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DOE OSTI2015

Origin of molecular conformational stability: Perspectives from molecular orbital interactions and density functional reactivity theory

To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF{sub 6} and CF{sub 3}I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF{sub 6} molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation. (laser separation of isotopes)

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2017

Outer membrane cytochromes/flavin interactions in Shewanella spp.—A molecular perspective

Extracellular electron transfer (EET) is intrinsically associated with the core phenomena of energy harvesting/energy conversion in natural ecosystems and biotechnology applications. But, the mechanisms associated with EET are complex and involve molecular interactions that take place at the “bionano interface” where biotic/abiotic interactions are usually explored. Our work provides molecular perspective on the electron transfer mechanism(s) employed by Shewanella oneidensis MR-1. Molecular docking simulations were used to explain the interfacial relationships between two outer-membrane cytochromes (OMC) OmcA and MtrC and riboflavin (RF) and flavin mononucleotide (FMN), respectively. OMC-flavin interactions were analyzed by studying the electrostatic potential, the hydrophilic/hydrophobic surface properties, and the van der Waals surface of the OMC proteins. As a result, it was proposed that the interactions between flavins and OMCs are based on geometrical recognition event. The possible docking positions of RF and FMN to OmcA and MtrC were also shown.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors

We performed analyses of compounds in clinical development which have shown that ligand efficient-molecules with privileged physical properties and low dose are less likely to fail in the various stages of clinical testing, have fewer postapproval withdrawals, and are less likely to receive black box safety warnings. However, detailed side-by-side examination of molecular interactions and properties within single drug classes are lacking. As a class, VEGF receptor tyrosine kinase inhibitors (VEGFR TKIs) have changed the landscape of how cancer is treated, particularly in clear cell renal cell carcinoma, which is molecularly linked to the VEGF signaling axis. Despite the clear role of the molecular target, member molecules of this validated drug class exhibit distinct clinical efficacy and safety profiles in comparable renal cell carcinoma clinical studies. The first head-to-head randomized phase III comparative study between active VEGFR TKIs has confirmed significant differences in clinical performance [Rini BI, et al. (2011) Lancet 378:193–1939]. To elucidate how fundamental drug potency–efficiency is achieved and impacts differentiation within the VEGFR TKI class, we determined potencies, time dependence, selectivities, and X-ray structures of the drug–kinase complexes using a VEGFR2 TK construct inclusive of the important juxtamembrane domain. Collectively, the studies elucidate unique drug–kinase interactions that are dependent on distinct juxtamembrane domain conformations, resulting in significant potency and ligand efficiency differences. Finally, the identified structural trends are consistent with in vitro measurements, which translate well to clinical performance, underscoring a principle that may be broadly applicable to prospective drug design for optimal in vivo performance.

McTigue, Michele↗

DOE OSTI2016

Interaction of Molecular Oxygen with a Hexagonally Reconstructed Au(001) Surface

Kinetics of molecular oxygen/Au(001) surface interaction has been studied at high temperature and near atmospheric pressures of O 2 gas with in situ X-ray scattering measurements. In this study, we find that the hexagonal reconstruction (hex) of Au(001) surface lifts to (1 × 1) in the presence of O 2 gas, indicating that the (1 × 1) is more favored when some oxygen atoms present on the surface. The measured lifting rate constant vs temperature is found to be highest at intermediate temperature exhibiting a “volcano”-type behavior. At low temperature, the hex-to-(1 × 1) activation barrier (E act = 1.3(3) eV) limits the lifting. At high temperature, oxygen adsorption energy (E ads = 1.6(2) eV) limits the lifting. The (1 × 1)-to-hex activation barrier (E hex = 0.41(14) eV) is also obtained from hex recovery kinetics. The pressure–temperature (PT) surface phase diagram obtained in this study shows three regions: hex at low P and T, (1 × 1) at high P and T, and coexistence of the hex and (1 × 1) at the intermediate P and T.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Polyethylene Glycol Surface Modification and Polythiophene Side-Chain Chemistry: A Combined Strategy toward High-Capacity Lithium-Ion Battery Anodes

In the development of high-capacity lithium-ion batteries (LIBs), the combined optimization of active material interfaces and polymer binder chemistry plays a critical role in improving electrode performance and longevity. This work explores a dual design strategy incorporating polyethylene glycol (PEG) surface modification and carboxylated polythiophene side-chain tailoring to enhance the electrochemical behavior of magnetite (Fe 3 O 4 )-based anodes. PEG is employed to improve interfacial stability, while carboxylated polythiophene binders with varying alkyl side-chain lengths─poly[3-(potassium-4-butanoate)thiophene-2,5-diyl] (P3KBT), poly[3-(potassium-5-pentanoate)thiophene-2,5-diyl] (P3KPT), and poly[3-(potassium-6-hexanoate)thiophene-2,5-diyl] (P3KHT)─are used to modulate molecular interactions and ion transport. Among these three analogs, the PEG–Fe 3 O 4 –P3KHT electrode exhibits superior ion-transfer kinetics, the highest capacity retention, and the lowest charge-transfer resistance after extended cycling. Compared to their non-PEG analogs, PEG-coated electrodes demonstrate enhanced structural integrity and electrochemical behavior, emphasizing the synergistic effects of surface modification and side-chain chemistry. These findings highlight the importance of interfacial interactions and molecular design in achieving robust and high-performance composite anodes for next-generation LIBs.

Fe3O4↗

DOE OSTI2015

Synchrotron-based X-ray Fluorescence Microscopy in Conjunction with Nanoindentation to Study Molecular-Scale Interactions of Phenol-Formaldehyde in Wood Cell Walls

Understanding and controlling molecular-scale interactions between adhesives and wood polymers are critical to accelerate the development of improved adhesives for advanced wood-based materials. The submicrometer resolution of synchrotron-based X-ray fluorescence microscopy (XFM) was found capable of mapping and quantifying infiltration of Br-labeled phenolformaldehyde (BrPF) into wood cell walls. Cell wall infiltration of five BrPF adhesives with different average molecular weights (MWs) was mapped. Nanoindentation on the same cell walls was performed to assess the effects of BrPF infiltration on cell wall hygromechanical properties. For the same amount of weight uptake, lower MW BrPF adhesives were found to be more effective at decreasing moisture-induced mechanical softening. This greater effectiveness of lower MW phenolic adhesives likely resulted from their ability to more intimately associate with water sorption sites in the wood polymers. Evidence also suggests that a BrPF interpenetrating polymer network (IPN) formed within the wood polymers, which might also decrease moisture sorption by mechanically restraining wood polymers during swelling.

adhesive↗

DOE OSTI2014

The effect of cesium carbonate on 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 aggregation in films

Surface-pressure isotherms, X-ray reflectivity, and X-ray near-total reflection fluorescence were used to study the properties of 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 (PCBM) that was pre-mixed with cesium carbonate and spread as a film at the air-water interface. The pre-mixed PCBM with cesium carbonate demonstrated a strikingly strong effect on the organization of the film. Whereas films formed from pure PCBM solution were rough due to strong inter-molecular interactions, the films formed from the mixture were much smoother. This indicates that the cesium carbonate moderates the inter-molecular interactions among PCBM molecules, hinting that the cesium diffusion observed in inverted organic photovoltaics and the likely ensuing ionic Cs-PCBM interaction decrease aggregation tendency of PCBM. As a result, this implies that the use of cesium salts affects the morphology of the organic layer and consequently improves the efficiency of these devices.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Molecular Iodine Interactions with Fe, Ni, Cr, and Stainless Steel Alloys

The adsorption behavior of molecular iodine is important for understanding the spread of radioiodine in a nuclear accident. Prior experiments indicate that, in addition to the interaction with Fe, molecular iodine [i.e., I 2(g) ] also interacts with the next most abundant components of austenitic stainless steel (i.e., Ni, and Cr) at room temperature. Here, we investigate iodine adsorption on Fe, Ni, and Cr while focusing on understanding the variables affecting adsorption as well as the iodine compounds that are formed during adsorption. Scanning electron microscopy and energy-dispersive X-ray spectroscopy were used to characterize the surfaces of exposed metal particles and aid in the understanding of the morphology and chemistry of iodine interactions with the substrates. Inductively coupled plasma optical emission spectroscopy was used to detect low levels of metal iodides and X-ray photoelectron spectroscopy was used to confirm the formation of the metal iodides. The role of environmental factors (e.g., humidity and oxygen content) for iodine adsorption on metal substrates is addressed. The individual metals demonstrated formation of metal iodides for Fe and Ni particles from interaction with I 2(g) . The formation of metal iodides may indicate the affinity of iodine for the respective metal. In this study, the iodine affinities ranked Fe > Ni > Cr as determined by the quantity of chemisorbed iodine. This trend is also supported by the distributions and proportions of metals in the corrosion product of the stainless steels. The exposures without oxygen and humidity indicate the potential of a multistep iodine adsorption process where iodine first attacks the oxide layer and then chemisorbs to the exposed metal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

DETECTION OF EXTREMELY BROAD WATER EMISSION FROM THE MOLECULAR CLOUD INTERACTING SUPERNOVA REMNANT G349.7+0.2

We performed Herschel HIFI, PACS, and SPIRE observations toward the molecular cloud interacting supernova remnant G349.7+0.2. An extremely broad emission line was detected at 557 GHz from the ground state transition 1{sub 10}-1{sub 01} of ortho-water. This water line can be separated into three velocity components with widths of 144, 27, and 4 km s{sup −1}. The 144 km s{sup −1} component is the broadest water line detected to date in the literature. This extremely broad line width shows the importance of probing shock dynamics. PACS observations revealed three additional ortho-water lines, as well as numerous high-J carbon monoxide (CO) lines. No para-water lines were detected. The extremely broad water line is indicative of a high velocity shock, which is supported by the observed CO rotational diagram that was reproduced with a J-shock model with a density of 10{sup 4} cm{sup −3} and a shock velocity of 80 km s{sup −1}. Two far-infrared fine-structure lines, [O i] at 145 μm and [C ii] line at 157 μm, are also consistent with the high velocity J-shock model. The extremely broad water line could be simply from short-lived molecules that have not been destroyed in high velocity J-shocks; however, it may be from more complicated geometry such as high-velocity water bullets or a shell expanding in high velocity. We estimate the CO and H{sub 2}O densities, column densities, and temperatures by comparison with RADEX and detailed shock models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.

Zhu, Yitan↗

DOE OSTI2016

Thermodynamically controlled crystallization of glucose pentaacetates from amorphous phase

The α and β glucose pentaacetates are known sugar derivatives, which can be potentially used as stabilizers of amorphous phase of active ingredients of drugs (API). In the present work, crystallization behavior of equimolar mixture of α and β form in comparison to both pure anomers is revealed. It was shown that despite the same molecular interactions and similar molecular dynamics, crystallization from amorphous phase is significantly suppressed in equimolar mixture. Time dependent X-ray diffraction studies confirmed higher stability of the quenched amorphous equimolar mixture. Its tendency to crystallization is about 10 times lower than for pure anomers. Calorimetric studies revealed that the α and β anomers don’t form solid solutions and have eutectic point for x{sub α} = 0.625. Suppressed crystallization tendency in the mixture is probably caused by the altered thermodynamics of the system. The factors such as difference of free energy between crystalline and amorphous state or altered configurational entropy are probably responsible for the inhibitory effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Hadronic structure on the light front. VIII. Light scalar and vector mesons

We use the QCD instanton vacuum model to discuss the emergence of the light scalar and vector mesons on the light front. We take into account both the instanton and anti-instanton single and molecular interactions on the light quarks, in the form of nonlocal effective interactions. Although the molecular induced interactions are suppressed by a power of the packing fraction, they are still sufficient to bind the vector mesons, while keeping most of the scalar spectrum relatively unchanged. We explicitly derive the light front distribution amplitudes and partonic functions for the scalar and vector mesons, and compare them after pertinent QCD evolution, to the available empirical and lattice measured counterparts. The Dirac electric form factors for both the pion and ρ meson are derived, and shown to compare well with current data. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DOE OSTI2026

Primary biomolecular adsorption energetics of core–shell nanocomplexes: Implications for biological interactions

Molecular organization at the nano-bio interface governing the colloidal stability, reactivity, immune recognition, and drug delivery performance of nanoparticles remains difficult to predict. Quantifying the primary hydration energetics of biomolecule-coated nanomaterials can determine those interactions and provide a basis for engineered nanocarriers with tailored behavior in biological systems. Here, we measured the thermodynamics of water adsorption on patchy dry magnetite (Fe 3 O 4 ) nanoparticles coated with three model biomolecules, bovine serum albumin, potato starch, and lauric acid and compared these properties to the hydration energetics of the corresponding free dry biomolecules. The results demonstrate how the surface functionalization alters the hydrophilicity, the accessible hydrophilic surface, and the interaction potential of the nanocomplex surface with biological media. The protein coating increases the interaction potential of the surface of the nanocomplex. The weaker interaction potential of the polysaccharide coating and the relatively large hydrophilic surface area allow dynamic and reversible binding, while the fatty acid rearranges into a partial bilayer with very strong hydrophilicity. The findings establish the hydration enthalpy as a quantitative basis to determine and interpret nanoparticle interactions with proteins, membranes, and biological fluids, and provide a thermodynamic foundation for designing nanocarriers with predictable biological reactivity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Spin–orbit interaction mediated molecular dissociation

The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

Contamination Effects Due to Space Environmental Interactions

Molecular and particulate contaminants are commonly generated from the orbital spacecraft operations that are under the influence of the space environment. Once generated, these contaminants may attach to the surfaces of the spacecraft or may remain in the vicinity of the spacecraft. In the event these contaminants come to rest on the surfaces of the spacecraft or situated in the line-of-sight of the observation path, they will create various degrees of contamination effect which may cause undesirable effects for normal spacecraft operations, There will be circumstances in which the spacecraft may be subjected to special space environment due to operational conditions. Interactions between contaminants and special space environment may alter or greatly increase the contamination effect due to the synergistic effect. This paper will address the various types of contamination generation on orbit, the general effects of the contamination on spacecraft systems, and the typical impacts on the spacecraft operations due to the contamination effect. In addition, this paper will explain the contamination effect induced by the space environment and will discuss the intensified contamination effect resulting from the synergistic effect with the special space environment.

Chen, Philip T.↗

DOE OSTI2024

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗