Tiago E. de Oliveira

Effects of stereochemistry and copolymerization on the LCST of PNIPAm

Poly(N-isopropylacrylamide) (PNIPAm) is a smart polymer that presents a lower critical transition temperature (LCST) of 305 K. Interestingly, this transition point falls within the range of the human body temperature, making PNIPAm a highly suitable candidate for bio-medical applications. However, it is sometimes desirable to have a rather flexible tuning of the LCST of these polymers to further increase their range of applications. In this work, we use all-atom molecular dynamics simulations to study the LCST of PNIPAm-based (co-)polymers. We study different molecular architectures where the polymer sequences are tuned either by modifying its stereochemistry or by the co-polymerization of PNIPAm with acrylamide (Am) units. Our analysis connects global polymer conformations with the microscopic intermolecular interactions. These findings suggest that the collapse of a PNIPAm chain upon heating is dependent on the hydration structure around the monomers, which is strongly dependent on the tacticity and the presence of more hydrophilic acrylamide monomers. Our results are found to be in good agreement with the existing experimental data.

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C-IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within C-IBI compared to IBI. To validate the robustness, we apply C-IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Stability of a Split Streptomycin Binding Aptamer

Here we investigated the stability of an aptamer, which is formed by two RNA strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystal structure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycin binding with a free energy of ΔGbind° = −101.7 kJ mol–1. Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (koff-COMPLEX = 0.22 ± 0.16 s–1) for the aptamer–streptomycin complex compared to the aptamer having an empty binding pocket (koff-APTAMER = 0.49 ± 0.11 s–1). This decrease in the natural off-rate corresponds to a decrease in the Gibbs free energy of ΔΔGsheer ≈ −3.4 kJ mol–1. The simulated binding pattern and the experimental results led to the conclusion that...

Exploiting iminoquinone free radical production for thiol based drugs determination in pharmaceutical formulations

A spectrophotometric flow analysis procedure to determine Captopril (CPT) and N-acetyl-L-cysteine (NAC) in pharmaceutical formulations was developed based on the reaction with iminoquinone radical produced from the N,N-dimethyl-p-phenilenediamene (DMPD) oxidation in acid medium. The reagents addition order was evaluated and analytical parameters were optimized. The linear concentrations ranges were 2.5-90 and 5.0-50 mg L-1 for CPT and NAC, respectively. Limits of detection (3σ) were calculated at 0.22 and 1.8 mg L-1 and the relative standard deviation (N = 10) were lower than 1.0 and 2.1% for CPT and NAC, respectively. The procedure was employed for CPT and NAC determination in diverse pharmaceutical formulations and by applying paired t-test the results were in agreement with those obtained by reference methods for 95% confidence level.

Polyacrylamide “revisited”: UCST-type reversible thermoresponsive properties in aqueous alcoholic solutions

Combining experiments and all-atom molecular dynamics simulations, we study the conformational behavior of polyacrylamide (PAM) in aqueous alcohol mixtures over a wide range of temperatures. This study shows that even when the microscopic interaction is dictated by hydrogen bonding, unlike its counterparts that present a lower critical solution temperature (LCST), PAM shows a counterintuitive tunable upper critical solution temperature (UCST)-type phase transition in water/alcohol mixtures that was not reported before. The phase transition temperature was found to be tunable between 4 and 60 °C by the type and concentration of alcohol in the mixture as well as by the solution concentration and molecular weight of the polymer. In addition, molecular dynamics simulations confirmed a UCST-like behaviour of the PAM in aqueous alcoholic solutions. Additionally, it was observed that the PAM is more swollen in pure alcohol solutions than in 80% alcoholic solutions due to θ-like behaviour. Additionally, in the globular state, the size of the aggregates was found to increase with increasing solvent hydrophobicity and polymer concentration of the solutions. Above its phase transition temperature, PAM might be present as individual polymer chains in the coil state (≤10 nm). As PAM is a widespread polymer in many biomedical applications (gel electrophoresis, etc.), this finding could be of high relevance for many more practical applications in high performance pharmaceuticals and/or sensors.