Establishing Cost-Effective Computational Models for the Prediction of Lanthanoid Binding in [Ln(NO3)]2+ (with Ln = La to Lu)

Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions

Rapid and accurate approaches to characterizing the coordination structure of an ion are important for designing ligands and quantifying structure-property trends. Here, we introduce AFICS (Analysis of the First Ion Coordination Sphere), a tool written in Python 3 for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. The principal feature of AFICS is its ability to quantify the distortion a coordination geometry undergoes compared to uniform polyhedra. This work applies the toolkit to analyze molecular dynamics simulations of the well-defined coordination structure of aqueous Cr³⁺ along with the more ambiguous structure of aqueous Eu³⁺ chelated to ethylenediaminetetraacetic acid. The tool is targeted for analyzing ions with fluxional or irregular coordination structures (e.g., solution structures of f-block elements) but is generalized such that it may be applied to other systems.

Predicting lanthanide coordination structures in solution with molecular simulation

The chemical and physical properties of lanthanide coordination complexes can significantly change with small variations in their molecular structure. Further, in solution, coordination structures (e.g., lanthanide-ligand complexes) are dynamic. Resolving solution structures, computationally or experimentally, is challenging because structures in solution have limited spatial restrictions and are responsive to chemical or physical changes in their surroundings. To determine structures of lanthanide-ligand complexes in solution, a molecular simulation approach is presented in this chapter, which concurrently considers chemical reactions and molecular dynamics. Lanthanide ion, ligand, solvent, and anion molecules are explicitly included to identify, in atomic resolution, lanthanide coordination structures in solution. The computational protocol described is applicable to determining the molecular structure of lanthanide-ligand complexes, particularly with ligands known to bind lanthanides but whose structures have not been resolved, as well as with ligands not previously known to bind lanthanide ions. The approach in this chapter is also relevant to elucidating lanthanide coordination in more intricate structures, such as in the active site of enzymes.

Predicting Stability Constants for Terbium(III) Complexes with Dipicolinic Acid and 4-Substituted Dipicolinic Acid Analogues using Density Functional Theory

The relative stability constants of Tb(III) complexes exhibiting binding to a series of 4-substituted analogues of dipicolinic acid (2,6-pyridinedicarboxylic acid) (DPA) were calculated using density functional theory (DFT) with the standard thermodynamic cycle. DFT calculations showed that the strengths of the stability constants were modified by the substituents in the following (decreasing) order: -NH2 > -OH ∼ -CH2OH > -imidazole ∼ -Cl ∼ -Br ∼ -H > -F > -I, with the differences among them falling within one to two log units except for -NH2. Through population and structural analysis, we observed that the -NH2, -OH, -CH2OH, and halide substituents can donate electrons via resonance effect to the pyridine ring of DPA while inductively withdrawing electrons with different strengths, thus resulting in the different binding strengths of the 4-substituted DPAs to the Tb(III) ions. We believe that these observations possess utility not only in the ongoing development of luminescent probes for bioanalytical studies but also for more recent cross-industrial efforts to enhance reservoir surveillance capabilities using chemical tracers within the oil and gas sector.