Intermolecular interactions and tautomerism of nucleic acid bases and their analogues

doi:10.1016/0022-2860(90)80137-9

Journal of Molecular Structure

Volume 237, 15 September 1990, Pages 151-163

https://doi.org/10.1016/0022-2860(90)80137-9 Get rights and content

Abstract

The structures and stabilization energies of guanine—cytosine, guanine—thymine and adenine—thymine base pairs formed by “normal” amino-oxo and “rare” amino-hydroxy tautomers of guanine and the “normal” tautomers of adenine and thymine are studied using a combined quantum-mechanical approach, an ab initio calculation for relative stabilities of the isolated tautomers together with a calculation of intermolecular interaction energies using a multipolar expansion method developed by Claverie and co-workers. It is shown that the interaction between the components of the base pairs decreases the relative stability of the pairs involving “rare” tautomers of guanine; for the isolated molecules the stability of both tautomers of guanine is found to be approximately the same.

Our calculations include the base pairs formed by the “rare” hydroxy tautomer of guanine, whose existence has been reported in recent experimental studies of guanines isolated in an inert low-temperature matrix. Calculations for this amino-hydroxy form of guanine serve as a model for interactions of O⁶-methylguanine with pyrimidine bases.

References (22)

R. Czerminski et al.
J. Mol. Struct.
(1989)
R. Czerminski
J. Mol. Struct. (Theochem)
(1988)
J. Langlet et al.
Int. J. Quantum Chem.
(1981)
R. ReinP. Hobza et al.
J. Am. Chem. Soc.
(1987)
M.M. Szczesniak et al.
J. Phys. Chem.
(1983)
L.F. Sukhodub
Chem. Rev.
(1987)
E.D. Bergman et al.
J. Chem. Soc. B
(1970)
M.J. Nowak
(1980)
J.D. Watson et al.
Nature (London)
(1953)
J.D. Watson et al.
Nature (London)
(1953)
R.E. Franklin et al.
Acta Crystallogr.
(1953)
W. Saenger
(1984)
J. Elguero et al.
(1976)
M.D. Topal et al.
Nature (London)
(1976)
M.D. Topal et al.
Nature (London)
(1976)
C.M. Radding
Annu. Rev. Biochem.
(1978)
R.D. Hotchkiss
Annu. Rev. Microbiol.
(1974)
J.W. Drake
(1970)

A. Kornberg

(1980)

A.R. Fersht et al.

Nature (London)

(1985)

B. Kramer et al.

Cell

(1984)

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The Raman (3700–100 cm⁻¹), infrared (4000–200 cm⁻¹), mass spectrum and ¹H NMR temperature-dependent study of adenine have been recorded. Quantum chemical calculations were carried out for N(9)H-amino, N(7)H-amino, N(9)H-imino and N(7)H-imino adenine tautomers using RHF, B3LYP and MP2 with full electron correlation up to 6-311++G(d,p) basis set. The computational results reveal the non-planar N(9)H-amino conformer of adenine to be the most stable structure of adenine. The planar (C_s) form of N(9)H-amino adenine is found to represent a transition state, lying 8 cm⁻¹ above the non-planar conformer and with one imaginary frequency. Comparison between theoretical and experimental ¹H NMR spectra favors the assignment of the signals to N9(H) and N7(H)-amino tautomers over the corresponding imino tautomers. On the other hand, the recorded IR, Raman and ¹³C NMR spectra were fully consistent with N9(H)-amino adenine tautomer, therefore it is the only tautomer in both the gas and solid phases and in solution. Moreover, the results of NH₂ potential surface scans utilizing B3LYP and MP2 = full methods at 6-31G(d) basis also support the non-planarity of N(9)H-amino adenine. The mass spectral measurements indicate the presence of 3% adenine dimmer which indicates weak inter-molecular hydrogen bonding interactions in adenine. Additionally, intramolecular hydrogen bonding is also predicted between N₁ and H₁₅ atoms. The theoretical infrared and Raman spectra have been successfully simulated by means of both DFT and MP2 calculations, allowing the interpretation of the complex bands observed. Aided by normal coordinate analysis, potential energy distributions and the calculated force constants, a revised and accurate vibrational assignment for all fundamentals has been provided for the non-planar N(9)H-adenine tautomer. The results are reported herein and compared with similar molecules whenever appropriate.
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We have studied the quantum dynamics of the hydrogen bonds in the adenine–thymine base pair. Due to the position of hydrogen atoms, different tautomers are possible: the stable Watson–Crick A–T, the imino-enol A*–T* and the zwitterionic (the form with charge separation) A⁺–T⁻ and A⁻–T⁺ structures. The common idea in the literature is that only A–T exists either because the difference of energy among this tautomer and the others is large or because the other structures are transformed quickly in A–T. Here, we show a detailed theoretical study that suggests the following conclusion: A–T is the stablest tautomer, a partially charged system is important and a small amount of the imino-enol A*–T* tautomer is present at any time. The mechanism of passage from A–T tautomer to the others has also been investigated.
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Several pyridone-like compounds, where the extracyclic oxygen atom has been replaced by a sulfur atom or an imino NH group, have been studied using B3LYP/6-311+G** calculations. We found that the NH substituted species differ from the other ones: a single tautomeric form, i.e. the aminopyridine one, strongly dominates either in the gas phase or in the presence of a polar solvent like DMSO. In the gas phase or in solution, pyridinethiol species are more favoured than the pyridinol ones relatively to their corresponding tautomers. The zero point vibration energy and the entropic contribution to the free energy of the reaction play a more determining role for the sulphur containing species.
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^☆: Presented at the IXth Workshop on Horizons in Hydrogen Bond Research held at Zeist (Utrecht), The Netherlands, 10–15 September 1989.

¹: Permanent address: Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60680, U.S.A.

²: Permanent address: Institute of Physics, N. Copernicus University, 87-100 Torun, Poland.

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Intermolecular interactions and tautomerism of nucleic acid bases and their analogues☆

Abstract

J. Mol. Struct.

J. Mol. Struct. (Theochem)

Int. J. Quantum Chem.

J. Am. Chem. Soc.

J. Phys. Chem.

Chem. Rev.

J. Chem. Soc. B

Nature (London)

Nature (London)

Acta Crystallogr.

Nature (London)

Nature (London)

Annu. Rev. Biochem.

Annu. Rev. Microbiol.

Nature (London)

Cell