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.

Examines the history of work on optical activity and a harmonic oscillator model for this phenomenon.

A model for optical rotation

The extension of the significant structure theory of viscosity to the calculation of the viscosities of some selected liquid hydrocarbons such as n‐C12, n‐C15, and n‐C18, etc., has been made. In this derivation, the explicit functional expressions of the molar solidlike volume Vs and the intermolecular potential φ(a) were introduced. The agreement between theory and experiment over a wide temperature (35–135°C) and pressure range (1–3600 bars) is quite satisfactory. The advantage of this treatment is that thermodynamic as well as transport properties are calculated from this same model of the liquid state.

Theoretical Calculation of the Pressure Dependence of Liquid Hydrocarbon Viscosities

Comparison of Various Liquid Theories with the Significant Structure Theory

Thermodynamic treatment shows that for chemical reactions whose equilibrium constants go through maxima (or minima) the relationship ln K−ln Km=p(T−θ)2+q(T−θ)3+··· holds in the neighborhood of Tm=τ. Km is the extreme value of K. The constants p and q are equal to p=(ΔCp)θ2Rθ2;  q=−{(2/3)(ΔCp)θ−(1/6)(∂ΔCp∂T)θ1Rθ3. Equation (a), aside from the cubic and higher terms, has been proposed by Harned and Embree to apply to the experimental data on acidic dissociation. It is shown that for acidic dissociation in aqueous solution the properties of water almost completely determine the values of p and q. Estimates of these constants are made. The mechanism of the dissociation process is discussed, and it is shown that the equation for the dissociation of water can be represented by (m+n+2)H2O⇌H3+O(nH2O)+OH−(mH2O), where m+n+2≅16. This is in accord with the result of Harned and Fallon for mixtures of water and dioxane log10p0/p=12.2N2, in which p is the ion product for the mixture which contains a mole fraction N2 of...

Theory of Acid Strength. Temperature Effect

Considering the carbon‐hydrogen bond as an isolated unit, and including the effect of the interelectronic repulsions, a quantum‐mechanical calculation of the polarity of this bond is made The bond dipole is found to be C+H− On the basis of these calculations, the effect of change in hybridization on the C–H dipole, and the similar effect of replacement of hydrogen in a hydrocarbon by a highly electronegative substituent, is qualitatively discussed It is predicted that, in both cases, there will be a tendency for the dipole moment to reverse itself

Henry Eyring

Papers

A model for optical rotation

Theoretical Calculation of the Pressure Dependence of Liquid Hydrocarbon Viscosities

Comparison of Various Liquid Theories with the Significant Structure Theory

Theory of Acid Strength. Temperature Effect

An Averaged Field Calculation of the Polarity of the Carbon‐Hydrogen Bond