Jaana Tammiku-Taul

Computational Study of Cesium Cation Interactions with Neutral and Anionic Compounds Related to Soil Organic Matter

The gas-phase cesium cation affinities (CsCAs) and basicities (CsCBs) for 56 simple neutral compounds (mostly aromatic molecules) and 41 anions (carboxylates and phenolates) were calculated using density functional theory (DFT), in the context of the interaction of Cs(+) with soil organic matter (SOM). The B3LYP/def2-TZVP method gives in general CsCAs and CsCBs in a good agreement with experimental data. The strong deviations in case of NO(3)(-) and CsSO(4)(-) anions need further experimental investigations as the high-level CCSD(T) calculations support B3LYP results. Different cesium cation complexation patterns between Cs(+) and the neutral and anionic systems are discussed. As expected, the strongest CsCAs are observed for anions. The corresponding quantities are approximately by 4-5 times higher than for the neutral counterparts, being in the range 90-118 kcal/mol. The weakest cesium cation bonding is observed in the case of unsubstituted aromatic systems (11-15 kcal/mol).

NMR and DFT Study of the Copper(I)-Catalyzed Cycloaddition Reaction: H/D Scrambling of Alkynes and Variable Reaction Order of the Catalyst

Mechanism of an efficient and easily applicable catalytic system for the copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) reaction, consisting of phosphane‐ligated CuI carboxylates and apolar/aprotic solvent was investigated by means of 1H NMR reaction monitoring techniques, isotope exchange studies, and DFT calculations (at the M06L/6‐311++G(d,p)//B97D/cc‐pVDZ (SDD) level of theory). Kinetic analysis indicates 1st order kinetics with respect to [Azide] and nonlinear positive order in [Cu]. H/D scrambling between alkynes reveals a quickly reached equilibrium existing between CuI–carboxylates and CuI–acetylides and that proton transfer processes are mediated by acetate/acetic acid system. According to the computational results, the Cu–triazolide forms a dinuclear structure that equalizes the copper atoms in the catalytic complex.

Computational study on the reactivity of tetrazines toward organometallic reagents.

The possible reaction pathways between methyllithium and disubstituted 1,2,4,5-tetrazines (bearing methyl, methylthio, phenyl, and 3,5-dimethylpyrazolyl groups) were investigated by means of the density functional theory B3LYP/6-31G* method. Solvation was modeled using the supermolecule approach, adding one tetrahydrofuran molecule to the complexes. Comparison of the calculated energies and structures for the alternate azaphilic and nucleophilic addition pathways showed that the azaphilic addition is kinetically favored over nucleophilic addition, while thermodynamically the nucleophilic addition is usually preferred. The coordination of the tetrazine molecule with methyllithium was found to play a crucial role in the process. These findings provide the first rationale for the experimentally observed unique reactivity of tetrazines toward polar organometallic reagents, suggesting the presence of a kinetically controlled process.

A study of the cesium cation bonding to carboxylate anions by the kinetic method and quantum chemical calculations.

Collision-induced dissociation (CID) of the Cs(+) heterodimer adducts of the nitrate anion (NO(3)(-)) and a variety of substituted benzoates (XBenz(-)) [(XBenz(-))(Cs(+))(NO(3)(-))](-) produces essentially nitrate and benzoate ions. A plot of the natural logarithm of their intensity ratio, ln[I (NO(3)(-))/I(XBenz(-))], versus the calculated cesium cation affinity (DFT B3LYP) of the substituted benzoate ions (equivalent to the enthalpy of heterolytic dissociation of the salt) is reasonably linear. This suggests that the kinetic method can be used as a source of data on the intrinsic interaction between the anionic and the cationic moieties in a salt.

Interaction of the Cesium Cation with Mono-, Di-, and Tricarboxylic Acids in the Gas Phase. A Cs+ Affinity Scale for Cesium Carboxylates Ion Pairs

Humic substances (HS), including humic and fulvic acids, play a significant role in the fate of metals in soils. The interaction of metal cations with HS occurs predominantly through the ionized (anionic) acidic functions. In the context of the effect of HS on transport of radioactive cesium isotopes in soils, a study of the interaction between the cesium cation and model carboxylic acids was undertaken. Structure and energetics of the adducts formed between Cs+ and cesium carboxylate salts [Cs+RCOO−] were studied by the kinetic method and density functional theory (DFT). Clusters generated by electrospray ionization mass spectrometry from mixtures of a cesium salt (nitrate, iodide, trifluoroacetate) and carboxylic acids were quantitatively studied by CID. By combining the results of the kinetic method and the energetic data from DFT calculations, a scale of cesium cation affinity, CsCA, was built for 33 cesium carboxylates representing the first scale of cation affinity of molecular salts. The structural effects on the CsCA values are discussed.

INDOLE-LIKE TRK RECEPTOR ANTAGONISTS

The virtual screening for new scaffolds for TrkA receptor antagonists resulted in potential low molecular weight drug candidates for the treatment of neuropathic pain and cancer. In particular, the compound (Z)-3-((5-methoxy-1H-indol-3-yl)methylene)-2-oxindole and its derivatives were assessed for their inhibitory activity against Trk receptors. The IC50 values were computationally predicted in combination of molecular and fragment-based QSAR. Thereafter, based on the structure-activity relationships (SAR), a series of new compounds were designed and synthesized. Among the final selection of 13 compounds, (Z)-3-((5-methoxy-1-methyl-1H-indol-3-yl)methylene)-N-methyl-2-oxindole-5-sulfonamide showed the best TrkA inhibitory activity using both biochemical and cellular assays and (Z)-3-((5-methoxy-1-methyl-1H-indol-3-yl)methylene)-2-oxindole-5-sulfonamide was the most potent inhibitor of TrkB and TrkC.

Small-Molecule Ligands as Potential GDNF Family Receptor Agonists

To find out potential GDNF family receptor α1 (GFRα1) agonists, small molecules were built up by molecular fragments according to the structure-based drug design approach. Molecular docking was used to identify their binding modes to the biological target GFRα1 in GDNF-binding pocket. Thereafter, commercially available compounds based on the best predicted structures were searched from ZINC and MolPort databases (similarity ≥ 80%). Five compounds from the ZINC library were tested in phosphorylation and luciferase assays to study their ability to activate GFRα1–RET. A bidental compound with two carboxyl groups showed the highest activity in molecular modeling and biological studies. However, the relative position of these groups was important. The meta-substituted structure otherwise identical to the most active compound 2-[4-(5-carboxy-1H-1,3-benzodiazol-2-yl)phenyl]-1H-1,3-benzodiazole-5-carboxylic acid was inactive. A weaker activity was detected for a compound with a single carboxyl group, that is, 4-(1,3-benzoxazol-2-yl)benzoic acid. The substitution of the carboxyl group by the amino or acetamido group also led to the loss of the activity.

Molecular Dynamics Simulations of the Interactions between Glial Cell Line-Derived Neurotrophic Factor Family Receptor GFRα1 and Small-Molecule Ligands

The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) support the survival and functioning of various neuronal populations. Thus, they could be attractive therapeutic agents against a multitude of neurodegenerative diseases caused by progressive death of GFLs responsive neurons. Small-molecule ligands BT13 and BT18 show an effect on GDNF family receptor GFRα1 and RET receptor tyrosine kinase RetA function. Thus, their potential binding sites and interactions were explored in the GDNF–GFRα1–RetA complex using molecular docking calculations as well as molecular dynamics (MD) simulations. Three possible regions were examined: the interface between GDNF and GFRα1 (region A), the RetA interface with GFRα1 (region B), and a possible allosteric site in GFRα1 (region C). The results obtained by the docking calculations and the MD simulations indicate that the preferable binding occurs at the allosteric site. A less preferable binding site was detected on the RetA surface interfacing GFRα1. In the membrane-bound state of RetA this can enable compounds BT13 and BT18 to act as direct RetA agonists. The analysis of the MD simulations shows hydrogen bonds for BT13 and significant hydrophobic interactions with GFRα1 for BT13 and BT18 at the allosteric site.