Synthesis and conformational analysis of novel N(OCH3)-linked disaccharide analogues

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.     

Capillary isoelectric focusing-mass spectrometry for shotgun approach in proteomics

We report on capillary isoelectric focusing-mass spectrometry (CIEF-MS) of complex peptide mixtures in the absence of carrier ampholytes. Furthermore, the use of low concentrations of carrier ampholytes as mere spacers is investigated. Carrier ampholytes are complex mixtures of amphoteric compounds with high buffering capacity. Since all peptides are amphoteric compounds by themselves, the use of carrier ampholytes may be superfluous to establish a stable pH gradient in CIEF analysis of protein digests. Our research showed that when carrier ampholytes are omitted, the analyte ions are not focused at their isoelectric point. The analytes are charged, leading to electrophoretic mobility uncharacteristic for CIEF. The method was tested for a five-protein-mixture at 0.02 mg/mL per protein and 0.05 mg/mL per protein. At the lower concentration, the analytes were stacked during the focusing process in only a limited length of the capillary. Therefore, the higher concentration led to better separation efficiency. It was found that at low concentration (0.20%) the carrier ampholytes could work as spacers. Though it led to sensitivity losses of 15-45%, this was compensated by the higher separation efficiencies seen. The method was evaluated with an eight-protein-mixture, of which all could be identified after performing MS/MS.     

A hybrid approach combining energy density analysis with the interaction energy decomposition method

We propose a new analysis technique for characterizing molecular interactions that combines an energy decomposition scheme, such as the Kitaura-Morokuma decomposition method, with energy density analysis, which partitions the total energy of the system into atomic contributions. The combined scheme, termed Interaction-EDA, enables us to estimate the local contribution of interaction energy components, such as electrostatic, exchange, polarization, and charge transfer. The evaluation of the local interaction energy is rather important in large systems. For a numerical assessment, the Interaction-EDA method is applied to the process of CO adsorption on Si(100) - (2 x 1) surface.     

Novel Chiral Aminophosphine Ligand:Synthesis and Application in Saymmetric Catalytic Hydrogenation Reaction

A new chiral aminophosphine ligand 6,6′-dimethoxy-2,2′-bis(diphenylphosphinoamino)biphenyl(DMBDPPABP) was prepared and its rhodium complex was found to be an effective catalyst for the asymmetric hydrogenation of amidoacrylic acid and its dervatives.The effects of solvent and reaction temperature on enantioselectivity were also studied.     

Polyazoxyfurazans in reactions with ammonia

The reaction of 4,4"-bis(4-nitrofurazan-3-yl-NNO-azoxy)azoxyfurazan with ammonia affords a product of nucleophilic substitution for the furazanyldiazene oxide fragment, while the nitro groups remain intact.     

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

A comparative study between inductively and capacitively coupled plasma deposited polystyrene films: chemical and morphological characterizations

Thin polystyrene films were deposited on stainless steel substrates by capacitively and inductively coupled radio frequency glow discharge plasma, in order to compare their chemical and morphological properties. The films were characterized by Fourier‐transform infrared spectroscopy (FTIR), X‐Ray photoelectron spectroscopy (XPS), time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), atomic force microscopy (AFM) and scanning electron microscope (SEM). Wettability properties were also determined by contact angle measurements. Ageing effect was studied by analysing films aged for 15 min and for 1 week. Results from both capacitively and inductively plasma polymerized polystyrene (pPS) films aged for 15 min showed that the chemical structure of the bulk, chemical composition of the surface (depth < 10 nm) and wettability properties were rather similar. Only their microstructures were very different: the pPS_capa film's microstructure showed homogeneous distribution of spherical particles of about 100 nm in diameter but the pPS_ind film's microstructure seemed to be mainly influenced by the surface of the metallic substrate: orientated ‘lamellae‐like layers’ of polymers were observed on each metallic grain. Ageing for 1 week in ambient air induced low oxygen uptake in the surface of both pPS films. The pPS_ind topmost surface (depth < 3 nm) was more oxidized than that of pPS_capa but no modification of the chemical structure of the bulk or of the morphology was noticed after ageing. Copyright © 2006 John Wiley & Sons, Ltd.     

Variable Mott-Schottky plots acquisition by potentiodynamic electrochemical impedance spectroscopy

Potentiodynamic electrochemical impedance spectroscopy provides extraction of potential-dependent space charge layer capacitance from potentiodynamic impedance spectra of non-stationary semiconductor–electrolyte interface. The new technique has been applied for acquisition of Mott-Schottky plots of cathodically treated TiO₂ anodic films. Cathodic treatment in 1 M H₂SO₄ increases donor density and flat band potential of TiO₂. Freshly doped films show hysteresis in the space charge layer capacitance in cyclic potential scans. The subsequent cycling eliminates the hysteresis but preserves the greater part of the doping effect. Presented at the 4th Baltic Conference on Electrochemistry, Greifswald, 13–16 March 2005