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Thermodynamic Analysis of Silk Fibroin–Graphite Hybrid Materials and Their Morphology
Silk fibroin (SF) is a β-sheet-rich protein that is responsible for the remarkable tensile strength of silk. In addition to its mechanical properties, SF is biocompatible and biodegradable, making it an attractive candidate for use in biotic/abiotic hybrid materials. A pairing of particular interest is the use of SF with graphene-based nanomaterials (GBNs). The properties of this interface drive the formation of well-ordered nanostructures and can improve the electronic properties of the resulting hybrid. It was previously demonstrated that SF can form lamellar nanostructures in the presence of graphite; however, the equilibrium morphology and associated driving interactions are not fully understood. Here, in this study, we characterize these interactions between SF and SF lamellar with graphite using molecular dynamics (MD) simulations and umbrella sampling (US). We find that SF lamellar nanostructures have strong orientational and spatial preferences on graphite that are driven by the hydrophobic effect, destabilizing solvent–protein interactions and stabilizing protein–protein and protein–graphite interactions. Finally, we show how careful consideration of these underlying interactions can be applied to rationally modify the nanostructure morphology.
Adsorption of Molecular Nitrogen in Electrical Double Layers near Planar and Atomically Sharp Electrodes
Here, the adsorption of gas molecules at electrode–electrolyte interfaces is an important step in electrochemical reactions. Using molecular dynamics simulations, we investigate the adsorption of dissolved N 2 in the electrical double layers (EDLs) of an aqueous electrolyte near planar and 1 nm radius spherical carbon electrodes. The adsorption of N 2 is found to be overall enriched near neutral electrodes regardless of their surface curvature, although it can be locally enriched or depleted depending on the distance from the electrode surface. In comparison, the adsorption of N 2 in the EDL near negatively charged electrodes is found to increase under a moderate surface charge density, but decrease under a high surface charge density, especially near a planar electrode. By analyzing the potential of mean force for dissolved N 2 , the solvent-induced effects are found to play important roles in influencing the adsorption of N 2 in the EDLs. The adsorption behavior of N 2 molecules, especially their dependence on the surface charge and curvature of electrodes, is further rationalized by examining the structure of interfacial water molecules, their interference with the hydration shell of N 2 , and their modification by the electrification of electrodes.
(Photo)Electrocatalytic CO 2 Reduction at the Defective Anatase TiO 2 (101) Surface
Excessive carbon dioxide (CO 2 ) emissions by combustion of fossil fuels are linked to global warming and rapid climate change. One promising route to lowering the concentration of CO 2 in the atmosphere is to reduce it to useful small molecules via photoelectrocatalytic hydrogenation, which would enable solar energy storage with a zero-carbon emission cycle and perform a more efficient separation of the photogenerated electron and hole pair than pure photocatalysis. Indeed, photoelectrocatalytic CO 2 reduction has been an intense focus of research. Using the density functional theory (DFT), we studied the CO 2 reduction reaction on the defective anatase TiO 2 (101) surface, at both the solvent/catalyst and the electrolyte/catalyst interfaces. The analysis of the electronic structure of the surface shows a contrast between the solvent/catalyst and the electrolyte/catalyst interfaces, which results in the two corresponding catalytic cycles being distinct. Furthermore, our study explains at the electronic and mechanistic levels why methanol is the main product in the presence of the electrolyte and why the overpotential is not only controlled by the reaction process but also by the diffusion process.
How Solvent Mediates the Catalytic Fate of 2-Methoxyphenol in Hydrodeoxygenation Catalysis?
Kinetic and isotopic assessments combined with theoretical calculations shed light on the mechanistic differences in terms of the number of hydrogen addition steps and the electronic charges of reactive hydrogen in the catalytic sequence leading to the Ar−OCH 3 scission of 2-methoxyphenol occurring at various interfaces of vapor−Ru, cyclohexane−Ru, and water−Ru. At vapor−Ru and cyclohexane−Ru interfaces, the initial hydrogen adatom (H*) additions on the phenyl ring disrupt its aromaticity, as a step required to occur before kinetically relevant Ar−OCH 3 scission on an ensemble of Ru sites. The number of H* addition events prerequisite to the formation of the kinetically relevant Ar−OCH 3 scission transition state, however, is larger at the cyclohexane−Ru interface than those at the vapor−Ru and water−Ru interfaces. The preferential solvation of 2-methoxyphenol derived reaction precursors and H* weakens their adsorption on Ru sites, which leads to a decrease in the activation barrier for the third H* addition step and in turn a larger number of H* additions. At the water−Ru interface, water as a polar protic solvent promotes the Ar−OCH 3 scission by enabling a mechanistically distinct catalytic route an adjacent water molecule from the solvent layer assists with the intramolecular proton shuttling from the hydroxyl group (−OH) to the vicinal methoxy group (−OCH 3 ) of 2-methoxyphenol, evolving a highly charged transition state that is further stabilized by the water solvent layer, thereby leading to Ar−OCH 3 scission rate constants that are much higher than those at the vapor−Ru interface and, when comparing at the same H 2 chemical potential, higher Ar−OCH 3 scission turnovers. Furthermore, these distinct mechanistic details of the Ar−OCH 3 scission at various reaction interfaces, inferred from experiment and theory, illustrate how a solvent either solvates reaction intermediates and transition states or directly participates in the formation of kinetically relevant transition states, leading to changes in the free energy landscape, thus rewriting the catalytic fates in hydrodeoxygenation reactions.
A Simple Bond-Additivity Model Explains Large Decreases in Heats of Adsorption in Solvents Versus Gas Phase: A Case Study with Phenol on Pt(111) in Water
Previously, we reported the low-coverage heat of adsorption of phenol on Pt(111) facets of a Pt wire in aqueous phase to be approximately 21 kJ/mol (relative to aqueous phenol) on the basis of measurements of the adsorption equilibrium constant. This is much smaller than the heat we reported for gas-phase phenol adsorption at this same low coverage on single-crystal Pt(111) under ultrahigh vacuum (200 kJ/mol) on the basis of adsorption calorimetry measurements. Here we quantitatively analyze the individual contributions that give rise to this 179 kJ/mol difference using a simple pairwise bond-additivity model, taking advantage of experimental data from the literature to estimate the bond energies. The dominant contribution to the lowering in heat when phenol is adsorbed in water is the energy cost to break the strong bond of liquid water to Pt(111) (~116 kJ per mole of phenol area). The water–phenol bonding is lost on one face of the phenol, and this costs ~50 kJ/mol, but this is nearly compensated by the new water–water bonding (~53 kJ/mol of phenol area). The results indicate that the intrinsic bond energy between phenol and Pt(111) is not very different in the gas versus the aqueous phase, provided one takes into consideration the expectation that water forces phenol into islands of high local coverage even at low average coverage (for the same reason that phenol has limited solubility in water). Furthermore, this explains the lack of a strong coverage dependence in the heat of adsorption when it is measured in aqueous phase, whereas it decreases by ~57 kJ/mol with coverage when it is measured in gas phase. This bond-additivity analysis presented here can be easily generalized to other adsorbates, surfaces, and solvents. It clarifies why catalysis with molecules such as phenol which have very strong bonding to Pt-group metals can proceed rapidly at room temperature in liquid solvents such as water but would never proceed in the gas phase at room temperature due to irreversible site poisoning.
Controlling Solid–Liquid Conversion Reactions for a Highly Reversible Aqueous Zinc–Iodine Battery
Aqueous rechargeable batteries are desirable for many energy storage applications due to their low cost and high safety. However, low capacity and short cycle life are the significant obstacles to their practical applications. Here, we demonstrate a highly reversible aqueous zinc-iodine battery using encapsulated iodine in microporous active carbon fibers (ACFs) as cathode materials through the rational control of solid-liquid conversion reactions. The experiments and density function theory (DFT) calculations were employed to investigate the effects of solvents and properties of carbon hosts, e.g. pore size, surface chemistries, on the adsorption of iodine species. The rational manipulation of the competition between the adsorption in carbon and solvation in electrolytes for iodine species is responsible for the high reversibility and cycling stability. The zinc-iodine batteries deliver a high capacity of 180 mAh g-1 at 1C and a stable cycle life over 3000 cycles with ~90% capacity retention as well as negligible self-discharge. We believe the principles for stabilizing the zinc-iodine system could provide new insight into conversion systems such as Li-S systems.
Solvent–Solvent Correlations across Graphene: The Effect of Image Charges
Wetting experiments show pure graphene to be weakly hydrophilic, but its contact angle (CA) also reflects the character of the supporting material. Measurements and Molecular Dynamics simulations on suspended and supported graphene often reveal a CA reduction due to the presence of the supporting substrate. A similar reduction is consistently observed when graphene is wetted from both sides. The effect has been attributed to transparency to molecular interactions across the graphene sheet, however, the possibility of substrate-induced graphene polarization has also been considered. Computer simulations of CA on graphene have so far been determined by ignoring the material’s conducting properties. We improve the graphene model by incorporating its conductivity according to the Constant Applied Potential Molecular Dynamics. Using this method, we compare the wettabilities of suspended graphene and graphene supported by water by measuring the CA of cylindrical water drops on the sheets. The inclusion of graphene conductivity and concomitant polarization effects lead to a lower CA on suspended graphene but the CA reduction is significantly bigger when the sheets are also wetted from the opposite side. The stronger adhesion is accompanied by a profound change in the correlations among water molecules across the sheet. While partial charges on water molecules interacting across an insulator sheet attract charges of the opposite sign, apparent attraction among like charges is manifested across the conducting graphene. The change is associated with graphene polarization, as the image charges inside the conductor attract equally signed partial charges of water molecules on both sides of the sheet. Additionally, by using a non-polar liquid (diiodomethane), we affirm a detectable wetting translucency when liquid-liquid forces are dominated by dispersive interactions. Furthermore, our findings are important for predictive modeling toward a variety of applications including sensors, fuel cell membranes, water filtration, and graphene-based electrode materials in high-performance supercapacitors.
Unraveling the Dynamic Network in the Reactions of an Alkyl Aryl Ether Catalyzed by Ni/γ-Al 2 O 3 in 2-Propanol
The reductive cleavage of aryl ether linkages is a key step in the disassembly of lignin to its monolignol components, where selectivity is determined by the kinetics of multiple parallel and consecutive liquid-phase reactions. Triphasic hydrogenolysis of 13 C-labeled benzyl phenyl ether (BPE, a model compound with the same C-O bond energy as the major β-O-4 linkage in lignin), catalyzed by Ni/γ-Al 2 O 3 , was observed directly at elevated temperatures (150 - 175 °C) and pressures (79-89 bar) using operando magic-angle spinning NMR spectroscopy. Liquid-vapor partitioning in the NMR rotor was quantified using the 13 C NMR resonances for the 2-propanol solvent, whose chemical shifts report on the internal reactor temperature. At 170 °C, BPE is converted to toluene and phenol with k 1 = 0.17 s -1 g cat -1 and an apparent activation barrier of (80 ± 8) kJ mol -1 . Subsequent phenol hydrogenation occurs much more slowly (k 2 = 0.0052 s -1 g cat -1 at 170-175 °C), such that cyclohexanol formation is significant only at higher temperatures. Toluene is stable under these reaction conditions, but its methyl group undergoes facile H/D exchange (k 3 = 0.046 s -1 g cat -1 at 175 °C). While the source of the reducing equivalents for both hydrogenolysis and hydrogenation is exclusively H 2 /D 2(g) rather than the alcohol solvent at these temperatures, the initial isotopic composition of adsorbed H/D on the catalyst surface is principally determined by the solvent isotopic composition (2-PrOH/D). All reactions are preceded by a pronounced induction period associated with catalyst activation. In air, Ni nanoparticles are passivated by a surface oxide monolayer, whose removal under H 2 proceeds with an apparent activation barrier of (72 ± 13) kJ mol -1 . Finally ,the operando NMR spectra provide molecularly-specific, time-resolved information about the multiple simultaneous and sequential processes as they occur at the solid-liquid interface.
Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations
Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.
Assessing health and environmental impacts of solvents for producing perovskite solar cells
Halide perovskites are poised as a game-changing semiconductor system with diverse applications in optoelectronics. Industrial entities aim to commercialize perovskite technologies because of high performance but also because this type of semiconductor can be processed from solution, a feature enabling low cost and fast production. In this work, we analyse the health and environmental impacts of eight solvents commonly used in perovskite processing. We consider first- and higher-order ramifications of each solvent on an industrial scale such as solvent production, use/removal, emissions and potential end-of-life treatments. Further, we consider the energy of evaporation for each solvent, air emission, condensation and subsequent incineration, reuse or distillation for solvent recycling, and apply a full end-of-life analysis. For human health impact, we use the ‘USEtox’ method but also consider toxicity data beyond carcinogenic classifications. We find that dimethyl sulfoxide has the lowest total impact, by being the most environmentally friendly and least deleterious to human health of the solvents considered. The analysis of the effects of these solvents on human health and the environment provides guidance for sustainable development of this new technology.
Ethylene glycol reforming on Pt(111): first-principles microkinetic modeling in vapor and aqueous phases
First-principles, periodic density functional theory (DFT) calculations and mean-field microkinetic modeling have been used to investigate the decomposition of ethylene glycol for hydrogen production on Pt(111) in vapor and aqueous phases. All dehydrogenated species derived from ethylene glycol (C 2 H x O 2 , x = 0–6) and methanol (CH y O, y = 0–4), and all elementary C–C, C–H, and O–H bond breaking steps are included in the microkinetic model. Reaction path analysis in vapor phase indicates that both initial C–H and O–H dehydrogenation steps are kinetically relevant at all temperatures (470–530 K). Initial O–H bond cleavage is reversible at low temperatures but accounts for an increasingly dominant fraction of the total reaction flux at higher temperatures. C–C bond scission is observed only after significant dehydrogenation (x ≤ 3) and is more likely to happen in surface intermediates where one of the cleavage products is CO. Here, the process is highly selective to the production of H2 compared to methanol. For aqueous-phase model development, free energies of solvation were computed for all surface intermediates and transition states using a continuum solvation approach. Our aqueous-phase microkinetic model predicts a 0.4 eV lower apparent activation energy and an order of magnitude larger turnover frequencies. Initial C–H bond cleavage becomes more important but the general trends are similar to the vapor phase, suggesting that the reaction chemistry is similar in both vapor and aqueous phases.
Efficient dual acidic carbo-catalyst for one-pot conversion of carbohydrates to levulinic acid
Levulinic acid (LA) is an important platform intermediate for several high value renewable bioproducts. One-pot synthesis of LA from carbohydrates is disadvantaged by the lack of proximity of the active sites required for sequential isomerization, dehydration and rehydration reactions. Herein, we report an efficient one-pot conversion of C 6 sugars to LA using a carbo-catalyst (ZrHyC), containing Lewis acidic zirconium and Brønsted acidic carboxyl and hydroxyl sites. The proximity of the two acid sites on a hydrothermally prepared carbon support makes the catalyst highly effective enabling a maximum 73% LA yield from glucose conversion. Fructose conversion achieved a higher LA yield (89%) because of a facile reaction without involving an isomerization step. The effects of solvents, the glucose to catalyst ratio, and the reaction time on glucose conversion and LA yield are systemically examined. Detailed characterization of the catalyst using FTIR, Raman spectroscopy, XPS, XRD, FESEM and NH 3 -TPD techniques are presented to elucidate the presence of the two acid sites and zirconium in the +4 oxidation state.
Weakly interacting solvation spheres surrounding a calixarene-protected tetrairidium carbonyl cluster: contrasting effects on reactivity of alkane solvent and silica support
The tetrairidium carbonyl cluster Ir 4 L 3 (CO) 9 (L = tert-butyl-calix[4]arene(OPr) 3 (OCH 2 PPh 2 ) (Ph = phenyl; Pr = propyl)) on a partially dehydroxylated silica support undergoes hydrogen activation at a rate and with a mechanism different from those pertaining to the cluster in alkane solution. These results are unobvious in view of the sterically bulky ligands protecting the cluster and the nearly identical CO band frequencies in the infrared spectra characterizing the supported and dissolved Ir 4 L 3 (CO) 9 , both before reaction and during reaction involving decarbonylation in the presence of either helium or H 2 (and H 2 reacted with the clusters to form hydrides with the same Ir–H band frequencies for clusters in alkane solvent and supported on silica). The initial rates of CO loss from the supported clusters in the presence of helium were the same as those in the presence of H 2 . In this work, the comparison demonstrates that the rate-determining step for hydride formation on the silica-supported cluster is CO dissociation. In contrast, the comparable dissociation of CO from the cluster in n-decane solution requires a higher temperature, 343 K, and is at least an order of magnitude slower than when the clusters were supported on silica. CO dissociation is not the rate-determining step for hydrogen activation on the cluster in n-decane, as the rate is influenced by reactant H 2 as well.
Evidence for I 2 loss from the perovskite–gas interface upon light-induced halide segregation
Sunlight-induced halide segregation in (CH 3 NH 3 )Pb(Br x I 1−x ) 3 (1 > x > 0.2), which limits obtainable voltages from solar cells with these perovskite absorbers, reverses upon resting in the dark. However, sustained illumination at ca. 1 sun opens a new decomposition pathway, leading to irreversible I 2 loss in an open system. We conclusively show I 2 off-gassing from halide-segregated (CH 3 NH 3 )Pb(Br 0.75 I 0.25 ) 3 by trapping gaseous I 2 and tracking the electronic conductivity of the perovskite, which increases from electron-doping as iodides are oxidized to iodine. Importantly, we show that this reaction occurs across the perovskite-air solid–gas interface, without confounding effects from solvent or reactive solid interfaces. This characterization was conducted under a nitrogen atmosphere, avoiding vacuum- and oxygen-driven I 2 loss pathways. Consistent observations of I 2 loss upon light-soaking CsPb(Br 0.75 I 0.25 ) 3 films show that this reaction is intrinsic to the inorganic framework. We propose that the disruption of iodide-rich domains in the halide-segregated films through I 2 loss can masquerade as a light-induced healing or apparent remixing of the segregated film, when in fact it leads to irreversible decomposition. Although I 2 off-gassing is less likely in bromide-rich solid solutions, light-induced halide segregation brings the iodides into proximity and forms electronic states that are energetically poised to trap and accumulate holes, providing a driving force for I 2 loss. Thus, even bromide-rich mixed-halide perovskite absorbers will benefit from I 2 -impermeable encapsulation for long-term stability.
Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures
Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.