Hierarchical helix of helix in the crystal: formation of variable-pitch helical π-stacked array of single-helical dinuclear metal complexes

Unique helix of helix structures were formed via intermolecular π-stacking and metal-metal interactions in the crystal of single-helical dinuclear complexes [L(2)M(2)] (M = Pd, Ni) having an acyclic bis(N(2)O(2))-type ligand. The difference in the helical winding angle of the constituents (401.7° for [L(2)Pd(2)]; 421.3° for [L(2)Ni(2)]) led to variation of the helical pitches of the helical array (7(2) helix for [L(2)Pd(2)]; 6(2) helix for [L(2)Ni(2)]).     

James D. Watson 88—the discovery of the double helix was an iconic event in structural chemistry

The ingenuity of James D. Watson and Francis Crick, the convergence of the advances in X-ray crystallography, the accumulated knowledge of structural chemistry, and the breakthroughs in chemical methods of analysis led to the discovery of the double helix structure of DNA. The discovery catapulted Watson to a career that helped DNA and the applications of the knowledge about its structure triumph in biomedical sciences. Watson’s eighty-eighth birthday is an occasion to have a look at his path to success, his personality, and assess his legacy.     

Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine

~~Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine~~     

Genetic algorithms as a tool for helix design – computational and experimental studies on prion protein helix 1

Summary Evolutionary computing is a general optimization mechanism successfully implemented for a variety of numeric problems in a variety of fields, including structural biology. We here present an evolutionary approach to optimize helix stability in peptides and proteins employing the AGADIR energy function for helix stability as scoring function. With the ability to apply masks determining positions, which are to remain constant or fixed to a certain class of amino acids, our algorithm is capable of developing stable helical scaffolds containing a wide variety of structural and functional amino acid patterns. The algorithm showed good convergence behaviour in all tested cases and can be parameterized in a wide variety of ways. We have applied our algorithm for the optimization of the stability of prion protein helix 1, a structural element of the prion protein which is thought to play a crucial role in the conformational transition from the cellular to the pathogenic form of the prion protein, and which therefore poses an interesting target for pharmacological as well as genetic engineering approaches to counter the as of yet uncurable prion diseases. NMR spectroscopic investigations of selected stabilizing and destabilizing mutations found by our algorithm could demonstrate its ability to create stabilized variants of secondary structure elements.     

Supramolecular double helix from capped γ-peptide

The single crystal X-ray diffraction study of capped γ-peptide reveal that the peptide adopts helical conformation which self-assemble to form a supramolecular parallel double helical structure using intermolecular hydrogen bonding as well as π-π stacking interactions in the solid state.     

Water molecule adsorption on short alanine peptides: how short is the shortest gas-phase alanine-based helix?

Water adsorption measurements have been performed under equilibrium conditions for unsolvated Ac-A(n)K+H(+) and Ac-KA(n)+H(+) peptides with n = 4 - 10. Previous work on larger alanine peptides has shown that two dominant conformations (helices and globules) are present for these peptides and that water adsorbs much more strongly to the globules than to the helices. All the Ac-KA(n)+H(+) peptides studied here (which are expected to be globular) adsorb water strongly, and so do the Ac-A(n)K+H(+) peptides with n < 8. However, for Ac-A(n)K+H(+) with n = 8-10 there is a substantial drop in the propensity to adsorb water. This result suggests that Ac-A(8)K+H(+) is the smallest Ac-A(n)K+H(+) peptide to have a significant helical content in the gas phase. Water adsorption measurements for Ac-V(n)K+H(+) and Ac-L(n)K+H(+) with n = 5-10 suggest that the helix emerges at n = 8 for these peptides as well.     

Playing with peptides: how to build a supramolecular peptide nanostructure by exploiting helix···helix macrodipole interactions

A novel method to build bicomponent peptide self-assembled monolayers (SAMs) has been developed, by exploiting helix···helix macrodipole interactions. In this work, a peptide-based self-assembled monolayer composed of two helical peptides was immobilized on a gold surface. Specifically, a pyrene-containing octapeptide, devoid of any sulfur atom (A8Pyr), and a hexapeptide, functionalized at the N-terminus with (S,R) lipoic acid, for binding to gold substrates (SSA4WA) via a Au-S linkage, have been employed. Both peptides investigated attain a helical structure, because they are almost exclusively formed by strongly folding inducer C(α)-tetrasubstituted α-amino acids. We demonstrate that the two peptides generate a stable supramolecular nanostructure (a densely packed bicomponent peptide monolayer), where A8Pyr is incorporated into the SSA4WA palisade by exploiting helix···helix macrodipole interactions. The presence of both peptides on the gold surface was investigated by spectroscopic and electrochemical techniques, while the morphology of the monolayer was analyzed by ultra high-vacuum scanning tunnelling microscopy. The composition of the bicomponent SAM on the surface was studied by a combination of electrochemical and spectroscopic techniques. In particular, the amount of Au-S linkages from the sulfur-containing peptides was quantified from reductive desorption of the peptide-based SAM, while the amount of A8Pyr was estimated by fluorescence spectroscopy. The antiparallel orientation of the A8Pyr and SSA4WA peptide chains minimizes the interaction energy between the helix dipoles, suggesting that this kind of electrostatic phenomenon is the driving force that stabilizes the bicomponent SAM.     

The Curl–Divergence equations for the electronic non-adiabatic coupling terms: study of the C2H molecule and the H2+H system

This Letter is part of an effort to use the Curl equations to calculate non-adiabatic coupling terms, subject to ab initio boundary conditions. As examples we consider two-state, planar, systems characterized by two coordinates, θ and q and treat the corresponding non-adiabatic coupling terms, namely, τ_θ(q,θ) and τ_q(q,θ). The theory, which yields τ_q(q,θ) once τ_θ(q,θ) is given, is applied to three cases: an analytical model and two ab initio treatments – one for the C₂H molecule and one for the H+H₂ molecular system. In all three cases encouraging agreements were obtained between the theoretical τ_q(q,θ) values and the ab initio ones.     

Comment on the possible role of the reaction H+H2O→H2+OH in the radiolysis of water at high temperatures

In a recent paper (Radiation Physics and Chemistry, 2005, vol. 74, pp. 210) it was suggested that the anomalous increase of molecular hydrogen radiolysis yields observed in high-temperature water is explained by a high activation energy for the reaction H+H₂O→H₂+OH. In this comment we present thermodynamic arguments to demonstrate that this reaction cannot be as fast as suggested. A best estimate for the rate constant is 2.2×10³ M⁻¹ s⁻¹ at 300 °C. Central to this argument is an estimate of the OH radical hydration free energy vs. temperature, ΔG_hyd(OH)=0.0278t−18.4 kJ/mole (t in °C, equidensity standard states), which is based on analogy with the hydration free energy of water and of hydrogen peroxide.     

Cooper and Zinc Superoxide dismutase from Peking duck erythrocytes forms a supramolecular double－helix in the crystal

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Reply to comment on the possible role of the reaction H+H2O→H2+OH in the radiolysis of water at high temperatures

In reply to “Comment on the possible role of reaction H+H₂O→H₂+OH in the radiolysis of water at high temperatures” (Bartels, 2009 Comment on the possible role of the reaction H+H₂O→H₂+OH in the radiolysis of water at high temperatures. Radiat. Phys. Chem. 78, 191–194) we present an alternative thermodynamic estimation of the reaction rate constant k. Based on the non-symmetric standard state convention we have calculated that the Gibbs energy of reaction Δ_rG=57.26 kJ mol^?1 and the reaction rate constant k=7.23×10^?5 M^?1 s^?1 at ambient temperature. Re-analysis of the thermodynamic estimation (Bartels, 2009 Comment on the possible role of the reaction H+H₂O→H₂+OH in the radiolysis of water at high temperatures. Radiat. Phys. Chem. 78, 191–194) showed that the upper limit for the rate constant at 573 K is k=1.75×10⁴ M^?1 s^?1 compared to the value predicted by the diffusion-kinetic modelling (3.18±1.25)×10⁴ M^?1 s^?1 (Swiatla-Wojcik, D., Buxton, G.V., 2005. On the possible role of the reaction H+H₂O→H₂+OH in the radiolysis of water at high temperatures. Radiat. Phys. Chem. 74(3–4), 210–219). The presented thermodynamic evaluation of k(573) is based on the assumption that k can be calculated from Δ_rG and the rate constant of the reverse reaction which, as discussed, are both uncertain at high temperatures.     

Temperature dependence of the substrate selectivity in the hydroxylation of alkylbenzenes in the H2O2−H2SO4 system

The substrate selectivity in the hydroxylation of methylbenzenes in the H₂O₂−H₂SO₄ (70 wt.%) system was studied at 15–55 °C. The activation entropy correlates with the basicity of the arenes, while the substrate selectivity and activation enthalpy correspond both with the basicity and ionization potentials of ArH. We concluded that the structure of the reaction transition state is intermediate between a charge transfer complex and σ-complex. L. M. Litvinenko Institute of Physical Organic and Coal Chemistry, National Academy of Sciences of Ukraine, 70 R. Lyuksemburg ul., Donetsk 340114, Ukraine. Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 35, No. 1, pp. 39–43, January–February, 1999.     

Can quasiclassical trajectory calculations reproduce the extreme kinetic isotope effect observed in the muonic isotopologues of the H + H2 reaction?

Rate coefficients for the mass extreme isotopologues of the H + H(2) reaction, namely, Mu + H(2), where Mu is muonium, and Heμ + H(2), where Heμ is a He atom in which one of the electrons has been replaced by a negative muon, have been calculated in the 200-1000 K temperature range by means of accurate quantum mechanical (QM) and quasiclassical trajectory (QCT) calculations and compared with the experimental and theoretical results recently reported by Fleming et al. [Science 331, 448 (2011)]. The QCT calculations can reproduce the experimental and QM rate coefficients and kinetic isotope effect (KIE), k(Mu)(T)/k(Heμ)(T), if the Gaussian binning procedure (QCT-GB)--weighting the trajectories according to their proximity to the right quantal vibrational action--is applied. The analysis of the results shows that the large zero point energy of the MuH product is the key factor for the large KIE observed.     

Study on the reaction of triple helix poly(A:2I) with Cu~(2+)

The effect of Cu2+ on the triple-stranded helical structure of poly(A:2I) was studied by means of circular dichroism spectral method with the help of ultraviolet spectral and ethidium bromide fluorescence probe methods. It was found that Cu2+ destabilizes the structure of the triple helix poly(A:2I) and induces its structural transformations, meanwhile, the transformations can be partially reversed by a higher NaCl concentration. The structural transformations may be expressed by the following scheme: poly(A:2I) - poly(A:I) + poly(I)- poly(A) + 2poly(I)     

Cleavage of the cyclic substituent in the [B10H9O2C4H8]−, [B10H9OC4H8]−, and [B10H9OC5H10]− anions upon the interaction with negatively charged N-nucleophiles

The interaction of the [B₁₀H₉O₂C₄H₈]^?, [B₁₀H₉OC₄H₈]^?, and [B₁₀H₉OC₅H₁₀]^? anions with negatively charged N-nucleophiles has been studied. It has been shown that such reactions yield doubly charged substituted closo-decaborates with a nitrogen-containing group attached to the cluster through an alkoxyl spacer. Compounds with pendant NO₂ ^?, N₃ ^?, N(CO)₂C₆H₄ ^?, and NHC₆H₅ groups have been synthesized.     

Theoretical studies of the radical reaction H2CSiH2 + H

Ab initio molecular orbital calculations on the transition states and barrier heights for the addition of atomic hydrogen to silaethylene are carried out. The activation energy for the addition to the silicon site is lower than that to the carbon site, while the exothermicity is smaller.     

Structures and cytotoxic properties of cucumariosides H₂, H₃ and H₄ from the sea cucumber Eupentacta fraudatrix

New triterpene glycosides, cucumariosides H? (1), H? (2) and H? (3), have been isolated from the Far Eastern sea cucumber Eupentacta fraudatrix. The structures of 1-3 were elucidated using extensive NMR spectroscopy (1H- and 13C-NMR, DEPT, 1H-1H COSY, 1D TOCSY, H2BC, HMBC, heteronuclear single-quantum coherence, and NOESY) and ESI-MS. Glycosides 1-3 are monosulphated branched pentaosides having rare 3-O-methyl-D-xylose as a terminal monosaccharide. Glycosides 1 and 3 contain holostane aglycones, whereas 2 has a 23,24,25,26,27-pentanorlanostane aglycone with an 18(16)-lactone, which is also uncommon for the sea cucumbers. Glycoside 3 contains a very rare ethoxyl radical at C-25 of the aglycone side chain, and it is most probably an artefact that was formed during long storage of the ethanolic extract. Cytotoxic activities of 1-3 against mouse spleen lymphocytes, haemolytic activity against mouse erythrocytes and Ehrlich carcinoma cells have been studied. The presence of 25-hydroxy group in aglycone moiety significantly decreased the activities.     

Algorithm for the calculation of the electronic structure of molecules by the expanded Hückel method

An algorithm is described for the calculation of quantum-chemical characteristics of molecules by the expanded Hückel method. The method for the calculation of the complete overlap matrix of Slater atomic orbitals of type ns, np, and nd was modified.