In chemistry, mechanism is the step-by-step sequence of elementary reactions by which overall chemical change occurs. [1] A reaction mechanism, said another way, is the way in which a particular chemical reaction occurs, described in terms of the steps involved. [2] In organic chemistry, one of the first reaction mechanisms proposed was that for the benzoin condensation, as shown below, where the proton transfers occur at (i) and (ii), by Scottish chemist Arthur Lapworth in 1903. [3]


Overview
In a mechanism, each step is characterized by a number of factors, such the reaction time in a single step, a specific movement or exchange, energy, entropy, and Gibbs free energy changes, among other factors. A mechanism describes in detail exactly what takes place at each stage of a chemical transformation. It describes the transition state and which bonds are broken, and in what order, which bonds are formed and in what order, and what the relative rates of the steps are. A complete mechanism must also account for all reactants used, the function of a catalyst, stereochemistry, as well as all products formed and the amount each reactant and product.

Life thermodynamics

See main: Life thermodynamics

The first to use thermodynamics to describe life mechanistically was French biologist Stéphane Leduc who in 1911 published a 197-page treatise on the mechanism of life, wherein, in his own words, he “endeavored to give as much of the science of energetics as can be treated without the use of formula; the conception of entropy and Carnot’s law of thermodynamics” to the explanation of the mechanism of life. He states, for instance, “a living being [is] a store of potential energy, to be set free by external stimulus.” [8]

The second to describe “mechanism” in relation to interactions between living entities, on the model of chemical mechanism, was English experimental biologist James Johnstone, beginning in 1914 and culminating with his 1921 book The Mechanism of Life in Relation to Modern Physical Theory. [4] Johnstone’s work later stimulated ideas on predator-prey mechanism as described in 1922 articles “Contribution to the Energetics of Evolution” and “Natural Selection as a Physical Principle” American physical chemist and mathematician Alfred Lotka. [5]


Human chemistry

See main: Human chemistry

In 2007, American chemical engineer Libb Thims used mechanist theory and depictions of mechanisms in the discussions of human chemical reactions occurring between “human molecules” (people), A or B, such as in the processes of relationship formation, divorce, or friendship rearrangement, etc., via its use in human collision theory, human molecular orbital theory, transition state theory, etc. [6] To cite one example, the classic model of reaction mechanism between two proteins R and L:


The first step in the reaction, R + L, brings the two protein molecules into close proximity, resulting in the first ‘macrocollision’ and yielding the encounter complex: R ∙∙∙ L. In the second step, short range electrostatic effects result in a well-oriented conformation called the ‘transition state’ or R – L. At this point, orbital overlap effects are not yet significant factors. The last step of the binding process is the latter stage transition from the favorable intermediates to the bound state unit RL. This is a process of induced fit, limited by a rate constant, which requires structural rearrangements overcoming mostly enthalpic energy barriers.

Thims explained this, in the human molecular perspective, such as if R and L were two human molecules, A and B, from one point of view, as an energetic analog to American psychologist John Money’s 1980 love map theory, but translated in the form of the modern drug-receptor thermodynamic conception of “free energy maps”, which corresponds to the sensory forces that guide the orientation, alignment, and development of a person’s life in proportion to measurements of neighboring ‘locking potentials’ of human molecules in close proximity. In this sense, in human life, forces or locking potentials drive the search leading to high-affinity binding of humans to other humans. [7]

References
1. March, Jerry (1985). Advanced Organic Chemistry, Reactions, Mechanisms and Structure. John Wiley & Sons.
2. Daintith, John. (2004). Oxford Dictionary of Chemistry. Oxford University Press.
3. Author. (1904), CXXII. — “Reactions involving the addition of hydrogen cyanide to carbon compounds. Part II. Cyanohydrins regarded as complex acids Arthur Lapworth”, Journal of the Chemical Society, Transactions, 85, 1206 - 1214.
4. (a) Johnstone, James. (1921). The Mechanism of Life in Relation to Modern Physical Theory, (pgs. 192-203). New York: Longmans, Green & Co.
(b) Johnstone, James. (1914). The Philosophy of Biology, (pg. 54). Cambridge: University Press.
(c) Lillie, Ralph S. (1914). “The Philosophy of Biology: Vitalism versus Mechanism”, Science, (pgs. 840-46), October 12.
(d) Paulist Fathers. (1922). “Book Review: The Mechanism of Life in Relation to Modern Physical Theory”, (pgs. 694-95). Catholic World.
5. (a) Lotka, Alfred J. (1922a) “Contribution to the energetics of evolution” [PDF]. Proc Natl Acad Sci, 8: pp. 147–51.
(b) Lotka, Alfred J. (1922b). “Natural selection as a physical principle” [PDF]. Proc Natl Acad Sci, 8, pp 151–54.
6. (a) Thims, Libb. (2007). Human Chemistry (Volume One), (preview), (Google books). Morrisville, NC: LuLu.
(b) Thims, Libb. (2007). Human Chemistry (Volume Two), (preview), (Google books). Morrisville, NC: LuLu.
7. ibid, Thims, Human Chemistry (Volume Two), (pgs. 144-45).
8. Leduc, Stephane. (1911). The Mechanism of Life, (ch. IX: Energetics, pgs. 97-113), 1914 Eng. Trans. By W. Deane Butcher, 197-pages (Scribd) (pdf) (target) (Half.com). London: William Heinemann.