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DOE OSTI2011

Photoassociation of a cold-atom-molecule pair. II. Second-order perturbation approach

The electrostatic interaction between an excited atom and a diatomic ground-state molecule in an arbitrary rovibrational level at large mutual separations is investigated with a general second-order perturbation theory, in the perspective of modeling the photoassociation between cold atoms and molecules. We find that the combination of quadrupole-quadrupole and van der Waals interactions competes with the rotational energy of the dimer, limiting the range of validity of the perturbative approach to distances larger than 100 Bohr radii. Numerical results are given for the long-range interaction between Cs and Cs{sub 2}, showing that the photoassociation is probably efficient for any Cs{sub 2} rotational energy.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2018

A Highly Crystalline Fused‐Ring n‐Type Small Molecule for Non‐Fullerene Acceptor Based Organic Solar Cells and Field‐Effect Transistors

Abstract N‐type organic small molecules (SMs) are attracting attention in the organic electronics field, due to their easy purification procedures with high yield. However, only a few reports show SMs that perform well in both organic field‐effect transistors (OFETs) and organic solar cells (OSCs). Here, the synthesis and characterization of an n‐type small molecule with an indacenodithieno[3,2‐b]thiophene (IDTT) core unit and linear alkylated side chain (C 16 ) (IDTTIC) are reported. Compared to the state‐of‐the‐art n‐type molecule IDTIC, IDTTIC exhibits smaller optical bandgap and higher absorption coefficient, which is due to the enhanced intramolecular effect. After mixing with the polymer donor PBDB‐T, IDTIC‐based solar cells deliver a power conversion efficiency of only 5.67%. In stark contrast, the OSC performance of IDTTIC improves significantly to 11.2%. It is found that the superior photovoltaic properties of PBDB‐T:IDTTIC blends are mainly due to reduced trap‐assisted recombination and enhanced molecular packing coherence length and higher domain purity when compared to IDTIC. Moreover, a significantly higher electron mobility of 0.50 cm 2 V −1 s −1 for IDTTIC in OFET devices than for IDTIC (0.15 cm 2 V −1 s −1 ) is obtained. These superior performances in OSCs and OFETs demonstrate that SMs with extended π‐conjugation of the backbone possess a great potential for application in organic electronic devices.

Song, Xin↗

DOE OSTI2023

Smartly Optimizing Crystallinity, Compatibility, and Morphology for Polymer Solar Cells by Small Molecule Acceptor with Unique 2D-EDOT Side Chain

A desired morphology is essential for achieving efficient polymer solar cells. Donors and acceptors with appropriate crystallization can lead to a suitable phase-separated morphology for effective photocurrent generation process. Inspired by the success of Y6 acceptors and the 2D side chain engineering on popular polymer donors and small molecule acceptors, the usage of unique 2D 3,4-ethylene dioxythiophene (EDOT) side chains on Y6 to regulate its crystallinity, compatibility, and thus the related blend morphology is explored. Here, in this study, two molecules of BTP-EDOT-4F and BTP-EDOT-4Cl with such unique 2D EDOT side chains are designed and synthesized. Due to the advantage of EDOT side chain, when these molecules are blended with PM6, the decent power conversion efficiencies (PCEs) of 16.78% and 15.87% are obtained. Furthermore, BTP-EDOT-4F is selected as the third component and added into PM6:L8-BO binary system to form ternary blends. The optimized crystallinity, compatibility, and morphology of such ternary blend are discovered in the presence of BTP-EDOT-4F, which enables efficient exciton dissociation and charge transport as well as decreased recombination, resulting in higher short circuit current density (J sc ) and fill factor. Finally, the outstanding PCE of 18.56% is achieved in ternary blends containing PM6, L8-BO, and BTP-EDOT-4F.

2D EDOT side chains↗

DOE OSTI2013

Nanowires and Nanostructures That Grow Like Polymer Molecules

Unique properties (e.g., rubber elasticity, viscoelasticity, folding, reptation) determine the utility of polymer molecules and derive from their morphology (i.e., one-dimensional connectivity and large aspect ratios) and flexibility. Crystals do not display similar properties because they have smaller aspect ratios, they are rigid, and they are often too large and heavy to be colloidally stable. We argue, with the support of recent experimental studies, that these limitations are not fundamental and that they might be overcome by growth processes that mimic polymerization. Furthermore, we (i) discuss the similarities between crystallization and polymerization, (ii) critically review the existing experimental evidence of polymer-like growth kinetic and behavior in crystals and nanostructures, and (iii) propose heuristic guidelines for the synthesis of “polymer-like” crystals and assemblies. Understanding these anisotropic materials at the boundary between molecules and solids will determine whether we can confer the unique properties of polymer molecules to crystals, expanding them with topology, dynamics, and information and not just tuning them with size.

36 MATERIALS SCIENCE↗

DOE OSTI2018

In Situ Analysis of Solvent and Additive Effects on Film Morphology Evolution in Spin-Cast Small-Molecule and Polymer Photovoltaic Materials

To elucidate the details of film morphology/order evolution during spin-coating, solvent and additive effects are systematically investigated for three representative organic solar cell (OSC) active layer materials using combined in situ grazing incidence wide angle x-ray scattering (GIWAXS) and optical reflectance. Two archetypical semiconducting donor (p-type) polymers, P3HT and PTB7, and semiconducting donor small-molecule, p-DTS(FBTTh 2 ) 2 are studied using three neat solvents (chloroform, chlorobenzene, 1,2-dichlorobenzene) and four processing additives (1-chloronaphthalene, diphenyl ether, 1,8-diiodooctane, and 1,6-diiodohexane). In situ GIWAXS identifies several trends: 1) for neat solvents, rapid crystallization occurs that risks kinetically locking the material into multiple crystal structures or crystalline orientations; and 2) for solvent + additive processed films, morphology evolution involves sequential transformations on timescales ranging from seconds to hours, with key divergences dependent on additive/semiconductor molecular interactions. When π-planes dominate the additive/semiconductor interactions, both polymers and small molecule films follow similar evolutions, completing in 1–5 min. When side chains dominate the additive/semiconductor interactions, polymer film maturation times are up to 9 h, while initial crystallization times <10 s are observed for small-molecule films. In conclusion, this study offers guiding information on OSC donor intermediate morphologies, evolution timescales, and divergent evolutions that can inform OSC manufacture.

25 ENERGY STORAGE↗

DOE OSTI2025

Late-Stage Oxidation of C( sp 3 )─H Bonds with High Efficiency and Alkyl Group Dihydroxylation of Complex Molecules

Here, the late-stage oxidation of C(sp 3 )─H bonds is highly valuable for modulating the solubility and binding of bioactive compounds and for diversification of complex molecules. Undirected methods for C(sp 3 )─H oxidation are valuable for the installation of hydroxyl groups at sites remote from other functional groups present in the molecule, but existing catalysts are limited by low turnover numbers and lengthy ligand syntheses. Perfluorinated ruthenium porphyrins are highly active catalysts for the oxidation of alkyl C─H bonds, but the scope of the transformation with complex molecules under conditions of limiting substrate has not been investigated. We report that carbonylruthenium(II) tetrakis(pentafluorophenyl)porphyrin [Ru(TPFPP)(CO)] catalyzes the selective oxidation of tertiary C(sp 3 )─H bonds in a broad range of complex natural products and drugs, with turnover numbers as high as 1000, and the tolerance of the reaction to various functional groups was rapidly assessed by performing a model reaction in the presence of additives. We show how the combination of this undirected C(sp 3 )─H oxidation and a directed C(sp 3 )─H silylation and oxidation provides rapid access to highly oxidized, 1,2-diol derivatives of natural products by a formal dihydroxylation of an alkyl group.

Alcohols↗

DOE OSTI2021

Bipolar Redox‐Active Molecules in Non‐Aqueous Organic Redox Flow Batteries: Status and Challenges

Abstract In this Review, recent advances in the development of organic bipolar redox‐active molecules (BRMs) for redox‐flow batteries (RFBs) are discussed, with special emphasis on their utilization in non‐aqueous systems. BRMs are single molecules that can be used as both anolyte and catholyte. Their unique redox chemistry enables identical components to be present in RFBs, which has distinct advantages in storage, mitigating crossover and compound degradation. Recent scientific innovations have uncovered three main strategies in preparing these bipolar species: developing stable radicals that are capable of both positive and negative redox reactions, covalently bridging electron donor‐acceptor motifs on one single molecule, and forming biredox eutectic mixtures through physically mixing active components. These approaches not only enabled symmetric flow battery design, but also resulted in electroactive materials with improved properties such as solubility, stability, and cell voltage. Nevertheless, much is still to be done. Importantly, developing BRMs that are competitive with vanadium RFBs in all performance indicators (e. g. solubility >1.0 M, voltage output >2.0 V, and cycling longevity >10 000 cycles) remains a challenge. Mechanistic studies including molecular dynamics, plausible degradation processes, and electrode/solution interface are necessary to peer into key parameters that dominate their battery performance. Accordingly, we review the current status and suggest future opportunities in these areas.

Li, Min↗

DOE OSTI2016

A Fundamental Tandem Mass Spectrometry Study of the Collision‐Activated Dissociation of Small Deprotonated Molecules Related to Lignin

AbstractThe collision‐activated fragmentation pathways and reaction mechanisms of 34 deprotonated model compounds representative of lignin degradation products were explored experimentally and computationally. The compounds were evaporated and ionized by using negative‐ion mode electrospray ionization doped with NaOH to produce abundant deprotonated molecules. The ions were isolated and subjected to collision‐activated dissociation (CAD). Their fragment ions were then isolated and also subjected to CAD. This was repeated until no further fragmentation was observed (up to MS6). This approach enabled the identification of characteristic reaction pathways and delineation of reasonable fragmentation mechanisms for deprotonated molecules containing various functional groups. The varying fragmentation patterns observed for different types of compounds allow for the identification of the functionalities in these compounds. This information was utilized to identify the presence of specific functionalities and their combinations in molecules in an organosolv lignin sample.

catalysis (homogeneous), catalysis (heterogeneous)↗

DOE OSTI2018

Modeling absorption spectra of molecules in solution

The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute–solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute–solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. Furthermore, we introduce our recent results combining the vertical excitation energies computed from an ensemble of solute–solvent configurations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Conjugation‐Curtailing of Benzodithionopyran‐Cored Molecular Acceptor Enables Efficient Air‐Processed Small Molecule Solar Cells

Abstract Small molecule solar cells (SMSCs) lag a long way behind polymer solar cells. A key limit is the less controllable morphology of small molecule materials, which can be aggravated when incorporating anisotropic nonfullerene acceptors. To fine‐tune the blending morphology within SMSCs, a π‐conjunction curtailing design is applied, which produces a efficient benzodithionopyran‐cored molecular acceptor for nonfullerene SMSCs (NF‐SMSCs). When blended with a molecular donor BDT3TR‐SF to fabricate NF‐SMSCs, the π‐conjunction curtailed molecular acceptor NBDTP‐M obtains an optimal power conversion efficiency (PCE) of up to 10.23%, which is much higher than that of NBDTTP‐M of longer π‐conjunction. It retains 93% of the PCE of devices fabricated in a glove box when all spin‐coating and post‐treating procedures are conducted in ambient air with relative humidity of 25%, which suggests the good air‐processing capability of π‐conjunction curtailed molecules. Detailed X‐ray scattering investigations indicate that the BDT3TR‐SF:NBDTP‐M blend exhibits a blend morphology featuring fine interpenetrating networks with smaller domains and higher phase purity, which results in more efficient charge generation, more balanced charge transport, and less recombination compared to the low‐performance BDT3TR‐SF:NBDTTP‐M blend. This work provides a guideline for molecular acceptors' design toward efficient, low‐cost, air‐processed NF‐SMSCs.

Wu, Hao↗

DOE OSTI2011

The effect of the target structure and composition on the ejection and transport of polymer molecules and carbon nanotubes in matrix-assisted pulsed laser evaporation

Matrix-assisted pulsed laser evaporation (MAPLE) is a prominent member of a broad and expanding class of laser-driven deposition techniques where a matrix of volatile molecules absorbs laser irradiation and provides the driving force for the ejection and transport of the material to be deposited. The mechanisms of MAPLE are investigated in coarse-grained molecular dynamic simulations focused on establishing the physical regimes and limits of the molecular transfer from targets with different structures and compositions. The systems considered in the simulations include dilute solutions of polymer molecules and individual carbon nanotubes (CNTs), as well as continuous networks of carbon nanotubes impregnated with solvent. The polymer molecules and nanotubes are found to be ejected only in the ablation regime and are incorporated into matrix-polymer droplets generated in the process of the explosive disintegration of the overheated matrix. The ejection and deposition of droplets explain the experimental observations of complex surface morphologies in films deposited by MAPLE. In simulations performed for MAPLE targets loaded with CNTs, the ejection of individual nanotubes, CNT bundles, and tangles with sizes comparable or even exceeding the laser penetration depth is observed. The ejected CNTs align along the flow direction in the matrix plume and tend to agglomerate into bundles at the initial stage of the ablation plume expansion. In a large-scale simulation performed for a target containing a network of interconnected CNT bundles, a large tangle of CNT bundles with the total mass of 50 MDa is separated from the continuous network and entrained with the matrix plume. No significant splitting and thinning of CNT bundles in the ejection process is observed in the simulations, suggesting that fragile structural elements or molecular agglomerates with complex secondary structures may be transferred and deposited to the substrate with the MAPLE technique.

Materials Science↗

DOE OSTI2012

Small molecule and peptide-mediated inhibition of Epstein-Barr virus nuclear antigen 1 dimerization

Highlights: Black-Right-Pointing-Pointer Evidence that targeting EBNA1 dimer, an EBV onco-antigen, can be achievable. Black-Right-Pointing-Pointer A small molecule and a peptide as EBNA1 dimerization inhibitors identified. Black-Right-Pointing-Pointer Both inhibitors associated with EBNA1 and blocked EBNA1 DNA binding activity. Black-Right-Pointing-Pointer Also, prevented its dimerization, and repressed viral gene transcription. -- Abstract: Latent Epstein-Barr virus (EBV) infection is associated with human B cell lymphomas and certain carcinomas. EBV episome persistence, replication, and gene expression are dependent on EBV-encoded nuclear antigen 1 (EBNA1)'s DNA binding domain (DBD)/dimerization domain (DD)-mediated sequence-specific DNA binding activity. Homodimerization of EBNA1 is essential for EBNA1 DNA binding and transactivation. In this study, we characterized a novel small molecule EBNA1 inhibitor EiK1, screened from the previous high throughput screening (HTS). The EiK1 compound specifically inhibited the EBNA1-dependent, OriP-enhanced transcription, but not EBNA1-independent transcription. A Surface Plasmon Resonance Biacore assay revealed that EiK1 associates with EBNA1 amino acid 459-607 DBD/DD. Consistent with the SPR data, in vitro gel shift assays showed that EiK1 suppressed the activity of EBNA1 binding to the cognate familial repeats (FR) sequence, but not control RBP-J{kappa} binding to the J{kappa} site. Subsequently, a cross-linker-mediated in vitro multimerization assay and EBNA1 homodimerization-dependent yeast two-hybrid assay showed that EiK1 significantly inhibited EBNA1 dimerization. In an attempt to identify more highly specific peptide inhibitors, small peptides encompassing the EBNA1 DBD/DD were screened for inhibition of EBNA1 DBD-mediated DNA binding function. The small peptide P85, covering EBNA1 a.a. 560-574, significantly blocked EBNA1 DNA binding activity in vitro, prevented dimerization in vitro and in vivo, associated with EBNA1 in vitro, and repressed EBNA1-dependent transcription in vivo. Collectively, this study describes two novel inhibitors of EBNA1 dimerization. This study demonstrates that EBNA1 homodimerization can be effectively targeted by a small molecule or peptide.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Direct detection of SERCA calcium transport and small-molecule inhibition in giant unilamellar vesicles

We have developed a charge-mediated fusion method to reconstitute the sarco/endoplasmic reticulum Ca{sup 2+}-ATPase (SERCA) in giant unilamellar vesicles (GUV). Intracellular Ca{sup 2+} transport by SERCA controls key processes in human cells such as proliferation, signaling, and contraction. Small-molecule effectors of SERCA are urgently needed as therapeutics for Ca{sup 2+} dysregulation in human diseases including cancer, diabetes, and heart failure. Here we report the development of a method for efficiently reconstituting SERCA in GUV, and we describe a streamlined protocol based on optimized parameters (e.g., lipid components, SERCA preparation, and activity assay requirements). ATP-dependent Ca{sup 2+} transport by SERCA in single GUV was detected directly using confocal fluorescence microscopy with the Ca{sup 2+} indicator Fluo-5F. The GUV reconstitution system was validated for functional screening of Ca{sup 2+} transport using thapsigargin (TG), a small-molecule inhibitor of SERCA currently in clinical trials as a prostate cancer prodrug. The GUV system overcomes the problem of inhibitory Ca{sup 2+} accumulation for SERCA in native and reconstituted small unilamellar vesicles (SUV). We propose that charge-mediated fusion provides a widely-applicable method for GUV reconstitution of clinically-important membrane transport proteins. We conclude that GUV reconstitution is a technological advancement for evaluating small-molecule effectors of SERCA.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Attenuation of macrophage accumulation and polarisation in obese diabetic mice by a small molecule significantly improved insulin sensitivity

Accumulation and polarization of anti-inflammatory M2 to proinflammatory M1 macrophage in the adipose tissue of obese diabetic mice is an important pathogenic signature. It worsens lipid induced inflammation and insulin resistance. Here we demonstrate that a small molecule, a peroxyvanadate compound i.e. DmpzH [VO(O{sub 2}){sub 2} (dmpz)] or dmp, could robustly decrease macrophage infiltration, accumulation and their polarization in high fat diet (HFD) induced obese diabetic mice. In searching the underlying mechanism it was revealed that SIRT1 level was strikingly low in the inflamed adipose tissue of HFD mice as compared to mice fed with standard diet (SD). Administration of dmp markedly increased SIRT1 level by inducing its gene expression with a consequent decrease in macrophage population. Elevation of SIRT1 coincided with the decrease of MCP1, Fetuin-A (FetA) and IFNγ. Since MCP1 and FetA drive macrophage to inflamed adipose tissue and IFNγ promotes M2 to M1 transformation, both recruitment and M1 induced inflammation were found to be significantly repressed by dmp. In addressing the question about how dmp induced excess SIRT1 could reduce MCP1, FetA and IFNγ levels, we found that it was due to the inactivation of NFκB because of its deacetylation by SIRT1. Since NFκB is the transcriptional regulator of these molecules, their expressions were significantly suppressed and that caused sharp decline in macrophage recruitment and their polarity to M1. This effected a marked fall in proinflammatory cytokine level which significantly improved insulin sensitivity. dmp is likely to be the first molecule that rescues inflammatory burden contributed by macrophage in obese diabetic mice adipose tissue which causes significant increase in insulin sensitivity therefore it may be a meaningful choice to treat type 2 diabetes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

The growth and assembly of organic molecules and inorganic 2D materials on graphene for van der Waals heterostructures

The unique properties of graphene have made it a promising material for integration in future electronic applications. The idealized surface of graphene, atomically-flat and without dangling bonds, offers the opportunity to understand the assembly of organic and inorganic molecules to form a wide range of ordered architectures and functional graphene-based heterostructures. In this review, we summarize recent progress in the growth of hierarchical nanostructures on graphene. The self-assembly of organic molecules and inorganic two-dimensional (2D) layers on graphene for the construction of various types of heterostructures are highlighted. Van der Waals interactions between the assembled molecules and graphene are shown to allow the formation of highly-ordered structures with preferred molecular orientations and stacking configurations that circumvent the strict lattice-matching requirements in traditional epitaxial growth. Lastly, we briefly discuss representative applications of graphene-based heterostructures in electronic and optoelectronics.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Artificial Transmembrane Channel Constructed from Shape-Persistent Covalent Organic Molecular Cages Capable of Ion and Small Molecule Transport

Shape-persistent arylene ethynylene molecular cages have been investigated as transmembrane channels for ions and small molecules. The molecular cages were obtained starting from tetrayne monomers through alkyne metathesis cyclooligomerization. We found these porphyrin-based rigid molecular cages can insert into the lipid bilayer and efficiently transport ions and small molecules (e.g., calcein). Our study reveals longer hydrophobic alkyl chains on the cage molecule promote the channeling efficiency, while shorter and/or more polar side chains impair such activity. Kinetic analysis shows linear correlation between the rate of proton transport and the concentration of the cage, suggesting the active species is likely a monomeric cage. We found that C70-encapsulated cages are nearly inactive for transmembrane ion transportation, indicating that ions are likely transported through the internal cavity of the cage. Discrete shape-persistent organic cages represent highly stable synthetic ion channels or pores, which could have interesting applications in biomimetic signaling and drug delivery.

alkyne metathesis↗

DOE OSTI2023

Compositional changes of dissolved organic molecules along water flow and their influencing factors in the Three Gorges Reservoir

Molecular composition of dissolved organic matter (DOM) and its influencing factors in river reservoirs remains elusive. Here, molecular compositions of DOM, bacterial community structures, and water physiochemistry were investigated in the field and microcosm samples of the Three Gorges Reservoir (TGR). The results showed that DOM molecular compositions were significantly (R 2 = 0.245, p < 0.001) correlated with bacterial community structures in the studied field samples, suggesting that bacteria may actively interact with DOM molecules. In this study, the molecular compositions of DOM in the studied field samples were significantly (p < 0.05) affected by the distance between the sample sites and the Three Gorges Dam and by bacterial groups of Actinobacteria and Alphaproteobacteria, suggesting that both hydrological and bacterial processes may contribute to the variation in DOM molecular composition in the TGR water. Furthermore, microcosm experiments demonstrated that both microbial and abiotic processes may transform and/or produce DOM in the TGR, thereby affecting DOM molecular composition. Microbial process increased the average aromaticity index and decreased the carbon number of DOM molecules with increasing incubation duration; whereas average oxygen number, double bond equivalent, and oxidation state of carbon of DOM molecules increased during the first 14 days of incubation and began to decrease thereafter. Taken together, this study expands our understanding of the impact of microbial process on the DOM molecular composition in reservoir ecosystems, and has great implications for carbon cycling in major rivers.

58 GEOSCIENCES↗

DOE OSTI2012

A Multi-State Single-Molecule Switch Actuated by Rotation of an Encapsulated Cluster within a Fullerene Cage

We demonstrate a single-molecule switch based on tunneling electron-driven rotation of a triangular Sc₃N cluster within an icosahedral C 80 fullerene cage among three pairs of enantiomorphic configura-tions. Scanning tunneling microscopy imaging of switching within single molecules and electronic structure theory identify the conformational isomers and their isomerization pathways. Bias-dependent actionspectra and modeling identify the antisymmetric stretch vibration of Sc 3N cluster to be the gateway for energy transfer from the tunneling electrons to the cluster rotation. Hierarchical switching of conductivity through the internal cluster motion among multiple stationary states while maintaining a constant shape, is advantageous for the integration of endohedral fullerene-based single-molecule memory and logic devices into parallel molecular computing arc.

Environmental Molecular Sciences Laboratory↗