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Flippin–Lodge Angle
The Flippin–Lodge angle is one of two angles used by organic and biological chemists studying the relationship between a molecule's chemical structure and ways that it reacts, for reactions involving "attack" of an electron-rich reacting species, the nucleophile, on an electron-poor reacting species, the electrophile. Specifically, the angles—the Bürgi–Dunitz, \alpha_, and the Flippin–Lodge, \alpha_—describe the "trajectory" or "angle of attack" of the nucleophile as it approaches the electrophile, in particular when the latter is planar in shape. This is called a nucleophilic addition reaction and it plays a central role in the biological chemistry taking place in many biosyntheses in nature, and is a central "tool" in the reaction toolkit of modern organic chemistry, e.g., to construct new molecules such as pharmaceuticals. Theory and use of these angles falls into the areas of synthetic and physical organic chemistry, which deals with chemical structure and react ...
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Carbonyl
In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a carbonyl group is often referred to as a carbonyl compound. The term carbonyl can also refer to carbon monoxide as a ligand in an inorganic or organometallic complex (a metal carbonyl, e.g. nickel carbonyl). The remainder of this article concerns itself with the organic chemistry definition of carbonyl, where carbon and oxygen share a double bond. Carbonyl compounds In organic chemistry, a carbonyl group characterizes the following types of compounds: Other organic carbonyls are urea and the carbamates, the derivatives of acyl chlorides chloroformates and phosgene, carbonate esters, thioesters, lactones, lactams, hydroxamates, and isocyanates. Examples of inorganic carbonyl compounds are carbon dioxide and carbonyl ...
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Organic Chemistry
Organic chemistry is a subdiscipline within chemistry involving the science, scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms.Clayden, J.; Greeves, N. and Warren, S. (2012) ''Organic Chemistry''. Oxford University Press. pp. 1–15. . Study of structure determines their structural formula. Study of properties includes Physical property, physical and Chemical property, chemical properties, and evaluation of Reactivity (chemistry), chemical reactivity to understand their behavior. The study of organic reactions includes the organic synthesis, chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study. The range of chemicals studied in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but also con ...
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Euclidean Geometry
Euclidean geometry is a mathematical system attributed to ancient Greek mathematician Euclid, which he described in his textbook on geometry: the ''Elements''. Euclid's approach consists in assuming a small set of intuitively appealing axioms (postulates) and deducing many other propositions ( theorems) from these. Although many of Euclid's results had been stated earlier,. Euclid was the first to organize these propositions into a logical system in which each result is '' proved'' from axioms and previously proved theorems. The ''Elements'' begins with plane geometry, still taught in secondary school (high school) as the first axiomatic system and the first examples of mathematical proofs. It goes on to the solid geometry of three dimensions. Much of the ''Elements'' states results of what are now called algebra and number theory, explained in geometrical language. For more than two thousand years, the adjective "Euclidean" was unnecessary because no other sort of geom ...
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Three Dimensional
Three-dimensional space (also: 3D space, 3-space or, rarely, tri-dimensional space) is a geometric setting in which three values (called '' parameters'') are required to determine the position of an element (i.e., point). This is the informal meaning of the term dimension. In mathematics, a tuple of numbers can be understood as the Cartesian coordinates of a location in a -dimensional Euclidean space. The set of these -tuples is commonly denoted \R^n, and can be identified to the -dimensional Euclidean space. When , this space is called three-dimensional Euclidean space (or simply Euclidean space when the context is clear). It serves as a model of the physical universe (when relativity theory is not considered), in which all known matter exists. While this space remains the most compelling and useful way to model the world as it is experienced, it is only one example of a large variety of spaces in three dimensions called 3-manifolds. In this classical example, when th ...
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Reaction Mechanism
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible, and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction. It also describes each reactive intermediate, activated complex, and transition state, and which bonds are broken (and in what order), and which bonds are formed (and in what order). A complete mechanism must also explain the reason for the reactants and catalyst used, the stereochemistry observed in reactants and products, all products formed and the amount of each. The electron or arrow pushing method is often used ...
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Physical Organic Chemistry
Physical organic chemistry, a term coined by Louis Hammett in 1940, refers to a discipline of organic chemistry that focuses on the relationship between chemical structures and reactivity, in particular, applying experimental tools of physical chemistry to the study of organic molecules. Specific focal points of study include the rates of organic reactions, the relative chemical stabilities of the starting materials, reactive intermediates, transition states, and products of chemical reactions, and non-covalent aspects of solvation and molecular interactions that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact reaction mechanism and rate for each organic reaction of interest. Application Physical organic chemists use theoretical and experimental approaches work to understand these foundational problems in organic chemistry, including classical and st ...
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Synthetic Chemistry
As a topic of chemistry, chemical synthesis (or combination) is the artificial execution of chemical reactions to obtain one or several products. This occurs by physical and chemical manipulations usually involving one or more reactions. In modern laboratory uses, the process is reproducible and reliable. A chemical synthesis involves one or more compounds (known as ''reagents'' or ''reactants'') that will experience a transformation when subjected to certain conditions. Various reaction types can be applied to formulate a desired product. This requires mixing the compounds in a reaction vessel, such as a chemical reactor or a simple round-bottom flask. Many reactions require some form of processing ("work-up") or purification procedure to isolate the final product. The amount produced by chemical synthesis is known as the ''reaction yield''. Typically, yields are expressed as a mass in grams (in a laboratory setting) or as a percentage of the total theoretical quanti ...
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Pharmaceuticals
A medication (also called medicament, medicine, pharmaceutical drug, medicinal drug or simply drug) is a drug used to diagnose, cure, treat, or prevent disease. Drug therapy (pharmacotherapy) is an important part of the medical field and relies on the science of pharmacology for continual advancement and on pharmacy for appropriate management. Drugs are classified in multiple ways. One of the key divisions is by level of control, which distinguishes prescription drugs (those that a pharmacist dispenses only on the order of a physician, physician assistant, or qualified nurse) from over-the-counter drugs (those that consumers can order for themselves). Another key distinction is between traditional small molecule drugs, usually derived from chemical synthesis, and biopharmaceuticals, which include recombinant proteins, vaccines, blood products used therapeutically (such as IVIG), gene therapy, monoclonal antibodies and cell therapy (for instance, stem cell therapies ...
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Biosynthesis
Biosynthesis is a multi-step, enzyme- catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of lipid membrane components and nucleotides. Biosynthesis is usually synonymous with anabolism. The prerequisite elements for biosynthesis include: precursor compounds, chemical energy (e.g. ATP), and catalytic enzymes which may require coenzymes (e.g. NADH, NADPH). These elements create monomers, the building blocks for macromolecules. Some important biological macromolecules include: proteins, which are composed of amino acid monomers joined via pe ...
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Nucleophilic Addition
In organic chemistry, a nucleophilic addition reaction is an addition reaction where a chemical compound with an electrophilic double or triple bond reacts with a nucleophile, such that the double or triple bond is broken. Nucleophilic additions differ from electrophilic additions in that the former reactions involve the group to which atoms are added accepting electron pairs, whereas the latter reactions involve the group donating electron pairs. Addition to carbon–heteroatom double bonds Nucleophilic addition reactions of nucleophiles with electrophilic double or triple bond (π bonds) create a new carbon center with two additional single, or σ, bonds.March Jerry; (1985). Advanced Organic Chemistry reactions, mechanisms and structure (3rd ed.). New York: John Wiley & Sons, inc. Addition of a nucleophile to carbon–heteroatom double or triple bonds such as >C=O or -C≡N show great variety. These types of bonds are polar (have a large difference in electronegativity b ...
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Trigonal Planar Molecular Geometry
In chemistry, trigonal planar is a molecular geometry model with one atom at the center and three atoms at the corners of an equilateral triangle, called peripheral atoms, all in one plane. In an ideal trigonal planar species, all three ligands are identical and all bond angles are 120°. Such species belong to the point group D3h. Molecules where the three ligands are not identical, such as H2CO, deviate from this idealized geometry. Examples of molecules with trigonal planar geometry include boron trifluoride (BF3), formaldehyde (H2CO), phosgene (COCl2), and sulfur trioxide (SO3). Some ions with trigonal planar geometry include nitrate (), carbonate (), and guanidinium (). In organic chemistry, planar, three-connected carbon centers that are trigonal planar are often described as having sp2 hybridization. Nitrogen inversion is the distortion of pyramidal amines through a transition state that is trigonal planar. Pyramidalization is a distortion of this molecular shape tow ...
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Nucleophile
In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are Lewis bases. ''Nucleophilic'' describes the affinity of a nucleophile to bond with positively charged atomic nuclei. Nucleophilicity, sometimes referred to as nucleophile strength, refers to a substance's nucleophilic character and is often used to compare the affinity of atoms. Neutral nucleophilic reactions with solvents such as alcohols and water are named solvolysis. Nucleophiles may take part in nucleophilic substitution, whereby a nucleophile becomes attracted to a full or partial positive charge, and nucleophilic addition. Nucleophilicity is closely related to basicity. History The terms ''nucleophile'' and ''electrophile'' were introduced by Christopher Kelk Ingold in 1933, replacing the terms ''anionoid'' and ''cation ...
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