Calculation of sequence‐dependent free energies of hydration of dipeptides formed by alanine and glycine

The relative free energies of hydration of the dipeptides glycylalanine and alanyl‐glycine in their naturally occurring form have been calculated both for the zwitterionic and protonated species. Emphasis was laid on comparisons between the conventional cutoff method and the Particle Mesh Ewald method to account for possible differences in electrostatic contributions to the free energy. Furthermore, the convergence behavior of the total free energy and its individual contributions were examined. The results, obtained by means of the thermodynamic integration technique as implemented in the free energy module of the AMBER program suite, suggest that in aqueous solution glycylalanine is more stable than alanylglycine by 2.7 kcal/mol in the zwitterionic form and by 3.5 kcal/mol in the protonated form. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 846–860, 2001     

A Combined QM/MM Molecular Dynamics Simulations Study of Nitrate Anion (NO3‐) in Aqueous Solution.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.     

Measurement of the dynamics of the compression of high aspect-ratio shell targets in the “Delfin-1” installation

With the help of a specific diagnostic system designed for the “DELFIN-1” installation we have measured implosion velocities ? 250 km/s, which are record values for experiments on compression at sufficiently high hydrodynamic efficiency of ablative shell targets. An empirical scaling is shown to agree well with the measured compression velocities.     

Shell-target laser-plasma images in the light of intrinsic and backlit X radiation

Results are presented of calculation of x-ray plasma images of glass shell targets with diagnostic additives Na, K, and Ca in the light of the intrinsic radiation of the resonance lines of H and He ions with Z_n = 8, ii, 14, and 20, and also in the light of cw radiation in the wavelength range = 1-300 Å. The calculation results are compared with laser-plasma images obtained in experiments with the Del'fin-l thermonuclear facility. The temperature and density of the plasma, the rate of corona expansion, the target mass ablation rate, and the hydrodynamic coefficient of laser-energy transfer into kinetic energy of the ablating shell are determined. The plasma images obtained by backlighting the shell target with an auxiliary x-ray source are analyzed with account taken of the radiation refraction. The required energy, temporal, and spectral characteristics of the auxiliary source are determined.Laser-Plasma Laboratory, Lebedev Physics Institute. Translated from Preprint No. 70 of the Lebedev Physics Institute, Academy of Sciences of the USSR, Moscow, 1989.     

Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP

Free energy perturbation calculations have been applied to evaluate the relative free energies of binding of 2'-deoxyuridine-5'-monophosphate (dUMP) and its 2- and/or 4-thio and/or 5-fluoro analogues to the wild-type E. coli thymidylate synthase (ecTS). The results accurately reproduce experimentally measured differences in the free energy of binding of dUMP versus 5-fluoro-dUMP to thymidylate synthase. They indicate that preferred binding of dUMP compared to 5-fluoro-dUMP in the binary complex is equally related to (i) more favorable electrostatic interactions of the dUMP molecule in the enzyme active site, and (ii) its less favorable solvation in the aqueous solution. The relative free energies of binding in the binary complex show moderate and qualitatively indistinguishable discrimination among the studied fluorinated and non-fluorinated 2- and/or 4-thio analogues of dUMP. The binding free energies of monothio analogues of dUMP and 5-fluoro-dUMP correspond quite well with experimentally measured activities of these nucleotides in the thymidylate synthase reaction. On the other hand, the binding free energies of both dithio analogues, 2,4-dithio-dUMP and 2,4-dithio-FdUMP, show lack of such correlation. The latter suggests that very low activities of the dithio analogues of dUMP and 5-fluoro-dUMP may relate more to the covalent reaction of these nucleotides within the ternary complex with TS and 5,10-methylenetetrahydrofolate, than to their pre-covalent binding. We speculate that a lack of substrate activity of 2,4-dithio-dUMP is related to the high aromaticity of its pyrimidine ring that prevents the Michael addition of the active site cysteine thiol to the pyrimidine C6 atom. A stronger affinity of the fluorinated analogues of dUMP to thymidylate synthase, compared to the non-fluorinated congeners, results from the fluorine substituent producing a local strain in the C6 region in the pyrimidine ring, thus sensitizing C6 to the Michael addition of the cysteine thiol.     

The “Del'fin” high-power laser facility for heating spherical thermonuclear targets

The Del'fin H twelve-channel laser facility for high-temperature heating of thermonuclear targets in a spherical geometry is described. It consists of a neodymium driver laser with maximum energy ~10 kJ, pulse duration 10^-10–10^-9 sec, andbeam divergence ~5·10^–4 rad, a vacuum chamber in which the laser radiation interacts with the plasma, and the devices for the diagnostics of the laser and plasma parameters. The Del'fin focusing system, which ensures a high degree of symmetry of the spherical irradiation of the target at a maximum flux density on its surface ~10¹⁵ W/cm², is described. The problem of realizing the maximum ability of heating spherical thermonuclear targets by radiation from high-power laser systems is considered.Translated from Trudy Ordena Lenina Fizicheskogo Instituta im. P.N. Lebedeva, Vol. 103, pp. 3–51, 1978.     

Solvent structures around Na+ and Cl− ions in water

The structural orientation of water in the hydration shells of Na⁺ and Cl^– has been obtained from a Monte Carlo simulation of a 0.55 molal NaCl solution, using the MCY model for water. The probability of first shell coordination numbers has been calculated and is compared with data of previous studies using various model systems.

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Zur Lösungsmittel-Struktur rund um Na⁺ und Cl^– Ionen in Wasser

Zusammenfassung Es wurde mittels einer Monte Carlo-Simulation einer 0.55 molalen NaCl-Lösung unter Verwendung des MCY-Modells für Wasser die Lösungsmittel-orientierung von Wasser in der Hydrat-Hülle von Na⁺ und Cl^–-Ionen erhalten. Die wahrscheinlichsten Koordinationszahlen der ersten Hydrat-Schale werden diskutiert und mit den Daten aus früheren Untersuchungen verschiedener Modellsysteme verglichen.

     

A quantum chemical investigation of CO, NF, SO, CF2 and their combination products

The combination products of the compounds CO, NF, SO and CF₂ have been investigated by semiempirical and ab initio SCF methods. The semiempirical standard procedures lead to satisfactory molecular geometries except for sulfur compounds. The stabilisation energies, however, are unreasonable. Ab initio calculations with minimal basis sets lead to more satisfactory results, as far as stabilisation energies are concerned.     

Ab initioSCF-Berechnungen von JO2F3

Two possible monomers of IO₂F₃ (C_2v, trigonal-bipyramidal and C_s, tetragonal-pyramidal) have been calculated by theLCGO?MO?SCF-method. The calculations indicate the C_2v conformation to be strongly favoured by its total energy. The electronic structure of the compound is discussed on the basis of population analysis and electron density maps. A comparison of the¹⁹F-NMR spectrum of (IO₂F₃) _n , with these calculated data supports the results indicated by the energy values.