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DOE OSTI2020

Water Catalysis of the Reaction of Methanol with OH Radical in the Atmosphere is Negligible

Abstract Faced with the contradictory results of two recent experimental studies [Jara‐Toro et al., Angew. Chem. Int. Ed . 2017 , 56 , 2166 and Chao et al., Angew. Chem. Int. Ed . 2019 , 58 , 5013] of the possible catalytic effect of water vapor on CH 3 OH + OH reaction, we report calculations that corroborate the conclusion made by Chao et al. and extend the rate constant evaluation down to 200 K. The rate constants of the CH 3 OH + OH reaction catalyzed by a water molecule are computed as functions of temperature and relative humidity using high‐level electronic structure and kinetics calculations. The Wuhan–Minnesota Scaling (WMS) method is used to provide accurate energetics to benchmark a density functional for direct dynamics. Both high‐frequency and low‐frequency anharmonicities are included. Variational and tunneling effects are treated by canonical variational transition state theory with multidimensional small‐curvature tunneling. And, most significantly, we include multistructural effects in the rate constant calculations. Our calculations show that the catalytic effect of water vapor is not observable at 200–400 K.

Wu, Junjun↗

DOE OSTI2020

Hydrogen Bonding Enhances the Electrochemical Hydrogenation of Benzaldehyde in the Aqueous Phase

Abstract The hydrogenation of benzaldehyde to benzyl alcohol on carbon‐supported metals in water, enabled by an external potential, is markedly promoted by polarization of the functional groups. The presence of polar co‐adsorbates, such as substituted phenols, enhances the hydrogenation rate of the aldehyde by two effects, that is, polarizing the carbonyl group and increasing the probability of forming a transition state for H addition. These two effects enable a hydrogenation route, in which phenol acts as a conduit for proton addition, with a higher rate than the direct proton transfer from hydronium ions. The fast hydrogenation enabled by the presence of phenol and applied potential overcompensates for the decrease in coverage of benzaldehyde caused by competitive adsorption. A higher acid strength of the co‐adsorbate increases the intensity of interactions and the rates of selective carbonyl reduction.

Sanyal, Udishnu↗

DOE OSTI2022

Maximum Impact of Ionic Strength on Acid‐Catalyzed Reaction Rates Induced by a Zeolite Microporous Environment

Abstract The intracrystalline ionic environment in microporous zeolite can remarkably modify the excess chemical potential of adsorbed reactants and transition states, thereby influencing the catalytic turnover rates. However, a limit of the rate enhancement for aqueous‐phase dehydration of alcohols appears to exist for zeolites with high ionic strength. The origin of such limitation has been hypothesized to be caused by the spatial constraints in the pores via, e.g., size exclusion effects. It is demonstrated here that the increase in turnover rate as well as the formation of a maximum and the rate drop are intrinsic consequences of the increasingly dense ionic environment in zeolite. The molecularly sized confines of zeolite create a unique ionic environment that monotonically favors the formation of alcohol‐hydronium ion complexes in the micropores. The zeolite microporous environment determines the kinetics of catalytic steps and tailors the impact of ionic strength on catalytic rates.

Liu, Qiang↗

DOE OSTI2024

Facile Access to Organostibines via Selective Organic Superbase Catalyzed Antimony‐Carbon Protonolysis

Abstract The selective formation of antimony‐carbon bonds via organic superbase catalysis under metal‐ and salt‐free conditions is reported. This novel approach utilizes electron‐deficient stibine, Sb(C 6 F 5 ) 3 , to give upon base‐catalyzed reactions with weakly acidic aromatic and heteroaromatic hydrocarbons access to a range of new aromatic and heteroaromatic stibines, respectively, with loss of C 6 HF 5 . Also, the significantly less electron‐deficient stibines, Ph 2 SbC 6 F 5 and PhSb(C 6 F 5 ) 2 smoothly underwent base‐catalyzed exchange reactions with a range of terminal alkynes to generate the stibines of formulae PhSb(C≡CPh) 2 , and Ph 2 SbC≡CR [R=C 6 H 5 , C 6 H 4 ‐NO 2 , COOEt, CH 2 Cl, CH 2 NEt 2 , CH 2 OSiMe 3 , Sb(C 6 H 5 ) 2 ], respectively. These formal substitution reactions proceed with high selectivity as only the C 6 F 5 groups serve as a leaving group to be liberated as C 6 HF 5 upon formal proton transfer from the alkyne. Kinetic studies of the base‐catalyzed reaction of Ph 2 SbC 6 F 5 with phenyl acetylene to form Ph 2 SbC≡CPh and C 6 HF 5 suggested the empirical rate law to exhibit a first‐order dependence with respect to the base catalyst, alkyne and stibine. DFT calculations support a pathway proceeding via a concerted σ‐bond metathesis transition state, where the base catalyst activates the Sb‐C 6 F 5 bond sequence through secondary bond interactions.

Culvyhouse, Jacob↗

DOE OSTI2020

Water Catalysis of the Reaction of Methanol with OH Radical in the Atmosphere is Negligible

Not provided.

Chemistry↗

DOE OSTI2020

Enantioselective Intramolecular Allylic Substitution via Synergistic Palladium/Chiral Phosphoric Acid Catalysis: Insight into Stereoinduction through Statistical Modeling

The mode of asymmetric induction in an enantioselective intramolecular allylic substitution reaction catalyzed by a combination of palladium and a chiral phosphoric acid was investigated by a combined experimental and statistical modeling approach. Experiments to probe nonlinear effects, the reactivity of deuterium-labeled substrates, and control experiments revealed that nucleophilic attack to the π-allylpalladium intermediate is the enantio-determining step, in which the chiral phosphate anion is involved in stereoinduction. Here, using multivariable linear regression analysis, we determined that multiple noncovalent interactions with the chiral environment of the phosphate anion are integral to enantiocontrol in the transition state. The synthetic protocol to form chiral pyrrolidines was further applied to the asymmetric construction of C-O bonds at fully substituted carbon centers in the synthesis of chiral 2,2-disubstituted benzomorpholines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Maximum Impact of Ionic Strength on Acid‐Catalyzed Reaction Rates Induced by a Zeolite Microporous Environment

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Vinyl Halide-Modified Unsaturated Cyclitols are Mechanism-Based Glycosidase Inhibitors

Suitably configured allyl ethers of unsaturated cyclitols act as substrates of β-glycosidases, reacting via allylic cation transition states. Incorporation of halogens at the vinylic position of these carbasugars, along with an activated leaving group, generates potent inactivators of β-glycosidases. Enzymatic turnover of these halogenated cyclitols (F, Cl, Br) displayed a counter-intuitive trend wherein the most electronegative substituents yielded the most labile pseudo-glycosidic linkages. Structures of complexes with the Sulfolobus β-glucosidase revealed similar enzyme-ligand interactions to those seen in complexes with a 2-fluorosugar inhibitor, the lone exception being displacement of tyrosine 322 from the active site by the halogen. Mutation of Y322 to Y322F largely abolished glycosidase activity, consistent with lost interactions at O5, but minimally affected (7-fold) rates of carbasugar hydrolysis, yielding a more selective enzyme for unsaturated cyclitol ether hydrolysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Facile Access to Organostibines via Selective Organic Superbase Catalyzed Antimony‐Carbon Protonolysis

The selective formation of antimony-carbon bonds via organic superbase catalysis under metal- and salt-free conditions is reported. Here, this novel approach utilizes electron-deficient stibine, Sb(C 6 F 5 ) 3 , to give upon base-catalyzed reactions with weakly acidic aromatic and heteroaromatic hydrocarbons access to a range of new aromatic and heteroaromatic stibines, respectively, with loss of C 6 HF 5 . Also, the significantly less electron-deficient stibines, Ph 2 SbC 6 F 5 and PhSb(C 6 F 5 ) 2 smoothly underwent base-catalyzed exchange reactions with a range of terminal alkynes to generate the stibines of formulae PhSb(C≡CPh) 2 , and Ph 2 SbC≡CR [R=C 6 H 5 , C 6 H 4 -NO 2 , COOEt, CH 2 Cl, CH 2 NEt 2 , CH 2 OSiMe 3 , Sb(C 6 H 5 ) 2 ], respectively. These formal substitution reactions proceed with high selectivity as only the C 6 F 5 groups serve as a leaving group to be liberated as C 6 HF 5 upon formal proton transfer from the alkyne. Kinetic studies of the base-catalyzed reaction of Ph 2 SbC 6 F 5 with phenyl acetylene to form Ph 2 SbC≡CPh and C 6 HF 5 suggested the empirical rate law to exhibit a first-order dependence with respect to the base catalyst, alkyne and stibine. DFT calculations support a pathway proceeding via a concerted σ-bond metathesis transition state, where the base catalyst activates the Sb-C 6 F 5 bond sequence through secondary bond interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Variations of Alloying Site Density in Pd 1 Cu Single‐Atom Alloy Catalysts Lead to Shifted Product Yields in Electrochemical CO Reduction

Single-atom alloy (SAA) catalysis research often reports that a SAA catalyst, in the general formulation of a single-atom metal M1 alloyed on the surface of the host metal M2, facilitates a probe reaction. However, for catalytic reactions that present decoupled rate- and selectivity-limiting steps, the alloying site density may significantly manipulate these independent steps, but it has rarely been explicitly examined for any SAA systems. Herein, using the electrocatalytic CO reduction as a probe reaction, we report that the nominal Pd 1 Cu cube SAA catalysts exhibit distinctive high reactivity toward ethylene or ethanol, respectively, depending on whether the Pd atoms are in dilute or crowded forms. Although the presence of single-atom Pd embedded on Cu uniformly promotes CHO* formation and C─C coupling, the dilute-Pd 1 Cu favors ethylene formation by enabling low-barrier C─O cleavage from a flat CH 2 CH 2 OH* intermediate, whereas the crowded-Pd 1 Cu promotes ethanol formation by stabilizing an upright hydrogenation transition state of the same intermediate. Furthermore, we present evidence that the catalytic chemistry of crowded Pd 1 species differs from that of the Pd 2 -dimer; the latter, albeit unstable, steers reaction selectivity to acetate instead. In conclusion, these results uncovered the underappreciated importance of controlling SAA catalytic chemistry from the perspective of single-atom site densities.

Jin, Zehua [Clemson University, SC (United States)↗

DOE OSTI2022

Consequences of Intrapore Liquids on Reactivity, Selectivity, and Stability for Aldol Condensation Reactions on Anatase TiO 2 Catalysts

Abstract This study provides evidence and mechanistic interpretations for the significant consequences of intrapore non‐polar liquids on acetone aldol condensation turnover rates, selectivity to primary dimer products, and catalyst stability for reactions at Lewis acid‐base site pairs on TiO 2 surfaces. These non‐polar liquids confer such benefits through the preferential stabilization of transition states (TS) for adsorption (“entry”) and desorption (“exit”) steps, which place their respective reactants or products within a solvating outer sphere environment. The extent to which non‐polar fluids ( n ‐heptane) form an intrapore liquid phase within TiO 2 voids was obtained from N 2 uptakes using established formalisms that consider the different molal volume, surface tension, and volatility between N 2 and n ‐heptane. Acetone condensation rates are limited by C−H activation, an “entry” step that forms bound prop‐1‐en‐2‐olates via a TS stabilized by intrapore liquids, leading to higher aldol condensation turnover rates as n ‐heptane pressure increases and active TiO 2 surfaces become increasingly immersed within a non‐polar liquid phase. These liquids solvate the late TS structures that mediate the desorption of primary C 6 condensation products even more effectively than those involved in prop‐1‐en‐2‐olate formation or in nucleophilic attack events that later form C−C bonds. Such preferential solvation favors desorption over C−C coupling events, thus disfavoring the formation of larger oligomers that become stranded at active sites, thus leading to much slower deactivation. Moreover, solvation by non‐polar liquids also leads to C 6 alkanones as the sole products formed in a single surface sojourn. These effects of a non‐polar dense phase circumvent the inherent stability, reactivity, and selectivity hurdles that have precluded practical aldol condensation catalysis on Lewis acid‐base pairs at oxide surfaces; these consequences are demonstrated here for TiO 2 catalysts, acetone aldol condensation reactions, and n ‐heptane as the non‐polar liquid but through strategies, concepts, and mechanistic features that extend to other systems. More generally, these observations and their mechanistic origins demonstrate how a contacting liquid preferentially solvates TS structures for elementary steps that involve either reactants arriving from or products entering into an outer sphere environment that contains a dense non‐polar phase.

Kadam, Shashikant A.↗

DOE OSTI2021

Hydrosilane σ‐Adduct Intermediates in an Adaptive Zinc‐Catalyzed Cross‐dehydrocoupling of Si−H and O−H Bonds

Abstract Three‐coordinate Ph BOX ZnR ( Ph BOX =phenyl‐(4,4‐dimethyl‐oxazolinato; R=Me: 2 a , Et: 2 b ) catalyzes the dehydrocoupling of primary or secondary silanes and alcohols to give silyl ethers and hydrogen, with high turnover numbers (TON; up to 10 7 ) under solvent‐free conditions. Primary and secondary silanes react with small, medium, and large alcohols to give various degrees of substitution, from mono‐ to tri‐alkoxylation, whereas tri‐substituted silanes do not react with MeOH under these conditions. The effect of coordinative unsaturation on the behavior of the Zn catalyst is revealed through a dramatic variation of both rate law and experimental rate constants, which depend on the concentrations of both the alcohol and hydrosilane reactants. That is, the catalyst adapts its mechanism to access the most facile and efficient conversion. In particular, either alcohol or hydrosilane binds to the open coordination site on the Ph BOX ZnOR catalyst to form a Ph BOX ZnOR(HOR) complex under one set of conditions or an unprecedented σ‐adduct Ph BOX ZnOR(H−SiR′ 3 ) under other conditions. Saturation kinetics provide evidence for the latter species, in support of the hypothesis that σ‐bond metathesis reactions involving four‐centered electrocyclic 2σ–2σ transition states are preceded by σ‐adducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Gas–Phase Synthesis of 3–Vinylcyclopropene via the Crossed Beam Reaction of the Methylidyne Radical (CH; X 2 Π) with 1,3–Butadiene (CH 2 CHCHCH 2 ; X 1 Ag)

The crossed molecular beam reactions of the methylidyne radical (CH; X 2 Π) with 1,3-butadiene (CH 2 CHCHCH 2 ; X 1 Ag) along with their (partially) deuterated counterparts were performed at collision energies of 20.8 kJ mol -1 under single collision conditions. Combining our laboratory data with ab initio calculations, we reveal that the methylidyne radical may add barrierlessly to the terminal carbon atom and/or carbon-carbon double bond of 1,3-butadiene, leading to doublet C 5 H 7 intermediates with life times longer than the rotation periods. Furthermore, these collision complexes undergo non-statistical unimolecular decomposition through hydrogen atom emission yielding the cyclic cis- and trans-3-vinyl-cyclopropene products with reaction exoergicities of 119±42 kJ mol -1 . Since this reaction is barrierless, exoergic, and all transition states are located below the energy of the separated reactants, these cyclic C 5 H 6 products are predicted to be accessed even in low-temperature environments, such as in hydrocarbon-rich atmospheres of planets and cold molecular clouds such as TMC-1.

3-vinylcyclopropene↗

DOE OSTI2025

Mechanistic Insights into the Demethylation of Lignin‐Derived Structures Using Protic Ionic Liquids: A Density Functional Theory Study

Lignin valorization is restricted by the stability of its methoxy groups, creating a critical need for efficient demethylation strategies. Here, in this study, density functional theory (DFT) is employed to dissect the mechanistic pathways of demethylation in lignin model compounds, guaiacol and syringol, using protic ionic liquids (PILs) that act as both solvent and catalyst. Conductor‐like Screening Model for Real Solvents (COSMO‐RS) analysis identifies monoethanolammonium acetate ([MEOA][Ace]) as the most promising medium, attributed to its strong hydrogen bonding network and solvation ability. By integrating implicit and explicit solvation models, it is revealed that an acid‐catalyzed hydrolytic mechanism governs demethylation, with PILs stabilizing crucial transition states and intermediates. Complementary electronic structure evaluations, including highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO‐LUMO) gap analysis, charge distribution, and electrostatic potential mapping, demonstrate how PILs lower energetic barriers and enhance reactivity. To simulate realistic environments, this study is extended to lignin dimer complexes with varying water content, uncovering how water‐bridged solvation reverses demethylation preference from guaiacyl to syringyl units. This mechanistic shift aligns with experimental observations showing faster S‐unit reactivity in hydrated systems. Together, these findings provide atomic‐level insight into lignin demethylation dynamics and highlight how tuning acid concentration in PILs can accelerate kinetics, enabling a rational pathway toward next‐generation biomass conversion technologies.

COSMO-RS↗

DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗

DOE OSTI2022

Chemical transformations and transport phenomena at interfaces

Abstract Interfaces, the boundary that separates two or more chemical compositions and/or phases of matter, alters basic chemical and physical properties including the thermodynamics of selectivity, transition states, and pathways of chemical reactions, nucleation events and phase growth, and kinetic barriers and mechanisms for mass transport and heat transport. While progress has been made in advancing more interface‐sensitive experimental approaches, their interpretation requires new theoretical methods and models that in turn can further elaborate on the microscopic physics that make interfacial chemistry so unique compared to the bulk phase. In this review, we describe some of the most recent theoretical efforts in modeling interfaces, and what has been learned about the transport and chemical transformations that occur at the air–liquid and solid–liquid interfaces. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Materials Science Software > Quantum Chemistry Software > Simulation Methods

Hao, Hongxia↗

DOE OSTI2024

The role of stereochemistry in combustion processes

Stereochemical effects significantly influence chemical processes, yet it is not well understood if they are a leading source of uncertainty in combustion modeling. Stereochemistry influences a combustion model (i) at the earliest stage of its construction when mapping the reaction network, (ii) in the computation of individual thermochemical and rate parameters, and (iii) in the prediction of combustion observables. The present work reviews the importance of enumerating stereochemical species and reactions at each of these steps. Further, it analyzes the separate influence of several types of stereochemistry, including geometric, optical, and fleeting transition state diastereomers. Three reaction networks serve to examine which stages of low-temperature oxidation are most affected by stereochemistry, including the first and second oxidation of n-butane, the third oxidation of n-pentane, and the early stages of pyrolysis of 1- and 2-pentene. The 149 reactions in the n-butane mechanism are expanded to 183 reactions when accounting for diastereomerism. Each of these 183 reactions is parameterized with ab initio kinetics computations to determine that, for the n-butane mechanism, the median factor of diastereomeric deviation is 3.5 at 360 K for rate constants and as high as 1.6 for mechanism reactivity, in terms of ignition delay times, as opposed to a mechanism without stereochemical expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Gravitational index of the heterotic string

The fundamental heterotic string has a tower of BPS states whose supersymmetric index has an exponential growth in the charges. We construct the saddle-point of the gravitational path integral corresponding to this index. The saddle-point configuration is a supersymmetric rotating non-extremal Euclidean black hole. This configuration is singular in the two-derivative theory. We show that the addition of higher-derivative terms in four-dimensional N = 2 supergravity resolves the singularity. In doing so, we extend the recently-developed “new attractor mechanism” to include the effect of higher-derivative terms. Remarkably, the one-loop, four-derivative F-term contribution to the prepotential leads to a precise match of the gravitational and microscopic index. We also comment, using the effective theory near the horizon, on the possibility of a string-size near-extremal black hole. Our results clarify the meaning of different descriptions of this system in the literature. The thermal state transitions to a winding condensate and a gas of strings without ever reaching a small black hole, while the index is captured by the rotating Euclidean black hole solution and is constant and thus smoothly connected to the microscopic ensemble.

79 ASTRONOMY AND ASTROPHYSICS↗