Publications

Abstract Recent density-functional theory (DFT) calculations raised the possibility that diamond could be degenerate with graphite at very low temperatures. Through high-accuracy calorimetric experiments closing gaps in available data, we reinvestigate the relative thermodynamic stability of diamond and graphite. For T400 K, graphite is always more stable than diamond at ambient pressure. At low temperatures, the stability is enthalpically driven, and entropy terms add to the stability at higher temperatures. We also carried out DFT calculations: B86bPBE-25X-XDM//B86bPBE-XDM and PBE0-XDM//PBE-XDM results overlap with the experimental -T Delta S results and bracket the experimental values of Delta H and Delta G, displaced by only about 2x the experimental uncertainty. Revised values of the standard thermodynamic functions for diamond are Delta H-f(o)=-2150 +/- 150 J mol(-1), Delta S-f(o)=3.44 +/- 0.03 J K-1 mol(-1) and Delta(f)G(o)=-3170 +/- 150 J mol(-1).

Abstract Hypothesis: Amphiphilic molecules spontaneously adsorb to fluid polar-nonpolar interfaces. The time scale of such adsorption depends on the molecular size and structure of the solute. This process should be accompanied by a power heat exchange that could be detected by commercial isothermal calorimeters. Experiments: Air is injected in the bulk of different aqueous solutions contained in the sample cell of an isothermal titration calorimeter. The formation of the resulting bubbles leads to a liquid/air interface to which the solute molecules spontaneously adsorb. Continuous injection experiments to produce multiple bubbles as well as experiments with static bubbles stand from the capillary tip, aiming to observe slow adsorption processes, were performed. Findings: The power associated with the formation, growth and release of air bubbles in different liquids was measured. Different independent contributions that can be associated to the pressure change in the gas phase, the evaporation-condensation of the solvent, the increase of interfacial area, the change in the heat capacity of the sample cell content, and the release of the bubble were observed. The periodic pattern produced by the continuous injection of air at a constant rate is used to determine the surface tension of different liquids, including solutions of different molecules and (bio)macromolecules.

Abstract Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus–minus the standard deviation. However, in general, the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change ΔGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and ΔGb are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and ΔGb values is to consistently report 95% confidence intervals, in line with other authors’ suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC. © 2021, European Biophysical Societies' Association.

Abstract Antimicrobial peptides are viewed as a promising alternative to conventional antibiotics, as their activity through membrane targeting makes them less prone to resistance development. Among them, antimicrobial D,L-alpha-cyclic peptides (CPs) have been proposed as an alternative, specially due to their cyclic nature and to the presence of D-alpha-amino acids that increases their resistance to proteases. In present work, second generation D,L-alpha-cyclic peptides with proven antimicrobial activity are shown to form complex macromolecular assemblies in the presence of membranes. We addressed the CPs:membrane interactions through a combination of experimental techniques (DSC and ATR-FTIR) with coarse-grained molecular dynamics (CG-MD) simulations, aiming at understanding their interactions, macromolecular assemblies and eventually unveil their mechanism of action. DSC shows that the interaction depends heavily on the negatively charge content of the membrane and on lipid/peptide ratio, suggesting different mechanisms for the different peptides and lipid systems. CG-MD proved that CPs can self-assemble at the lipid surface as nanotubes or micellar aggregates, depending on the peptide, in agreement with ATR-FTIR results. Finally, our results shed light into possible mechanisms of action of the peptides with pending hydrocarbon tail, namely membrane extensive segregation and/or membrane disintegration through the formation of disk-like lipid/peptide aggregates.

Abstract The thermodynamic properties and band gap energies were evaluated for six ortho- and peri-fused polycyclic aromatic hydrocarbons (PAHs): triphenylene; benzo[a]pyrene; benzo[e]pyrene; perylene; benzo[ghi]perylene; coronene. The standard molar enthalpies of formation in the crystalline state and the standard molar enthalpies of sublimation were measured by high precision combustion calorimetry and Knudsen effusion methodology, respectively. The combination of the molar enthalpies of formation in the crystalline state with the respective enthalpies of sublimation was used to evaluate the energetics of the progressive peri-fusion of the aromatic moieties from triphenylene to coronene aiming to investigate the hypothetical superaromaticity character of coronene. The linear trend of the enthalpy of formation in crystalline and gaseous phases in the series (from benzo[e]pyrene to coronene) is an irrefutable indication of a non-superaromaticity character of coronene. High accurate thermodynamic properties of sublimation (volatility, enthalpy, and entropy of sublimation) were derived by the measurement of vapor pressures as a function of temperature, using a Knudsen/quartz crystal effusion methodology. Furthermore, the p-electronic conjugation of these compounds was explored by evaluation of the optical band gaps along with this series of compounds. The morphology of perylene, benzo[ghi]perylene, and coronene thin films, deposited by physical vapor deposition onto transparent conductive oxide substrates (ITO and FTO), was used to analyze the nucleation and growth mechanisms. The morphologies observed were found to be related to the cohesive energy and entropy of the bulk.

Abstract Isothermal titration calorimetry (ITC) is currently widely used in many applied areas of research, spanning protein-ligand binding, metal-ligand interactions, DNA/DNA or protein/DNA interactions, partition to membranes, and polymer surfactant interactions, to mention just a few. This is due to the availability of commercial instruments, and thus the production and spread of an accepted and widely followed SOP is felt by most users, in an effort to produce results that are scientifically correct and comparable. Therefore, within the efforts of Working Group 4 of the ARBRE-MOBIEU COST Action (CA15126), this ITC SOP was generated, alongside SOPs for several other biophysical techniques. Here, we discuss the factors that are fundamental for good experimental design and that need to be carefully considered, as well as machine calibration, in particular chemical calibration, linked to another outcome of Working Group 4 on ITC benchmarking, to be also published in this Special Issue.

Abstract Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) has been used for the structural characterization of peptides and their interactions with membranes. Antimicrobial peptides (AMPs) are part of our immune system and widely studied in recent years. Many linear AMPs have been studied, but their cyclization was shown to enhance the peptide's activity. We have used cyclic peptides (CPs) of an even number of alternating D- and L-alpha-amino acids, an emerging class of potential AMPs. These CPs can adopt a flat-ring shape that can stack into an antiparallel structure, forming intermolecular hydrogen bonds between different units, creating a tubular beta-sheet structure - self-assembled cyclic peptide nanotubes (SCPNs). To get the structural information on peptides in solution and/or in contact with membranes, Amide I and II absorptions are used as they can adopt frequency and shape band characteristics that are influenced by the strength of existing hydrogen bonds between the amide CO and NH involved in secondary structures such as helix, beta-sheet or aperiodic structures. The combination of polarized lens with ATR-FTIR provides an important tool to study the orientation of peptides when interacting with lipid membranes as the information can be derived on the position relative to the membrane normal. This work shows how ATR-FTIR used together with polarized light was successfully used to characterize structurally two CPs (RSKSWPgKQ and RSKSWX(C10)KQ) in solution and upon interaction with negatively charged membranes of DMPG, assessing the formation and orientation of tubular structures (SCPNs) that were shown to be enhanced by the presence of the lipid membrane.

Abstract A small-scale ITC benchmarking study was performed involving 9 biophysics laboratories/facilities, to evaluate inter-laboratory and intra-laboratory basal levels of uncertainty. Our prime goal was to assess a number of important factors that can influence both the data gathered by this technique and the thermodynamic parameter values derived therefrom. In its first part, the study involved 5 laboratories and 13 different instruments, working with centrally prepared samples and the same experimental protocol. The second part involved 4 additional laboratories and 6 more instruments, where the users prepared their own samples according to provided instructions and did the experiments following the same protocol as in the first part. The study design comprised: (1) selecting a minimal set of laboratories; (2) providing very stable samples; (3) providing samples not requiring preparation or manipulation; and (4) providing a well-defined and detailed experimental protocol. Thus, we were able to assess: (i) the variability due to instrument and data analysis performed by each user on centrally prepared samples; (ii) the comparability of data retrieved when using 4 different software packages to analyze the same data, besides the data analysis carried out by the different users on their own experimental results; and (iii) the variability due to local sample preparation (second part of the study). Individual values, as well as averages and standard deviations for the binding parameters for EDTA-cation interaction, were used as metrics for comparing the equilibrium association constant (logK), enthalpy of interaction (Delta H), and the so-called "stoichiometry" (n), a concentration-correction factor.