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

Abstract

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.py

Communicated by Ramaswamy H. Sarma

Keywords:

• Palladium
• square planar
• Cis-Trans
• AMBER
• molecular dynamics
• bonded metal force field

Acknowledgements

I would like to thank Prof. David A. Case of Rutgers University for providing me with the AMBER license. Additionally, I am grateful to Assoc. Prof. Ilyas Yildirim from Florida Atlantic University for assisting me with the setup of the pmemd.cuda program under WSL2. I also extend my gratitude to my friends, Dr. Serhat Uzan of Batman University and Dr. Murat Evcil of Dicle University, for their invaluable support in calculating the electrostatic charges of palladium complexes during my preliminary studies. The numerical calculations presented in this paper were partially conducted at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).

Disclosure statement

No potential conflict of interest was reported by the authors.

Data and software availability

All data and software can be found here: https://github.com/bkurt00/palladiumFF/and https://github.com/bkurt00/palladiumFF2 (Please see readme.md file for details).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.