CHARMM Molecular Simulation Observations of Carbonaceous Materials as Possible Templates for Prebiotic Nucleic Acid Oligomer Formation

25 April 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


This research utilizes CHARMM molecular simulations for the purposes of an initial qualitative observational study of diamond-like carbon and related carbonaceous substrates as potential templates for the abiotic formation of RNA polymers,. While a number of research group have looked at nanodiamond, graphite and other carbon and non-carbon-based materials (especially clays) as possible solid templates for early life, we propose that diamond-like carbon (DLC, also known as amorphous diamond or aD) may have been a plausible ideal template. This is due largely to the fact that DLC is a heterogeneous material, essentially an aggregation of various constituent carbon species (for instance, graphene, graphite, CNT, etc.), depending on formation conditions. Further, DLC exhibits a range of superlative material properties shared by diamond and graphitic materials It possesses high thermal diffusivity and conductivity along all planes due to its inherent anisotropism. Internal and surface structure variability could have played a crucial role in facilitating the molecular interactions that accelerated the abiotic formation of RNA oligomers, potentially supporting the RNA World hypothesis. Significant outside energy is not needed to enable oligomer formation. Entropy, in the form of heat, is a driving force that provides conditions necessary for oligomer formation. To reduce computational and financial costs, we investigate artificial intelligence-driven methodologies to inform optimal MD input parameters with the goal of generating key qualitative endpoints. As MD simulations are extremely computationally expensive due to the large quantity of electronegativity and force field interactions for trajectory calculations, we initially used a lightweight MD system combined with a transformer model to better predict the likelihood of achieving collisions between target molecules, and thus increase the chance of observing exemplar endpoints. Various key endpoints were observed, including Van der Waals oligomer-template attachment, translocation/rotation potentially leading to more complex configurations, quasi-elongation and bridging, as well as detachment). The observations of these endpoints suggest that carbonaceous materials such as DLC could plausibly have served as templates for the formation of early nucleic acid oligomers. Further simulations and physical experiments are needed to confirm these results, and to develop a supporting statistical model.


RNA world
diamond like carbon

Supplementary materials

Supplemental Information - data files and instructions for use of VMD
DCD trajectory output files demonstrating exemplar endpoints, associated PDB structure files and brief instructions for use of VMD visualization software


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