Conformational preferences of the base substituent in hypermodified nucleotide queuosine 5`-monophosphate ?pQ? and its protonated form ?pQH+? have been studied using quantum chemical Perturbative Configuration Interaction with Localized Orbitals PCILO method. The salient points have also been examined using molecular mechanics force field MMFF, parameterized modified neglect of differential overlap PM3 and Hartree Fock-Density Functional Theory HF DFT (pBP/DN*) approaches. Aqueous solvation of pQ and pQH+ has also been studied using molecular dynamics simulations. Consistent with the observed crystal structure, in isolated protonated form pQH+, the quaternary amine HN(13)⁺H, of the sidechain having 7-aminomethyl linkage, hydrogen bonds with the carbonyl oxygen O(10) of the base. However, N(13)H?O(10) hydrogen bonding is not preferred for unprotonated pQ, whether isolated or hydrated. Interaction between the 5´-phosphate and the 7-aminomethyl group is more likely for isolated pQ. The cyclopentenediol hydroxyl group O4´´H may hydrogen bond with the O(10) in isolated pQ as well as in pQH+. The O4´´H may hydrogen bond with the 5´-phosphate as well. The presence of -CH2-NH- and O´´H groups in pQ and pQH+ allows interesting possibilities for intranucleotide hydrogen bonds and interactions across the anticodon loop. Simultaneous hydrogen bonds O2P?HN(13)+H?O(10) are indicated for hydrated pQH+. Unlike weak involvement of O4´´H, these interactions also persist in hydrated pQH+ and may much reduce backbone flexibility. Resulting sub-optimal Q:C base pairing leads to unbiased reading of U or C as the third codon letter. Cyclopentenediol hydroxyl groups may interact with other biomolecules, allowing specific recognition. Prospective pQ₃₄ and pQ₃₄H+ sites for codon-anticodon base pairing remain unhindered, but non canonical Q:G base pairing (amber-suppression) is ruled out.

Key words: conformational preferences, queuosine 5´-monophosphate, protonation, hypermodified nucleotides, tRNA anticodon loop, PCILO, MMFF, PM3, HF DFT(pBP/DN*).