Notes

Potential RNA experimental sources to refit espaloma

• Frechet, D., Ehrlich, R., Remy, P., & Gabarro-Arpa, J. (1979). Thermal perturbation differential spectra of ribonucleic acids. U. Nearest neighbour interactions. Nucleic Acids Research, 7(7), 1981–2001. doi:10.1093/nar/7.7.1981

Thermodynamic properties of dinucleotide monophosphates (delta H, delta S, and fraction of stacking and unstacking).
Two-state model to U.V. melting curves.

• Ezra, F. S., Lee, C.-H., Kondo, N. S., Danyluk, S. S., & Sarma, R. H. (1977). Conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates. Biochemistry, 16(9), 1977–1987. doi:10.1021/bi00628a035

Chemical shift, coupling constants, and popultaion distribution of conformers (stacked ratio, C3'-endo, etc.).
Ribose coupling constants via NMR.

• Lee, C.-H., Ezra, F. S., Kondo, N. S., Sarma, R. H., & Danyluk, S. S. (1976). Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines. Biochemistry, 15(16), 3627–3639. doi:10.1021/bi00661a034

Chemical shift, coupling constants, and popultaion distribution of conformers (stacked ratio, C3'-endo, etc.).
Ribose coupling constants via NMR.

• Yildirim, I. Stern, H. A., Kennedy, S. D., Tubbs, J. D. & Turner, D. H. (2010). Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine. JCTC, 6(5), 1520-1531. doi:10.1021/ct900604a

J-couplings, C2'- and C3'-endo, anti/syn population of nucleosides.

Learning from experiments

• Li, D., Brüschweiler, R., Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins, 2011, JCTC
• Cesari, A., Gil-Ley, A., Bussi, G., Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement, JCTC, 2016
• Cesari, A., Bottaro, A., Lindorff-Larsen, K., Banáš, P., Šponer, J., Bussi, G., Fitting Corrections to an RNA Force Field Using Experimental Data, JCTC, 2019
• Köfinger, J., Hummer, G., Empirical optimization of molecular simulation force fields by Bayesian inference, Eur. Phys. J. B, 2021
• Fröhlking, T., Mlýnský, V., Janeček, M., Kührová, P., Krepl, M., Banáš, P., Šponer, J., Bussi, G., Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field, 2022, JCTC

Dynamical behaviors of RNA systems reported by previous literatures

• Zhao, J., Kennedy, S. D., Berger, K. D., & Turner, D. H. (2020). Nuclear Magnetic Resonance of Single Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.9b00912

Intercalated tetramer systems inconsistent with NMR spectra for r(CAAU), r(AAAA), and r(GACC)

Useful RNA experimental summary

• Bernetti. M, Bussi. G, Integrating experimental data with molecular simulations to investigate RNA structural dynamics, Curr Opin Struct Biol, 2023, 102503