A theoretical investigation of tautomeric equilibria and proton transfer in isolated and monohydrated cytosine and isocytosine molecules (original) (raw)
Related papers
International Journal of Quantum Chemistry, 1998
The results of an ab initio post-Hartree᎐Fock study of the molecular structures, relative stabilities, and mechanisms of intermolecular proton transfer in isolated and monohydrated cytosine complexes are reported. The geometries of the local minima and transition states were optimized without symmetry restrictions by the gradient procedure at the HF and the MP2 levels of theory and were verified by energy Ž . second-derivative calculations. The standard 6-31G d basis set was used. The single-point Ž . Ž . Ž . calculations were performed at the MP4 SDQ r6-31 q G d, p rrMP2r6-31G d and Ž . Ž . MP2r6-311qqG d, p rrMP2r6-31G d approximations. All values of the total energies were corrected for scaled zero-point energy contributions. The post-Hartree᎐Fock ab initio theory predicts the height of the proton-transfer barrier for monohydrated cytosine complexes to be approximately three times lower for the tautomeric oxo-hydroxo reaction Ž compared with non-water-assisted processes. The influence of polar media Onsager's . self-consistent reaction-field model slightly changes these values according to the order of the stability of the tautomers in a polar solution. The interaction with one water molecule changes the order of the relative stability of cytosine tautomers from the gas Correspondence to: J. Leszczynski.
The tautomeric equilibria of cytosine studied by NQR spectroscopy and HF, MP2 and DFT calculations
Journal of Molecular Structure, 2003
A study was undertaken to check if such parameters as NQR frequencies, quadrupole coupling constants and the asymmetry parameters determined from the 14 N NQR spectra can provide sufficient information to infer about the tautomeric form of a compound studied. The influence of the choice of functional on the 14 N NQR parameters calculated by ab initio and DFT methods was analysed. Moreover, the influence of the neighbouring molecules on the NQR parameters was checked for the assumed symmetric planar environment of the cytosine molecule in which it is hydrogen-bonded to four other cytosine molecules. Since the use of a finite basis set is always a source of uncertainties in the electric field gradient tensor components, the final calculations for a layer were performed in two different basis sets: middle and extended. q
Tautomerism of cytosine, cytidine, and deoxycytidine: Proton transfer through water bridges
International Journal of Quantum Chemistry, 2022
Altogether six tautomers of cytosine and three tautomers of cytidine and deoxycytidine are studied theoretically in the gas phase and in a microhydrated environment. Their structures are optimized at MP2/6-31 + G(d,p) level. The relative energies of the isolated and the hydrated tautomers included the correction to higher correlation energy terms evaluated at the SCS-MP2, MP4, and CCSD(T) levels. The free energies at 298 K and higher temperatures are based on the above-mentioned relative energies and temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31 + G(d,p) level. Theoretical predictions for the coexistence of five species for cytosine in the gas phase (canonical, trans-and cis-enol-amino, transand cis-imino-oxo forms) fully agree with recent experimental results. Five-hydrated cytosine tautomeric forms of are investigated at CPCM/SCS-MP2/6-31 + G(d,p) level to evaluate the interconversion barriers between them and to explain the coexistence, experimentally proven, of two amino-oxo and one imino-oxo tautomers of cytosine in aqueous solution. The presence of coordinated water molecules acting as
Tautomerism in 7-Hydroxyquinoline: A Combined Experimental and Theoretical Study in Water
The Journal of Physical Chemistry A, 2011
A large number of low-molecular-weight compounds bind reversibly to proteins and are widely used as extrinsic probes to explore the interior properties of biological systems. 1,2 Molecules possessing one or more hydrogen bonds in their structure show a large sensitivity in their spectroscopy to solvent polarity. We have used some of these molecules to probe protein binding sites 3À7 and photoinduced tautomerization in DNA. 8À10 Recently, we examined one of the drug-binding sites of human serum albumin using 7-hydroxyquinoline (7HQ) as a local reporter. 11 The results point to the existence of water inside the binding site and to the role of water in molecular recognition and ligand binding. 7HQ is useful in this regard due to the high sensitivity of its spectroscopy to protic solvents and the unique spectroscopic signatures in aqueous solution. A molecule such as 7HQ that has both acidic and basic functional groups may serve as a model to study proton transfer in enzymes and proteins. 12À14 Herein, we characterize the spectroscopy of 7HQ in different solvents, particularly in aqueous medium, to understand the photophysics of the reversible interaction of 7HQ with water molecules.
The Tautomerism of Cytosine and Hydroxycytosine. A Quantum-Mechanical Study
Zeitschrift für Naturforschung C, 1982
Semi-empirical studies by the MNDO and MINDO-3 methods together with ab initio studies by the Hartree Fock method, have been performed on the tautomers of cytosine (C) and hydroxycytosine (HC), in each case with full optimisation of the molecular skeleton. The results are in agreement with recent solution studies of these systems, and show that the amino form of C and the oxime form of HC are the lowest energy tautomers. Thus the property is one of the ring system rather than environment. Various conformers of the imino tautomer of 5-methyl-N(4)-hydroxycytosine were studied by MINDO/3 and PCILO calculations; although only partial geometry optimisation was performed, it seems unlikely that the molecule can be a complementary base to adenine in the Watson-Crick sense.`
Chemical Physics Letters, 1996
The structures and relative stabilities of the four different forms of hydroxypyridine and hydroxyquinoline (normal, protonated cation, deprotonated anion and zwitterion) in the gas phase have been calculated at the M¢ller-Plesset (MP) perturbation and coupled-cluster theory levels with basis sets up to 6-3 I+G**. The solvation free energies of the reactions were treated with the SMx series of aqueous solvation models by Cramer and Truhlar. By combining the PM3-SM3 model for solvation with the MP2/6-31 +G** level treatment for the gas-phase species, it is found that the free energy changes of the proton transfer reactions can be predicted reasonably well.
Journal of Molecular …, 2000
The geometries, harmonic vibrational frequencies and energies of the two stable cyclic structures of the keto tautomer of cytosine complexed with water are computed using density functional theory (B3LYP) combined with the 6-31ϩϩG(d,p) basis set. The effect of complex formation with water on the pyramidalization of the amino group is discussed. The proton affinities of the oxygen and nitrogen atoms and the deprotonation enthalpies of the three NH bonds of cytosine are computed at the same level of theory. The deprotonation enthalpies of the two NH bonds of the amino group differ by 23 kJ mol Ϫ1 from each other and this reflects the asymmetric deformation of the amino group. The most stable hydrogen bond between cytosine and water is formed at the acceptor atom characterized by the lowest proton affinity and at the NH group having the highest acidity. The results are compared with data obtained at the same level of theory for the uracil-and thymine-water complexes. For the three nucleobases, the intermolecular distances and the energies of the hydrogen bonds formed at the different sites depend on the proton affinity and the deprotonation enthalpy of these sites. The dominance of the proton donor capacity in determining the hydrogen-bond energies and the cooperativity in the cyclic structures are discussed. ᭧
A Theoretical Study of Chloroquine Tautomerism
Journal of Computational and Theoretical Nanoscience, 2011
A theoretical study about the chloroquine was executed using DFT method (B3LYP/6-31G * ) to clarify anti-malarial influence of 4-amine-quinoline (AQ) tautomerism. Stability and reactivity were determined by geometric and energetic parameters in gas phase for AQ as simplified model of chloroquine (CQ) and compared with water and chloroform solvents using PCM methods. The results have shown that AQ is more stable than 4-imine-quinoline (IQ) on the gas phase and these relative energy differences of the tautomers were increased by solvent effect influence.