Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures.     

Structural characteristics of p‐t‐Octylphenol formaldehyde resole resins using molecular simulation

p‐t‐Octylphenol formaldehyde resole resins have two linkage types of methylene‐ and dimethylene ether‐linkages and have three terminal types of hydrogen, methylol, and o‐methylene quinone. Variation of structural characteristics of the resins due to different types of linkages and terminals were studied using molecular dynamics and molecular mechanics. The structural characteristics of the methylene‐bridged resins were intramolecular hydrogen bonds between hydroxyl groups of the adjacent p‐t‐octylphenols. In the dimethylene ether‐bridged resin, the intramolecular hydrogen bonds between oxygen atoms of the dimethylene ether‐linkages and hydroxyl groups of the neighboring phenolic units were found. For the resins with both methylol terminals, one of both terminals of the resins was hidden at the center of the molecule when the resin size is large. The number of hydrogen bonds in the resins with the methylol terminal was larger than for the resins with the o‐methylene quinone terminal. Variation of the structural characteristics of the resins by dehydration of the terminal methylol was discussed. Using the calculated results, dissociation of the dimethylene ether linkage and crosslinking reaction of rubber chains by the resin were explained. Copyright © 2002 John Wiley & Sons, Ltd.     

Water oxidation with inhomogeneous metal-silicon interfaces

Silicon (Si) is a prime candidate for manufacturing water-splitting photoelectrochemical cells, however, the stability of this material remains a serious bottleneck. This is particularly true for the photoanode, subject to severe deactivation mechanisms. So far, thin film homogeneity has been the paradigm in the quest for stable and efficient Si-based photoanodes, which involved the use of vapor deposition methods to produce conformal thin films ensuring Si protection and efficient catalysis during operation. Conversely, recent reports on n-Si/metal thin film junctions have highlighted the benefits of the junction heterogeneity, generated in situ. In addition, results obtained from n-Si photoanodes partially covered with discontinuous films of Co and Ni nanoparticles lately suggested that homogeneity is not a prerequisite to reach efficiency and stability. Such findings may open new protection routes for Si-based photoanodes, breaking with classical strategies and allowing the use of liquid phase modification methods such as electrodeposition.     

Electrochemical Determination of Sulfide at High Temperatures via Its Electrochemically Initiated Reaction with Diethyl‐p‐phenylenediamine in Dimethylformamide

The electrochemical oxidation of DEPD proceeds via an EC_revECE mechanism in dimethylformamide. It has been investigated at elevated temperatures up to 130 °C at both micro and macro platinum and glassy carbon electrodes. Kinetic and thermodynamic parameters for the reaction process have been calculated for each temperature. Further, the voltammetric response of DEPD shows enhanced limiting currents in the presence of sulfide. The analytical utility of the approach has been investigated with linear range from 50 to 850 μM sulfide concentration observed and a corresponding limit of detection of 20 μM achievable at temperatures of 70 °C.     

Simultaneous Determination of Palladium and Platinum by On‐Line Enrichment Followed by Rapid Column High Performance Liquid Chromatography

In this paper, a new method for the simultaneous determination of palladium and platinum ions was developed using a rapid column high performance liquid chromatograph equipped with an on‐line enrichment technique. The palladium and platinum ions were pre‐column derivatized with 5‐(p‐aminobenzylidene)‐thiorhodanine (ABTR) to form colored chelates. The Pd‐ABTR, Pt‐ABTR chelates can be absorbed onto the front of an enrichment column when they were injected into the injector and sent to the enrichment column [ZORBAX Stable Bound, 4.6 × 10 mm, 1.8 μm] with a buffer solution of 0.05 mol/L sodium acetate‐acetic acid buffer solution (pH 3.5) as mobile phase. After the enrichment had finished, by switching the six‐ports switching valve, the retained chelates were back‐flushed by mobile phase and traveled towards the analytical column. These chelates separation on the analytical column [ZORBAX Stable Bound, 4.6 × 50 mm, 1.8 μm] was satisfactory with 65% methanol (containing 0.05 mol/L of pH 3.5 sodium acetate‐acetic acid buffer salt and 0.01 mol/L of tritonX‐100) as mobile phase. The palladium and platinum were separated completely within 2 min. The detection limits (S/N = 3) of palladium and platinum are 1.4 ng/L and 1.6 ng/L, respectively. This method was applied to the determination of palladium and platinum in water and urine samples with good results.     

Ab initio Study of β-lactam antibiotics

Ab initio SCF-MO-LCAO calculations have been performed with a 7s3p/3s GTO basis set for the CH₃O--lactam + OH^– reaction which is related to the mode of action of -lactam antibiotics. The comparison of the present results with the previous ones for -lactam + OH^– and 3-cephem + OH^– shows that the CH₃O substitution has a negligible effect on the amidic bond breaking of -lactam, so that this group probably influences other steps of the antibiotic reactivity of cephaloporins.     

Triterpene Glycosides from Plants of the Astragalus Genus. Structure of Cyclounifolioside A from Astragalus unifoliolatus

The known compound oleanolic acid (1) and a new cycloartane glycoside cyclounifolioside A (2), which has the structure 6,16-di-O-acetyl-24R-cycloartan-6,16,24,25-pentaol 3-O--D-glucopyranoside, were isolated from Astragalus unifoliolatus Bunge. The structures of the isolated compounds were established using chemical transformations and two-dimensional spectra (TOCSY, ROESY, HMBC, HSQC, COSY).     

Calculation of some electronic excited states of formaldehyde

The optimized MO's of several excited states of formaldehyde have been calculated by means of a large basis set of modified Gaussian functions; particular attention has been paid to the * transition. The total energy of the various states has been obtained as the sum of the SCF and correlation energies; the last one has been calculated as a functional of the electronic density. The calculated values for the transition energies are in good agreement with the experiment. A strong interaction of the * state with the continuum is evidentiated; this fact can justify the absence of the * band in the absorption spectrum.     

Thermodynamic parameters for the interaction of adenosine 5′-diphosphate,and adenosine 5′-triphosphate with Mg2+ from 323.15 to 398.15 K

The interaction of adenosine 5-diphosphate (ADP) and adenosine 5-triphosphate (ATP) with Mg²⁺ in water has been studied calorimetrically at 323.15, 348.15, 373.15, and 398.15 K for ATP and at 348.15 and 373.15 K for ADP. The enthalpies of reaction of Mg²⁺ with ADP and ATP were obtained from the heats of mixing of aqueous solutions of tetramethylammonium salts of ADP and ATP with MgCl₂ solutions in an isothermal flow calorimeter. Equilibrium constant (K), enthalpy change (H°), entropy change (S°), and heat capacity change (Cp°) values were calculated for the interaction: Mg²⁺+L^n–=MgL^2–n and Mg²⁺+MgL^2–n=Mg₂L^4–n, where n=4 for L=ATP and n=3 for L=ADP. The results are consistent with those at lower temperatures. For the two nucleotides studied, the above two reactions are endothermic and entropy-driven in the temperature range studied. Large Cp° values for the interaction of Mg²⁺ with ADP with ATP indicate the involvement of phosphate groups of nucleotides in the coordination of Mg²⁺. The coordination of the first and second Mg²⁺ ions involves the phosphate chain in both ADP and ATP. No evidence was found for the involvement of the adenine ring or the ribose moiety in the coordination of Mg²⁺ with these nucleotides. Approximate values of logK, H°, and S°, and Cp° for the self-association of ADP and ATP in the presence of Mg²⁺ are also given.     

Reaction of pyridoxal 5′-phosphate with TRIS

Kinetic and equilibrium studies are presented on the reaction of pyridoxal 5-phosphate withTris. Upon raising thepH from 7.3 to 9.3 at 25°C, the second-order rate constant increases from 1.05 M^–1 s^–1 to 3.79 M^–1 s^–1, whereas the apparent dissociation constant varies from 2 to 8 mM. These results demonstrate the significance of this reaction whenTris buffer is used in studies of pyridoxal 5-phosphate-dependent enzymes.

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Reaktion von Pyridoxal-5-phosphat mit TRIS

Zusammenfassung Es werden Untersuchungen über die Kinetik und das Gleichgewicht der Reaktion von Pyridoxal-5-phosphat mitTRIS vorgelegt. Wenn derpH bei 25°C von 7,3 auf 9,3 erhöht wird, steigt die Geschwindigkeitskonstante zweiter Ordnung von 1,05 M^–1 s^–1 auf 3,79 M^–1 s^–1, während die scheinbare Dissoziationskonstante sich im Bereich von 2 bis 8 mM verändert. Die Ergebnisse zeigen, welche Bedeutung diese Reaktion für Untersuchungen von Pyridoxal-5-phosphat-abhängigen Enzymen bei Verwendung vonTRIS-Puffer hat.