Understanding solvent effects on adsorption and protonation in porous catalysts

Solvent effect in H-BEA catalyzed cyclohexanol dehydration reaction

The solvent effect on H-BEA catalyzed cyclohexanol dehydration was investigated in water, dioxane, and cyclohexanol. The dynamic evolution of the Brønsted acid site of zeolite and its interaction with reactant molecules in different solvents were explored with ab initio molecular dynamics simulations, providing reliable configuration sampling to obtain configurations at equilibrium. Solvent profoundly changes the adsorption as well as the dehydration reaction of cyclohexanol in H-BEA, where the reaction is determined to follow the E2 mechanism in water and dioxane but the E1 mechanism in cyclohexanol untill saturation uptake. Near saturation uptake, all three solvents significantly reduce the cyclohexanol dehydration rates in H-BEA. Cyclohexanol loading also dramatically affects the kinetics of the dehydration reaction, displaying an overall decreasing trend with a local minimum present at intermediate loading of 6 molecules per unit cell, which is a result of the entropic effect associated with greater freedom of motion of the transition state. Rigorous quantification of enthalpy and entropy contributions to cyclohexanol adsorption and activation shed light on the solvent effect of zeolite-catalyzed alcohol dehydration.

Multilevel quantum mechanical calculations show the role of promoter molecules in the dehydration of methanol to dimethyl ether in H-ZSM-5

Methyl carboxylate esters promote the formation of dimethyl ether (DME) from the dehydration of methanol in H-ZSM-5 zeolite. We employ a multilevel quantum method to explore the possible associative and dissociative mechanisms in the presence, and absence, of six methyl ester promoters. This hybrid method combines density functional theory, with dispersion corrections (DFT-D3), for the full periodic system, with second-order Møller-Plesset perturbation theory (MP2) for small clusters representing the reaction site, and coupled cluster with single, double, and perturbative triple substitution (CCSD(T)) for the reacting molecules. The calculated adsorption enthalpy of methanol, and reaction enthalpies of the dehydration of methanol to DME within H-ZSM-5, agree with experiment to within chemical accuracy (∼4 kJ mol-1). For the promoters, a reaction pathway via an associative mechanism gives lower overall reaction enthalpies and barriers compared to the reaction with methanol only. Each stage of this mechanism is explored and related to experimental data. We provide evidence that suggests the promoter's adsorption to the Brønsted acid site is the most important factor dictating its efficiency.

In Situ Observation of Solvent-Mediated Cyclic Intermediates during the Alkene Epoxidation/Hydration over a Ti-Beta/H2O2 System

Solvent effects in catalytic reactions have received widespread attention as they can promote reaction rates and product selectivities by orders of magnitude. It is well accepted that the stable five-membered cyclic intermediates formed between the solvent molecules and Ti species are crucial to the alkene epoxidation in a heterogeneous Ti(IV)-H2O2 system. However, the direct spectroscopic evidence of these intermediates is still missing and the corresponding reaction pathway for the alkene epoxidation remains unclear. By combining in situ 13C MAS NMR, two-dimensional (2D) 1H-13C heteronuclear correlation (HETCOR) NMR spectroscopy and theoretical calculations, the five-membered ring structures, where the protic solvents (ROH), and aprotic solvent (acetone), coordinate and stabilize the active Ti species, are identified for the first time over Ti-Beta/H2O2 system. Moreover, the role of these cyclic intermediates in the alkene epoxidation/hydration conversion is clarified. These results provide new insights into the solvent effect in liquid-phase epoxidation/hydration reactions over Ti(IV)-H2O2 system.

Isotherm and kinetic studies on adsorption of gasoline and kerosene using jujube and barberry tree stem powder and commercially available activated carbon

Herein, the application of granular activated carbon, jujube, and barberry tree stem powder for the removal of gasoline and kerosene from water was investigated. Kerosene removal rates upwards of 68.48, 83.87, and 99.02% were achieved using jujube tree stem powder, barberry tree stem powder, and granular activated carbon, respectively. Besides, gasoline removal rates upwards of 69.35, 55.02, and 95.59% were attained using jujube tree stem powder, barberry tree stem powder, and granular activated carbon, respectively. Isotherm data were further investigated and fitted using Langmuir, Freundlich, and Elovich models. The results indicated that the adsorption onto jujube adsorbent is a multilayer adsorption process over a heterogeneous surface, which is best illustrated by the Temkin (Ave. R2= 0.95) model. It was found that the Temkin isotherm (Ave. R2= 0.81) best describes the properties of barberry stem powder in the adsorption of gasoline and kerosene from water. Moreover, the best models to describe the characteristics of granular activated carbon in the adsorption of gasoline and kerosene from water were Freundlich (Ave. R2= 0.74) and Langmuir (Ave. R2= 0.73) isotherms, respectively. The adsorption kinetics showed that the pseudo-second-order was appropriate in modeling the adsorption kinetics of gasoline and kerosene to the studied adsorbents (R2>0.74).

A new insight into the surface adsorption in the solution phase: A modification of the Langmuir isotherm

The Langmuir isotherm, originally developed to study the adsorption of gases, has been modified in this research to investigate the adsorption of solutes in the solution phase. The modification considers the adsorption of solvent molecules and the interactions between adsorbed particles and the species in the solution. Three equations have been obtained to calculate the contribution of these additional effects on the Gibbs free energy, enthalpy, and entropy of solute adsorption based on the new isotherm. The study evaluated the efficiency of the new isotherm in the adsorption of some metal ions in an aqueous solution and found that it is more accurate than the Langmuir isotherm and provides a deeper insight into the adsorption process in the solution phase. PRACTITIONER POINTS: Modification of the Langmuir isotherm for adsorption in solution. Comparison of the efficiency of the Langmuir and modified Langmuir isotherms. Accurate determination of∆ H ads o $$ \Delta {H}_{ads}^o $$ and∆ S ads o $$ \Delta {S}_{ads}^o $$ for Pb(II), Cd(II), and Ni(II) adsorption.

Water structures on acidic zeolites and their roles in catalysis

The local reaction environment of catalytic active sites can be manipulated to modify the kinetics and thermodynamic properties of heterogeneous catalysis. Because of the unique physical-chemical nature of water, heterogeneously catalyzed reactions involving specific interactions between water molecules and active sites on catalysts exhibit distinct outcomes that are different from those performed in the absence of water. Zeolitic materials are being applied with the presence of water for heterogeneous catalytic reactions in the chemical industry and our transition to sustainable energy. Mechanistic investigation and in-depth understanding about the behaviors and the roles of water are essentially required for zeolite chemistry and catalysis. In this review, we focus on the discussions of the nature and structures of water adsorbed/stabilized on Brønsted and Lewis acidic zeolites based on experimental observations as well as theoretical calculation results. The unveiled functions of water structures in determining the catalytic efficacy of zeolite-catalyzed reactions have been overviewed and the strategies frequently developed for enhancing the stabilization of zeolite catalysts are highlighted. Recent advancement will contribute to the development of innovative catalytic reactions and the rationalization of catalytic performances in terms of activity, selectivity and stability with the presence of water vapor or in condensed aqueous phase.

Exploiting Cation Structure and Water Content in Modulating the Acidity of Ammonium Hydrogen Sulfate Protic Ionic Liquids

In this paper, we investigated the effect of cation structure and water content on proton dissociation in alkylammonium [HSO4]- protic ionic liquids (ILs) doped with 20 wt % water and correlated this with experimental Hammett acidities. For pure systems, increased cation substitution resulted in a reduction in the number of direct anion-anion neighbors leading to larger numbers of small aggregates, which is further enhanced with addition of water. We also observed spontaneous proton dissociation from [HSO4]- to water only for primary amine-based protic ILs, preceded by the formation of an anion trimer motif. Investigation using DFT calculations revealed spontaneous proton dissociation from [HSO4]- to water can occur for each of the protic ILs investigated; however, this is dependent on the size of the anion aggregates. These findings are important in the fields of catalysis and lignocellulosic biomass, where solvent acidity is a crucial parameter in biomass fractionation and lignin chemistry.

Spectroscopy-Guided Deep Learning Predicts Solid-Liquid Surface Adsorbate Properties in Unseen Solvents

Accurately and rapidly acquiring the microscopic properties of a material is crucial for catalysis and electrochemistry. Characterization tools, such as spectroscopy, can be a valuable tool to infer these properties, and when combined with machine learning tools, they can theoretically achieve fast and accurate prediction results. However, on the path to practical applications, training a reliable machine learning model is faced with the challenge of uneven data distribution in a vast array of non-negligible solvent types. Herein, we employ a combination of the first-principles-based approach and data-driven model. Specifically, we utilize density functional theory (DFT) to calculate theoretical spectral data of CO-Ag adsorption in 23 different solvent systems as a data source. Subsequently, we propose a hierarchical knowledge extraction multiexpert neural network (HMNN) to bridge the knowledge gaps among different solvent systems. HMNN undergoes two training tiers: in tier I, it learns fundamental quantitative spectra-property relationships (QSPRs), and in tier II, it inherits the fundamental QSPR knowledge from previous steps through a dynamic integration of expert modules and subsequently captures the solvent differences. The results demonstrate HMNN's superiority in estimating a range of molecular adsorbate properties, with an error range of less than 0.008 eV for zero-shot predictions on unseen solvents. The findings underscore the usability, reliability, and convenience of HMNN and could pave the way for real-time access to microscopic properties by exploiting QSPR.

CO Binding Energy is an Incomplete Descriptor of Cu-Based Catalysts for the Electrochemical CO2 Reduction Reaction

CO binding energy has been employed as a descriptor in the catalyst design for the electrochemical CO2 reduction reactions (CO2 RR). The reliability of the descriptor has yet been experimentally verified due to the lack of suitable methods to determine CO binding energies. In this work, we determined the standard CO adsorption enthalpies (Δ H C O ∘ ${\Delta {H}_{CO}^{^\circ{}}}$ ) of undoped and doped oxide-derived Cu (OD-Cu) samples, and for the first time established the correlation ofΔ H C O ∘ ${\Delta {H}_{CO}^{^\circ{}}}$ with the Faradaic efficiencies (FE) for C2+ products. A clear volcano shaped dependence of the FE for C2+ products onΔ H C O ∘ ${\Delta {H}_{CO}^{^\circ{}}}$ is observed on OD-Cu catalysts prepared with the same hydrothermal durations, however, the trend becomes less clear when all catalysts investigated are taken into account. The relative abundance of Cu sites active for the CO2 -to-CO conversion and the further reduction of CO is identified as another key descriptor.

Accelerating explicit solvent models of heterogeneous catalysts with machine learning interatomic potentials

Realistically modelling how solvents affect catalytic reactions is a longstanding challenge due to its prohibitive computational cost. Typically, an explicit atomistic treatment of the solvent molecules is needed together with molecular dynamics (MD) simulations and enhanced sampling methods. Here, we demonstrate the utility of machine learning interatomic potentials (MLIPs), coupled with active learning, to enable fast and accurate explicit solvent modelling of adsorption and reactions on heterogeneous catalysts. MLIPs trained on-the-fly were able to accelerate ab initio MD simulations by up to 4 orders of magnitude while reproducing with high fidelity the geometrical features of water in the bulk and at metal-water interfaces. Using these ML-accelerated simulations, we accurately predicted key catalytic quantities such as the adsorption energies of CO*, OH*, COH*, HCO*, and OCCHO* on Cu surfaces and the free energy barriers of C-H scission of ethylene glycol over Cu and Pd surfaces, as validated with ab initio calculations. We envision that such simulations will pave the way towards detailed and realistic studies of solvated catalysts at large time- and length-scales.

Diffuse reflectance infrared spectroscopy of adsorbates in liquid phase

Infrared spectroscopy is widely used to analyse the surface of solid materials central to modern chemical processes. For liquid phase experiments, the attenuated total reflection mode (ATR-IR) requires the use of waveguides that can limit a broader applicability of the technique for catalysis studies. Here, we demonstrate that high quality spectra of the solid-liquid interface can be collected in diffuse reflectance mode (DRIFTS) thus opening future applications of infrared spectroscopy.

The application of QM/MM simulations in heterogeneous catalysis

The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.

Correlating the Experimentally Determined CO Adsorption Enthalpy with the Electrochemical CO Reduction Performance on Cu Surfaces

CO binding energy has been widely employed as a descriptor for effective catalysts in the electrochemical CO₂ and CO reduction reactions (CO₍₂₎ RR), however, it has yet to be determined experimentally at electrochemical interfaces due to the lack of suitable techniques. In this work, we developed a method to determine the standard adsorption enthalpy of CO on Cu surfaces with quantitative surface enhanced infrared absorption spectroscopy. On dendritic Cu at -0.75 V vs. SHE, the standard adsorption enthalpy, entropy and Gibbs free energy were determined to 1.5±0.5 kJ mol^-1 , ≈37.9±13.4 J/(mol K), and ≈-9.8±4.0 kJ mol^-1 , respectively. Comparison of the standard adsorption enthalpy of oxide-derived Cu and dendritic Cu, as well as their CORR activities, suggests the presence of stronger binding sites on OD Cu, which could favor multicarbon products. The method developed in this work will help establish the correlation between the CO binding energy and the CO₍₂₎ RR activity.

Preparation of pure active water for auto-catalytic reactions performed in it

In catalyzed electrochemical reactions, a general strategy is to modify electrode materials to increase the efficiency of the reaction. From the viewpoint of environmental protection, electrochemical reactions should be performed in an inert green water phase. In this study, we report active pure liquid water (named PV), which was collected from the condensed vapor of heated gold (Au)-containing plasmon-activated water (PAW) with a distinct structure of electron-doping and reduced hydrogen bonding (HB). The resulting PV also exhibited distinct properties of the formation of stronger intermolecular HB with alcohols, and notable activities in catalytic electrochemical reactions, compared to bulk deionized water (DIW). Moreover, the measured diffusion coefficients of water increased by ca. 30% in PV solutions. Two typical electrochemical reactions significantly increased peak currents observed in oxidation-reduction cycles (ORCs) with roughening of the Au substrate and in a model of reversible oxidation-reduction reactions on a platinum (Pt) substrate. Also, PV enhanced hydrogen evolution reactions (HERs) on catalytic Pt and inert stainless steel substrates in PV-based solutions at different pH values, compared to DIW. Moreover, these activities of PV were more marked, even better than those of PAW, when PV was collected under a higher heating rate used to heat PAW. Active pure PV has emerged as a promising green solvent applicable to various chemical reactions with more efficiency.

Liquid-Phase Effects on Adsorption Processes in Heterogeneous Catalysis

Aqueous solvation free energies of adsorption have recently been measured for phenol adsorption on Pt(111). Endergonic solvent effects of ∼1 eV suggest solvents dramatically influence a metal catalyst's activity with significant implications for the catalyst design. However, measurements are indirect and involve adsorption isotherm models, which potentially reduces the reliability of the extracted energy values. Computational, implicit solvation models predict exergonic solvation effects for phenol adsorption, failing to agree with measurements even qualitatively. In this study, an explicit, hybrid quantum mechanical/molecular mechanical approach for computing solvation free energies of adsorption is developed, solvation free energies of phenol adsorption are computed, and experimental data for solvation free energies of phenol adsorption are reanalyzed using multiple adsorption isotherm models. Explicit solvation calculations predict an endergonic solvation free energy for phenol adsorption that agrees well with measurements to within the experimental and force field uncertainties. Computed adsorption free energies of solvation of carbon monoxide, ethylene glycol, benzene, and phenol over the (111) facet of Pt and Cu suggest that liquid water destabilizes all adsorbed species, with the largest impact on the largest adsorbates.

CTAB-functionalized δ-FeOOH for the simultaneous removal of arsenate and phenylarsonic acid in phenylarsenic chemical warfare

This study prepared a cetyltrimethylammonium bromide (CTAB) functionalized δ-FeOOH using the coprecipitation method to remove arsenate and phenylarsonic acid in water polluted by phenylarsonic chemical warfare agents. Under neutral conditions, the adsorption capacity for arsenate and phenylarsonic acid was 45.7 and 85.3 mg g^-1, respectively. The adsorption process conformed to the pseudo-second-order kinetics and Freundlich isothermal adsorption model, and the adsorption was spontaneous and endothermic. The CTAB-functionalized δ-FeOOH could effectively resist the interference of coexisting anions except for CO₃^2-, SiO₃^2- and PO₄^3-. Furthermore, the adsorption mechanism was proposed by combining the adsorption experimental results, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and density functional theory analyses. The results showed that the adsorption of arsenate by the CTAB-functionalized δ-FeOOH was mainly through the formation of bidentate-dinuclear inner-sphere complexes and electrostatic interactions. While for phenylarsonic acid, the formation of monodentate-mononuclear inner-sphere complexes on (100) and (110) crystal facets, and the formation of bidentate-dinuclear inner-sphere complexes on the (002) crystal facet, as well as hydrogen bonding, electrostatic interaction, and π-hydrophobic interaction between organic compounds were the primary mechanism. Moreover, the CTAB-functionalized δ-FeOOH could maintain about 60% of the adsorption capacity for the two pollutants after five cycles. Overall, CTAB-functionalized δ-FeOOH has good potential for the remediation of inorganic and organic arsenic-contaminated water bodies.

Driving Forces of Cationic Dye Adsorption, Confinement, and Long-Range Correlation in Zeolitic Materials

Zeolitic materials are commonly used to capture emergent contaminants in water or complex aqueous effluents. The efficiency of this adsorption depends strongly on the guest-host interactions and on the surrounding environment with possible coadsorption of the solvent. Only a few experimental techniques are available to probe in situ the sequestration processes at the solid/liquid interface. We propose in the present work to combine the second harmonic scattering technique with isothermal titration calorimetry in order to investigate the adsorption and the confinement of a hemicyanine dye adsorbed inside faujasite materials. The methodology described here permits the quantification of the correlations between the confined dyes in the material and thus gives local information about the organization at the nanometer scale. Various impacts, such as the effect of the solvent type and the silicon to aluminum ratio of the zeolitic adsorbent, are quantitatively estimated and discussed. This work highlights that the most correlated system matches the higher adsorption capacity associated with the lower entropic contribution.

Influence of solvent structure and hydrogen bonding on catalysis at solid-liquid interfaces

Solvent molecules interact with reactive species and alter the rates and selectivities of catalytic reactions by orders of magnitude. Specifically, solvent molecules can modify the free energies of liquid phase and surface species via solvation, participating directly as a reactant or co-catalyst, or competitively binding to active sites. These effects carry consequences for reactions relevant for the conversion of renewable or recyclable feedstocks, the development of distributed chemical manufacturing, and the utilization of renewable energy to drive chemical reactions. First, we describe the quantitative impact of these effects on steady-state catalytic turnover rates through a rate expression derived for a generic catalytic reaction (A → B), which illustrates the functional dependence of rates on each category of solvent interaction. Second, we connect these concepts to recent investigations of the effects of solvents on catalysis to show how interactions between solvent and reactant molecules at solid-liquid interfaces influence catalytic reactions. This discussion demonstrates that the design of effective liquid phase catalytic processes benefits from a clear understanding of these intermolecular interactions and their implications for rates and selectivities.

Molecular Insights on Solvent Effects in Organic Reactions as Obtained through Computational Chemistry Tools

Molecular understanding of the role of protic solvents in a gamut of organic transformations can be developed using density functional and ab initio computational studies focused on the reaction mechanism. Inclusion of explicit solvent molecules in the vital TSs has been proven to be valuable toward improving the energetic estimates of organocatalytic as well as transition-metal-catalyzed organic reactions. Herein, we provide an overview of the importance of an explicit-implicit solvation model using a number of interesting examples.

Tunable Proton Conductivity and Color in a Nonporous Coordination Polymer via Lattice Accommodation to Small Molecules

Nonporous coordination polymers (npCPs) able to accommodate molecules through internal lattice reorganization are uncommon materials with applications in sensing and selective gas adsorption. Proton conduction, extensively studied in the analogue metal-organic frameworks under high-humidity conditions, is however largely unexplored in spite of the opportunities provided by the particular sensitivity of npCPs to lattice perturbations. Here, AC admittance spectroscopy is used to unveil the mechanism behind charge transport in the nonporous 1·2CH3 CN. The conductance in the crystals is found to be of protonic origin. A vehicle mechanism is triggered by the dynamics of the weakly coupled acetonitrile molecules in the lattice that can be maintained by a combination of thermal cycles, even at low humidity levels. An analogue 1·pyrrole npCP is formed by in situ exchange of these weakly bound acetonitrile molecules by pyrrole. The color and conduction properties are determined by the molecules weakly bonded in the lattice. This is the first example of acetonitrile-mediated proton transport in an npCP showing distinct optical response to different molecules. These findings open the door to the design of switchable protonic conductors and capacitive sensors working at low humidity levels and with selectivity to different molecules.

Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations

In hybrid simulations, such as the QM/MM approach, the system is partitioned into regions that are treated at different levels of theory. The key question then becomes how to evaluate the interactions between particles on opposite sides of the boundary. One approach is to place the boundary in such a way that particles near the boundary on both sides are of the same type, thus simplifying the evaluation of the interactions. If mobile particles are present, such as solvent molecules, and particles are allowed to cross the boundary, the conservation of energy and atomic forces is problematic unless the computational effort is increased significantly. By preventing particles from crossing the boundary but allowing the boundary to be flexible, an accurate estimate of average thermodynamic properties is obtained in principle as illustrated by the flexible inner region ensemble separator (FIRES) method [C. Rowley and B. Roux, J. Chem. Theory Comput. 2012, 8, 3526]. In FIRES, a harmonic restraint is applied to particles near the boundary. Therefore, it can occur that particle cross the boundary to some extent resulting in anomalies in the particle density. Here, a constraint approach is presented where particles instantaneously scatter from the boundary. This scattering-adapted FIRES (SAFIRES) implementation makes use of a variable-time-step propagation algorithm where the time step is scaled automatically to identify the moment a collision should occur. If the length of the time step is kept constant, this propagator reduces to a regular Langevin dynamics algorithm, and to the velocity Verlet algorithm for conservative dynamics if the friction coefficient is set to zero. Correct average ensemble statistics are obtained as demonstrated in simulations where, for testing purposes, the particles in the two regions are treated at the same level of theory, namely, a homogeneous Lennard-Jones (LJ) liquid and liquid water based on the TIP4P potential function. In order to illustrate this approach in solid-liquid interface simulations, a LJ liquid in contact with the surface of a crystal is also simulated. The simulations using SAFIRES are shown to reproduce the unconstrained reference simulations without significant deviations in the particle density and the dynamics are shown to conserve energy when coupling to the heat bath is turned off.

What Is Being Measured with P-Bearing NMR Probe Molecules Adsorbed on Zeolites?

Elucidating the nature, strength, and siting of acid sites in zeolites is fundamental to fathom their reactivity and catalytic behavior. Despite decades of research, this endeavor remains a major challenge. Trimethylphosphine oxide (TMPO) has been proposed as a reliable probe molecule to study the acid properties of solid acid catalysts, allowing the identification of distinct Brønsted and Lewis acid sites and the assessment of Brønsted acid strengths. Recently, doubts have been raised regarding the assignment of the ³¹P NMR resonances of TMPO-loaded zeolites. Here, it is shown that a judicious control of TMPO loading combined with two-dimensional ¹H-³¹P HETCOR solid-state NMR, DFT, and ab initio molecular dynamics (AIMD)-based computational modeling provides an unprecedented atomistic description of the host-guest and guest-guest interactions of TMPO molecules confined within HZSM-5 molecular-sized voids. ³¹P NMR resonances usually assigned to TMPO molecules interacting with Brønsted sites of different acid strength arise instead from both changes in the probe molecule confinement effects at ZSM-5 channel system and the formation of protonated TMPO dimers. Moreover, DFT/AIMD shows that the ¹H and ³¹P NMR chemical shifts strongly depend on the siting of the framework aluminum atoms. This work overhauls the current interpretation of NMR spectra, raising important concerns about the widely accepted use of probe molecules for studying acid sites in zeolites.

Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection

DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl₂ solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm², respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg²⁺), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm², suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.

Kinetic effects of molecular clustering and solvation by extended networks in zeolite acid catalysis

Reactions catalyzed within porous inorganic and organic materials and at electrochemical interfaces commonly occur at high coverage and in condensed media, causing turnover rates to depend strongly on interfacial structure and composition, collectively referred to as "solvent effects". Transition state theory treatments define how solvation phenomena enter kinetic rate expressions, and identify two distinct types of solvent effects that originate from molecular clustering and from the solvation of such clusters by extended solvent networks. We review examples from the recent literature that investigate reactions within microporous zeolite catalysts to illustrate these concepts, and provide a critical appraisal of open questions in the field where future research can aid in developing new chemistry and catalyst design principles.

Ordered Hydrogen-Bonded Alcohol Networks Confined in Lewis Acid Zeolites Accelerate Transfer Hydrogenation Turnover Rates

The disruption of ordered water molecules confined within hydrophobic reaction pockets alters the energetics of adsorption and catalysis, but a mechanistic understanding of how nonaqueous solvents influence catalysis in microporous voids remains unclear. Here, we use kinetic analyses coupled with IR spectroscopy to study how alkanol hydrogen-bonding networks confined within hydrophobic and hydrophilic zeolite catalysts modify reaction free energy landscapes. Hydrophobic Beta zeolites containing framework Sn atoms catalyze the transfer hydrogenation reaction of cyclohexanone in a 2-butanol solvent 10× faster than their hydrophilic analogues. This rate enhancement stems from the ability of hydrophobic Sn-Beta to inhibit the formation of extended liquid-like 2-butanol oligomers and promote dimeric H-bonded 2-butanol networks. These different intraporous 2-butanol solvent structures manifest as differences in the activation and adsorption enthalpies and entropies that comprise the free energy landscape of transfer hydrogenation catalysis. The ordered H-bonding solvent network present in hydrophobic Sn-Beta stabilizes the transfer hydrogenation transition state to a greater extent than the liquid-like 2-butanol solvent present in hydrophilic Sn-Beta, giving rise to higher turnover rates on hydrophobic Sn-Beta. Additionally, reactant adsorption within hydrophobic Sn-Beta is driven by the breakup of intraporous solvent-solvent interactions, resulting in positive enthalpies of adsorption that are partially compensated by an increase in the solvent reorganization entropy. Collectively, these results emphasize the ability of the zeolite pore to regulate the structure of confined nonaqueous H-bonding solvent networks, which offers an additional dimension to modulate adsorption and reactivity.

pH-Dependent Water Clusters in Photoacid Solution: Real-Time Observation by ToF-SIMS at a Submicropore Confined Liquid-Vacuum Interface

Water clusters are ubiquitously formed in aqueous solutions by hydrogen bonding, which is quite sensitive to various environment factors such as temperature, pressure, electrolytes, and pH. Investigation of how the environment has impact on water structure is important for further understanding of the nature of water and the interactions between water and solutes. In this work, pH-dependent water structure changes were studied by monitoring the changes for the size distribution of protonated water clusters by in-situ liquid ToF-SIMS. In combination with a light illumination system, in-situ liquid ToF-SIMS was used to real-time measure the changes of a light-activated organic photoacid under different light illumination conditions. Thus, the proton transfer and pH-mediated water cluster changes were analyzed in real-time. It was found that higher concentration of free protons could lead to a strengthened local hydrogen bonding network as well as relatively larger protonated water clusters in both organic acid and inorganic acid. Besides, the accumulation of protons at the liquid-vacuum interface under light illumination was observed owing to the affinity of organic molecules to the low-pressure gas phase. The application of in-situ liquid ToF-SIMS analysis in combination with in-situ light illumination system opened up an avenue to real-time investigate light-activated reactions. Besides, the results regarding water structure changes in acidic solutions showed important insights in related atmospheric and physiochemical processes.

Structure and solvation of confined water and water-ethanol clusters within microporous Brønsted acids and their effects on ethanol dehydration catalysis

Water networks confined within zeolites solvate clustered reactive intermediates and must rearrange to accommodate transition states that differ in size and polarity, with thermodynamic penalties that depend on the shape of the confining environment.

Aqueous-phase reactions within microporous Brønsted acids occur at active centers comprised of water-reactant-clustered hydronium ions, solvated within extended hydrogen-bonded water networks that tend to stabilize reactive intermediates and transition states differently. The effects of these diverse clustered and networked structures were disentangled here by measuring turnover rates of gas-phase ethanol dehydration to diethyl ether (DEE) on H-form zeolites as water pressure was increased to the point of intrapore condensation, causing protons to become solvated in larger clusters that subsequently become solvated by extended hydrogen-bonded water networks, according to in situ IR spectra. Measured first-order rate constants in ethanol quantify the stability of S_N2 transition states that eliminate DEE relative to (C₂H₅OH)(H⁺)(H₂O)_n clusters of increasing molecularity, whose structures were respectively determined using metadynamics and ab initio molecular dynamics simulations. At low water pressures (2–10 kPa H₂O), rate inhibition by water (–1 reaction order) reflects the need to displace one water by ethanol in the cluster en route to the DEE-formation transition state, which resides at the periphery of water–ethanol clusters. At higher water pressures (10–75 kPa H₂O), water–ethanol clusters reach their maximum stable size ((C₂H₅OH)(H⁺)(H₂O)_4–5), and water begins to form extended hydrogen-bonded networks; concomitantly, rate inhibition by water (up to –3 reaction order) becomes stronger than expected from the molecularity of the reaction, reflecting the more extensive disruption of hydrogen bonds at DEE-formation transition states that contain an additional solvated non-polar ethyl group compared to the relevant reactant cluster, as described by non-ideal thermodynamic formalisms of reaction rates. Microporous voids of different hydrophilic binding site density (Beta; varying H⁺ and Si–OH density) and different size and shape (Beta, MFI, TON, CHA, AEI, FAU), influence the relative extents to which intermediates and transition states disrupt their confined water networks, which manifest as different kinetic orders of inhibition at high water pressures. The confinement of water within sub-nanometer spaces influences the structures and dynamics of the complexes and extended networks formed, and in turn their ability to accommodate the evolution in polarity and hydrogen-bonding capacity as reactive intermediates become transition states in Brønsted acid-catalyzed reactions.

Discussing the performance of beta zeolites in aqueous-phase valorization of xylose

Beta zeolites are potential catalysts for xylose upgrade to bioproducts and selectivity is determined by the balance between water-tolerant Lewis and Brønsted acid sites.