Molecular dynamics simulation study of translocation of fullerene C60 through skin bilayer: effect of concentration on barrier properties

The molecular level permeation mechanism of fullerenes and its derivatives through human skin could open a vast area for designing novel nanoparticles for cosmetics and drug delivery applications. In this study, we report the permeation mechanism of pristine fullerene C60 for the first time through the skin lipid layer, as determined via prolonged unconstrained and constrained coarse-grained molecular dynamics simulations. The skin layer was modelled as an equimolar ratio of ceramides, cholesterol and free fatty acids. It was observed that at lower concentrations fullerenes formed small clusters (3 or 5 molecules) in the aqueous phase, which further spontaneously permeated inside the bilayer and remained dispersed inside the bilayer interior. On the other hand, at higher concentrations fullerenes aggregated in the aqueous layer, penetrated in that form and remained aggregated in the bilayer interior. Lower concentrations of fullerenes did not induce...  Read more

Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide?

Physical Chemistry Chemical Physics
The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents. Denaturants such as urea are instrumental in the unfolding of proteins while protecting osmolytes favour the folded ensemble. Recently, room temperature ionic liquids (ILs) have been shown to counteract the deleterious effect of urea on proteins. In this paper, using atomistic molecular dynamics we show that a ternary mixture containing a particular ammonium-based IL, triethylammonium acetate (TEAA), and urea (in 1 : 5 molar ratio) helps a small 15-residue S-peptide analogue regain most of its native structure, whereas a binary aqueous mixture containing a large amount of urea alone completely distorts it. Our simulations show that the denaturant urea directly interacts with the peptide...  Read more

Dynamics of solvation dictates conformation of polyethylene oxide in aqueous, isobutyric acid and binary solutions

Physical Chemistry Chemical Physics
Polymers hydrogen-bonding with solvent represent an important broad class of polymers, properties of which depend on solvation. Using atomistic molecular dynamics simulations with the OPLS/AA force field we investigate the effect of hydrogen bonding on PEO conformation and chain motility by comparing its behavior in isobutyric acid and aqueous solutions. In agreement with experimental data, we found that in isobutyric acid PEO forms a rather rigid extended helical structure, while in water it assumes highly flexible coil conformation. We show that the difference in PEO conformation and flexibility is the result of the hydrogen bond stability and overall solvent dynamics near PEO. Isobutyric acid forms up to one hydrogen bond per repeat unit of PEO and interacts with PEO for a prolonged period of time thereby stabilizing the helical structure of the polymer and reducing its segmental mobility. In contrast, water forms on average 1.2 hydrogen bonds per repeat unit of PEO (with 60% of...  Read more

Interfacial water effect on cooperativity and signal communication in Scapharca dimeric hemoglobin

Physical Chemistry Chemical Physics
Cooperativity is important in controlling the biological functions of allosteric proteins. Understanding the detailed mechanisms of cooperativity and allosteric regulation in such proteins is essential to understanding their function; however, the mechanism by which allosteric proteins undergo conformational transitions to aid the ligand escape process and its relevance to interfacial water molecules is not well understood. Here, we perform molecular dynamics simulations to examine these issues in Scapharca dimeric hemoglobin. The effects of interfacial water on dimeric motion, ligand escape probability, gate function, and cross-correlation are considered. The results reveal that interfacial water exhibits an unbalanced stress distribution in the interface region, leading to a bias helix bundle motion that not only can expedite the escape of the first ligand but also can increase the interval between the escape of both ligands. Correspondingly, the gate function follows the...  Read more

The staging mechanism of AlCl4 intercalation in a graphite electrode for an aluminium-ion battery

Physical Chemistry Chemical Physics
Identifying a suitable electrode material with desirable electrochemical properties remains a primary challenge for rechargeable Al-ion batteries. Recently an ultrafast rechargeable Al-ion battery was reported with high charge/discharge rate, (relatively) high discharge voltage and high capacity that uses a graphite-based cathode. Using calculations from first-principles, we have investigated the staging mechanism of AlCl4 intercalation into bulk graphite and evaluated the stability, specific capacity and voltage profile of AlCl4 intercalated compounds. Ab initio molecular dynamics is performed to investigate the thermal stability of AlCl4 intercalated graphite structures. Our voltage profiles show that the first AlCl4 intercalation step could be a more sluggish step than the successive intercalation steps. However, the diffusion of AlCl4 is very...  Read more

Microwave reduction of graphene oxide rationalized by reactive molecular dynamics

Obtaining graphene (GRA) in industrial quantities is among the most urgent goals in today's nanotechnology. Elegant methods involve the oxidation of graphite with its subsequent solvent-assisted exfoliation. The reduction of graphene oxide (GO) is challenging leading to a highly-disordered oxygen-rich material. A particularly successful microwave-induced reduction of GO was reported recently (Science, 2016, 353, 1413–1416). We mimic the experiment by reactive molecular dynamics and establish the molecular mechanisms of reduction and their time scales as functions of temperature. We show that the rapid removal of oxygen groups achieved by microwave heating leaves GRA sheets intact. The epoxy groups are most stable within GO. They can rearrange into the carbonyl groups upon quick heating. It is important to avoid creating holes upon graphite oxidation. They cannot be healed easily and undermine GRA thermal stability and electronic properties. The edge oxygen...  Read more

Computational study of phononic resonators and waveguides in monolayer transition metal dichalcogenides

Physical Chemistry Chemical Physics
Using molecular dynamics and semi-empirical potentials, large scale transition metal dichalcogenides monolayers (TMDM) were examined. The focus of the study was the modification of the phonon spectrum of TMDMs by engineering substitutional defects to produce phononic resonators and waveguides on the atomic scale. The resonant frequencies of the aforementioned structures can be tuned by applying tensile or compressive stresses. The TMDMs exhibited wide phononic band gaps (PBG) in their phonon spectrum because they consist of atoms with quite different atomic masses. The PBG from the present semi-empirical calculations were found to be in reasonable agreement with previous ab initio calculations. The problem is very broad since many varieties of TMDMs (with or without defects) can be made. The present study focused on MX2 composites with M being Mo or W and X being S or Se. The most interesting behavior was found in WS2 with...  Read more

Dynamical descriptors of bioactivity: a correlation between chemical durability and ion migration in biodegradable glasses

Physical Chemistry Chemical Physics
Ion migration in two fluorinated bioactive glasses of significantly different durability was modeled through molecular dynamics simulations. Whereas the very different biodegradation of these glasses cannot be explained on the basis of their structural features alone, the analysis of the diffusive data highlights a strong connection between the glass durability determined experimentally and the activation barriers for ion diffusion extracted by the simulations, clarifying the source of the different solubility and suggesting that “dynamical” descriptors of bioactivity could represent a key tool to predict the macroscopic behavior of a biomaterial, in some cases more effectively than with the current structural descriptors.Read more

Negative Poisson's ratio in graphene oxide

We perform molecular dynamics simulations to investigate the Poisson's ratio of graphene oxide. We find that the Poisson's ratio can be effectively tuned by increasing the degree of oxidation of graphene oxide. More specifically, the Poisson's ratio decreases linearly from positive to negative with increasing oxidation, turning negative at room temperature for a degree of oxidation of 0.27, and reaching a value of −0.567 for fully oxidized graphene. The oxidation dependence of the Poisson's ratio is attributed to the tension-induced suppression of the ripples resulting from the oxidation, whose amplitude increases with increasing oxidation. Finally, we also demonstrate the temperature dependence of the Poisson's ratio in the graphene oxide.Read more

Transdermal cellular membrane penetration of proteins with gold nanoparticles: a molecular dynamics study

Physical Chemistry Chemical Physics
Transdermal delivery, where the skin acts as the route for local or systemic distribution, presents a lot of advantages over conventional routes such as oral and intravenous and intramuscular injections. However, the delivery of large biomolecules like proteins through the skin is challenging due to their size and structural properties. A molecular level understanding of their transport across the skin barrier is desirable to design successful formulations. We have employed constrained and unconstrained coarse grained molecular dynamics simulation techniques to obtain the molecular mechanism of penetration of the horseradish peroxidase (HRP) protein into the skin, in the presence and absence of gold nanoparticles (AuNPs). Unconstrained simulations show that HRP, when considered individually, was not able to breach the skin barrier, while in the presence of AuNPs, it first binds to the AuNPs and then breaches the barrier. The constrained simulations revealed that there was a free...  Read more

Temperature dependence of ion diffusion coefficients in NaCl electrolyte confined within graphene nanochannels

Physical Chemistry Chemical Physics
The behavior of ion diffusion in nano-confined spaces and its temperature dependence provide important fundamental information about electric double-layer capacitors (EDLCs) employing nano-sized active materials. In this work, the ion diffusion coefficients of NaCl electrolyte confined within neutral and charged graphene nanochannels at different temperatures are investigated using molecular dynamics simulations. The results show that ions confined in neutral nanochannels diffuse faster (along the graphene surfaces) than those in bulk solution, which could be attributed to the relatively smaller concentration in confined spaces and the solvophobic nature of graphene surfaces. In charged nanochannels where the electrostatic interactions between counter-ions and charged channel surfaces govern the motion of ions, the diffusion coefficients are found to be lower than those in the neutral counterparts. The increase of temperature will lead to enhanced vibrant thermal motion of ions. Due...  Read more

Light-driven rotary molecular motors without point chirality: a minimal design

Physical Chemistry Chemical Physics
A fundamental requirement for achieving photoinduced unidirectional rotary motion about an olefinic bond in a molecular motor is that the potential energy surface of the excited state is asymmetric with respect to clockwise and counterclockwise rotations. In most available light-driven rotary molecular motors, such asymmetry is guaranteed by the presence of a stereocenter. Here, we present non-adiabatic molecular dynamics simulations based on multiconfigurational quantum chemistry to demonstrate that this chiral feature is not essential for inducing unidirectional rotary motion in molecules that incorporate a cyclohexenylidene moiety into a protonated Schiff-base framework. Rather, the simulations show that it is possible to exploit the intrinsic asymmetry of the puckered cyclohexenylidene to control the direction of photoinduced rotation.Read more

Transient inhomogeneous flow patterns in supercooled liquids under shear

Soft Matter
Supercooled liquids and other soft glassy systems show characteristic spatial inhomogeneities in their local dynamical properties. Using detailed molecular dynamics simulations, we find that for sufficiently low temperatures and sufficiently high shear rates supercooled liquids also show transient inhomogeneous flow patterns (shear banding) in the start-up of steady shear flow, similar to what has already been observed for many other soft glassy systems. We verify that the onset of transient shear banding coincides quite well with the appearance of a stress overshoot for temperatures in the supercooled regime. We find that the slower bands adapt less well to the imposed deformation and therefore accumulate higher shear stresses compared to the fast bands at comparable local shear rates. Our results also indicate that the shear rates of the fast and slow bands are adjusted such that the local dissipation rate is approximately the same in both bands.Read more

Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study

Soft Matter
Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in “hydration state”. In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase...  Read more

Cation ordering and oxygen transport behaviour in Sr1−3x/2LaxTiO3 perovskites

Journal of Materials Chemistry A
Molecular dynamics simulations and genetic algorithms are used to identify the mechanisms by which oxygen is transported through the Sr1−3x/2LaxTiO3 family of perovskites as a function of x. Across this compositional range the relative stability of ordered structures and random arrangements of cations and vacancies on the A sublattice is established. O and Ti Frenkel pair formation is then predicted for the considered compositions. These results show that Ti defects are more favourable for all La-containing compositions, but have a larger defect volume than O defects for low x. Oxygen diffusion at high temperature is determined using Molecular dynamics simulations. Two types of oxygen transport mechanisms are identified, that each contribute to oxygen diffusion in ordered structures. These mechanism involve transient O and Ti defects respectively, and provide means for O...  Read more

Influence of Orientation Mismatch on Charge Transport Across Grain Boundaries in Tri-isopropylsilylethynyl (TIPS) Pentacene Thin Films

Physical Chemistry Chemical Physics
We present a multi-scale model for charge transport across grain boundaries in molecular electronic materials that incorporates packing disorder, electrostatic and polarisation effects. We choose quasi two-dimensional films of tri-isopropylsilylethynyl pentacene (TIPS-P) as a model system of technologically relevant crystalline organic semiconductors. We use atomistic molecular dynamics, with a force-field specific for TIPS-P, to generate and equilibrate polycrystalline two-dimensional thin films. The energy landscape is obtained by calculating contributions from electrostatic interactions and polarization. The variation in these contributions leads to energetic barriers between grains. Subsequently, charge transport is simulated using a kinetic Monte-Carlo algorithm. Two-grain systems with varied mutual orientation are studied. We find relatively little effect of long grain boundaries due to the presence of low impedence pathways. However, effects could be more pronounced for systems...  Read more

Controlled propulsion and separation of helical particles at the nanoscale

Soft Matter
Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann molecular dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet...  Read more

Hydrophilicities of amylose and natural cellulose are regulated by the linkage between sugar rings

Comparative studies of single molecule force spectroscopy and molecular dynamics simulations indicate that natural cellulose is more hydrophobic than amylose at the single-chain level, implying that the hydrophobicities of these polymeric isomers are regulated by only one parameter in the chains, the linkage between the sugar rings.Read more

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins

Physical Chemistry Chemical Physics
The development of polarizable water models at coarse-grained (CG) levels is of much importance to CG molecular dynamics simulations of large biomolecular systems. In this work, we combined the newly developed two-bead multipole force field (TMFF) for proteins with the two-bead polarizable water models to carry out CG molecular dynamics simulations for benchmark proteins. In our simulations, two different two-bead polarizable water models are employed, the RTPW model representing five water molecules by Riniker et al. and the LTPW model representing four water molecules. The LTPW model is developed in this study based on the Martini three-bead polarizable water model. Our simulation results showed that the combination of TMFF with the LTPW model significantly stabilizes the protein's native structure in CG simulations, while the use of the RTPW model gives better agreement with all-atom simulations in predicting the residue-level fluctuation dynamics. Overall, the TMFF...  Read more

Oxygen Solubility and Transport in Li-Air Battery Electrolytes: Establishing Criteria and Strategies for Electrolyte Design

Energy & Environmental Science
Li-air or Li-oxygen batteries promise significantly higher energies than existing commercial battery technologies, yet their development has been hindered by a lack of suitable electrolytes. In this article, we evaluate the physical properties of varied electrolyte compositions to form generalized criteria for electrolyte design. We show that oxygen transport through non-aqueous electrolytes has a critical impact on the discharge rate and capacity of Li-air batteries. Through experiments and molecular dynamics simulations, we highlight that the choice of salt species and concentration have an outsized influence on oxygen solubility, while solvent choice is the major influence on oxygen diffusivity. The stability of superoxide reaction intermediates, key to the oxygen reduction mechanism, is also affected by variations in salt concentration and the choice of solvent. The importance of reactant transport is confirmed through Li-air cell discharge, which demonstrates good agreement...  Read more