Intermolecular Packing and Cooperative Stabilization in Nucleotide Monophosphate Crystals
Abstract
We examine the known polymorphs of cytidine 5′-monophosphate (CMP) using dispersion-corrected density functional theory. The monoclinic phase is predicted to be the most stable, lying 1.76 and 3.00 kcal/mol per molecular unit below the orthorhombic and triclinic forms, respectively. Monoclinic CMP contains a ribose-based H-bonding motif along the crystallographic b⃗ direction, comprising alternating intra- and intermolecular interactions, motivating an investigation of cooperative stabilization along this pathway. We employ chain-of-molecules (COM) and chain-of-slabs (COS) models to quantify the direction- and size-dependent stabilization and extend the analysis to the corresponding 5′-monophosphates of thymidine, uridine, adenosine, and guanosine. Successive dimer-addition energies reveal the strongest size-dependent cooperative stabilization along the b⃗ direction, whereas growth along a⃗ and c⃗ exhibits substantially weaker size dependence. Among the nucleotides examined, adenosine 5′-monophosphate shows the strongest chain-growth stabilization in the COM model, whereas the uridine variant shows the strongest stabilization in the COS model. Guanosine 5′-monophosphate exhibits the weakest response in both models. Minimal-basis iterative stockholder (MBIS) analysis further supports molecular polarization along the growing assemblies. These results demonstrate how nucleobase identity and the surrounding crystal environment modulate direction-dependent cooperative stabilization associated with extended hydrogen-bond networks.
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BibTeX
@misc{duraisamy2026intermolecular,
title = {{Intermolecular Packing and Cooperative Stabilization in Nucleotide Monophosphate Crystals}},
author = {Parimala Devi Duraisamy and Raghunathan Ramakrishnan},
howpublished = {arXiv},
year = {2026},
month = oct,
doi = {10.48550/arxiv.2610.26068},
eprint = {2610.26068},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2610.26068},
}
RIS
TY - UNPB
TI - Intermolecular Packing and Cooperative Stabilization in Nucleotide Monophosphate Crystals
AU - Parimala Devi Duraisamy
AU - Raghunathan Ramakrishnan
PY - 2026
DA - 2026/10/19
PB - arXiv
DO - 10.48550/arxiv.2610.26068
UR - https://arxiv.org/abs/2610.26068
AB - We examine the known polymorphs of cytidine 5^′-monophosphate (CMP) using dispersion-corrected density functional theory. The monoclinic phase is predicted to be the most stable, lying 1.76 and 3.00 kcal/mol per molecular unit below the orthorhombic and triclinic forms, respectively. Monoclinic CMP contains a ribose-based H-bonding motif along the crystallographic b⃗ direction, comprising alternating intra- and intermolecular interactions, motivating an investigation of cooperative stabilization along this pathway. We employ chain-of-molecules (COM) and chain-of-slabs (COS) models to quantify the direction- and size-dependent stabilization and extend the analysis to the corresponding 5^′-monophosphates of thymidine, uridine, adenosine, and guanosine. Successive dimer-addition energies reveal the strongest size-dependent cooperative stabilization along the b⃗ direction, whereas growth along a⃗ and c⃗ exhibits substantially weaker size dependence. Among the nucleotides examined, adenosine 5^′-monophosphate shows the strongest chain-growth stabilization in the COM model, whereas the uridine variant shows the strongest stabilization in the COS model. Guanosine 5^′-monophosphate exhibits the weakest response in both models. Minimal-basis iterative stockholder (MBIS) analysis further supports molecular polarization along the growing assemblies. These results demonstrate how nucleobase identity and the surrounding crystal environment modulate direction-dependent cooperative stabilization associated with extended hydrogen-bond networks.
ER -