Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Solid state characterization of an antioxidant alkaloid boldine using vibrational spectroscopy and quantum chemical calculations

Boldo (Peumus boldus Mol.), a Chilean tree traditionally employed in folk medicine and recognized as a herbal remedy in a number of pharmacopoeias, mainly for the treatment of liver ailment, has recently been the subject of increasing attention. Boldine, in particular, the major and most characteristic alkaloid constituent of this plant species, now emerges as its most interesting active principle from the pharmacological viewpoint.In the present work the structural and spectral characteristics of boldine have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and infrared spectra of boldine molecule.     

丙烯腈废水中有机物的高压放电法降解机理

利用气相色谱-质谱探讨了丙烯腈废水中有机物的高压放电法降解机理.结果表明:丙烯腈的氰基首先被破坏生成丙烯酸,丙烯酸进一步被氧化生成乙酸,乙酸降解为甲酸,最后生成CO2.丁二腈首先降解为丁二酸,丁二酸再生成丙酸,并逐步降解为乙酸、甲酸,最后生成CO2.二氰乙基胺在降解过程中依次生成丙腈、丙酸、乙酸和甲酸,最后生成CO2....     

Flow through Porous Media XVI: Electrokinetic Transport Coefficients of Aqueous Solutions of Mercuric Chloride and Glycine through a Sintered Disc Impregnated with a Cellulose Acetate Membrane under a Magnetic Field

The effect of the magnetic field on the electrokinetic transport coefficients (permeability coefficient and electro-osmotic permeability coefficient) of water and aqueous solutions of mercuric chloride and glycine through a sintered disc impregnated with cellulose acetate at different potentials, concentrations, and magnetic fields varying up to 21 kg/cm² are reported at 308.15 K. The phenomenological coefficients characterizing the electro-osmotic flow and the membrane characteristics are also estimated for the various solutions with the object of determining the efficiencies of electrokinetic energy conversion and ζ potential. The effect of magnetic field has been attributed to the molecular orientation of dipoles in solutions and to the change in the structure of the membrane.     

Investigation of the interaction mechanism of the recombinant human antibody MDJ8 and its fragments with chromatographic apatite phases

The chromatographic behaviour of a recombinant human antibody (IgG₁-subtype, κ-light chain, MW: 149.5 kD, pI: 9.3) was investigated as a function of the buffer pH and buffer type (HEPES, phosphate, borate) on fluoroapatite and hydroxyapatite stationary phases. HEPES buffer was used at pH 7.0, phosphate buffer at pH 8.2 and borate buffer between pH 8.5 and 11. Elution was by a double gradient method of first a salt gradient from 0 to 1 M NaCl in the corresponding buffer, followed by a step gradient to 0.4 M sodium phosphate. Regardless of the pH and buffer type, the antibody eluted in the NaCl gradient; capacity factors decreased with increasing pH. At pH 11 the antibody eluted in the flow-through. Retention was thus dominated by electrostatic interaction throughout the investigated pH-range. Investigation of antibody fragments obtained by papain digestion (fc- and fab-fragments) and deglycosylated fc-fragments showed that the sugar structures had no influence on the chromatographic behaviour. Instead the chromatographic behaviour was dominated by that of the fab-fragment. ζ-Potential measurements verified that the apatite surface bore a negative surface charge in the investigated pH range, while the antibody net surface charge switched from positive to negative as the pH increased. The corresponding isoionic point was a function of both the buffer concentration and the buffer species. However, above a pH of 8.3 the ζ-potential of the antibody generally was negative. Simulations of the molecular electrostatic potential of the antibody and the two fragments revealed the presence of a positively charged patch within the fab-fragment, which only disappeared above a pH of 10. Most likely this patch was responsible for the observed behaviour.     

Synthesis and pharmacological evaluation of potential metabolites of the potassium-competitive acid blocker BYK 405879

Four potential metabolites of the potassium-competitive acid blocker BYK 405879 (1) were synthesized which might be formed in vivo by enzymatic oxidation of the pyran moiety or the methyl groups attached to the (hetero) aromatic system. In all cases, the oxidation of the parent compound 1 was accompanied by a significant loss of pharmacological activity and by a decrease in lipophilicity. The target compounds 6, 14, 20, and 21 constitute valuable tool substances for the investigation of the metabolic fate of BYK 405879 (1).     

Study of geometrical parameters in N-H...N type of hydrogen bonds

Geometrical parameters associated with N-H ... N types of hydrogen bonds have been analysed using crystal structure data on nucleic acids, amino acids and related compounds. Histograms depicting the frequency distribution of N-H ... N length (l) and H-N ... N angle (θ) have been drawn and conclusions on the favoured geometry of such bonds have been arrived at. The distribution ofl shows a pronounced maximum in the range between 2.9? and 3.0? with an overall average of 2.98 ?. The θ distribution shows a pronounced maximum for the hydrogen bond angle in the range 0°-10°, with a rapid fall-off in frequency for nonlinear hydrogen bonds. The frequency shows a cos⁶θ dependence as compared to cos²θ dependence term used earlier to predict the angular dependence of hydrogen bond potential energy in proteins and polypeptides.     

Stretching vibrations and structure of (HF) n (n=4–8) clusters

IR spectra of 24 structural isomers of (HF) _n (n=4–8) clusters were calculated in the framework of semiempirical theory of polyatomic molecule vibrations. Based on the results obtained and available experimental data it is proposed that (HF) _n associates comprising 3–5-membered cycles with attached monomeric HF units are present in molecular beams and gas phase.Ab initio calculations performed by the SCF method show the existence of local minima corresponding to such structures on the potential energy surface of (HF) _n clusters (n=4–6). Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 435–443, March, 1997.     

双电层相互作用时胶体表面电位的分布及电荷密度的计算

本文以实验为基础,运用计算机数值解解出双电层相互作用时平面胶体表面电位ψ随距离X的分布,依据作者导出的双电层相互作用时胶体表面阴离子负吸附方程,计算出胶体表面外Hclmhotz面(OHP)处的表面电荷密度σ_δ;讨论了双电层相互作用程度(ψ_d/ψ_δ)对胶体表面电位分布及其表面电荷密度的影响。     

Ab initio molecular orbital study of potential energy surface for the H2NO(B1)→NO(Π)+H2 reaction

The mechanism of the H₂NO(²B₁)→NO(²Π)+H₂ reaction has been examined using ab initio molecular orbital methods. Ground-state and first-excited-state potential surfaces were plotted at the FOCI/cc-pVTZ level of theory as functions of two appropriate internal degrees of freedom. A conical intersection was found on the C_s pathway that is symmetric with respect to the plane perpendicular to the molecular plane of C_2v H₂NO(²B₁). It is therefore considered that trajectories that start from H₂NO(²B₁) towards the product region detour around the conical intersection, pass through the neighborhood of the transition state that is located at the saddle point on the C_s pathway, and finally reach the products, NO(²Π)+H₂. Thus we can explain the mechanism of the H₂NO(²B₁)→NO(²Π)+H₂ reaction, which has remained unclear to date.