Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular-dynamics simulations of urea nucleation from aqueous solution.

ABSTRACT: Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

SUBMITTER: Salvalaglio M

PROVIDER: S-EPMC4291617 | biostudies-other | 2015 Jan

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis.

Project description:Although the crystal structure of the disaccharide sucrose was solved more than 30 years ago, its conformational distribution in aqueous solution is still a matter of debate. We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron-mediated spin-spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably overstabilized in the calculations.

| S-EPMC3290335 | biostudies-literature

Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease.

Project description:We present the results of molecular dynamics simulations on the urea/urease system. The starting structure was prepared from the 2.0 A crystal structure of Benini et al. [(1999) Struct. Folding Des. 7, 205-216] of DAP-inhibited urease (PDB code ), and the trimeric structure (2479 residues) resulted in 180K atoms after solvation by water. The force field parameters were derived using the bonded model approach described by Hoops et al. [(1991) J. Am. Chem. Soc. 113, 8262-8270]. Three different systems were analyzed, each one modeling a different protonation pattern for the His320 and His219 residues. In each case, the three monomers of urease have been analyzed separately. The time-averaged structures observed in the three monomers suggest that urease could follow two different competitive mechanisms. A "protein-assisted proton transfer" mechanism points to Asp221 as crucial for catalysis. An "Asp-mediated proton transfer" involves the transfer of a proton from the bridging OH to an NH2 moiety of urea, assisted by Asp360 in the active site. The impact of the simulation results on our understanding of urease catalysis is discussed in detail.

| S-EPMC2505355 | biostudies-literature

Molecular dynamics simulations of lignin peroxidase in solution.

Project description:The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.

| S-EPMC1302970 | biostudies-literature

Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation.

Project description:We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic ? and ? torsion angles. NMR relaxation parameters, including longitudinal (R?) and transverse (R?) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ?-? values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.

| S-EPMC3306822 | biostudies-literature

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.

Project description:Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.

| S-EPMC3189405 | biostudies-literature

Molecular dynamics simulation of four typical surfactants in aqueous solution.

Project description:The thermodynamic values of the four surfactants, anionic surfactants, nonionic surfactants, zwitterion surfactants and gemini surfactants, were calculated by molecular dynamics simulation. The calculated results of thermodynamic parameters showed that the four surfactant can form micelles spontaneously. The mainly force for micellization process is entropy-driven, and as the temperature increases, the entropy-driven contribution is gradually reduced. There are linear enthalpy-entropy compensation phenomena for the four surfactants. Among the studied four surfactants, the gemini surfactant is the easiest to form micelles and has good stability, the zwitterion surfactant is the second, and the anionic surfactant is the least stable.

| S-EPMC9059947 | biostudies-literature

Deciphering solution scattering data with experimentally guided molecular dynamics simulations.

Project description:Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.

| S-EPMC4325560 | biostudies-literature

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

Project description:Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties.

| S-EPMC4685891 | biostudies-literature

Fluorescence of KCl Aqueous Solution: A Possible Spectroscopic Signature of Nucleation.

Project description:Ion pairing in water solutions alters both the water hydrogen-bond network and ion solvation, modifying the dynamics and properties of electrolyte water solutions. Here, we report an anomalous intrinsic fluorescence of KCl aqueous solution at room temperature and show that its intensity increases with the salt concentration. From the ab initio density functional theory (DFT) and time-dependent DFT modeling, we propose that the fluorescence emission could originate from the stiffening of the hydrogen bond network in the hydration shell of solvated ion-pairs that suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway. Because computations suggest that the fluorophores are the local ion-water structures present in the prenucleation phase, this band could be the signature of the incoming salt precipitation.

| S-EPMC8996234 | biostudies-literature

Comparative molecular dynamics simulations of thermal conductivities of aqueous and hydrocarbon nanofluids.

Project description:The addition of metal oxide nanoparticles to fluids has been used as a means of enhancing the thermal conductive properties of base fluids. This method formulates a heterogeneous fluid conferred by nanoparticles and can be used for high-end fluid heat-transfer applications, such as phase-change materials and fluids for internal combustion engines. These nanoparticles can enhance the properties of both polar and nonpolar fluids. In the current paper, dispersions of nanoparticles were carried out in hydrocarbon and aqueous-based fluids using molecular dynamic simulations (MDS). The MDS results have been validated using the autocorrelation function and previous experimental data. Highly concurrent trends were achieved for the obtained results. According to the obtained results of MDS, adding CuO nanoparticles increased the thermal conductivity of water by 25% (from 0.6 to 0.75 W·m-1·K-1). However, by adding these nanoparticles to hydrocarbon-based fluids (i.e., alkane) the thermal conductivity was increased three times (from 0.1 to 0.4 W·m-1·K-1). This approach to determine the thermal conductivity of metal oxide nanoparticles in aqueous and nonaqueous fluids using visual molecular dynamics and interactive autocorrelations demonstrate a great tool to quantify thermophysical properties of nanofluids using a simulation environment. Moreover, this comparison introduces data on aqueous and nonaqueous suspensions in one study.

| S-EPMC9273982 | 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