Identifying representative sequences of protein families using submodular optimization.

Identifying representative sequences for groups of functionally similar proteins and enzymes poses significant computational challenges. In this study, we applied submodular optimization, a method effective in data summarization, to select representative sequences for thioesterase enzyme families. We introduced and validated two algorithms, Greedy and Bidirectional Greedy, using curated protein sequence data from the ThYme (Thioester-active enzYmes) database.

Predicting Magnetic Barriers in Lanthanide Complexes with Electrostatic Potential Charges.

Single-molecule magnets (SMMs) with slow relaxation of magnetization and blocking temperatures above that of liquid nitrogen are essential for practical applications in high-density data storage devices and quantum computers. A rapid and accurate prediction of the effective magnetic relaxation barrier () is needed to accelerate the discovery of high-performance SMMs. Using density functional theory and multireference calculations, we explored correlations between , partial atomic charges, and the anisotropic barrier for a series of sandwich-type lanthanide complexes containing cyclooctatetraene, substituted cyclopentadiene, phospholyl, boratabenzene, or borane ligands.

Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution.

-average sampling of structures from molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures.

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 Gd 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 Gd ion coordinated to 0-3 DEHP ligands in either water, 1-octanol, or hexane solvents and at the water-organic interfaces.

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 Nd and Dy. G-macropa maintains the same thermodynamic preference for the large REEs as macropa, but shows smaller thermodynamic stability constants.

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 , , 2022, , 10263-10271, https://doi.org/10.

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.

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.

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.

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 Eu 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 Eu ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions.

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

The aqueous hydration structure of the Bi 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 Bi ion are dramatically controlled by the water stabilization of a lone-pair electronic state involving the mixed 6s and 6p orbitals.

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

Increasing atmospheric concentrations of greenhouse gases due to industrial activity have led to concerning levels of global warming. Reducing carbon dioxide (CO) emissions, one of the main contributors to the greenhouse effect, is key to mitigating further warming and its negative effects on the planet. CO capture solvent systems are currently the only available technology deployable at scales commensurate with industrial processes.

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 La, Eu, Gd, and Lu 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.

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.

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 (Ln) 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 Ln (Ce, Sm, and Lu) aqua ions.

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.

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]4f) and large-core ([Xe]4f5d) options that successfully reproduce the structures and energetics, particularly redox processes.

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.

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.

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

To resolve the fleeting structures of lanthanide Ln aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln 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 Ln ions (Nd, Dy, Er, Lu) 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.

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

Water-lean CO capture solvents show promise for more efficient and cost-effective CO 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 CO. 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.

Molecular-Level Overhaul of γ-Aminopropyl Aminosilicone/Triethylene Glycol Post-Combustion CO -Capture Solvents.

Capturing carbon dioxide from post-combustion gas streams is an energy-intensive process that is required prior to either converting or sequestering CO . Although a few commercial 1st and 2nd generation aqueous amine technologies have been proposed, the cost of capturing CO with these technologies remains high. One approach to decrease costs of capture has been the development of water-lean solvents that aim to increase efficiency by reducing the water content in solution.

Norm-Conserving Pseudopotentials and Basis Sets To Explore Lanthanide Chemistry in Complex Environments.

A complete set of pseudopotentials and accompanying basis sets for all lanthanide elements are presented based on the relativistic, norm-conserving, separable, dual-space Gaussian-type pseudopotential protocol of Goedecker, Teter, and Hutter (GTH) within the generalized gradient approximation (GGA) and the exchange-correlation functional of Perdew, Burke, and Ernzerhof (PBE). The corresponding basis sets have been molecularly optimized (MOLOPT) using a contracted form with a single set of Gaussian exponents for the s, p, and d states. The f states are uncontracted explicitly with Gaussian exponents.