RESUMO

The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.

Assuntos

RESUMO

Extracting reliable information on certain physical properties of materials, such as thermal transport, can be computationally very demanding. Aiming to overcome such difficulties in the particular case of lattice thermal conductivity (LTC) of 2D nanomaterials, we propose a simple, fast, and accurate semi-empirical approach for LTC calculation. The approach is based on parameterized thermochemical equations and Arrhenius-like fitting procedures, thus avoiding molecular dynamics or ab initio protocols, which frequently require computationally expensive simulations. As a proof of concept, we obtain the LTC of some prototypical physical systems, such as graphene (and other 2D carbon allotropes), hexagonal boron nitride (hBN), silicene, germanene, binary, and ternary BNC lattices and two examples of the fullerene network family. Our obtained values are in good agreement with other theoretical and experimental estimations, nonetheless, being derived in a rather straightforward way, at a fraction of the usual computational cost.

RESUMO

Boron nitride nanotube peapods (BNNT-peapod) are composed of linear chains of C60molecules encapsulated inside BNNTs, they were first synthesized in 2003. In this work, we investigated the mechanical response and fracture dynamics of BNNT-peapods under ultrasonic velocity impacts (from 1 km s-1up to 6 km s-1) against a solid target. We carried out fully atomistic reactive molecular dynamics simulations using a reactive force field. We have considered the case of horizontal and vertical shootings. Depending on the velocity values, we observed tube bending, tube fracture, and C60ejection. Furthermore, the nanotube unzips for horizontal impacts at certain speeds, forming bi-layer nanoribbons 'incrusted' with C60molecules. The methodology used here is applicable to other nanostructures. We hope it motivates other theoretical investigations on the behavior of nanostructures at ultrasonic velocity impacts and aid in interpreting future experimental results. It should be stressed that similar experiments and simulations were carried out on carbon nanotubes trying to obtain nanodiamonds. The present study expands these investigations to include BNNT.

RESUMO

Recently, a new two-dimensional carbon allotrope named biphenylene network (BPN) was experimentally realized. The BPN structure consists of four-, six-, and eight-membered rings of sp2-hybridized carbon atoms. In this work, we carried out fully-atomistic reactive (ReaxFF) molecular dynamics simulations to study the mechanical properties and fracture patterns of non-defective and defective (nanocracks) BPN. Results show that, under uniaxial tensile loading, BPN is converted into four distinct morphologies before fracture starts. This conversion process is dependent on the stretching direction. Some of the formed structures contain mainly eight-membered rings, which have different shapes in each morphology. In one of them, a graphitization process occurs before the complete fracture. Importantly, in the presence of nanocracks, no new morphologies are formed. BPN exhibits a distinct fracture process when contrasted to graphene. After the critical strain threshold, the graphene transitions from an elastic to a brittle regime, while BPN can exhibit different inelastic stages. These stages are associated with the appearance of new morphologies. However, BPN shares some of the exceptional graphene properties. BPN Young's modulus and melting point are comparable to graphene, about 1019.4 GPa and 4024 K, respectively.

RESUMO

Carbon-based tubular materials have sparked a great interest in future electronics and optoelectronics device applications. In this work, we computationally studied the mechanical properties of nanotubes generated from popgraphene (PopNTs). Popgraphene is a 2D carbon allotrope composed of 5-8-5 rings. We carried out fully atomistic reactive (ReaxFF) molecular dynamics for PopNTs of different chiralities ( n,0 and 0,n ) and/or diameters and at different temperatures (from 300 up to 1200 K). Results showed that the tubes are thermally stable (at least up to 1200 K). All tubes presented stress/strain curves with a quasi-linear behavior followed by an abrupt drop of stress values. Interestingly, armchair-like PopNTs ( 0,n ) can stand a higher strain load before fracturing when contrasted to the zigzag-like ones ( n,0 ). Moreover, it was obtained that Young's modulus (YMod ) (750-900 GPa) and ultimate strength (σUS ) (120-150 GPa) values are similar to the ones reported for conventional armchair and zigzag carbon nanotubes. YMod values obtained for PopNTs are not significantly temperature-dependent. While the σUS values for the 0,n showed a quasi-linear dependence with the temperature, the n,0 exhibited no clear trends.

RESUMO

The behavior of nanostructures under high strain-rate conditions has been the object of theoretical and experimental investigations in recent years. For instance, it has been shown that carbon and boron nitride nanotubes can be unzipped into nanoribbons at high-velocity impacts. However, the response of many nanostructures to high strain-rate conditions is still unknown. In this work, we have investigated the mechanical behavior of carbon (CNS) and boron nitride nanoscrolls (BNS) colliding against solid targets at high velocities, using fully atomistic reactive (ReaxFF) molecular dynamics (MD) simulations. CNS (BNS) are graphene (boron nitride) membranes rolled up into papyrus-like structures. Their open-ended topology leads to unique properties not found in their close-ended analogs, such as nanotubes. Our results show that collision products are mainly determined by impact velocities and by two orientation angles, which define the position of the scroll (i) axis and (ii) open edge relative to the target. Our MD results showed that for appropriate velocities and orientations, large-scale deformations and nanoscroll fractures could occur. We also observed unscrolling (scrolls going back to quasi-planar membranes), scroll unzipping into nanoribbons, and significant reconstruction due to breaking and/or formation of new chemical bonds. For particular edge orientations and velocities, conversion from open to close-ended topology is also possible, due to the fusion of nanoscroll walls.

RESUMO

In this work we report new silicon and germanium tubular nanostructures with no corresponding stable carbon analogues. The electronic and mechanical properties of these new tubes were investigated through ab initio methods. Our results show that these structures have lower energy than their corresponding nanoribbon structures and are stable up to high temperatures (500 and 1000 K, for silicon and germanium tubes, respectively). Both tubes are semiconducting with small indirect band gaps, which can be significantly altered by both compressive and tensile strains. Large bandgap variations of almost 50% were observed for strain rates as small as 3%, suggesting their possible applications in sensor devices. They also present high Young's modulus values (0.25 and 0.15 TPa, respectively). TEM images were simulated to help in the identification of these new structures.

RESUMO

As graphene has become one of the most important materials, there is renewed interest in other similar structures. One example is silicene, the silicon analogue of graphene. It shares some of the remarkable graphene properties, such as the Dirac cone, but presents some distinct ones, such as a pronounced structural buckling. We have investigated, through density functional based tight-binding (DFTB), as well as reactive molecular dynamics (using ReaxFF), the mechanical properties of suspended single-layer silicene. We calculated the elastic constants, analyzed the fracture patterns and edge reconstructions. We also addressed the stress distributions, unbuckling mechanisms and the fracture dependence on the temperature. We analysed the differences due to distinct edge morphologies, namely zigzag and armchair.

RESUMO

Boron nitride nanoribbons (BNNRs) exhibit very interesting magnetic properties, which could be very useful in the development of spintronic based devices. One possible route to obtain BNNRs is through the unzipping of boron nitride nanotubes (BNNTs), which have been already experimentally realized. In this work, different aspects of the unzipping process of BNNTs were investigated through fully atomistic molecular dynamics simulations using a classical reactive force field (ReaxFF). We investigated multiwalled BNNTs of different diameters and chiralities. Our results show that chirality plays a very important role in the unzipping process, as well as the interlayer coupling. These combined aspects significantly change the fracturing patterns and several other features of the unzipping processes in comparison to the ones observed for carbon nanotubes. Also, similar to carbon nanotubes, defective BNNTs can create regions of very high curvature which can act as a path to the unzipping process.

RESUMO

Recently, Geblinger et al. [Nat. Nanotechnol. 3, 195 (2008)] reported the experimental realization of carbon nanotube S-like shaped nanostructures, the so-called carbon nanotube serpentines. We report here results from multimillion fully atomistic molecular dynamics simulations of their formation. We consider one-µm-long carbon nanotubes placed on stepped substrates with and without a catalyst nanoparticle on the top free end of the tube. A force is applied to the upper part of the tube during a short period of time and turned off; then the system is set free to evolve in time. Our results show that these conditions are sufficient to form robust serpentines and validates the general features of the "falling spaghetti model" proposed to explain their formation.