Category:Transition states: Difference between revisions
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A '''transition state''' in chemistry refers to a high-energy, short-lived configuration that occurs during a chemical reaction as reactants transform into products. At this point, the reaction's progress is maximized. In other words, the transition state is a metastable structure that corresponds to a saddle point on the high-dimensional potential surface. Identifying the transition state is essential for understanding reaction mechanisms, energy barriers, and reaction rates. There are various methods available to pinpoint transition states in VASP. | |||
== Improved dimer method == | |||
[[Category:VASP|Transition States]] | The dimer method{{Cite|henkelman:jpc:1999}} is a technique for determining activated transitions without knowledge of the final state. In VASP, the improved dimer method (IDM) by Heyden et al. is implemented. The modification reduces the number of gradient calculations per cycle, improving algorithm performance. A detailed presentation of the method can be found in their paper{{Cite|heyden:jpc:2005}}. The main tag is {{TAG|IBRION}}=44. | ||
Follow the how-to in order to learn [[Improved dimer method|how to perform an IDM calculation]]. | |||
== Nudged elastic bands == | |||
The nudged elastic band (NEB) method{{cite|mills:surf-sci:1995}}{{cite|jonsson:book:1998}} involves the creation of an initial path connecting the system's initial and final states, utilizing a set of intermediate configurations ({{TAG|IMAGES}}). Hence, as a prerequisite, the initial and final state (e.g., reactant and product) must be known. The ''images'' are interconnected by springs, forming a flexible ''band''. Through iterative adjustments (''nudging''), the positions of the images along the band are modified, minimizing energy until a minimum energy pathway, referred to as the ''nudged elastic band'', is attained. | |||
Learn [[Nudged elastic bands|how to perform an NEB calculation]]. | |||
== Intrinsic reaction coordinate == | |||
Following the intrinsic reaction coordinate (IRC) implies following the steepest descent path from the transition state to reactants and products. The IRC method employs a classical trajectory integration method with fixed velocity, i.e., the damped-velocity Verlet algorithm, incorporating an adaptive time step such that the dynamic reaction pathway resembles the IRC. Hence, as a prerequisite, the transition state must be known. | |||
Learn [[IRC calculations|how to perform an IRC calculation]]. | |||
== References == | |||
[[Category:VASP|Transition States]][[Category:Ionic minimization]] | |||
Revision as of 14:29, 12 November 2023
A transition state in chemistry refers to a high-energy, short-lived configuration that occurs during a chemical reaction as reactants transform into products. At this point, the reaction's progress is maximized. In other words, the transition state is a metastable structure that corresponds to a saddle point on the high-dimensional potential surface. Identifying the transition state is essential for understanding reaction mechanisms, energy barriers, and reaction rates. There are various methods available to pinpoint transition states in VASP.
Improved dimer method
The dimer method[1] is a technique for determining activated transitions without knowledge of the final state. In VASP, the improved dimer method (IDM) by Heyden et al. is implemented. The modification reduces the number of gradient calculations per cycle, improving algorithm performance. A detailed presentation of the method can be found in their paper[2]. The main tag is IBRION=44.
Follow the how-to in order to learn how to perform an IDM calculation.
Nudged elastic bands
The nudged elastic band (NEB) method[3][4] involves the creation of an initial path connecting the system's initial and final states, utilizing a set of intermediate configurations (IMAGES). Hence, as a prerequisite, the initial and final state (e.g., reactant and product) must be known. The images are interconnected by springs, forming a flexible band. Through iterative adjustments (nudging), the positions of the images along the band are modified, minimizing energy until a minimum energy pathway, referred to as the nudged elastic band, is attained.
Learn how to perform an NEB calculation.
Intrinsic reaction coordinate
Following the intrinsic reaction coordinate (IRC) implies following the steepest descent path from the transition state to reactants and products. The IRC method employs a classical trajectory integration method with fixed velocity, i.e., the damped-velocity Verlet algorithm, incorporating an adaptive time step such that the dynamic reaction pathway resembles the IRC. Hence, as a prerequisite, the transition state must be known.
Learn how to perform an IRC calculation.
References
- ↑ G. Henkelman and H. Jónsson, A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives, J. Chem. Phys. 111, 7010–7022 (1999).
- ↑ A. Heyden, A. T. Bell, and F. J. Keil, Efficient methods for finding transition states in chemical reactions: Comparison of improved dimer method and partitioned rational function optimization method, J. Chem. Phys. 123, 224101 (2005).
- ↑ G. Mills, H. Jonsson and G. K. Schenter, Reversible work transition state theory: application to dissociative adsorption of hydrogen, Surf. Sci., 324, 305 (1995).
- ↑ H. Jonsson, G. Mills and K. W. Jacobsen, Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions, in Classical and Quantum Dynamics in Condensed Phase Simulations, ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998).
Pages in category "Transition states"
The following 17 pages are in this category, out of 17 total.