be a risk factor for COPD and reduced lung function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Modeling the aqueous interface of amorphous TiO 2 using deep potential molecular dynamics

Amorphous titanium dioxide (a-TiO 2 ) is widely used as a coating material in applications such as electrochemistry and self-cleaning surfaces where its interface with water has a central role. However, little is known about the structures of the a-TiO 2 surface and aqueous interface, particularly at the microscopic level. In this work, we construct a model of the a-TiO 2 surface via a cut-melt-and-quench procedure based on molecular dynamics simulations with deep neural network potentials (DPs) trained on density functional theory data. After interfacing the a-TiO 2 surface with water, we investigate the structure and dynamics of the resulting system using a combination of DP-based molecular dynamics (DPMD) and ab initio molecular dynamics (AIMD) simulations. Both AIMD and DPMD simulations reveal that the distribution of water on the a-TiO 2 surface lacks distinct layers normally found at the aqueous interface of crystalline TiO 2 , leading to an ~10 times faster diffusion of water at the interface. Bridging hydroxyls (Ti 2 –O b H) resulting from water dissociation decay several times more slowly than terminal hydroxyls (Ti–O w H) due to fast Ti–O w H 2 → Ti–O w H proton exchange events. These results provide a basis for a detailed understanding of the properties of a-TiO 2 in electrochemical environments. Moreover, the procedure of generating the a-TiO 2 -interface employed here is generally applicable to studying the aqueous interfaces of amorphous metal oxides.

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

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes

The metal centers in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.

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

Atomically Precise Membranes for the Separation of Gases

Industrial separations require enormous amounts of energy, accounting for approximately half the industrial energy use and 10–15% of the total energy consumption. Distillation alone accounts for about half the energy demand for industrial separations. If these processes could be replaced by an energy-efficient membrane separation process, this energy demand could be reduced by 90%. However, although some membrane processes have made inroads into thermal distillation, for membrane-based separations to replace the distillation process to a far more significant and practical level, new membranes with higher robustness, selectivity, and flux still need be developed. In this membrane development program, we leveraged Temple University’s prior work in spiroligomers to develop robust membrane structures. These structures can be formed into atomically precise pores by controlling the chemical synthesis and the oligomer building blocks to first build precisely controlled macrocycles and then subsequently crosslinking these macrocycles to produce a membrane. Furthermore, through the highly controllable chemistry of our molecular building blocks, not only can we integrate pores with highly controllable and reproducible size and morphology, but we can also target internal functionalization. By using a range of scalable membrane synthesis approaches, combined with control of each and every pores internal chemistry and molecular conformation we can achieve membrane structures that can display the ultimate in high selectivity and permeance. The Mainstream-Temple University membranes can be designed to achieve ultra-selective separations based on the key factors of molecular size, shape, and functionality. In our approach to fabricate scalable atomically precise membranes, we used our molecular Lego nanostructures. We demonstrated an approach to create atomically precise pores within the membrane with pores that are the dimensions of the molecule we are trying to separate. Moreover, in addition to controlling the morphology of the membrane structure by controlling the size of every pore, we can also decorate every pore with precisely targeted and placed functional groups. These accurately placed functional groups can provide selective binding to molecules and provide enhanced selectivity via a facilitated transport mechanism. In Phase II, the Mainstream-Temple University team demonstrated the scalable synthesis of oligomers and the ability to control the pore internal and external functionality, or chemistry, to allow the fabrication of a thin-film membrane. The initial steps of the spiroligomer synthesis to produce the two key bis-amino enantiomer building blocks were scaled from the gram scale to the kilogram scale, obtaining 25 kg of the materials by transferring the procedure to a toll manufacturer. Finally, we successfully optimized the fabrication of these macrocycles into robust membranes. We successfully transitioned from a laboratory based, hard-to-scale Langmuir trough synthesis to a highly scalable, roll-to-roll applicable, interfacial polymerization process. During this Phase II program, we established a platform of atomically precise membranes where our highly controllable, atomically precise macrocycles served as a scaffold with precisely and uniformly controlled pores. Furthermore, this layer can be tailored to accommodate a diverse range of functional groups, which both further controlled the pore size to enhance the sieving effect as well as imparting precisely controlled targeted selectivity through biomimetic molecular interactions. In this Phase II, we established and scaled up a platform approach to both tune the pore size and chemistry as well as scale it to produce membranes that can be applied to a wide range of industries. In future development, the project team expects to scale up both the macrocycle building block production and interfacial polymerization process to produce the atomically precise membrane with targeted pore sizes and pore chemistries.

36 MATERIALS SCIENCE↗
DOE OSTI2023

DFT (and DMFT) for DFT users

The interesting properties of f -electron systems comes from a simultaneous existence of free and discrete level electrons. The challenge we have is to describe free electrons and discrete level electrons equally well in a unified picture. The ELF index can be used to find regions in real space where discrete level physics needs to be taken into account. We have identified the HO gas as a model system that can be used to gain insight about this kind of physics. We will use the HO gas model system for creating a functional suitable for these systems via the subsystem functional scheme. With a predictive capability for the rare earths and lanthindes, we can identify new materials with new/improved properties. This is crucial for, e.g., developing material and technology substitutes for addressing the challenges associated with the use of rare earth elements and other critical materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Commensurate states and pattern switching via liquid crystal skyrmions trapped in a square lattice

Using continuum based simulations we show that a rich variety of skyrmion liquid crystal states can be realized in the presence of a periodic obstacle array. As a function of the number of skyrmions per obstacle we find hexagonal, square, dimer, trimer and quadrimer ordering, where the n-mer structures are a realization of a molecular crystal state of skyrmions. As a function of external field and obstacle radius we show that there are transitions between the different crystalline states as well as mixed and disordered structures. Here, we discuss how these states are related to commensurate effects seen in other systems, such as vortices in type-II superconductors and colloids interacting with two dimensional substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Selective heterogeneous capture and release of actinides using carborane-functionalized electrodes

Here we report the heterogenization of molecular, electrochemically switchable ortho-substituted carboranes ( PO Cb, PO Cb-Pyr) for selective metal capture. Films of PO Cb and PO Cb-Pyr on glassy carbon and carbon fiber (CF) electrodes demonstrated heterogeneous electrochemical behaviour that was enhanced by the inclusion of single-walled carbon nanotubes (CNTs). Galvanostatically charged CF|CNT| PO Cb and CF|CNT| PO Cb-Pyr electrodes selectively captured and released actinides (Th 4+ , UO 2 2+ ) from mixed solutions containing alkali (Cs + ), lanthanide (Nd 3+ , Sm 3+ ) and actinide (Th 4+ , UO 2 2+ ) metal ions.

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

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A strain density function to analyze particle size effects during high velocity impacts of yttria

Here, the impact behavior of a single yttria (Y 2 O 3 ) nanoparticle onto a Y 2 O 3 substrate is studied as a function of particle velocity (300–1200 m/s) and diameter (12–50 nm) using molecular dynamics simulations. To analyze the results, a strain density function is developed to provide both quantitative and qualitative information about the deformation mechanisms that contribute to the final state of the system. This function provides both clear evidence of shear localization and insight into the conditions for which localization occurs during the impact of Y 2 O 3 particles as they approach experimentally relevant sizes. Further analysis shows that localization and fragmentation only occur for Y 2 O 3 impacts with diameters of at least 50 nm, while particles with diameters of 25 nm and smaller deform primarily by amorphization and viscous flow. Implications for the deposition of films of Y 2 O 3 and other rare-earth oxides via the micro cold spray process are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Multi-reward Reinforcement Learning Based Bond-Order Potential to Study Strain-Assisted Phase Transitions in Phosphorene

Here, we introduce a multi-reward reinforcement learning (RL) approach to train a flexible bond-order potential (BOP) for 2D phosphorene based on ab initio training data sets. Our approach is based on a continuous action space Monte Carlo tree search algorithm that is general and scalable and presents an efficient multiobjective optimization scheme for high-dimensional materials design problems. As a proof-of-concept, we deploy this scheme to parametrize multiple structural and dynamical properties of 2D phosphorene polymorphs. Our RL-trained BOP model adequately captures the structure, energetics, transformation barriers, equation of state, elastic constants, and phonon dispersions of various 2D P polymorphs. We use this model to probe the impact of temperature and strain rate on the phase transition from black (α-P) to blue phosphorene (β-P) through molecular dynamics simulations. A decrease in critical strain for this phase transition with increase in temperature is observed, and the underlying atomistic mechanisms are discussed.

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

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Comparing the Effects of Side Chain Dipole–Dipole Interactions and Hydrogen Bonding on the Mechanical and Electrical Properties of Poly(3-hexylthiophene)

Poly(3-alkylthiophenes) are simple conjugated polymers with good electrical properties, but tend to be brittle, limiting their application. Here, we investigate how side chain modifications can improve their toughness without compromising their charge transport. Specifically, we compare a weak dipole–dipole interaction of ester groups with a stronger hydrogen-bonding interaction of the hydroxyl groups. Two copolymers with targeted 5 and 10 mol % ester-functionalized side chains were synthesized and hydrolyzed in the solid state to introduce hydroxyl groups. Both hydrolyzed polymers became insoluble in most organic solvents, providing a path to layer-by-layer solution processing. All polymers’ optical, thermal, structural, electrical, and mechanical properties were investigated. Optical spectroscopy revealed that functionalization at these low levels did not significantly affect aggregation or π–π stacking. Differential scanning calorimetry indicated reduced crystallinity in the functionalized copolymers compared to that of P3HT. Grazing-incidence wide-angle X-ray diffraction data showed that functionalization led to an increase in lamellar spacing without altering molecular orientation or π–π stacking. Mechanical testing highlighted that at the lower functionalization level, both ester and hydroxyl groups similarly enhanced toughness, suggesting that disorder, rather than the specific nature of the functional group, was responsible for these improvements. At the higher functionalization level, hydroxyl groups significantly increased the elastic modulus while also negatively impacting charge carrier mobility. This study suggests that with stronger hydrogen-bonding groups, only very small amounts can improve P3HT’s toughness. For a wider tunable range, it may be a better strategy to use weak interactions such as dipole–dipole interactions of ester groups.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Dynamical electron correlation and the chemical bond. I. Covalent bonds in AH and AF (A = B–F)

Dynamical electron correlation has a major impact on the computed values of molecular properties and the energetics of molecular processes. This study focused on the effect of dynamical electron correlation on the spectroscopic constants ($R$ e , $ω$ e , $D$ e ), and potential energy curves, Δ$E$($R$), of the covalently bound AH and AF molecules, A = B–F. The changes in the spectroscopic constants (Δ$R$ e , Δ$ω$ e , Δ$D$ e ) caused by dynamical correlation are erratic and, at times, even surprising. These changes can be understood based on the dependence of the dynamical electron correlation energies of the AH and AF molecules as a function of the bond distance, i.e., Δ$E$ DEC ($R$). At large $R$, the magnitude of Δ$E$ DEC ($R$) increases nearly exponentially with decreasing $R$, but this increase slows as $R$ continues to decrease and, in many cases, even reverses at very short $R$. The changes in Δ$E$ DEC ($R$) in the region around $R$ e were as unexpected as they were surprising, e.g., distinct minima and maxima were found in the curves of Δ$E$ DEC ($R$) for the most polar molecules. The variations in Δ$E$ DEC ($R$) for $R$ ≲ $R$ e are directly correlated with major changes in the electronic structure of the molecules as revealed by a detailed analysis of the spin-coupled generalized valence bond wave function. In conclusion, the results reported here indicate that we have much to learn about the nature of dynamical electron correlation and its effect on chemical bonds and molecular properties and processes.

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

Combining Experimental and Theoretical Techniques to Gain an Atomic Level Understanding of the Defect Binding Mechanism in Hard Carbon Anodes for Sodium Ion Batteries

Sodium ion batteries (NIBs) are an attractive alternative to lithium–ion batteries in applications that require large–scale energy storage due to sodium's high natural abundance and low cost. Hard carbon (HC) is the most promising anode material for NIBs; however, there is a knowledge gap in the understanding of the sodium binding mechanism that prevents a rational design of HC. This study tunes sucrose–derived HC via synthesis temperature then evaluates the structural, physical, and electrochemical properties. Neutron total scattering is used to generate structural models by fitting pair distribution functions (PDF) with a combination of molecular dynamics and reverse Monte Carlo methods. From this model, the number and type of structural features are identified, quantified, and correlated to the galvanostatic charge/discharge. A method of PDF “fingerprinting” binding sites using Na probe atoms is developed and analyzing these PDFs reveals an atomistic view of ion binding sites responsible for “defect” storage mechanisms. Combining these techniques results in an atomic–level study that provides a big picture of the Na–binding mechanism in NIBs, which allows for more precise tuning of the structure–property relationships in the future. Finally, the methodologies developed will also enable new strategies for the analysis of amorphous functional materials.

25 ENERGY STORAGE↗
DOE OSTI2025

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. Here, we analyze assemblies of an amphiphile (C 16 K 2 ), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

ionization↗