Automated Search For The Low-lying Energy Isomers of Rhamnolipids and Related Organometallic Complexes

14 February 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Rhamnolipids (RMLs) are a widely studied biosurfactant due to its high biodegradability, low toxicity, and environmentally friendly production, which has the bacterium Pseudomonas aeruginosa as producer and renewable source of feedstock. However, the knowledge of the structure-property relationship of several RMLs congeners is imperative for the design of a high efficient application. Aiming to a better understanding of RMLs at a molecular level, we performed a automated search for low energy structures of the most abundant congeners, namely, Rha-C10, Rha-C10-C10, Rha-Rha-C10 and Rha-Rha-C10-C10 and their respective congener with two carbon atoms (C2) at the side chain. Besides that, selected neutral metal complexes were also considered. We thus performed a metadynamics search followed by DFT optimizations of selected geometries. In addition, molecular dynamics simulations were also applied. Our results show a plethora of low energy structures for each congener. Although several of them have internal hydrogen bonds, this interaction alone cannot explain the stability. Moreover, geometries in closed conformation were always more stable than ”open” ones and the effect of chain length on the geometry was found to be more prominent between Rha-Rha-C2-C2 and Rha-Rha-C10-C10 . Finally, the energy differences between open and closed conformations for K+ , Ni2+ , Cu2+ and Zn2+ complexes were found to be 23.5 kcal mol−1, 62.8 kcal mol−1 , 24.3 kcal mol−1 and 41.6 kcal mol−1 , respectively, indicating a huge structural reorganization after the complex formation.


density functional theory
organometallic complex
global minimum search

Supplementary materials

Electronic Supplementary Information of "Automated Search For The Low-lying Energy Isomers of Rhamnolipids and Related Organometallic Complexes"
Electronic Supplementary Information (ESI) containing structures and cartesian coordinates (XYZ format) of low-lying energy structures present in the Manuscript.


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.