Intrinsic kinetic model for oxidative dehydrogenation of ethane over MoVTeNb mixed metal oxides: A mechanistic approach
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Donaubauer, Philipp J.↗
SEARCH · Engineering Papers
Results for “hydrogen bonds”
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Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex
The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Nanoscale Ternary Amide‐rGO Composite with Boosted Kinetics for Reversible H 2 Storage
Abstract Metal amides are attractive candidates for hydrogen storage due to their high volumetric and gravimetric hydrogen densities. However, the sluggish kinetics and competing side reactions during hydrogen uptake and release limit their practical use. Here, a novel nanoconfined Li 2 Mg(NH) 2 @reduced graphene oxide (rGO) composite is presented, which is fabricated using a melt‐infiltration method with a minimum weight penalty of only 2 wt.%. The presence of rGO ensures close contact between the active phases, effectively preventing aggregation during cycling process. As a result, the reversible capacity of Li 2 Mg(NH) 2 @rGO reaches 4.42 wt.%, with no capacity degradation observed after multiple cycling. Theoretical calculations show that rGO catalyzes the hydrogen bond cleavage at the Mg‐amide/Li hydride interface, leading to local dehydrogenation hotspots and significantly improves kinetics of dehydrogenation compared to the bulk counterpart. This study provides a promising strategy for designing metal imide‐based composites to overcome the kinetic limitations and improve their reversible hydrogen storage performance.
08 HYDROGEN↗
Atomically Precise Single Metal Oxide Cluster Catalyst with Oxygen–Controlled Activity
Single cluster catalysts (SCCs) consisting of atomically precise metal nanoclusters dispersed on supports represent a new frontier of heterogeneous catalysis. However, the ability to synthesize SCCs with high loading and to precisely introduce non-metal atoms to further tune their catalytic activity and reaction scope of SCCs have been longstanding challenges. In this work, a new interface confinement strategy is developed for the synthesis of a high density of atomically precise Ru oxide nanoclusters (Ru 3 O 2 ) on reduced graphene oxide (rGO), attributed to the suppression of diffusion-induced metal cluster aggregation. Ru 3 O 2 /rGO exhibits a significantly enhanced activity for oxidative dehydrogenation of 1,2,3,4-tetrahydroquinoline (THQ) to quinoline with a high yield (≈86%) and selectivity (≈99%), superior to Ru and RuO 2 nanoparticles, and homogeneous single/multiple-site Ru catalysts. In addition, Ru 3 O 2 /rGO is also capable of efficiently catalyzing more complex oxidative reactions involving three reactants. The theoretical calculations reveal that the presence of two oxygen atoms in the Ru 3 O 2 motif not only leads to a weak hydrogen bonding interaction between the THQ reactant and the active site, but also dramatically depletes the density of states near the Fermi level, which is attributed to the increased positive valence state of Ru and the enhanced oxidative activity of the Ru 3 O 2 cluster for hydrogen abstraction.
36 MATERIALS SCIENCE↗
Mechanism and dynamics of fatty acid photodecarboxylase
Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Surface molecular pump enables ultrahigh catalyst activity
The performance of electrocatalysts is critical for renewable energy technologies. While the electrocatalytic activity can be modulated through structural and compositional engineering following the Sabatier principle, the insufficiently explored catalyst-electrolyte interface is promising to promote microkinetic processes such as physisorption and desorption. By combining experimental designs and molecular dynamics simulations with explicit solvent in high accuracy, we demonstrated that dimethylformamide can work as an effective surface molecular pump to facilitate the entrapment of oxygen and outflux of water. Dimethylformamide disrupts the interfacial network of hydrogen bonds, leading to enhanced activity of the oxygen reduction reaction by a factor of 2 to 3. This strategy works generally for platinum-alloy catalysts, and we introduce an optimal model PtCuNi catalyst with an unprecedented specific activity of 21.8 ± 2.1 mA/cm 2 at 0.9 V versus the reversible hydrogen electrode, nearly double the previous record, and an ultrahigh mass activity of 10.7 ± 1.1 A/mg Pt .
Science & Technology - Other Topics↗
Methanol adsorption and dissociation on GaP(110) studied by ambient pressure X-ray photoelectron spectroscopy
Ambient pressure X-ray photoelectron spectroscopy (AP-XPS) was used to investigate methanol (CH 3 OH) adsorption and reaction on the GaP(110) surface. Exposure of CH 3 OH to GaP(110) at room temperature led to the formation of at least four different surface species as indicated by analysis of C 1s and O 1s XPS features. By combining AP-XPS data with density functional theory calculations, the surface species were identified as methoxy (CH 3 O*), formaldehyde (CH 2 O*), and paired methanol (p-CH 3 O*H) and methoxy (p-CH 3 O*) species, where “paired” means that they belong to a hydrogen-bonded methoxy-methanol complex. Asterisk * here indicates an adsite. The formation of CH 2 O* via the dehydrogenation of CH 3 O* was shown to be limited by the availability of vacant phosphorus (P) sites on GaP(110). With an increase in CH 3 OH pressure, the fractional coverage of CH 3 O* species reached 0.55, and the surface P sites were completely saturated with hydrogen. Under a constant CH 3 OH pressure of 0.5 Torr, the surface concentration of the paired species and of CH 2 O* remained constant until 400 K. At higher temperatures, thermally driven reactions led to a significant increase in the concentration of surface CH x * species, which suggests that C-O bond cleavage of the CH 3 O group is the dominant decomposition mechanism on GaP(110). In conclusion, based on the reactivity of GaP(110) toward CH 3 OH dehydrogenation, elevated temperatures and CH 3 OH pressures may be used to functionalize this surface.
36 MATERIALS SCIENCE↗
Hydration structure of flat and stepped MgO surfaces
We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. Here, these species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Rapid and efficient hydrogen clathrate hydrate formation in confined nanospace
Clathrate hydrates are crystalline solids characterized by their ability to accommodate large quantities of guest molecules. Although CH 4 and CO 2 are the traditional guests found in natural systems, incorporating smaller molecules (e.g., H 2 ) is challenging due to the need to apply higher pressures to stabilize the hydrogen-bonded network. Another critical limitation of hydrates is the slow nucleation and growth kinetics. Here, we show that specially designed activated carbon materials can surpass these obstacles by acting as nanoreactors promoting the nucleation and growth of H 2 hydrates. The confinement effects in the inner cavities promote the massive growth of hydrogen hydrates at moderate temperatures, using pure water, with extremely fast kinetics and much lower pressures than the bulk system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cellular Phosphate Sensing and Anion Binding by an Azacrown‐Calixpyrrole Hybrid
A hybrid receptor-sensor for anions originating from the merging of positively charged ammonium moieties for electrostatic attraction/stronger binding of azacrowns with directionality of calixpyrrole hydrogen bond donors for selectivity is investigated. As demonstrated this hybrid receptor-sensor shows a remarkable selectivity for orthophosphate even in the presence of other phosphates and anions found in cellular materials (K assoc H 2 PO 4 − >H 2 P 2 O 7 2− >AMP − ≫ADP 2− or ATP 3− over halides, nitrate, or hydrogen sulfate; all Na + salts in water) but also cellular polyphosphate or phospholipids. This selectivity is harnessed in a real-time monitoring of cell lysis by lysozyme, which releases orthophosphate and other phosphates and anions from the cells. This sensitive (LOD 0.4 μM) fluorescence-based microscale method compares favorably with the state-of-the-art techniques but can easily be practiced in a high-throughput screening (HTS) manner. The anion binding and selectivity in aqueous solutions were investigated by NMR and put in context with phosphate binding of the parent calix[4]pyrrole. The microscopic understanding of anion binding by the hybrid receptor was then obtained from a combination of density functional theory (DFT), classical molecular dynamics (MD) with explicit water solvation, and ab initio MD (AIMD) simulations. Correlating the NMR and fluorescence binding data with studies of solvation of the receptor, phosphate anion, and the resulting complex confirms the binding is largely driven by entropic component (TΔS) associated with receptor and anion desolvation.
Anions↗
Bonding and reactivity of isostructural uranyl and neptunyl peroxide phases
Understanding the reactivity of actinide peroxides is critical for predicting the behavior of spent nuclear fuel in radiolytic environments. Herein, we report the synthesis and characterization of a lithium neptunyl(VI) hydroxo peroxo compound (LiNp), which is isostructural to the uranyl analogue (LiU). Single-crystal X-ray diffraction reveals that LiNp contains both [NpO 2 (O 2 ) 3 ] 4- and [NpO 2 (OH) 4 ] 2- units stabilized by Li + and hydrogen bonding and Raman spectroscopy shows systematic redshifts in neptunyl vibrational modes relative to uranyl. DFT calculations highlight the importance of secondary coordination in reproducing vibrational and structural features, but challenges remain with correctly modeling strong sigma donors. Solid-state EPR spectroscopy and DFT confirm superoxide stabilization within LiU and calculations suggest favorability of the analogous radical species in LiNp. Solution state EPR spectroscopy with the radical spin trap 5-tert-butoxycarbonyl-5-methyl-1-pyrroline N-oxide (BMPO) reveal evidence of superoxide in the LiU and LiNp phases and suggests stabilization of superoxide within actinyl triperoxide complexes, forming [AnO 2 (O 2 ) 2 (O) 2 • ] 3- .
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
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↗
Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila
Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila , can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidase enzyme OgpA, which cleaves peptide bonds at the N-terminus of serine (Ser) or threonine (Thr) residues carrying O-glycan substitutions, with selectivity influenced by the O-glycan functional groups. Using molecular dynamics (MD) simulations and quantum chemistry calculations, we explored how different O-glycan groups affect OgpA's selectivity. Our results show that peptides bind to the enzyme via hydrogen bonds, π–π interactions, van der Waals forces and electrostatic interactions, with key residues, including Tyr90, Val138, Gly176, Tyr210 and Glu91, playing important roles. The primary determinant of selectivity is the interaction between the peptide's functional group and the enzyme's binding cavity, while peptide–enzyme interface interactions are secondary. Quantum chemistry calculations reveal that OgpA prefers peptides with a lower electrophilic character. This study provides new insights into mucin degradation by gut microbiota enzymes, advancing our understanding of this critical biological process.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Microwave spectra of van der Waals complexes of importance in planetary atmospheres
The Fourier-transform Fabry-Perot pulsed-molecular-beam microwave spectrometer at NIST was used to study the microwave spectra of a number of molecular dimers and trimers that may be present in planetary atmospheres. The weak van der Waals bonds associated with these species usually give rise to rotational-tunneling splittings in the microwave spectra. The microwave spectrum of the water dimer species was used to illustrate the complications that can arise in the study of the rotational spectra of these loosely bound species. In addition to the water dimer species, the microwave spectra of the following hydrogen-bonded and van der Waals complexes were studied: (CO2)2-H2O, CO2-(H2O)2, CO2-H2S, N2-H2O, CO-H2O, SO2-H2O, and O3-H2O.
Suenram, R. D.↗
Photoelectron Spectroscopy and Computational Study on Microsolvated [B 10 H 10 ] 2– Clusters and Comparisons to Their [B 12 H 12 ] 2– Analogues
Microhydrated closo-Boranes have attracted great interests due to their superchaotropic activity related to well-known Hofmeister effect and important applications in biomedical and battery fields. In this work, we report a combined negative ion photoelectron spectroscopy and quantum chemical investigation on hydrated closo-decaborate clusters [B 10 H 10 ] 2- ·nH 2 O (n = 1 – 7) with a direct comparison to their analogues [B 12 H 12 ] 2- ·nH 2 O and free water clusters. A single H 2 O molecule is found sufficient to stabilize the intrinsically unstable [B 10 H 10 ] 2- dianion. The first two water molecules strongly interact with the solute forming B-H···H-O dihydrogen bonds while additional water molecules show substantially reduced binding energies. Unlike [B 12 H 12 ] 2- ·nH 2 O possessing highly structured water network with the attached H 2 O molecules arranged in a unified pattern by maximizing B-H···H-O dihydrogen bonding, distinct structural arrangements of the water clusters within [B 10 H 10 ] 2– ·nH 2 O are achieved with the water cluster networks from trimer to heptamer resembling free water clusters. Such a distinct difference arises from the variations in size, symmetry, and charge distributions between these two dianions. Finally, the present finding again confirms the structural diversity of hydrogen-bonding networks in microhydrated closo-boranes and enrich our understanding of aqueous borate chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantification of the carbon bonding state in amorphous carbon materials: A comparison between EELS and NEXAFS measurements
In this report the quantitative determination of the carbon hybridization is critical for establishing processing-structure-properties relationships for carbon-based materials, including amorphous carbon coatings. While several techniques have been employed to characterize the amount of sp 2 and sp 3 carbon in these materials, direct comparisons between analytical results are limited. Here, we compare near edge X-ray absorption fine structure (NEXAFS) spectra of a silicon- and oxygen-containing hydrogenated amorphous carbon (a-C:H:Si:O) coating acquired in synchrotron-based scanning transmission X-ray microscopy (STXM) mode with electron energy loss spectra (EELS) obtained from the same a-C:H:Si:O lamella. While the fractions of sp 2 carbon computed from STXM and EELS spectra are in close agreement, the comparison of NEXAFS spectra acquired in STXM mode with NEXAFS spectra collected in partial electron yield mode on a flat a-C:H:Si:O surface indicated that the destructive preparation of thin lamellae for STXM analyses induces variations in the structure of a-C:H:Si:O, namely the breakage of carbon-silicon and carbon-hydrogen bonds, a change in ordering of sp 2 -bonded carbon, and an increase in the sp 2 carbon fraction. These findings can help scientists in the careful interpretation of spectroscopic results obtained from the analysis of samples made of metastable materials after the destructive preparation of specimens for analytical purposes.
36 MATERIALS SCIENCE↗
Concordant Mode Approach (CMA): Vibrational Analysis of New and Upgraded Intermolecular Benchmarks for Noncovalent Bonding
The Concordant Mode Approach (CMA) is a novel method that offers tremendous potential for increasing the system size and the level of theory attainable in quantum chemical computations of molecular vibrational frequencies. To investigate the extension of CMA to intermolecular vibrations, computations with coupled cluster singles and doubles with perturbative triples theory [CCSD(T)] using two augmented correlation-consistent polarized-valence triple-ζ basis sets (aug-cc-pVTZ or h-aug-ccpVTZ) were performed on 17 prototypical loosely bound complexes of hydrogen-bonded, dispersion, and mixed character. These Level A results provide new and upgraded benchmarks for noncovalent bonding and a severe test for CMA vibrational analyses. The Level A target frequencies were recovered remarkably well using second-order Møller−Plesset perturbation theory (MP2) with h-aug-cc-pVTZ for generating the underlying (Level B) normal modes of the CMA scheme. Employing this Level B within the lowest-rung CMA-0A method reproduces the 435 benchmark frequencies with a mean absolute error (MAE) of 0.23 cm −1 and a corresponding standard deviation (σ) of 0.84 cm −1 ; strikingly, the corresponding subset of 106 interfragment frequencies exhibits MAE = 0.34 cm −1 and σ = 0.90 cm −1 . Subsequent application of the higher-rung CMA-2A scheme eliminates all outliers and reduces the overall MAE to a minuscule 0.08 cm −1 with the inclusion of only 3.0% of the off-diagonal couplings not accounted for by CMA-0A. Accordingly, the highly efficient CMA methodology proves to be robust even for vibrations on flat potential energy surfaces.
Aromatic compounds↗
The Role of the Solvent in the Condensed-Phase Dynamics and Identity of Chemical Bonds: The Case of the Sodium Dimer Cation in THF
When a solute molecule is placed in solution, is it acceptable to presume that its electronic structure is essentially the same as in the gas phase? In this paper, we address this question from a simulation perspective for the case of the sodium dimer cation (Na 2 + ) molecule in both liquid Ar and liquid tetrahydrofuran (THF). In previous work, we showed that when local specific interactions between a solute and solvent are energetically on the order of a hydrogen bond, the solvent can become part of the chemical identity of the solute. Here, using mixed quantum/classical molecular dynamics simulations, we see that for the Na 2 + molecule, solute--solvent interactions lead to two stable, chemically-distinct coordination states (Na(THF) 4 -Na(THF) 5 + and Na(THF) 5 -Na(THF) 5 + ) that are not only stable themselves as gas-phase molecules but that also have a completely new electronic structure with important implications for the excited-state photodissociation of this molecule in the condensed phase. Furthermore, we show through a set of comparative classical simulations that treating the solute's bonding electron explicitly quantum mechanically is necessary to understand both the ground-state dynamics and chemical identity of this simple diatomic molecule; even use of the quantum-derived potential of mean force is insufficient to describe the behavior of the molecule classically. Lastly, we calculate the results of a proposed transient hole-burning experiment that could be used to spectroscopically disentangle the presence of the different coordination states.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗