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Topology and polarity of dislocation cores dictate the mechanical strength of monolayer MoS2
摘要： In contrast to homoelemental graphene showing common dislocation dipole with pentagon-heptagon (5|7) core, heteroelemental MoS2 is observed to contain diverse dislocation cores that tune the chemical and physical properties. Yet, how the inevitable dislocation cores in MoS2 affect the mechanical behaviours remains virtually unexplored. Herein, we report direct atomistic simulations of mechanical characteristics of isolated dislocation-embedded MoS2 monolayers under tensile load. All isolated dislocation cores in MoS2 monolayer rise polar stress-concentration, while those with larger Burgers vector are less energetically-favorable configurations but show local wrinkling behaviour. It is revealed that the intrinsic tensile strength of MoS2 is dictated by topology and polarity of dislocation cores. There is a strong inverse correlation between the maximum residual stresses induced by the dislocation cores and the strength of MoS2 monolayers. Mechanical failure initiates from the bond at dislocation polygon on which side there is a missing atomic chain. Armchair-oriented 4|8 dislocation exhibits sole brittle failure, however, dual brittle/ductile fractures occur in zigzag-oriented dislocations; Mo-S-Mo angle-oriented crack is brittle, while the S-Mo-S angle-oriented crack becomes ductile. Our findings shed sights on mechanical design of heteroelemental 2D materials via dislocation engineering for practical application.
关键词： Mechanical strength,Fracture characteristics,Monolayer MoS2,Molecular dynamics simulations,Dislocation cores
更新于2025-09-23 15:23:52
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Wetting Transition from the Cassie–Baxter State to the Wenzel State on Regularly Nanostructured Surfaces Induced by an Electric Field
摘要： When droplets are placed on hydrophobic textured surfaces, different wetting state Cassie-Baxter (CB) state or Wenzel (W) state may occur depending on materials and structures of surfaces, types and sizes of droplets, thermal fluctuations, and external stimuli. The wetting transition from the CB to the W state and the opposite process have attracted a great deal of attention due to their primary importance for designing and fabricating textured surfaces. In this work, molecular dynamics (MD) simulations are employed to understand the mechanism behind the CB-to-W transition for a nanoscale water film placed on a surface decorated with a single nanogroove when an external electric field is applied. The free energy variation during the transition process is computed on the basis of the restrained MD simulations. Water intrusion into the groove is observed by simulation snapshots, which provides a direct evidence for the electric-field-induced CB-to-W transition. In the previous experiments, however, only a sharp reduction in the apparent contact angle is employed to judge whether the transition takes place. The free energy curves reveal that there are two energy barriers separating the CB and W states (?E1) as well as separating the W and CB states (?E2). Owing to the presence of ?E1, although the CB state has a higher free energy than the W state, it cannot spontaneously convert to the W state. When the external energy input exceeds ?E1, the CB-to-W transition can be triggered, otherwise the transition will stop, and the water film will return to the CB state. Moreover, it is found that the maximum of free energy always occurs after the film touches the groove bottom. Thus, the requirement of the film touching the groove bottom is responsible for the presence of the energy barrier ?E1. Finally, the dependences of the two energy barriers on the electric field strength, groove aspect ratio, and intrinsic contact angle of the groove are also discussed.
关键词： Cassie-Baxter state,wetting transition,Wenzel state,energy barrier,free energy,molecular dynamics simulations.
更新于2025-09-23 15:23:52
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Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites
摘要： Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as biosensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed.
关键词： plastoquinone binding site,molecular dynamics simulations,plastoquinone,Molecular docking,protein dynamics,Photosystem II
更新于2025-09-23 15:22:29
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Density, Structure, and Stability of Citrate <sup>3–</sup> and H <sub/>2</sub> Citrate <sup>–</sup> on Bare and Coated Gold Nanoparticles
摘要： We simulate the packing of citrate3– and H2citrate– onto gold nanoparticles (AuNPs) to understand how citrate anions cap and stabilize AuNPs. We determine the molecular configurations of citrate on 4, 6, and 8 nm AuNP surfaces as a function of charge state and packing density and find that both the distribution of configurations and maximum packing density are independent of AuNP size. A combination of molecular dynamics simulations and in situ Fourier transform infrared spectroscopy (FTIR) is employed to compare the molecular configurations, stability, and density of citrate on 4 nm citrate-coated (cit-AuNPs) and within polycation-wrapped 4 nm cit-AuNPs. FTIR experiments indicate the presence of H2citrate– within polycation-wrapped cit-AuNPs with coordination between the H2citrate– layer and polycation layer in agreement with simulations. Intermolecular hydrogen bonding between terminal carboxylic-acid groups of H2citrate– stabilizes the anionic layer at the interface between cit-AuNPs and adsorbing charged molecules. The calculated total density of H2citrate– on AuNPs decreases from 3.3 × 10-10 mol/cm2 to 3.0 × 10-10 mol/cm2 upon adsorption of a polycation due to some displacement of dangling H2citrate– hydrogen bonded to the surface-bound layer. The density of the surface-bound layer is consistently 2.8 × 10-10 mol/cm2 with and without polycation adsorption. We provide all-atom level insight into the distribution and organization of experimentally derived binding modes of citrate on bare and coated cit-AuNPs. The citrate density and surface charge density are determined for all-atom and coarse-grained modeling of cit-AuNPs, their functionalization, and transformations in complex environments.
关键词： polycation adsorption,gold nanoparticles,FTIR spectroscopy,citrate,molecular dynamics simulations
更新于2025-09-23 15:21:21
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Characterizing Molecular Adsorption on Biodegradable MnO <sub/>2</sub> Nanoscaffolds
摘要： Biodegradable MnO2 nanoscaffolds have recently been designed for advanced stem cell therapy. These nanomaterials strongly bind extracellular matrix proteins and effectively deliver therapeutic molecules, which significantly enhance stem cell survival and neuronal differentiation both in vitro and in vivo. In this work, we combine molecular dynamics simulations, density functional theory calculations and UV-Vis spectroscopy experiments to examine the selectivity and efficiency of a MnO2 nanosheet in adsorbing neurogenic drugs. To uncover the fundamental principles governing the drug loading process, we have systematically examined a series of model aromatic and alkyl compounds with characteristic functional groups and demonstrated that molecular adsorption on the MnO2 nanosheet results from an interplay of dispersion, electrostatic and charge transfer interactions. We have then proposed a metric that efficiently predicts the qualitative adsorption affinity of a guest molecule on the MnO2 nanosheet based on its structural and chemical features, which will facilitate the experimental screening of proper adsorbates for efficient molecular delivery and aid the development of MnO2-based nanoscaffolds for biomedical applications.
关键词： adsorption affinity,molecular dynamics simulations,density functional theory,MnO2 nanoscaffolds,neurogenic drugs,UV-Vis spectroscopy
更新于2025-09-23 15:21:21
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Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption
摘要： Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.
关键词： molecular dynamics simulations,Graphene quantum dots,oxidation level,ssDNA,adsorption,noncovalent functionalization,fluorescence quenching
更新于2025-09-23 15:21:01
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Structure and Conformation of a Crystalline P3HT Film Adsorbed on an Alkanethiol Self-Assembled Monolayer Deposited on Gold
摘要： All-atom molecular dynamics simulations are performed to investigate the structural and conformational properties of a regioregular poly(3-hexylthiophene) (P3HT) crystal in the presence of a gold (Au) substrate terminated with an n-alkanethiol self-assembled monolayer (SAM). The employed orientation of the P3HT crystals deposited on the SAM is the edge-on, since this orientation is believed to be the most energetically favorable and stable, also yielding the highest charge carrier mobility in organic thin-film transistors. The unit cell of the overall Au/SAM interfacial layer is obtained through detailed ab initio calculations. Systems with a varying number of P3HT stacks on the Au/SAM substrate are studied with an all-atom force field in order to elucidate the effect of polymer thickness on the structural properties of the system. All final structures are found to be stable and well-equilibrated. Insights into the P3HT crystal structure are provided for the P3HT layers in direct contact with the SAM, but also for those deeper in the polymer film. According to the simulations, the majority of conformational and packing properties of the P3HT film are practically similar to those of the bulk crystalline P3HT material, implying that its structure remains unaffected by the presence of the underlying Au/SAM substrate.
关键词： DFT calculations,semiconducting polymers,molecular dynamics simulations,self-assembled monolayers,P3HT
更新于2025-09-23 15:19:57
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Unveiling the photophysics of thiourea from CASPT2/CASSCF potential energy surfaces and singlet/triplet excited state molecular dynamics simulations
摘要： This work describes the decay mechanism of photoexcited thiourea, both in gas phase and in solution, from the information inferred from the topography of the excited and ground state potential energy surfaces and mixed singlet/triplet quantum classical molecular dynamics simulations. Our gas phase results reveal T1/S0 intersystem crossing as the dominant (49%) intrinsic decay channel to the ground state, which reaches a population of 0.28 at the final time of our simulations (10 ps). Population of the T1, would occur after internal conversion to the S1 from the spectroscopic S2 electronic state, followed by S1->T2 intersystem crossing and T2->T1 internal conversion processes. Minor decay channels occurring exclusively along the singlet manifold, i.e. S2->S0 (33%) and S1->S0 (18%), were also observed to play a role in the relaxation of photoexcited thiourea in the gas phase. The explicit incorporation of water-thiourea interactions in our simulations was found to provoke a very significant delay in the decay to the ground state of the system, with no transitions to the S0 being registered during the first 10 ps of our simulations. Intermolecular vibrational energy redistribution and explicit hydrogen bond interaction established between water molecules and the NH2 group of thiourea were found to structurally or energetically hamper the access to the intersystem crossing or internal conversion funnels with the S0.
关键词： intersystem crossing,internal conversion,CASPT2 calculations,thiourea,molecular dynamics simulations
更新于2025-09-19 17:15:36
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The effect of pulse duration on nanoparticle generation in pulsed laser ablation in liquids: Insights from large-scale atomistic simulations
摘要： The generation of colloidal solutions of chemically clean nanoparticles through pulsed laser ablation in liquids (PLAL) has evolved into a thriving research field that impacts industrial applications. The complexity and multiscale nature of PLAL make it difficult to untangle the various processes involved in the generation of nanoparticles and establish the dependence of nanoparticle yield and size distribution on the irradiation parameters. Large-scale atomistic simulations have yielded important insights into the fundamental mechanisms of ultrashort (femtoseconds to tens of picoseconds) PLAL and provided a plausible explanation of the origin of the experimentally observed bimodal nanoparticle size distributions. In this paper, we extend the atomistic simulations to short (hundreds of picoseconds to nanoseconds) laser pulses and focus our attention on the effect of the pulse duration on the mechanisms responsible for the generation of nanoparticles at the initial dynamic stage of laser ablation. Three distinct nanoparticle generation mechanisms operating at different stages of the ablation process and in different parts of the emerging cavitation bubble are identified in the simulations. These mechanisms are (1) the formation of a thin transient metal layer at the interface between the ablation plume and water environment followed by its decomposition into large molten nanoparticles, (2) nucleation, growth, and rapid cooling/solidification of small nanoparticles at the very front of the emerging cavitation bubble, above the transient interfacial metal layer, and (3) spinodal decomposition of a part of the ablation plume located below the transient interfacial layer, leading to the formation of a large population of nanoparticles growing in a high-temperature environment through inter-particle collisions and coalescence. The coexistence of the three distinct mechanisms of the nanoparticle formation at the initial stage of the ablation process can be related to the broad nanoparticle size distributions commonly observed in nanosecond PLAL experiments. The strong dependence of the nanoparticle cooling and solidification rates on the location within the low-density metal-water mixing region has important implications for the long-term evolution of the nanoparticle size distribution, as well as for the ability to quench the nanoparticle growth or dope them by adding surface-active agents or doping elements to the liquid environment.
关键词： phase explosion,pulsed laser ablation in liquids,molecular dynamics simulations,hydrodynamic instability,atomistic simulations,nanoparticles,nucleation and growth
更新于2025-09-19 17:13:59
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Effect of liquid environment on single-pulse generation of laser induced periodic surface structures and nanoparticles
摘要： The effect of a liquid environment on the fundamental mechanisms of surface nanostructuring and generation of nanoparticles by single pulse laser ablation is investigated in a closely integrated computational and experimental study. A large-scale molecular dynamics simulation of spatially-modulated ablation of Cr in water reveals a complex picture of dynamic interaction between the ablation plume and water, which involves rapid deceleration of the ablation plume by water environment, formation and prompt disintegration of a hot metal layer at the interface between the ablation plume and water, lateral redistribution and redeposition of a major fraction of the ablation plume, and eventual formation of smooth frozen surface features. A good agreement between the shapes of the surface features predicted in the simulation and the ones generated in single pulse laser ablation experiments performed for Cr in water supports the mechanistic insights revealed in the simulations. The results of this study suggest that the presence of liquid environment can eliminate the sharp features of surface morphology, reduce the amount of material removed from the target by more than an order of magnitude, and narrow down the nanoparticle size distribution as compared to laser ablation in vacuum. Moreover, the computational predictions of the effective incorporation of molecules constituting the liquid environment into the surface region of the irradiated target and the generation of high vacancy concentrations exceeding the equilibrium levels by more than an order of magnitude suggest a potential for hyperdoping of laser-generated surfaces by solutes present in the liquid environment.
关键词： Laser-Induced Periodic Surface Structures (LIPSS),Generation of Nanoparticles,Crystal Defects,Surface Morphology,Hyperdoping,Molecular Dynamics Simulations,Pulsed Laser Ablation in Liquids
更新于2025-09-19 17:13:59