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Basilevsky MV Leontyev IV Luschekina SV Kondakova OA Sulimov VB 《Journal of computational chemistry》2006,27(5):552-570
A new approach for computing hydration free energies DeltaG(solv) of organic solutes is formulated and parameterized. The method combines a conventional PCM (polarizable continuum model) computation for the electrostatic component DeltaG(el) of DeltaG(solv) and a specially detailed algorithm for treating the complementary nonelectrostatic contributions (DeltaG(nel)). The novel features include the following: (a) two different cavities are used for treating DeltaG(el) and DeltaG(nel). For the latter case the cavity is larger and based on thermal atomic radii (i.e., slightly reduced van der Waals radii). (b) The cavitation component of DeltaG(nel) is taken to be proportional to the volume of the large cavity. (c) In the treatment of van der Waals interactions, all solute atoms are counted explicitly. The corresponding interaction energies are computed as integrals over the surface of the larger cavity; they are based on Lennard Jones (LJ) type potentials for individual solute atoms. The weighting coefficients of these LJ terms are considered as fitting parameters. Testing this method on a collection of 278 uncharged organic solutes gave satisfactory results. The average error (RMSD) between calculated and experimental free energy values varies between 0.15 and 0.5 kcal/mol for different classes of solutes. The larger deviations found for the case of oxygen compounds are probably due to a poor approximation of H-bonding in terms of LJ potentials. For the seven compounds with poorest fit to experiment, the error exceeds 1.5 kcal/mol; these outlier points were not included in the parameterization procedure. Several possible origins of these errors are discussed. 相似文献
2.
G Fuchs K-H Müller J Freudenberger K Nenkov S-L Drechsler SV Shulga D Lipp A Gladun T Cichorek P Gegenwart 《Pramana》2002,58(5-6):791-797
The effect of substitutional disorder on the superconducting properties of YNi2B2C was studied by partially replacing yttrium and nickel by Lu and Pt, respectively. For the two series of (Y, Lu)Ni2B2C and Y(Ni, Pt)2B2C compounds, the upper critical field H
c2(T) and the specific heat c
p(T, H) in the superconducting mixed state have been investigated. Disorder is found to reduce several relevant quantities such
as T
c, the upper critical field H
c2(0) at T=0 and a characteristic positive curvature of H
c2(T) observed for these compounds near T
c. The H
c2(T) data point to the clean limit for (Y, Lu) substitutions and to a transition to the quasi-dirty limit for (Ni, Pt) substitutions.
The electronic specific heat contribution γ(H) exhibits significant deviations from the usual linear γ(H) law. These deviations reduce with growing substitutional disorder but remain even in the quasidirty limit which is reached
in the Y(Ni1−x
, Pt
x
)2B2C samples for x=0.1. 相似文献
3.
Non-resonant microwave absorption (NRMA) studies of superconducting MgB2 and a sample containing ∼10% by weight of MgO in MgB2 are reported. The NRMA results indicate near absence of intergranular weak links in the pure MgB2 sample. A linear temperature dependence of the lower critical field H
c1 is observed indicating a non-s wave superconductivity. However, the phase reversal of the NRMA signal which could suggest d wave symmetry is also not observed. In the MgB2 + MgO sample, much larger low field dependent absorption is observed indicating the presence of intergranular weak links.
The hysteretic behavior of NRMA is compared and contrasted in the two samples. In the pure MgB2 sample, a large hysteresis is observed between the forward and the reverse scans of the magnetic field indicating strong
pinning of flux lines. This hysteresis saturates a few degrees below T
c while in the MgB2 + MgO sample, a much slower increase of hysteresis with decreasing temperature is observed, a signature of weaker pinning. 相似文献
4.
E. Nikitina V. Sulimov F. Grigoriev O. Kondakova S. Luschekina 《International journal of quantum chemistry》2006,106(8):1943-1963
An approach to quantum mechanical investigation of interactions in protein–ligand complexes has been developed that treats the solvation effect in a mixed scheme combining implicit and explicit solvent models. In this approach, the first solvation shell of the solvent around the solute is modeled with a limited number of hydrogen bonded explicit solvent molecules. The influence of the remaining bulk solvent is treated as a surrounding continuum in the conductor‐like screening model (COSMO). The enthalpy term of the binding free energy for the protein–ligand complexes was calculated using the semiempirical PM3 method implemented in the MOPAC package, applied to a trimmed model of the protein–ligand complex constructed with special rules. The dependence of the accuracy of binding enthalpy calculations on size of the trimmed model and number of optimized parameters was evaluated. Testing of the approach was performed for 12 complexes of different ligands with trypsin, thrombin, and ribonuclease with experimentally known binding enthalpies. The root‐mean‐square deviation (RMSD) of the calculated binding enthalpies from experimental data was found as ~1 kcal/mol over a large range. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 相似文献
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