Biomedical subjects

Erin R Johnson

Publications and source records attributed to Erin R Johnson.

7 recordsLinked to original sources

PubMed2006

A post-Hartree-Fock model of intermolecular interactions: inclusion of higher-order corrections.

We have previously demonstrated that the dipole moment of the exchange hole can be used to derive intermolecular C(6) dispersion coefficients [J. Chem. Phys. 122, 154104 (2005)]. This was subsequently the basis for a novel post-Hartree-Fock model of intermolecular interactions [J. Chem. Phys. 123, 024101 (2005)]. In the present work, the model is extended to include higher-order dispersion coefficients C(8) and C(10). The extended model performs very well for prediction of intermonomer separations and binding energies of 45 van der Waals complexes. In particular, it performs twice as well as basis-set extrapolated MP2 theory for dispersion-bound complexes, with minimal computational cost.

Journal Article↗

PubMed2006

Exchange-hole dipole moment and the dispersion interaction: high-order dispersion coefficients.

In recent publications [A. D. Becke and E. R. Johnson, J. Chem. Phys. 122, 154104 (2005); E. R. Johnson and A. D. Becke 123, 024101 (2005)] we have demonstrated that the position-dependent dipole moment of the exchange hole can be used to generate dispersion interactions between closed-shell systems. Remarkably accurate C6 coefficients and intermolecular potential-energy surfaces can be obtained from Hartree-Fock occupied orbitals and polarizability data alone. In the present work, our model is extended to predict C8 and C10 coefficients as well. These higher-order coefficients are obtained as easily as C6 and with comparable accuracy.

Journal Article↗

PubMed2005

A density-functional model of the dispersion interaction.

We have recently introduced [J. Chem. Phys. 122, 154104 (2005)] a simple parameter-free model of the dispersion interaction based on the instantaneous in space, dipole moment of the exchange hole. The model generates remarkably accurate interatomic and intermolecular C6 dispersion coefficients, and geometries and binding energies of intermolecular complexes. The model involves, in its original form, occupied Hartree-Fock or Kohn-Sham orbitals. Here we present a density-functional reformulation depending only on total density, the gradient and Laplacian of the density, and the kinetic-energy density. This density-functional model performs as well as the explicitly orbital-dependent model, yet offers obvious computational advantages.

Journal Article↗

PubMed2005

A post-Hartree-Fock model of intermolecular interactions.

Intermolecular interactions are of great importance in chemistry but are difficult to model accurately with computational methods. In particular, Hartree-Fock and standard density-functional approximations do not include the physics necessary to properly describe dispersion. These methods are sometimes corrected to account for dispersion by adding a pairwise C6R6 term, with C6 dispersion coefficients dependent on the atoms involved. We present a post-Hartree-Fock model in which C6 coefficients are generated by the instantaneous dipole moment of the exchange hole. This model relies on occupied orbitals only, and involves only one, universal, empirical parameter to limit the dispersion energy at small interatomic separations. The model is extensively tested on isotropic C6 coefficients of 178 intermolecular pairs. It is also applied to the calculation of the geometries and binding energies of 20 intermolecular complexes involving dispersion, dipole-induced dipole, dipole-dipole, and hydrogen-bonding interactions, with remarkably good results.

Journal Article↗

PubMed2005

Exchange-hole dipole moment and the dispersion interaction.

A simple model is presented in which the instantaneous dipole moment of the exchange hole is used to generate a dispersion interaction between nonoverlapping systems. The model is easy to implement, requiring no electron correlation (in the usual sense) or time dependence, and has been tested on various atomic and molecular pairs. The resulting C6 dispersion coefficients are remarkably accurate.

Journal Article↗

PubMed2005

Efficient silicon surface and cluster modeling using quantum capping potentials.

A one-electron, silicon quantum capping potential for use in capping the dangling bonds formed by artificially limiting silicon clusters or surfaces is developed. The quantum capping potentials are general and can be used directly in any computational package that can handle effective core potentials. For silicon clusters and silicon surface models, we compared the results of traditional hydrogen atom capping with those obtained from capping with quantum capping potentials. The results clearly show that cluster and surface models capped with quantum capping potentials have ionization potentials, electron affinities, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps that are in very good agreement with those of larger systems. The silicon quantum capping potentials should be applied in cases where one wishes to model processes involving charges or low-energy excitations in silicon clusters and surfaces consisting of more than ca. 150 atoms.

Journal Article↗

PubMed2002

Naphthalene diols: a new class of antioxidants intramolecular hydrogen bonding in catechols, naphthalene diols, and their aryloxyl radicals.

1,8-Naphthalenediol, 5, and its 4-methoxy derivative, 6, were found to be potent H-atom transfer (HAT) compounds on the basis of their rate constants for H-atom transfer to the 2,2-di(4-t-octylphenyl)-1-picrylhydrazyl radical (DOPPH*), k(ArOH/DOPPH)*, or as antioxidants during inhibited styrene autoxidation, k(ArOH/ROO)*, initiated with AIBN. The rate constants showed that 5 and 6 are more active HAT compounds than the ortho-diols, catechol, 1, 2,3-naphthalenediol, 2, and 3,5-di-tert-butylcatechol, 3. Compound 6 has almost twice the antioxidant activity, k(ArOH/ROO)* = 6.0 x 10(6) M(-)(1) s(-1), of that of the vitamin E model compound, 2,2,5,7,8-pentamethyl-6-chromanol, 4. Calculations of the O-H bond dissociation enthalpies compared to those of phenols, (deltaBDEs), of 1-6 predict a HAT order of reactivity of 2 < 1 < 3 approximately 4 < 5 < 6 in general agreement with kinetic results. Calculations on the diols show that intramolecular H-bonding stabilizes the radicals formed on H-atom transfer more than it does the parent diols, and this effect contributes to the increased HAT activity of 5 and 6 compared to the activities of the catechols. For example, the increased stabilization due to the intramolecular H-bond of 5 radical over 5 parent of 8.6 kcal/mol was about double that of 2 radical over 2 parent of 4.6 kcal/mol. Linear free energy plots of log k(ArOH/DOPPH)* and log k(ArOH/ROO)* versus deltaBDEs for compounds 1-6 along with available literature values for nonsterically hindered monophenols placed the compounds on common scales. The derived Evans-Polanyi constants from the plots for the two reactions, alpha(DOPPH)* = 0.48 > alpha(ROO)* = 0.32, gave the expected order, since the ROO* reaction is more exothermic than the DOPPH* reaction. Compound 6 is sufficiently reactive to react directly with oxygen, and it lies off the log k(ArOH/ROO)* versus deltaBDE plot.

Antioxidants↗