Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Enantiomerically pure 4-amino-1,2,3-trihydroxybutylphosphonic acids

(1S,2R,3S)-, (1R,2R,3S)- and (1S,2R,3R)-4-amino-1,2,3-trihydroxybutylphosphonic acids were synthesised. The synthetic strategy involved preparation of the respective 4-azido-2,3-O-isopropylidene-l-threose or -d-erythrose, addition of dialkyl phosphites, separation of C-1 epimeric O,O-dibenzyl phosphonates, the reduction of azides and the removal of the protecting groups. The (2R,3S) and (2R,3R) configurations in the final products were secured by employing diethyl l-tartrate and d-isoascorbic acid as starting materials. The stereochemical course of the addition to the carbonyl groups in 4-azido-2,3-O-isopropylidene-l-threose or -d-erythrose followed that established earlier for 2,3-O-isopropylidene-d-glyceraldehyde and similar (3:1-4:1) diastereoselectivities were achieved.     

New Molecular Receptors with Cyclophosphazene Subunits: Synthesis, Reactivity, and Structure-Property Relationships

A series of hydrophopic ( 2 and 3) and new hydrophilic ( 4– 7) molecular receptors of the PNP-lariat ether with tetra-substituted cyclotriphosphazene subunits have been prepared by the complete nucleophilic substitution of chlorine atoms in the reactive PNP-crown precursor 1 with the respective sodium cation-paired oxyanions (phenoxy 2, -naphthoxy 3, and methoxytrioxyethylenoxy 4) and aliphatic amines (n-propylamine 5 aziridine 6, and pyrrolidine 7). Their structures were established by MS and ³¹P NMR spectroscopy and their metal ion complexing properties tested by a TLC method. Comparison of the complexation behaviour for ligands 1– 7 shows that the affinity for particular cations is strongly substituent-dependent and, in general, is significantly enhanced by cooperation of the side arm donor atoms (O or N) with the parent PNP-crown structure in the binding process. The remarkable affinity of some ligands for selected cations, in particular lithium, cesium, and silver ions, is interpreted in terms of structure-property relationships.     

Correction to: Foreword to the memorial issue for Professor Roberto Marassi

Journal of Solid State Electrochemistry -     

New Insight on Carbon Dioxide-Mediated Hydrogen Production**

A new approach to hydrogen production from water is described. This simple method is based on carbon dioxide-mediated water decomposition under UV radiation. The water contained dissolved sodium hydroxide, and the solution was saturated with gaseous carbon dioxide. During saturation, the pH decreased from about 11.5 to 7–8. The formed bicarbonate and carbonate ions acted as scavengers for hydroxyl radicals, preventing the recombination of hydroxyl and hydrogen radicals and prioritizing hydrogen gas formation. In the presented method, not yet reported in the literature, hydrogen production is combined with carbon dioxide. For the best system with alkaline water (0.2 m NaOH) saturated with CO₂ under UV-C, the hydrogen production amounted to 0.6 μmol h⁻¹ during 24 h of radiation.     

Lipase-catalyzed kinetic resolution approach toward enantiomerically enriched 1-(β-hydroxypropyl)indoles

In a route towards enantiomerically enriched 1-(β-hydroxypropyl)indoles, which are potentially useful building blocks for high value-added chemicals synthesis, a kinetic resolution approach by means of lipase-catalyzed enantioselective acylation as well as hydrolysis/methanolysis has been elaborated for the first time. The enzymatic resolution of chiral N-substituted indole-based sec-alcohols was successfully accomplished, yielding both enantiomeric forms of the employed derivatives with up to >99% enantiomeric purity via an enantioselective transesterification under mild reaction conditions. The most selective resolutions were obtained using fungal (CAL-B and TLL) and bacterial (PFL and BCL) lipases and vinyl acetate as the acyl?group donor. The synthetic protocol described herein is very simple, user-friendly and efficient, thus paving the way for future access towards more complex compounds of this type. The absolute configurations of novel enantiomeric derivatives, and thus stereoselectivity of the described enzymatic reactions were confirmed by application of CDA-based NMR methodology and single-crystal X-ray diffraction analysis.     

Pentafluorophenyl Esters as Exchangeable Stoppers for the Construction of Photoactive [2]Rotaxanes

Stable pillar[5]arene-containing [2]rotaxane building blocks with pentafluorophenyl ester stoppers have been efficiently prepared on a multi-gram scale. Reaction of these building blocks with various nucleophiles gave access to a wide range of [2]rotaxanes with amide, ester or thioester stoppers in good to excellent yields. The rotaxane structure is fully preserved during these chemical transformations. Actually, the addition-elimination mechanism at work during these transformations totally prevents the unthreading of the axle moiety of the mechanically interlocked system. The stopper exchange reactions were optimized both in solution and under mechanochemical solvent-free conditions. While amide formation is more efficient in solution, the solvent-free conditions are more powerful for the transesterification reactions. Starting from a fullerene-functionalized pillar[5]arene derivative, this new strategy gave easy access to a photoactive [2]rotaxane incorporating a C₆₀ moiety and two Bodipy stoppers. Despite the absence of covalent connectivity between the Bodipy and the fullerene moieties in this photoactive molecular device, efficient through-space excited state interactions have been evidenced in this rotaxane.     

Effectiveness of the Oxygenation over Classical Protonolysis Reactions: A Case of Alkylzinc Complexes Incorporating an Aminoalcoholate Ligand

Alkylzinc aminoalcoholates have emerged as powerful catalysts in organic synthesis and polymerization processes. Despite extensive research, difficulties in the rational design of these catalytic systems and in-depth understanding of their modes of action have hitherto been encountered. Most of the major obstacles stem largely from the relatively limited knowledge of the structure-activity relationship of zinc catalysts. In fact, the key active species are often generated in situ via the protonolysis of the alkylzinc precursors, which precludes their isolation and detailed characterization. Herein, the effectiveness of the oxygenation over the classical protonolysis in the synthesis of zinc alkylperoxides stabilized by an aminoalcoholate ligand is demonstrated. The controlled oxygenation of a tert-butylzinc complex incorporating a pridinolum (prinol) ligand leads to well-defined a dinuclear adduct of a (prinol)ZnOOtBu moiety with the parent tBuZn(prinol) complex and a novel dimer [tBuOOZn(prinol)]₂ with terminal alkylperoxide groups. The observed reaction outcomes strongly depend on the reaction conditions. Although sparse examples of heteroleptic adducts of the [RZn(L)]_x[ROOZn(L)]_y-type are known, the herein reported homoleptic [ROOZn(L)]_x aggregate is unprecedented. Strikingly, comparative studies involving reactions between tBuZn(prinol) and tert-butylhydroperoxide or ethanol revealed that the respective seemingly simple zinc alkylperoxides, or zinc alkoxides, respectively, are not accessible via the classical alcoholysis. We believe that these game-changing results concerning multifaceted chemistry of organozinc aminoalcoholates should pave the way for more rational development of various Zn-based catalytic systems.     

Unravelling Structural Mysteries of Simple Organozinc Alkoxides

Simple RZnOR’ alkoxides are among the first known organozinc compounds, and widespread interest in their multifaced chemistry has been driven by their fundamental significance and potential applications including various catalytic reactions. Nevertheless, their chemistry in solution and in the solid state remains both relatively poorly understood and a subject of constant debate. Herein, the synthesis and structural characterization of long-sought structural forms, a roof-like trimer [(tBuZn)₃(μ-OC(H)Ph₂)₂(μ₃-OC(H)Ph₂)] and a ladder-type tetramer [(PhZn)₄(μ-OC(H)Ph₂)₂(μ₃-OC(H)Ph₂)₂], incorporating diphenylmethanolate as a model alkoxide ligand, are reported. Both novel aggregates are robust in the solid state and resistant towards mechanical force. By using ¹H NMR and diffusion-order spectroscopy, it is demonstrated that new RZnOR’ alkoxides are kinetically labile in solution and readily undergo ligand scrambling, such as in the case of Schlenk equilibrium. The elucidated key structural issues, which have remained undiscovered for decades, significantly advance the chemistry of RZnOR’ alkoxides and should support the rational design of zinc alkoxide-based applications.     

Design,synthesis and application of new bile acid ligands with 1,2,3-triazole ring

New dimers have been obtained from propargyl ester of bile acids and α,α′-diazide-m-xylene by intermolecular 1,3-dipolar cycloaddition. These compounds have been used as ligands to form intermolecular hydrogen bonds with various aromatic acids. The structures of all products were confirmed by spectroscopic (¹H NMR, ¹³C NMR and FT-IR) analysis, mass spectrometry (ESI, MALDI) and PM5 semiempirical methods.