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Atomic Radii (atomic + radius)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Test and modification of the van der Waals' radii employed in the default PCM model

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2008
Wei-Hua Mu
Abstract High level ab initio calculations at the B3LYP/6-311++G(d,p) and MP2(full)/6-311++G(d,p) levels employing PCM/UA0 model with different van der Waals' radii for the systems that contain lithium atoms have been carried out, in order to see if the van der Waal's radius for lithium atom employed in the default PCM/UA0 model is proper or not. Comparative analysis indicated that the van der Waals' radius for alkali metals, especially for lithium atom in the default PCM/UA0 model within the Gaussian 03 package, is too small, which causes erroneous redundant imaginary frequencies (RIFs) in the characterization of Li-containing compounds from moderate to big size. A new set of van der Waals' atomic radii based on QTAIM, proposed by Bader, was suggested for a better choice in the characterization of compounds containing alkali metals, for which it can effectively avoid the erroneous RIFs for corresponding geometries of these Li-containing systems. © 2008 Wiley Periodicals, Inc. Int. J. Quantum Chem, 2008 [source]

Converging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,Raf

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004
Holger Gohlke
Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source]

The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2002
Li Xie
Abstract We present a model to calculate the free energies of solvation of small organic compounds as well as large biomolecules. This model is based on a generalized Born (GB) model and a self-consistent charge-density functional theory-based tight-binding (SCC-DFTB) method with the nonelectrostatic contributions to the free energy of solvation modeled in terms of solvent-accessible surface areas (SA). The parametrization of the SCC-DFTB/GBSA model has been based on 60 neutral and six ionic molecules composed of H, C, N, O, and S, and spanning a wide range of chemical groups. Effective atomic radii as parameters have been obtained through Monte Carlo Simulated Annealing optimization in the parameter space to minimize the differences between the calculated and experimental free energies of solvation. The standard error in the free energies of solvation calculated by the final model is 1.11 kcal mol,1. We also calculated the free energies of solvation for these molecules using a conductor-like screening model (COSMO) in combination with different levels of theory (AM1, SCC-DFTB, and B3LYP/6-31G*) and compared the results with SCC-DFTB/GBSA. To assess the efficiency of our model for large biomolecules, we calculated the free energy of solvation for a HIV protease-inhibitor complex containing 3204 atoms using the SCC-DFTB/GBSA and the SCC-DFTB/COSMO models, separately. The computed relative free energies of solvation are comparable, while the SCC-DFTB/GBSA model is three to four times more efficient, in terms of computational cost. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1404,1415, 2002 [source]

Determination of cubic equation of state parameters for pure fluids from first principle solvation calculations

AICHE JOURNAL, Issue 8 2008
Chieh-Ming Hsieh
Abstract A new method for estimation of parameters in cubic equations of state from ab initio solvation calculations is presented. In this method, the temperature-dependent interaction parameter a(T) is determined from the attractive component of solvation free energy, whereas the volume parameter b is assumed to be that of solvation cavity. This method requires only element-specific parameters, i.e., atomic radius and dispersion coefficient, and nine universal parameters for electrostatic and hydrogen-bonding interactions. The equations of state (EOS) parameters so determined allow the description of the complete fluid phase diagram, including the critical point. We have examined this method using the Peng,Robinson EOS for 392 compounds and achieved an accuracy of 43% in vapor pressure, 17% in liquid density, 5.4% in critical temperature, 11% in critical pressure, and 4% in critical volume. This method is, in principle, applicable to any chemical species and is especially useful for those whose experimental data are not available. © 2008 American Institute of Chemical Engineers AIChE J, 2008 [source]