Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.

Effect of Charge and Phosphine Ligands on the Electronic Structure of the Au8 Cluster

In this work, we use density functional theory calculations with a hybrid exchange-correlation functional and effective core pseudopotentials to determine the geometry of bare and phosphine-protected Au₈ nanoclusters and characterize their electronic structure. Au₈ clusters were bonded to four and eight PH₃ ligands in order to evaluate the effect of ligand concentration on the electronic structure, while different positional configurations were also tried for four ligands attached to the cluster. We show that the neutral clusters become more nucleophilic as the ligands bind to the clusters at stable sites. The ground-state planar configuration of Au₈ is maintained depending on the concentration and position of ligands. The effect of ionizing to the +2 charge state results in disruption of planar geometry in some cases because of inoccupation of a molecular orbital with the Au-Au bonding character. Natural bond order charge analyses showed that Au atoms oxidize upon ionization, instead of phosphine. The net positive charge makes the clusters more electrophilic with a capacity to absorb electrons from nucleophiles depending on the concentration and position of ligands and on the concentration of low-coordinated gold atoms. Besides, ionization energies and electron affinities were calculated through different mechanisms, finding that both variables are much higher for charged systems and change inversely with the concentration of ligands.

Direct evidence of atomic-scale structural fluctuations in catalyst nanoparticles

Rational catalyst design requires an atomic scale mechanistic understanding of the chemical pathways involved in the catalytic process. A heterogeneous catalyst typically works by adsorbing reactants onto its surface, where the energies for specific bonds to dissociate and/or combine with other species (to form desired intermediate or final products) are lower. Here, using the catalytic growth of single-walled carbon nanotubes (SWCNTs) as a prototype reaction, we show that the chemical pathway may in-fact involve the entire catalyst particle, and can proceed via the fluctuations in the formation and decomposition of metastable phases in the particle interior. We record in situ and at atomic resolution, the dynamic phase transformations occurring in a Cobalt catalyst nanoparticle during SWCNT growth, using a state-of-the-art environmental transmission electron microscope (ETEM). The fluctuations in catalyst carbon content are quantified by the automated, atomic-scale structural analysis of the time-resolved ETEM images and correlated with the SWCNT growth rate. We find the fluctuations in the carbon concentration in the catalyst nanoparticle and the fluctuations in nanotube growth rates to be of complementary character. These findings are successfully explained by reactive molecular dynamics (RMD) simulations that track the spatial and temporal evolution of the distribution of carbon atoms within and on the surface of the catalyst particle. We anticipate that our approach combining real-time, atomic-resolution image analysis and molecular dynamics simulations will facilitate catalyst design, improving reaction efficiencies and selectivity towards the growth of desired structure.

Nanocatalyst shape and composition during nucleation of single-walled carbon nanotubes

The dynamic evolution of nanocatalyst particle shape and carbon composition during the initial stages of single-walled carbon nanotube growth by chemical vapor deposition synthesis is investigated. Classical reactive and ab initio molecular dynamics simulations are used, along with environmental transmission electron microscope video imaging analyses. A clear migration of carbon is detected from the nanocatalyst/substrate interface, leading to a carbon gradient showing enrichment of the nanocatalyst layers in the immediate vicinity of the contact layer. However, as the metal nanocatalyst particle becomes saturated with carbon, a dynamic equilibrium is established, with carbon precipitating on the surface and nucleating a carbon cap that is the precursor of nanotube growth. A carbon composition profile decreasing towards the nanoparticle top is clearly revealed by the computational and experimental results that show a negligible amount of carbon in the nanoparticle region in contact with the nucleating cap. The carbon composition profile inside the nanoparticle is accompanied by a well-defined shape evolution of the nanocatalyst driven by the various opposing forces acting upon it both from the substrate and from the nascent carbon nanostructure. This new understanding suggests that tuning the nanoparticle/substrate interaction would provide unique ways of controlling the nanotube synthesis.

Engineering preferential adsorption of single-walled carbon nanotubes on functionalized ST-cut surfaces of quartz

Horizontal alignment during synthesis of single-walled carbon nanotubes has been found experimentally along certain directions of well-defined quartz surfaces. The reasons for such alignment are here examined using first-principles computational analysis, as a function of structure and chemistry of the specific exposed facet, presence and location of OH and H functional groups, and degree of hydration of the surface. It is found that selective functionalization of low-coordinated surface sites may cause exposure of low-coordinated Si atoms that bond strongly to nanotube walls. On the other hand, saturation of low-coordinated oxygen also favors carbon nanotube adhesion to the substrate. As found previously on bare silica surfaces, a chirality preference is confirmed on functionalized surfaces toward zigzag over armchair nanotubes. Magnetization effects on the surface originated by the presence of adsorbed functional groups are found to enhance adsorption of arm-chair nanotubes compared to that on clean surfaces. On the basis of the findings, it is suggested that surfaces may be engineered to favor horizontal adsorption of specific chiralities along preferential directions.

Carbon nanotubes: engineering biomedical applications

Carbon nanotubes (CNTs) are cylinder-shaped allotropic forms of carbon, most widely produced under chemical vapor deposition. They possess astounding chemical, electronic, mechanical, and optical properties. Being among the most promising materials in nanotechnology, they are also likely to revolutionize medicine. Among other biomedical applications, after proper functionalization carbon nanotubes can be transformed into sophisticated biosensing and biocompatible drug-delivery systems, for specific targeting and elimination of tumor cells. This chapter provides an introduction to the chemical and electronic structure and properties of single-walled carbon nanotubes, followed by a description of the main synthesis and post-synthesis methods. These sections allow the reader to become familiar with the specific characteristics of these materials and the manner in which these properties may be dependent on the specific synthesis and post-synthesis processes. The chapter ends with a review of the current biomedical applications of carbon nanotubes, highlighting successes and challenges.