Study of the solvent-dependent crystal shape of theophylline using constant chemical potential molecular dynamics simulations.

The crystal habit of an organic crystalline material impacts its properties, processing, and performance, especially in pharmaceuticals. In solution crystallization, solvents play a crucial role in modulating the crystal habits by interacting with the different growing facets - either enhancing or inhibiting the growth of specific facets. Thus, an in-depth understanding of the role of the solvent in crystal shape selection is of paramount importance for the design and growth of crystals. In this work, we used constant chemical potential molecular dynamics (CµMD) to simulate the growth of theophylline crystals in solvents with decreasing polarity, i.e. water, isopropyl alcohol, and dimethylformamide. Our results indicate that as the polarity of the solvent increases, theophylline crystallizes into rod-shaped crystals; the aspect ratio is modulated by the relative growth of the (001) and (010) facets. Furthermore, solvent profile analyses revealed that the desolvation of the crystal facets plays a major role in the growth process.

Unveiling the Role of Solvent in Solution Phase Chemical Reactions using Deep Potential-Based Enhanced Sampling Simulations.

We have used a deep learning-based active learning strategy to develop ab initio level accurate machine-learned (ML) potential for a solution-phase reactive system. Using this ML potential, we carried out enhanced sampling simulations to sample the reaction process efficiently. Multiple transitions between the reactant and product states allowed us to calculate the converged free energy surface for the reaction. As a prototypical example, we have investigated the Menshutkin reaction, a classic bimolecular nucleophilic substitution reaction (SN2) in aqueous medium. Our analyses revealed that water stabilizes the ionic product state by enhanced solvation, facilitating the reaction and making it more spontaneous. Our approach expands the scope of studying the chemical reaction under realistic conditions, such as explicit solvents at finite temperatures, closely mimicking experiments.

Polymorph-Specific Solubility Prediction of Urea Using Constant Chemical Potential Molecular Dynamics Simulations.

Molecular dynamics simulations offer a robust approach to understanding the material properties within a system. Solubility is defined as the analytical composition of a saturated solution expressed as a proportion of designated solute in a designated solvent, according to IUPAC. It is a critical property of compounds and holds significance across numerous fields. Various computational techniques have been explored for determining solubility, including methods based on chemical potential determination, enhanced sampling simulation, and direct coexistence simulation, and lately, machine learning-based methods have shown promise. In this investigation, we have utilized Constant Chemical Potential Molecular Dynamics, a method rooted in direct coexistence simulation, to predict the solubility of urea polymorphs in aqueous solution. The primary purpose of using this method is to overcome the limitation of the direct simulation method by maintaining a constant chemical potential for a sufficiently long time. Urea is chosen as a prototypical system for our study, with a particular focus on three of its polymorphs. Our approach effectively discriminates between the polymorphs of urea based on their respective solubility values; polymorph III is found to have the highest solubility, followed by forms IV and I.

Graph Neural Networks for Predicting Solubility in Diverse Solvents Using MolMerger Incorporating Solute-Solvent Interactions.

The prediction of solubility is a complex and challenging physicochemical problem that has tremendous implications for the chemical and pharmaceutical industry. Recent advancements in machine learning methods have provided a great scope for predicting the reliable solubility of a large number of molecular systems. However, most of these methods rely on using physical properties obtained from experiments and expensive quantum chemical calculations. Here, we developed a method that utilizes a graphical representation of solute-solvent interactions using "MolMerger," which captures the strongest polar interactions between molecules using Gasteiger charges and creates a graph incorporating the true nature of the system. Using these graphs as input, a neural network learns the correlation between the structural properties of a molecule in the form of node embedding and its physicochemical properties as the output. This approach has been used to calculate molecular solubility by predicting the Log solubility values of various organic molecules and pharmaceuticals in diverse sets of solvents.

Diastereoselective cyclopropanation of α,ß-unsaturated carbonyl compounds with vinyl sulfoxonium ylides.

Herein, we report a three-component stereoselective cyclopropanation of vinyl sulfoxonium ylides with indane 1,3-dione and aldehydes under mild reaction conditions. In contrast to previous reports, the present work shows that electrophilic addition selectively takes place at the α-position of the vinyl sulfoxonium ylide. The interesting feature of this approach is that the multicomponent reaction selectively proceeds because of the difference in nucleophilic reactivity of vinyl sulfoxonium ylides and indane 1,3-dione with electrophilic partners, such as aldehydes and in situ generated arylidenes. Additionally, density functional theory (DFT) studies were conducted to investigate the difference in the reactivity of these reactants, as well as to unveil the mechanism of this three-component reaction. Furthermore, non-covalent interactions of selectivity-determining transition states explain the origin of the diastereoselectivity of cyclopropanation.

A molecular dynamics study on the ion-mediated self-assembly of monolayer-protected nanoclusters.

We studied the effects of metal and molecular cations on the aggregation of atomically precise monolayer-protected nanoclusters (MPCs) in an explicit solvent using atomistic molecular dynamics simulations. While divalent cations such as Zn2+ and Cd2+ promote aggregation by forming ligand-cation-ligand bridges between the MPCs, molecular cations such as tetraethylammonium and cholinium inhibit their aggregation by getting adsorbed into the MPC's ligand shell and reducing the ligand's motion. Here, we studied the aggregation of Au25(SR)18 nanoclusters with two types of ligands, para-mercaptobenzoic acid and D-penicillamine, as prototypical examples.

Insights into the mechanism of peptide fibril growth on gold surface.

Understanding the formation of ß-fibrils over the gold surface is of paramount interest in nano-bio-medicinal Chemistry. The intricate mechanism of self-assembly of neurofibrillogenic peptides and their growth over the gold surface remains elusive, as experiments are limited in unveiling the microscopic dynamic details, in particular, at the early stage of the peptide aggregation. In this work, we carried out equilibrium molecular dynamics and enhanced sampling simulations to elucidate the underlying mechanism of the growth of an amyloid-forming sequence of tau fragments over the gold surface. Our results disclose that the collective intermolecular interactions between the peptide chains and peptides with the gold surface facilitate the peptide adsorption, followed by integration, finally leading to the fibril formation.

Visible Light-Promoted Regioselective Benzannulation of Vinyl Sulfoxonium Ylides with Ynoates.

Herein, we report a highly regioselective [4 + 2]-annulation of vinyl sulfoxonium ylides with ynoates under light-mediated conditions. The reaction proceeds through the new dienyl sulfoxonium ylide, which undergoes photolysis under blue light irradiation to give highly substituted naphthalene scaffolds. The method presented here operates at room temperature and does not require the addition of an external photosensitizer. The in situ-generated dienyl sulfoxonium ylide absorbs light and acts as a photosensitizer for the formation of arenes. The synthetic potential of these benzannulations was further illustrated by various synthetic transformations and a scale-up reaction. Moreover, control experiments and quantum chemical calculations reveal the mechanistic details of the developed reaction.

Carbene-mediated stereoselective olefination of vinyl sulfoxonium ylides with diazo compounds and acetals.

The development of stereoselective olefination using sulfur ylide-derived vinyl carbenes with diazo esters and acetals is reported. Both reactions proceed through nucleophilic addition to electrophiles at the γ-position of an in situ-generated 2-alkoxy furan intermediate. The synthetic utility of the developed method is demonstrated by the total synthesis of rubrolide E. Detailed mechanistic investigations and quantum chemical calculations provide insight into the reaction mechanism.

Electrostatic-Driven Self-Assembly of Janus-like Monolayer-Protected Metal Nanoclusters.

The generation of controlled microstructures of functionalized nanoparticles has been a crucial challenge in nanoscience and nanotechnology. Efforts have been made to tune ligand charge states that can affect the aggregation propensity and modulate the self-assembled structures. In this work, we modeled zwitterionic Janus-like monolayer ligand-protected metal nanoclusters (J-MPCs) and studied their self-assembly using atomistic molecular dynamics and on-the-fly probability-based enhanced sampling simulations. The oppositely charged ligand functionalization on two hemispheres of a J-MPC elicits asymmetric solvation, primarily driven by distinctive hydrogen bonding patterns in the ligand-solvent interactions. Electrostatic interactions between the oppositely charged residues in J-MPCs guide the formation of one-dimensional and ring-like self-assembled superstructures with molecular dipoles oriented in specific patterns. The pertinent atomistic insights into the intermolecular interactions governing the self-assembled structures of zwitterionic J-MPCs obtained from this work can be used to design a general strategy to create tunable microstructures of charged MPCs.

Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters.

Monolayer-protected atomically precise metal nanoclusters (MPCs) have potential applications in catalysis, imaging, and drug delivery. Understanding their interactions with biomolecules such as peptides is of paramount interest for their use in cell imaging and drug delivery. Here we have carried out atomistic molecular dynamics simulations to investigate the interactions between MPCs and an anticancer peptide, melittin. Melittin gets attached to the MPCs surface by the formation of multiple hydrogen bonds between its amino acid residues with MPCs ligands. Additionally, the positively charged Lys, Arg, and peptide's N-terminal strongly anchor the peptide to the MPC metal surface, providing extra stabilization.

Elucidating the Role of Atomically Dilute Copper Centers Impregnating a Phosphamide Polymer for the Preferential Hydrogen Evolution Reaction over CO2 Reduction.

Organic polymers have attracted considerable interest in designing a multifunctional electrocatalyst. However, the inferior electro-conductivity of such metal-free polymers is often regarded as a shortcoming. Herein, a nitrogen- and phosphorus-rich polymer with phosphamide functionality (PAP) in the repeating unit has been synthesized from diaminopyridine (DAP) and phenylphosphonic dichloride (PPDC) precursors. The presence of phosphamide oxygen and pyridine nitrogen in the repeating unit of PAP leads to the coordination of the CuII ion and the incorporation of 3.29 wt % in the polymer matrix (Cu30@PAP) when copper salt is used to impregnate the polymer. Combined with a spectroscopic, microscopic, and DFT study, the coordination and geometry of copper in the PAP matrix has been established to be a distorted square planar CuII in a N2O2 ligand environment where phosphamide oxygen and pyridine nitrogen of the PAP coordinate to the metal center. The copper incorporation in the PAP modulates its electrocatalytic activity. On the glassy carbon electrode, PAP shows inferior activity toward the hydrogen evolution reaction (HER) in 0.5 M H2SO4 while 3 wt % copper incorporation (Cu30@PAP) significantly improves the HER performance with an overpotential of 114 mV at 10 mA cm-2. The notable electrochemical activity with Cu30@PAP occurs due to the impregnation of Cu(II) in PAP, improved electro-kinetics, and better charge transfer resistance (Rct). When changing the electrolyte from H2SO4 to CO2-saturated bicarbonate solution at nearly neutral pH, PAP shows HER as the dominant pathway along with the partial reduction of CO2 to formate. Moreover, the use of Cu30@PAP as an electrolcatalyst could not alter the predominant HER path, and only 20% Faradaic efficiency for the CO2 reduced products has been achieved. Post-chronoamperometric characterization of the recovered catalyst suggests an unaltered valence state of the copper ion and the intact chemical structure of PAP. DFT studies unraveled that the copper sites of Cu30@PAP promote water adsorption while phosphamide-NH of the PAP can weakly hold the CO2 adduct via a hydrogen bonding interaction. A detailed calculation has pointed out that the tetra-coordinated copper centers present in the PAP frame are the reactive sites and that the formation of the [CuI-H] intermediate is the rate-limiting step for both HER and its competitive side reaction, i.e., CO2 reduction to formate or CO formation. The high proton concentration in the electrolyte of pH < 7 leads to HER as the predominant pathway. This combined experimental and theoretical study has highlighted the crucial role of copper sites in electrocatalysis, emphasizing the plausible reason for electrocatalytic selectivity.

Divergent Approach to Highly Substituted Arenes via [3 + 3] Annulation of Vinyl Sulfoxonium Ylides with Ynones.

Herein, we report the divergent benzannulation for highly substituted arenes using vinyl sulfoxonium ylides and ynones. The addition of ynone at the γ-position of vinyl sulfoxonium ylides leads to dienyl sulfoxonium ylide that can undergo selective annulation under different conditions to give m-terphenyls and parabens. Moreover, control experiments and quantum chemical calculations reveal two distinct reaction mechanisms for both annulations.

Synthesis and Applications of π-Conjugation-Extended Vinyl Sulfoxonium Ylides.

Herein, we report the synthesis of π-conjugation-extended vinyl sulfoxonium ylides from vinyl sulfoxonium ylide and electron-deficient alkynes. The new dienoate ylides are used in various transformations, such as X-H (X = S, O) insertion, halogenation, carbene-mediated transformation, and radical-mediated reductions to obtain a variety of conjugated dienoates.

Thermodynamic Window for Size-Controlled Pore Formation in Graphene for Large-Scale Molecular Sieves.

Nanopores in graphene monolayers are a promising option for molecular separation applications, such as desalination and carbon capture. Graphene's atomic thickness allows for an optimal balance between molecular selectivity and permeability, while its chemical stability and robust mechanical properties make it appealing for a wide range of commercial applications. However, scaling to large areas with controlled pore size distribution is an open challenge in ultrathin membranes. Here, using first-principles calculations, we identify a suitable thermodynamic window in a chemical vapor deposition system for directly growing graphene monolayers with a controlled pore size distribution. As an example, our calculations show that a postgrowth annealing step with a supersaturation range of 19.7-25 kJ/mol at 1000 K results in the creation of a controllable pore density at graphene grain boundaries, with pore sizes falling within the range of 5-8 Å. Such pores isolate hydrated Cl ions from water molecules, effectively desalinating seawater. Thus, it allows the design of targeted synthesis of large-scale 2D layers for membrane applications.

Cu(I)/N,N-Imine Ligand Catalyzed C(sp3)-C(sp) Coupling of Alkyl Bromides with Alkynes: Scope and Mechanistic Investigation.

We have developed an efficient Cu/N,N-bidentate imine ligand catalytic system for C(sp3)-C(sp) coupling to obtain internal alkynes, di/trisubstituted allenes and strained bridged cyclic lactams in moderate to excellent yields from readily available alkyl(benzyl) bromides in one-pot transformation. Density Functional Theory (DFT) assisted mechanistic study along with control experiments support the involvement of bialkynylated copper species which undergo single electron transfer (SET) with alkyl halides to generate radical intermediate in the reaction. The N,N-bidentate imine ligand plays a vital role in stabilization of intermediate copper complex and facilitates the product formation.

Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters.

Monolayer-protected atomically precise nanoclusters (MPCs) are an important class of molecules due to their unique structural features and diverse applications, including bioimaging, sensors, and drug carriers. Understanding the atomistic and dynamical details of their self-assembly process is crucial for designing system-specific applications. Here, we applied molecular dynamics and on-the-fly probability-based enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in aqueous and methanol solutions. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and crystals. The dimerization free energy profiles reveal a pivotal role of the ligand charged state and solvent mediating the molecular aggregation. Furthermore, MPCs' ligands exhibit suppressed conformational flexibility in the solid phase due to facile intercluster hydrogen bonds and π-stacks. Our work provides unprecedented molecular-level dynamical details of the aggregation process and conformational dynamics of MPCs ligands in solution and crystalline phases.

Expanded triazolophanes: a topological analysis of vesicular assembly.

Triazolophanes with larger ring sizes such as 40- and 42- were designed and synthesized. Ultramicroscopic studies on a variety of expanded triazolophanes and larger acyclic systems revealed vesicular self-assembly. The role of molecular topology on vesicular assembly was systematically investigated by studying a series of molecules with increasing curvature.

Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations.

ConspectusConcentration-driven processes in solution, i.e., phenomena that are sustained by persistent concentration gradients, such as crystallization and surface adsorption, are fundamental chemical processes. Understanding such phenomena is crucial for countless applications, from pharmaceuticals to biotechnology. Molecular dynamics (MD), both in- and out-of-equilibrium, plays an essential role in the current understanding of concentration-driven processes. Computational costs, however, impose drastic limitations on the accessible scale of simulated systems, hampering the effective study of such phenomena. In particular, due to these size limitations, closed system MD of concentration-driven processes is affected by solution depletion/enrichment that unavoidably impacts the dynamics of the chemical phenomena under study. As a notable example, in simulations of crystallization from solution, the transfer of monomers between the liquid and crystal phases results in a gradual depletion/enrichment of solution concentration, altering the driving force for phase transition. In contrast, this effect is negligible in experiments, given the macroscopic size of the solution volume. Because of these limitations, accurate MD characterization of concentration-driven phenomena has proven to be a long-standing simulation challenge. While disparate equilibrium and nonequilibrium simulation strategies have been proposed to address the study of such processes, the methodologies are in continuous development.In this context, a novel simulation technique named constant chemical potential molecular dynamics (CµMD) was recently proposed. CµMD employs properly designed, concentration-dependent external forces that regulate the flux of solute species between selected subregions of the simulation volume. This enables simulations of systems under a constant chemical drive in an efficient and straightforward way. The CµMD scheme was originally applied to the case of crystal growth from solution and then extended to the simulation of various physicochemical processes, resulting in new variants of the method. This Account illustrates the CµMD method and the key advances enabled by it in the framework of in silico chemistry. We review results obtained in crystallization studies, where CµMD allows growth rate calculations and equilibrium shape predictions, and in adsorption studies, where adsorption thermodynamics on porous or solid surfaces was correctly characterized via CµMD. Furthermore, we will discuss the application of CµMD variants to simulate permeation through porous materials, solution separation, and nucleation upon fixed concentration gradients. While presenting the numerous applications of the method, we provide an original and comprehensive assessment of concentration-driven simulations using CµMD. To this end, we also shed light on the theoretical and technical foundations of CµMD, underlining the novelty and specificity of the method with respect to existing techniques while stressing its current limitations. Overall, the application of CµMD to a diverse range of fields provides new insight into many physicochemical processes, the in silico study of which has been hitherto limited by finite-size effects. In this context, CµMD stands out as a general-purpose method that promises to be an invaluable simulation tool for studying molecular-scale concentration-driven phenomena.