Self-association-driven transition of the β-peptidic H12 helix to the H18 helix

Various patterns of foldameric oligomers formed by trans-ABHC ((1S,2S,3S,5S)-2-amino-6,6-dimethylbicyclo[3.3.1]heptane-3-carboxylic acid) and β(3)-hSer residues were studied. NMR, ECD and molecular modelling demonstrated that octameric and nonameric sequences with multiple i-i+3 ABHC pair repulsions attain the β-H18 helix in CD(3)OH. As a close relative of the α-helix, this helix type is stabilized by i-i+4 backbone H-bond interactions. The formation of the β-H18 helix was found to be solvent- and concentration-dependent. Upon dilution, the β-H18 → β-H12 helix transition was revealed by concentration-dependent ECD, DOSY-NMR and TEM measurements.     

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.     

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.     

Time-dependent wave mechanical study of the wings to the lyman-α line in H + H2 reactive collisions

We have predicted the absorption spectrum of the transition state configurations for the collinear reaction H + H₂ → H₃ → H₂ + H by solving the time-dependent Schrödinger equation for the nuclear motion. The spectral features have been interpreted in terms of the build up of the probability density function in the inner repulsive wall of the potential-energy surface.     

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.     

Reactivity of the Ge–H,Sn–H,P–H,and Se–H Bonds in Radical Abstraction Reactions

The experimental data for the liquid- and gas-phase reactions of atoms and radicals with organoelement compounds R _{n – 1}E–H

A theoretical study of the H2SO4+H2O → HSO4 −+H3O+ reaction at the surface of aqueous aerosols

The surface region of sulfate aerosols (supercooled aqueous concentrated sulfuric acid solutions) is the likely site of a number of important heterogeneous reactions in various locations in the atmosphere, but the surface region ionic composition is not known. As a first step in exploring this issue, the first acid ionization reaction for sulfuric acid, H₂SO₄ + H₂O HSO₄^– + H₃O⁺, is studied via electronic structure calculations at the Hartree–Fock level on an H₂SO₄ molecule embedded in the surface region of a cluster containing 33 water molecules. An initial H₂SO₄ configuration is selected which could produce H₃O⁺ readily available for heterogeneous reactions, but which involves reduced solvation and is consistent with no dangling OH bonds for H₂SO₄. It is found that at 0 K and with zero-point energy included, the proton transfer is endothermic by 3.4 kcal/mol. This result is discussed in the context of reactions on sulfate aerosol surfaces and, further, more complex calculations.Contribution to the Jacopo Tomasi Honorary Issue     

Polymorphic effects at the eutectic melting in the H2O–glycine system

Solid mixtures of ice with three glycine polymorphs were heated up to the eutectic melting and the DSC has detected the eutectic temperatures of ?2.8 °C for α-, ?3.6 °C for β-, and ?2.8 °C for γ-glycine. DSC peaks of the eutectic melting are rather strange in shape, indicating unclear processes in the solutions. Accurate DSC measurements of extremely small samples can probably provide us with the physicochemical tool for the investigation of polymorphic differences among different solutions. This may be important in relation to different bioavailability of solutions prepared from different polymorphs. Eutectic temperature of ?4.7 °C in water–glycine system allows us to suggest that the unknown polymorph of glycine exists.     

Disruptive influence of the host cage C60 on the guest He–H+ bond and bonding in H3+

Although a helium atom prefers to stay at the centre of a fullerene (C₆₀) cage and a proton binds with one of the carbon atoms from inside, DFT(MN15)/cc-pVTZ and DLPNO-MP2/def2-TZVP calculations show that the helium atom and the proton in HeH⁺ prefer to stay away from the centre of the cage, weakening the He–H⁺ covalent bond considerably. Both the helium atom and the proton exhibit noncovalent interactions with the carbon atoms of two pentagons at the opposite ends of the fullerene cage. Our calculations also show that a linear arrangement of H₃⁺ (inside C₆₀), pointing towards the centres of two pentagons opposite to each other, with the proton breaking away from H_2, is energetically more favored over the equilateral triangle geometry of free H₃⁺.     

How short can the H...H intermolecular contact be? New findings that reveal the covalent nature of extremely strong interactions

Ab initio calculations at the MP2/6-311++G(d,p) and MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ levels have been performed for the following complexes: H2OH+...HBeH, H2OH+...HBeBeH, H2OH+...HBeF, HClOH+...HBeH, Cl2OH+...HBeH, and Cl2OH+...HBeF. For all dimers considered, extremely short H...H intermolecular contacts (1.0-1.3 A) were obtained. These are the shortest intermolecular distances which have ever been reported, with binding energies within the range of 13.7-24.3 kcal/mol (MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ level). The interaction energies of the complexes analyzed were also extrapolated to the complete basis set (CBS) limit. To explain the nature of such strong interactions, the Bader theory was applied, and the characteristics of the bond critical points (BCPs) were analyzed. It was pointed out that for the major part of the H...H contacts considered here the Laplacian of the electron density at H...H BCP is negative indicating the partly covalent nature of such a connection. The term "covalent character of the hydrogen bond" used sometimes in recent studies is discussed. An analysis of the interaction energy components for dihydrogen bonded systems considered indicates that in contrast to conventional hydrogen bonded systems the attractive electrostatic term is outweighed by the repulsive exchange energy term and that the higher order delocalization energy term is the most important attractive term.     

Capture and dissociation in the complex-forming CH + H2 → CH2 + H, CH + H2 reactions

The rate coefficients for the capture process CH + H(2)→ CH(3) and the reactions CH + H(2)→ CH(2) + H (abstraction), CH + H(2) (exchange) have been calculated in the 200-800 K temperature range, using the quasiclassical trajectory (QCT) method and the most recent global potential energy surface. The reactions, which are of interest in combustion and in astrochemistry, proceed via the formation of long-lived CH(3) collision complexes, and the three H atoms become equivalent. QCT rate coefficients for capture are in quite good agreement with experiments. However, an important zero point energy (ZPE) leakage problem occurs in the QCT calculations for the abstraction, exchange and inelastic exit channels. To account for this issue, a pragmatic but accurate approach has been applied, leading to a good agreement with experimental abstraction rate coefficients. Exchange rate coefficients have also been calculated using this approach. Finally, calculations employing QCT capture/phase space theory (PST) models have been carried out, leading to similar values for the abstraction rate coefficients as the QCT and previous quantum mechanical capture/PST methods. This suggests that QCT capture/PST models are a good alternative to the QCT method for this and similar systems.     

Exploring the C–H…O Interactions in Glycoproteins

Glycoproteins are an important class of proteins that play a significant role in many cellular events. In the present study, we analyze the influence of C–H…O interactions in relation to other environmental preferences in glycoproteins. CH…O interactions are now accepted as a genuine hydrogen bond. Main chain–main chain interactions are predominant. Proline residues stabilize strands by C–H…O interactions in glycoproteins. Majority of the C–H…O interacting residues were conserved and had one or more stabilization centers. CH…O interactions might be responsible for the global conformational stability, since long-range CH…O contacts were predominant. The results presented in this study might be useful for structural stability studies in glycoproteins.     

The TST-CEQ calculations on the light-heavy-light H+ClH reaction

The calculated TST-CEQ state-selected reaction cross sections and rate constants forthe exchange reaction of H+ClH are reported.It is found that,although the collinear proba-bilities exhibit the oscillating behaviour,the TST-CEQ cross sections do not oscillate.Compa-rison of the different state-selected cross sections at a constant total energy indicates thattranslational energy is more effective than vibrational energy in promoting the reaction H+ClH.We also find that,the larger the vibrational quantum number of the reactant,the larger thereactive rate constant k~(TST-CEQ)(T,v)is at a given temperature.The state-selected rate constantsare then averaged to yield the thermal rate constants which are shown to be in good agreementwith our VTST calculations and those by Schwenke et al..     

Theoretical Study on the Reaction Mechanism of SiCl_4 with H in the Gas Phase

1 INTRODUCTION Semiconductor silicon materials are vital for mi- croelectronic and information industry. Silicon has many advantages, for example, rich resource, out- standing quality and sophisticated processing tech- nology. So it has been widely used in semiconduc- tor industry. One of the key techniques of mo- dern microelectronic industry is epitaxial growth of single crystal thin film on single crystal silicon and its ba- cking materials. In the chemical vapour deposition of Si, g…