The Journal of Physical Chemistry B
Article
Combination with the gas phase results clearly indicates that
intermolecular interactions or solvation effects will stabilize
reaction products 38−40 more than uridine itself, thus leading
to a larger driving force for intramolecular transfer hydro-
genation. We should add that these types of hydrogen exchange
reactions are equally possible between sugar components of
one nucleotide and the base of the adjacent nucleotide in 3′ or
(5) Kistiakowsky, G. B.; Nickle, A. G. Ethane−Ethylene and
Propane−Propylene Equilibria. Faraday Discuss. Chem. Soc. 1951, 10,
1
75−187.
(6) Pedley, J. P.; Naylor, R. D.; Kirby, S. P. Thermochemical Data of
Organic Compounds, 2nd ed.; Chapman and Hall: London, 1986; see
also values compiled in ref 7.
(
7) Chase, M. W., Jr. NIST-JANAF Themochemical Tables, 4th ed. J.
Phys. Chem. Ref. Data, Monogr. 1998, 9, 1−1951.
8) Dolliver, M. A.; Gresham, T. L.; Kistiakowsky, G. B.; Smith, E. A.;
5′ position.
(
The rather similar hydrogenation enthalpies found here for
Vaughan, W. E. Heats of Organic Reactions. VI. Heats of
Hydrogenation of Some Oxygen-Containing Compounds. J. Am.
Chem. Soc. 1938, 60, 440−450.
some of the sugar and the base components of nucleosides raise
the question how the information stored in oligonucleotides
can be preserved under the potential threat of internal
hydrogen transfer reactions. Most RNA maturing steps such
as C5′ end-capping and methylation of the C2′ hydroxy groups
of nucleotides located at the C3′ terminus, or the
polyadenylation of the C3′ terminus all reduce the potential
of intramolecular transfer hydrogenation by simply removing
the respective hydroxy groups as redox partners or by
positioning redox-inactive bases at the respective termini.
DNA systems, in contrast, are much less prone to this type of
redox process due to removal of the C2′ hydroxy group and the
replacement of uridine by thymine. This limits the risk of
transfer hydrogenation to the terminal C3′ and C5′ positions
carrying thymine as the most easily reduced base. Avoidance of
this base at the very last position as well as any end-capping
process (including the formation of cyclic DNA) will, of course,
eliminate the risk of transfer hydrogenation as an unwanted
redox process.
(9) Kistiakowsky, G. B.; Romeyn, H., Jr.; Ruhoff, J. R.; Smith, H. A.;
Vaughan, W. E. Heats of Organic Reactions. I. The Apparatus and the
Heat of Hydrogenation of Ethylene. J. Am. Chem. Soc. 1935, 57, 65−
7
5.
(10) Rogers, D. W. Experimental and Computational Hydrogen
Thermochemistry of Organic Compounds; World Scientific Publishing
Company: Singapore, 2006).
(11) Wiberg, K. B.; Crocker, L. S.; Morgan, K. M. Thermochemical
Studies of Carbonyl Compounds. 5. Enthalpies of Reduction of
Carbonyl Compounds. J. Am. Chem. Soc. 1991, 113, 3447−3450.
(12) Lide, D. R. CRC Handbook of Chemistry and Physics, 89th ed.;
CRC Taylor & Francis: Boca Raton, FL, 2008.
(13) Galvao, T. L. P.; Rocha, I. M.; Ribeiro da Silva, M. D. M. C.;
Ribeiro da Silva, M. A. V. Is Uracil Aromatic? The Enthalpies of
Hydrogenation in the Gaseous and Crystalline Phases, and in Aqueous
Solution, as Tools to Obtain an Answer. J. Phys. Chem. A 2013, 117,
5
(
826−5836.
14) Galvao, T. L. P.; Ribeiro da Silva, M. D. M. C.; Ribeiro da Silva,
M. A. V. From 2,4-Dimethoxypyrimidine to 1,3-Dimethyluracil:
Isomerization and Hydrogenation Enthalpies and Noncovalent
ASSOCIATED CONTENT
Interactions. J. Phys. Chem. A 2014, 118, 4816−4823.
■
−1
(
15) Using Δ H(CH NCH ) = +44 ± 8 kJ mol from Peerboom,
f
3
2
*
S
Supporting Information
R. A. L.; Ingemann, S.; Nibbering, N. M. M.; Liebman, J. F. Proton
Full experimental details for the synthesis of nucleobase
derivatives and measurements of their heats of hydrogenation,
energies and coordinates for all theoretical calculations, and
Affinities and Heats of Formation of the Imines CH NH, CH
2
2
NMe and PhCHNH. J. Chem. Soc., Perkin Trans. 2 1990, 1825−
−1
1828 and Δ H(CH NHCH ) = −18.8 kJ mol from ref 12.
f
3
3
(16) Seidel, C. A.; Schulz, A.; Sauer, M. H. Nucleobase-Specific
Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox
Potentials and Their Correlation with Static and Dynamic Quenching
Efficiencies. J. Phys. Chem. 1996, 100, 5541−5553.
AUTHOR INFORMATION
■
(17) Aflatooni, K.; Gallup, G. A.; Burrow, P. D. Electron Attachment
Energies of the DNA Bases. J. Phys. Chem. A 1998, 102, 6205−6207.
(18) Green, E. A.; Rosenstein, R. D.; Shiono, R.; Abraham, D. J.;
*
Trus, B. L.; Marsh, R. E. The Crystal Structure of Uridine. Acta
Crystallogr. 1975, B31, 102−107.
Notes
The authors declare no competing financial interest.
(19) Leulliot, N.; Ghomi, M.; Scalmani, G.; Berthier, G. Ground
State Properties of the Nucleic Acid Constituents Studied by Density
Functional Calculations. I. Conformational Features of Ribose,
Dimethyl Phosphate, Uridine, Cytidine, 5′-Methyl Phosphate-Uridine,
and 3′-Methyl Phosphate-Uridine. J. Phys. Chem. A 1999, 103, 8716−
ACKNOWLEDGMENTS
■
This work was supported by the Deutsche Forschungsgemein-
schaft, DFG, in its priority program SPP 1071. The work has
been supported by the Russian Government Program of
Competitive Growth of Kazan Federal University.
8
724.
20) Saenger, W. Structure and Function of Nucleosides and
Nucleotides. Angew. Chem., Int. Ed. 1973, 12, 591−682.
(
REFERENCES
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(
1) Cooke, M. S.; Evans, M. D.; Dizdaroglu, M.; Lunec, J. Oxidative
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195−1214.
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(
3) Calculated using the following standard heats of formation Δ H:
f
−
1
−
1
4
Δ H(H , 1) = 0.0 kJ mol ; Δ H(CH O, 2) = −108.6 ± 0.5 kJ mol ;
f
2
f
2
4
Δ H(CH OH, 3) = −201.5 ± 0.1 kJ mol-1; and for reaction 2 the
f
3
heats of hydrogenation reported in ref 4 and ref 5.
4) Cox, J. D.; Pilcher, G. Thermochemistry of Organic and
Organometallic Compounds; Academic Press: San Diego, CA, 1970.
(
1
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dx.doi.org/10.1021/jp507855k | J. Phys. Chem. B 2014, 118, 10426−10429