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  • 1
    ISSN: 1432-2234
    Keywords: Key words: Chemical reactivity ; Density functional ; Non-local reactivity ; Response function ; CN ; Cyanide ion reactivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Activation is a fundamental and well-known concept in chemistry. It may be qualitatively defined as an increase in the chemical reactivity pattern of a molecule at a given site k when the system is locally perturbed at a different site l, say. This external perturbation arise from a localized molecular rearrangement, a substitution, a selective solvation or simply by the approach of a reagent of variable hardness. This work presents a theoretical approach intending to quantify this activation concept in the density functional framework. This is done here by first calculating the fluctuation of the electron density at a given site k for the ground state of the isolated substrate (static reactivity model) and then incorporating the substrate and model electrophile reagents in a spatial disposition related to a virtual transition structure for the parent system. This perturbation is assumed representable by local changes in the external potential. It is shown that a local approximation to the softness kernel s(r, r′) yields a simple expression for the fluctuation of the electron density δρ(r k ), which shows that this change becomes proportional to the variation of an effective potential δu(r k ), containing the information on the variation in the chemical potential and the external perturbing potential at site k; the proportionality constant being the local softness s 0(r k) at that site. The strong local approximation made to the kernel s(r, r′) causes the second reactivity site (l) to implicitly appear in the formulation through the changes in the electronic chemical potential term. It is shown that the introduction of a less restrictive approach to the linear response function, obtained from a model Kohn-Sham one-electron density matrix, leads to the same result. Non-locality is therefore self-contained in the electronic chemical potential contribution to the modified potential, and may be associated with an intramolecular charge transfer between the active sites of the ambident nucleophilic/electrophilic substrate, promoted by the presence of the reagents. The resulting formulation of pair-site reactivity is illustrated for the electrophilic attack on the CN− ion by different model electrophile agents of variable hardness. It is shown that correct reactivity indexes are obtained only when the topology of the transition structure is used as a vantage point to perturb the CN− ion. The calculations were performed at both density functional theory and ab-initio Hartree-Fock levels. The results show that the proposed model is independent of the method used to obtain ρ(r).
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0887-3585
    Keywords: computer simulation ; force-field analysis ; molecular dynamics of proteins ; water solvation properties ; van der Waals interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A critical evaluation is presented of the sensitivity of the results of molecular dynamics simulations of proteins to changes in the parameters describing water-protein and protein-protein van der Waals interactions in the GROMOS force field. The origin of the van der Waals and electrostatic parameters of the GROMOS standard force field is reviewed, and possible weaknesses are discussed. Four alternate sets of van der Waals parameters for the oxygen types of the GROMOS force field that have been suggested by different authors are then tested against the original force field. Six 500 ps molecular dynamics simulations of the potato carboxypeptidase inhibitor (PCI) in solution using the different parameter sets are analyzed and the results compared with the available X-ray and NMR data. It is shown that the behavior of the molecular system is very sensitive to changes in the van der Waals parameters of the oxygens, especially when affecting the interactions between water and aliphatic or aromatic groups. It is also shown that correction of just the repulsive van der Waals parameter of the water oxygen for its interactions with nonpolar groups is sufficient to correct the main deficiency of the original GROMOS parameter set. Nevertheless, the present study suggests that further refinement of the current parameters is still needed for a proper representation of nonbonded interactions. © 1996 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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