João P. Prates Ramalho

Accounting for van der Waals interactions between adsorbates and surfaces in density functional theory based calculations: selected examples

This article reviews the different density functional theory (DFT) methods available in the literature for dealing with dispersion interactions and recent applications of DFT approaches including van der Waals corrections in the study of the interaction of atoms and molecules with several different surfaces. Focus is given to the interaction of atoms and molecules with metal, metal oxide and graphite surfaces or more complex systems. It will be shown that DFT approaches including van der Waals corrections present significant advances over standard exchange–correlation functionals for treating systems dominated by weak interactions.

Effect of Amphipathic HIV Fusion Inhibitor Peptides on POPC and POPC/Cholesterol Membrane Properties: A Molecular Simulation Study

T-20 and T-1249 fusion inhibitor peptides were shown to interact with 1-palmitoyl-2-oleyl-phosphatidylcholine (POPC) (liquid disordered, ld) and POPC/cholesterol (1:1) (POPC/Chol) (liquid ordered, lo) bilayers, and they do so to different extents. Although they both possess a tryptophan-rich domain (TRD), T-20 lacks a pocket binding domain (PBD), which is present in T-1249. It has been postulated that the PBD domain enhances FI interaction with HIV gp41 protein and with model membranes. Interaction of these fusion inhibitor peptides with both the cell membrane and the viral envelope membrane is important for function, i.e., inhibition of the fusion process. We address this problem with a molecular dynamics approach focusing on lipid properties, trying to ascertain the consequences and the differences in the interaction of T-20 and T-1249 with ld and lo model membranes. T-20 and T-1249 interactions with model membranes are shown to have measurable and different effects on bilayer structural and dynamical parameters. T-1249’s adsorption to the membrane surface has generally a stronger influence in the measured parameters. The presence of both binding domains in T-1249 appears to be paramount to its stronger interaction, and is shown to have a definite importance in membrane properties upon peptide adsorption.

Adenine as an organocatalyst for the ring-opening polymerization of lactide: scope, mechanism and access to adenine-functionalized polylactide

Nucleobase-functionalized polymers are widely used in the fields of supramolecular chemistry and self-assembly, and their development for biomedical applications is also an area of interest. They are usually synthesized by tedious multistep procedures. In this study, we assess adenine as an organoinitiator/organocatalyst for the ring-opening polymerization of lactide. L-Lactide can be quantitatively polymerized in the presence of adenine. Reaction conditions involving short reaction times and relatively low temperatures enable the access to adenine end-capped polylactide in a simple one-step procedure, in bulk, without additional catalyst. DFT calculations show that the polymerization occurs via hydrogen bond catalysis. The mechanism involves (i) a hydrogen bond between the NH9 of adenine and the carbonyl moiety of lactide, leading to an electron deficient carbon atom, and (ii) a second hydrogen bond between the N3 of adenine and the NH2 of a second adenine molecule, followed by a nucleophilic attack of the latter activated amine on the former electron deficient carbon on the monomer. For longer reaction times and higher temperatures, macrocyclic species are formed, and a mechanism involving the imidazole ring of adenine is proposed based on literature studies. Depending on the reaction conditions, adenine can thus be considered as an organoinitiator or an organocatalyst for the ring-opening polymerization of lactide.

A magnetic controllable tool for the selective enrichment of dimethoate from olive oil samples: A responsive molecular imprinting-based approach

Aiming to develop a straightforward magnetic-based sample preparation methodology for the selective extraction of dimethoate from olive oil, the synthesis of dimethoate-imprinted polymer on the surface of modified magnetic nanoparticles has been attempted. Molecular recognition assays have proven their suitability for the selective pre-concentration of dimethoate. Mechanistic basis for template selective recognition has been explored using a quantum chemical approach, providing new insights about the mechanisms underlying template recognition. Thus, a magnetic molecularly imprinted solid-phase extraction method was developed allowing the extraction of dimethoate from spiked olive oil samples, at levels similar to the maximum residue limits imposed by legislation, followed by the quantification of their levels by high-performance liquid chromatography with diode-array detection. Recoveries of 94.55% were obtained, with relative standard deviations lower than 0.53% (n = 3). The developed sample preparation technique enables a selective pre-concentration/enrichment of dimethoate from olive oil matrix with minimum handling and less solvent consumption.

Conformational Preference and Spectroscopical Characteristics of the Active Pharmaceutical Ingredient Levetiracetam

The analysis of the possible conformers and the conformational change between solid and liquid states of a particular drug molecule are mandatory not only for describing reliably its spectroscopical properties but also for understanding the interaction with the receptor and its mechanism of action. Therefore, here we investigated the free-energy conformational landscape of levetiracetam (LEV) in gas phase as well as in water and ethanol, aiming to describe the 3-dimensional structure and energetic stability of its conformers. Twenty-two unique conformers were identified, and their energetic stability was determined at density functional theory B3LYP/6-31+G(2d,2p) level of theory. The 6 most stable monomers in water, within a relative free-energy window of 0.71 kcal mol-1 and clearly separated in energy from the remaining subset of 16 conformers, as well as the 3 most stable dimers were then used to compute the Boltzmann populations-averaged UV-Vis and NMR spectra of LEV. The conformational landscape in solution is distinctly different from that corresponding to gas phase, particularly due to the relative orientations of the butanamide group. Aiming to clarify the stability of the possible dimers of LEV, we also investigated computationally the structure of a set of 11 nonhydrated and hydrated homochiral hydrogen-bonded LEV dimers.

A photoswitchable “host-guest” approach for the selective enrichment of dimethoate from olive oil

This work describes the development of a new selective photocontrollable molecularly imprinted-based sorbent for the selective enrichment/pre-concentration of dimethoate from spiked olive oil samples. To achieve this goal an improved molecularly imprinted strategy relying on the embedding of a functional monomer containing an azobenzene chromophore as light-responsive element, on the crosslinked tridimensional molecular imprinted network, has been assessed. To address the mechanisms underlying template recognition and uptake/release of the analyte from the functional imprinted material, computational studies using a quantum chemical approach, have been explored. This new functional sorbent provides a straightforward controllable uptake/release of the target template using light as the stimuli tool, which is highly advantageous due to light manipulation characteristics, such as superior clean, precision and remote controllable properties. In general, this work will contribute to the implementation of a photoswitchable analytical methodology that proves to be suitable for the selective isolation and further quantification of dimethoate from olive oil matrices at levels similar to the maximum residues limits imposed by the legislation. The limits of detection, calculated based on 3σ, was 1.6 mgL-1 and the limit of quantification, based on 10σ, was 5.2 mgL-1. The implemented sample preparation shows high reproducibility and recoveries (93.3 ± 0.4%).