Intramolecular hydrogen bonding of nucleobases

Preparation and DFT Study for New Three-Ring Supramolecular H-Bonded Induced Liquid Crystal Complexes

Supramolecular three-ring Schiff base novel liquid crystal complexes have been prepared and investigated. Schiff bases of para-substituted aniline derivatives and para-pyridine carbaldehyde have been prepared and then mixed in equimolar quantities with para-alkoxy benzoic acids. On one side, the alkoxy chain length varies from 8 to 16 carbon atoms. On the other side, terminal small compact groups substituting aniline with various polarities are used. Hydrogen-bonding interaction was elucidated by FTIR spectroscopy. The mesomorphic thermal and optical characteristics of the samples were obtained by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). All samples exhibit enantiotropic mesophases. Experimental results obtained for the induced mesophases were correlated with density functional theory (DFT) theoretical calculations. The results revealed that both the polar compact groups' polarity and the alkoxy chain lengths contribute strongly to mesomorphic characteristics and thermal stabilities of the mesophases. Surprisingly, the observed values of enthalpy changes associated with the crystalline mesomorphic transitions lie in the range of 2.2-12.5 kJ/mol. However, the enthalpy changes corresponding to the mesomorphic-isotropic transitions vary from 0.9 to 13.9 kJ/mol, depending on the polarity of para-attached groups to the aniline moiety.

Pyridine-Based Three-Ring Bent-Shape Supramolecular Hydrogen Bond-Induced Liquid Crystalline Complexes: Preparation and Density Functional Theory Investigation

A series of new supramolecular three-ring bent-shape Schiff base liquid crystal (LC) complexes were prepared and studied. On one side, two alkoxy chain lengths of the carboxylic acids were used, namely eight and sixteen carbons. Moreover, on the other side, terminal small compact groups, which substituted aniline, with different polarities were utilized. Furthermore, the hydrogen-bonding interactions in the formed complexes were elucidated by Fourier-transform infrared (FT–IR) spectroscopy. The mesomorphic thermal and optical characteristics of the samples were determined by differential thermal analysis (DSC) and polarized optical microscopy (POM). The complexes exhibited enantiotropic and dimorphic mesophase behaviors. The results indicate that the polarity of the compact groups and the lengths of the alkoxy chains greatly impacted the mesomorphic characteristics and thermal stabilities of the mesophases. The observed values of the enthalpy changes (ΔH) associated with the crystalline smectic-A (TCr-SmA) transitions were extremely small compared with the conventional values that characterize supramolecular hydrogen-bonded liquid crystalline complexes. ΔH, which corresponded to the nematic isotropic transitions (TN-I), varied from 0.13 to 9.54 kJ/mol depending mainly on the polarity of the groups that were para-attached to the aniline moiety. Finally, the theoretical results obtained by density functional theory (DFT) calculations were discussed. The DFT geometrical structures showed non-coplanar structures. The mesomorphic range was correlated with the calculated dipole moment, polarizability and the aspect ratios of the investigated compounds.

Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance

Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H₂O, HCOOH, and the HCOOHH₂O group to facilitate the tautomerism of the Cyt2t⁺ to CytN3⁺ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol^-1, respectively, when the reaction is carried out in the absence and presence of H₂O, HCOOH, or the HCOOHH₂O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t⁺ to CytN3⁺ isomer remains unfavorable, and the HCOOH and HCOOHH₂O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3⁺HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t⁺HCOOH) (τ_99.9% = 3.84 × 10^-12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3⁺HCOOH complex (τ = 8.33 × 10^-9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3⁺ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.

N3 and O2 protonated tautomeric conformations of 2'-deoxycytidine and cytidine coexist in the gas phase

Infrared multiple photon dissociation action spectra of the protonated forms of the cytidyl nucleosides, 2'-deoxycytidine, [dCyd+H](+), and cytidine, [Cyd+H](+), are acquired over the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level to determine the stable low-energy tautomeric conformations of these species generated upon electrospray ionization (ESI) and to generate the linear IR absorption spectra of these protonated nucleosides. Comparison between the experimental and theoretical spectra allows the tautomeric conformations of [dCyd+H](+) and [Cyd+H](+) populated by ESI to be determined. B3LYP predicts N3 as the preferred protonation site for both [dCyd+H](+) and [Cyd+H](+), whereas MP2 suggests that protonation at O2 is more favorable. The 2'-hydroxyl substituent does not significantly alter the structures of the B3LYP N3 and MP2 O2 protonated ground tautomeric conformations of [dCyd+H](+) vs [Cyd+H](+). [dCyd+H](+) and [Cyd+H](+) exhibit very similar spectral signatures in both regions. Nonetheless, the 2'-hydroxyl does affect the relative intensities of the IRMPD bands of [dCyd+H](+) vs [Cyd+H](+). The spectral features observed in the hydrogen-stretching region complement those of the fingerprint region and allow the N3 and O2 protonated tautomeric conformations to be readily distinguished. Comparison between the measured and computed spectra indicates that both N3 and O2 protonated tautomeric conformations coexist in the experiments, and the populations are dominated by the most stable N3 and O2 protonated tautomeric conformations. Least-squares fitting of the IRMPD spectra to the IR spectra for these most stable conformers suggests relative populations of ∼55% N3 vs 45% O2 protonated conformers of [dCyd+H](+), whereas ∼47% N3 vs 53% O2 protonated conformers of [Cyd+H](+). This change in the preferred site of protonation indicates that the 2'-hydroxyl substituent plays an important role in controlling the reactivity of the cytidyl nucleosides.

Synthesis and antiviral properties of novel 7-heterocyclic substituted 7-deaza-adenine nucleoside inhibitors of Hepatitis C NS5B polymerase

Previous investigations in our laboratories resulted in the discovery of a novel series of potent nucleoside inhibitors of Hepatitis C virus (HCV) NS5B polymerase bearing tetracyclic 7-substituted 7-deaza-adenine nucleobases. The planarity of such modified systems was suggested to play a role in the high inhibitory potency observed. This paper describes how we envisaged to maintain the desired planarity of the modified nucleobase by means of an intra-molecular H-bond, engaging a H-bond donor atom on an appropriately substituted 7-heterocyclic residue with the adjacent amino group of the nucleobase. The success of this strategy is reflected by the identification of several novel potent nucleoside inhibitors of HCV NS5B bearing a 7-heterocyclic substituted 7-deaza-adenine nucleobase. Amongst these, the 1,2,4-oxadiazole analog 11 showed high antiviral potency against HCV replication in replicon cells and efficient conversion to the corresponding NTP in vivo, with high and sustained levels of NTP measured in rat liver following intravenous and oral administration.

A specific molecular beacon probe for the detection of human prostate cancer cells

The small-molecule, water-soluble molecular beacon probe 1 is hydrolyzed by the lysate and living cells of human prostate cancer cell lines (LNCaP), resulting in strong green fluorescence. In contrast, probe 1 does not undergo significant hydrolysis in either the lysate or living cells of human nontumorigenic prostate cells (RWPE-1). These results, corroborated by UV-Vis spectroscopy and fluorescent microscopy, reveal that probe 1 is a sensitive and specific fluorogenic and chromogenic sensor for the detection of human prostate cancer cells among nontumorigenic prostate cells and that carboxylesterase activity is a specific biomarker for human prostate cancer cells.

Synthesis and EPR studies of 2'-deoxyuridines with alkynyl, rodlike linkages

Sonogashira coupling of diacetyl 5-ethynyl-2'-deoxyuridine with diacetyl 5-iodo-2'-deoxyuridine gave the acylated ethynediyl-linked 2'-deoxyuridine dimer (3 b; 63%), which was deprotected with ammonia/methanol to give ethynediyl-linked 2'-deoxyuridines (3 a; 79%). Treatment of 5-ethynyl-2'-deoxyuridine (1 a) with 5-iodo-2'-deoxyuridine gave the furopyrimidine linked to 2'-deoxyuridine (78%). Catalytic oxidative coupling of 1 a (O(2), CuI, Pd/C, N,N-dimethylformamide) gave butadiynediyl-linked 2'-deoxyuridines (4; 84 %). Double Sonogashira coupling of 5-iodo-2'-deoxyuridine with 1,4-diethynylbenzene gave 1,4-phenylenediethynediyl-bridged 2'-deoxyuridines (5; 83%). Cu-catalyzed cycloisomerization of dimers 4 and 5 gave their furopyrimidine derivatives. One-electron addition to 1 a, 3 a, and 4 gave the anion radical, the EPR spectra of which showed that the unpaired electron is largely localized at C6 of one uracil ring (17 G doublet) at 77 K. The EPR spectra of the one-electron-oxidized derivatives of ethynediyl- and butadiynediyl-linked uridines 3 a and 4 at 77 K showed that the unpaired electron is delocalized over both rings. Therefore, structures 3 a and 4 provide an efficient electronic link for hole conduction between the uracil rings. However, for the excess electron, an activation barrier prevents coupling to both rings. These dimeric structures could provide a gate that would separate hole transfer from electron transport between strands in DNA systems. In the crystal structure of acylated dimer 3 b, the bases were found in the anti position relative to each other across the ethynyl link, and similar anti conformation was preserved in the derived furopyrimidine-deoxyuridine dinucleoside.