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Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations.
J Am Chem Soc. 2007 Jan 24; 129(3):569-80.JA

Abstract

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.

Authors+Show Affiliations

Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17227020

Citation

Wu, Ronghu, and Terry B. McMahon. "Investigation of Proton Transport Tautomerism in Clusters of Protonated Nucleic Acid Bases (cytosine, Uracil, Thymine, and Adenine) and Ammonia By High-pressure Mass Spectrometry and Ab Initio Calculations." Journal of the American Chemical Society, vol. 129, no. 3, 2007, pp. 569-80.
Wu R, McMahon TB. Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations. J Am Chem Soc. 2007;129(3):569-80.
Wu, R., & McMahon, T. B. (2007). Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations. Journal of the American Chemical Society, 129(3), 569-80.
Wu R, McMahon TB. Investigation of Proton Transport Tautomerism in Clusters of Protonated Nucleic Acid Bases (cytosine, Uracil, Thymine, and Adenine) and Ammonia By High-pressure Mass Spectrometry and Ab Initio Calculations. J Am Chem Soc. 2007 Jan 24;129(3):569-80. PubMed PMID: 17227020.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations. AU - Wu,Ronghu, AU - McMahon,Terry B, PY - 2007/1/18/pubmed PY - 2007/5/1/medline PY - 2007/1/18/entrez SP - 569 EP - 80 JF - Journal of the American Chemical Society JO - J Am Chem Soc VL - 129 IS - 3 N2 - The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules. SN - 0002-7863 UR - https://www.unboundmedicine.com/medline/citation/17227020/Investigation_of_proton_transport_tautomerism_in_clusters_of_protonated_nucleic_acid_bases__cytosine_uracil_thymine_and_adenine__and_ammonia_by_high_pressure_mass_spectrometry_and_ab_initio_calculations_ L2 - https://doi.org/10.1021/ja065088g DB - PRIME DP - Unbound Medicine ER -