Theoretical Assessment of the Ligand/Metal/Quadruplex Recognition in the Non-Canonical Nucleic Acids Structures.

Quadruplexes (GQs), peculiar DNA/RNA motifs concentrated in specific genomic regions, play a vital role in biological processes including telomere stability and, hence, represent promising targets for anticancer therapy. GQs are formed by folding guanine-rich sequences into square planar G-tetrads which stack onto one another. Metal cations, most often potassium, further stabilize the architecture by coordinating the lone electron pairs of the O atoms.

Small Heterocyclic Ligands as Anticancer Agents: QSAR with a Model G-Quadruplex.

G-quadruplexes (GQs) have become valid targets for anticancer studies in recent decades due to their multifaceted biological function. Herewith, we aim to quantify interactions of potential heterocyclic ligands (Ls) with model GQs. For seven 4-aminoquinazolines and three 2-heteroaryl perimidines, seven of this ten-membered group so far unknown, we use routine quantum chemical modeling.

Biological activity of quinazoline analogues and molecular modeling of their interactions with G-quadruplexes.

Background: Quinazolines 1 to 6, with an aromatic or aryl-vinyl substituent in position 2 are selected with the aim to compare their structures and biological activity. The selection includes a natural alkaloid, schizocommunin, and the synthetic 2-(2'-quinolyl)-3H-quinazolin-4-one, known to interact with guanine-quadruplex dependent enzymes, respectively telomerase and topoisomerase.

Methods: Breast cancer cells of the MDA cell line have been used to study the bioactivity of the tested compounds by the method of Comet Assay and FACS analyses.

Solvent induced shifts of electronic spectra IV. Computational study on PRODAN fluorescence and implications to the excited state structure.

Vertical S(1)-S(0) electronic transitions of the highly solvent-sensitive fluorescence label 2-propionyl-6-dimethylamino naphthalene (PRODAN) are modeled by semiempirical CISD AM1 and TD DFT calculations in a large number of solvents of different polarity and hydrogen donating ability. Calculations correctly reproduce the observed solvent induced shifts of the emission maxima. The fluorescence Frank-Condon transition energies in solvent can be predicted quantitatively at the AM1 SM5.

Origins of stereoselectivity in the Diels-Alder addition of chiral hydroxyalkyl vinyl ketones to cyclopentadiene: a quantitative computational study.

Modest basis set level MP2/6-31G(d,p) calculations on the Diels-Alder addition of S-1-alkyl-1-hydroxy-but-3-en-2-ones (1-hydroxy-1-alkyl methyl vinyl ketones) to cyclopentadiene correctly reproduce the trends in known experimental endo/exo and diastereoface selectivity. B3LYP theoretical results at the same or significantly higher basis set level, on the other hand, do not satisfactorily model observed endo/exo selectivities and are thus unsuitable for quantitative studies. The same is valid also with regard to subtle effects originating from, for example, conformational distributions of reactants.

Correlated MO study of the low-barrier intramolecular motions in donor-acceptor ethenes.

Correlated MP2 and MCSCF MO calculations of several model push-pull ethenes in most cases indicate no great participation of excited singlet and triplet electronic configurations in either the minima or the transition structures for the suggested facilitated intramolecular rotation about the polarized C=C bond. This situation changes significantly only in molecules with sulfur atoms in the molecule as either donors or acceptors. The outstanding contribution of sulfur atoms as either donors or acceptors is a significant increase of push-pull ethene molecular polarizabilities.

Thorpe-Ingold effects in cyclizations to five-membered and six-membered rings containing planar segments. The rearrangement of N(1)-alkyl-substituted dihydroorotic acids to hydantoinacetic acids in base.

While the gem-dimethyl effect (GDME) is quantitatively similar for cyclizations to cyclopentane and cyclohexane rings and their homomorphs, in systems containing planar segments the GDME is stronger for the formation of five-membered rings. Planar pentagons have smaller angles than planar hexagons and their formation is helped by the decrease in the potential internal bond angle caused by substituents, as suggested by Thorpe and Ingold for small rings. The phenomenon is illustrated with crystal structure data on five-membered hydantoins and six-membered dihydrouracils containing four-atom planar segments.

Schiff base addition to cyclic dicarboxylic anhydrides: an unusual concerted reaction. An MO and DFT theoretical study.

The existing controversy as to whether dicarboxylic anhydride iminolysis by Schiff bases is a concerted [4 + 2] addition or a stepwise reaction following either a Perkin-like route or occurs as iminolysis via zwitterionic intermediates is solved computationally by DFT and MO theory. Both types of theory favor a concerted mechanism starting as bimolecular addition of imine to the carbonyl carbon of anhydride monoenol, accompanied by simultaneous elimination of carboxylate. The reaction proceeds further without forming any intermediate and completes as intramolecular charge transfer from enol HOMO to imine LUMO with ring closure.

Fluorinated alcohols enable olefin epoxidation by H2O2: template catalysis.

Experimental observations show that direct olefin epoxidation by H(2)O(2), which is extremely sluggish otherwise, occurs in fluorinated alcohol (R(f)OH) solutions under mild conditions requiring no additional catalysts. Theoretical calculations of ethene and propene epoxidation by H(2)O(2) in the gas phase and in the presence of methanol and of two fluorinated alcohols, presented in this paper, show that the fluoro alcohol itself acts as a catalyst for the reaction by providing a template that stabilizes specifically the transition state (TS) of the reaction. Thus, much like an enzyme, the fluoro alcohol provides a complementary charge template that leads to the reduction of the barrier by 5-8 kcal mol(-)(1).