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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structure Activity Relationship Approach toward the Improved Separation of Rare-Earth Elements Using Diglycolamides

The separation of adjacent lanthanides continues to be a challenge worldwide because of the similar physical and chemical properties of these elements and a necessity to advance the use of clean-energy applications. In this paper, a systematic structure–performance relationship approach toward understanding the effect of N-alkyl group characteristics in diglycolamides (DGAs) on the separation of lanthanides(III) from a hydrochloric acid medium is presented. In addition to the three most extensively studied DGA complexants [N,N,N',N'-tetra(n-octyl)diglycolamide, TODGA; N,N,N',N'-tetra(2-ethylhexyl)diglycolamide, TEHDGA; N,N'-dimethyl-N,N'-di(n-octyl)diglycolamide, DMDODGA], 12 new extracting agents with varying substitution patterns were designed to study the interplay of steric and electronic effects that control rare-earth element extraction. Subtle changes in the structure around diglycolamide carbonyl oxygen atoms result in dramatic shifts in the lanthanide extraction strength and selectivity. The effects of the chain length and branching position of N-alkyl substituents in DGAs are elaborated on with the use of experimental, computational, and solution-structure characterization techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Carbon Dioxide Promoted H + Reduction Using a Bis(imino)pyridine Manganese Electrocatalyst

Heating a 1:1 mixture of (CO) 5 MnBr and the phosphine-substituted pyridine diimine ligand, Ph2PPr PDI, in THF at 65 °C for 24 h afforded the diamagnetic complex [( Ph2PPr PDI)Mn(CO)][Br] (1). Higher temperatures and longer reaction times resulted in bromide displacement of the remaining carbonyl ligand and the formation of paramagnetic ( Ph2PPr PDI)MnBr (2). The molecular structure of 1 was determined by single crystal X-ray diffraction, and density functional theory (DFT) calculations indicate that this complex is best described as low-spin Mn(I) bound to a neutral Ph2PPr PDI chelating ligand. The redox properties of 1 and 2 were investigated by cyclic voltammetry (CV), and each complex was tested for electrocatalytic activity in the presence of both CO 2 and Brønsted acids. Although electrocatalytic response was not observed when CO 2 , H 2 O, or MeOH was added to 1 individually, the addition of H2O or MeOH to CO 2- saturated acetonitrile solutions of 1 afforded voltammetric responses featuring increased current density as a function of proton source concentration ($i$ cat /$i$ p up to 2.4 for H 2 O or 4.2 for MeOH at scan rates of 0.1 V/s). Bulk electrolysis using 5 mM 1 and 1.05 M MeOH in acetonitrile at -2.2 V vs Fc +/0 over the course of 47 min gave H 2 as the only detectable product with a Faradaic efficiency of 96.7%. Electrochemical experiments indicate that CO 2 promotes 1-mediated H 2 production by lowering apparent pH. While evaluating 2 for electrocatalytic activity, this complex was found to decompose rapidly in the presence of acid. Although modest H + reduction activity was realized, the experiments described herein indicate that care must be taken when evaluating Mn complexes for electrocatalytic CO 2 reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Noninnocent Proton-Responsive Ligand Facilitates Reductive Deprotonation and Hinders CO 2 Reduction Catalysis in [Ru(tpy)(6DHBP)(NCCH 3 )] 2+ (6DHBP = 6,6'-(OH) 2 bpy)

Ruthenium complexes with proton-responsive ligands [Ru(tpy)(nDHBP)(NCCH 3 )](CF 3 SO 3 ) 2 (tpy = 2,2':6',2"-terpyridine; nDHBP = n,n'-dihydroxy-2,2'-bipyridine, n = 4 or 6) were examined in this study for reductive chemistry and as catalysts for CO 2 reduction. Electrochemical reduction of [Ru(tpy)(nDHBP)(NCCH 3 )] 2+ generates deprotonated species through interligand electron transfer in which the initially formed tpy radical anion reacts with a proton source to produce singly and doubly deprotonated complexes that are identical to those obtained by base titration. A third reduction (i.e., reduction of [Ru(tpy)(nDHBP–2H + )] 0 ) triggers catalysis of CO 2 reduction; however, the catalytic efficiency is strikingly lower than that of unsubstituted [Ru(tpy)(bpy)(NCCH 3 )] 2+ (bpy = 2,2'-bipyridine). Cyclic voltammetry, bulk electrolysis, and spectroelectrochemical infrared experiments suggest the reactivity of CO 2 at both the Ru center and the deprotonated quinone-type ligand. Lastly, the Ru carbonyl formed by the intermediacy of a metallocarboxylic acid is stable against reduction, and mass spectrometry analysis of this product indicates the presence of two carbonates formed by the reaction of DHBP–2H + with CO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions. Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies

Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand–binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f , 25i , and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g- bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand–binding site interactions are possibly responsible for their potent activity.

Ghosh, Arun K.↗
DOE OSTI2015

Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes with menin. Here, we found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Lastly, considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker

A novel series of macrocyclic FXIa inhibitors was designed based on our lead acyclic phenyl imidazole chemotype. Our initial macrocycles, which were double-digit nanomolar FXIa inhibitors, were further optimized with assistance from utilization of structure-based drug design and ligand bound X-ray crystal structures. This effort resulted in the discovery of a macrocyclic amide linker which was found to form a key hydrogen bond with the carbonyl of Leu41 in the FXIa active site, resulting in potent FXIa inhibitors. Here, the macrocyclic FXIa series, exemplified by compound 16, had a FXIa K i = 0.16 nM with potent anticoagulant activity in an in vitro clotting assay (aPTT EC 1.5x = 0.27 μM) and excellent selectivity against the relevant blood coagulation enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular Mechanism of Inhibition of Acid Ceramidase by Carmofur

Human acid ceramidase (AC) is a lysosomal cysteine amidase, which has received a great deal of interest in recent years as a potential target for the development of new therapeutics against melanoma and glioblastoma tumors. Despite the strong interest in obtaining structural information, only the structures of the apo-AC enzyme in its zymogen and activated conformations are available. In this work, the crystal structure of AC in complex with the covalent carmofur inhibitor is presented. Carmofur is an antineoplastic drug containing an electrophilic carbonyl reactive group that targets the catalytic cysteine. This novel structural data explains the basis of the AC inhibition, provides insights into the enzymatic properties of the protein, and is a great aid toward the structure-based drug design of potent inhibitors for AC, providing the detailed mechanism, which has eluded the scientific community for more than 30 years, of carmofur's mysterious 5-fluorouracil-independent antitumor activity.

Dementiev, Alexey↗
DOE OSTI2021

Dramatic Conformer-Dependent Reactivity of the Acetaldehyde Oxide Criegee Intermediate with Dimethylamine Via a 1,2-Insertion Mechanism

The reactivity of carbonyl oxides has previously been shown to exhibit strong conformer and substituent dependencies. Through a combination of synchrotron multiplexed photoionization mass spectrometry experiments (298 K, 4 Torr) and high-level theory (CCSD(T)-F12/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ with an added CCSDT(Q) correction), we explore the conformer dependence of the reaction of acetaldehyde oxide (CH 3 CHOO) with dimethyl amine (DMA). The experimental data supports the theoretically predicted 1,2-insertion mechanism and the formation of an amine-functionalized hydroperoxide reaction product. Tunable-VUV photoionization probing of anti- or anti- + syn-CH 3 CHOO reveals a strong conformer dependence of the title reaction. Here, the rate coefficient of DMA with anti-CH 3 CHOO is predicted to exceed that for the reaction with syn-CH 3 CHOO by a factor of ~34,000, which is attributed to submerged barrier (syn) vs. barrierless (anti) mechanisms for energetically downhill reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues

We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR–IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. Here, these observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Excited-State Dynamics during Primary C–I Homolysis in Acetyl Iodide Revealed by Ultrafast Core-Level Spectroscopy

In typical carbonyl-containing molecules, bond dissociation events follow initial excitation to $nπ_{C=O}$$^*$ states. However, in acetyl iodide, the iodine atom gives rise to electronic states with mixed $nπ_{C=O}$$^*$ and $nπ_{C–I}$$^*$ character, leading to complex excited-state dynamics, ultimately resulting in dissociation. Using ultrafast extreme ultraviolet (XUV) transient absorption spectroscopy and quantum chemical calculations, we present an investigation of the primary photodissociation dynamics of acetyl iodide via time-resolved spectroscopy of core-to-valence transitions of the I atom after 266 nm excitation. The probed I 4d-to-valence transitions show features that evolve on sub-100-fs time scales, reporting on excited-state wavepacket evolution during dissociation. These features subsequently evolve to yield spectral signatures corresponding to free iodine atoms in their spin–orbit ground and excited states with a branching ratio of 1.1:1 following dissociation of the C–I bond. Calculations of the valence excitation spectrum via equation-of-motion coupled cluster with single and double substitutions (EOM-CCSD) show that initial excited states are of spin-mixed character. From the initially pumped spin-mixed state, we use a combination of time-dependent density functional theory (TDDFT)-driven nonadiabatic ab initio molecular dynamics and EOM-CCSD calculations of the N$_{4,5}$ edge to reveal a sharp inflection point in the transient XUV signal that corresponds to rapid C–I homolysis. Here, by examining the molecular orbitals involved in the core-level excitations at and around this inflection point, we are able to piece together a detailed picture of C–I bond photolysis in which d → σ* transitions give way to d → p excitations as the bond dissociates. We also report theoretical predictions of short-lived, weak 4d → 5d transitions in acetyl iodide, validated by weak bleaching in the experimental transient XUV spectra. This joint experimental–theoretical effort has thus unraveled the detailed electronic structure and dynamics of a strongly spin–orbit coupled system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Bimolecular Reaction of Methyl-Ethyl-Substituted Criegee Intermediate with SO 2

Methyl-ethyl-substituted Criegee intermediate (MECI) is a four-carbon carbonyl oxide that is formed in the ozonolysis of some asymmetric alkenes. MECI is structurally similar to the isoprene-derived methyl vinyl ketone oxide (MVK-oxide) but lacks resonance stabilization, making it a promising candidate to help us unravel the effects of size, structure, and resonance stabilization that influence the reactivity of atmospherically important, highly functionalized Criegee intermediates. We present experimental and theoretical results from the first bimolecular study of MECI in its reaction with SO 2 , a reaction that shows significant sensitivity to the Criegee intermediate structure. Using multiplexed photoionization mass spectrometry, we obtain a rate coefficient of (1.3 ± 0.3) × 10 –10 cm 3 s –1 (95% confidence limits, 298 K, 10 Torr) and demonstrate the formation of SO 3 under our experimental conditions. Through high-level theory, we explore the effect of Criegee intermediate structure on the minimum energy pathways for their reactions with SO 2 and obtain modified Arrhenius fits to our predictions for the reaction of both syn and anti conformers of MECI with SO 2 (k syn = 4.42 × 10 11 T –7.80 exp(-1401/T) cm 3 s –1 and k anti = 1.26 × 10 11 T –7.55 exp(-1397/T) cm 3 s –1 ). In conclusion, our experimental and theoretical rate coefficients (which are in reasonable agreement at 298 K) show that the reaction of MECI with SO 2 is significantly faster than MVK-oxide + SO 2 , demonstrating the substantial effect of resonance stabilization on Criegee intermediate reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2026

Photodissociation and Infrared Spectroscopy of U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n Cation-Molecular Complexes

Laser vaporization of uranium in a pulsed supersonic expansion of carbon dioxide is used to produce complexes of the form U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n . These ions are selected in a reflectron time-offlight mass spectrometer and studied with visible laser photodissociation and tunable infrared laser photodissociation spectroscopy in the region of the CO 2 antisymmetric stretch. The dissociation patterns and spectroscopy of these ions indicate that CO 2 ligands are intact molecules. Although reaction products that form oxide-carbonyl or oxalate species are predicted to be stable, there is no direct evidence in the frequency range studied for the formation of these species. There is no clear indication for the coordination numbers for singly charged uranium and its oxide complexes with CO 2 . However, there is strong support in the vibrational patterns for an eight-coordinate complex of the doubly charged UO 2+ species, i.e., UO 2+ (CO 2 ) 8 .

Cluster chemistry↗
DOE OSTI2016

Probing the Heterogeneous Ozonolysis of Squalene Nanoparticles by Photoemission

The heterogeneous reaction of ozone (O 3 ) with 200 nm squalene nanoparticles is studied in this paper using near-edge X-ray absorption fine structure (NEXAFS) and ultraviolet (UPS) and X-ray photoelectron spectroscopy (XPS). Photoelectrons are detected from free nanoparticle beams using a velocity map imaging (VMI) spectrometer capable of detecting photoelectrons with up to 40 eV of kinetic energy. Heterogeneous kinetics are quantified using changes in the UPS, XPS, and NEXAFS spectrum, yielding uptake coefficients for the decay of the double bonds in squalene of (3.1 ± 0.7) × 10 –4 , (2.6 ± 0.6) × 10 –4 , and (2.9 ± 0.7) × 10 –4 , respectively. When comparing these values with the uptake coefficient, (1.0 ± 0.2) × 10 –3 , determined by the molecular decay of squalene measured with aerosol mass spectrometry, it is found that on average 1.6 ± 0.2 double bonds are removed for each ozone-squalene reactive collision, suggesting the importance of evaporation of small molecular weight reaction products from the aerosol. From further analysis of the nanoparticle XPS spectrum, it is found that ozonolysis increases the oxygen-to-carbon (O:C) ratio of the aerosol to 0.43 ± 0.03 and produces 16 ± 4% and 84 ± 4% secondary ozonides and carbonyls, respectively. Finally, the methods developed here show how aerosol photoemission can be used to quantify heterogeneous reaction on free nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Understanding Trends in Autoignition of Biofuels: Homologous Series of Oxygenated C5 Molecules

Oxygenated biofuels provide a renewable, domestic source of energy that can enable adoption of advanced, high-efficiency internal combustion engines, such as those based on homogeneously charged compression ignition (HCCI). Of key importance to such engines is the cetane number (CN) of the fuel, which is determined by the autoignition of the fuel under compression at relatively low temperatures (550-800 K). For the plethora of oxygenated biofuels possible, it is desirable to know the ignition delay times and the CN of these fuels to help guide conversion strategies so as to focus efforts on the most desirable fuels. For alkanes, the chemical pathways leading to radical chain-branching reactions giving rise to low-temperature autoignition are well-known and are highly coincident with the buildup of reactive radicals such as OH. Key in the mechanisms leading to chain branching are the addition of molecular oxygen to alkyl radicals and the rearrangement and dissociation of the resulting peroxy radials. Prediction of the temperature and pressure dependence of reactions that lead to the buildup of reactive radicals requires a detailed understanding of the potential energy surfaces (PESs) of these reactions. In this study, we used quantum mechanical modeling to systematically compare the effects of oxygen functionalities on these PESs and associated kinetics so as to understand how they affect experimental trends in autoignition and CN. The molecules studied here include pentane, pentanol, pentanal, 2-heptanone, methylpentyl ether, methyl hexanoate, and pentyl acetate. All have a saturated five-carbon alkyl chain with an oxygen functional group attached to the terminal carbon atom. The results of our systematic comparison may be summarized as follows: (1) Oxygen functionalities activate C-H bonds by lowering the bond dissociation energy (BDE) relative to alkanes. (2) The R-OO bonds in peroxy radicals adjacent to carbonyl groups are weaker than corresponding alkyl systems, leading to dissociation of ROO radicals and reducing reactivity and hence CN. (3) Hydrogen atom transfer in peroxy radicals is important in autoignition, and low barriers for ethers and aldehydes lead to high CN. (4) Peroxy radicals formed from alcohols have low barriers to form aldehydes, which reduce the reactivity of the alkyl radical. In conclusion, these findings for the formation and reaction of alkyl radicals with molecular oxygen explain the trend in CN for these common biofuel functional groups.

09 BIOMASS FUELS↗
DOE OSTI2017

Aerosol Fragmentation Driven by Coupling of Acid–Base and Free-Radical Chemistry in the Heterogeneous Oxidation of Aqueous Citric Acid by OH Radicals

A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity. The reaction scheme, containing both free-radical and acid-base elementary reaction steps with physically validated rate coefficients, accurately predicts the experimentally observed molecular composition, particle size, and average elemental composition of the aerosol upon oxidation. The difference between the two reaction channels centers on the reactivity of carboxylic acid groups. Free-radical reactions mainly add functional groups to the carbon skeleton of neutral citric acid, because carboxylic acid moieties deactivate the unimolecular fragmentation of alkoxy radicals. In contrast, the conjugate carboxylate groups originating from acid-base equilibria activate both acyloxy radical formation and carbon-carbon bond scission of alkoxy radicals, leading to the formation of low molecular weight, highly oxidized products such as oxalic and mesoxalic acid. Subsequent hydration of carbonyl groups in the oxidized products increases the aerosol hygroscopicity and accelerates the substantial water uptake and volume growth that accompany oxidation. These results frame the oxidative lifecycle of atmospheric aerosol: it is governed by feedbacks between reactions that first increase the particle oxidation state, then eventually promote water uptake and acid-base chemistry. When coupled to free-radical reactions, acid-base channels lead to formation of low molecular weight gas-phase reaction products and decreasing particle size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Reaction Pathways, Thermodynamics, and Kinetics of Cyclopentanone Oxidation Intermediates: A Theoretical Approach

Despite the promising role of cyclopentanone as a bio-derived fuel, thermodynamic and kinetic data are lacking for low temperature oxidation regimes. In this study, ab initio calculations at the CBS-QB3 level explore the subsequent reactivity that results from O 2 -addition to 2- and 3-oxo cyclopentyl radicals, including expected reaction classes such as intra-H migration, HO 2 -elimination, cyclic ether formation and β-scission along with their thermodynamic parameters. Some of the rates are similar to the analogous reactions of cyclopentane, but some other reactions of cyclopentanone are very different. The carbonyl group hinders H-migration from the α’ position but promotes HO 2 -elimination. Enol peroxy formation from some hydroperoxy alkyl radicals of cyclopentanone is unexpectedly important, and so is HO 2 -elimination by β-scission. Our calculations also indicated that at engine relevant conditions the α-RO 2 prefers to go back to reactants 2-oxo cyclopentyl radical and O 2 . Therefore, the reactions resulting from HO2-addition to 2-oxo cyclopentyl is also provided. The lowest barrier channel identified on the singlet surface corresponds to an unexpected intra OH-migration path concerted with ring opening. In conclusion, this valuable information will advance the construction of improved kinetic models for the oxidation of cylopentanone.

09 BIOMASS FUELS↗
DOE OSTI2025

Photoactivation Transition State and Dynamical Response of the Orange Carotenoid Protein

The orange carotenoid protein (OCP) regulates light harvesting in cyanobacteria by acting as a photoreceptor in its resting form, OCP O , and by effecting the quenching of bilin excitons upon binding to the core of the phycobilisome in its photoactivated red form, OCP R . We show herein using fluorescence anisotropy measurements and the action spectra for the rate constants of the two light-driven steps in the mechanism that the photoactivation of the OCP from Synechocystis sp. PCC 6803 is triggered by excited-state motions of the canthaxanthin chromophore that yield a twisted and bent conformation. Well-tempered metadynamics simulations reveal that a bicycle-pedal configuration, due to twisting of the two adjacent C=C bonds at the C13−C14 and C15−C15′ positions in the center of canthaxanthin’s π-conjugated isoprenoid backbone, can be accommodated by the binding site in the OCP, with the energy of a captured photon required to cross the local activation energy barriers from the dark equilibrium structure. The bicycle-pedal configuration breaks the conserved hydrogen-bonding interactions between the carbonyl substituent of the β-ionone end ring of canthaxanthin and the adjacent W288 and Y201 residues in the C-terminal domain. The action spectra are modulated by the vibronic excitation prepared by absorption transitions to the S 2 state, indicating that the photoactivation reactions are triggered by the canthaxanthin chromophore well prior to vibrational equilibration. These findings show that an ultrafast structural response of the OCP protein to the excited-state motions of the canthaxanthin chromophore controls the photoactivation yield and the sensing of blue light.

Fluorescence↗