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.

The significant‐structure theory of liquids is applied to describe a two‐dimensional liquid of hard disks. The results are in quite good agreement with the molecular‐dynamics calculations. However, the virial expansion of the equation of state is in only fair agreement with the machine calculations. Cell theory is also applied to the two‐dimensional liquid; it is found that although the agreement with the molecular‐dynamics data is poor in the liquid range, the cell theory shows good agreement in the solid region.

Significant‐Structure Theory and Cell Theory for Two‐Dimensional Liquids of Hard Disks

The nature of the luciferin-luciferase system

The magnetic circular dichroism of benzene and indole derivatives was measured down to 190 nM. The following pairs of molecules have magnetic circular dichroisms of the opposite sign in the B2u absorption region: aniline and benzonitrile, indene and indoline, indole and 4-aminoindole, and 4-aminoindole and 5-aminoindole. The sign and magnitude of the magnetic circular dichroisms observed are in good agreement with those calculated by the semiempirical self-consistent field with configuration interaction Pariser-Parr-Pople method with incorporation of variable π-electronegativity and σ-polarization. The energy dominator in the magnetic rotational strength expression serves to limit the important contributions to a few terms only.

Molecular Orbital Calculations of Magnetic Circular Dichroism Spectra: A Benzene-Indole Sequence

It is pointed out that chemiluminescent reactions are necessarily nonadiabatic, since emission of radiation can only occur by transition from an upper to a lower potential energy surface. The restriction imposed by the second law of thermodynamics on the photon yield is, [open phi]⩽ΔF/E, where [open phi] is the ratio of quanta evolved to molecules reacted, ΔF is the free energy decrease in the reaction, and E is the energy of the photon emitted. Upper potential energy surfaces are reached either by activation by radiation, which may be that of a black body at the temperature of the reaction, or by the ``crossing'' of potential energy surfaces. From Audubert's data on the radiation produced by the thermal decomposition of sodium azide approximate surfaces which account for the observations are constructed.

Nonadiabatic Reactions, Chemiluminescence

Significant liquid-structure theory has been used to calculate the transport properties of the alkali metals. Unlike previous calculations, the volume and temperature dependence of the solid-like structure has been taken into consideration. Equations for the potential energy as a function of volume of the alkali metals, which lead to agreement between calculated and experimental values of thermodynamic and transport properties, are given. The calculated results are in satisfactory agreement with the experimental data.

https://www.pnas.org/content/pnas/69/6/1342.full.pdf

Henry Eyring

Papers

Significant‐Structure Theory and Cell Theory for Two‐Dimensional Liquids of Hard Disks

The nature of the luciferin-luciferase system

Molecular Orbital Calculations of Magnetic Circular Dichroism Spectra: A Benzene-Indole Sequence

Nonadiabatic Reactions, Chemiluminescence

Significant liquid-structure theory of viscosity and self-diffusion of the alkali metals.