This study provides a comprehensive investigation of the structural and vibrational properties of protonated cytosine monomers and dimers. Experimental IRPD spectroscopy, combined with theoretical calculations, revealed distinct behaviors for monomers and dimers. We find that protonated cytosine monomers predominantly adopt the enol form in the gas phase, with a contribution from the keto form between 25% and 33%. For dimers, our computations predict a keto-enol configuration to be more stable than the keto-keto form by 1.5 kcal mol-1. However, experimentally, the keto-keto form emerged as the dominant structure. The theoretically most stable keto-enol configuration undergoes a structural reorganization in MD simulations with explicit methanol, forming the dynamically unstable neutral-keto-protonated-keto complex. This reorganization highlights the role of environmental factors in modulating tautomer populations.

Department of Chemistry and Biochemistry University of California Santa Barbara CA 93106 9510 USA

Department of Chemistry School of Science Institute of Science Tokyo H 68 Main Building B19A 2 12 2 Ookayama Meguro ku Tokyo 152 8550 Japan

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542 2 160 00 Praha 6 Czech Republic

Laboratory for Chemistry and Life Science Institute of Innovative Research Institute of Science Tokyo 4259 Nagatsuta cho Midori ku Yokohama 226 8503 Japan

Research and Development Initiative Chuo University 1 13 27 Kasuga Bunkyo ku Tokyo 112 8551 Japan

Tokyo Tech World Research Hub Initiative Institute of Innovation Research Institute of Science Tokyo 4259 Nagatsuta cho Midori ku Yokohama 226 8503 Japan

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