Vacancy-induced MnO6 distortion and its impacts on structural transition of Li2MnO3

Physical Chemistry Chemical Physics
As a new class of high-capacity cathode materials, the Li-rich Mn-based layer-structured xLi2MnO3·(1 − x)LiMO2 (M = Ni, Co, Mn, etc.) is a promising candidate for constructing high energy-density Li-ion batteries. Unfortunately, drawbacks such as oxygen evolution, poor rate performance and potential fading during cycling hinder their commercial applications. Migration of the transition metal (Mn) into the Li layer of Li2MnO3 and the resultant irreversible structural transition are believed to be responsible for these issues. Therefore, it is essential to explore the driving force for the Mn migration. In this study, we show, starting from understanding the impact of O and Li vacancies on the migration of the Mn atoms by the first-principles molecular dynamics simulation, that Mn migration is closely involved in the breaking and...  Read more

Tensile and compressive behaviors of prestrained single-layer black phosphorus: a molecular dynamics study

Nanoscale
The effect of prestrain on tensile and compressive behaviors of single-layer black phosphorus (SLBP) in both armchair and zigzag directions is investigated by using molecular dynamics simulations. Prestrain is carried out by stretching or compressing SLBP in an orthogonal in-plane direction. The results show that the overall mechanical properties of SLBP, including Young's modulus, tensile strength, compressive strength, and yield strength are enhanced with an increase in compressive prestrain but are reduced with an increased tensile prestrain. With the same value of prestrain, SLBP exhibits unidirectional-homogeneous characteristics for tensile and compressive deformation. It is demonstrated that the armchair-oriented prestrain leads to a more significant improvement in the overall mechanical properties than the zigzag-oriented prestrain, indicating the anisotropic deformation behavior due to the characteristic puckers in SLBP. This work also reveals the mechanisms of prestrain...  Read more

Partitioning of caffeine in lipid bilayers reduces membrane fluidity and increases membrane thickness

Physical Chemistry Chemical Physics
Caffeine is a small amphiphilic molecule, which is widely consumed as a stimulant to prevent fatigue, but is also used as a common drug adjuvant in modern medicine. Here, we show that caffeine interacts with unsaturated lipid membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). By combining X-ray diffraction and molecular dynamics simulations, we present evidence that caffeine partitions in lipid membranes and locates at the head group–tail group interface of the bilayers. By attracting water molecules from neighboring lipid molecules, it leads to the formation of “water pockets”, i.e., a local increase of water density at this interface. Through this mechanism, caffeine leads to an overall decrease of the gauche defect density in the membranes and an increase of membrane thickness, indicating a loss of membrane fluidity. These non-specific membrane interactions may increase the efficacy of analgesic drugs through changes in the...  Read more

Stability of reverse micelles in rare-earth separation: a chemical model based on a molecular approach

Physical Chemistry Chemical Physics
Molecular complexes formed in the organic phase during solvent extraction may self-assemble as reverse micelles, and therefore induce a supramolecular organization of this phase. In most of the cases, water molecules play an essential role in the organization of this non polar medium. The aim of this work is to investigate the speciation of the aggregates formed in the organic phase during solvent extraction, and especially to assess their stability as a function of the number of water molecules included in their polar core. We have focused on malonamide extractants that have already been investigated experimentally. Different stoichiometries of reverse micelles in the organic phase have been studied by means of classical molecular dynamics simulations. Furthermore, umbrella-sampling molecular dynamics simulations have been used to calculate the equilibrium constant (K°) representing the association/dissociation pathways of water molecules in the aggregates and the...  Read more

Adsorption dynamics of molecular nitrogen at an Fe(111) surface

Physical Chemistry Chemical Physics
We present an extensive theoretical study of N2 adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N2 adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states. Our QCT calculations confirm that there are activated and nonactivated paths for the adsorption of N2 on the Fe(111) surface, which is in agreement with previous experimental investigations. Molecular dynamics at a surface temperature Ts = 300 K...  Read more

Prediction of tunable quantum spin Hall effect in methyl-functionalized tin film

Journal of Materials Chemistry C
The quantum spin Hall (QSH) effect may promote revolutionary device development due to dissipationless propagation of spin currents. The bottleneck preventing applications from the QSH effect, however, is a lack of large nontrivial bulk gap and highly stable two-dimensional (2D) films. In this work, we design a novel 2D honeycomb lattice, namely a SnCH3 monolayer, using comprehensive density-functional theory (DFT) computations. The structural stability is confirmed using a phonon spectrum and molecular dynamics simulations. Interestingly, its nontrivial bulk gap can reach up to 0.34 eV, which is further tunable via external strain. The nontrivial topology stems mainly from band inversion between the s–px,y orbitals, demonstrated by the nonzero topological invariant Z2 and a single pair of gapless helical edge states located in the bulk gap. The effects of a growth...  Read more

Molecular Dynamics Investigations of Membrane-Bound CYP2C19 Polymorphisms Reveal Distinct Mechanisms for Peripheral Variants by Long-Range Effects on the Enzymatic Activity

Molecular BioSystems
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reaction. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzyme and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analysis carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unraveled at the atomic level. To this end, we have investigated the mutation effects on structural characteristics and tunnel geometry upon single point mutations to elucidate the underlying molecular mechanism for the enzymatic activities deficiencies by using the fully atomistic molecular dynamics simulations in their native, membrane-bound cellular environment. The...  Read more

Understanding the microscopic binding mechanism of hydroxylated and sulfated polybrominated diphenyl ethers with transthyretin by molecular docking, molecular dynamics simulations and binding free energy calculations

Molecular BioSystems
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood–brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites. However, experimentally determined data for the TTR binding potential of the sulfated PBDEs are still not available. Therefore, molecular docking and molecular dynamics (MD) simulations were employed in the present study to probe the molecular basis of TTR interacting with hydroxylated and sulfated PBDEs at the atomic level. The docking scores of LeDock were used to construct the structure-based predictive model. The...  Read more

Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus

Molecular BioSystems
The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations...  Read more

Poly(Vinyl Alcohol) as a Water Protecting Agent for a Silver Nanoparticle: A Role of Polymer Size and Structure

Physical Chemistry Chemical Physics
Chemical modification of a silver nanoparticle (AgNP) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in its shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of a stabilizing mechanism of PVA is still poorly understood. For better understanding of a role of PVA in water protecting of a silver nanoparticle, we developed an atomistic molecular model of AgNP grafted with single-chain PVA of various length. Our model, designed for classical molecular dynamics (MD) simulations, approximates AgNP as a quasi-spherical silver nanocrystal with diameter 3.9 nm and uses a united-atom representation for PVA with a polymer chain length varied from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee &...  Read more

Adsorption behaviors and vibrational spectra of hydrogen peroxide molecules at quartz/water interfaces

Physical Chemistry Chemical Physics
The effect of H2O2 concentration on the change of H-bonds at a water/quartz interface was systematically examined by surface-specific sum-frequency generation (SFG) spectroscopy. Molecular dynamics (MD) simulation was further utilized to interpret the specific molecular dynamics as well as the configuration and evolution of water and H2O2 molecules at the interface. The results from this study demonstrated the important role of surface H-bonds on determination of the stability of adsorbed H2O2 at solvated, silica, xerogel surfaces. It was revealed that prior to reaching the surface saturation with H2O2 molecules (less than 20% in bulk solution), multiple H-bonds were formed with silanols at relatively short interactive distances. These H-bonds proved to be strong enough to enable...  Read more

The dynamic mechanism of RASSF5 and MST kinase activation by Ras

Physical Chemistry Chemical Physics
As a tumor suppressor, RASSF5 (NORE1A) activates MST1/2 thereby modulating the Hippo pathway. Structurally, activation involves RASSF5 and MST1/2 swapping their SARAH domains to form a SARAH heterodimer. This exposes the MST1/2 kinase domain which homodimerizes, leading to trans-autophosphorylation. The SARAH–SARAH interaction shifts RASSF5 away from its autoinhibited state and relieves MST1/2 autoinhibition. Separate crystal structures are available for the RA (Ras association) domain and SARAH dimer, where SARAH is a long straight α-helix. Using all-atom molecular dynamics simulations, we modeled the RASSF5 RA with a covalently connected SARAH to elucidate the dynamic mechanism of how SARAH mediates between autoinhibition and Ras triggered-activation. Our results show that in inactive RASSF5 the RA domain retains SARAH, yielding a self-associated conformation in which SARAH is in a kinked α-helical motif that increases the binding interface. When RASSF5 binds...  Read more

Probing the origins of vibrational mode specificity in intramolecular dynamics through picosecond time-resolved photoelectron imaging studies

Physical Chemistry Chemical Physics
We have studied the intramolecular dynamics induced by selective photoexcitation of two near-isoenergetic vibrational states in S1p-fluorotoluene using picosecond time-resolved photoelectron imaging. We find that similar dynamics ensue following the preparation of the 13111 and 7a111 states that lie at 1990 cm−1 and 2026 cm−1, and that these dynamics are mediated by a single strongly coupled doorway state in each case. However, the lifetimes differ by a factor of three, suggesting an influence of the vibrational character of the modes involved. Our results clearly show the contribution of torsion-vibration coupling to the dynamics; this is further corroborated by comparison with the 7a111 state in...  Read more

2D MoS2/polyaniline heterostructures with enlarged interlayer spacing for superior lithium and sodium storage

Journal of Materials Chemistry A
The exploitation of high-capacity and long-life MoS2-based materials is highly important for developing lithium ion batteries (LIBs) and sodium ion batteries (SIBs). Herein, we demonstrate the confined synthesis of 2D MoS2/polyaniline (MoS2/PANI) nanosheet heterostructures with well-defined interfaces, in which the interlayer distance of MoS2 is greatly enlarged from 0.62 nm to 1.08 nm. The introduction of such a big interlayer distance for efficient Li+/Na+ storage has never been demonstrated before. The unique MoS2/PANI nanosheets can address well the key challenges of traditional MoS2 anode materials related to low conductivity particularly in the vertical direction, easy restacking/aggregation, large volumetric change and sluggish...  Read more

Comparing Solvophobic and Multivalent Induced Collapse in Polyelectrolyte Brushes

ACS Macro Letters
Coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role of multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent...  Read more

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

Macromolecules
How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and...  Read more

Theoretical and numerical analysis of nano-actuators based on grafted polyelectrolytes in electric field

Faraday Discussions
We analyze theoretically and by means of molecular dynamics (MD) simulations the generation of mechanical force by a polyelectrolyte (PE) chain grafted to a plane and exposed to an external electric field; the free end of the chain is linked to a deformable target body. Varying the field, one can alter the length of the non-adsorbed (bulk) part of the chain and hence the deformation of the target body and the arising force. We focus on the impact of added salt on the magnitude of the generated force, which is especially important for applications. In particular, we develop a simple variational theory for the double layer formed near electrodes to compute the electric field acting on the bulk part of the chain. Our theoretical predictions agree well with the MD simulations. Next, we study the effectiveness of possible PE-based nano-vices, comprised of two clenching planes connected by PEs exposed to an external electric field. We analyze a novel phenomenon - two-dimensional diffusion...  Read more

Designing an efficient multi-epitope oral vaccine against Helicobacter pylori using immunoinformatics and structural vaccinology approaches

Molecular BioSystems
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and “CTGKSC” peptide motif that target epithelial microfold cells (M cells) to enhance vaccine...  Read more

Toward accurately modeling N-methylated cyclic peptides

Physical Chemistry Chemical Physics
Cyclic peptides have unique properties and can target protein surfaces specifically and potently. N-Methylation provides a promising way to further optimize the pharmacokinetic and structural profiles of cyclic peptides. The capability to accurately model structures adopted by N-methylated cyclic peptides would facilitate rational design of this interesting and useful class of molecules. We apply molecular dynamics simulations with advanced enhanced sampling methods to efficiently characterize the structural ensembles of N-methylated cyclic peptides, while simultaneously evaluating the overall performance of several simulation force fields. We find that one of the residue-specific force fields, RSFF2, is able to recapitulate experimental structures of the N-methylated cyclic peptide benchmarks tested here when the correct amide isomers are used as initial configurations and enforced during the simulations. Thus, using our simulation approach, it is...  Read more

Tailoring the Schiff base photoswitching – a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer

Physical Chemistry Chemical Physics
Small molecular systems exhibiting Excited State Intramolecular Proton Transfer (ESIPT) attract considerable attention due to their possible role as ultrafast, efficient, and photostable molecular photoswitches. Here, by means of static potential energy profile scan and on-the-fly non-adiabatic dynamics simulations we study the photodeactivation process of a minimal-chromophore aromatic Schiff base, salicylidene methylamine (SMA), and its two derivatives 6-cyano-salicylidene methylamine (6-CN-SMA) and 3-hydroxy-salicylidene methylamine (3-OH-SMA). We show that the dominant character of the lowest excited singlet state – ππ* vs. nπ* – plays a crucial role in the system's photophysics and controls the ESIPT efficiency. We also show that the relative alignment of the ππ* and nπ* states may be controlled through chemical substitutions made to the aromatic ring of the Schiff-base molecule. We believe that our findings will improve the rational-design strategies employed...  Read more