Search results for "Nucleobase"
showing 9 items of 69 documents
Determination of the lowest-energy oxidation site in nucleotides: 2'-deoxythymidine 5'-monophosphate anion.
2006
High level ab initio computations anticipate nucleobases as the most favorable sites for oxidation in nucleotides. At the CASPT2 level, the lowest ionization channel for the 2'-deoxythymidine 5'-monophosphate anion is related to a pi-orbital of the thymine base. The present findings lead to revision of the recent assignments of the photodetachment photoelectron spectra of mononucleotide anions in the gas phase and support the classical view of the nucleobase being the main actor in the oxidation process of both nucleosides and nucleotides.
DNA nucleobase properties and photoreactivity: Modeling environmental effects
2009
Abstract The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more acc…
B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double…
2013
actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…
Receptors for Nucleotides
2012
Recognition and activation of nucleotides by polyammonium receptors constitute an important target in supramolecular chemistry since the very beginning of this field. Nucleotides have three components: (i) the polyphosphate chain, (ii) the sugar moiety, and (iii) the nucleobase, which permit their multipoint binding through attractions between opposite charges, hydrogen bonding, π-stacking, CH–π interactions, and so on. In this chapter, different receptors for nucleotides, most but not all of them consisting polyamines, are examined, focusing on their molecular structure that enables different binding modes to be operated. Also, a number of examples of nucleotide binding through metal compl…
Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d, e]-anellated isoquinoline derivative with base paired deo…
1996
Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form π,π-charge-transfer interactions with the purine…
Cyclobutane Pyrimidine Photodimerization of DNA/RNA Nucleobases in the Triplet State
2010
The photoinduced formation of cyclobutane pyrimidine dimers in the triplet excited state of the DNA/RNA pyrimidine nucleobases pairs has been studied at the CASPT2 level of theory. A stepwise mechanism through the triplet state of the homodimer is proposed for the pairs of nucleobases cytosine, thymine, and uracil involving a singlet−triplet crossing intermediary structure of biradical character representing the most favorable triplet state conformation of the nucleobases as found in the DNA environment. The efficiency of the mechanism will be modulated by two factors: the effectiveness of the triplet−triplet energy transfer process from a donor photosensitizer molecule, which relates to th…
A Gadolinium(III) Complex Based on the Thymine Nucleobase with Properties Suitable for Magnetic Resonance Imaging
2021
The paramagnetic gadolinium(III) ion is used as contrast agent in magnetic resonance (MR) imaging to improve the lesion detection and characterization. It generates a signal by changing the relaxivity of protons from associated water molecules and creates a clearer physical distinction between the molecule and the surrounding tissues. New gadolinium-based contrast agents displaying larger relaxivity values and specifically targeted might provide higher resolution and better functional images. We have synthesized the gadolinium(III) complex of formula [Gd(thy)2(H2O)6](ClO4)3·2H2O (1) [thy = 5-methyl-1H-pyrimidine-2,4-dione or thymine], which is the first reported compound based on gadolinium…
Multifacial Recognition in Binary and Ternary Cocrystals from 5-Halouracil and Aminoazine Derivatives
2018
A systematic analysis using single crystal X-ray diffraction was performed to explore the role exerted by potential intercomponent proton-transfer reactions in the supramolecular structures of A–B cocrystals formed by 5-haloderivatives of uracil (A), coupled with 2-aminoadenine simulants (aminoazines, B). Twelve new heterodimers were synthesized in different stoichiometries and cocrystallized by solvent cogrinding followed by solution crystallization. In the binary cocrystals, uracil or 1-methyluracil with halide modification at the 5 position (F, Cl, Br, I) was coupled with amino-aromatic N-heterocycles (melamine, 2,4,6-triaminopyrimidine, 2,6-diaminopyridine) as a multivalent site for pyr…
6-Methyluracil: a redetermination of polymorph (II)
2019
6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, molecules form ribbons approximately running parallel to the c-axis direction through N—H...O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms…