Quantum biochemical analysis of the TtgR regulator and effectors.

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.

Lattice thermal conductivity of 2D nanomaterials: a simple semi-empirical approach.

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.

Boron nitride nanotube peapods at ultrasonic velocity impacts: a fully atomistic molecular dynamics investigation.

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.

On the mechanical properties and fracture patterns of the nonbenzenoid carbon allotrope (biphenylene network): a reactive molecular dynamics study.

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.

On the Mechanical Properties of Popgraphene-Based Nanotubes: a Reactive Molecular Dynamics Study.

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.

Virtually imprinted polymers (VIPs): understanding molecularly templated materials via molecular dynamics simulations.

Molecularly imprinted polymers are advanced recognition materials selectively rebinding a target molecule present during the synthesis of the polymer matrix. It is commonly understood that the templating process is based on embedding the complex formed between a template and functional monomers into a co-polymer matrix. This happens by a polymerization of the complex with a cross-linker while maintaining their spatial arrangement forming a molecular imprint. Template removal then leads to synthetic recognition sites ready to selectively rebind their targets, which are complementary in functionality, size and shape to the target. In this study, an innovative theoretical concept using fully atomistic molecular dynamics simulations for modeling molecular templating processes is introduced yielding virtually imprinted polymers (VIPs). VIPs created for the template 17-ß-estradiol and applied in modeled chromatography experiments demonstrated selectivity for their template. This evidenced the creation of virtual imprints as a result of a templated synthesis protocol, which represents a theoretical confirmation of the governing imprinting theory.

Efficient prediction of suitable functional monomers for molecular imprinting via local density of states calculations.

Synthetic molecular recognition materials, such as molecularly imprinted polymers (MIPs), are of increasing importance in biotechnology and analytical chemistry, as they are able to selectively bind their respective template. However, due to their specificity, each MIP has to be individually designed for the desired target leading to a molecularly tailored synthesis strategy. While trial-and-error remains the common approach for selecting suitable functional monomers (FMs), the study herein introduces a radically new approach towards rationally designing MIPs by rapidly screening suitable functional monomers based on local density of states (LDOS) calculations in a technique known as Electronic Indices Methodology (EIM). An EIM-based method of classification of FMs according to their suitability for imprinting was developed. Starting from a training set of nine different functional monomers, the prediction of suitability of four functional monomers was possible. These predictions were subsequently experimentally confirmed.

Structural transformations of carbon and boron nitride nanoscrolls at high impact collisions.

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.

STRETCHY ELECTRONICS. Hierarchically buckled sheath-core fibers for superelastic electronics, sensors, and muscles.

Superelastic conducting fibers with improved properties and functionalities are needed for diverse applications. Here we report the fabrication of highly stretchable (up to 1320%) sheath-core conducting fibers created by wrapping carbon nanotube sheets oriented in the fiber direction on stretched rubber fiber cores. The resulting structure exhibited distinct short- and long-period sheath buckling that occurred reversibly out of phase in the axial and belt directions, enabling a resistance change of less than 5% for a 1000% stretch. By including other rubber and carbon nanotube sheath layers, we demonstrated strain sensors generating an 860% capacitance change and electrically powered torsional muscles operating reversibly by a coupled tension-to-torsion actuation mechanism. Using theory, we quantitatively explain the complementary effects of an increase in muscle length and a large positive Poisson's ratio on torsional actuation and electronic properties.

One-dimensional silicon and germanium nanostructures with no carbon analogues.

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.

Mechanical properties and fracture dynamics of silicene membranes.

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.

Dynamical aspects of the unzipping of multiwalled boron nitride nanotubes.

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.

Dynamics of the formation of carbon nanotube serpentines.

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.

Graphene to fluorographene and fluorographane: a theoretical study.

We report here a fully reactive molecular dynamics study on the structural and dynamical aspects of the fluorination of graphene membranes (fluorographene). Our results show that fluorination tends to produce defective areas on the graphene membranes with significant distortions of carbon-carbon bonds. Depending on the amount of incorporated fluorine atoms, large membrane holes were observed due to carbon atom losses. These results may explain the broad distribution of the structural lattice parameter values experimentally observed. We have also investigated the effects of mixing hydrogen and fluorine atoms on the graphene functionalization. Our results show that, when in small amounts, the presence of hydrogen atoms produces a significant decrease in the rate of fluorine incorporation onto the membrane. On the other hand, when fluorine is the minority element, it produces a significant catalytic effect on the rate of hydrogen incorporation. We have also observed the spontaneous formation of new hybrid structures with different stable configurations (chair-like, zigzag-like and boat-like) which we named fluorographane.

On the unzipping of multiwalled carbon nanotubes.

Graphene nanoribbons (GNRs) are very interesting structures which can retain graphene's high carrier mobility while presenting a finite bandgap. These properties make GNRs very valuable materials for the building of nanodevices. Unzipping carbon nanotubes (CNTs) is considered one of the most promising approaches for GNR controlled and large-scale production, although some of the details of the CNT unzipping processes are not completely known. In this work we have investigated CNT unzipping processes through fully atomistic molecular dynamics simulations using reactive force fields (ReaxFF). Multiwalled CNTs of different dimensions and chiralities under induced mechanical stretching were considered. Our results show that fracture patterns and stress profiles are highly CNT chirality dependent. Our results also show that the 'crests' (partially unzipped CNT regions presenting high curvature), originating from defective CNT areas, can act as a guide for the unzipping processes, which can explain the almost perfectly linear cuts frequently observed in unzipped CNTs.

Electronic properties of Fibonacci and random Si-Ge chains.

In this paper we address a theoretical calculation of the electronic spectra of an Si-Ge atomic chain that is arranged in a Fibonacci quasi-periodic sequence, by using a semi-empirical quantum method based on the Hückel extended model. We apply the Fibonacci substitutional sequences in the atomic building blocks A(Si) and B(Ge) through the inflation rule or a recursion relation. In our ab initio calculations we use only a single point, which is sufficient for considering all the orbitals and charge distribution across the entire system. Although the calculations presented here are more complete than the models adopted in the literature which take into account the electronic interaction only up to the second and third neighbors, an interesting property remains in their electronic spectra: the fractality (which is the main signature of this kind of system). We discuss this fractality of the spectra and we compare them with the random arrangement of the Si-Ge atomic chain, and with previous results based on the tight-binding approximation of the Schrödinger equation considering up to the nearest neighbor.

Ordered phases of encapsulated diamondoids into carbon nanotubes.

Diamondoids are hydrogen-terminated nanosized diamond fragments that are present in petroleum crude oil at low concentrations. These fragments are found as oligomers of the smallest diamondoid, adamantane (C(10)H(16)). Due to their small size, diamondoids can be encapsulated into carbon nanotubes to form linear arrangements. We have investigated the encapsulation of diamondoids into single walled carbon nanotubes with diameters between 1.0 and 2.2 nm using fully atomistic simulations. We performed classical molecular dynamics and energy minimizations calculations to determine the most stable configurations. We observed molecular ordered phases (e.g. double, triple, 4- and 5-stranded helices) for the encapsulation of adamantane, diamantane, and dihydroxy diamantane. Our results also indicate that the functionalization of diamantane with hydroxyl groups can lead to an improvement on the molecular packing factor when compared to non-functionalized compounds. Comparisons to hard-sphere models revealed differences, especially when more asymmetrical diamondoids were considered. For larger diamondoids (i.e., adamantane tetramers), we have not observed long-range ordering but only a tendency to form incomplete helical structures. Our calculations predict that thermally stable (at least up to room temperature) complex ordered phases of diamondoids can be formed through encapsulation into carbon nanotubes.

Mechanical deformation of nanoscale metal rods: when size and shape matter.

Face centered cubic metals deform mainly by propagating partial dislocations generating planar fault ribbons. How do metals deform if the size is smaller than the fault ribbons? We studied the elongation of Au and Pt nanorods by in situ electron microscopy and ab initio calculations. Planar fault activation barriers are so low that, for each temperature, a minimal rod size is required to become active for releasing elastic energy. Surface effects dominate deformation energetics; system size and shape determine the preferred fault gliding directions which induce different tensile and compressive behavior.

Intrinsic stability of the smallest possible silver nanotube.

Recently, Lagos et al. [Nature Nanotech. 4, 149 (2009)] reported the discovery of the smallest possible Ag nanotube with a square cross section. Ab initio density functional theory calculations strongly support that the stability of these hollow structures is structurally intrinsic and not the result of contamination by light atoms. We also report the first experimental observation of the theoretically predicted corrugation of the hollow structure. Quantum conductance calculations predict a unique signature of 3.6 G0 for this new family of nanotubes.

Temperature effects on the occurrence of long interatomic distances in atomic chains formed from stretched gold nanowires.

The origin of long interatomic distances in suspended gold atomic chains formed from stretched nanowires remains the object of debate despite the large amount of theoretical and experimental work. Here, we report new atomic resolution electron microscopy observations acquired at room and liquid-nitrogen temperatures and theoretical results from ab initio quantum molecular dynamics on chain formation and stability. These new data are suggestive that the long distances are due to contamination by carbon atoms originating from the decomposition of adsorbed hydrocarbon molecules.