Calculation of the van der Waals volumes of organic molecules

A new and more precise method is proposed for calculating van der Waals atomic and molecular volumes of organic compounds. The method provides for intersections of three or more spheres at one point of space. Such a possibility is essential for calculating the volumes of sterically overcrowded molecules and of molecules with intramolecular hydrogen bonds. A computer program for IBM PC/AT(XT) is developed. Depending on the atomic environment in the molecule, the average values of the volume increments for atoms C, N, O, H, F, Cl, and S are obtained using the data from the Cambridge Structural Database.N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 117071. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 922–931, April, 1992.     

Thermodynamics of molecular interactions in ethyl iodide+toluene mixtures

The excess Gibb's free energy of mixing, G^E, for ethyl iodide+toluene at 25°C have been obtained from the measured vapor pressuure data. The H^E and G^E values for ethyl iodide+toluene are positive throughout the ethyl iodide concentration range and G^E>H^E. The results have been analyzed in terms of Flory and ideal associated model theory of nonelectrolyte solutions. It has been observed that the ideal associated model approach which assumes the presence of AN and A₂B molecular species describes well (within±10 J-mol^–1 in the worst case) the general dependence of H^E on X_A (mole fraction of ethyl iodide) over the whole composition range for ethyl iodide+toluene mixtures. The equilibrium constants for A+A AB and 2A+BA₂B reactions along with the enthalpies of formation of AB and A₂B molecular species have been calculated.     

Zur Chemie der Pyrrolpigmente, 54. Mitt.: Phytochrommodellstudien: Ein 2,3-Dihydrobilatrien-abc-3-Cholesterylderivat

The diastereomeric 2,3-Dihydrobilatrienes-abc derivatives (4Z, 9Z, 15Z)-7 and (4Z, 9Z, 15E)-7 bearing a cholesterylacetate moiety in position 3 of the chromophore are prepared. The reaction sequence contains an isomerisation step providing quantitative enantioselective formation of the chiral center in position 3. Configurations and conformations of the diastereomers are elucidated using¹H- and¹³C-NMR spectra, NOE-difference spectra, 2D-NMR experiments (NOESY) and arguments from UV-VIS and CD data. It is concluded that the hydrophobic interactions between chromophore and cholesteryl-fragment yield a compact conformation where the two substructures are in close contact with each other. On the other hand these interactions seem to be too weak to induce significant changes in the chemistry, absorption spectra and conformational characterics of the bile pigment chromophore. Therefore hydrophobic interactions between chromophor and apolar amino acid residues of the protein in phytochrome should be of minor relevance for determining spectroscopic shifts.

     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Finite extensibility and orientational effects in rubbers. A physical interpretation of the ‘van der Waals equation’ for the elastic force

We propose a physical interpretation of the so-called van der Waals equation of state for rubbers, which gives a relation between the force and the deformation. On a phenomenological basis this equation takes the finite extensibility and a non-defined interaction into account. Here the fininte extensibility is discussed for the dilute case (no entanglements) and the highly entangled limit. The intramolecular interactions are described by orientational effects. The resulting equation of state for the force shows the same features as the van der Waals equation.Dedicated to Prof. H.-G. Kilian on the occasion of his 60th birthday.     

The Weak Interaction on CO2 …CO van der Waals Complex : A Theoretical Study

The geometries of van der Waals complex CO2…CO were optimized at DFT and second-order Moller-Plesset perturbation(MP2) levels with the large basis set,three stable structures were found.The most stable structure has a T-shape geometry in which the CO lies along the C2 axis of CO2,with the two C atoms direct contact and R(C…C)=0.3227nm.The corresponding energies of the most stable structure were calculated by means of MP2,MP4D,MP4DQ,MP4SDTQ,MP4SDQ,CCSD and CCSD(T) methods,The BSSE (basis set superposition error) wads eliminated by the Boys-Bernardi counterpoise correction(CP) method.According to thermodynamics data.van der Waals complex CO2…CO can found at a low temperature and or a high pressure,There is a little charge transferred between the two interacted subunits.In the most stable structure,CO2 is the acceptor and CO is the donor.     

Molecular structure of di-aryl-aldimines by multinuclear magnetic resonance and X-ray diffraction

The complete ¹H, ¹³C and ¹⁵N NMR analyses for a series of 25 diaryl-aldimines containing phenyl, pyridyl, pyrazolone and furanyl moieties are described herein. Detailed evaluation of substituent chemical shift and coupling constant effects showed that interaction between the lone pair of the pyrazolone carbonyl group or the nitrogen of 2-substitued pyridines with the aldimine hydrogen increases the value and shifts the resonance signal for this hydrogen to high frequency, in the ¹H NMR spectra. The X-ray crystal structure analysis of pyrazolone substituted aldimines evidenced the planarity of the aryl groups which are conjugated with the CN double bond. In the case of the N-(2-pyridinemethylene)-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one, two rotamers were observed in the same unit cell.     

Some ideas on minimization in ultra micro elemental analysis

Summary The problems encountered in the development of ultra micro methods or trace methods of elemental analysis are generally discussed. It is shown that process analyses (e.g. titrations) are preferable to meet needs of accuracy and sensitivity. Moreover, continuous systems of chemical process analyses seem to give a solution to the generally stated problems.

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Überlegungen zur Minimalisierung in der Ultramikroelementaranalyse

Zusammenfassung Die Probleme bei der Entwicklung von Ultramikro- oder Spurenmethoden in der Elementaranalyse werden allgemein diskutiert. Es wird gezeigt, daß Prozeßanalysen (z.B. Titrationen) den Anforderungen an Genauigkeit und Empfindlichkeit entsprechen. Darüber hinaus scheinen kontinuierliche Systeme chemischer Prozeßanalysen eine Lösung der aufgezeigten Probleme zu ermöglichen.

We thank the Czechoslovak Academy of Sciences, the Analytical Department of the Charles University of Prague and the High School for Chemical Technology of Pardubice for the possibility given to one of us (B.G.) to discuss with many colleagues in the SSR, the ideas presented in this article.     

Calculations of concentration dependences of chemical shifts for acrylamide in water—DMSO mixed solvent

The lattice model of associated solutions was used to calculate the concentration dependences of the chemical shifts of¹³C magnetic nuclei in the acrylamide molecule in water—DMSO solvent. Each pair of bonds between the acrylamide group containing a magnetic nucleus and the neighboring solvent molecule was assumed to additively contribute to the change in the chemical shift of the nucleus in question. The new approach affords the same accuracy in describing the experimental data at any ratios of the solution components. It was shown that the chemical shifts and the excess heat of mixing of the water—DMSO binary solution can be simultaneously described using the same set of energy parameters of the model. The model makes it possible to employ experimental data on chemical shifts for studying intermolecular interactions in solutions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1983–1987, October, 1998.     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.