Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Liquid water contains the building blocks of diverse ice phases.

ABSTRACT: Water molecules can arrange into a liquid with complex hydrogen-bond networks and at least 17 experimentally confirmed ice phases with enormous structural diversity. It remains a puzzle how or whether this multitude of arrangements in different phases of water are related. Here we investigate the structural similarities between liquid water and a comprehensive set of 54 ice phases in simulations, by directly comparing their local environments using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, lattice energies, and vibrational properties of the ices. The finding that the local environments characterising the different ice phases are found in water sheds light on the phase behavior of water, and rationalizes the transferability of water models between different phases.

SUBMITTER: Monserrat B

PROVIDER: S-EPMC7666157 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Liquid water contains the building blocks of diverse ice phases.

Monserrat Bartomeu B Brandenburg Jan Gerit JG Engel Edgar A EA Cheng Bingqing B

Nature communications 20201113 1

Water molecules can arrange into a liquid with complex hydrogen-bond networks and at least 17 experimentally confirmed ice phases with enormous structural diversity. It remains a puzzle how or whether this multitude of arrangements in different phases of water are related. Here we investigate the structural similarities between liquid water and a comprehensive set of 54 ice phases in simulations, by directly comparing their local environments using general atomic descriptors, and also by demonst ...[more]

PMID: 33188195

Similar Datasets

Reconfigurable Magnetic Liquid Building Blocks for Constructing Artificial Spinal Column Tissues.

Project description:All-liquid molding can be used to transform a liquid into free-form solid constructs, while maintaining internal fluidity. Traditional biological scaffolds, such as cured pre-gels, are normally processed in solid state, sacrificing flowability and permeability. However, it is essential to maintain the fluidity of the scaffold to truly mimic the complexity and heterogeneity of natural human tissues. Here, this work molds an aqueous biomaterial ink into liquid building blocks with rigid shapes while preserving internal fluidity. The molded ink blocks for bone-like vertebrae and cartilaginous-intervertebral-disc shapes, are magnetically manipulated to assemble into hierarchical structures as a scaffold for subsequent spinal column tissue growth. It is also possible to join separate ink blocks by interfacial coalescence, different from bridging solid blocks by interfacial fixation. Generally, aqueous biomaterial inks are molded into shapes with high fidelity by the interfacial jamming of alginate surfactants. The molded liquid blocks can be reconfigured using induced magnetic dipoles, that dictated the magnetic assembly behavior of liquid blocks. The implanted spinal column tissue exhibits a biocompatibility based on in vitro seeding and in vivo cultivating results, showing potential physiological function such as bending of the spinal column.

| S-EPMC10477840 | biostudies-literature

Diverse N-Substituted Azole-Containing Amino Acids as Building Blocks for Cyclopeptides.

Project description:The preparation of 16 oxazole- or thiazole-containing amino esters bearing a wide array of N-substitution is reported. These were accessed in 40-92% yield via an AgClO4-promoted substitution reaction between a primary amine and a chloromethyl-functionalized thiazole or oxazole. These new synthetic building blocks will be useful for the preparation of new cyclopeptide analogues bearing heterocyclic backbone modifications. Four macrocyclic N-substituted oligoamides that include thiazole or oxazole heterocycles were obtained, following cyclooligomerization reactions of azole-modified N-substituted amino acids.

| S-EPMC6977196 | biostudies-literature

Quasi-liquid layers on ice crystal surfaces are made up of two different phases.

Project description:Ice plays crucially important roles in various phenomena because of its abundance on Earth. However, revealing the dynamic behavior of quasi-liquid layers (QLLs), which governs the surface properties of ice crystals at temperatures near the melting point, remains an experimental challenge. Here we show that two types of QLL phases appear that exhibit different morphologies and dynamics. We directly visualized the two types of QLLs on ice crystal surfaces by advanced optical microscopy, which can visualize the individual 0.37-nm-thick elementary steps on ice crystal surfaces. We found that they had different stabilities and different interactions with ice crystal surfaces. The two immiscible QLL phases appeared heterogeneously, moved around, and coalesced dynamically on ice crystal surfaces. This picture of surface melting is quite different from the conventional picture in which one QLL phase appears uniformly on ice crystal surfaces.

| S-EPMC3268306 | biostudies-literature

Direct Substitution of Arylalkynyl Carbinols Provides Access to Diverse Terminal Acetylene Building Blocks.

Project description:To develop next generation antifolates for the treatment of trimethoprim-resistant bacteria, synthetic methods were needed to prepare a diverse array of 3-aryl-propynes with various substitutions at the propargyl position. A direct route was sought whereby nucleophilic addition of acetylene to aryl carboxaldehydes would be followed by reduction or substitution of the resulting propargyl alcohol. The direct reduction, methylation, and dimethylation of these readily available alcohols provide efficient access to this uncommon functional array. In addition, an unusual silane exchange reaction was observed in the reduction of the propargylic alcohols.

| S-EPMC5253071 | biostudies-literature

Water Mobility in the Interfacial Liquid Layer of Ice/Clay Nanocomposites.

Project description:At solid/ice interfaces, a premelting layer is formed at temperatures below the melting point of bulk water. However, the structural and dynamic properties within the premelting layer have been a topic of intense debate. Herein, we determined the translational diffusion coefficient Dt of water in ice/clay nanocomposites serving as model systems for permafrost by quasi-elastic neutron scattering. Below the bulk melting point, a rapid decrease of Dt is found for charged hydrophilic vermiculite, uncharged hydrophilic kaolin, and more hydrophobic talc, reaching plateau values below -4 °C. At this temperature, Dt in the premelting layer is reduced up to a factor of two compared to supercooled bulk water. Adjacent to charged vermiculite the lowest water mobility was observed, followed by kaolin and the more hydrophobic talc. Results are explained by the intermolecular water interactions with different clay surfaces and interfacial segregation of the low-density liquid water (LDL) component.

| S-EPMC8048683 | biostudies-literature

Ice is born in low-mobility regions of supercooled liquid water.

Project description:When an ice crystal is born from liquid water, two key changes occur: (i) The molecules order and (ii) the mobility of the molecules drops as they adopt their lattice positions. Most research on ice nucleation (and crystallization in general) has focused on understanding the former with less attention paid to the latter. However, supercooled water exhibits fascinating and complex dynamical behavior, most notably dynamical heterogeneity (DH), a phenomenon where spatially separated domains of relatively mobile and immobile particles coexist. Strikingly, the microscopic connection between the DH of water and the nucleation of ice has yet to be unraveled directly at the molecular level. Here we tackle this issue via computer simulations which reveal that (i) ice nucleation occurs in low-mobility regions of the liquid, (ii) there is a dynamical incubation period in which the mobility of the molecules drops before any ice-like ordering, and (iii) ice-like clusters cause arrested dynamics in surrounding water molecules. With this we establish a clear connection between dynamics and nucleation. We anticipate that our findings will pave the way for the examination of the role of dynamical heterogeneities in heterogeneous and solution-based nucleation.

| S-EPMC6369743 | biostudies-literature

Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice.

Project description:Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 μs.

| S-EPMC9883474 | biostudies-literature

ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water.

Project description:Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, T(g) = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called "no man's land" (the range 150-235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at approximately 225 K. The reorientation of the probe molecules decouples from the viscosity below approximately 225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes-Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974-12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360:324-328] and the fragile-to-strong dynamic cross-over at approximately 228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-to-strong liquid transition in water. Nature 398:492-494].

| S-EPMC2710679 | biostudies-literature

Enantiodiscriminating Lipophilic Liquid Membrane-Based Assay for High-Throughput Nanomolar Enantioenrichment of Chiral Building Blocks.

Project description:The reported optical resolution method was designed to support high-throughput enantioseparation of molecular building blocks obtained by automated small-scale synthetic methods. Lipophilic esters of common resolving agents were prepared and used as liquid membranes on the indifferent polymer surface of a microtiter assay. Chiral model compounds were enriched in one of the enantiomers starting from the aqueous solutions of their racemic mixture. Enantiodiscrimination was provided by forming diastereomeric coordination complexes of lipophilic enantiopure esters with the enantiomers of the chiral building blocks inside the liquid membranes. This enantiomeric recognition resulted in a greater distribution ratio of the preferred isomer in the membrane phase, thus the process enables a simultaneous enantioenrichment of the solutions outside the membrane. This paper reports a novel microplate-integrated stereoselective membrane enrichment technique satisfying the need for automatable enantioseparation on a subpreparative scale.

| S-EPMC9862411 | biostudies-literature

Accuracy of Approximations to the Poynting Correction for Ice and Liquid Water.

Project description:Rigorous calculation of the Poynting correction, which describes the effect of pressure on the fugacity of a condensed phase, requires time-consuming evaluation of a thermodynamic potential such as the International Association for the Properties of Water and Steam (IAPWS-95) formulation for water. Simplifying approximations are used in many applications, but the error introduced by the approximations is seldom evaluated. In this work, first-order and second-order approximations were developed for the Poynting correction for both ice and liquid water (including supercooled liquid water), and their errors were evaluated by comparison to the full thermodynamic potentials. The range of conditions covered is from -100 °C to 200 °C at pressures to 20 MPa. Some implications for the calculation of the enhancement factor used in humidity metrology are discussed.

| S-EPMC7351569 | 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