New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

Reverse-docking as a computational tool for the study of asymmetric organocatalysis

A novel methodology for 'reverse-docking' a cationic peptide-based organocatalyst to a rigid anionic transition state (TS) model for the conjugate addition of azide to alpha,beta-unsaturated carbonyl substrates is described. The resulting docking poses serve as simplified TS models for enantioselective catalysis. Molecular mechanics-based scoring and ranking of the docking poses, followed by clustering and structural analysis, reveal a clear energetic preference for docking to the S-enantiomeric azidation TS model, in agreement with experiment. Clear energetic trends emerged from docking the catalyst to both enantiomers of all six azidation TS models of this study. Structural analysis of the most favorable pose suggests a mechanism for enantioselective catalysis that is consistent with principles of molecular recognition, catalysis, and experimental data.     

Tetrakis(thiadiazolo)porphyrazines. 3. Acid-base Properties and Stability of Tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine in Sulfuric Acid Solutions

AM1 calculations gave the proton affinities of different types of donor sites in tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine, H₂{[SN₂)₄PA}, and protonation of the meso-nitrogen atoms was found to be favored. A spectrometric study showed that the basicity of the meso-nitrogen atoms of the porphyrazine macrocycle is strongly diminished and these atoms in CF₃CO₂H are involved in an incomplete acid-base interaction (ABI) to give acid solvates, while a complete ABI (protonation) is found only in the presence of sulfuric acid. The basicity constants of the meso-nitrogen atoms were determined spectrophotometrically in CF₃CO₂H-H₂SO₄. The kinetics of decomposition of the macrocyclic chromophore in concentrated sulfuric acid was studied and a possible mechanism for this process was proposed.__________Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 278–287, February, 2005.     

A structural analysis of the complexes of (S,S)-dimethylpyridino-18-crown-6 with (R) and (S)-[α-(1-naphthyl)ethyl]ammonium perchlorate by NMR techniques and molecular modeling

Significant - interaction is found in the complexes of (S, S)-dimethylpyridino-18-crown-6 with (R)- and (S)-[-(1-naphthyl)ethyl]ammonium perchlorate. This finding is supported by the¹H NOESY NMR spectral technique, greater chemical shift changes of aromatic protons in both host and guest molecules upon complexation, and by molecular mechanics calculations. Because of the flexibility of the ligand, the tripod hydrogen bonding causes¹³C relaxation times of all periphery carbons to decrease without significant selectivity. Rotational energy barrier calculations of the methyl groups of the complexed ligand also show that the (S, S)-host-(R)-guest is the more stable complex.     

Computer simulation of conformational movement based on interconversion phenomena

A computer method has been developed which is an alternative to molecular dynamics in the sense that it pictures conformational motion. It simulates propagation in conformational movement based on conformational interconversion phenomena. The method starts with the knowledge of the topology of the conformational potential energy hyper-surface, which is described by the minima and the transition states. The topology is obtained by the recently described software . The simulation of conformational motion is based on the Boltzmann statistics of movement between the minima and the transition states at a given temperature. The method is illustrated for methyl--glucopyranoside and - -galNAc(1-3)[- -Fuc(1-2)]Gal-O-Me molecules. Conformational transitions of hydroxyl groups as well as glycosidic linkages are discussed.     

Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minima

The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers.     

Surface modification of soft-glass capillaries for gas chromatography by treatment with water vapour

“Leaching” or “etching” by strong mineral acids seems to be a necessary pretreatment step for the most commonly used deactivation procedures of glass capillaries by reaction with either polyethylene glycol or silylation reagents. The acidic sites which are formed on the surface during this acid treatment cannot be completely removed by the subsequent deactivation process. This drawback can be overcome by performing the leaching with water vapour, resulting in an accumulation of cations at the surface and a decrease in the number of silanol groups. Capillaries of this type show excellent properties for the chromatography of strongly basic compounds. After the wash-out of the alkaline surface layer, the acidity of the support is suited for the chromatography of strongly basic as well as strongly acidic compounds. Due to a lack of reactive acidic sites, special deactivation procedures have to be applied to capillaries produced in this way.     

Crystal Structure of Lappaconitine Hydrobromide Hydrate

The structure of lappacontine hydrobromide hydrate was solved by an x-ray structure analysis.     

Conformational analysis of 2-oxo-1,2,3,4,-tetrahydropyridine and its alkyl- and phenyl-substituted derivatives

The molecular geometries and inversion barriers of the rings in 2-oxo-1,2,3,4-tetrahydropyridine and its alkyl-substituted (Me, Et, Prⁱ, or Bu^t) and phenyl-substituted derivatives were calculated by the molecular mechanics method. The introduction of substituents has no substantial effect on the equilibrium conformation of the heterocycle (a distorted sofa). For 4-alkyl- and 3-alkyl-substituted derivatives (except for 4-Me and 4-Et derivatives), an axial orientation of the alkyl group is more favorable. The phenyl substituents have equatorial and axial orientations at postions 4 and 3, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1584–1586, September, 1997.     

Some Comments on the Matter Wave-light Wave Hypothesis

From the de Broglie matter wave hypothesis and Planck’s energy quantization law, and assuming conservation of energy in the absorption of a photon and its consequent conversion to kinetic energy of motion by a material particle initially at rest, one can deduce a simple mathematical relationship between the wavelength λ (or frequency ν), of the photon absorbed by the particle at rest, and the resulting de Broglie matter wave length, λ_D, of the particle with kinetic energy of motion of mv²/2. The relationship so deduced, λ_D∝√λ, suggests that visible wavelengths of light, from about 4000 ?, in the violet, to beyond about 7000 ?, in the red, on absorption by an electron at rest, lead to material electron wavelengths, λ_D, of the order of the size of the electron transfer proteins seen in the photosynthetic reaction centers of photosynthesizing organisms, at about a size of 50–100 ?. In addition to understanding the mechanism of photosynthesis as a material wave mediated phenomenon, further areas of importance of the relations pointed out in this paper are in the design of experiments to gain a deeper understanding of the basic tenets of wave mechanics, and in the use of tunable lasers to probe various properties of material waves, and to precisely control their properties for applications including lithography.