Development and validation of a general-purpose ReaxFF reactive force field for earth material modeling.

ReaxFF reactive force field bridges the gap between nonreactive molecular simulations and quantum mechanical calculations and has been widely applied during the past two decades. However, its application to earth materials, especially those under high T-P conditions relevant to Earth's interior, is still limited due to the lack of available parameters. Here, we present the development and validation of a ReaxFF force field containing several of the most common elements in Earth's crust, i.e., Si/Al/O/H/Na/K. The force field was trained against a large data set obtained from density functional theory (DFT) calculations, including charges, bond/angle distortion curves, equation of states, ion migration energy profiles, and condensation reaction energies. Different coordination environments were considered in the training set. The fitting results showed that the current force field can well reproduce the DFT data (the Pearson correlation coefficient, Rp, is 0.95). We validated the force field on mineral-water interfaces, hydrous melts/supercritical geofluids, and bulk crystals. It was found that the current force field performed excellently in predicting the structural, thermodynamic, and transport properties of various systems (Rp = 0.95). Moreover, possible applications and future development have been discussed. The results obtained in this study suggest that the current force field holds good promise to model a wide range of processes and thus open opportunities to advance the application of ReaxFF in earth material modeling.

The Role of Chloride ion in the Silicate Condensation Reaction from ab Initio Molecular Dynamics Simulations.

The comprehension of silicate oligomer formation during the initial stage of zeolite synthesis is of significant importance. In this study, we investigated the effect of chloride ions (Cl-) on silicate oligomerization using ab initio molecular dynamics simulations with explicit water molecules. The results show that the presence of Cl- increases the free energy barriers of all reactions compared to the case without the anion. The formation of the 4-ring structure has the lowest free energy barrier (73 kJ/mol), while the formation of the 3-ring structure has the highest barrier (98 kJ/mol) in the presence of Cl-. These findings suggest that Cl- suppresses the formation of 3-rings and favors the formation of larger oligomers in the process of zeolite synthesis. Our study provides important insights into the directing role of Cl- in silicate oligomerization by regulating thermodynamic and kinetic parameters. An important point to consider is the impact of the anion on aqueous reactions, particularly in altering the hydrogen bond network around reactive species. These results also provide a basis for further studies of the formations of larger silicate oligomers in solution.

Insight into the role of excess hydroxide ions in silicate condensation reactions.

The formation of silicate oligomers in the early stages is key to zeolite synthesis. The pH and the presence of hydroxide ions are important in regulating the reaction rate and the dominant species in solutions. This paper describes the formation of silicate species, from dimers to 4-membered rings, using ab initio molecular dynamics simulations in explicit water molecules with an excess hydroxide ion. The thermodynamic integration method was used to calculate the free energy profile of the condensation reactions. The hydroxide group's role is not only to control the pH of the environment, but also to actively participate in the condensation reaction. The results show that the most favorable reactions are linear-tetramer and 4-membered-ring formation, with overall barriers of 71 kJ mol-1 and 73 kJ mol-1, respectively. The formation of trimeric silicate, with the largest free-energy barrier of 102 kJ mol-1, is the rate-limiting step under these conditions. The excess hydroxide ion aids in the stabilization of the 4-membered-ring structure over the 3-membered-ring structure. Due to a relatively high free-energy barrier, the 4-membered ring is the most difficult of the small silicate structures to dissolve in the backward reaction. This study is consistent with the experimental observation that silicate growth in zeolite synthesis is slower in a very-high-pH environment.

Elucidating the Role of Tetraethylammonium in the Silicate Condensation Reaction from Ab Initio Molecular Dynamics Simulations.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is important. The use of organic structure-directing agents (OSDAs) is known to be a key factor in the formation of different silicate species and the final zeolite structure. For example, tetraethylammonium ion (TEA+) is a commonly used organic template for zeolite synthesis. In this study, ab initio molecular dynamics (AIMD) simulation is used to provide an understanding of the role of TEA+ in the formation of various silicate oligomers, ranging from dimer to 4-ring. Calculated free-energy profiles of the reaction pathways show that the formation of a 4-ring structure has the highest energy barrier (97 kJ/mol). The formation of smaller oligomers such as dimer, trimer, and 3-ring has lower activation barriers. The TEA+ ion plays an important role in regulating the predominant species in solution via its coordination with silicate structures during the condensation process. The kinetics and thermodynamics of the oligomerization reaction indicate a more favorable formation of the 3-ring over the 4-ring structure. The results from AIMD simulations are in line with the experimental observation that TEA+ favors the 3-ring and double 3-ring in solution. The results of this study imply that the role of OSDAs is not only important for the host-guest interaction but also crucial for controlling the reactivity of different silicate oligomers during the initial stage of zeolite formation.

Understanding the Heterogeneous Nucleation of Heavy Metal Phyllosilicates on Clay Edges with First-Principles Molecular Dynamics.

The nucleation and precipitation of heavy metal phyllosilicates can occur in the course of sorption onto clay edges, which will provide a long-term stabilization of heavy metal pollutants. However, a quantitative understanding of their reaction mechanisms is still lacking. Taking Ni2+ as the model cation, we characterized the atomic scale structures and thermodynamics of the early stage of nucleation by carrying out systematic first-principles molecular dynamics (FPMD) simulations, and the microscopic nucleation mechanisms were revealed. Two possible nucleation pathways were examined: a stepwise pathway (denoted as Path1) and a synchronous pathway (denoted as Path2). In Path1, Ni(OH)2 forms first and then transforms to Ni phyllosilicate via silicification; in Path2, Ni phyllosilicate forms on clay edges directly. The computed free energies of complexation and condensation reactions indicate that Path2 is much more thermodynamically favorable than Path1, meaning that, given that the solution contains dissolved Si initially, heavy metal phyllosilicates will nucleate on clay edges through Path2. By comparing these free energies with their counterpart values of the reaction in bulk solution, the effect of the surface has been uncovered. These findings provide valuable insights for an improved understanding of the stabilization and transformation of heavy metal elements in nature. The derived results form a quantitative basis for future studies on the heterogenous nucleation and precipitation of heavy metal cations.

Elucidating cation effects in homogeneously catalyzed formic acid dehydrogenation.

In this work, we use density functional theory based molecular dynamics with an explicit description of methanol solvent to study the effect of cations on formic acid dehydrogenation catalyzed by a ruthenium PNP pincer complex (RuPNP). Formic acid dehydrogenation is a two step process that involves the reorientation of the formate moiety bound via its oxygen to a H bound intermediate, followed by the hydride transfer step to form CO2 and the hydrogenated catalyst. We find the reorientation step to proceed with a low barrier in methanol solvent and in the presence of a Li+ cation, while the hydride transfer is significantly hindered by the presence of cations (Li+ and K+). The cation seems to strongly stabilize the negatively charged formate moiety, hindering complete hydride transfer and resulting in a high barrier for this step. This study is a first step towards addressing the exact role of cations in formic acid dehydrogenation reactions.

Dynamic Interplay between Defective UiO-66 and Protic Solvents in Activated Processes.

UiO-66, composed by Zr-oxide inorganic bricks [Zr6 (µ3 -O)4 (µ3 -OH)4 ] and organic terephthalate linkers, is one of the most studied metal-organic frameworks (MOFs) due to its exceptional thermal, chemical, and mechanical stability. Thanks to its high connectivity, the material can withstand structural deformations during activation processes such as linker exchange, dehydration, and defect formation. These processes do alter the zirconium coordination number in a dynamic way, creating open metal sites for catalysis and thus are able to tune the catalytic properties. In this work, it is shown, by means of first-principle molecular-dynamics simulations at operating conditions, how protic solvents may facilitate such changes in the metal coordination. Solvent can induce structural rearrangements in the material that can lead to undercoordinated but also overcoordinated metal sites. This is demonstrated by simulating activation processes along well-chosen collective variables. Such enhanced MD simulations are able to track the intrinsic dynamics of the framework at realistic conditions.

Ultrastrong Absorption Meets Ultraweak Absorption: Unraveling the Energy-Dissipative Routes for Dye-Sensitized Upconversion Luminescence.

Dye sensitization is becoming a new dimension to highly improve the upconversion luminescence (UCL) of lanthanide-doped upconversion nanoparticles (UCNPs). However, there is still a lack of general understanding of the dye-UCNPs interactions, especially the confused large mismatch between the inputs and outputs. By taking dye-sensitized NaYF4:Yb/Er@NaYF4:Nd UCNPs as a model system, we not only revealed the in-depth energy-dissipative process for dye-sensitized UCL but also confirmed the first ever experimental observation of the energy back transfer (EBT) in the dye-sensitized UCL. Furthermore, this energy-dissipative EBT restricted the optimal ratio of dyes to UCNP. By unearthing all of the energy loss behind the EBT, energy transfer, and energy migration processes, this paper sheds light on the further design of effective dye-sensitized nanosystems for UCL or even downconversion luminescence.

How Solvent Affects C-H Activation and Hydrogen Production Pathways in Homogeneous Ru-Catalyzed Methanol Dehydrogenation Reactions.

Insights into the mechanism of the catalytic cycle for methanol dehydrogenation catalyzed by a highly active PNP pincer ruthenium complex in methanol solvent are presented, using DFT-based molecular dynamics with an explicit description of the solvent, as well as static DFT calculations using microsolvation models. In contrast to previous results, we find the amido moiety of the catalyst to be permanently protonated under catalytic conditions. Solvent molecules actively participate in crucial reaction steps and significantly affect the reaction barriers when compared to pure gas-phase models, which is a direct result of the enhanced solvent stabilization of methoxide anion intermediates. Further, the calculations reveal that this system does not operate via the commonly assumed Noyori-type outer-sphere metal-ligand cooperative pathway. Our results show the importance of incorporating a molecular description of the solvent to gain a deeper and accurate understanding of the reaction pathways, and stress on the need to involve explicit solvent molecules to model complex catalytic processes in a realistic manner.

Impact of the Ligand Flexibility and Solvent on the O-O Bond Formation Step in a Highly Active Ruthenium Water Oxidation Catalyst.

By advanced molecular dynamics simulations, we show that for a highly active ruthenium-based water oxidation catalyst the dangling carboxylate group of the catalyst plays an important role in the crucial O-O bond formation step. The interplay of the flexible group and solvent molecules facilitates two possible pathways: a direct pathway with a single solvent water molecule or a mediated pathway involving two solvent water molecules, which have similar activation barriers. Our results provide an example for which a realistic molecular dynamics approach, incorporating an explicit description of the solvent, is required to reveal the full complexity of an important catalytic reaction in aqueous solvent.

Precisely Tailoring Upconversion Dynamics via Energy Migration in Core-Shell Nanostructures.

Upconversion emission dynamics have long been believed to be determined by the activator and its interaction with neighboring sensitizers. Herein this assumption is, however, shown to be invalid for nanostructures. We demonstrate that excitation energy migration greatly affects upconversion emission dynamics. "Dopant ions' spatial separation" nanostructures are designed as model systems and the intimate link between the random nature of energy migration and upconversion emission time behavior is unraveled by theoretical modelling and confirmed spectroscopically. Based on this new fundamental insight, we have successfully realized fine control of upconversion emission time behavior (either rise or decay process) by tuning the energy migration paths in various specifically designed nanostructures. This result is significant for applications of this type of materials in super resolution spectroscopy, high-density data storage, anti-counterfeiting, and biological imaging.

Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites.

Acidity Constant (pKa ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods.

pH-Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa ). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.

On the slowdown mechanism of water dynamics around small amphiphiles.

Aqueous solvation of small amphiphilic molecules exhibits a unique and complex dynamics, that is only partially understood. A recent series of studies on the hydration of small organic compounds, such as tetramethylurea (TMU), trimethylamine N-oxide (TMAO) and urea, has provided strong evidence of a slowdown of the dynamics of the hydrating water molecules. However, the mechanism of this slowdown is still a matter of debate. We analyze the slowdown mechanism by combining molecular dynamics (MD) simulations, using ab initio and classical force field methods, with mid-infrared pump-probe spectroscopy. Aqueous solutions of TMU and of urea were studied at a 0.1 solute/solvent ratio, where we decompose the contribution of different solvating groups to the orientational dynamics. Our results reveal that two competing processes govern the H-bond breaking mechanism: H-bond switching through an associative partner exchange and a dissociative breaking characterized by an unbound state. H-bond switches are shown to occur less often near hydrophobic groups, thus creating a subset of OH groups that do not switch and therefore do not significantly reorient within the lifetime of one H-bond, but will require at least a second H-bond to be formed and broken before it may switch. Our results shed new light on the role of hydrophobic solvation in the water orientational dynamics and help to conciliate the controversy regarding the timescale separation, providing a mechanistic explanation for the observed slow component.

The role of a structure directing agent tetramethylammonium template in the initial steps of silicate oligomerization in aqueous solution.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is of fundamental scientific and technological importance. The use of different organic structure directing agents is known to be a key factor in the formation of different silicate species, and the final zeolite structure. Tetramethylammonium (TMA(+)), for example, is indispensable for the formation of the LTA zeolite type. However, the role of a TMA(+) template has not yet been elucidated at the molecular level. In this study, ab initio molecular dynamic simulations were combined with thermodynamic integration to arrive at an understanding of the role of TMA(+) in the formation of various silicate species, ranging from dimer to 4-ring. Free energy profiles show that trimer and 3-ring silicate are less favourable than other oligomers such as linear tetramer, branched tetramer and 4-ring structures. TMA(+) exhibits an important role in controlling the predominant species in solution via its coordination with silicate structures during the reaction process. This can explain that formation of D4R·8TMA crystals, as observed in experiment, is controlled by the single 4-ring formation step.

Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics.

The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.

Force sensing in surgical sutures.

The tension in a suture is an important factor in the process of wound healing. If there is too much tension in the suture, the blood flow is restricted and necrosis can occur. If the tension is too low, the incision opens up and cannot heal properly. The purpose of this paper is to describe the design and evaluation of the Stitch Force (SF) sensor and the Hook-In Force (HIF) sensor. These sensors were developed to measure the force on a tensioned suture inside a closed incision and to measure the pulling force used to close the incision. The accuracy of both sensors is high enough to determine the relation between the force in the thread of a stitch and the pulling force applied on the suture by the physician. In a pilot study, a continuous suture of 7 stitches was applied on the fascia of the abdominal wall of multiple pigs to study this relationship. The results show that the max force in the thread of the second stitch drops from 3 (SD 1.2) to 1 (SD 0.3) newton after the 4(th) stitch was placed. During placement of the 5(th), 6(th) and 7(th) stitch, the force in the 2(nd) stitch was not influenced anymore. This study indicates that in a continuous suture the force in the thread remains constant up to more than 3 stiches away from the pulled loose end of the suture. When a force feedback tool is developed specially for suturing in surgery on patients, the proposed sensors can be used to determine safety threshold for different types of tissue and sutures.

Conformational study of Z-Glu-OH and Z-Arg-OH: dispersion interactions versus conventional hydrogen bonding.

The gas-phase conformational preferences of the model dipeptides Z-Glu-OH and Z-Arg-OH have been studied in the low-temperature environment of a supersonic jet. IR-UV ion-dip spectra obtained using the free electron laser FELIX provide conformation-specific IR spectra, which in combination with density functional theory (DFT) allow us to determine the conformational structures of the peptides. Molecular dynamics modeling using simulated annealing generates a variety of low-energy structures, for which geometry optimization and frequency calculations are then performed using the B3LYP functional with the 6-311+G(d,p) basis set. By comparing experimental and theoretical IR spectra, three conformations for Z-Glu-OH and two for Z-Arg-OH have been identified. For three of the five structures, the dispersion interaction provides an important contribution to the stabilization, emphasizing the importance of these forces in small peptides. Therefore, dispersion-corrected DFT functionals (M05-2X and B97D) have also been employed in our theoretical analysis. Second-order Møller-Plesset perturbation theory (MP2) has been used as benchmark for the relative energies of the different conformational structures. Finally, we address the ongoing debate on the gas-phase structure of arginine by elucidating whether isolated arginine is canonical, tautomeric, or zwitterionic.