Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Driving forces of conformational changes in single-layer graphene oxide.

ABSTRACT: The extensive oxygen-group functionality of single-layer graphene oxide proffers useful anchor sites for chemical functionalization in the controlled formation of graphene architecture and composites. However, the physicochemical environment of graphene oxide and its single-atom thickness facilitate its ability to undergo conformational changes due to responses to its environment, whether pH, salinity, or temperature. Here, we report experimental and molecular simulations confirming the conformational changes of single-layer graphene oxide sheets from the wet or dry state. MD, PM6, and ab initio simulations of dry SLG and dry and wetted SLGO and electron microscopy imaging show marked differences in the properties of the materials that can explain variations in previously observed results for the pH dependent behavior of SLGO and electrical conductivity of chemically modified graphene-polymer composites. Understanding the physicochemical responses of graphene and graphene oxide architecture and performing selected chemistry will ultimately facilitate greater tunability of their performance.

SUBMITTER: Whitby RL

PROVIDER: S-EPMC3357922 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

An iron-based green approach to 1-h production of single-layer graphene oxide.

Project description:As a reliable and scalable precursor of graphene, graphene oxide (GO) is of great importance. However, the environmentally hazardous heavy metals and poisonous gases, explosion risk and long reaction times involved in the current synthesis methods of GO increase the production costs and hinder its real applications. Here we report an iron-based green strategy for the production of single-layer GO in 1?h. Using the strong oxidant K2FeO4, our approach not only avoids the introduction of polluting heavy metals and toxic gases in preparation and products but also enables the recycling of sulphuric acid, eliminating pollution. Our dried GO powder is highly soluble in water, in which it forms liquid crystals capable of being processed into macroscopic graphene fibres, films and aerogels. This green, safe, highly efficient and ultralow-cost approach paves the way to large-scale commercial applications of graphene.

| S-EPMC4354147 | biostudies-literature

p-wave triggered superconductivity in single-layer graphene on an electron-doped oxide superconductor.

Project description:Electron pairing in the vast majority of superconductors follows the Bardeen-Cooper-Schrieffer theory of superconductivity, which describes the condensation of electrons into pairs with antiparallel spins in a singlet state with an s-wave symmetry. Unconventional superconductivity was predicted in single-layer graphene (SLG), with the electrons pairing with a p-wave or chiral d-wave symmetry, depending on the position of the Fermi energy with respect to the Dirac point. By placing SLG on an electron-doped (non-chiral) d-wave superconductor and performing local scanning tunnelling microscopy and spectroscopy, here we show evidence for a p-wave triggered superconducting density of states in SLG. The realization of unconventional superconductivity in SLG offers an exciting new route for the development of p-wave superconductivity using two-dimensional materials with transition temperatures above 4.2 K.

| S-EPMC5253682 | biostudies-literature

Atomic Layer Deposition of Titanium Oxide on Single-Layer Graphene: An Atomic-Scale Study toward Understanding Nucleation and Growth.

Project description:Controlled synthesis of a hybrid nanomaterial based on titanium oxide and single-layer graphene (SLG) using atomic layer deposition (ALD) is reported here. The morphology and crystallinity of the oxide layer on SLG can be tuned mainly with the deposition temperature, achieving either a uniform amorphous layer at 60 °C or ∼2 nm individual nanocrystals on the SLG at 200 °C after only 20 ALD cycles. A continuous and uniform amorphous layer formed on the SLG after 180 cycles at 60 °C can be converted to a polycrystalline layer containing domains of anatase TiO2 after a postdeposition annealing at 400 °C under vacuum. Using aberration-corrected transmission electron microscopy (AC-TEM), characterization of the structure and chemistry was performed on an atomic scale and provided insight into understanding the nucleation and growth. AC-TEM imaging and electron energy loss spectroscopy revealed that rocksalt TiO nanocrystals were occasionally formed at the early stage of nucleation after only 20 ALD cycles. Understanding and controlling nucleation and growth of the hybrid nanomaterial are crucial to achieving novel properties and enhanced performance for a wide range of applications that exploit the synergetic functionalities of the ensemble.

| S-EPMC5364723 | biostudies-literature

Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes.

Project description:Accurate free-energy calculations provide mechanistic insights into molecular recognition and conformational equilibrium. In this work, we performed free-energy calculations to study the thermodynamic properties of different states of molecular systems in their equilibrium basin, and obtained accurate absolute binding free-energy calculations for protein-ligand binding using a newly developed M2 algorithm. We used a range of Asp-Phe-Gly (DFG)-in/out p38α mitogen-activated protein kinase inhibitors as our test cases. We also focused on the flexible DFG motif, which is closely connected to kinase activation and inhibitor binding. Our calculations explain the coexistence of DFG-in and DFG-out states of the loop and reveal different components (e.g., configurational entropy and enthalpy) that stabilize the apo p38α conformations. To study novel ligand-binding modes and the key driving forces behind them, we computed the absolute binding free energies of 30 p38α inhibitors, including analogs with unavailable experimental structures. The calculations revealed multiple stable, complex conformations and changes in p38α and inhibitor conformations, as well as balance in several energetic terms and configurational entropy loss. The results provide relevant physics that can aid in designing inhibitors and understanding protein conformational equilibrium. Our approach is fast for use with proteins that contain flexible regions for structure-based drug design.

| S-EPMC3400776 | biostudies-literature

Aqueous proton transfer across single-layer graphene.

Project description:Proton transfer across single-layer graphene proceeds with large computed energy barriers and is therefore thought to be unfavourable at room temperature unless nanoscale holes or dopants are introduced, or a potential bias is applied. Here we subject single-layer graphene supported on fused silica to cycles of high and low pH, and show that protons transfer reversibly from the aqueous phase through the graphene to the other side where they undergo acid-base chemistry with the silica hydroxyl groups. After ruling out diffusion through macroscopic pinholes, the protons are found to transfer through rare, naturally occurring atomic defects. Computer simulations reveal low energy barriers of 0.61-0.75 eV for aqueous proton transfer across hydroxyl-terminated atomic defects that participate in a Grotthuss-type relay, while pyrylium-like ether terminations shut down proton exchange. Unfavourable energy barriers to helium and hydrogen transfer indicate the process is selective for aqueous protons.

| S-EPMC4382684 | biostudies-literature

Comparative studies on single-layer reduced graphene oxide films obtained by electrochemical reduction and hydrazine vapor reduction.

Project description:The comparison between two kinds of single-layer reduced graphene oxide (rGO) sheets, obtained by reduction of graphene oxide (GO) with the electrochemical method and hydrazine vapor reduction, referred to as E-rGO and C-rGO, respectively, is systematically studied. Although there is no morphology difference between the E-rGO and C-rGO films adsorbed on solid substrates observed by AFM, the reduction process to obtain the E-rGO and C-rGO films is quite different. In the hydrazine vapor reduction, the nitrogen element is incorporated into the obtained C-rGO film, while no additional element is introduced to the E-rGO film during the electrochemical reduction. Moreover, Raman spectra show that the electrochemical method is more effective than the hydrazine vapor reduction method to reduce the GO films. In addition, E-rGO shows better electrocatalysis towards dopamine than does C-rGO. This study is helpful for researchers to understand these two different reduction methods and choose a suitable one to reduce GO based on their experimental requirements.

| S-EPMC3309976 | biostudies-literature

Lipid-protein forces predict conformational changes in a mechanosensitive channel.

Project description:The mechanosensitive TREK-2 potassium channel, a member of the K2P family, has essential physiological roles and is, therefore, a pharmaceutical target. A combination of experimental and computational studies have established that of the two known conformations, "up" and "down", membrane tension directly favors the "up" state, which displays a higher conductance. However, these studies did not reveal the exact mechanism by which the membrane affects the channel conformation. In this work, we show that changes in protein-lipid interaction patterns suffice in predicting this conformational change, and pinpoint potentially important residues involved in this phenomenon.

| S-EPMC8071793 | biostudies-literature

Selective Growth of MAPbBr<sub>3</sub> Rounded Microcrystals on Micro-Patterned Single-Layer Graphene Oxide/Graphene Platforms with Enhanced Photo-Stability.

Project description:The synergistic combination of hybrid perovskites with graphene-related materials is leading to optoelectronic devices with enhanced performance and stability. Still, taking advantage of the solution processing of perovskite onto graphene is especially challenging. Here, MAPbBr3 perovskite is grown on single-layer graphene/graphene oxide (Gr/GO) patterns with 120 µm periodicity using a solution-processed method. MAPbBr3 rounded crystals are formed with sizes ranging from nanometers to microns, either forming continuous films or dispersed particles. A detailed morphological and structural study reveals a fully oriented perovskite and very different growth habits on the Gr/GO micro-patterns, which we relate to the substrate characteristics and the nucleation rate. A simple method for controlling the nucleation rate is proposed based on the concentration of the precursor solution and the number of deposited perovskite layers. The photoluminescence is analyzed in terms of the crystal size, strain, and structural changes observed. Notably, the growth on top of Gr/GO leads to a huge photostability of the MAPbBr3 compared with that on glass. Especially outstanding is that of the microcrystals, which endure light densities as high as 130 kW/cm2. These results allow for anticipating the design of integrated nanostructures and nanoengineered devices by growing high-stability perovskite directly on Gr/GO substrates.

| S-EPMC10538007 | biostudies-literature

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding.

Project description:Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy-enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy-enthalpy compensation.

| S-EPMC3523842 | biostudies-literature

Forces Driving Chaperone Action.

Project description:It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client's affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins.

| S-EPMC4947014 | 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