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

/pdf/aging-a-theory-based-on-free-radical-and-radiation-chemistry-2cbm9l3kiz.pdf

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.

Symmetry is used to reduce exactly the secular equation for nine monovalent atoms forming a body‐centered cube from an equation of forty‐second degree to equations of third degree and lower. Application of the results is then made to calculate approximately the energy of the isolated unit cell for sodium. The vector method recently put forward by Van Vleck is shown to be a valuable check on such calculations.

Molecular Symmetry and the Reduction of the Secular Equation. Part II

Electrode depolarization kinetics on open circuit1

The statistical effect of internal irradiation on the survival of beagles is similar to that of aging, with the exception that death occurs earlier. Since biological processes are close to equilibrium most of the time, the above observation suggests that death ensues when the rate of insult has exceeded the rate of recovery to a sufficient extent that the reserves are depleted and the steady state can no longer be maintained. The steady-state theory of mutation rates is derived from first principles, and, through absolute rate theory, is completely general and is not limited to a specific kind of cellular alteration. However, the nature of the cellular alterations that lead to nonsurvival are considered. The young growing system is also considered in the context of this theory.

The Dynamics of Life, II. The Steady-State Theory of Mutation Rates

Resolution of Crossed Bond Eigenfunctions in Terms of the Uncrossed Set

A model designated “The elastomeric rack” is discussed with reference to the mechanism of enzyme catalysis and the necessity of large protein molecules in the process. This model, which represents an extension of the earlier “Rack mechanism,” stems from experimental evidence demonstrating large volume changes of activation or of reaction accompanying various biochemical reactions and more complicated physiological processes. For reasons discussed, the volume changes, as revealed through the influence of increased hydrostatic pressure on reaction rates and equilibria, prove that there are large conformational changes in the protein which, because of numerous cross links in a complex network, lead to additive stress on the substrate-enzyme complex, and thereby to increased reactivity. The manner in which the model serves to account for the influence of changes in the environment (temperature, pressure, chemical composition, electrical fields) on the activity of the protein catalyst, and the modifying action of particular inhibitory or activating substances, alone or in combination, is briefly discussed. The bearing of various considerations on protein denaturation, excitation of nerve, contraction of muscle, specific precipitation, and the divers physiological processes in living cells, including mutation, cancer, and the degenerative diseases of aging, is also briefly discussed.

Henry Eyring

Papers

Molecular Symmetry and the Reduction of the Secular Equation. Part II

Electrode depolarization kinetics on open circuit1

The Dynamics of Life, II. The Steady-State Theory of Mutation Rates

Resolution of Crossed Bond Eigenfunctions in Terms of the Uncrossed Set

The elastomeric rack in biology.