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.

An equation for the viscosity of a liquid in terms of the energy of vaporization and the molal volume is developed from the reaction rate theory of viscosity due to Eyring. The degree of freedom corresponding to flow is assumed to be a translational one, and the energy of activation for the elementary flow process is assumed to be some fraction, 1/n, of the energy of vaporization. On applying this equation to a large number of normal liquids it is found that molecules possessing spherical symmetry have n = 3, while nonspherical molecules have n greater than 3, usually about 4. It is shown that the ratio ΔEvap/ΔEvis,  where  ΔEvis=R(d ln η)/(d(1/T)), can be taken as an index of the size and shape of the molecule, or more precisely, of the unit of flow in the liquid. The activation energy for flow in liquid metals is a very small fraction of the energy of vaporization, ranging from 1/10 to 1/25, leading to the conclusion that the metal ions flow without their valence electrons. Viscosity data confirm the S8...

Theory of the Viscosity of Liquids as a Function of Temperature and Pressure

The possible individual processes that may occur in a gaseous system under irradiation from alpha‐particles have been examined from the theoretical standpoint. The ionization, clustering and the fate of the ions have been studied. The ortho‐para hydrogen conversion under the influence of alpha‐particles has been chosen as an example with which to illustrate the method of treatment. Recent experimental data by Capron have been analyzed to confirm his conclusion that atomic hydrogen is responsible for the large ratio of molecules converted to ions produced (M/N = (700 to 1000)/1). It is also shown that clustering is unimportant in this case and that the paramagnetism of the ions is of negligible importance in producing the spin‐isomerization. The role of mercury atoms in removing atomic hydrogen from the system is found to be negligible. Removal of atoms by three body collision of two atoms with molecular hydrogen is slow compared with removal at the walls of the reaction vessel. Analysis of this latter pro...

The Theoretical Treatment of Chemical Reactions Produced by Ionization Processes Part I. The Ortho‐Para Hydrogen Conversion by Alpha‐Particles

Diffusion, Thermal Conductivity, and Viscous Flow of Liquids

Advances and Perspectives

The limitations of the simple collision theory for reactions are discussed. The Menschutkin and related reactions are shown to involve the formation of an activated complex with an electric moment of a magnitude which is calculated for the various cases. The free energy of activation for proton transfer is found from the experiments on conductance in water and the dispersion effects on polarization in ice. A partition function for liquid H2O and D2O based upon experimental quantities is given. The abnormal rapidity of the denaturation of proteins in spite of an enormous activation energy is typical of reactions, involving the simultaneous breaking of many bonds.

Henry Eyring

Papers

Theory of the Viscosity of Liquids as a Function of Temperature and Pressure

The Theoretical Treatment of Chemical Reactions Produced by Ionization Processes Part I. The Ortho‐Para Hydrogen Conversion by Alpha‐Particles

Diffusion, Thermal Conductivity, and Viscous Flow of Liquids

Advances and Perspectives

The Deduction of Reaction Mechanisms from the Theory of Absolute Rates