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.

A molecular model in terms of which the elastic viscous properties of rubber‐like substances can be interpreted is presented. Experiments on stress relaxation at constant extension, creep under constant load, extrusion, vibration, and breaking are discussed in terms of a mathematical formulation of this molecular model.

Mechanical Properties of Polymeric Materials

The theory of absolute reaction rates is developed for condensed phases. The equation for the rate of a reaction of any order in any phase where the slow process is the passage over an energy barrier consists of the product of a transmission coefficient κ, a frequency kT/h, an equilibrium constant between an activated complex and the reactants and an activity coefficient factor. Previous theories of reaction rates such as Bronsted's, the collision theory of Mc C. Lewis, etc., are seen to be special cases of the general theory. A variety of examples are considered.

The Absolute Rate of Reactions in Condensed Phases

The relaxation process of viscous flow may be visualized as the sudden shifting of some small patch on one side of a shear surface with respect to the neighboring material on the other side of the shear surface. Any shear surface will divide a mosaic of such patches lying on the two sides of the surface. Except for the simplest systems, this mosaic of patches will be heterogeneous and can be described by groups each characterized by its mean relaxation time βn, by xn the fractional area of the shear surface which the group occupies and by αn, a characteristic shear volume divided by kT. The resulting generalized expression for viscosity is η= ∑ n=1nxnβnαnsinh−1βnṡβnṡ, where ṡ is the rate of shear. This equation is applied to masticated natural rubber, polystyrene, X‐672 GR‐S, X‐518 GR‐S rubber, and Vistanex LM‐S polyisobutylene. All applications give good agreement with experiment. The known criticisms of Eyring's simple relaxation theory for viscous flow are reviewed, and are apparently taken care of in ...

Theory of Non‐Newtonian Flow. I. Solid Plastic System

Diffusion and Membrane Permeability.

A RECENT communication by D. D. Eley and D. C. Pepper1 describes experiments on the plastic flow of plasticized cellulose derivatives. They find that the flow velocity of compression of cylinders and extension of rods depends exponentially on stress at moderate stresses as the simple relaxation theory predicts2,3, but at higher stresses flow velocity approaches linearity with stress. This behaviour at high stress leads them to question the applicability of the relaxation theory in general to flow problems.

Henry Eyring

Papers

Mechanical Properties of Polymeric Materials

The Absolute Rate of Reactions in Condensed Phases

Theory of Non‐Newtonian Flow. I. Solid Plastic System

Diffusion and Membrane Permeability.

Mechanisms for the Relaxation Theory of Viscosity