Naphthalene crystal shape prediction from molecular dynamics simulations

We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys., 142, 2015, 144113]. To bring the crystal growth within the timescale of a molecular dynamics simulation we applied Well-Tempered Metadynamics with a spatially constrained collective variable, which focuses the sampling on the growing layer. We estimated that the resulting steady state crystal shape corresponds to a rhombic prism, which is in line with experiments. Further, we observed that at the investigated supersaturations, the $\{00\bar{1}\}$ face grows in a two step two dimensional nucleation mechanism while the considerably faster growing faces $\{1\bar{1}0\}$ and $\{20\bar{1}\}$ grow new layers with a one step two dimensional nucleation mechanism

Non-Equilibrium Modelling of Concentration-Driven Processes with Constant Chemical Potential Molecular Dynamics Simulations

Concentration-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

Influence of SiO(2) and Al(2)O(3) Fillers on Thermal and Dielectric Properties of Barium Zinc Borate Glass Microcomposites for Barrier Rib of Plasma Display Panels (PDPs)

In a lead-free low temperature sinterable multicomponent barium zinc borate glass system, BaO-ZnO-B(2)O(3)- SiO(2)-Li(2)O-Na(2)O (BZBSLN), the influence of SiO(2) (amorphous) and Al(2)O(3) (crystalline, a-alumina) ceramic fillers on the softening point (T(s)), glass transition temperature (T(g)), coefficient of thermal expansion (CTE), and dielectric constant (epsilon(r)) has been investigated with a view to its use as the barrier ribs of plasma display panels (PDPs). The interaction of fillers with glass which occurred during sintering at 570 degrees C has also been studied by XRD and FTIR spectroscopic analyses. It is observed that the filler has partially dissolved in the glass at the sintering temperature leaving some residual filler which results in ceramic-glass microcomposites. The distribution of fillers in the glass matrix and microstructures of the composites have been analyzed by SEM images. It has been seen that the T(s), T(g), CTE and epsilon(r) slightly increased with the increase of Al(2)O(3) content. In the case of SiO(2) filler, the T(s) and T(g) gradually, increased whereas CTE and epsilon(r) gradually decreased along with the addition or SiO(2). These experimentally measured properties have also been compared with the theoretically predicted values. Both the experimental and theoretical predictions of these properties with added filler contents have been found to be correlated very well. In consideration of the desired properties of barrier rib of PDPs with respect to use on PD200 glass substrates, the addition of Al(2)O(3) filler to BZBSLN glass has been found to be more preferable than SiO(2) filler

Understanding Molecular Aggregation of Ligand-protected Atomically-Precise Metal Nanoclusters

Atomically precise ligand-protected nanoclusters (MPC) have emerged as an important class of molecules due to their unique structural features and diverse potential applications, including nano-electronics, bio-imaging, as sensors and drug carriers. Understanding the atomistic details of their intermolecular interaction is of paramount interest for designing, synthesizing, and system-specific applications. Crystal structures of various MPCs provide details related to molecular packing and intermolecular interactions. While these experiments reveal macroscopic, mostly static properties, they are often limited by the spatial and temporal resolutions in delineating the microscopic dynamical details. Here we apply molecular dynamics and enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in the solution phase. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and periodic crystals. The free energy profiles obtained from enhanced sampling simulations of dimerization reveal a pivotal role of the protonated states of the ligands as well as the solvation shell in mediating the molecular aggregation process in solution. In the solid phase, the MPCs’ ligands have suppressed conformational flexibility owing to many facile intermolecular hydrogen bonds and π- stacks. Our work provides unprecedented molecular-level details of the aggregation process and conformational dynamics of MPCs ligands in the solution and crystalline phases, which will help rational design of new MPCs with specific properties

Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO₂ Release from AMDase and Its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter

Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules phenylacetate (PAC) and carbon dioxide (CO₂), from the wild-type (WT) and its G74C/C188S mutant enzymes. Both of the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior. A higher free energy barrier for the release of PAC from G74C/C188S compared to that in the WT is consistent with the experimentally observed compromised efficiency of the mutant. The release of CO₂ precedes that of PAC; free energy barriers for CO₂ and PAC release in the WT enzyme are calculated to be ∼1–2 and ∼23 kcal/mol, respectively. Postdecarboxylation, CO₂ moves toward a hydrophobic pocket formed by Pro 14, Leu 38, Leu 40, Leu 77, and the side chain of Tyr 48 which serves as its temporary “reservoir”. CO₂ releases following a channel mainly decorated by apolar residues, unlike in the case of oxalate decarboxylase where polar residues mediate its transport

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

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

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