Combined matrix-isolation FT-IR and ab initio 6-31++G** study of H-bonded complexes between water and molecules modelling cytosine or isocytosine

Smets, Johan; Adamowicz, Ludwik; Maes, Guido

doi:10.1016/0022-2860(94)87026-8

Cited by 31 publications

(37 citation statements)

References 26 publications

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“…Depending on the contribution in the tautomeric mixture, individual tautomers can be considered as major (10% < x < 100%), minor (0.1% < x < 10%), or rare forms ( x < 0.1%). The major and minor isomers can be detected experimentally by various spectroscopic techniques, some of them already applied to nucleobases ,− and also to neutral isocytosine. ,,, However, the rare forms possible in the isomeric mixture can only be investigated theoretically. ,,,,,− ,− ,− ,− ,− Quantum-chemical methods applied to all possible isomers of tautomeric system give complete information on tautomeric conversions and on amounts of each isomer in the tautomeric mixture. This kind of information is not accessible on the basis of experimental spectroscopic investigations, particularly for short-lived charged radicals.…”

Section: Resultsmentioning

confidence: 99%

“…For neutral isocytosine, a change of tautomeric preferences has already been discovered when proceeding from the gas phase to aqueous solution and in the solid state. ,,,,− For investigations, various spectroscopic techniques and quantum-chemical calculations have been applied and the following conclusions reported. The isomer iC3 (Figure ), possessing the canonical tautomeric functions like for G in DNA or RNA (Figure S1 (SI)), is favored in aqueous solution, whereas the isomer iC1 , corresponding to the rare form G *, predominates in the gas phase or apolar environment.…”

Section: Introductionmentioning

confidence: 99%

“…The experiments, carried out for selected charged radicals of nucleobases, encouraged us to continue quantum-chemical calculations for pyrimidine bases undertaken about ten years ago. , Generally, quantum-chemical methods complete experimental results. − They give the possibility to study all possible forms of tautomeric systems, whereas experiments lead usually to detection of favored isomers. ,,− ,− Signals of rare tautomers are exceptionally difficult to distinguish from the background. Their amounts (<0.1%) are too small and cannot be detected experimentally.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Raczyńska

Makowski

2018

J. Phys. Chem. A

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Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC), and negative ionization, called one-electron reduction (iC + e → iC), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC is close to that of the iC conjugate acid, and basicity of iC is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC, iC, U, U, U, C, C, and C are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Raczyńska

Makowski

2018

J. Phys. Chem. A

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“…To find a system which involves chemical bonding changes with low barriers and low energy changes, we considered ways in which this process has been optimized biologically and chose to examine tautomerization reactions amongst the conjugate acids of heterocyclic nitrogen bases 3 including cytosine 4 and many others. Such systems have already been shown by Aviram et al 5 to have interesting molecular electronic properties.…”

Section: Introductionmentioning

confidence: 99%

“…6 Quite frequently (see, for example, Refs. 4,7–14) pyridinol/pyridinone tautomerization is used as a model for biological systems, a key feature of which is that the relative energies of the OXO and HYDROXY tautomers are very similar so that large energy penalties are not encountered.…”

Section: Introductionmentioning

confidence: 99%

Chemical Control of Tautomerization‐Based Molecular Electronic and Color Switches

Reimers

Hall

Hush

et al. 1998

Annals of the New York Academy of Sciences

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Many schemes which have been suggested for the chemical control of molecular electronic devices are impractical because of the large energy changes associated with bond breaking and reforming: these would result in unacceptably large amounts of energy being required for device operation. We have chosen to look in detail at a class of chemical reactions prominent in biological systems that, on energetic grounds, could produce a feasible device: tautomerization reactions of heterocyclic bases. In particular, we concentrate on a model reaction, the 4‐pyridinol/4(1H)‐pyridinone tautomerization, through which an aromatic pyridinol unit is converted into a π‐localized pyridinone unit. In these molecules the functionalities are arranged para, allowing the possibility that the molecules align in a solid phase in linear hydrogen‐bonded chains. The change in the π electronic structure associated with reactions of this type is quite large, as illustrated, for example, in the conversion of quinacridone, a brightly colored pigment, to quinacridol, an uncolored species with strong UV absorption. Our primary purpose is to calculate energy changes and reaction barrier heights to see whether such tautomerization reactions could provide the basis for an operational chemically controlled molecular electronic device. We also consider, briefly, other required properties in a practicable device.

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Water and alcohol(s): what's the difference? A proton NMR and DFT study of hetero‐association with pyridine

Lomas

Maurel

2008

J of Physical Organic Chem

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Hetero‐association of water and some simple aliphatic alcohols with pyridine in benzene has been studied by 1H nuclear magnetic resonance (NMR) spectroscopy at very low donor concentration, where self‐association is negligible. Association constants for the formation of 1:1 and 2:1 pyridine:water complexes can then be determined without recourse to ad hoc computer programmes. That for association of a second pyridine with water is about 10 times lower than for the first. Reaction parameters for the first association with water are very similar to those for the alcohols, whereas the reaction enthalpy for the second association is somewhat smaller. The chemical shift of the OH protons and the HCOH coupling constants for alcohols at high dilution in benzene are almost identical with gas‐phase data. The change in chemical shift upon association with pyridine correlates with the free energy of the reaction. Quantum mechanical calculations [BPE0 functional, 6‐311+G(d,p) basis set and a polarized continuum model of the solvent (IEFPCM)] have been run on complexes of pyridine with water, both 1:1 and 2:1, and with four alcohols. Calculated reaction enthalpies are in qualitative and, in some cases, almost quantitative agreement with the experimental data. The association constants for 1:1 complexation of pyridine with alcohols follow a rough Taft correlation in terms of polar substituent constants. Substituent size, even in the case of very bulky groups, seems to be unimportant. Copyright © 2008 John Wiley & Sons, Ltd.

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Combined matrix-isolation FT-IR and ab initio 6-31++G** study of H-bonded complexes between water and molecules modelling cytosine or isocytosine

Cited by 31 publications

References 26 publications

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Chemical Control of Tautomerization‐Based Molecular Electronic and Color Switches

Water and alcohol(s): what's the difference? A proton NMR and DFT study of hetero‐association with pyridine

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