skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information
  1. DOE STTR Phase I Final Report Report: Machine-learning Based Prediction of Thermal Limits for Conjugated Organic Materials

    The SCANN-DT Phase I STTR project led by NLM Photonics and partnering with the National Renewable Energy Laboratory (NREL) sought to apply machine learning techniques based on graph neural networks (GNNs) towards the prediction of decomposition temperatures (Td) of organic semiconductors, based on prior work on bond dissociation energy (BDE) prediction as implemented in NREL’s ALFABET prediction tool. Using a curated set of experimental decomposition energies, the project examined GNN-based, classical quantitative structure-property relationship (QSPR) based on DFT calculations, and combinations of both methods to predict Td. While the best MAEs in Td achieved were near 40°C, below project targets,more » the project led to improvements in the ALFABET model, improvements in cloud-based implementations of NWChem software, and a substantial dataset of calculations on medium-sized conjugated organic molecules.« less
  2. Mechanical coupling in the nitrogenase complex

    The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex asmore » a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.« less
  3. Unraveling Excitonic Effects for the First Hyperpolarizabilities of Chromophore Aggregates

    Excitonic interactions often significantly affect the optoelectronic properties of molecular materials. However, their role in determining the nonlinear optical response of organic electro-optic materials remains poorly understood. In this paper, we explore the effects of excitonic interactions on the first hyperpolarizability for aggregates of donor–acceptor chromophores. We show that calculations of the first hyperpolarizabilty of chromophore aggregates based on a two-state model agree well with the more rigorous coupled perturbed Hartree–Fock method. We then use both time-dependent density functional theory calculations and the molecular exciton approximation to parametrize the two-state model. Use of the molecular exciton approximation to the two-statemore » model (i) is appropriate for disordered aggregates (unlike band theory), (ii) is computationally efficient enough for calculating the first hyperpolarizability of materials that consist of thousands of interacting chromophores, and (iii) allows the unraveling of the effects of both excitonic interactions and electrostatic polarization of the chromophore electron density by its environment on the first hyperpolarizability of molecular materials. We find that use of the molecular exciton approximation to the two-state model does not introduce significant additional errors compared to those introduced by applying the two-state model alone. We determine that the absolute change to the first hyperpolarizability of chromophore aggregates due to excitonic interactions increases with the size of the aggregate. For all sizes of disordered aggregates of chromophores considered in this paper, the inclusion of excitonic interactions on average decreases the magnitude of the first hyperpolarizability by 12–14% compared to the case of non-interacting chromophores. Lastly, we present a method for analytically calculating the first hyperpolarizability of a one-dimensional periodic array of chromophores within the molecular exciton approximation to the two-state model. This technique can be used to include an approximate correction for excitonic effects when simulating the electro-optic response of disordered and ordered organic materials.« less
  4. Mechanism of Catalytic O2 Reduction by Iron Tetraphenylporphyrin

    The catalytic reduction of O2 to H2O is important for energy transduction in both synthetic and natural systems. Herein, we report a kinetic and thermochemical study of the oxygen reduction reaction (ORR) catalyzed by iron tetraphenylporphyrin (Fe(TPP)) in N,N'-dimethylformamide using decamethylferrocene as a soluble reductant and para-toluenesulfonic acid (pTsOH) as the proton source. This work identifies and characterizes catalytic intermediates and their thermochemistry, providing a detailed mechanistic understanding of the system. Specifically, reduction of the ferric porphyrin, [FeIII(TPP)]+, forms the ferrous porphyrin, FeII(TPP), which binds O2 reversibly to form the ferric-superoxide porphyrin complex, FeIII(TPP)(O2•–). The temperature dependence of both themore » electron transfer and O2 binding equilibrium constants has been determined. Kinetic studies over a range of concentrations and temperatures show that the catalyst resting state changes during the course of each catalytic run, necessitating the use of global kinetic modeling to extract rate constants and kinetic barriers. The rate-determining step in oxygen reduction is the protonation of FeIII(TPP)(O2•–) by pTsOH, which proceeds with a substantial kinetic barrier. Computational studies indicate that this barrier for proton transfer arises from an unfavorable preassociation of the proton donor with the superoxide adduct and a transition state that requires significant desolvation of the proton donor. Together, these results are the first example of oxygen reduction by iron tetraphenylporphyrin where the pre-equilibria among ferric, ferrous, and ferric-superoxide intermediates have been quantified under catalytic conditions. This work gives a generalizable model for the mechanism of iron porphyrin-catalyzed ORR and provides an unusually complete mechanistic study of an ORR reaction. More broadly, this study also highlights the kinetic challenges for proton transfer to catalytic intermediates in organic media.« less
  5. DANPY (dimethylaminonaphthylpyridinium): an economical and biocompatible fluorophore

    Dyes with nonlinear optical (NLO) properties enable new imaging techniques and photonic systems. We have developed a dye (DANPY-1) for photonics applications in biological substrates such as nucleic acids; however, the design specification also enables it to be used for visualizing biomolecules. It is a prototype dye demonstrating a water-soluble, NLO-active fluorophore with high photostability, a large Stokes shift, and a favorable toxicity profile. A practical and scalable synthetic route to DANPY salts has been optimized featuring: (1) convergent Pd-catalyzed Suzuki coupling with pyridine 4-boronic acid, (2) site-selective pyridyl N-methylation, and (3) direct recovery of crystalline intermediates without chromatography. Wemore » characterize the optical properties, biocompatibility, and biological staining behavior of DANPY-1. In addition to stability and solubility across a range of polar media, the DANPY-1 chromophore shows a first hyperpolarizability similar to common NLO dyes such as Disperse Red 1 and DAST, a large two-photon absorption cross section for its size, substantial affinity to nucleic acids in vitro, an ability to stain a variety of cellular components, and strong sensitivity of its fluorescence properties to its dielectric environment.« less
  6. Electron anions and the glass transition temperature

    Properties of glasses are typically controlled by judicious selection of the glass-forming and glass-modifying constituents. Through an experimental and computational study of the crystalline, molten, and amorphous [Ca12Al14O32]2+ ∙ (e)2, we demonstrate that electron anions in this system behave as glass-modifiers that strongly affect solidification dynamics, the glass transition temperature, and spectroscopic properties of the resultant amorphous material. Here, concentration of such electron anions is a consequential control parameter: it invokes materials evolution pathways and properties not available in conventional glasses, which opens a new avenue in rational materials design.

Search for:
All Records
Author / Contributor
000000027412073X

Refine by:
Resource Type
Availability
Publication Date
Author / Contributor
Research Organization