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.

Reversible assembly of nanoparticles: theory, strategies and computational simulations

The significant advances in synthesis and functionalization have enabled the preparation of high-quality nanoparticles that have found a plethora of successful applications. The unique physicochemical properties of nanoparticles can be manipulated through the control of size, shape, composition, and surface chemistry, but their technological application possibilities can be further expanded by exploiting the properties that emerge from their assembly. The ability to control the assembly of nanoparticles not only is required for many real technological applications, but allows the combination of the intrinsic properties of nanoparticles and opens the way to the exploitation of their complex interplay, giving access to collective properties. Significant advances and knowledge gained over the past few decades on nanoparticle assembly have made it possible to implement a growing number of strategies for reversible assembly of nanoparticles. In addition to being of interest for basic studies, such advances further broaden the range of applications and the possibility of developing innovative devices using nanoparticles. This review focuses on the reversible assembly of nanoparticles and includes the theoretical aspects related to the concept of reversibility, an up-to-date assessment of the experimental approaches applied to this field and the advanced computational schemes that offer key insights into the assembly mechanisms. We aim to provide readers with a comprehensive guide to address the challenges in assembling reversible nanoparticles and promote their applications.

Carbon dioxide adsorption and activation on ionic liquid decorated Au(111) surface: A DFT study

We use first principle approaches to study the adsorption and catalytic activation mechanism of CO₂ on ionic liquids (ILs, [C_nMIm]⁺[Cl]^- (n = 0-6)) attached to a Au(111) surface. The adsorption of CO₂ at this liquid-solid model interface occurs via either (i) parallel π-stacking mode or (ii) CO₂ oxygen lone pair (lp)···π interaction. These CO₂ physisorption modes, which depend on the CO₂ landing angle at this interface, are identified as an efficient way to activate CO₂ and its further conversion into value-added products. For illustration, we discuss the conversion of CO₂ into formic acid where the ILs@Au(111) decorated interface allows reduction of the activation energy for the CO₂ + H₂ → HCOOH reaction. In sum, our electrode/electrolyte based interface model provides valuable information to design novel heterogeneous catalysts for CO₂ conversion. Indeed, our work establishes that a suitable interface material is enough to activate CO₂.

Modulation of Nanoparticle Diffusion by Surface Ligand Length and Charge: Analysis with Molecular Dynamics Simulations

To help better interpret experimental measurement of nanoparticle size, it is important to understand how their diffusion depends on the physical and chemical features of surface ligands. In this study, explicit solvent molecular dynamics simulations are used to probe the effect of ligand charge and flexibility on the diffusion of small gold nanoparticles. The results suggest that despite a high bare charge (+18 e), cationic nanoparticles studied here have reduced diffusion constants compared to a hydrophobic gold nanoparticle by merely a modest amount. Increasing the ligand length by 10 CH₂ units also has a limited impact on the diffusion constant. For the three particles studied here, the difference between estimated hydrodynamic radius and radius of gyration is on the order of one solvent layer (3-5 Å), confirming that the significant discrepancies found in the size of similar nanoparticles by recent transmission electron microscopy and dynamic light scattering measurements were due to aggregation under solution conditions. The limited impact of electrostatic friction on the diffusion of highly charged nanoparticles is found to be due to the strong anticorrelation between electrostatic and van der Waals forces between nanoparticle and environment, supporting the generality of recent observation for proteins by Matyushov and co-workers. Including the first shell of solvent molecules as part of the diffusing particle has a minor impact on the total force autocorrelation function but reduces the disparity in relaxation time between the total force and its electrostatic and van der Waals components.

Removal of azo dye from aqueous solution by a low-cost activated carbon prepared from coal: adsorption kinetics, isotherms study, and DFT simulation

The high-risk organic pollutants produced by industries are of growing concern. The highly porous coal-based activated carbon (AC) having a specific surface area of 3452.8 m²/g is used for the adsorption of azo dye from synthetic solution. The sorbent is characterized through BET, SEM, TEM, XRD, FT-IR, TGA, and zeta potential. The sorbent exhibits - 18.7 mV surface charge, which is high enough for making suspension. The maximum dye uptake of 333 mg/g is observed in sorbent under acidic medium. The thermodynamics parameters like ∆G, ∆H, and ΔS were found to be - 12.40 kJ mol^-1, 39.66 kJ mol^-1, and 174.55 J mol^-1 K^-1 at 293 K, respectively, revealing that the adsorption mechanism is spontaneous, endothermic, and feasible. The experimental data follows the Langmuir and D-R models. The adsorption follows pseudo 2nd-order kinetics. DFT investigation shows that the dye sorption onto AC in configuration No. 4 (CFG-4) is more effective, as this configuration has high ∆H (enthalpy change) and adsorption energy (E_ads). This is confirmed by Mullikan atomic charge transfer phenomenon.

Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.

Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules

The molecular features that dictate interactions between functionalized nanoparticles and biomolecules are not well understood. This is in part because for highly charged nanoparticles in solution, establishing a clear connection between the molecular features of surface ligands and common experimental observables such as ζ potential requires going beyond the classical models based on continuum and mean field models. Motivated by these considerations, molecular dynamics simulations are used to probe the electrostatic properties of functionalized gold nanoparticles and their interaction with a charged peptide in salt solutions. Counterions are observed to screen the bare ligand charge to a significant degree even at the moderate salt concentration of 50 mM. As a result, the apparent charge density and ζ potential are largely insensitive to the bare ligand charge densities, which fall in the range of ligand densities typically measured experimentally for gold nanoparticles. While this screening effect was predicted by classical models such as the Manning condensation theory, the magnitudes of the apparent surface charge from microscopic simulations and mean-field models are significantly different. Moreover, our simulations found that the chemical features of the surface ligand (e.g., primary vs. quaternary amines, heterogeneous ligand lengths) modulate the interfacial ion and water distributions and therefore the interfacial potential. The importance of interfacial water is further highlighted by the observation that introducing a fraction of hydrophobic ligands enhances the strength of electrostatic binding of the charged peptide. Finally, the simulations highlight that the electric double layer is perturbed upon binding interactions. As a result, it is the bare charge density rather than the apparent charge density or ζ potential that better correlates with binding affinity of the nanoparticle to a charged peptide. Overall, our study highlights the importance of molecular features of the nanoparticle/water interface and underscores a set of design rules for the modulation of electrostatic driven interactions at nano/bio interfaces.

Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data

Nanoparticles used in biological settings are exposed to proteins that adsorb on the surface forming a protein corona. These adsorbed proteins dictate the subsequent cellular response. A major challenge has been predicting what proteins will adsorb on a given nanoparticle surface. Instead, each new nanoparticle and nanoparticle modification must be tested experimentally to determine what proteins adsorb on the surface. We propose that any future predictive ability will depend on large datasets of protein-nanoparticle interactions. As a first step towards this goal, we have developed an automated workflow using a liquid handling robot to form and isolate protein coronas. As this workflow depends on magnetic separation steps, we test the ability to embed magnetic nanoparticles within a protein nanoparticle. These experiments demonstrate that magnetic separation could be used for any type of nanoparticle in which a magnetic core can be embedded. Higher-throughput corona characterization will also require lower-cost approaches to proteomics. We report a comparison of fast, low-cost, and standard, slower, higher-cost liquid chromatography coupled with mass spectrometry to identify the protein corona. These methods will provide a step forward in the acquisition of the large datasets necessary to predict nanoparticle-protein interactions.

How cations affect the electric double layer and the rates and selectivity of electrocatalytic processes

Electrocatalysis is central to the production of renewable fuels and high-value commodity chemicals. The electrolyte and the electrode together determine the catalytic properties of the liquid/solid interface. In particular, the cations of the electrolyte can greatly change the rates and reaction selectivity of many electrocatalytic processes. For this reason, the careful choice of the cation is an essential step in the design of catalytic interfaces with high selectivity for desired high-value products. To make such a judicious choice, it is critical to understand where in the electric double layer the cations reside and the various distinct mechanistic impacts they can have on the electrocatalytic process of interest. In this perspective, we review recent advances in the understanding of the electric double layer with a particular focus on the interfacial distribution of cations and the cations' hydration states in the vicinity of the electrode under various experimental conditions. Furthermore, we summarize the different ways in which cations can alter the rates and selectivity of chemical processes at electrified interfaces and identify possible future areas of research in this field.

Conformation-Dependent Coordination of Carboxylic Acids with Fe3O4 Nanoparticles Studied by ATR-FTIR Spectral Deconvolution

The coordination of valeric acid (VA), glutaric acid (GA), and tricarballylic acid (TA) with Fe-OH on the Fe₃O₄ nanoparticle surface has been systematically studied to elucidate the effects of COOH, molecular configuration, and ligand concentration on the coordination by the combined use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) and thermogravimetric analysis (TGA). The results show that the binding ability of the acids increases with the increase in the COOH number. Multiple conformations coexist for the dicarboxylic and tricarboxylic acid coordinated on the iron oxide NPs. Saturated coordination formed with only a one-, two-, or three-COOH conformation for VA, GA, and TA, respectively, occurs under ligand-scarce conditions, while unsaturated coordination formed with the mixture of uncoordinated, one-, and/or two-COOH conformations for VA, GA, and TA, respectively, exists under ligand-abundant conditions. The maximum coordination numbers for monolayer adsorption for VA, GA, and TA on Fe₃O₄ NPs are 9, 2.4, and 2.7 nm^-2, respectively. This study helps us to understand the fine coordination mechanism caused by the acid molecules with different configurations and elucidates, for the first time, the fine conformational variance incurred by the surrounding ligand with different concentrations and the way in which the ligand is added.

Microscopy and Cell Biology: New Methods and New Questions

Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.