Conformational isomerism in the context of Ring strain

In the field of molecular biology, nuclear receptors are a class of proteins responsible for sensing steroids, thyroid hormones, vitamins, and certain other molecules. These intracellular receptors work with other proteins to regulate the expression of specific genes, thereby controlling the development, homeostasis, and metabolism of the organism.

Nuclear receptors bind directly to DNA regulating the expression of adjacent genes; hence these receptors are classified as transcription factors. The regulation of gene expression by nuclear receptors often occurs in the presence of a ligand—a molecule that affects the receptor's behavior. Ligand binding to a nuclear receptor results in a conformational change activating the receptor. The result is up- or down-regulation of gene expression.

In chemistry, an enantiomer (/ɪˈnænti.əmər, ɛ-, -oʊ-/ ih-NAN-tee-ə-mər), also known as an optical isomer, antipode, or optical antipode, is one of a pair of molecular entities which are mirror images of each other and non-superposable.

Enantiomer molecules are like right and left hands: one cannot be superposed onto the other without first being converted to its mirror image. It is solely a relationship of chirality and the permanent three-dimensional relationships among molecules or other chemical structures: no amount of re-orientation of a molecule as a whole or conformational change converts one chemical into its enantiomer. Chemical structures with chirality rotate plane-polarized light. A mixture of equal amounts of each enantiomer, a racemic mixture or a racemate, does not rotate light.

In chemistry and physics, a molecular entity, or chemical entity, is "any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity". A molecular entity is any singular entity, irrespective of its nature, used to concisely express any type of chemical particle that can exemplify some process: for example, atoms, molecules, ions, etc. can all undergo a chemical reaction.

Chemical species is the macroscopic equivalent of molecular entity and refers to sets or ensembles of molecular entities.

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ligare, which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure.

Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association or docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition of ligand in metalorganic and inorganic chemistry, in biochemistry it is ambiguous whether the ligand generally binds at a metal site, as is the case in hemoglobin. In general, the interpretation of ligand is contextual with regard to what sort of binding has been observed.

In chemistry, a space-filling model, also known as a calotte model, is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei, all in the same scale. Atoms of different chemical elements are usually represented by spheres of different colors.

Space-filling calotte models are also referred to as CPK models after the chemists Robert Corey, Linus Pauling, and Walter Koltun, who over a span of time developed the modeling concept into a useful form. They are distinguished from other 3D representations, such as the ball-and-stick and skeletal models, by the use of the "full size" space-filling spheres for the atoms. The models are tactile and manually rotatable. They are useful for visualizing the effective shape and relative dimensions of a molecule, and (because of the rotatability) the shapes of the surface of the various conformers. On the other hand, these models mask the chemical bonds between the atoms, and make it difficult to see the structure of the molecule that is obscured by the atoms nearest to the viewer in a particular pose. For this reason, such models are of greater utility if they can be used dynamically, especially when used with complex molecules (e.g., see the greater understanding of the molecules shape given when the THC model is clicked on to rotate).

Cis–trans isomerism, also known as geometric isomerism, describes certain arrangements of atoms within molecules. The prefixes "cis" and "trans" are from Latin: "this side of" and "the other side of", respectively. In the context of chemistry, cis indicates that the functional groups (substituents) are on the same side of some plane, while trans conveys that they are on opposing (transverse) sides. Cis–trans isomers are stereoisomers, that is, pairs of molecules which have the same formula but whose functional groups are in different orientations in three-dimensional space. Cis and trans isomers occur both in organic molecules and in inorganic coordination complexes. Cis and trans descriptors are not used for cases of conformational isomerism where the two geometric forms easily interconvert, such as most open-chain single-bonded structures; instead, the terms "syn" and "anti" are used.

According to IUPAC, "geometric isomerism" is an obsolete synonym of "cis–trans isomerism".

In organometallic chemistry, a sandwich compound is a chemical compound featuring a metal bound by haptic, covalent bonds to two arene (ring) ligands. The arenes have the formula C_nH_n, substituted derivatives (for example C_n(CH₃)_n) and heterocyclic derivatives (for example BC_nH_n+1). Because the metal is usually situated between the two rings, it is said to be "sandwiched". A special class of sandwich complexes are the metallocenes.

The term sandwich compound was introduced in organometallic nomenclature in 1956 in a report by J. D. Dunitz, L. E. Orgel and R. A. Rich, who confirmed the structure of ferrocene by X-ray crystallography. The correct structure, in which the molecule features an iron atom sandwiched between two parallel cyclopentadienyl rings, had been proposed several years previously by Robert Burns Woodward and, separately, by Ernst Otto Fischer. The structure helped explain puzzles about ferrocene's conformers. This result further demonstrated the power of X-ray crystallography and accelerated the growth of organometallic chemistry.

The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.

In molecular biology, proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of angstroms to nm) and time scales (ns to s),and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.

The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves.These two perspectives—kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm:highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively.

In chemistry, a molecule or ion is called chiral (/ˈkaɪrəl/) if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality (/kaɪˈrælɪti/). The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property.

A chiral molecule or ion exists in two stereoisomers that are mirror images of each other, called enantiomers; they are often distinguished as either "right-handed" or "left-handed" by their absolute configuration or some other criterion. The two enantiomers have the same chemical properties, except when reacting with other chiral compounds. They also have the same physical properties, except that they often have opposite optical activities. A homogeneous mixture of the two enantiomers in equal parts, a racemic mixture, differs chemically and physically from the pure enantiomers.

A cyclic compound (or ring compound) is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon (i.e., are carbocycles), none of the atoms are carbon (inorganic cyclic compounds), or where both carbon and non-carbon atoms are present (heterocyclic compounds with rings containing both carbon and non-carbon). Depending on the ring size, the bond order of the individual links between ring atoms, and their arrangements within the rings, carbocyclic and heterocyclic compounds may be aromatic or non-aromatic; in the latter case, they may vary from being fully saturated to having varying numbers of multiple bonds between the ring atoms. Because of the tremendous diversity allowed, in combination, by the valences of common atoms and their ability to form rings, the number of possible cyclic structures, even of small size (e.g., < 17 total atoms) numbers in the many billions.

• Cyclic compound examples: All-carbon (carbocyclic) and more complex natural cyclic compounds
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  Cycloalkanes, the simplest carbocycles, including cyclopropane, cyclobutane, cyclopentane, and cyclohexane. Note, elsewhere an organic chemistry shorthand is used where hydrogen atoms are inferred as present to fill the carbon's valence of 4 (rather than their being shown explicitly).
• 
  Ingenol, a complex, terpenoid natural product, related to but simpler than the paclitaxel that follows, which displays a complex ring structure including 3-, 5-, and 7-membered non-aromatic, carbocyclic rings.
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  Paclitaxel, another complex, plant-derived terpenoid, also a natural product, displaying a complex multi-ring structure including 4-, 6-, and 8-membered rings (carbocyclic and heterocyclic, aromatic and non-aromatic).

Adding to their complexity and number, closing of atoms into rings may lock particular atoms with distinct substitution (by functional groups) such that stereochemistry and chirality of the compound results, including some manifestations that are unique to rings (e.g., configurational isomers). As well, depending on ring size, the three-dimensional shapes of particular cyclic structures – typically rings of five atoms and larger – can vary and interconvert such that conformational isomerism is displayed. Indeed, the development of this important chemical concept arose historically in reference to cyclic compounds. Finally, cyclic compounds, because of the unique shapes, reactivities, properties, and bioactivities that they engender, are the majority of all molecules involved in the biochemistry, structure, and function of living organisms, and in man-made molecules such as drugs, pesticides, etc.

In chemistry, folding is the process by which a molecule assumes its shape or conformation. The process can also be described as intramolecular self-assembly, a type of molecular self-assembly, where the molecule is directed to form a specific shape through noncovalent interactions, such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions, and electrostatic effects.

The most active area of interest in the folding of molecules is the process of protein folding, which analyses the specific sequences of amino acids in a protein. The shape of the folded protein can be used to understand its function and design drugs to influence the processes that it is involved in.

In biochemistry and nutrition, a polyunsaturated fat is a fat that contains a polyunsaturated fatty acid (abbreviated PUFA), which is a subclass of fatty acid characterized by a backbone with two or more carbon–carbon double bonds.Some polyunsaturated fatty acids are essentials. Polyunsaturated fatty acids are precursors to and are derived from polyunsaturated fats, which include drying oils.

Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is generally a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape (conformation) and reactivity of ions and molecules. Steric effects complement electronic effects, which dictate the shape and reactivity of molecules. Steric repulsive forces between overlapping electron clouds result in structured groupings of molecules stabilized by the way that opposites attract and like charges repel.