Organic contaminants and atmospheric nitrogen at the graphene-water interface: a simulation study

Real-Time Monitoring of Volatile Organic Compound-Mediated Plant Intercommunication Using Surface-Enhanced Raman Scattering Nanosensor

Plants communicate through volatile organic compounds (VOCs), but real-time monitoring of VOCs for plant intercommunication is not practically possible yet. A nanobionic VOC sensor plant is created to study VOC-mediated plant intercommunication by incorporating surface-enhanced Raman scattering (SERS) nanosensors into a living plant. This sensor allows real-time monitoring of VOC with a sensitivity down to the parts per trillion level. A quantitative VOC diffusion model in plants is proposed to describe this extreme sensitivity. The sensor plant is paired with a customized portable Raman device, demonstrating its ability to detect multiple VOCs on-field. The sensor demonstrated that plants collect VOCs emitted from neighboring plants and hazardous volatile chemicals in the air at a certain distance. As a feasibility study, this nanobionic VOC sensor plant successfully monitored the early stages of fungal infection in strawberry fruits. This result suggests that interfacing nanosensors with plants offers an innovative approach to studying interplant communication and can be used as a compelling tool for monitoring VOC occurrence.

Environmental Influence on Stripe Formation at the Graphite-Water Interface

Understanding the characteristics of graphite-water interfaces is of scientific significance and practical importance. Ordered stripe structures have been observed at this interface, with their origins debated between condensed gas molecules and airborne hydrocarbons. Atomic force microscopy (AFM) studies have revealed variations in the morphology, formation and growth of these ordered structures. Here, we investigate the graphite-water interface under different environmental conditions using PeakForce Quantitative Nanomechanical (PF-QNM) AFM. Our findings reveal that stripe structures with 4 nm width and 0.5 nm periodicity, form and grow under wet laboratory conditions but not in pure inert gas or cleanroom environments. These stripes appear more readily when the graphite surface is immersed in water, with growth associated with gas nanodomains on the surface. This suggests that atmospheric contaminants migrate to the water-graphite interface, potentially facilitated by gas states. These findings underscore the impact of environmental conditions on graphitic materials, providing new insights into the mechanisms underlying stripe formation and growth.

Interfacial Water Is Separated from a Hydrophobic Silica Surface by a Gap of 1.2 nm

The interaction of liquid water with hydrophobic surfaces is ubiquitous in life and technology. Yet, the molecular structure of interfacial liquid water on these surfaces is not known. By using a 3D atomic force microscope, we characterize with angstrom resolution the structure of interfacial liquid water on hydrophobic and hydrophilic silica surfaces. The combination of 3D AFM images and molecular dynamics simulations reveals that next to a hydrophobic silica surface, there is a 1.2 nm region characterized by a very low density of water. In contrast, the 3D AFM images obtained of a hydrophilic silica surface reveal the presence of hydration layers next to the surface. The gap observed on hydrophobic silica surfaces is filled with two-to-three layers of straight-chain alkanes. We developed a 2D Ising model that explains the formation of a continuous hydrocarbon layer on hydrophobic silica surfaces.

Chiral organic molecular structures supported by planar surfaces

We employ the molecular dynamics simulations to study the dynamics of acetanilide (ACN) molecules placed on a flat surface of planar multilayer hexagonal boron nitride. We demonstrate that the ACN molecules, known to be achiral in the three-dimensional space, become chiral after being placed on the substrate. Homochirality of the ACN molecules leads to stable secondary structures stabilized by hydrogen bonds between peptide groups of the molecules. By employing molecular dynamics simulations, we reveal that the structure of the resulting hydrogen-bond chains depends on the isomeric composition of the molecules. If all molecules are homochiral (i.e., with only one isomer being present), they form secondary structures (chains of hydrogen bonds in the shapes of arcs, circles, and spirals). If the molecules at the substrate form a racemic mixture, then no regular secondary structures appear, and only curvilinear chains of hydrogen bonds of random shapes emerge. A hydrogen-bond chain can form a zigzag array only if it has an alternation of isomers. Such chains can create two-dimensional (2D) regular lattices or 2D crystals. The melting scenarios of such 2D crystals depend on density of its coverage of the substrate. At 25% coverage, melting occurs continuously in the temperature interval 295-365 K. For a complete coverage, melting occurs at 415-470 K due to a shift of 11% of all molecules into the second layer of the substrate.

Interfacial Liquid Water on Graphite, Graphene, and 2D Materials

The optical, electronic, and mechanical properties of graphite, few-layer, and two-dimensional (2D) materials have prompted a considerable number of applications. Biosensing, energy storage, and water desalination illustrate applications that require a molecular-scale understanding of the interfacial water structure on 2D materials. This review introduces the most recent experimental and theoretical advances on the structure of interfacial liquid water on graphite-like and 2D materials surfaces. On pristine conditions, atomic-scale resolution experiments revealed the existence of 1-3 hydration layers. Those layers were separated by ∼0.3 nm. The experimental data were supported by molecular dynamics simulations. However, under standard working conditions, atomic-scale resolution experiments revealed the presence of 2-3 hydrocarbon layers. Those layers were separated by ∼0.5 nm. Linear alkanes were the dominant molecular specie within the hydrocarbon layers. Paradoxically, the interface of an aged 2D material surface immersed in water does not have water molecules on its vicinity. Free-energy considerations favored the replacement of water by alkanes.

Interfacial layering of hydrocarbons on pristine graphite surfaces immersed in water

Interfacial water participates in a wide range of phenomena involving graphite, graphite-like and 2D material interfaces. Recently, several high-spatial resolution experiments have questioned the existence of hydration layers on graphite, graphite-like and 2D material surfaces. Here, 3D AFM was applied to follow in real-time and with atomic-scale depth resolution the evolution of graphite-water interfaces. Pristine graphite surfaces upon immersion in water showed the presence of several hydration layers separated by a distance of 0.3 nm. Those layers were short-lived. After several minutes, the interlayer distance increased to 0.45 nm. At longer immersion times (∼50 min) we observed the formation of a third layer. An interlayer distance of 0.45 nm characterizes the layering of predominantly alkane-like hydrocarbons. Molecular dynamics calculations supported the experimental observations. The replacement of water molecules by hydrocarbons on graphite is spontaneous. It happens whenever the graphite-water volume is exposed to air.

Design of Peptides that Fold and Self-Assemble on Graphite

The graphite-water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite-water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite-water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.