Effect of ion to ligand ratio on the aqueous to organic relative solubility of a lanthanide-ligand complex.

In the solvent extraction of rare earth elements, mechanistic aspects remain unclear regarding where and how extractant molecules coordinate metal ions and transport them from the aqueous phase into the organic phase. Molecular dynamics simulations were used to examine how unprotonated di(2-ethylhexyl)phosphoric acid (DEHP-) ligands that coordinate the Gd3+ ion can transfer the ion across the water-organic interface. Using the umbrella sampling technique, potential of mean force profiles were constructed to quantify the relative solubility of the Gd3+ ion coordinated to 0-3 DEHP- ligands in either water, 1-octanol, or hexane solvents and at the water-organic interfaces. The simulations show the Gd-DEHP- complexes, at varying Ln-ligand ratios, preferentially solvate on water-organic interfaces. While the Gd(DEHP-)3 complex will diffuse past the aqueous-organic interface into the octanol solvent, it is thermodynamically preferred for the Gd(DEHP-)3 complex to remain in the water-hexane interface when there is no amphiphilic layer of excess ligand.

Chelator-Assisted Precipitation-Based Separation of the Rare Earth Elements Neodymium and Dysprosium from Aqueous Solutions.

The rare earth elements (REEs) are critical resources for many clean energy technologies, but are difficult to obtain in their elementally pure forms because of their nearly identical chemical properties. Here, an analogue of macropa, G-macropa, was synthesized and employed for an aqueous precipitation-based separation of Nd3+ and Dy3+. G-macropa maintains the same thermodynamic preference for the large REEs as macropa, but shows smaller thermodynamic stability constants. Molecular dynamics studies demonstrate that the binding affinity differences of these chelators for Nd3+ and Dy3+ is a consequence of the presence or absence of an inner-sphere water molecule, which alters the donor strength of the macrocyclic ethers. Leveraging the small REE affinity of G-macropa, we demonstrate that within aqueous solutions of Nd3+, Dy3+, and G-macropa, the addition of HCO3 - selectively precipitates Dy2(CO3)3, leaving the Nd3+-G-macropa complex in solution. With this method, remarkably high separation factors of 841 and 741 are achieved for 50 : 50 and 75 : 25 mixtures. Further studies involving Nd3+:Dy3+ ratios of 95 : 5 in authentic magnet waste also afford an efficient separation as well. Lastly, G-macropa is recovered via crystallization with HCl and used for subsequent extractions, demonstrating its good recyclability.

Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms.

Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.

Correction: The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation.

Correction for 'The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation' by Ravi D. O'Brien et al., Phys. Chem. Chem. Phys., 2022, 24, 10263-10271, https://doi.org/10.1039/D2CP01081J.

Mutation Space of Spatially Conserved Amino Acid Sites in Proteins.

The mutation space of spatially conserved (MSSC) amino acid residues is a protein structural quantity developed and described in this work. The MSSC quantifies how many mutations and which different mutations, i.e., the mutation space, occur in each amino acid site in a protein. The MSSC calculates the mutation space of amino acids in a target protein from the spatially conserved residues in a group of multiple protein structures. Spatially conserved amino acid residues are identified based on their relative positions in the protein structure. The MSSC examines each residue in a target protein, compares it to the residues present in the same relative position in other protein structures, and uses physicochemical criteria of mutations found in each conserved spatial site to quantify the mutation space of each amino acid in the target protein. The MSSC is analogous to scoring each site in a multiple sequence alignment but in three-dimensional space considering the spatial location of residues instead of solely the order in which they appear in a protein sequence. MSSC analysis was performed on example cases, and it reproduces the well-known observation that, regardless of secondary structure, solvent-exposed residues are more likely to be mutated than internal ones. The MSSC code is available on GitHub: "https://github.com/Cantu-Research-Group/Mutation_Space".

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.

Solution Structures of Europium Terpyridyl Complexes with Nitrate and Triflate Counterions in Acetonitrile.

Lanthanide-ligand complexes are key components of technological applications, and their properties depend on their structures in the solution phase, which are challenging to resolve experimentally or computationally. The coordination structure of the Eu3+ ion in different coordination environments in acetonitrile is examined using ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. AIMD simulations are conducted for the solvated Eu3+ ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions. EXAFS spectra are calculated directly from AIMD simulations and then compared to experimentally measured EXAFS spectra. In acetonitrile solution, both nitrate and triflate anions are shown to coordinate directly to the Eu3+ ion forming either ten- or eight-coordinate solvent complexes where the counterions are binding as bidentate or monodentate structures, respectively. Coordination of a terpyridyl ligand to the Eu3+ ion limits the available binding sites for the solvent and anions. In certain cases, the terpyridyl ligand excludes any solvent binding and limits the number of coordinated anions. The solution structure of the Eu-terpyridyl complex with nitrate counterions is shown to have a similar arrangement of Eu3+ coordinating molecules as the crystal structure. This study illustrates how a combination of AIMD and EXAFS can be used to determine how ligands, solvent, and counterions coordinate with the lanthanide ions in solution.

Water Defect Stabilizes the Bi3+ Lone-Pair Electronic State Leading to an Unusual Aqueous Hydration Structure.

The aqueous hydration structure of the Bi3+ ion is probed using a combination of extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) simulations of ion-water clusters and condensed-phase solutions. Anomalous features in the EXAFS spectra are found to be associated with a highly asymmetric first-solvent water shell. The aqueous chemistry and structure of the Bi3+ ion are dramatically controlled by the water stabilization of a lone-pair electronic state involving the mixed 6s and 6p orbitals. This leads to a distinct multimodal distribution of water molecules in the first shell that are separated by about 0.2 Å. The lone-pair structure is stabilized by a collective response of multiple waters that are localized near the lone-pair anti-bonding site. The findings indicate that the lone-pair stereochemistry of aqueous Bi3+ ions plays a major role in the binding of water and ligands in aqueous solutions.

Advanced Theory and Simulation to Guide the Development of CO2 Capture Solvents.

Increasing atmospheric concentrations of greenhouse gases due to industrial activity have led to concerning levels of global warming. Reducing carbon dioxide (CO2) emissions, one of the main contributors to the greenhouse effect, is key to mitigating further warming and its negative effects on the planet. CO2 capture solvent systems are currently the only available technology deployable at scales commensurate with industrial processes. Nonetheless, designing these solvents for a given application is a daunting task requiring the optimization of both thermodynamic and transport properties. Here, we discuss the use of atomic scale modeling for computing reaction energetics and transport properties of these chemically complex solvents. Theoretical studies have shown that in many cases, one is dealing with a rich ensemble of chemical species in a coupled equilibrium that is often difficult to characterize and quantify by experiment alone. As a result, solvent design is a balancing act between multiple parameters which have optimal zones of effectiveness depending on the operating conditions of the application. Simulation of reaction mechanisms has shown that CO2 binding and proton transfer reactions create chemical equilibrium between multiple species and that the agglomeration of resulting ions and zwitterions can have profound effects on bulk solvent properties such as viscosity. This is balanced against the solvent systems needing to perform different functions (e.g., CO2 uptake and release) depending on the thermodynamic conditions (e.g., temperature and pressure swings). The latter constraint imposes a "Goldilocks" range of effective parameters, such as binding enthalpy and pK a, which need to be tuned at the molecular level. The resulting picture is that solvent development requires an integrated approach where theory and simulation can provide the necessary ingredients to balance competing factors.

The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation.

Ligand selectivity to specific lanthanide (Ln) ions is key to the separation of rare earth elements from each other. Ligand selectivity can be quantified with relative stability constants (measured experimentally) or relative binding energies (calculated computationally). The relative stability constants of EDTA (ethylenediaminetetraacetic acid) with La3+, Eu3+, Gd3+, and Lu3+ were predicted from relative binding energies, which were quantified using electronic structure calculations with relativistic effects and based on the molecular structures of Ln-EDTA complexes in solution from density functional theory molecular dynamics simulations. The protonation state of an EDTA amine group was varied to study pH ∼7 and ∼11 conditions. Further, simulations at 25 °C and 90 °C were performed to elucidate how structures of Ln-EDTA complexes varying with temperature are related to complex stabilities at different pH conditions. Relative stability trends are predicted from computation for varying Ln3+ ions (La, Eu, Gd, Lu) with a single ligand (EDTA at pH ∼11), as well as for a single Ln3+ ion (La) with varying ligands (EDTA at pH ∼7 and ∼11). Changing the protonation state of an EDTA amine site significantly changes the solution structure of the Ln-EDTA complex resulting in a reduction of the complex stability. Increased Ln-ligand complex stability is correlated to reduced structural variations in solution upon an increase in temperature.

Ionic Contraction across the Lanthanide Series Decreases the Temperature-Induced Disorder of the Water Coordination Sphere.

In liquid, temperature affects the structures of lanthanide complexes in multiple ways that depend upon complex interactions between ligands, anions, and solvent molecules. The relative simplicity of lanthanide aqua ions (Ln3+) make them well suited to determine how temperature induces structural changes in lanthanide complexes. We performed a combination of ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) measurements, both at 25 and 90 °C, to determine how temperature affects the first- and second-coordination spheres of three Ln3+ (Ce3+, Sm3+, and Lu3+) aqua ions. AIMD simulations show first lanthanide coordination spheres that are similar at 25 and 90 °C, more so for the Lu3+ ion that remains as eight-coordinate than for the Ce3+ and Sm3+ ions that change their preferred coordination number from nine (at 25 °C) to eight (at 90 °C). The measured EXAFS spectra are very similar at 25 and 90 °C, for the Ce3+, Sm3+, and Lu3+ ions, suggesting that the dynamical disorder of the Ln3+ ions in liquid water is sufficient such that temperature-induced changes do not clearly manifest changes in the structure of the three ions. Both AIMD simulations and EXAFS measurements show very similar structures of the first coordination sphere of the Lu3+ ion at 25 and 90 °C.

Thioesterase enzyme families: Functions, structures, and mechanisms.

Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.

Computational Prediction of All Lanthanide Aqua Ion Acidity Constants.

The protonation state of lanthanide-ligand complexes, or lanthanide-containing porous materials, with many Brønsted acid sites can change due to proton loss/gain reactions with water or other heteroatom-containing compounds. Consequently, variations in the protonation state of lanthanide-containing species affect their molecular structure and desired properties. Lanthanide(III) aqua ions undergo hydrolysis and form hydroxides; they are the best characterized lanthanide-containing species with multiple Brønsted acid sites. We employed constrained ab initio molecular dynamics simulations and electronic structure calculations to determine all acidity constants of the lanthanide(III) aqua ions solely from computation. The first, second, and third acidity constants of lanthanide(III) aqua ions were predicted, on average, within 1.2, 2.5, and 4.7 absolute pKa units from experiment, respectively. A table includes our predicted pKa values alongside most experimentally measured pKa values known to date. The approach presented is particularly suitable to determine the Brønsted acidity of lanthanide-containing systems with multiple acidic sites, including those whose measured acidity constants cannot be linked to specific acid sites.

Norm-Conserving Pseudopotentials and Basis Sets to Explore Actinide Chemistry in Complex Environments.

We have developed a new set of norm-conserving pseudopotentials and companion Gaussian basis sets for the actinide (An) series (Ac-Lr) using the Goedecker, Teter, and Hutter (GTH) formalism with the Perdew, Burke, and Ernzerhof (PBE) exchange-correlation functional of generalized gradient approximation. To test the accuracy and reliability of the newly parameterized An-GTH pseudopotentials and basis sets, a variety of benchmarks on actinide-containing molecules were carried out and compared to all-electron and available experimental results. The new pseudopotentials include both medium- ([Xe]4f14) and large-core ([Xe]4f145d10) options that successfully reproduce the structures and energetics, particularly redox processes. The medium-core size set, in particular, reproduces all-electron calculations over multiple oxidation states from 0 to VII, whereas the large-core set is suitable only for the early series elements and low oxidation states. The underlying reason for these transferability issues is discussed in detail. This work fills a critical void in the literature for studying the chemistry of 5f-block elements in the condensed phase.

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.

Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy.

To resolve the fleeting structures of lanthanide Ln3+ aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln3+ aqua ions in explicit water solvent using pseudopotentials and basis sets recently optimized for lanthanides and (ii) measured the symmetry of the hydrating waters about Ln3+ ions (Nd3+, Dy3+, Er3+, Lu3+) for the first time with extended X-ray absorption fine structure (EXAFS). EXAFS spectra were measured experimentally and generated from AIMD trajectories to directly compare simulation, which concurrently considers the electronic structure and the atomic dynamics in solution, with experiment. We performed a comprehensive evaluation of EXAFS multiple-scattering analysis (up to 6.5 Å) to measure Ln-O distances and angular correlations (i.e., symmetry) and elucidate the molecular geometry of the first hydration shell. This evaluation, in combination with symmetry-dependent L3- and L1-edge spectral analysis, shows that the AIMD simulations remarkably reproduces the experimental EXAFS data. The error in the predicted Ln-O distances is less than 0.07 Å for the later lanthanides, while we observed excellent agreement with predicted distances within experimental uncertainty for the early lanthanides. Our analysis revealed a dynamic, symmetrically disordered first coordination shell, which does not conform to a single molecular geometry for most lanthanides. This work sheds critical light on the highly elusive coordination geometry of the Ln3+ aqua ions.

Solution structure of a europium-nicotianamine complex supports that phytosiderophores bind lanthanides.

We report the solution structure of a europium-nicotianamine complex predicted from ab initio molecular dynamics simulations with density functional theory. Emission and excitation spectroscopy show that the Eu3+ coordination environment changes in the presence of nicotianamine, suggesting complex formation, such as what is seen for the Eu3+-nicotianamine complex structure predicted from computation. We modeled Eu3+-ligand complexes with explicit water molecules in periodic boxes, effectively simulating the solution phase. Our simulations consider possible chemical events (e.g. coordination bond formation, protonation state changes, charge transfers), as well as ligand flexibility and solvent rearrangements. Our computational approach correctly predicts the solution structure of a Eu3+-ethylenediaminetetraacetic acid complex within 0.05 Å of experimentally measured values, backing the fidelity of the predicted solution structure of the Eu3+-nicotianamine complex. Emission and excitation spectroscopy measurements were also performed on the well-known Eu3+-ethylenediaminetetraacetic acid complex to validate our experimental methods. The electronic structure of the Eu3+-nicotianamine complex is analyzed to describe the complexes in greater detail. Nicotianamine is a metabolic precursor of, and structurally very similar to, phytosiderophores, which are responsible for the uptake of metals in plants. Although knowledge that nicotianamine binds europium does not determine how plants uptake rare earths from the environment, it strongly supports that phytosiderophores bind lanthanides.

Subtle changes in hydrogen bond orientation result in glassification of carbon capture solvents.

Water-lean CO2 capture solvents show promise for more efficient and cost-effective CO2 capture, although their long-term behavior in operation has yet to be well studied. New observations of extended structure solvent behavior show that some solvent formulations transform into a glass-like phase upon aging at operating temperatures after contact with CO2. The glassification of a solvent would be detrimental to a carbon-capture process due to plugging of infrastructure, introducing a critical need to decipher the underlying principles of this phenomenon to prevent it from happening. We present the first integrated theoretical and experimental study to characterize the nano-structure of metastable and glassy states of an archetypal single-component alkanolguanidine carbon-capture solvent and assess how minute changes in atomic-level interactions convert the solvent between metastable and glass-like states. Small-angle neutron scattering and neutron diffraction coupled with small- and wide-angle X-ray scattering analysis demonstrate that minute structural changes in solution precipitae reversible aggregation of zwitterionic alkylcarbonate clusters in solution. Our findings indicate that our test system, an alkanolguanidine, exhibits a first-order phase transition, similar to a glass transition, at approximately 40 °C-close to the operating absorption temperature for post-combustion CO2 capture processes. We anticipate that these phenomena are not specific to this system, but are present in other classes of colvents as well. We discuss how molecular-level interactions can have vast implications for solvent-based carbon-capture technologies, concluding that fortunately in this case, glassification of water-lean solvents can be avoided as long as the solvent is run above its glass transition temperature.