Assign_v2: a novel bonded-force field parameterization software for square planar palladium molecular dynamics simulations.

In the present study, a requisite bonded force field for conducting molecular dynamics simulations of palladium compounds was derived utilizing a novel technique termed the "numbering system," implemented through a program named assign.py. A significant challenge in deriving a bonded force field for square-planar palladium compounds emanates from their cis-trans characteristics, whereby the bond angles of identical atoms diverge across different compounds due to the presence of cis and trans isomers. To navigate this challenge, atoms surrounding the palladium were assigned numerical identifiers; consecutively numbered neighboring atoms were designated as "cis," while atoms alternately numbered were regarded as "trans" relative to each other. Through the employment of the newly developed assign.py program, atoms common to GAFF were automatically assigned, facilitating the seamless integration of GAFF with the newly derived force field for cis and trans configurations. The tested innovative force field demonstrated results in close proximity to experimental findings. This research introduced two novel elements: firstly, a comparatively extensive force field was derived for palladium compounds, enabling the simulation of the previously non-simulable square planar geometry of palladium. Secondly, new software, assign.py, was developed, capable of amalgamating "numbering system atom types" with GAFF atom types into a unified force field. Conclusive tests within the study affirmed that the innovative bonded force field and technique utilizing the assign.py program was successful, simulating the square-planar geometry of palladium in a manner highly congruent with the experimental geometry. The program, licensed under Apache2, can be accessed via the following link: https://github.com/bkurt00/palladiumFF2/blob/main/assign_v2/assign_v2.pyCommunicated by Ramaswamy H. Sarma.

Mitochondrial iron transporter (MIT) gene in potato (Solanum tuberosum): comparative bioinformatics, physiological and expression analyses in response to drought and salinity.

Mitochondrial iron transporter (MIT) genes are essential for mitochondrial acquisition/import of iron and vital to proper functioning of mitochondria. Unlike other organisms, research on the MITs in plants is limited. The present study provides comparative bioinformatics assays for the potato MIT gene (StMIT) as well as gene expression analyses. The phylogenetic analyses revealed monocots-dicot divergence in MIT proteins and it was also found clade specific motif diversity. In addition, docking analyses indicated that Asp172 and Gly100 residues to be identified as the closest residues binding to ferrous iron. The percentage of structure overlap of the StMIT 3D protein model with Arabidopsis, maize and rice MIT proteins was found between 80.18% and 85.71%. The transcript analyses exhibited that the expression of StMIT was triggered under drought and salinity stresses. The findings of the present study would provide valuable leads for further studies targeting specifically the MIT gene and generally the plant iron metabolism.

Regulation of SEI Formation by Anion Receptors to Achieve Ultra-Stable Lithium-Metal Batteries.

Despite high specific capacity (3860 mAh g-1 ), the utilization of Li-metal anodes in rechargeable batteries are still hampered due to their insufficient cyclability. Herein, we report an anion-receptor-mediated carbonate electrolyte with improved performance and can ameliorate the solid electrolyte interphase (SEI) composition comparing to the blank electrolyte. It demonstrates a high average Coulombic efficiency (97.94 %) over 500 cycles in the Li/Cu cell at a capacity of 1 mAh cm-2 . Raman spectrum and molecular modelling further clarify the screening effects of the anion receptor on the Li+ -PF6 - ion coupling that results in the enhanced ion dynamics. The X-ray photoelectron spectroscopy (XPS) distinguishes the disparities in the SEI components of the developed electrolyte and the blank one, which is rationalized by the molecular insights of the Li-metal/electrolyte interface. Thus, we prepare a 2.5 Ah prototype pouch cell, exhibiting a high energy density (357 Wh kg-1 ) with 90.90 % capacity retention over 50 cycles.

Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation.

Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.

A key gene bHLH115 in iron homeostasis: comprehensive bioinformatics analyses in Arabidopsis, tomato, rice, and maize.

bHLH115 transcription factor (TF) is a positive regulator of the Fe-deficiency and plays essential roles in the stress-related regulation network. In this study, orthologous bHLH115 genes in Arabidopsis, tomato, rice, and maize were analyzed using in silico methods. All bHLH115 proteins contained PF00010 (HLH: Helix-loop-helix DNA-binding domain) domain structure and their sub-cellular localizations were predicted as nucleus. The bHLH115 orthologues in monocots and dicots clearly diverged from each other. The expression analyses revealed that orthologous genes of bHLH115 in queried species were highly expressed in seed parts, leaf, stem, and flower parts. The bHLH115 genes were co-expressed with genes in plant defense system, and with genes involving in biotic and abiotic stress responses. In terms of protein structures, OsbHLH115 and ZmbHLH115, and AtbHLH115 and SlbHLH115 had the highest protein structure similarities. In addition, bHLH115 proteins have bZIP, bHLH and MYB transcription factor binding sites strengthens their engagement in various metabolic ways. Molecular docking analyses showed the different binding sites based on plant species, suggesting functional flexibilities of bHLH115 gene.