On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Electron attachment step in electron capture dissociation (ECD) and electron transfer dissociation (ETD)

We have made use of classical dynamics trajectory simultions and ab initio electronic structure calculations to estimate the cross sections with which electrons are attached (in electron capture dissociation (ECD)) or transferred (in electron transfer dissociation (ETD)) to a model system that contained both an S-S bond that is cleaved and a -NH(3)(+) positively charged site. We used a Landau-Zener-Stueckelberg curve-crossing approximation to estimate the ETD rates for electron transfer from a CH(3)(-) anion to the -NH(3)(+) Rydberg orbital or the S-S sigma* orbital. We draw conclusions about ECD from our ETD results and from known experimental electron-attachment cross sections for cations and sigma-bonds. We predict the cross section for ETD at the positive site of our model compound to be an order of magnitude larger than that for transfer to the Coulomb-stabilized S-S bond site. We also predict that, in ECD, the cross section for electron capture at the positive site will be up to 3 orders of magnitude larger than that for capture at the S-S bond site. These results seem to suggest that attachment to such positive sites should dominate in producing S-S bond cleavage in our compound. However, we also note that cleavage induced by capture at the positive site will be diminished by an amount that is related to the distance from the positive site to the S-S bond. This dimunition can render cleavage through Coulomb-assisted S-S sigma* attachment competitive for our model compound. Implications for ECD and ETD of peptides and proteins in which SS or N-C(alpha) bonds are cleaved are also discussed, and we explain that such events are most likely susceptible to Coulomb-assisted attachment, because the S-S sigma* and C=O pi* orbitals are the lowest-lying antibonding orbitals in most peptides and proteins.     

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.     

Empirical parameters of lewis acidity and basicity for aqueous binary solvent mixtures

Empirical parameters of Lewis acidity, E^N_T, introduced by Reichardt et al., and Lewis basicity, B_KT , introduced by Kamlet and Taft, have been determined for mixtures of water with ten organic solvents. In the case of water/alcohol mixtures a distinct dependence between these acidity and basicity parameters have been found. For the other solvent mixtures the E^N_T on B_KT dependence is more complex even if these parameters are purified from non-specific solute/solvent interactions.     

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.     

Determination of oxygen content in YBa2Cu3O6.5+x

A method for determining the oxygen content of the high-temperature superconductor YBa₂Cu₃O_6.5+x is described. The superconductor is dissolved in 4.4 M hydrobromic acid, forming bromine. The mixture is then diluted with hydrochloric acid to obtain a solution of bromine and Cu(II) in 0.44 M hydrobromic acid and 1.1 M hydrochloric acid. As(III) is added in slight excess of that required to react with the bromine and the unreacted As(III) is determined by titration with potassium bromate. Oxygen does not interfere. The results of this method are in agreement with those of other iodimetric procedures. The dissolution of the superconductor in 4.4 M hydrobromic acid is much faster than in hydrochloric acid, the medium used in one iodimetric technique. YBa₂Cu₃O_6.5+x sintered fibers and powder samples weighing from ca. 0.5 to 200 mg were analyzed for oxygen content.     

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.