Guilherme Colherinhas

Graphene and graphene-derived electrodes combined with ionic liquid electrolytes provide atomically well-defined, high-surface-area interfaces and wide electrochemical windows, making them benchmark platforms for supercapacitor research. Understanding how molecular-scale structure at this interface controls macroscopic capacitance requires molecular dynamics simulation since neither continuum theory nor experiment alone resolves the relevant length and time scales. This review treats the electrode-charging methods available─fixed and constant-charge, constant potential, electronic-structure-aware variants, and applied fields─together with force-field choice, as a toolbox of complementary tools suited to different questions, not a hierarchy of accuracy. We use this framework to organize findings on interfacial structure, electrode curvature, defects, doping, and nanoconfinement, emphasizing how these factors affect both the electric double layer and quantum capacitance. We conclude that progress toward predictive simulation will depend less on selecting a single optimal method than on integrating electrolyte polarizability, realistic electrode electronic response, structural complexity, and transferable machine-learning potentials within experimentally validated frameworks.

Water uptake alters the interfacial organization and charge storage response of ionic-liquid supercapacitors, but its effects in the presence of multivalent cations remain poorly understood. Here, atomistic molecular dynamics simulations were used to investigate dry N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide, [Pyr14][TFSI], the corresponding humid electrolyte, and humid systems containing Al3+, Ca2+, Mg2+, or Zn2+ at a 1:1 metal-to-water ratio. The electrolytes were confined between oppositely charged graphene electrodes over surface-charge magnitudes of 0.00−0.30 e/nm2. Interfacial organization was characterized using number- and charge-density profiles and species populations within the electric double layer. Projected and differential capacitances were obtained from the charge−potential relationship, and stored energies were compared at a common potential difference of 2.0 V. The principal [Pyr14]+/[TFSI]− layering was broadly preserved, whereas metal-cation accumulation and water redistribution were strongly composition-dependent. Hydration yielded a slightly lower total projected capacitance in the global fit analysis (2.23 ± 0.12 to 2.10 ± 0.10 μF/cm2), although the block-level comparison revealed no statistically significant difference between the dry and humid electrolytes (Welch’s two-sample t-test, p = 0.85). Al3+ yielded a central value closest to the dry-electrolyte reference (2.21 ± 0.16 μF/cm2), while Ca2+and Zn2+ remained close to the metal-free humid system; none of these differences was clearly resolved within the present uncertainty. Mg2+produced the largest reduction, reaching 1.58 ± 0.13 μF/cm2, with lower capacitance at both electrode interfaces. At 2.0 V, hydration decreased the stored energy relative to the dry electrolyte, and Mg2+ produced the largest decrease among the metal-containing systems (26.3%), whereas Al3+ was the only system whose central stored energy exceeded that of the dry electrolyte, with a correspondingly larger block-to-block uncertainty (±0.68 versus ≤0.12 μJ/cm2 for the other humid electrolytes). These results demonstrate that multivalent-cation addition produces composition- and voltage-dependent changes in interfacial screening rather than a uniform recovery of the dry electrolyte response.

Accurate predictions of capacitance and energy storage in electrochemical systems depend critically on how the charge–potential response is sampled. In this work, we investigate how data resolution and sampling strategy affect capacitance and energy estimates in graphene-based supercapacitors using molecular dynamics (MD) simulations of a partially hydrated ionic liquid. To this end, we compare projected and differential capacitance approaches and their associated energy estimates using complete, uniformly reduced, and nonuniformly sampled data sets. Linear fits of the potential–charge relationship, Φ(σ), provide a robust estimate of the average projected capacitance and are relatively insensitive to sampling density. However, because the projected approach compresses the full electrostatic response into a single effective slope, it cannot resolve local capacitance variations or directly determine the capacitance at the point of zero charge (PZC). In contrast, the differential capacitance, derived from cubic fits of the charge–potential relationship, σ(Φ), provides a local, potential-resolved reconstruction of the electrostatic response, but is more sensitive to sparse or uneven sampling because it depends on the curvature of the fitted response. These methodological differences are propagated into the energy estimates: the projected energy follows the ideal quadratic voltage dependence of a constant-capacitance model, whereas the integrated energy reflects the voltage-dependent capacitance profile and captures deviations from ideal linear-capacitor behavior. By comparing edge-dominated and PZC-centered data sets, we show that different regions of the electrostatic phase space probe distinct electrostatic regimes. Sampling near the PZC captures the near-equilibrium response, whereas edge-dominated sampling emphasizes the strongly polarized regime. These results provide practical guidelines for molecular simulations of electrochemical interfaces and show that reliable capacitance and energy estimates require control not only over the number of sampled points, but also over their distribution across the full polarization range.

Classical molecular dynamics simulations were used to investigate the effect of fullerene C60 on the interfacial structure and electrostatic response of graphene-based supercapacitors containing the ionic liquid [Bmim][PF6]. Systems with different C60 loadings were analyzed within a fixed-charge framework, and polarized and nonpolarized fullerene descriptions were compared at the highest loading. The simulations show that C60 preferentially accumulates near the graphene/electrolyte interfaces, partially displacing adsorbed ions while preserving the layered structure of the electrical double layer. This interfacial redistribution reduces conventional ionic screening and increases the relative contribution of fullerene–graphene dispersion interactions. Although increasing C60 content lowers the calculated capacitance, the solvent-polarized fixed-charge model produces a larger corrected electrostatic potential difference and, consequently, a higher model-derived energy-density estimate than the corresponding nonpolarized model at the same fullerene loading. These results suggest that fullerene adsorption and solvent-induced charge anisotropy can jointly modulate the electrostatic response of ionic-liquid graphene supercapacitors. The reported values should be interpreted as comparative trends within the adopted molecular model rather than as direct predictions of experimental operating voltages.

Self-assembled biomolecular materials provide a promising route for designing soft, sustainable, and molecularly tunable electrostatic interfaces that are relevant to energy storage, iontronics, and bioinspired electrochemical systems. However, the molecular mechanisms by which charged peptide assemblies organize confined ionic environments and generate interfacial electrostatic gradients remain poorly understood. Here, we use fully atomistic molecular dynamics simulations to investigate self-assembled peptide nanomembranes composed of the bolaamphiphilic sequences EFL4FE and RFL4FR immersed in the ionic liquid [PYR][TFSI]. We examine these nanosheets as intrinsically charged supramolecular interfaces, whose surface charges arise from peptide composition, predefined protonation states, and supramolecular organization. The distinct charge characteristics of the two peptide sequences produce sequence-dependent ionic organization with preferential recruitment of cations or anions according to the local sign of the peptide charge. In both systems, localized peptide charges induce compact counterion accumulation, co-ion depletion, charge density oscillations, and electrical double-layer (EDL)-like organization. Consequently, the confined ionic liquid exhibits pronounced interfacial structuring and electrostatic potential gradients governed by the spatial distribution of charges within the peptide nanomembranes. Moreover, the electrostatic potential profiles indicate that the interfacial perturbation extends into the supramolecular membrane rather than being restricted to the electrolyte-facing surface. Within the limitations of the nonreactive classical fixed-charge model, these results provide molecular-level evidence that intrinsically charged peptide nanomembranes can organize confined ionic liquids and sustain electrostatic gradients across supramolecular interfaces. Their potential use as electrostatic transduction elements or components of iontronic and electrochemical devices requires further investigation, explicitly addressing electronic transport, external electrical coupling, and device-level operation.

West Nile virus (WNV) is a neurotropic flavivirus lacking approved antiviral therapies. Here, we evaluated the repurposing potential of ten HIV protease inhibitors as inhibitors of the WNV NS2B–NS3 protease using molecular docking followed by molecular dynamics simulations. Structural, energetic, and interaction analyses revealed substantial differences in binding stability under dynamic conditions. Indinavir and Atazanavir consistently showed strong and stable interactions, low structural and positional fluctuations, persistent hydrogen bonding, and favorable binding free energies. In contrast, several inhibitors displayed transient binding despite favorable docking scores. These findings emphasize the importance of molecular dynamics in drug repurposing studies and identify Indinavir and Atazanavir as promising candidates for further experimental evaluation against WNV.

Electrode spacing is frequently considered a parameter in supercapacitor optimization, yet its intrinsic impact on capacitance and energy storage under nanoconfinement remains uncertain. In this study, classical molecular dynamics simulations were performed for graphene-based supercapacitors containing the ionic liquid [emim][ala] confined between planar electrodes separated by 4–12 nm. Electric potential profiles enabled the calculation of differential and total capacitances as well as stored energy densities. Mass density analyses show well-defined electric double layers (EDLs) at both electrodes. Strong overlap is observed at short separations, whereas a bulk-like central region is preserved at larger ones. Nevertheless, the total capacitance remains nearly constant (∼2.40–2.58 μF/cm²), and the differential capacitance at zero charge varies only slightly across all separations, indicating a surface-dominated storage mechanism. The integrated areal energy density up to 2.5 V is also essentially independent of spacing (∼7.4–7.7 μJ/cm²). In contrast, gravimetric and volumetric energy densities decrease with increasing separation due to mass and volume normalization effects. These results demonstrate that electrode spacing modulates EDL structure but only weakly affects intrinsic capacitive performance.

Deep eutectic solvents (DESs) based on choline chloride and phenol (CCPhe) have attracted increasing attention due to their tunable physicochemical properties and structural versatility. In this work, molecular dynamics (MD) simulations were performed for CCPhe systems at molar ratios of 1:2, 1:3, and 1:4 with water contents ranging from 0 to 30%. Energetic, hydrogen-bond, dielectric, transport, and structural analyses were combined to establish a multiscale description of hydration effects. Hydration promotes a progressive redistribution of stabilization from chloride-phenol and choline-chloride interactions toward chloride-water interactions, accompanied by increased water-mediated hydrogen bonding and reduced hydrogen-bond lifetimes. The dielectric constant increases significantly with water content, reaching 15.93 for the 1:4 system at 30% hydration, while the infinite-system Kirkwood factor reveals enhanced cooperative dipolar correlations at high hydration levels. Diffusion coefficients increase by nearly an order of magnitude between dry and highly hydrated systems, indicating substantial mobility enhancement. Radial distribution functions show that hydration modifies the first solvation shell of choline through competitive coordination between chloride and water without altering the characteristic contact distance. These results demonstrate that controlled hydration acts as an effective tuning parameter in CCPhe systems, modulating energetic balance, hydrogen-bond connectivity, collective polarization, and molecular transport in a composition-dependent manner.

The increasing concentration of atmospheric CO₂ demands the development of advanced and sustainable materials for carbon capture. Peptide-based nanostructures have emerged as promising candidates due to their tunable chemistry, biocompatibility, and ability to self-assemble into ordered supramolecular architectures. In this work, we investigate the adsorption behavior of CO₂ on self-assembled A₆H and A₆R peptide membranes through classical molecular dynamics simulations. The A₆H and A₆R sequences consist of six alanine residues capped by a terminal histidine or arginine residue, respectively, and self-assemble into stable β-sheet membrane structures whose surface charge distribution and hydration organization are governed by the nature of the terminal residue. After equilibrating the membranes in an aqueous medium, water molecules were removed, and CO₂ was introduced into the simulation box to evaluate gas–surface interactions under idealized gas-phase contact conditions. The results reveal distinct adsorption mechanisms governed by headgroup chemistry: the imidazole-terminated A₆H interface exhibits preferential electrostatic and hydrogen-bond-driven interactions with CO₂, whereas the guanidinium-terminated A₆R membrane, characterized by a higher surface charge density, promotes enhanced electrostatic attraction and a larger number of CO₂ binding events. These findings highlight how the chemistry of peptide terminal residues modulates CO₂ affinity at ordered, self-assembled membrane interfaces, underscoring the potential of bioinspired peptide membranes as tunable platforms for carbon capture. By focusing on experimentally validated supramolecular architectures rather than peptide aggregates or hybrid systems, this study provides molecular-level insights that can inform the rational design of peptide-based sorbent materials for sustainable CO₂ sequestration.