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.

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.

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.

Cooperative Friedel-Crafts Alkylation of Electron-Deficient Arenes via Catalyst Activation with Hexafluoroisopropanol.

A Friedel-Crafts alkylation of electron-deficient arenes with aldehydes through ''catalyst activation'' is presented. Through hydrogen bonding interactions, the solvent 1,1,1,3,3,3, -hexafluoroisopropanol (HFIP) interacted with the added Brønsted acid catalyst pTSA•H2 O, increasing its acidity. This activated catalyst enabled the Friedel-Crafts alkylation of electron-neutral as well as electron-deficient arenes. Strongly electron withdrawing arenes including arenes with multiple halogen atoms, NO2 , CHO, CO2 R, and CN, groups acted as efficient nucleophiles in this reaction. DFT studies reveal multiple roles of solvent HFIP viz; increasing the Brønsted acidity of the catalyst pTSA•H2 O, and stabilization of the transition states through a concerted pathway enabling the challenging reaction.

Ion-Mediated Protein Stabilization on Nanoscopic Surfaces.

The emergence of nanoparticles in biomedical applications has made their interactions with proteins inevitable. Nanoparticles conjugated with proteins and peptide-based constructs form an integral part of nanotherapeutics and have recently shown promise in treating a myriad of diseases. The proper functioning of proteins is critical to achieve their biological functions. However, interface issues result in the denaturation of proteins, and the loss of orientation and steric hindrance can adversely affect the function of the conjugate. Furthermore, surface-induced denaturation also triggers protein aggregation, resulting in amyloid-like species. Understanding the mechanistic underpinnings of protein-nanoparticle interactions and controlling their interfacial characteristics are critical and challenging due to the complex nature of the conjugates. In this milieu, we demonstrate that ionic liquids can be suitable candidates for stabilizing protein-nanoparticle interactions by virtue of their excellent protein-preserving properties. We also probe the previously unexplored mechanism of ion-mediated stabilization of the protein molecules on the nanoparticle surface. The protein-nanoparticle conjugates consist of lysozyme and choline-based ionic liquids characterized by optical and electron microscopy techniques combined with surface-sensitive plasmon-enhanced Raman spectroscopy. Furthermore, atomistic molecular dynamics simulations of the conjugates delineate interfacial interactions of the protein molecules and the modulation by the ions, particularly the conformational changes and the dynamic correlation when the protein and specific ionic liquid molecules are adsorbed on the nanoparticle surface. The combined experimental and computational studies showed the synergistic behavior of the ions of the ionic liquids, specifically the orientation and coverage of the anions aided by the cations to control the surface interactions and hence the overall protein stability. These studies pave the way for using ionic liquids, particularly their biocompatible counterparts in nanoparticle-based complexes, as stabilizing agents for biomedical applications.

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.

A Catalyst and Solvent Free Route for the Synthesis of N-Substituted Pyrrolidones from Levulinic Acid.

An efficient, metal-free, catalyst-free and solvent-free methodology for the reductive amination of levulinic acid with different anilines has been developed using HBpin as the reducing reagent. This protocol offers an excellent method to avoid solvents and added catalysts on the synthesis of different kinds of N-substituted pyrrolidones under metal free conditions. It is also the first report for the synthesis of different pyrrolidones by solvent-free as well as catalyst-free methods. The proposed mechanism for the formation of pyrrolidone has been supported by DFT calculations and control experiments.

Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation.

Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or ß-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.

Liquid-Liquid Critical Point in Phosphorus.

The study of liquid-liquid phase transitions has attracted considerable attention. One interesting example of this phenomenon is phosphorus, for which the existence of a first-order phase transition between a low density insulating molecular phase and a conducting polymeric phase has been experimentally established. In this Letter, we model this transition by an ab initio quality molecular dynamics simulation and explore a large portion of the liquid section of the phase diagram. We draw the liquid-liquid coexistence curve and determine that it terminates into a second-order critical point. Close to the critical point, large coupled structure and electronic structure fluctuations are observed.

Role of W181 in modulating kinetic properties of Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferase.

Hypoxanthine-guanine-xanthine phosphoribosyltransference (HGXPRT), a key enzyme in the purine salvage pathway of the malarial parasite, Plasmodium falciparum (Pf), catalyses the conversion of hypoxanthine, guanine, and xanthine to their corresponding mononucleotides; IMP, GMP, and XMP, respectively. Out of the five active site loops (I, II, III, III', and IV) in PfHGXPRT, loop III' facilitates the closure of the hood over the core domain which is the penultimate step during enzymatic catalysis. PfHGXPRT mutants were constructed wherein Trp 181 in loop III' was substituted with Ser, Thr, Tyr, and Phe. The mutants (W181S, W181Y and W181F), when examined for xanthine phosphoribosylation activity, showed an increase in Km for PRPP by 2.1-3.4 fold under unactivated condition and a decrease in catalytic efficiency by more than 5-fold under activated condition as compared to that of the wild-type enzyme. The W181T mutant showed 10-fold reduced xanthine phosphoribosylation activity. Furthermore, molecular dynamics simulations of WT and in silico W181S/Y/F/T PfHGXPRT mutants bound to IMP.PPi.Mg2+ have been carried out to address the effect of the mutation of W181 on the overall dynamics of the systems and identify local changes in loop III'. Dynamic cross-correlation analyses show a communication between loop III' and the substrate binding site. Differential cross-correlation maps indicate altered communication among different regions in the mutants. Changes in the local contacts and hydrogen bonding between residue 181 with the nearby residues cause altered substrate affinity and catalytic efficiency of the mutant enzymes. Proteins 2016; 84:1658-1669. © 2016 Wiley Periodicals, Inc.

Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase.

Atomistic molecular dynamics (MD) simulations coupled with the metadynamics technique were carried out to delineate the product (PPi.2Mg and IMP) release mechanisms from the active site of both human (Hs) and Plasmodium falciparum (Pf) hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (HG(X)PRT). An early movement of PPi.2Mg from its binding site has been observed. The swinging motion of the Asp side chain (D134/D145) in the binding pocket facilitates the detachment of IMP, which triggers the opening of flexible loop II, the gateway to the bulk solvent. In PfHGXPRT, PPi.2Mg and IMP are seen to be released via the same path in all of the biased MD simulations. In HsHGPRT too, the product molecules follow similar routes from the active site; however, an alternate but minor escape route for PPi.2Mg has been observed in the human enzyme. Tyr 104 and Phe 186 in HsHGPRT and Tyr 116 and Phe 197 in PfHGXPRT are the key residues that mediate the release of IMP, whereas the motion of PPi.2Mg away from the reaction center is guided by the negatively charged Asp and Glu and a few positively charged residues (Lys and Arg) that line the product release channels. Mutations of a few key residues present in loop II of Trypanosoma cruzi (Tc) HGPRT have been shown to reduce the catalytic efficiency of the enzyme. Herein, in silico mutation of corresponding residues in loop II of HsHGPRT and PfHGXPRT resulted in partial opening of the flexible loop (loop II), thus exposing the active site to bulk water, which offers a rationale for the reduced catalytic activity of these two mutant enzymes. Investigations of the product release from these HsHGPRT and PfHGXPRT mutants delineate the role of these important residues in the enzymatic turnover.

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.

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.

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.

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.

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.

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.

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.

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.