Calculation method for the conductance of mesoscopic systems: assembly of Tight Binding Hamiltonians with spin effects-revisited.

We discretize the Schrödinger equation in the approximation of the effective mass for the two-dimensional electron gas of GaAs, without magnetic field and on the other hand, with magnetic field. This discretization leads naturally to Tight Binding (TB) Hamiltonians in the approximation of the effective mass. An analysis of this discretization allows us to gain insight into the role of site and hopping energies, which allows us to model the TB Hamiltonian assembly with spin: Zeeman and spin-orbit coupling effects, especially the case Rashba. With this tool we can assemble Hamiltonians of quantum boxes, Aharanov-Bohm interferometers, anti-dots lattices and effects of imperfections, as well as disorder in the system. The extension to mount quantum billiards is natural. We also explain here how to adapt the recursive equations of Green's functions for the case of spin modes, apart from transverse modes, for the calculation of conductance in these mesoscopic systems. The assembled Hamiltonians allow to identify the matrix elements (depending on the different parameters of the system) associated with splitting or spin flipping, which gives a starting point to model specific systems of interest, manipulating certain parameters. In general, the approach of this work allows us to clearly see the relationship between the wave and matrix description of quantum mechanics. We discuss here also, the extension of the method for 1D and 3D systems, for the extension apart from the first neighbors and for the inclusion of other types of interaction. The way we approach the method, has the objective of showing how specifically the site and hopping energies change in the presence of new interactions. This is very important in the case of spin interactions, because by looking at the matrix elements (site or hopping) we can directly identify the conditions that can lead to splitting, flipping or a mixture of these effects. Which is essential for the design of devices based on spintronics. Finally, we discuss spin-conductance modulation (Rashba spin precession) for the states of an open quantum dot (resonant states). Unlike the case of a quantum wire, the spin-flipping observed in the conductance is not perfectly sinusoidal, there is an envelope that modulates the sinusoidal component, which depends on the discrete-continuous coupling of the resonant states.

Isolation and Characterization of NpCI, a New Metallocarboxypeptidase Inhibitor from the Marine Snail Nerita peloronta with Anti-Plasmodium falciparum Activity.

Metallocarboxypeptidases are zinc-dependent peptide-hydrolysing enzymes involved in several important physiological and pathological processes. They have been a target of growing interest in the search for natural or synthetic compound binders with biomedical and drug discovery purposes, i.e., with potential as antimicrobials or antiparasitics. Given that marine resources are an extraordinary source of bioactive molecules, we screened marine invertebrates for new inhibitory compounds with such capabilities. In this work, we report the isolation and molecular and functional characterization of NpCI, a novel strong metallocarboxypeptidase inhibitor from the marine snail Nerita peloronta. NpCI was purified until homogeneity using a combination of affinity chromatography and RP-HPLC. It appeared as a 5921.557 Da protein with 53 residues and six disulphide-linked cysteines, displaying a high sequence similarity with NvCI, a carboxypeptidase inhibitor isolated from Nerita versicolor, a mollusc of the same genus. The purified inhibitor was determined to be a slow- and tight-binding inhibitor of bovine CPA (Ki = 1.1·× 10-8 mol/L) and porcine CPB (Ki = 8.15·× 10-8 mol/L) and was not able to inhibit proteases from other mechanistic classes. Importantly, this inhibitor showed antiplasmodial activity against Plasmodium falciparum in an in vitro culture (IC50 = 5.5 µmol/L), reducing parasitaemia mainly by inhibiting the later stages of the parasite's intraerythrocytic cycle whilst having no cytotoxic effects on human fibroblasts. Interestingly, initial attempts with other related proteinaceous carboxypeptidase inhibitors also displayed similar antiplasmodial effects. Coincidentally, in recent years, a metallocarboxypeptidase named PfNna1, which is expressed in the schizont phase during the late intraerythrocytic stage of the parasite's life cycle, has been described. Given that NpCI showed a specific parasiticidal effect on P. falciparum, eliciting pyknotic/dead parasites, our results suggest that this and related inhibitors could be promising starting agents or lead compounds for antimalarial drug discovery strategies.

A General Use QSAR-ARX Model to Predict the Corrosion Inhibition Efficiency of Drugs in Terms of Quantum Mechanical Descriptors and Experimental Comparison for Lidocaine.

A study of 250 commercial drugs to act as corrosion inhibitors on steel has been developed by applying the quantitative structure-activity relationship (QSAR) paradigm. Hard-soft acid-base (HSAB) descriptors were used to establish a mathematical model to predict the corrosion inhibition efficiency (IE%) of several commercial drugs on steel surfaces. These descriptors were calculated through third-order density-functional tight binding (DFTB) methods. The mathematical modeling was carried out through autoregressive with exogenous inputs (ARX) framework and tested by fivefold cross-validation. Another set of drugs was used as an external validation, obtaining SD, RMSE, and MSE, obtaining 6.76%, 3.89%, 7.03%, and 49.47%, respectively. With a predicted value of IE% = 87.51%, lidocaine was selected to perform a final comparison with experimental results. By the first time, this drug obtained a maximum IE%, determined experimentally by electrochemical impedance spectroscopy measurements at 100 ppm concentration, of about 92.5%, which stands within limits of 1 SD from the predicted ARX model value. From the qualitative perspective, several potential trends have emerged from the estimated values. Among them, macrolides, alkaloids from Rauwolfia species, cephalosporin, and rifamycin antibiotics are expected to exhibit high IE% on steel surfaces. Additionally, IE% increases as the energy of HOMO decreases. The highest efficiency is obtained in case of the molecules with the highest ω and ΔN values. The most efficient drugs are found with pKa ranging from 1.70 to 9.46. The drugs recurrently exhibit aromatic rings, carbonyl, and hydroxyl groups with the highest IE% values.

Stability conditions of armchair graphene nanoribbon bipolarons.

Graphene nanoribbons are 2D hexagonal lattices with semiconducting band gaps. Below a critical electric field strength, the charge transport in these materials is governed by the quasiparticle mechanism. The quasiparticles involved in the process, known as polarons and bipolarons, are self-interacting states between the system charges and local lattice distortions. To deeply understand the charge transport mechanism in graphene nanoribbons, the study of the stability conditions for quasiparticles in these materials is crucial and may guide new investigations to improve the efficiency for a next generation of graphene-based optoelectronic devices. Here, we use a two-dimensional version of the Su-Schrieffer-Heeger model to investigate the stability of bipolarons in armchair graphene nanoribbons (AGNRs). Our findings show how bipolaron stability is dependent on the strength of the electron-phonon interactions. Moreover, the results show that bipolarons are dynamically stable in AGNRs for electric field strengths lower than 3.0 mV/Å. Remarkably, the system's binding energy for a lattice containing a bipolaron is smaller than the formation energy of two isolated polarons, which suggests that bipolarons can be natural quasiparticle solutions in AGNRs. Graphical Abstract Charge localization of bipolarons in armchair garphene nanoribbons.

Asymmetric synthesis and evaluation of epoxy-α-acyloxycarboxamides as selective inhibitors of cathepsin L.

Cathepsin L plays important roles in physiological processes as well as in the development of many pathologies. Recently the attentions were turned to its association with tumor progress what makes essential the development of more potent and selective inhibitors. In this work, epoxipeptidomimetics were investigated as new cathepsin inhibitors. This class of compounds is straightforward obtained by using a green one-pot asymmetric epoxidation/Passerini 3-MCR. A small library of 17 compounds was evaluated against cathepsin L, and among them LSPN423 showed to be the most potent. Investigations of the mechanism suggested a tight binding uncompetitive inhibition.

Identification of Tight-Binding Plasmepsin II and Falcipain 2 Inhibitors in Aqueous Extracts of Marine Invertebrates by the Combination of Enzymatic and Interaction-Based Assays.

Natural products from marine origin constitute a very promising and underexplored source of interesting compounds for modern biotechnological and pharmaceutical industries. However, their evaluation is quite challenging and requires specifically designed assays to reliably identify the compounds of interest in a highly heterogeneous and interfering context. In the present study, we describe a general strategy for the confident identification of tight-binding protease inhibitors in the aqueous extracts of 62 Cuban marine invertebrates, using Plasmodium falciparum hemoglobinases Plasmepsin II and Falcipain 2 as model enzymes. To this end, we first developed a screening strategy that combined enzymatic with interaction-based assays and then validated screening conditions using five reference extracts. Interferences were evaluated and minimized. The results from the massive screening of such extracts, the validation of several hits by a variety of interaction-based assays and the purification and functional characterization of PhPI, a multifunctional and reversible tight-binding inhibitor for Plasmepsin II and Falcipain 2 from the gorgonian Plexaura homomalla, are presented.

Electron-Lattice Coupling in Armchair Graphene Nanoribbons.

We report the effects of electron-lattice coupling on the charge density distribution study of armchair graphene nanoribbons (GNRs). Here, we perform a theoretical investigation explaining the unexpected electronic density states observed experimentally. By means of a tight-binding approach with electron-lattice coupling, we obtained the same characteristic pattern of charge density along the C-C bonds suggested by both scanning tunneling and transmission electron microscopic measurements. Our results suggest electronic localized states whose sizes are dependent on the GNR width. We also show that our model rescues the quasi-particle charge-transport mechanism in GNRs. The remarkable agreement with experimental evidence allows us to conclude that our model could be, in many aspects, a fundamental tool when it comes to the phenomenological understanding of the charge behavior in this kind of system.