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  2. Reaction coordinate - Wikipedia

    en.wikipedia.org/wiki/Reaction_coordinate

    In chemistry, a reaction coordinate [1] is an abstract one-dimensional coordinate chosen to represent progress along a reaction pathway. Where possible it is usually a geometric parameter that changes during the conversion of one or more molecular entities, such as bond length or bond angle. For example, in the homolytic dissociation of ...

  3. Energy profile (chemistry) - Wikipedia

    en.wikipedia.org/wiki/Energy_profile_(chemistry)

    Figure 6:Reaction Coordinate Diagrams showing reactions with 0, 1 and 2 intermediates: The double-headed arrow shows the first, second and third step in each reaction coordinate diagram. In all three of these reactions the first step is the slow step because the activation energy from the reactants to the transition state is the highest.

  4. Transition state theory - Wikipedia

    en.wikipedia.org/wiki/Transition_state_theory

    At 298 K, a reaction with ΔG ‡ = 23 kcal/mol has a rate constant of k ≈ 8.4 × 10 −5 s −1 and a half life of t 1/2 ≈ 2.3 hours, figures that are often rounded to k ~ 10 −4 s −1 and t 1/2 ~ 2 h. Thus, a free energy of activation of this magnitude corresponds to a typical reaction that proceeds to completion overnight at room ...

  5. Root mean square deviation of atomic positions - Wikipedia

    en.wikipedia.org/wiki/Root_mean_square_deviation...

    where δ i is the distance between atom i and either a reference structure or the mean position of the N equivalent atoms. This is often calculated for the backbone heavy atoms C, N, O, and C α or sometimes just the C α atoms.

  6. Potential energy surface - Wikipedia

    en.wikipedia.org/wiki/Potential_energy_surface

    The transition state is a maximum in the reaction coordinate and a minimum in the coordinate perpendicular to the reaction path. The advance of time describes a trajectory in every reaction. Depending on the conditions of the reaction the process will show different ways to get to the product formation plotted between the 2 axes.

  7. Jacobi coordinates - Wikipedia

    en.wikipedia.org/wiki/Jacobi_coordinates

    In the theory of many-particle systems, Jacobi coordinates often are used to simplify the mathematical formulation. These coordinates are particularly common in treating polyatomic molecules and chemical reactions, [3] and in celestial mechanics. [4] An algorithm for generating the Jacobi coordinates for N bodies may be based upon binary trees. [5]

  8. More O'Ferrall–Jencks plot - Wikipedia

    en.wikipedia.org/wiki/More_O'Ferrall–Jencks_plot

    In this type of plot (Figure 1), each axis represents a unique reaction coordinate, the corners represent local minima along the potential surface such as reactants, products or intermediates and the energy axis projects vertically out of the page. Changing a single reaction parameter can change the height of one or more of the corners of the plot.

  9. Reaction–diffusion system - Wikipedia

    en.wikipedia.org/wiki/Reaction–diffusion_system

    Reaction–diffusion systems are naturally applied in chemistry. However, the system can also describe dynamical processes of non-chemical nature. Examples are found in biology, geology and physics (neutron diffusion theory) and ecology. Mathematically, reaction–diffusion systems take the form of semi-linear parabolic partial differential ...