A modification of the nudged elastic band method for finding minimum energy paths is presented. One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#

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A climbing image nudged elastic band method for finding saddle points and minimum energy paths

The phenomenon of growth, decline and death—aging—has been the source of considerable speculation (1, 8, 10). This cycle seems to be a more or less direct function of the metabolic rate and this in turn depends on the species (animal or plant) on which are superimposed the factors of heredity and the effects of the stresses and strains of life—which alter the metabolic activity. The universality of this phenomenon suggests that the reactions which cause it are basically the same in all living things. Viewing this process in the light of present day free radical and radiation chemistry and of radiobiology, it seems possible that one factor in aging may be related to deleterious side attacks of free radicals (which are normally produced in the course of cellular metabolism) on cell constituents.* Irradiation of living things induces mutation, cancer, and aging (9). Inasmuch as these also arise spontaneously in nature, it is natural to inquire if the processes might not be similar. It is believed that one mechanism of irradiation effect is through liberation of OH and HO 2 radicals (12). There is evidence, although indirect, that these two highly active free radicals are produced normally in living systems. In the first place, free radicals are present in living cells; this was recently demonstrated in vivo by a paramagnetic resonance absorption method (3). Further, it was shown that the concentration of free radicals increased with increasing metabolic activity in conformity with the postulates set forth some years ago that free radicals were involved in biologic oxidation-reduction reactions (11, 13). Are some of these free radicals OH and/or HO2, or radicals of a similar high order of reactivity, and where might they arise in the cell? The most likely source of OH and HO2 radicals, at least in the animal cell, would be the interaction of the respiratory enzymes involved

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Aging: A Theory Based on Free Radical and Radiation Chemistry

/pdf/brownian-motion-in-a-field-of-force-and-the-diffusion-model-2nbbzrdubb.pdf

Brownian motion in a field of force and the diffusion model of chemical reactions

Stanford Moore, William Stein, and Anfinsen were awarded the Nobel Prize in Chemistry in 1972 for \"their contribution\n to the understanding of the connection between chemical structure and catalytic activity of the active center of the ribonuclease\n molecule.\" In his Nobel Lecture, Anfinsen provided a sketch of the rich history of research that provided the foundation\n for his work on protein folding and the \"Thermodynamic Hypothesis,\" and outlined potential avenues of current and\n future scientific exploration.

https://web.iitd.ac.in/~amittal/1973_Anfinsen_Science.pdf

Principles that Govern the Folding of Protein Chains

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

: Work on ionization in flames and related subjects such as combustion and pyrolysis is critically reviewed. It is assumed that saturated hydrocarbons and high molecular weight unsaturated hydrocarbons produce acetylene and the acetylene-oxygen mixture is responsible for the production of the most abundant ion. This assumption is justified by subsequent literature survey. Acetylene undergoes further chemical changes producing the CH radical which is directly responsible for the production of the most abundant ion. The probable chain reactions for the production of the CH radical are proposed. The mechanism of the formation of the most abundant ion and less abundant ions are illustrated. The high ionization in hydrocarbon flames is shown to be caused by electronically excited species. Reasons for the lack of high ionization in carbon monoxide and hydrogen flames are discussed. (Author)

Ions in flames

A study of the dependence of the energy calculations for the linear triatomic hydrogen ion system H3, on a single polarization (electron cloud displacement) parameter g, and on two effective orbital charge parameters Z0 and Zm is presented. The studies, with separate screening parameters for the central and outer atomic orbitals, used normalized approximate integrals. The individual variation of Z0, the charge associated with the outer orbitals, and of Zm, the charge associated with the central orbital, gave little improvement of the energy calculation. From these results with approximate integrals, calculations, at this time, using the exact integrals appear unprofitable.Only exact integrals are used in the study dealing with the off‐center electron cloud parameter, g. These exact integral calculations led to an energy of — 158.07 kcal/mole which is 2.74 kcal/mole better than the best previously obtained value for this linear system.

Energy Calculations for the Linear H3+ Ion System*

The authors present a theory of valency that accounts for a variety of organic and inorganic structures in a clear and easily understood manner.

The principle of minimum bending of orbitals

A method is presented for localizing molecular orbitals, based on diagonalizing subunits of the density matrix. First, nonbonding orbitals are found by diagonalizing the monatomic subunits; then, diatomic σ or π bonding and antibonding orbitals are obtained from the diatomic subunits for all bonded pairs of atoms; finally, the delocalized π-orbitals for particular chromophores are found by projecting the first set out of the self-consistent field (SCF) Hamiltonian. The results show good general agreement with other localization methods, with advantages in the ability to display group orbitals in complex molecules which most closely resemble the SCF orbitals for simple prototypes.

http://www.pnas.org/content/76/7/3042.full.pdf

Henry Eyring

Papers

Ions in flames

Energy Calculations for the Linear H3+ Ion System*

The principle of minimum bending of orbitals

Density matrix method for orbital localization.

Strain Electrometry and Corrosion. II. Chemical Effects with Copper Electrodes