Efficient search for all low energy conformations of polypeptides by Monte Carlo methods

The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below ?10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below ?10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.     

Probing the glycosidic linkage: UV and IR ion-dip spectroscopy of a lactoside

The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.     

Orientational aspect of transient absorption in solutions

In picosecond spectroscopy transient absorption methods are utilized to measure ground-state repopulation kinetics. Since linearly polarized light pulses from mode-locked lasers are used, the transient absorption characteristics in solutions are governed by the rotational diffusion of the absorbing molecules, too. The theory for isotropic diffusion is given and compared to a measurement on the rhodamine 6G molecule dissolved in solvents of different viscosity using a novel pulse spectrophotometer.     

Facts and artifacts about aromatic stability estimation

The stability of a set of 105 five-membered π-electron systems (involving aromatic, non-aromatic and anti-aromatic species) was evaluated using six isodesmic reactions of which two belong to the subclass of homodesmotic reactions, which are based on cyclic and acyclic reference systems. We demonstrate that the ‘Resonance Energies’ derived from isodesmotic schemes have obvious flaws and do not correct or cancel other contributions to the energy, such as the changes of hybridization, homoconjugation of heterosubstituted cyclopentadienes, conjugative interactions of CC or CX (X=N or P) with a π or pseudo π orbital at Y (Y=O, S, NH, PH), strain, etc. as effectively as possible. Likewise, ‘aromatic stabilization energies (ASE)’ derived from homodesmotic schemes based on the acyclic reference compounds do not give satisfactory results. We strongly recommend that only cyclic reference compounds should be used for ASE and other aromaticity evaluations. The analysis is based on ab initio optimized geometries at B3LYP/6-311+G^∗∗.     

Microwave-assisted extraction of zearalenone from wheat and corn

A microwave-assisted extraction (MAE) method has been developed for determination of zearalenone in wheat and corn by LC-MS with an atmospheric pressure chemical ionization interface (APCI). Matrix effects were minimized by use of matrix-matched standard curves for quantification of the analyte. The limit of quantification (LOQ) of the method was 30 ng g(-1) in wheat and 20 ng g(-1) in corn. The rapid LC-MS method enabled analysis of the extracts without clean-up, thereby reducing analyte losses, the time required for the analytical procedure, and costs. A factorial design approach was used to examine the effect on extraction efficiency of the main extraction conditions - time, temperature, and solvent. On the basis of results from statistical assessment extraction was performed with 1:1 (v/v) methanol-acetonitrile at 80 degrees C for 5 min. When these extraction conditions were applied to a wheat sample from a recently conducted international proficiency test, 92% (103 ng g(-1)) of the assigned zearalenone concentration (112 ng g(-1)) in the test material was obtained. This result was within the uncertainty (u) range of the assigned value of the test material (u=+/-15.8 ng g(-1), alpha=0.05) thereby demonstrating the accuracy of the method was sufficient. The precision of the whole method was also confirmed to be adequate, because the observed relative standard deviation (RSD) of 12% (n=10) also fulfils the quality criteria recommended by European guidelines for in-house method validation.     

Delocalization resonance energy of the allylic radical from the geometrical isomerization of hexa-1,3,5-trienes

Thermal cis, trans geometrical isomerization theoretically involves a 90° twisted, singlet diradical-like transition state which may serve as a base for the examination of structural perturbations. Although thermal rearrangement of hexa-1, trans-3,5-triene (and all-trans octa-2,4,6-triene) to the cis isomer cannot be followed directly owing to subsequent cyclization and 1,5 hydrogen shifts, activation parameters for disappearance have been determined. Experimental complications and mechanistic uncertainties which make interpretation difficult are removed in the bicyclic hexatriene, cyclopentenylidenecyclopentene. These geometrical isomers undergo uncomplicated thermal cis, trans isomerization in vessels of lead-potash glass: log k₁ = 12·03±0·32?41·7±0·8/(0·004575T_abs). Extraction of a value for allylic delocalization energy from the behavior of hexa-1, trans-3,5-triene [log k₁ = 12·91 ± 0·47?44·3±1·2/(0·004575 T_abs)] requires corrections of the Dewar-Schmeising type for changes in hybridization of the σ bonds. Depending on whether ethylene or trans-butene is taken as standard, values of 12·2 and 13·1 kcal/mol are obtained (estimated uncertainty ± 2 kcal/mol).     

Proton-impact excitation of HeI triplet levels

We investigated the excitation of the λ(1s3d ³ D?1s2p ³ P)=588 nm line of atomic helium by proton and deuteron impact for projectile energies 10 keV≦E _p≦25 keV. In apparent contradiction to Wigner's spin conservation rule, the emission cross section does not vanish. By measuring the intensity of the impact radiation as a function of homogeneous magnetic and electric fields applied to the collision volume, it has been shown thatp- andd-impact excitation of the 1s3d ³ D level of HeI proceeds via 1snl states withl≧3, which populate the 3³ D states by cascade decays. The well-known strong singlet-triplet mixing of these 1snl states enables a population of triplet states in accord with Wigner's rule. Accordingly, we determine the excitation cross section of the 1s4f multiplet from the measured emission cross section of the 588 nm line. The field-dependent signals give evidence that predominantly substates with |m _L|≦1 are excited.     

One-Bond 13C, 13C-Spin Coupling in η4-, η3- and η2-Olefin Transition Metal Complexes

One-bond ¹³C, ¹³C-spin-coupling constants have been measured, with natural isotope abundance, in η⁴-diene, η³-allyl and η²-ene transition-metal carbonyl complexes. Typical values of ¹J(C,C) are given for Fe-, Ru- and Os-complexes with the three types of olefinic ligands. The effects of substituents and the structural significance of the C,C-coupling constants are discussed.     

Carbohydrate chain of ganglioside GM1 as a ligand: identification of the binding strategies of three 15 mer peptides and their divergence from the binding modes of growth-regulatory galectin-1 and cholera toxin

The branched pentasaccharide chain of ganglioside GM1 is a prominent cell surface ligand, for example, for cholera toxin or tumor growth-regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N-terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross-linking capacity of the natural lectins by peptide attachment to a suitable scaffold.     

As12Se44—: ein neuartiges Selenoarsenatanion mit einem Polyarsenkäfig in der Verbindung [Co(NH3)6]2As12Se4 · 12 NH3

As₁₂Se₄^4—: a New Selenoarsenate Anion with a Polyarsenic Cage in the Compound [Co(NH₃)₆]₂As₁₂Se₄ · 12 NH₃ Orange coloured crystals of [Co(NH₃)₆]₂As₁₂Se₄ · 12 NH₃ were prepared by the reduction of As₄Se₄ with a solution of sodium in liquid ammonia and subsequent precipitation with CoBr₂. The X‐ray structure determination shows them to contain the selenoarsenate anion As₁₂Se₄^4—, which consists of a central As₁₂‐cage with four exo‐bonded, formally negatively charged Se atoms. The structure of the As₁₂‐cage is equivalent to the main polyphosphorus building unit of a known organopolyphosphane and of tubular P₁₂ in the compound (CuI)₃P₁₂.