Disclosing gate-opening/closing events inside a flexible metal-organic framework loaded with CO2 by reactive and essential dynamics.

We have combined reactive molecular dynamics simulations with principal component analysis to provide a clearer view of the interactions and motion of the CO2 molecules inside a metal-organic framework and the movements of the MOF components that regulate storage, adsorption, and diffusion of the guest species. The tens-of-nanometer size of the simulated model, the capability of the reactive force field tuned to reproduce the inorganic-organic material confidently, and the unconventional use of essential dynamics have effectively disclosed the gate-opening/closing phenomenon, possible coordinations of CO2 at the metal centers, all the diffusion steps inside the MOF channels, the primary motions of the linkers, and the effects of their concerted rearrangements on local CO2 relocations.

An Atomically Dispersed Mn-Photocatalyst for Generating Hydrogen Peroxide from Seawater via the Water Oxidation Reaction (WOR).

In this work, we have fabricated an aryl amino-substituted graphitic carbon nitride (g-C3N4) catalyst with atomically dispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibited excellent reactivity, obtaining up to 2230 µM H2O2 in 7 h from alkaline water and up to 1800 µM from seawater under identical conditions. More importantly, the catalyst was quickly recovered for subsequent reuse without appreciable loss in performance. Interestingly, unlike the usual two-electron oxygen reduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction (WOR) process in which both the direct and indirect WOR processes occurred; namely, photoinduced h+ directly oxidized H2O to H2O2 via a one-step 2e- WOR, and photoinduced h+ first oxidized a hydroxide (OH-) ion to generate a hydroxy radical (•OH), and H2O2 was formed indirectly by the combination of two •OH. We have characterized the material, at the catalytic sites, at the atomic level using electron paramagnetic resonance, X-ray absorption near edge structure, extended X-ray absorption fine structure, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, magic-angle spinning solid-state NMR spectroscopy, and multiscale molecular modeling, combining classical reactive molecular dynamics simulations and quantum chemistry calculations.

Stability and potential degradation of the α',ß'-epoxyketone pharmacophore on ZnO nanocarriers: insights from reactive molecular dynamics and density functional theory calculations.

We investigate the structure and dynamics of a zinc oxide nanocarrier loaded with Carfilzomib, an epoxyketone proteasome inhibitor developed for treating multiple myeloma. We demonstrate that, even though both bare and functionalized zinc oxide supports have been used for drug delivery, their interactions with the reactive functional groups of the ligands could be detrimental. This is because pharmacophores like α',ß'-epoxyketones should preserve the groups required for the drug activity and be capable of leaving the vehicle at the target site. Earlier studies showed that even when ZnO is functionalized with oleic acid surfactants, the drug could reach parts of the surface and remain stably adsorbed. Herein, we have used reactive molecular dynamics simulations and quantum chemistry calculations to explore the potential interactions of the Carfilzomib functional groups with the typical surfaces of ZnO supports. We have found that Carfilzomib can adsorb on the (0001)Zn-terminated polar surface through the carbonyl oxygens and the epoxyketone moiety. These strong connections could prevent the drug release and induce the epoxy ring opening with its consequential inactivation. Therefore, regulating the dosage to maintain the desired level of drug bioavailability is paramount. These findings emphasize the need for appropriate carrier functionalizations to efficiently entrap, transport, and release the cargo at the target sites and the crucial role played by predictive/descriptive computational techniques to complement and drive experiments to the most appropriate selections of the materials to optimize drug delivery.

Role of the redox state of cerium oxide on glycine adsorption: an experimental and theoretical study.

The role of the oxidation state of cerium cations in a thin oxide film in the adsorption, geometry, and thermal stability of glycine molecules was studied. The experimental study was performed for a submonolayer molecular coverage deposited in vacuum on CeO2(111)/Cu(111) and Ce2O3(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by ab initio calculations for prediction of the adsorbate geometries, C 1s and N 1s core binding energies of glycine, and some possible products of the thermal decomposition. The molecules adsorbed on the oxide surfaces at 25 °C in the anionic form via the carboxylate oxygen atoms bound to cerium cations. A third bonding point through the amino group was observed for the glycine adlayers on CeO2. In the course of stepwise annealing of the molecular adlayers on CeO2 and Ce2O3, the surface chemistry and decomposition products were analyzed and found to relate to different reactivities of glycinate on Ce4+ and Ce3+ cations, observed as two dissociation channels via C-N and C-C bond scission, respectively. The oxidation state of cerium cations in the oxide was shown to be an important factor, which defines the properties, electronic structure, and thermal stability of the molecular adlayer.

Π-Π Stacking Complex Induces Three-Component Coupling Reactions To Synthesize Functionalized Amines.

π-π stacking and ion-pairing interactions induced the generation of α-amino radicals under the irradiation of visible light without the requirement of an expensive photocatalyst. This strategy enabled the construction of functionalized amines via three-component coupling reactions with broad scope (we report >50 examples with an up to 90 % yield). This synthetic pathway also delivered complex functionalized amines with a very high yield. Quantum chemistry Density Functional Theory (DFT) calculations identified π-π stacked ionic complexes; time-dependent DFT was employed to simulate the absorption spectra, and nudged elastic band (NEB) methodology provided a possible interaction/reaction picture of the selected species.

Exploring the mechanisms of drug-delivery by decorated ZnO nanoparticles through predictive ReaxFF molecular dynamics simulations.

Herein, we study the assembling of a drug delivery nanocarrier through reactive molecular dynamics simulations based on an appropriately tuned force field. First, we focus on the combination of the various components (all selected in agreement with experiments), namely nanoparticle (ZnO), functional chains (oleic acid), drug (carfilzomib), and solvent molecules (ethanol), and then on the ability of the assembled nanotool to release its cargo in a physiological environment (water). The simulation results reveal that reactivity is crucial for characterizing the stability of the functionalized ZnONP, its dynamics, and its interactions with lipid chains and drug molecules. The chains are stably chemisorbed on the ZnONP through monodentate or bidentate binding of the carboxyls to the Zn atoms (the hydrogens are released to the surface oxygens). Chains' self-interactions reinforce the lipid cover's stability and distribution on the ZnONP interface. The added drug migrates from the solution to the nano assembly and is captured by the lipids. The molecules are entrapped among the oleic acid chains and adsorbed on the uncoated regions of the nanoparticle surface, partially physisorbed or chemisorbed. The analysis of the simulations confirms that the supramolecular assembly is compact and stable in ethanol. However, upon injection into the water, the size of the aggregate gradually increases, and the lipids start to swell with the aqueous medium. The system evolves towards an unpacked structure where the chains are elongated, separated, and prone to release the cargo depending on local water activity and depth of cargo insertion. All the results agree with the literature confirming the reliability of our predictive computational procedure for disclosing the structure and dynamics of complex materials relevant to the medicinal chemistry field.

Molecularly Imprinted Nanoparticles towards MMP9 for Controlling Cardiac ECM after Myocardial Infarction: A Predictive Experimental-Computational Chemistry Investigation.

The recent advances in nanotechnology are revolutionizing preventive and therapeutic approaches to treating cardiovascular diseases. Controlling the extracellular matrix metalloproteinase (MMP) activation and expression in the failing human left ventricular myocardium represents a significant therapeutic target for heart disease. In this study, we used molecularly imprinting polymers (MIPs) to restore the correct balance between MMPs and their tissue inhibitors (TIMPs), and explored the potential of this technique exhaustively through chemical synthesis, physicochemical and biological characterizations, and computational chemistry methods. By molecular dynamics simulations based on classical force fields, we simulated the early stages of the imprinting process in solution disclosing the pivotal interaction established between the monomers and the MMP9 protein template. The average interaction energies of methacrylic acid (MAA) and poly (ethylene glycol) ethyl ether methacrylate (PEG) units were in the ranges 17-22 and 30-37 kcal/mol, respectively. At low coverage, the PEG monomers seemed firmly anchored to the protein surface and were not displaced by water, while only about 20% of MAA was replaced by water. The synthesis of MIPs was successfully with a monomer conversion higher than 99% and the production of spherical particles with average diameter of 344 ± 33 nm. HPLC analysis showed a specific recognition factor of MMP9 on MIPs of about 1.3. FT-IR Chemical Imaging confirmed the mechanisms necessary to generate a "selective memory" of the MIPs towards the enzyme. HPLC results indicated that the rebound amount of both TIMP1 and MMP2 to MIPs is lower than that of the template, showing a selectivity factor of 2.1 and 2.3, respectively. Preliminary tests on the effect of MIPs on H9C2 cells revealed that this treatment has no cytotoxic effects.

Lignin-Supported Heterogeneous Photocatalyst for the Direct Generation of H2O2 from Seawater.

The development of smart and sustainable photocatalysts is in high priority for the synthesis of H2O2 because the global demand for H2O2 is sharply rising. Currently, the global market share for H2O2 is around 4 billion US$ and is expected to grow by about 5.2 billion US$ by 2026. Traditional synthesis of H2O2 via the anthraquinone method is associated with the generation of substantial chemical waste as well as the requirement of a high energy input. In this respect, the oxidative transformation of pure water is a sustainable solution to meet the global demand. In fact, several photocatalysts have been developed to achieve this chemistry. However, 97% of the water on our planet is seawater, and it contains 3.0-5.0% of salts. The presence of salts in water deactivates the existing photocatalysts, and therefore, the existing photocatalysts have rarely shown reactivity toward seawater. Considering this, a sustainable heterogeneous photocatalyst, derived from hydrolysis lignin, has been developed, showing an excellent reactivity toward generating H2O2 directly from seawater under air. In fact, in the presence of this catalyst, we have been able to achieve 4085 µM of H2O2. Expediently, the catalyst has shown longer durability and can be recycled more than five times to generate H2O2 from seawater. Finally, full characterizations of this smart photocatalyst and a detailed mechanism have been proposed on the basis of the experimental evidence and multiscale/level calculations.

An augmented (multi-descriptor) grouping algorithm to optimize chemical ordering in nanoalloys.

We propose the Augmented Grouping Approach (AugGA) and its deployment in the Augmented Grouping GO (AugGGO) scheme, for an efficient exploration of the chemical ordering (or compositional structure) of multi-component (alloyed) nanoparticles. The approach is based on a 'grouping' strategy (previously proposed for high-symmetry structures) by which the number of compositional degrees of freedom of the system is decreased by defining sets of atoms (groups, or orbits, or shells) that are constrained to be populated by the same element. Three fundamental advances are here included with respect to previous proposals: (i) groups are defined on the basis of descriptors (no point-group symmetry is assumed), (ii) bulk groups can exploit general chemical ordering patterns taken from databases, and (iii) sub-grouping is realized via a multi-descriptor strategy (here using two basic descriptors: the atomic energy and a few types of geometry patterns). The AugGGO approach is applied to two prototypical examples of binary nanoalloys: Pd-Pt and Ag-Cu, with a size between ≈500 and ≈1300 atoms, in different configurations, and the convex hull of the mixing energy as a function of composition is derived. It is shown how the three advances here proposed decisively extend the power and scope of the grouping approach: (i) making it applicable to any generic structural framework, (ii) achieving a thorough sampling of the core regions of nanoparticles, and (iii) catching exotic/unexpected chemical ordering arrangements, at a computational cost which is 1-2 orders of magnitude smaller than that of traditional Monte Carlo single-exchange techniques.

Structural Refinement of Carbimazole by NMR Crystallography.

The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave's disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.

Correction: 2D oxides on metal materials: concepts, status, and perspectives.

Correction for '2D oxides on metal materials: concepts, status, and perspectives' by Giovanni Barcaro et al., Phys. Chem. Chem. Phys., 2019, 21, 11510-11536, DOI: 10.1039/C9CP00972H.

Diverse Phases of Carbonaceous Materials from Stochastic Simulations.

Amorphous carbon systems are emerging to have unparalleled properties at multiple length scales, making them the preferred choice for creating advanced materials in many sectors, but the lack of long-range order makes it difficult to establish structure/property relationships. We propose an original computational approach to predict the morphology of carbonaceous materials for arbitrary densities that we apply here to graphitic phases at low densities from 1.15 to 0.16 g/cm3, including glassy carbon. This approach, dynamic reactive massaging of the potential energy surface (DynReaxMas), uses the ReaxFF reactive force field in a simulation protocol that combines potential energy surface (PES) transformations with global optimization within a multidescriptor representation. DynReaxMas enables the simulation of materials synthesis at temperatures close to experiment to correctly capture the interplay of activated vs entropic processes and the resulting phase morphology. We then show that DynReaxMas efficiently and semiautomatically produces atomistic configurations that span wide relevant regions of the PES at modest computational costs. Indeed, we find a variety of distinct phases at the same density, and we illustrate the evolution of competing phases as a function of density ranging from uniform vs bimodal distributions of pore sizes at higher and intermediate density (1.15 g/cm3 and 0.50 g/cm3) to agglomerated vs sparse morphologies, further partitioned into boxed vs hollow fibrillar morphologies, at lower density (0.16 g/cm3). Our observations of diverse phases at the same density agree with experiment. Some of our identified phases provide descriptors consistent with available experimental data on local density, pore sizes, and HRTEM images, showing that DynReaxMas provides a systematic classification of the complex field of amorphous carbonaceous materials that can provide 3D structures to interpret experimental observations.

New Mechanistic Insights into the Lignin ß-O-4 Linkage Acidolysis with Ethylene Glycol Stabilization Aided by Multilevel Computational Chemistry.

Acidolysis in conjunction with stabilization of reactive intermediates has emerged as one of the most powerful methods of lignin depolymerization that leads to high aromatic monomer yields. In particular, stabilization of reactive aldehydes using ethylene glycol results in the selective formation of the corresponding cyclic acetals (1,3-dioxolane derivatives) from model compounds, lignin, and even from softwood lignocellulose. Given the high practical utility of this method for future biorefineries, a deeper understanding of the method is desired. Here, we aim to elucidate key mechanistic questions utilizing a combination of experimental and multilevel computational approaches. The multiscale computational protocol used, based on ReaxFF molecular dynamics, represents a realistic scenario, where a typical experimental setup can be reproduced confidently given the explicit molecules of the solute, catalyst, and reagent. The nudged elastic band (NEB) approach allowed us to characterize the key intermolecular interactions involved in the reaction paths leading to crucial intermediates and products. The high level of detail obtained clearly revealed for the first time the unique role of sulfuric acid as a proton donor and acceptor in lignin ß-O-4 acidolysis as well as the reaction pathways for ethylene glycol stabilization, and the difference in reactivity between compounds with different methoxy substituents.

Modeling generation and growth of iron oxide nanoparticles from representative precursors through ReaxFF molecular dynamics.

Detailed dynamical characterization of the mechanisms responsible for the formation and growth of iron oxide nanoparticles remains a significant challenge not only for experimental techniques but also for theoretical methodologies due to the nanoparticle size, long simulation times, and complexity of the environments. In this work, we have designed a fast computational protocol based on atomistic reactive molecular dynamics, which is capable of simulating the whole synthetic and proliferation process of the nanoparticles (greater than 10 nm) in a homogeneous medium from organometallic precursors. We have defined appropriate growth accelerating strategies based on the observed reactions, which consisted of the formation of Fe-O-Fe bridges, linking separate precursors, and Fe˙ and FeO˙ radicals. This reduced drastically the computational time allowing the simulation of NPs made of thousands of atoms (full nanometric range). We have identified the most probable reaction environments and summarized them under two distinct conditions: reductive and oxidative. The first one leads to the formation of nanoparticles with FeO stoichiometry typical of wustite, whereas the second one stabilizes stoichiometries between Fe3O4 (magnetite), and Fe2O3 (maghemite). In the latter case, the obtained NPs adopted, from the very early stages of the growth process, a cubic crystalline structure, typical of the oxidized FeOx bulk phases. The excellent agreement of our results with the experimental data demonstrates that the proposed protocol can provide a powerful predictive tool to describe structural features developed by the metal oxide nanoparticles and establish clear structure-property relationships.

Phosphorene and Black Phosphorus: The 31P NMR View.

This work aims at characterizing for the first time the 31P spin interactions determining the nuclear magnetic resonance (NMR) properties of solid black phosphorus (bP) and of its few-layer exfoliated form (fl-bP). Indeed, the knowledge of these properties is still very poor, despite the great interest received by this layered phosphorus allotrope and its exfoliated 2D form, phosphorene. By combining density functional theory (DFT) calculations and solid-state NMR experiments on suspensions of fl-bP nanoflakes and on solid bP, it has been possible to characterize the 31P homonuclear dipolar and chemical shift interactions, identifying the network of 31P nuclei more strongly dipolarly coupled and highlighting two kinds of magnetically nonequivalent 31P nuclei. These results add an important missing piece of information to the fundamental chemico-physical knowledge of bP and support future extensive applications of NMR spectroscopy to the characterization of phosphorene-based materials.

2D oxides on metal materials: concepts, status, and perspectives.

Oxide materials at the two-dimensional limit, in particular in the form of ultrathin films of oxides (UTOx) grown on metal surfaces, represent promising materials in view of both fundamental science and technological applications. While the former aspect is widely recognized, these systems have not yet realized their full potential in terms of the latter (technological) aspect. In the present perspective, we review the field and its basic underlying concepts, and at the same time we provide an overview of the most promising future directions with a focus on their potential toward and relationships with real-world exploitation.

Core Shell Investigation of 2-nitroimidazole.

Tunability and selectivity of synchrotron radiation have been used to study the excitation and ionization of 2-nitroimidazole at the C, N, and O K-edges. The combination of a set of different measurements (X-ray photoelectron spectroscopy, near-edge photoabsorption spectroscopy, Resonant Auger electron spectroscopy, and mass spectrometry) and computational modeling have successfully disclosed local effects due to the chemical environment on both excitation/ionization and fragmentation of the molecule.

Experimental and theoretical elucidation of catalytic pathways in TiO2-initiated prebiotic polymerization.

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

Modeling Nucleation and Growth of ZnO Nanoparticles in a Low Temperature Plasma by Reactive Dynamics.

The very first stages of nucleation and growth of ZnO nanoparticles in a plasma reactor are studied by means of a multiscale computational paradigm where the DFT-GGA approach is used to evaluate structure and electronic energy of small (ZnO) N clusters ( N ≤ 24) that are employed as a training set (TS) for the optimization of a Reactive Force Field (ReaxFF). Reactive Molecular Dynamics (RMD) simulations based on this tuned ReaxFF are carried out to reproduce nucleation and growth in a realistic environment. Inside the reaction chamber the temperature is around 1200 K, and the zinc atoms are oxidized in an oxygen-rich atmosphere at high pressure (about 20 atm), whereas in the quenching chamber where the temperature is lower (about 800 K) the ZnO embryo-nanoclusters are grown. The main processes ruling gas-phase nucleation and growth of ZnO nanoclusters are identified and discussed together with the dependence of the inception time and average stoichiometry of nanoclusters of different size on the composition of precursor material and physical parameters.

Molecular dynamics simulations of melting and sintering of Si nanoparticles: a comparison of different force fields and computational models.

Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential. The capability of our parametrization of a reactive force field ReaxFF to describe such processes is assessed through a comparison with formally simpler Stillinger-Weber and Tersoff potentials, which are frequently used for simulating silicon-based materials. A substantial dependence of both the predicted melting point and its variation as a function of the nanoparticle size on the simulation model is also highlighted. The outcomes of the molecular dynamics simulations suggest that the trend of the nanoparticulate sintering/coalescence time vs. temperature could provide a valid tool to determine the melting points of nanoparticles theoretically/experimentally.