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To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D.
MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size.
Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
We recommend a set of internally consistent ΔGof, REEX for 119 end-members of REE oxides, hydroxides, chlorides, fluorides, carbonates, hydrous carbonates, and ferrites. These ΔGof, REEX are combined with experimental or predicted values of So, Vo, and Cpo from the literature and incorporated into a new SUPCRT database, which allows the calculations of thermodynamic properties to high P-T conditions (e.g., up to 1000 oC and 5 kb). The log Ksp of REE solid dissociation reactions were incorporated into a modified USGS program PHREEQC for calculations of speciation, solubility, and reactive transport. These thermodynamic databases will also be incorporated into the MINES database to be used together with the GEMS code package in the future.
Citation to related publication:
Title:
Linear correlations of Gibbs free energy for rare earth element oxide, hydroxide, chloride, fluoride, carbonate, and ferrite minerals and crystalline solids
Rare Earth Elements (REE) are critical minerals (metals) for the transition from fossil fuels to renewable and clean energy. Accurate thermodynamic properties of REE minerals and other crystalline solids are crucial for geochemical modeling of the solubility, speciation, and transport of REE in ore formation, extraction, chemical processing, and recycling processes. However, the Gibbs free energies of formation (∆Gof, REEX) for these solids from different sources vary by 10s kJ/mol. We applied the Sverjensky linear free energy relationship (LFER) to evaluate their internal consistency and predict the unavailable ∆Gof of the REE solids. By considering both the effects of ionic radius size and corresponding aqueous ion properties, the Sverjensky LFER,
allows estimates with much accuracy and precision. Here, rREEZ+ represents the Shannon-Prewitt ionic radii (Å) of REEZ+, and ∆Gon, REEZ+ denotes the non-solvation contribution to the ∆Gof of the aqueous REEZ+ ion. X represents the remainder of the compounds. In this study, the parameters aREEX, bREEX, and βREEX were regressed from ∆Gof compilations in the literature for 13 isostructural families. Based on these linear relationships, we recommend a set of internally consistent ∆Gof, REEX for 119 end-members of REE oxides, hydroxides, chlorides, fluorides, carbonates, hydrous carbonates, and ferrites. These ∆Gof, REEX are combined with experimental or predicted values of So, Vo, and Cpo from the literature and incorporated into a new SUPCRT database, which allows the calculations of thermodynamic properties to high P-T conditions (e.g., up to 1000 oC and 5 kb). The log Ksp of REE solid dissociation reactions were incorporated into a modified USGS program PHREEQC for calculations of speciation, solubility, and reactive transport. These thermodynamic databases will also be incorporated into the MINES database to be used together with the GEMS code package in the future.
Citation to related publication:
Title:
Linear correlations of Gibbs free energy for rare earth element oxide, hydroxide, chloride, fluoride, carbonate, and ferrite minerals and crystalline solids
