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.     

Facile one-pot synthesis of BINOL- and H8-BINOL-based aryl phosphites and their use in palladium catalysed asymmetric allylation

Novel P-monodentate aryl phosphite ligands have been synthesised in one step from (R)-BINOL, (R)-H₈-BINOL and (R)-H₈-3,3′-dibromo-BINOL. With the new aryl phosphites, up to 86% ee was observed in the asymmetric Pd-catalysed amination of 1,3-diphenyl-2-propenyl acetate with sodium diformylamide. In the enantioselective alkylation of 1,3-diphenyl-2-propenyl acetate with dimethyl malonate, up to 97% enantioselectivity was achieved.     

A method for the palladium-catalyzed allylic oxidation of olefins

Olefins are converted into allylic acetates by treatment in acetic acid with a catalytic amount of palladium bis(trifluoroacetate) and one equivalent of benzoquinone as oxidant. The reaction is selective for oxidation of a terminal methyl group of geranylacetone.     

The cleavage of heterocyclic compounds in organic synthesis II Use of 5‐nitroisatine for synthesis of various nitrogenous heterocycles

The reactions of 5‐nitroisatine were studied with nucleophiles like heterocyclic amines and alkaline hydroxide. With the use of alkaline hydroxide it was converted into 2‐amino‐5‐nitrophenylglyoxylic acid 2 , with piperidine, morpholine and carbethoxypiperazine to its amides 4a‐4c or by oxidation to 5‐nitroanthranilic acid 7. This acid was used for synthesis of 3‐hydroxy‐6‐nitro‐2‐phenyl‐1H‐quinolin‐4‐one 10. Semicarbazone of 5‐nitroisatine 11 was converted to 5‐(2‐amino‐5‐nitrophenyl)‐2,3,4,5‐tetrahydro‐1,2,4‐triazine‐3,5‐dione 12. Cyclocondensation of this compound to afford 8‐nitro‐2,3‐dihydro‐5H‐[1,2,4]triazino‐[5,6‐b]indol‐3‐one 13 was unsuccessful.     

Metal complexes with an aminosubstituted tricarbollide ligand

The reaction of the tricarbollide salt Tl[7-tBuNH-7,8,9-C₃B₈H₁₀] (Tl1) with [(cod)Rh(THF)_x]⁺ gives the rhodium complex [1-(cod)-12-tBuNH-1,2,4,12-RhC₃B₈H₁₀] in almost quantitative yield. Analogous reactions of Tl1 with [(ring)M(THF)_x]²⁺ ((ring)M = Cp*Rh and (1,3,5-C₆H₃Me₃)Ru) afford the corresponding metallatricarbollides [1-(ring)-12-tBuNH-1,2,4,12-MC₃B₈H₁₀] in ca. 50% yield. Refluxing Tl1 with [Mn(CO)₃(MeCN)₃]⁺ in THF give the tricarbollide analogue of cymantrene, [1,1,1-(CO)₃-12-tBuNH-1,2,4,12-MnC₃B₈H₁₀], the structure of which was determined by single-crystal X-ray diffraction analysis. In all cases, the formation of the metallatricarbollide complexes is accompanied by polyhedral rearrangement leading to the maximum separation of the cage carbon atoms.     

The Remarkable Structure of Lithium Cyanide/Isocyanide

Electron correlation corrections have a considerable influence on the relative stabilities of lithium isocyanide ( 1 ), lithium cyanide ( 2 ), and the bridged form, 3 . While Hartree-Fock theory finds 1 to be most stable and 3 not to be a minimum, MP2/6-31G* optimization indicates 3 to be the global minimum. At higher levels employing full fourth-order Møller-Plesset theory and a quadruply split valence and polarized basis set (MP4STDQ/6-311+G*), 2 is only about 2 kcal/mol less stable than 1 and 3 , which are indicated to have nearly the same energy. LiNC thus is similar to C(Na)N and C(K)N, both of which are known to prefer T-shaped (bridged) structures in the gas phase. However, to an even greater extent than formerly realized, rotation of the lithium cation around the cyanide anion nucleus should be practically free. ΔH (LiCN) = 32.8 kcal/mol is estimated from the calculated lithium cation affinity of 151.2 kcal/mol. In addition, we find at the MP4SDTQ/6-31+G*//MP2/6-31G* level that the bridged form of NaCN is favored by 2–3 kcal/mol over the corresponding linear forms, which have nearly the same energy.     

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine homodimers were determined by the MP2 and CCSD(T) calculations utilizing a wide range of split-valence, correlation-consistent, and bond-functions basis sets. Complete basis set MP2 (CBS MP2) stacking energies extrapolated using aug-cc-pVXZ (X = D, T, and for pyrimidine dimer Q) basis sets equal to -5.3, -12.3, and -11.2 kcal/mol for the first three dimers, respectively. Higher-order correlation corrections estimated as the difference between MP2 and CCSD(T) stacking energies amount to 2.0, 0.7, and 0.9 kcal/mol and lead to final estimates of the genuine stacking energies for the three dimers of -3.4, -11.6, and -10.4 kcal/mol. The CBS MP2 stacking-energy estimate for guanine dimer (-14.8 kcal/mol) was based on the 6-31G(0.25) and aug-cc-pVDZ calculations. This simplified extrapolation can be routinely used with a meaningful accuracy around 1 kcal/mol for large aromatic stacking clusters. The final estimate of the guanine stacking energy after the CCSD(T) correction amounts to -12.9 kcal/mol. The MP2/6-31G(0.25) method previously used as the standard level to calculate aromatic stacking in hundreds of geometries of nucleobase dimers systematically underestimates the base stacking by ca. 1.0-2.5 kcal/mol per stacked dimer, covering 75-90% of the intermolecular correlation stabilization. We suggest that this correction is to be considered in calibration of force fields and other cheaper computational methods. The quality of the MP2/6-31G(0.25) predictions is nevertheless considerably better than suggested on the basis of monomer polarizability calculations. Fast and very accurate estimates of the MP2 aromatic stacking energies can be achieved using the RI-MP2 method. The CBS MP2 calculations and the CCSD(T) correction, when taken together, bring only marginal changes to the relative stability of H-bonded and stacked base pairs, with a slight shift of ca. 1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases.     

Continuous chemiluminescence determination of formaldehyde in air based on Trautz-Schorigin reaction

A new continuous method for the determination of formaldehyde in air is described. A cylindrical wet effluent diffusion denuder is used for the collection of formaldehyde from air into a thin film of absorption liquid (distilled-deionized water). Formaldehyde in the denuder concentrate is on-line detected employing a chemiluminescence flow method based on a reaction of formaldehyde and gallic acid with hydrogen peroxide in an alkaline solution. The collection efficiency of formaldehyde is quantitative at the air flow rate of 0.5 L min⁻¹ (absorption liquid flow rate of 336 μL min⁻¹). The limit of detection (S/N = 3) is 0.60 μg m⁻³ HCHO (0.49 ppb). The calibration graph is linear up to 300 μg m⁻³ HCHO (244 ppb). The relative standard deviations of chemiluminescence method for 1 × 10⁻⁶ and 5 × 10⁻⁶ M HCHO are 2.87% and 1.49%, respectively. Acetaldehyde interferes negligible, other compounds do not interfere. The method was employed for formaldehyde measurement in ambient air. The comparison measurement illustrates the good agreement of results obtained by proposed method with those obtained by reference fluorimetric method.     

Beitrag zur Stickstoffschnellbestimmung nach Merz

Zusammenfassung Einige Änderungen an der Apparatur zur Stickstoffschnellbestimmung nachMerz wurden vorgenommen. Dadurch wird erreicht, daß zwischen den einzelnen Verbrennungen Sauerstoff das Verbrennungsrohr durchspült und vor dem Reduktionsrohr nach außen tritt. Der Verbrennungsraum ist daher bereits zu Beginn jeder Analyse mit Sauerstoff gefüllt, wodurch günstigere Bedingungen für die schlagartige Verbrennung erzielt werden. Der Umbau der von der Firma Heraeus gelieferten Apparatur und die Herstellung eines Oxydationskatalysators (Kobaltoxid-Wolframoxid) werden beschrieben.

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Contribution to the rapid nitrogen determination according to merz

Summary The apparatus for rapid nitrogen determination according toMerz has been modified. Between each two combustions, oxygen is flushed through the combustion tube and is vented before the reduction tube. Therefore, at the beginning of each analysis, the combustion chamber is filled with oxygen, providing a more favorable atmosphere for the rapid ignition. The alterations in the Hereaus apparatus and the preparation of an oxidation catalyst (cobalt oxide and tungsten oxide) are described.