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DOE OSTI2025

A cobalamin-dependent pathway of choline demethylation from the human gut acetogen Eubacterium limosum

Elevated serum levels of trimethylamine N-oxide (TMAO) are reported to promote the development of atherosclerosis. TMAO is produced by hepatic oxidation of trimethylamine (TMA) produced by the gut microbiome from dietary quaternary amines such as choline. Net TMA production in the gut depends on microbial enzymes that either produce or consume TMA and its precursors. Here we report the elucidation of a novel microbial pathway consuming choline without TMA production. The human gut acetogen Eubacterium limosum grows by demethylating choline to N-N-dimethylaminoethanol. Quantitative mass spectral analysis of the proteome revealed a multi-protein choline to tetrahydrofolate (THF) methyltransferase system present only in choline-grown cells. The components are encoded in a gene cluster on the genome and include MthB, an MttB superfamily member; MthC, homologous to methylotrophic cobalamin-binding proteins; MthA, homologous to cobalamin:THF methyltransferases; and MthK, a protein related to serine kinases. Together, MthB, MthC, and MthA methylate THF with phosphocholine, but not choline or other quaternary amines. MthB specifically methylates Co(I)-MthC with phosphocholine. MthK acts as a bifunctional choline kinase which can utilize ATP or the MthB demethylation product, N,N-dimethylaminoethanol phosphate, to phosphorylate choline. Together, MthK, MthB, MthC, and MthA are proposed to carry out the methylation of THF with choline. These results outline a THF methylation pathway in which choline is first activated with ATP to phosphocholine prior to demethylation to form N,N-dimethylaminoethanol phosphate. Furthermore, the latter can be recycled by MthK to form more phosphocholine without expending additional ATP, thus minimizing energy utilization during choline-dependent acetogenesis.

acetogenesis↗

DOE OSTI2022

Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetanyl peroxy radicals

2,4,dimethyloxetane is an important cyclic ether intermediate that is produced from hydroperoxyalkyl (QOOH) radicals in the low-temperature combustion of n-pentane. However, the reaction mechanisms and rates of consumption pathways remain unclear. In the present work, the pressure- and temperature-dependent kinetics of seven cyclic ether peroxy radicals, which stem from 2,4,dimethyloxetane via H-abstraction and O 2 addition, were determined. The automated kinetic workflow code, KinBot, was used to model the complexity of the chemistry in a stereochemically resolved manner and solve the resulting master equations from 300–1000 K and from 0.01–100 atm. The main conclusions from the calculations include (i) diastereomeric cyclic ether peroxy radicals show significantly different reactivities, (ii) the stereochemistry of the peroxy radical determines which QOOH isomerization steps are possible, (iii) conventional QOOH decomposition pathways, such as cyclic ether formation and HO 2 elimination, compete with ring-opening reactions, which primarily produce OH radicals, the outcome of which is sensitive to stereochemistry. Ring-opening reactions lead to unique products, such as unsaturated, acyclic peroxy radicals, that form direct connections with species present in other chemical kinetics mechanisms through "cross-over" reactions that may complicate the interpretation of experimental results from combustion of n-pentane and, by extension, other alkanes. For example, one cross-over reaction involving 1-hydroperoxy-4-pentanone-2-yl produces 2-(hydroperoxymethyl)-3-butanone-1-yl, which is an iso-pentane-derived ketohydroperoxide (KHP). At atmospheric pressure, the rate of chemical reactions of all seven peroxy radicals compete with that of collisional stabilization, resulting in well-skipping reactions. However, at 100 atm, only one out of seven peroxy radicals undergoes significant well-skipping reactions. Here, the rates produced from the master equation calculations provide the first foundation for the development of detailed sub-mechanisms for cyclic ether intermediates. In addition, analysis of the complex reaction mechanisms of 2,4-dimethyloxetane-derived peroxy radicals provides insights into the effects of stereoisomers on reaction pathways and product yields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

High-Octane Gasoline from Lignocellulosic Biomass via Syngas and Methanol/Dimethyl Ether Intermediates: 2020 State of Technology

The 2020 state of technology (SOT) serves as an update to the 2019 SOT report and details the techno-economic analysis (TEA) results for producing high-octane gasoline (HOG) via indirect liquefaction (IDL). This report only describes changes to the experimental and analysis results from previous SOTs; more details regarding the full process design can be found in the 2015 design report. The conversion pathway presented in this report includes the gasification of biomass, steam reforming and cleanup of the syngas, followed by the conversion of the syngas to HOG via methanol and dimethyl-ether (DME) intermediates. Research efforts in 2020 included the collection of experimental results over a variety of isobutane (iC4) to DME ratios in the feed of the DME-to-HOG reactor, enabling the TEA to identify the effect on modeled product yield and cost. Additionally, a significant re-build of the Aspen Plus model allowed for better integration of new research, however underlying conceptual and economic assumptions remain the same as those detailed in the 2015 deign report. The 2020 SOT also considers the potential for federal carbon tax credits from CO 2 capture in the acid-gas removal step and the impact on the final minimum fuel selling price.

09 BIOMASS FUELS↗

DOE OSTI2023

Urban mining from biomass, brine, sewage sludge, phosphogypsum and e-waste for reducing the environmental pollution: Current status of availability, potential, and technologies with a focus on LCA and TEA

We discuss how rapid industrialization, improved standards of living, growing economies and ever-increasing population has led to the unprecedented exploitation of the finite and non-renewable resources of minerals in past years. It was observed that out of 100 BMT of raw materials processed annually only 10% is recycled back. This has resulted in a strenuous burden on natural or primary resources of minerals (such as ores) having limited availability. Moreover, severe environmental concerns have been raised by the huge piles of waste generated at landfill sites. To resolve these issues, ‘Urban Mining’ from waste or secondary resources in a Circular Economy’ concept is the only sustainable solution. The objective of this review is to critically examine the availability, elemental composition, and the market potential of the selected secondary resources such as lignocellulosic/algal biomass, desalination water, sewage sludge, phosphogypsum, and e-waste for minerals sequestration. This review showed that, secondary resources have potential to partially replace the minerals required in different sectors such as macro and microelements in agriculture, rare earth elements (REEs) in electrical and electronics industry, metals in manufacturing sector and precious elements such as gold and platinum in ornamental industry. Further, inputs from the selected life cycle analysis (LCA) & techno economic analysis (TEA) were discussed which showed that although, urban mining has a potential to reduce the greenhouse gaseous (GHG) emissions in a sustainable manner however, process improvements through innovative, novel and cost-effective pathways are essentially required for its large-scale deployment at industrial scale in future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Environmental and Economic Assessments and Uncertainties of Multiple Lignocellulosic Biomass Utilization for Bioenergy Products: Case Studies

Life-cycle assessment (LCA) and techno-economic analysis (TEA) were applied to assess the economic feasibility and environmental benefits of utilizing multiple biomass feedstocks for bioenergy products under three different technological pathways with consideration of uncertainties. Three cases were studied for the production of pellets, biomass-based electricity, and pyrolysis bio-oil. A Monte Carlo simulation was used to examine the uncertainties of fossil energy consumption, bioenergy conversion efficiency, stochastic production rate, etc. The cradle-to-gate LCA results showed that pellet production had the lowest greenhouse gas (GHG) emissions, water and fossil fuels consumption (8.29 kg CO2 eq (equivalent), 0.46 kg, and 105.42 MJ, respectively). The conversion process presented a greater environmental impact for all three bioenergy products. When producing 46,929 Mg of pellets, 223,380 MWh of electricity, and 78,000 barrels of pyrolysis oil, the net present values (NPV) indicated that only pellet and electricity production were profitable with NPVs of $1.20 million for pellets, and $5.59 million for biopower. Uncertainty analysis indicated that pellet production showed the highest uncertainty in GHG emission, and bio-oil production had the least uncertainty in GHG emission but had risks producing greater-than-normal amounts of GHG. Biopower production had the highest probability to be a profitable investment with 85.23%.

09 BIOMASS FUELS↗

NASA NTRS1997

The ethylene signal transduction pathway in Arabidopsis

The gaseous hormone ethylene is an important regulator of plant growth and development. Using a simple response of etiolated seedlings to ethylene as a genetic screen, genes involved in ethylene signal transduction have been identified in Arabidopsis. Analysis of two of these genes that have been cloned reveals that ethylene signalling involves a combination of a protein (ETR1) with similarity to bacterial histidine kinases and a protein (CTR1) with similarity to Raf-1, a protein kinase involved in multiple signalling cascades in eukaryotic cells. Several lines of investigation provide compelling evidence that ETR1 encodes an ethylene receptor. For the first time there is a glimpse of the molecular circuitry underlying the signal transduction pathway for a plant hormone.

NASA Discipline Plant Biology↗

NASA NTRS2000

Systematic Sensitivity Analysis of Metabolic Controllers During Reductions in Skeletal Muscle Blood Flow

An acute reduction in oxygen delivery to skeletal muscle is generally associated with profound derangements in substrate metabolism. Given the complexity of the human bioenergetic system and its components, it is difficult to quantify the interaction of cellular metabolic processes to maintain ATP homeostasis during stress (e.g., hypoxia, ischemia, and exercise). Of special interest is the determination of mechanisms relating tissue oxygenation to observed metabolic responses at the tissue, organ, and whole body levels and the quantification of how changes in oxygen availability affect the pathways of ATP synthesis and their regulation. In this study, we apply a previously developed mathematical model of human bioenergetics to study effects of ischemia during periods of increased ATP turnover (e.g., exercise). By using systematic sensitivity analysis the oxidative phosphorylation rate was found to be the most important rate parameter affecting lactate production during ischemia under resting conditions. Here we examine whether mild exercise under ischemic conditions alters the relative importance of pathways and parameters previously obtained.

Radhakrishnan, Krishnan↗

DOE OSTI2022

Building a better framework for evaluating human well-being impacts in global change analysis: The example of energy security

Human well-being can be greatly impacted by the global environmental and socio-economic change captured in Integrated Models of Global Change (IMGCs). Though most IMGCs address some aspects of well-being, their underlying modeling approach and ‘philosophy’ differ widely, and some key elements – like energy security – are omitted. In this report, we describe a project in which we set out to a create a framework through which the well-being dimensions of the household are connected to key drivers of socio-economic and environmental change – and how the needed metrics, data and modeling methods can be brought to bear. We focus on the well-being dimensions of energy, and lay out the necessary elements to capturing household energy security – using household energy burden as the relevant metric. We begin by showing the conceptual linkage of energy burden to environmental drivers like temperature change, using a simple and straightforward conceptual framework. We then go further to use the example of GCAM-USA to show how some key analytical features of the model can provide insight into how energy security across different groups can change along alternative pathways to sustainability. We compare our preliminary assessment of household energy burden to existing data and suggest further steps to improve and refine this analysis in future research.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Pathways for Agricultural Decarbonization in the United States

In the United States, agricultural production is both a significant source of greenhouse gases (GHGs) (Environmental Protection Agency (EPA), 2022) and uniquely susceptible to climate change impacts (Vermeulen et al., 2012). Decarbonization solutions have been proposed for addressing agricultural GHGs; however, research has been limited in synthesizing qualitative and quantitative analysis of potential GHG mitigation solutions in the United States. In this report, we review U.S. agricultural GHG sources by activity and quantify potential mitigation solutions based on a comprehensive data and literature analysis. We also discuss agricultural carbon sequestration options to offset GHG emissions. In our analysis, we identified two significant and hard-to-abate GHG sources (N 2 O from soil management, and CH 4 from enteric fermentation from livestock) as well as high-impact GHG mitigation solutions (e.g. agroforestry, reforestation, and biochar application) and cross-cutting GHG mitigation solutions (renewable energy production, precision agriculture, no-till, integrated nutrient management, and biochar). This report is meant to provide initial analysis and establish a foundation for future agricultural decarbonization research - it is not an exhaustive analysis of all available studies. However, to our knowledge this report is the most comprehensive assessment of agricultural GHG emissions and associated mitigation opportunities in the United States to date. Future empirical research is recommended to close research gaps in different climates, soils, and agricultural systems. Meta-analyses for all mitigation solutions would increase confidence in the estimated GHG mitigation potentials. To conclude this report, we discuss short-term and long-term pathways for agricultural decarbonization in the United States, the importance of accounting for total GHG fluxes, potential co-benefits of agricultural decarbonization, analysis of study data confidence, and research gaps.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Chapter 6: Recycling Plastic Waste to Produce Chemicals - A Techno-Economic Analysis and Life-Cycle Assessment

This study presents the results of a preliminary assessment on the technology, economics, and sustainability of using waste plastics as a feedstock to produce low molecular weight olefins via pyrolysis and gasification pathways. We also studied the formation of formaldehyde - an important polymer precursor - via the gasification of waste plastics. Process pathways for recovery of ethylene and propylene and production of formaldehyde from a simulated mixed plastic waste were constructed based on literature data. They included direct and indirect pathways based on either gasification or pyrolysis as the primary conversion step. Results of these studies have shown that significant economic challenges exist of producing olefins via pyrolysis and gasification, with the latter pathway especially difficult. Base costs of pyrolysis naphtha from waste plastics are higher when compared to the same material produced from fossil feedstocks. Base olefin costs for one direct route are two times higher than comparable costs from steam cracking of fossil naphtha. These costs are driven primarily by feedstock costs; some pyrolysis scenarios become more economically feasible when very low feedstock costs are used. Similarly, for gasification, the cost of methanol - the central intermediate - was found to be noticeable higher when produced by gasification of waste plastics compared to current selling prices, which negatively impacts all pathways that go through methanol as the central intermediate. Life-cycle assessment indicates that the production of pyrolysis naphtha from plastics is a carbon intensive operation; no major advantages were found in terms of greenhouse gas emissions for any of the pathways producing C2 and C3 olefins. The results of this study can serve as the baseline for future comparison to other plastic waste valorization processes.

BIOMASS FUELS,ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (~50°C; pH~10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ~2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO 2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H + /Na + pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group “OPB41.” We propose to name this bacterium ‘Candidatus Hakubanella thermoalkaliphilus.'

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Towards cost-competitive middle distillate fuels from ethanol within a market-flexible C2 platform-based biorefinery concept

Ethanol to middle distillates (ETMD) is a promising pathway to produce sustainable liquid fuels to decarbonize the hard-to-electrify transportation sectors due to (1) the abundant sugar/starch and lignocellulosic biomass, (2) the existing deployment scale of fuel ethanol production (similar to 29 billion gallons per year globally), and (3) emerging opportunities in C2+ alcohol synthesis from CO2. Here we report a conceptual market-responsive biorefinery centered around a new ETMD pathway based on one-step ethanol to butene-rich olefins (ETO) over a Cu-Zn-Y/Beta catalyst. Specifically, this ethanol conversion pathway comprises one-step ETO, oligomerization, and hydrotreating. This ETO is distinct from that in the conventional ethanol-to-jet process which is based on two-step ethanol to ethylene and ethylene oligomerization to butenes. Butene-rich olefins can be shifted to butadiene-rich products by simply changing the reaction atmosphere from hydrogen to inert gas over the same ETO catalyst. Leveraging the experimental results, baseline techno-economic analysis (TEA) and sensitivity analysis indicate that the ethanol conversion cost is $0.60 per gallon gasoline equivalent (GGE), with opportunities for further cost reduction via improving the liquid hydrocarbon yield and space velocities, and process optimization on balancing dewatering of ethanol feed prior to the ETO step. The minimum fuel selling price (MFSP) of liquid hydrocarbons derived from corn starch ethanol with butadiene as coproduct is $1.64 per GGE, in the range that is cost competitive with petroleum kerosene-type jet fuel. Projected MFSP for cellulosic ethanol (corn stover) derived hydrocarbons is below $3.00 per GGE and co-production of butadiene further reduces the MFSP to $1.70 per GGE. The Well-to-Wake life-cycle analysis indicates that 85% greenhouse gas emission reduction can be achieved when using corn stover compared to petroleum reference and the associated carbon credits will provide significant economic incentives to favor the cellulosic ethanol-derived hydrocarbon fuels. This study demonstrates a low-cost pathway to middle distillate fuels leveraging existing ethanol infrastructure, where catalysis innovation drives the reduction of process complexity and flexible coproduction of a value-added chemical product.

Zhang, Junyan↗

DOE OSTI2022

Mechanistic pathways and role of oxygen in oxidative coupling of methane derived from transient kinetic studies

Oxidative coupling of methane (OCM) is a promising industrial process to upgrade natural gas to high value chemicals. In this study, Temporal Analysis of Products (TAP) and steady-state experiments were conducted to distinguish how the composition of surface and gas phase oxygen influence mechanistic details of the selective conversion of CH 4 to C 2 H 4 over the Mn-Na 2 WO 4 /SiO 2 catalyst. The results from TAP studies indicate that methane activation on this catalyst proceeds predominantly via a short-lived, transient surface oxygen species and there is a competition for this species to form either CO or methyl radicals on the surface. This active species has a total lifetime of 3 s and is identified to have a dioxygen (e.g. O 2 2- or O 2 -) form. We show that the concentration of the transient surface oxygen species significantly impacts the OCM performance. Oxygen attributed to the catalyst lattice (in a singular form e.g., O - ), is found to activate methane to a lesser degree, but exclusively forms CO 2 . Evidence for these surface pathways for methyl radical, CO and CO 2 formation identified by TAP are also validated through steady-state experiments. Finally, by distinguishing different catalyst oxygen species and their role in selective/nonselective pathways, important screening criteria have been identified for the advancement of superior catalyst formulations.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges

Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production have intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of ‘user-friendly’ biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Techno-Economic Case Study: Low-Temperature Conversion Performance Based on Isolated Anatomical Fractions of Corn Stover

This report summarizes analysis conducted to support a case study under the Feedstock Conversion Interface Consortium (FCIC) focused on techno-economic analysis (TEA) modeling to quantify the process yield and resulting process cost impacts for processing isolated anatomical fractions of corn stover through a low-temperature conversion (biochemical) pathway. It is hypothesized that different individual anatomical fractions of corn stover vary in both composition and recalcitrance, giving biorefineries options in whether and how to deal with fractionated or whole biomass feedstock. By quantifying the techno-economic impacts of this variability, we provide actionable information for end users to understand tradeoffs in conversion system yields and economics in considering feedstock processing decisions at the biorefinery gate. For this study, we worked with FCIC researchers to obtain data on the compositional analysis and conversion performance of whole corn stover alongside three individual anatomical fractions (cobs, husks, and stalks) across key steps of the biorefinery conversion process within FCIC’s research scope—pretreatment and enzymatic hydrolysis. This TEA screening assessment highlighted biorefinery economic trade-offs observed through this approach. Namely, relative to processing whole stover biomass, two of the three anatomical fractions for which composition/conversion data were available (cobs and husks) demonstrated the ability to achieve higher fuel yields and lower minimum fuel selling prices (MFSPs), while the third fraction (stalks) led to the opposite result, as a composite reflection of compositional differences and process convertibility.

cost impacts↗

DOE OSTI2023

A systematic multicriteria-based approach to support product portfolio selection in microalgae biorefineries

Here this work proposes and applies a sequential approach of objective methods to aid the decision-making process for the deployment of microalgae biorefineries. The strategy combines Multicriteria Decision Analysis (MCDA) and weight assignment methods to simultaneously consider technical, economic, and environmental criteria to (1) outrank the best bioproduct options from different biomass fractions present in microalgae biomass at different ratios (namely carbohydrates, lipids, and protein) and (2) define the most suitable biorefining pathways associated with specific pairings of microalgae strains and cultivation conditions. The first part of the assessment identified succinic acid, acrylic acid, and citric acid as the top-ranked bioproducts from carbohydrates, polyurethane from lipids, and thermoplastic extrusion co-feed from protein. The second step of the analysis determined that, when production of a hydrocarbon fuel is desired, the compositional profile of a strain is paramount in defining the biorefining setup that should be pursued. In summary, microalgae lipids should be sent to the production of hydrocarbon fuels if the ratio between neutral lipids and fermentable carbohydrates is higher than roughly 1, with carbohydrates and protein being converted to the higher-value products noted above. Finally, this result was corroborated through process simulations, which indicated superior economic and environmental metrics when strains are paired with suitable conversion pathways identified through MCDA based on their compositional profiles. The outcomes of this work provide clear, objective, guidelines for establishing the best biorefining approach for a large suite of biochemical compositions as a screening method prior to employing detailed process simulations alongside rigorous techno-economic and life-cycle assessments.

09 BIOMASS FUELS↗

DOE OSTI2024

The Acetylene Bridge in Intramolecular Singlet Fission: A Boon or A Nuisance?

Various analogues of the alkylsilylacetylene group are frequently used as auxiliary groups to enhance the solubility and stability of the acene dimer core, widely used as platforms to investigate intramolecular singlet fission (iSF) mechanisms. However, while in the 2,2’-linked dimers they are primarily auxiliary groups, these are essential fragments of the bridging units in 6,6’/5,5’-linked dimers, the two preferred choices for dimerization. The starkly different iSF dynamics observed in the two variants raise the question of what role the acetylene bridges play. Here, we systematically designed a set of (oligo-)para-phenylene bridged 2,2’-linked pentacene dimers with an additional acetylene fragment in the bridging unit to mimic the structure of 6,6’-linked dimers. Contrasting the results with previously reported analogous 2,2’-linked and 6,6’-linked pentacene dimers reveals that the acetylene bridges contribute to significant conformational freedom. This effect provides a mechanism to promote spin evolution within the triplet pair to achieve free triplets but also offers new parasitic pathways for triplet-pair recombination, revealing that this structural motif can be both a boon and a nuisance. Additionally, our analysis reveals that these bridges directly modify the electronic states, highlighting significant pitfalls of the standard chromophore-bridge-chromophore framework used to design and interpret photophysics of iSF materials.

14 SOLAR ENERGY↗

DOE OSTI2020

Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.

59 BASIC BIOLOGICAL SCIENCES↗