Chemical Structure & Reactivity Concepts

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Abstractions about molecular structure and reactivity, including bonding and hybridization, catalytic cycles, protein secondary-structure rules, and empirical relationships like Clar's rule, spanning organic, inorganic and biochemical phenomena.

22 abstractions in this family — domain-specific abstractions that sit near one another in structural-signature space (k-means over structural-signature embeddings). Each is shown with its short description.

• Arrow Pushing — Use curved arrows to specify a local formal reassignment of electrons in a chemical structural drawing.
• Brønsted–Lowry Acid–Base Theory — A proton-transfer framework that assigns acid and base roles to interacting species and relates each to its conjugate partner.
• Catalytic cycle — In chemistry, a catalytic cycle is a multistep reaction mechanism that involves a catalyst.
• Clar's rule — In organic and physical organic chemistry, Clar's rule is an empirical rule that relates the chemical stability of a molecule to its aromaticity.
• Conjugated System — A bonded molecular segment whose adjacent compatible orbitals interact across intervening sigma bonds to form a coupled electronic path.
• Corey–Pauling rules — In biochemistry, the Corey–Pauling rules are a set of three basic statements that govern the secondary nature of proteins, in particular, the CO-NH peptide link.
• Determination of equilibrium constants — Equilibrium constants are determined in order to quantify chemical equilibria.
• Half-Reaction — A balanced, electron-explicit chemical equation representing one oxidation or reduction component of a redox process.
• Harpoon Reaction — A neutral-reactant reaction mechanism in which long-range electron transfer creates an ion pair whose attraction draws the partners closer before subsequent chemistry.
• Isovalent Hybridization — In chemistry, isovalent or second order hybridization is an extension of orbital hybridization, the mixing of atomic orbitals into hybrid orbitals which can form chemical bonds, to include fractional numbers of atomic orbitals of each type (s, p, d).
• LCP theory — The consistency of the interligand distances (F-F and O-F) in the above molecules is striking and this phenomenon is repeated across a wide range of molecules and forms the basis for LCP theory.
• Light-oxygen-voltage-sensing domain — A Light-oxygen-voltage-sensing domain (LOV domain) is a protein sensor used by a large variety of higher plants, microalgae, fungi and bacteria to sense environmental conditions.
• Linear molecular geometry — Linear organic molecules, such as acetylene (), are often described by invoking sp orbital hybridization for their carbon centers.
• Molecule mining — Molecule mining is the process of data mining, or extracting and discovering patterns, as applied to molecules.
• Multiple Bond — In chemistry, bond order is a formal measure of the multiplicity of a covalent bond between two atoms.
• Nucleic-Acid Secondary Structure — Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers.
• Radical Disproportionation — The most thoroughly studied radical disproportionation reactions have been conducted with alkyl radicals, but there are many organic molecules that can exhibit more complex, multi-step disproportionation reactions.
• Tetranucleotide hypothesis — In that form there is an implication that the four bases are present in equal amounts in DNA, and small variations in the experimental values were assumed to be the result of experimental error.
• Transition-State Analog — Transition state analogs (transition state analogues), are chemical compounds with a chemical structure that resembles the transition state of a substrate molecule in an enzyme-catalyzed chemical reaction.
• Umpolung — In organic chemistry, umpolung () or polarity inversion is the chemical modification of a functional group with the aim of the reversal of polarity of that group.
• Universality–diversity paradigm — The universality–diversity paradigm (UDP) is the analysis of biological materials based on the universality and diversity of its fundamental structural elements and functional mechanisms.
• Valence Bond Theory — In chemistry, valence bond (VB) theory is one of the two basic theories, along with molecular orbital (MO) theory, that were developed to use the methods of quantum mechanics to describe chemical bonding.