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71.
Carlos Alemn Enric I. Canela Rafael Franco Modesto Orozco 《Journal of computational chemistry》1991,12(6):664-674
A new strategy for the determination of force parameters is presented. The equilibrium values appearing in the force field equations representing the “stretching” and “bending” of bonds are directly determined from quantum mechanical calculations without geometrical restrictions. The determination of the force parameters is carried out by means of a rigorous fitting between the quantum mechanic and the molecular mechanical energy variations arising from the perturbation of the geometric variables. The strategy presented here has been incorporated into a computer program named PAPQMD, which was developed in order to provide nonquantum mechanical experts with a powerful tool for the determination of approximate force parameters. The program was developed upon the assumption that force parameters are not universal, but they strongly depend on the molecular environment. This implies that the parametrization procedure should be done in a molecular model close to the molecule or molecules to be studied by means of molecular mechanical or dynamic methods, and consequently, it is no longer supposed that the variation of one geometrical parameter does not affect the rest of the molecular geometry. PAPQMD performs the fitting between molecular mechanics and quantum mechanical energies considering all the perturbations that the modification in one geometric variable causes in all the others, enabling the parametrization even of large molecules. The ability of our method to reproduce experimentally derived force parameters is discussed and compared with the widely used Hopfinger's strategy. The study of the behavior of PAPQMD and Hopfinger's strategies for reproducing the force parameters of two complex molecules demonstrates the superiority of the methodology presented here. 相似文献
72.
The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc. 相似文献
73.
Crespo A Martí MA Kalko SG Morreale A Orozco M Gelpi JL Luque FJ Estrin DA 《Journal of the American Chemical Society》2005,127(12):4433-4444
Mycobacterium tuberculosis is the causative agent of human tuberculosis. The nitric oxide reaction with oxy-truncated hemoglobin N (trHbN) has been proposed to be responsible for the resistance mechanism by which this microorganism can evade the toxic effects of NO. In this work, we explore the molecular basis of the NO detoxification mechanism using a combination of classical and hybrid quantum-classical (QM-MM) simulation techniques. We have investigated the structural flexibility of the protein, the ligand affinity properties, and the nitric oxide reaction with coordinated O2. The analysis of the classical MD trajectory allowed us to identify Phe62 as the gate of the main channel for ligand diffusion to the active site. Moreover, the opening of the channel stems from the interplay between collective backbone motions and local rearrangements in the side chains of the residues that form the bottleneck of the tunnel. Even though the protein environment is not found to make a significant contribution to the heme moiety catalyzed reaction, the binding site influences the physiological function of the enzyme at three different levels. First, by isolating the intermediates formed in the reaction, it prevents nondesired reactions from proceeding. Second, it modulates the ligand (O2, NO) affinity of the protein, which can be ascribed to both distal and proximal effects. Finally, the stabilization of the Tyr33-Gln58 pair upon O2 binding might alter the essential dynamics of the protein, leading in turn to a mechanism for ligand-induced regulation. 相似文献
74.
Suaud N Gaita-Ariño A Clemente-Juan JM Sánchez-Marín J Coronado E 《Journal of the American Chemical Society》2002,124(50):15134-15140
We present a quantitative evaluation of the influence of the electron transfer on the magnetic properties of mixed-valence polyoxometalates reduced by two electrons. For that purpose, we extract from valence-spectroscopy ab initio calculations on embedded fragments the value of the transfer integrals between W nearest-neighbor atoms in a mixed-valence alphaPW(12)O(40) polyoxowolframate Keggin anion. In contradiction with what is usually assumed, we show that the electron transfer between edge-sharing and corner-sharing WO(6) octahedra have very close values. Considering fragments of various ranges, we analyze the accuracy of calculations on fragments based on only two WO(5) pyramids which should allow a low cost general study of transfer parameters in polyoxometalates. Finally, these parameters are introduced in an extended Hubbard Hamiltonian that models the whole anion. It permits to prove that electron transfers induce a large energy gap between the singlet ground state and the lowest triplet states providing a clear explanation of the diamagnetic properties of the mixed-valence Keggin ions reduced by two electrons. 相似文献
75.
We report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc. 相似文献
76.
Salichs A López M Segarra V Orozco M Luque FJ 《Journal of computer-aided molecular design》2002,16(8-9):569-583
The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. Attention is paid to i) the reliability of semiempirical versus
ab initio treatments of the quantum mechanical molecule, ii) the role of solvation, and iii) the effect of including the polarization energy component in the calculation of the GMIPp functional. The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds. 相似文献
77.
Giorgio Giorgiani David Modesto Sonia Fernández‐Méndez Antonio Huerta 《国际流体数值方法杂志》2013,73(10):883-903
Three Galerkin methods—continuous Galerkin, Compact Discontinuous Galerkin, and hybridizable discontinuous Galerkin—are compared in terms of performance and computational efficiency in 2‐D scattering problems for low and high‐order polynomial approximations. The total number of DOFs and the total runtime are used for this correlation as well as the corresponding precision. The comparison is carried out through various numerical examples. The superior performance of high‐order elements is shown. At the same time, similar capabilities are shown for continuous Galerkin and hybridizable discontinuous Galerkin, when high‐order elements are adopted, both of them clearly outperforming compact discontinuous Galerkin. Copyright © 2013 John Wiley & Sons, Ltd. 相似文献
78.
79.
The francium atom offers an excellent laboratory to study electron-nucleus interactions. As the heaviest alkali, its atomic
properties can be calculated with high precision, and laser trapping methods now allow precision optical spectroscopy of many
isotopes. Recent measurements of the 7P1/2 hyperfine structure, when coupled with previous measurements of the ground state hyperfine structure reveal a hyperfine anomaly.
The change in anomaly between an even-N isotope and an odd-N isotope is sensitive to the radial distribution of the neutron magnetization.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
80.
Axel Bidon-Chanal Oscar Huertas Modesto Orozco F. Javier Luque 《Theoretical chemistry accounts》2009,123(1-2):11-20
The balance between electrostatic and non-electrostatic enthalpic contributions to the free energy of solvation of a series of neutral solutes in water and n-octanol is examined by means of continuum solvation calculations based on the Miertus–Scrocco–Tomasi (MST) method. The experimental data indicate that the solvation enthalpy of hydrocarbons is very similar in water and n-octanol, and that the enthalpic contribution measured for polar compounds is larger in water than in n-octanol. According to MST calculations, the different magnitude of the solvation enthalpy found for polar compounds in the two solvents can be largely attributed to the electrostatic contribution. Moreover, the results point out that there is close resemblance between the non-electrostatic components for both hydrocarbons and polar compounds in the two solvents. Finally, the results show the power of current continuum models like MST to dissect the total free energy of solvation in entropic and enthalpic contributions and suggest that new refinements of continuum solvation models should include not only the fitting to solvation free energies, but also their enthalpic components. 相似文献