A theoretical study of tautomerism of cytosine, thymine, uracil and their 1-methyl analogues in the gas and aqueous phases using AM1 and PM3

Civcir, Pervin Ünal

doi:10.1016/s0166-1280(00)00556-x

Cited by 67 publications

(38 citation statements)

References 50 publications

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“…Tautomers differ in heat and energy of formation, proton affinities, dipole moments, and ionization potentials [see examples in Refs. [272,273]]. There are numerous studies of tautomers in gas or aqueous solution, however, little is known about tautomerism of ligands in the binding site of proteins.…”

Section: Tautomerism and Bindingmentioning

confidence: 99%

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

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The effect of weak intermolecular interactions on the binding affinity between ligand-protein complexes plays an important role in stabilizing a ligand at the interface of a protein structure. In this review article, we will explore the different ways of taking into account these interactions, mainly intramolecular hydrogen bonds, in docking calculations. Their possible limitations and their suitable application domains are highlighted. Inspection of the outliers of this study probed very stimulating, as it provides opportunities and inspiration to medicinal chemists, being a reminder of the impact that minimal chemical modifications can have on biological activities.

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Section: Tautomerism and Bindingmentioning

confidence: 99%

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

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“…Implementation of increased basis sets of atomic orbitals and electron correlation effects, which are critical for capturing stacking interactions, has led theoreticians to claim more accurate and realistic values for tautomeric equilibria. [123][124][125][126] Typically, these studies give free energies that disfavor rare tautomers by ϳ5-10 kcal/mol under aqueous conditions, with protonated tautomers disfavored by an additional 5 kcal/mol or so at neutral pH. Although these values are likely to get adjusted as methods are refined, the fact that they cluster suggests that they may be used as reasonable estimates of the energetics that a ribozyme would have to provide in order to have a reasonable population of a tautomer.…”

Section: Kinetic Complexity and The Possible Involvement Of Tautomersmentioning

confidence: 99%

Catalytic roles for proton transfer and protonation in ribozymes

Bevilacqua

Brown

Nakano³

et al. 2003

Biopolymers

149

185

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Utilization of proton transfer in catalysis, which is well known in the mechanisms of protein enzymes, has been described only relatively recently for RNA enzymes. In this article, we present a current understanding of proton transfer by nucleic acids. Rate enhancement and specificity conferred by general acid-base catalysis are discussed. We also present possibilities for electrostatic catalysis from general acids and bases as well as cationic base pairs. The microenvironments of a large RNA provide the possibility of histidine-like pK(a)s for proton transfer, as well as lysine- and arginine-like pK(a)s for electrostatic catalysis. Discussion on proton transfer focuses on the hepatitis delta virus (HDV) and hairpin ribozymes, with select examples drawn from the protein literature. Discussion on electrostatic catalysis also draws on these two ribozymes, and a postulate for electrostatic catalysis by a cationic base pair in the mechanism of peptidyl transfer in the ribosome is presented. We also provide a perspective on possibilities for phosphoryl transfer mechanisms involving phosphorane intermediates and unusual tautomeric forms of the bases. Lastly, a distinction is made between ground state and "transition state" pK(a)s. We favor a model in which changes in pH lead to changes in the distribution of reactive and nonreactive ionizations of the ribozyme molecules in the ground state, and therefore suggest that "pK(a) changes in the transition state" do not provide an acceptable explanation for observed pH-rate profiles.

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“…Our notation is based on the literature from reference. 7,34 The "2" tautomer was found to be most stable in their gas phase at the level of B3LYP, whereas the "1" tautomer appeared to be more stable than the "2" tautomer by only 1.7 and 2.1 kcal/ mol at the level of HF and MP2, respectively. The zwitter ionic "4" tautomer was calculated to be least stable for the gas phase presumably due to its charge repulsion as listed in Table 3.…”

Section: Resultsmentioning

confidence: 98%

“…The six tautomeric forms that could be coordinated to metal atoms were considered among many possibilities. 7 The geometry optimization for the tautomers was carried out starting from many possible orientations. During the geometry optimization, no geometric constraints such as planarity were used for the present calculation.…”

Section: Calculation Methodsmentioning

confidence: 99%

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Tautomerism of Cytosine on Silver, Gold, and Copper: Raman Spectroscopy and Density Functional Theory Calculation Study

2008

Bulletin of the Korean Chemical Society

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Tautomerism of pyrimidine base cytosine has been comparatively examined on nanoparticle and roughened plate surfaces of silver, gold, and copper by surface-enhanced Raman scattering (SERS). The SERS spectrum was found to be different depending on the metals and their substrate conditions suggesting the dissimilar population of various tautomers of cytosine on the surfaces. The ab initio calculations were performed at the levels of B3LYP, HF, and MP2 levels of theory with the LanL2DZ basis set to estimate the energetic stability of the tautomers with the metal complexes as well as the gas phase state. The amino group and N 3 -coordinated tautomer was predicted to be more favorable for bonding to Au, whereas the hydroxyl and N 1 -coordinated zwitter ionic form is most stable with Ag and Cu as a bidentate form from the DFT calculation. The binding energy with the Ag atom is calculated to be smaller than those with the Au and Cu atoms in line with the temperature-dependent SERS spectra of cytosine.

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A theoretical study of tautomerism of cytosine, thymine, uracil and their 1-methyl analogues in the gas and aqueous phases using AM1 and PM3

Cited by 67 publications

References 50 publications

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Catalytic roles for proton transfer and protonation in ribozymes

Tautomerism of Cytosine on Silver, Gold, and Copper: Raman Spectroscopy and Density Functional Theory Calculation Study

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