Interplay of thermochemistry and Structural Chemistry,the journal (volume 29, 2018, issues 3–4) and the discipline

The contents of issues 3 and 4 of Structural Chemistry from the calendar year 2018 are summarized in the present review. A brief thermochemical commentary and recommendations for future research have been added to the summary of each paper.

     

Determination of the Molar-Mass Averages of Random Poly(aspartate-co-lactide) Copolymers by Tuning the Ionic Strength of the Solvent

Water-soluble sodium poly(aspartate-co-lactide) (PALNa) copolymers with a molar ratio of aspartate-to-lactide units equal to 1:0.6, 1:1.0 and 1:1.5 were studied using NMR spectroscopy to determine the composition as well as SEC-MALS and static light-scattering measurements to determine the molar-mass characteristics of the copolymers. In the copolymer aqueous solutions, high-molar-mass species were detected, most probably due to the incomplete dissolution of the samples. The molar-mass averages determined in water with added simple electrolyte, i.e., NaCl, were much lower than the values determined in pure water. The concentration of the salt, which allows dissolution on a molecular level, and the separation predominantly according to a size-exclusion mechanism depend on the chemical composition of the PALNa copolymers. The optimal mobile phase for the PALNa-1/0.6 and the PALNa-1/1.0 copolymers was 0.1 M NaCl at pH 9, and for the PALNa-1/1.5 copolymer with a higher content of lactide units it was 0.05 M NaCl at pH 9. The molar-mass averages of the PALNa-1/1.0 copolymer, determined by SEC-MALS and static light-scattering measurements, were comparable.

     

Interplay of thermochemistry and Structural Chemistry, the journal (volume 23, 2012, issues 1–3) and the discipline

In the current review of the journal Structural Chemistry, the contents of the issues 1–3 for the calendar year 2012 are related to thermochemistry. A brief thermochemical commentary is added to the summary of each article.     

Bis­(tetra­methyl­ammonium) hexa­molyb­date hydrate, [(CH3)4N]2[Mo6O19]·H2O

The crystal and molecular structure of the title compound, (C₄H₁₂N)₂[Mo₆O₁₉]·H₂O, has been determined from X‐ray diffraction data. The poly­oxo­anion [Mo₆O₁₉]^2? is built up from six distorted MoO₆ octa­hedra sharing common edges and one common vertex at the central O atom, and has crystallographic m3m (O_h) symmetry. The cation has crystallographic 3m symmetry.     

Relationships between structure, retention and biological activity of some Schiff base ligands and their complexes

The lipophilicity of a series of Schiff base ligands and their complexes with nickel(II) and copper(II) has been determined by reversed-phase thin-layer chromatography using binary dioxane-water mobile phase. Chelate ligands were prepared by condensation of diamine and the corresponding beta-diketone. Copper(II) and nickel(II) complexes with chelate ligands containing ethane-1,2-diamine or propane-1,2-diamine as the amine part and pentane-2,4-dione and/or 1-phenylbutane-1,3-dione, pentane-2,4-dione and/or 1,1,1-trifluoropentane-2,4-dione, or 1,1,1-trifluoropentane-2,4-dione and/or 1-phenylbutane-1,3-dione as the beta-diketone part were synthesized. Some of investigated compounds were screened for their in vitro antifungal activity against Sacharomyces cerevisiae and antibacterial activity against Escherichia coli. Chromatographically obtained lipophilicity parameters were correlated both with calculated n-octanol-water partition coefficient C log P and antimicrobial activities. Satisfactory correlations were obtained. Chromatographic data proved to be reliable parameters for describing the lipophilic properties of the investigated compounds. Additionally, the principal components analysis was performed on the data chromatographically obtained. This statistical method was useful for distinguishing compounds and objective comparison of their lipophilicity parameters.     

Calculations of pH-dependent binding of proteins to biological membranes

Binding of proteins to membranes is often accompanied by titration of ionizable residues and is, therefore, dependent on pH. We present a theoretical treatment and computational approach for predicting absolute, pH-dependent membrane binding free energies. The standard free energy of binding, DeltaG, is defined as -RTln(P(b)/P(f)), where P(b) and P(f) are the amounts of bound and free protein. The apparent pK(a) of binding is the pH value at which P(b) and P(f) are equal. Proteins bind to the membrane in the pH range where DeltaG is negative. The components of the binding free energy are (a) the free energy cost of ionization state changes (DeltaG(ion)), (b) the effective energy of transfer from solvent to the membrane surface, (c) the translational/rotational entropy cost of binding, and (d) an ideal entropy term that depends on the relative volume of the bound and free state and therefore depends on lipid concentration. Calculation of the first term requires determination of pK(a) values in solvent and on the membrane surface. All energies required by the method are obtained from molecular dynamics trajectories on an implicit membrane (IMM1-GC). The method is tested on pentalysine and the helical peptide VEEKS, derived from the membrane-binding domain of phosphocholine cytidylyltransferase. The agreement between the measured and the calculated free energies of binding of pentalysine is good. The extent of membrane binding of VEEKS is, however, underestimated compared to experiment. Calculations of the interaction energy between two VEEKS helices on the membrane suggest that the discrepancy is mainly due to the neglect of protein-protein interactions on the membrane surface.     

Aptamer-based detection of thrombin by acoustic method using DNA tetrahedrons as immobilisation platform

The thickness shear mode acoustic method was used to study the binding of thrombin to DNA aptamers immobilised on the gold surface covered by DNA tetrahedrons. The binding of thrombin to conventional aptamers sensitive to fibrinogen (FBT) and heparin (HPT) exosites as well as to HPT in a loop configuration (HPTloop) made it possible to determine the constant of dissociation (K_D) and the limit of detection (LOD). The sensing system composed of a HPTloop was characterised by K_D = (66.7 ± 22.7) nM, which was almost twice as low as that of FBT and HPT. For this biosensor, a lower LOD of 5.2 nM compared with 17 nM for conventional HPT aptamers was also obtained. Less sensitive sensors based on FBT aptamers revealed an LOD of 30 nM which is in agreement with the lower affinity of these aptamers to thrombin in comparison with that of HPT. The surface concentration of DNA tetrahedrons was determined by the electrochemical method using [Ru(NH₃)₆]³⁺ as a redox probe. These experiments confirmed that the “step by step” method of forming the sensing layer, consisting first in chemisorption of DNA tetrahedrons onto a gold surface and then in hybridisation of the aptamer-supporting part with complementary oligos at the top of the tetrahedron, is preferable. In addition, atomic force microscopy was applied to analyse the topography of the gold layers modified stepwise by DNA tetrahedrons, DNA aptamers and thrombin. The height profiles of the layers were in reasonable agreement with the dimensions of the adsorbed molecules. The results indicate that DNA tetrahedrons represent an efficient platform for immobilisation of aptamers.