Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metadynamics studies of crystal nucleation.

ABSTRACT: Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation.

SUBMITTER: Giberti F

PROVIDER: S-EPMC4392418 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Metadynamics studies of crystal nucleation.

Giberti Federico F Salvalaglio Matteo M Parrinello Michele M

IUCrJ 20150210 Pt 2

Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are out ...[more]

PMID: 25866662

Similar Datasets

In situ X-ray studies of adlayer-induced crystal nucleation at the liquid-liquid interface.

Project description:Crystal nucleation and growth at a liquid-liquid interface is studied on the atomic scale by in situ Å-resolution X-ray scattering methods for the case of liquid Hg and an electrochemical dilute electrolyte containing Pb(2+), F(-), and Br(-) ions. In the regime negative of the Pb amalgamation potential ?(rp) = -0.70 V, no change is observed from the surface-layered structure of pure Hg. Upon potential-induced release of Pb(2+) from the Hg bulk at ? > ?(rp), the formation of an intriguing interface structure is observed, comprising a well-defined 7.6-Å-thick adlayer, decorated with structurally related 3D crystallites. Both are identified by their diffraction peaks as PbFBr, preferentially aligned with their axis along the interface normal. X-ray reflectivity shows the adlayer to consist of a stack of five ionic layers, forming a single-unit-cell-thick crystalline PbFBr precursor film, which acts as a template for the subsequent quasiepitaxial 3D crystal growth. This growth behavior is assigned to the combined action of electrostatic and short-range chemical interactions.

| S-EPMC3637733 | biostudies-literature

Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics.

Project description:Identification of correct protein-ligand binding poses is important in structure-based drug design and crucial for the evaluation of protein-ligand binding affinity. Protein-ligand coordinates are commonly obtained from crystallography experiments that provide a static model of an ensemble of conformations. Binding pose metadynamics (BPMD) is an enhanced sampling method that allows for an efficient assessment of ligand stability in solution. Ligand poses that are unstable under the bias of the metadynamics simulation are expected to be infrequently occupied in the energy landscape, thus making minimal contributions to the binding affinity. Here, the robustness of the method is studied using crystal structures with ligands known to be incorrectly modeled, as well as 63 structurally diverse crystal structures with ligand fit to electron density from the Twilight database. Results show that BPMD can successfully differentiate compounds whose binding pose is not supported by the electron density from those with well-defined electron density.

| S-EPMC7145342 | biostudies-literature

Unsupervised topological learning approach of crystal nucleation.

Project description:Nucleation phenomena commonly observed in our every day life are of fundamental, technological and societal importance in many areas, but some of their most intimate mechanisms remain however to be unravelled. Crystal nucleation, the early stages where the liquid-to-solid transition occurs upon undercooling, initiates at the atomic level on nanometre length and sub-picoseconds time scales and involves complex multidimensional mechanisms with local symmetry breaking that can hardly be observed experimentally in the very details. To reveal their structural features in simulations without a priori, an unsupervised learning approach founded on topological descriptors loaned from persistent homology concepts is proposed. Applied here to monatomic metals, it shows that both translational and orientational ordering always come into play simultaneously as a result of the strong bonding when homogeneous nucleation starts in regions with low five-fold symmetry. It also reveals the specificity of the nucleation pathways depending on the element considered, with features beyond the hypothesis of Classical Nucleation Theory.

| S-EPMC8873400 | biostudies-literature

Crystal Nucleation Using Surface-Energy-Modified Glass Substrates.

Project description:Systematic surface energy modifications to glass substrates can induce nucleation and improve crystallization outcomes for small molecule active pharmaceutical ingredients (APIs) and proteins. A comparatively broad probe for function is presented in which various APIs, proteins, organic solvents, aqueous media, surface energy motifs, crystallization methods, form factors, and flat and convex surface energy modifications were examined. Replicate studies (n ≥ 6) have demonstrated an average reduction in crystallization onset times of 52(4)% (alternatively 52 ± 4%) for acetylsalicylic acid from 91% isopropyl alcohol using two very different techniques: bulk cooling to 0 °C using flat surface energy modifications or microdomain cooling to 4 °C from the interior of a glass capillary having convex surface energy modifications that were immersed in the solution. For thaumatin and bovine pancreatic trypsin, a 32(2)% reduction in crystallization onset times was demonstrated in vapor diffusion experiments (n ≥ 15). Nucleation site arrays have been engineered onto form factors frequently used in crystallization screening, including microscope slides, vials, and 96- and 384-well high-throughput screening plates. Nucleation using surface energy modifications on the vessels that contain the solutes to be crystallized adds a layer of useful variables to crystallization studies without requiring significant changes to workflows or instrumentation.

| S-EPMC5613273 | biostudies-literature

Heterodimer formation and crystal nucleation of gramicidin D.

Project description:The linear pentadecapeptide antibiotic gramicidin D is a heterogeneous mixture of six components. Precise refinements of three-dimensional structures of naturally occurring gramicidin D in crystals obtained from methanol, ethanol, and n-propanol demonstrate the unexpected presence of stable left-handed antiparallel double-helical heterodimers that vary with the crystallization solvent. The side chains of Trp residues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor beta ribbon formation and stabilization of the antiparallel double helix that acts as a template for gramicidin folding and nucleation of different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation and crystal nucleation has potential applications to other systems in which anomalous behavior is exhibited by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins.

| S-EPMC1299886 | biostudies-other

Unveiling the self-association and desolvation in crystal nucleation.

Project description:As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent-solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute-solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute-solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

| S-EPMC8086163 | biostudies-literature

Two types of amorphous protein particles facilitate crystal nucleation.

Project description:Nucleation, the primary step in crystallization, dictates the number of crystals, the distribution of their sizes, the polymorph selection, and other crucial properties of the crystal population. We used time-resolved liquid-cell transmission electron microscopy (TEM) to perform an in situ examination of the nucleation of lysozyme crystals. Our TEM images revealed that mesoscopic clusters, which are similar to those previously assumed to consist of a dense liquid and serve as nucleation precursors, are actually amorphous solid particles (ASPs) and act only as heterogeneous nucleation sites. Crystalline phases never form inside them. We demonstrate that a crystal appears within a noncrystalline particle assembling lysozyme on an ASP or a container wall, highlighting the role of heterogeneous nucleation. These findings represent a significant departure from the existing formulation of the two-step nucleation mechanism while reaffirming the role of noncrystalline particles. The insights gained may have significant implications in areas that rely on the production of protein crystals, such as structural biology, pharmacy, and biophysics, and for the fundamental understanding of crystallization mechanisms.

| S-EPMC5338535 | biostudies-literature

Crystal Orientation Dynamics of Collective Zn dots before Preferential Nucleation.

Project description:The island nucleation in the context of heterogeneous thin film growth is often complicated by the growth kinetics involved in the subsequent thermodynamics. We show how the evolution of sputtered Zn island nucleation on Si(111) by magnetron sputtering in a large area can be completely understood as a model system by combining reflective second harmonic generation (RSHG), a 2D pole figure with synchrotron X-ray diffraction. Zn dots are then oxidized on the surfaces when exposed to the atmosphere as Zn/ZnO dots. Derived from the RSHG patterns of Zn dots at different growth times, the Zn dots grow following a unique transition from kinetic to thermodynamic control. Under kinetic-favoring growth, tiny Zn dots prefer arranging themselves with a tilted c-axis to the Si(111) substrate toward any of the sixfold in-plane Si<110> directions. Upon growth, the Zn dots subsequently evolve themselves to a metastable state with a smaller tilting angle toward selective <110> directions. As the Zn dots grow over a critical size, they become most thermodynamically stable with the c-axis vertical to the Si(111) substrate. For a system with large lattice mismatch, small volume dots take kinetic pathways with insignificant deviations in energy barriers.

| S-EPMC4515603 | biostudies-literature

Site-specific colloidal crystal nucleation by template-enhanced particle transport.

Project description:The monomer surface mobility is the single most important parameter that decides the nucleation density and morphology of islands during thin-film growth. During template-assisted surface growth in particular, low surface mobilities can prevent monomers from reaching target sites and this results in a partial to complete loss of nucleation control. Whereas in atomic systems a broad range of surface mobilities can be readily accessed, for colloids, owing to their large size, this window is substantially narrow and therefore imposes severe restrictions in extending template-assisted growth techniques to steer their self-assembly. Here, we circumvented this fundamental limitation by designing templates with spatially varying feature sizes, in this case moiré patterns, which in the presence of short-range depletion attraction presented surface energy gradients for the diffusing colloids. The templates serve a dual purpose: first, directing the particles to target sites by enhancing their surface mean-free paths and second, dictating the size and symmetry of the growing crystallites. Using optical microscopy, we directly followed the nucleation and growth kinetics of colloidal islands on these surfaces at the single-particle level. We demonstrate nucleation control, with high fidelity, in a regime that has remained unaccessed in theoretical, numerical, and experimental studies on atoms and molecules as well. Our findings pave the way for fabricating nontrivial surface architectures composed of complex colloids and nanoparticles as well.

| S-EPMC5087070 | biostudies-literature

Trapping crystal nucleation of cholesterol monohydrate: relevance to pathological crystallization.

Project description:Crystalline nucleation of cholesterol at the air-water interface has been studied via grazing incidence x-ray diffraction using synchrotron radiation. The various stages of cholesterol molecular assembly from monolayer to three bilayers incorporating interleaving hydrogen-bonded water layers in a monoclinic cholesterol.H(2)O phase, has been monitored and their structures characterized to near atomic resolution. Crystallographic evidence is presented that this multilayer phase is similar to that of a reported metastable cholesterol phase of undetermined structure obtained from bile before transformation to the triclinic phase of cholesterol.H(2)O, the thermodynamically stable macroscopic form. According to grazing incidence x-ray diffraction measurements and crystallographic data, a transformation from the monoclinic film structure to a multilayer of the stable monohydrate phase involves, at least initially, an intralayer cholesterol rearrangement in a single-crystal-to-single-crystal transition. The preferred nucleation of the monoclinic phase of cholesterol.H(2)O followed by transformation to the stable monohydrate phase may be associated with an energetically more stable cholesterol bilayer arrangement of the former and a more favorable hydrogen-bonding arrangement of the latter. The relevance of this nucleation process of cholesterol monohydrate to pathological crystallization of cholesterol from cell biomembranes is discussed.

| S-EPMC1305235 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data