Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study

Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method. All intercalators exhibit large charge delocalization, and none of them (including the DAPI dication) exhibits a site with dominant charge. All intercalators have large polarizability and are good electron acceptors, while base pairs are good electron donors. MP2/6-31G*(0.25) stabilization energies of intercalator...base pair complexes are large (E...AT, 22.4 kcal/mol; D...GC, 17.8 kcal/mol; EL...GC, 18.2 kcal/mol; DAPI...GC, 21.1 kcal/mol) and are well reproduced by modified AMBER potential (van der Waals radii of intercalator atoms are enlarged and their energy depths are increased). Standard AMBER potential underestimates binding, especially for DAPI-containing complexes. Because the DAPI dication is the best electron acceptor (among all intercalators studied), this difference is explained by the importance of the charge-transfer term, which is not included in the AMBER potential. For the neutral EL molecule, the standard AMBER force field provides correct results. The Hartree-Fock and DFT/B3LYP methods, not covering the dispersion energy, fail completely to reveal any energy minimum at the potential energy curve of the E...AT complex, and these methods thus cannot be recommended for a study of intercalation process. On the other hand, an approximate version of the DFT method, which was extended to cover London dispersion energy, yields for all complexes very good stabilization energies that are well comparable with referenced ab initio data. Besides the vertical dependence of the interaction, an energy twist dependence of the interaction energy was also investigated by a reference correlated ab initio method and empirical potentials. It is concluded that, despite the cationic (E +1, D +1, DAPI +2) or polar (EL) character of the intercalators investigated, it is the dispersion energy which predominantly contributes to the stability of intercalator...base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation.     

Zr-Porphyrin Metal–Organic Framework as nanoreactor for boosting the formation of hydrogen clathrates

We report the first experimental evidence for rapid formation of hydrogen clathrates under mild pressure and temperature conditions within the cavities of a zirconium-metalloporphyrin framework, specifically PCN-222. PCN-222 has been selected for its 1D mesoporous channels, high water-stability, and proper hydrophilic behavior. Firstly, we optimize a microwave (MW)-assisted method for the synthesis of nanosized PCN-222 particles with precise structure control (exceptional homogeneity in morphology and crystalline phase purity), taking advantage of MW in terms of rapid/homogeneous heating, time and energy savings, as well as potential scalability of the synthetic method. Second, we explore the relevance of the large mesoporous 1D open channels within the PCN-222 to promote the nucleation and growth of confined hydrogen clathrates. Experimental results show that PCN-222 drives the nucleation process at a lower pressure than the bulk system (1.35 kbar vs 2 kbar), with fast kinetics (minutes), using pure water, and with a nearly complete water-to-hydrate conversion. Unfortunately, PCN-222 cannot withstand these high pressures, which lead to a significant alteration of the mesoporous structure while the microporous network remains mainly unchanged.     

Application of MIP-AES as element specific detector for speciation analysis

An MIP-AES element specific detector has been directly coupled to an HPLC separation system by means of hydraulic high-pressure nebulization (HHPN) with an appropriate desolvation unit. This system was applied to Cr(III)/Cr(VI) speciation analysis. The linear dynamic range of Cr(III) and Cr(VI) determination was two orders of magnitude, absolute detection limits were 13 ng for Cr(III) and 18 ng for Cr (VI), respectively. The matrix effect caused by the easily ionizable elements (Na, Ca, K) was significant in real samples.     

Biomimetic carbocationic polymerizations III: Investigation of isoprene polymerization initiated by dimethyl allyl bromide

Natural rubber (poly(1,4‐cis‐isoprene), NR) is a polymer of considerable industrial importance due to its exceptional properties. It is mostly produced from the cultivation of Hevea brasiliensis, and to a limited extent from Parthenium argentatum. Till date none of the synthetic equivalent of NR exists. Recently we suggested that the mechanism of NR biosynthesis is based on carbocationic polymerization, similarly to that of natural oligoisoprenoids forming by enzyme‐catalyzed prenylation. In this article we present proof of concept of a new bio‐inspired synthetic route towards the synthesis of polyisoprenes based on carbocationic polymerization initiated by dimethyl allyl bromide (DMABr)/TiCl₄. It is shown that using this strategy, 1,4‐oligoisoprene carrying a dimethyl allyl head group is produced in both cis and trans configurations, together with cyclized sequences. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2172–2180, 2009     

Internal energy distribution in electrospray ionization

Internal energies and energy distributions were studied using the 'survival yield' method developed previously. In addition to conventional benzylpyridinium salts, protonated esters (fragmenting by rearrangement) and protonated leucine enkephalin were also used, extending the validity of the technique. Fragmentation processes were studied in the cone voltage region and modeled by the RRKM-based MassKinetics program. The results show that the shapes of the energy distributions are similar to thermal distributions. The mean internal energies are very similar for all compound classes studied, and show a linear increase with collision energy in the 10-50 eV region.     

Solid-phase syntheses of furopyridine and furoquinoline systems

[reaction: see text] Syntheses of 2-substituted furo[3,2-b]pyridines and furo[3,2-h]quinolines have been achieved for the first time in the solid-phase mode. The central enabling steps involved concomitant deprotection/cyclization promoted by the mild base K(2)CO(3). Reactions were monitored "in situ" in real time by a variety of spectroscopic techniques, which allowed full and accurate control of progress in these syntheses.     

Loss of Hoogsteen pairing ability upon N1 adenine platinum binding

Chloroform- and Freon-soluble mixed thymine, adenine complexes trans-[Pt(MeNH(2))(2)(ChmT-N3)(ChmA-N1)]NO(3) (2) and trans-[Pt(MeNH(2))(2)(ChmT-N3)(TBDMS-ado-N1)]BF(4) (3) (ChmT = anion of 1-cyclohexylmethylthymine ChmTH, ChmA = 9-cyclohexylmethyladenine, TBDMS-ado = 2',3',5'-tri-tert-butyldimethylsilyladenosine) have been prepared and characterized to study their propensity to undergo Hoogsteen and/or reversed Hoogsteen pairing in solution with free ChmTH and free 3',5'-diacetyl-2'-deoxyuridine, respectively. No Hoogsteen or reversed Hoogsteen pairing between 2 and ChmT takes place in CDCl(3). In Freon, partial H bonding between N1 platinated TBDMS-ado and 3',5'-diacetyl-2'-deoxyuridine as well as its [3-(15)N] labeled analogue is unambiguously observed only below 150 K. Comparison of (1)J ((15)N-(1)H) coupling constants of 3',5'-diacetyl-2'-deoxyuridine involved in Hoogsteen pairing with free and N1 platinated adenine suggests that the interaction is inherently weaker in the case of platinated adenine. To better understand the complete absence of hydrogen bonding between the ChmA ligand in 2 and free ChmTH, ab initio calculations (gas phase, 0 K) have been carried out for Hoogsteen pairs involving adenine (A) and thymine (T), as well as simplified analogues of 2 and T, both in the presence and absence of counteranions. The data strongly suggest that reduction of the effective positive charge of the heavy metal ion Pt(2+) by counterions diminishes interaction energies. With regard to mixtures of 2 and ChmTH in chloroform, this implies that ion pair formation between the cation of 2 and NO(3)(-) may be responsible for the lack of any measurable Hoogsteen pairing in this solvent.