Topological line defects in graphene represent an ideal way to produce highly controlled structures with reduced dimensionality that can be used in electronic devices. In this work we propose using extended line defects in graphene to improve nucleobase selectivity in nanopore-based DNA sequencing devices. We use a combination of QM/MM and non-equilibrium Green's functions methods to investigate the conductance modulation, fully accounting for solvent effects. By sampling over a large number of different orientations generated from molecular dynamics simulations, we theoretically demonstrate that distinguishing between the four nucleobases using line defects in a graphene-based electronic device appears possible. The changes in conductance are associated with transport across specific molecular states near the Fermi level and their coupling to the pore. Through the application of a specifically tuned gate voltage, such a device would be able to discriminate the four types of nucleobases more reliably than that of graphene sensors without topological line defects.

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In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green’s functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.

The mechanism of the alkylation reaction of the indanone anion through asymmetric phase-transfer catalysis has been unraveled by density functional theory calculations. Our results point out that the present view of the asymmetry induction mechanism determined by hydrogen bond and π–π stacking interactions is not correct. Rather, stabilization of the main reaction pathway takes place through both the hydrogen bond and electrostatic interaction involving the leaving chloride anion.

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Electrochemical immunosensors (EI) have been widely investigated in the last several years. Among them, immunosensors based on low-dimensional materials (LDM) stand out, as they could provide a substantial gain in fabricating point-of-care devices, paving the way for fast, precise, and sensitive diagnosis of numerous severe illnesses. The high surface area available in LDMs makes it possible to immobilize a high density of bioreceptors, improving the sensitivity in biorecognition events between antibodies and antigens. If on the one hand, many works present promising results in using LDMs as a sensing material in EIs, on the other hand, very few of them discuss the fundamental interactions involved at the interfaces. Understanding the fundamental Chemistry and Physics of the interactions between the surface of LDMs and the bioreceptors, and how the operating conditions and biorecognition events affect those interactions, is vital when proposing new devices. Here, we present a review of recent works on EIs, focusing on devices that use LDMs (1D and 2D) as the sensing substrate. To do so, we highlight both experimental and theoretical aspects, bringing to light the fundamental aspects of the main interactions occurring at the interfaces and the operating mechanisms in which the detections are based.

In this work, we present a multiscale approach based on first-principles calculations and classical molecular dynamics methods, to investigate the enhanced oil recovery via low-salinity water injection (EOR-LSWI). Salting-in effect, wettability, pH alteration, electrical double layer and the main geochemical reactions involved in the multicomponent ionic exchanges mechanism were analyzed in order to understand their contribution, also to provide an overall phenomenological perspective of the involved phenomena with a proposed feedback control system. The first-principles calculations were based on density functional theory, carry out in the Quantum-ESPRESSO package, to determine the adsorption energies of hydrocarbons (propionic and pentanoic acids and phenol) on calcite (CaCO3) {10.4} surface. In addition, we have obtained the free energy variations for the minerals dissolution processes. The solvent effect was taken into account for the geochemical reactions through a continuum dielectric. The interface between calcite and API brine was investigated through steered classical molecular dynamics, as implemented in the LAMMPs code to evaluate the brine ions adsorption/desorption on calcite surface and characterize the electrostatic environment in the vicinity of the calcite-brine-oil interfaces. Our results showed that the adsorption energies for the deprotonated molecules were lower than the ones for the neutral cases, highlighting the pH effect in the desorption processes. The pH also played a role in the calcite dissolution, since the free energy variation (ΔG) of the dissolution process mediated by H3O+ was lower than the ΔG for the neutral pH process. We found the lowest dissolution ΔG for the MgSO4 mineral (bulk), indicating that Mg2+ and SO42- ions would be abundant in the solution. In contrast, the other minerals exhibit a positive ΔG. Ions adsorption/desorption on calcite are isoergic and suggest an equilibrium between Ca2+ and CO32- ions. In contrast, the Na+ and Cl- ions adsorption were not found to be a spontaneous process. Moreover, the potential of mean force profile for Ca2+ and CO32- ions showed a layered structuring, which indicates that the ion hydration energy is related to the adsorption/desorption process. Such results may contribute to cause-effect understanding of correlations among the mechanisms in EOR-LSWI and help to propose an optimal brine composition to maximize the oil recovery.