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Computer models of Q5, Q6, and Q7. Top row is the view into the cavity and the bottom is the side view
Computer models of Q5, Q6, and Q7. Top row is the view into the cavity and the bottom is the side view

Cucurbiturils are macrocyclic molecules consisting of glycoluril repeat units. A macrocycle is as defined by IUPAC, "a cyclic macromolecule or a macromolecular cyclic portion of a molecule These compounds are particularly interesting to chemists because they are molecular containers that are capable of binding other molecules within their cavities. The name is derived from the resemblance of this molecule with a pumpkin of the family of Cucurbitaceae. Pumpkin is a Gourd -like squash of the genus Cucurbita and the family Cucurbitaceae (which also includes gourds Cucurbitaceae is a Plant family commonly known as Melons, gourds or cucurbits and includes crops like Cucumbers The cavity of cucurbit[6]uril has nanoscale dimensions with an approximate height of 9. 1 Å, outer diameter 5. 8 Å and inner diameter 3. 9 Å. [1]

Cucurbiturils were first synthesized in 1905 by Behrend[2] but their structure was not elucidated until 1981. [3] To date cucurbiturils composed of 5, 6, 7, 8, and 10 repeat units have all been isolated,3 which have internal cavity volumes of 82, 164, 279, 479, and 870 Å3 respectively. A cucurbituril composed of 9 repeat units has yet to be isolated. Other common molecular capsules that share a similar molecular shape with cucurbiturils include cyclodextrins and calixarenes. Cyclodextrins (sometimes called cycloamyloses make up a family of cyclic Oligosaccharides, composed of 5 or more α-D-glucopyranoside units linked 1->4 as in Amylose A calixarene is a Macrocycle or cyclic Oligomer based on a Hydroxyalkylation product of a Phenol and an Aldehyde.

Contents

Synthesis

Cucurbituril Synthesis

Cucurbiturils are aminals and synthesized from urea 1 and a diketone (e. A hemiaminal is a Functional group or type of Chemical compound that has a Hydroxyl group and an Amine attached to the same Carbon Urea is an Organic compound with the Chemical formula ( N[[hydrogen H]]22 C[[oxygen O]] A diketone is a molecule containing two Ketone groups The simpliest diketone is Diacetyl, also known as 23-butanedione g. , glyoxal 2) via a nucleophilic addition to give the intermediate glycoluril 3. Glyoxal is an Organic compound with the formula OCHCHO This yellow-coloured liquid is the smallest Dialdehyde (two Aldehyde groups In Organic chemistry, a nucleophilic addition reaction is an Addition reaction where in a Chemical compound a π bond is removed by the creation This intermediate is condensed with formaldehyde to give hexamer cucurbit[6]uril above 110 °C. A condensation reaction is a Chemical reaction in which two Molecules or moieties ( Functional groups) combine to form one single molecule together with In Chemistry, an oligomer consists of a limited number of Monomer units (ολιγος or oligos is Greek for "a few" in contrast to a Ordinarily, multifunctional monomers such as 3 would undergo a step-growth polymerization that would give a distribution of products, but due to favorable strain and an abundance of hydrogen bonding, the hexamer is the only reaction product isolated after precipitation. Step-growth polymerization is a Polymerization process that involves a Chemical reaction between multifunctional Monomer molecules In Chemistry a Molecule experiences strain when in a Chemical conformation there exist unfavorable bond angles or bond distances A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen [4]

Decreasing the temperature of the reaction to between 75 and 90 °C can be used to access other sizes of cucurbiturils including CB[5], CB[7], CB[8], CB[9], and CB[10]. CB[6] is still the major product; the other ring sizes are formed in smaller yields. The isolation of sizes other than CB[6] requires fractional crystallization and dissolution. CB[5], CB[6], CB[7], and CB[8] are all currently commercially available. The larger sizes are a particularly active area of research since they can bind larger and more interesting guest molecules, thus expanding their potential applications.

Crystal structure of the CB[10]•CB[5]complex including a chlorine anion.
Crystal structure of the CB[10]•CB[5]complex including a chlorine anion. [5]

Cucurbit[10]uril is particularly difficult to isolate. It was first discovered by Day and coworkers in 2002 as a inclusion complex containing CB[5] by fractional crystallization of the cucurbituril reaction mixture. In Host-guest chemistry an inclusion compound is a complex in which one Chemical compound (the "host" forms a cavity in which molecules of a [5] The CB[10]•CB[5] was unambiguously identified by single crystal X-ray structural analysis that revealed the complex resembled a molecular gyroscope. A gyroscope is a device for measuring or maintaining orientation, based on the principles of Angular momentum. In this case the free rotation of the CB[5] within the CB[10] cavity mimics the independent rotation of a flywheel within the frame of a gyroscope.

Isolation of pure CB[10] could not be accomplished by direct separation methods since the compound has such a high affinity for CB[5]. The strong binding affinity for the CB[5] can be understood since it has a complementary size and shape to the cavity of the CB[10]. Pure CB[10] was isolated by Isaacs and coworkers in 2005 by introducing a more strongly binding melamine diamine guest that is capable of displacing the CB[5]. This article is about the chemical substance called melamine The term "melamine" may also be used to refer to the plastic Melamine resin. [6] The melamine diamine guest was then separated from the CB[10] by reaction with acetic anhydride that converted the positively charged amine groups to neutrally charged amides. Acetic anhydride is the Chemical compound with the formula (CH3CO2O Cucurbiturils strongly bind cationic guests, but by removing the positive charge from the melamine diamine guest reduces the association constant to the point it can be removed by washing with methanol, DMSO, and water. Methanol, also known as methyl alcohol, carbinol, wood alcohol, wood naphtha or wood spirits, is a Chemical compound The CB[10] with its unusually large cavity (870 Å3) free and capable of binding extraordinarily large guests including a cationic calix[4]arene. A calixarene is a Macrocycle or cyclic Oligomer based on a Hydroxyalkylation product of a Phenol and an Aldehyde.

Applications

Supramolecular host molecules

Crystal structure of a host-guest complex with a p-xylylenediammonium bound within a cucurbit[6]uril reported by Freeman in Acta. Crystallogr. B, 1984, 382-387.
Crystal structure of a host-guest complex with a p-xylylenediammonium bound within a cucurbit[6]uril reported by Freeman in Acta. In Supramolecular chemistry, host-guest chemistry describes complexes that are composed of two or more Molecules or Ions held together in unique Crystallogr. B, 1984, 382-387.

Cucurbiturils are efficient host molecules in molecular recognition and have a particularly high affinity for positively charged or cationic compounds. The term molecular recognition refers to the specific interaction between two or more Molecules through Noncovalent bonding such as including hydrogen bonding High association constants with positively charged molecules are attributed to the carbonyl groups that line each end of the cavity and can interact with cations is a similar fashion to crown ethers. The affinity of cucurbiturils can be very high. For example the affinity equilibrium constant of cururbit[7]uril with the positively charged 1-aminoadamantane hydrochloride is experimentally determined at 4. For a general Chemical reaction \alpha A +\beta B. \rightleftharpoons \sigma S+\tau T. 23*1012. [7]

Host guest interactions also significantly influence solubility behavior of cucurbiturils. Cucurbit[6]uril dissolves poorly in just about any solvent but solubility is greatly improved in a solution of potassium hydroxide or in an acidic solution. Potassium hydroxide is the Inorganic compound with the formula K[[hydroxide OH]] In Computer science, ACID ( Atomicity Consistency Isolation Durability) is a set of properties that guarantee that Database transactions are The cavitand forms a positively charged inclusion compound with a potassium ion or a hydronium ion respectively which have much greater solubility that the uncomplexed neutral molecule. A cavitand is a container shaped molecule The cavity of the cavitand allows it to engage in Host-guest chemistry with guest molecules of a complementary shape and size In Host-guest chemistry an inclusion compound is a complex in which one Chemical compound (the "host" forms a cavity in which molecules of a [8]

CB[10] is large enough to hold other molecular hosts such as a calixarene molecule. A calixarene is a Macrocycle or cyclic Oligomer based on a Hydroxyalkylation product of a Phenol and an Aldehyde. With a calixarene guest different chemical conformations (cone, 1,2-alternate, 1,3-alternate) are in rapid equilibrium. In Chemistry, conformational isomerism is a form of Stereoisomerism in which Molecules with the same Structural formula (same connectivity Allosteric control is provided when an adamantane molecule forces a cone conformation with a calixarene - adamantane inclusion complex within a CB[10] molecule. In Biochemistry, allosteric regulation is the regulation of an Enzyme or other Protein by binding an effector molecule at the protein's allosteric Adamantane (tricyclodecane is a colourless crystalline compound with a Camphor -like odour

Rotaxane macrocycles

Given their high affinities to form inclusion complexes cucurbiturils have been employed as the macrocycles component of a rotaxane. A macrocycle is as defined by IUPAC, "a cyclic macromolecule or a macromolecular cyclic portion of a molecule A rotaxane is a mechanically-interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a " Macrocycle After formation of the supramolecular assembly or threaded complex with a guest molecule such as hexamethylene diamine the two ends of the guest can be reacted with bulky groups that will then act as a stoppers preventing the two separate molecules from dissociating. A supramolecular assembly or "supermolecule" is a well defined complex of molecules held together by noncovalent bonds. Hexamethylenediamine or 16-hexanediamine is a Diamine with a hexamethylene Hydrocarbon chain and Amine Functional groups [9]

In another rotaxane system with a CB[7] wheel, the axle is a 4,4'-bipyridinium or viologen subunit with two carboxylic acid terminated aliphatic N-substituents at both ends. The Viologens are diquaternary derivatives of 44'-bipyridyl The name comes from the fact that this class of compounds is easily reduced to the radical mono Carboxylic acids are Organic acids characterized by the presence of a Carboxyl group, which has the formula -C(=OOH usually written -COOH or -CO2H [10] In water at concentration higher than 0. 5 M complexation is quantitative without need of stoppers. At pH = 2 the carboxylic end-groups are protonated and the wheel shuttles back and forth between them as evidenced by the presence of just two aromatic viologen protons in the proton NMR spectrum. pH is the measure of the acidity or alkalinity of a Solution. An end-group in Polymer chemistry is a constitutional unit that is an extremity of a Macromolecule or Oligomer molecule Proton NMR (also Hydrogen-1 NMR, or 1HNMR) is the application of Nuclear magnetic resonance in NMR spectroscopy At pH = 9 the wheel is locked around the viologen center.

Drug delivery vehicles

Cucurbituril's host-guest properties have been explored for drug delivery vehicles. The potential of this application has been explored with cucurbit[7]uril that forms an inclusion compound with the important cancer fighting drug oxaliplatin. In Host-guest chemistry an inclusion compound is a complex in which one Chemical compound (the "host" forms a cavity in which molecules of a Oxaliplatin is a Platinum -based Chemotherapy drug in the same family as Cisplatin and Carboplatin. CB[7] was employed despite the fact that it is more difficult to isolate since it has much greater solubility in water and its larger cavity size can accommodate the drug molecule. The resulting complex was found to have increased stability and greater selectivity that may lead to less side effects. [11]

Supramolecular catalysts

Cucurbiturils have also been explored as supramolecular catalysts. Larger cucurbiturils, such as cucurbit[8]uril can bind multiple guest molecules. CB[8] forms a complex 2:1 (guest:host) with (E)-diaminostilbene dihydrochloride which is accommodated by CB[8]’s larger internal diameter of 8. 8 angstrom and height 9. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal 1 angstrom. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal [12] The close proximity and optimal orientation of the guest molecules within the cavity enhances the rate of the photochemical cyclization to give cyclobutane dimer with a 19:1 stereoselectivity for the syn configuration when bound to CB[8]. Photochemistry, a sub-discipline of Chemistry, is the study of the interactions between Atoms, small Molecules, and light (or Electromagnetic radiation Cyclobutane, C4H8 with a molecular mass of 56107g/mol is a four Carbon Alkane in which all the Carbon Atoms are arranged A dimer is a Chemical or Biological entity consisting of two subunits called Monomers which are held together by either Intramolecular forces In the absence of CB[8] the cyclization reaction does not occur, but only the isomerization of the trans isomer to the cis isomer is observed. Trans-2-butenesvg|right|thumb|Trans-2-butene]] In Chemistry, cis-trans isomerism or geometric isomerism or configuration isomerism is a form of Trans-2-butenesvg|right|thumb|Trans-2-butene]] In Chemistry, cis-trans isomerism or geometric isomerism or configuration isomerism is a form of [13]

Related compounds

Inverted cucurbiturils or iCB[x] are CB analogues with one glycoluril repeating unit inverted. In Polymer chemistry, a structural unit is a building block of a Polymer chain and related to the Repeat unit. [14] In this unit the methine protons actually point into the cavity and this makes the cavity less spacious. In chemistry methine (also known as methylidyne or methyne) is a tri-valent Functional group CH derived formally from Methane. Inverted cucurbiturils form as a side-product in CB-forming reactions, with yields between 2 and 0. 4%. Isolation of this type of CB compound is possible because it is more difficult to form inclusion compounds that ordinarily form with regular CB's. Inverted cucurbiturils are believed to be the kinetically controlled reaction products because the addition of deuterated hydrochloric acid or DCl to iCB[6] results in a mixture of CB[5], CB[6] and CB[7]in a 24:13:1 ratio. Thermodynamic reaction control or kinetic reaction control in a Chemical reaction can decide the composition in a reaction product when competing reactions lead to Deuterium, also called heavy hydrogen, is a Stable isotope of Hydrogen with a Natural abundance in the Oceans of Earth Hydrochloric acid is the Solution of Hydrogen chloride ( H[[Chlorine Cl]] in water

A cucurbituril cut in half along the equator is called a hemicucurbituril. A hemicucurbituril is a Macrocycle composed of alternating units of methylene (CH2 and N-substituted Ethylene urea units

Nomenclature

Cucurbiturils are commonly written as cucurbit[#]uril, where the number of repeat units is indicated within the brackets. A common abbreviation is CB[#] where again the number of repeat units is included within the brackets.

Systematic name

Cucurbit[6]uril goes by the systematic name of Dodecahydro-1H, 4H, 14H, 17H-2, 16:3, 15-dimethano-5H, 6H, 7H, 8H, 9H, 10H, 11H, 12H, 13H, 18H, 19H,20H, 21H, 22H, 23H, 24H, 25H, 26H-2, 3, 4a, 5a, 6a, 7a, 8a, 9a, 10a, 11a, 12a, 13a, 15, 16, 17a, 18a, 19a, 20a,21a, 22a, 23a, 24a, 25a, 26a-tetracosaazabispentaleno[1’’’, 6’’’:5’’, 6’’, 7’’]cycloocty[1’’, 2’’, 3’’:3’,4’]pentaleno (1’, 6’:5, 6, 7) -cycloocta (1, 2, 3-gh:1’, 2’, 3’-g’h’) cycloocta (1, 2, 3-cd:5, 6, 7-c’d’) dipentalene-1, 4,6, 8, 10, 12, 14, 17, 19, 21, 23, 25-dodecone [15]. Cucurbituril is considerably easier to remember.

References

  1. ^ Review: The Cucurbit[n]uril Family Jason Lagona, Pritam Mukhopadhyay, Sriparna Chakrabarti, Lyle Isaacs Angewandte Chemie International Edition Volume 44, Issue 31, Pages 4844 - 4870 2005 Abstract
  2. ^ Behrend et al Liebigs Ann. Angewandte Chemie is a weekly Peer-reviewed Chemistry journal that covers all disciplines of chemistry Chem. 1905, 339, 1.
  3. ^ Cucurbituril W. A. Freeman, W. L. Mock, and N. -Y. Shih J. Am. Chem. Soc., 1981, 103, 7367. The Journal of the American Chemical Society (usually abbreviated as J First Page
  4. ^ Cucurbituril Homologues and Derivatives: New Opportunities in Supramolecular Chemistry Acc. Chem. Res. , 36 (8), 621 -630, 2003. ref
  5. ^ a b A Cucurbituril-Based Gyroscane: A New Supramolecular Form AnthonyI. Day, Rodney J. Blanch, Alan P. Arnold, Susan Lorenzo, Gareth R. Lewis, and Ian Dance Angew. Chem. Int. Ed.; 2002; 41(2) pp 275-277. Angewandte Chemie is a weekly Peer-reviewed Chemistry journal that covers all disciplines of chemistry
  6. ^ Cucurbit[10]uril Simin Liu, Peter Y. Zavalij, and Lyle Isaacs J. Am. Chem. Soc.; 2005; 127(48) pp 16798 - 16799; (Communication) DOI: 10. The Journal of the American Chemical Society (usually abbreviated as J 1021/ja056287n Abstract
  7. ^ The Cucurbit[n]uril Family: Prime Components for Self-Sorting Systems Simin Liu, Christian Ruspic, Pritam Mukhopadhyay, Sriparna Chakrabarti, Peter Y. Zavalij, and Lyle Isaacs J. Am. Chem. Soc.; 2005; 127(45) pp 15959 - 15967; (Article) DOI: 10. The Journal of the American Chemical Society (usually abbreviated as J 1021/ja055013x Abstract cross-eyed stereoview More
  8. ^ U.S. Patent 6,365,734 
  9. ^ The complex formation of a, w-dicarboxylic acids and a, w-diols with cucurbituril and a-cyclodextrin. Stereoscopy, stereoscopic imaging or 3-D (three-dimensional imaging is any technique capable of recording three-dimensional visual the first step to the formation of rotaxanes and polyrotaxenes of thepolyester type Hans-Jürgen Buschmann, Klaus Jansen, Eckhard Schollmeyer Acta Chim. Slov. 1999, 46(3), pp. 405-411 Article
  10. ^ Switching a molecular shuttle on and off: simple, pH-controlled pseudorotaxanes based on cucurbit[7]uril Vladimir Sindelar, Serena Silvi, Angel E. Kaifer Chemical Communications, 2006, 2185 - 2187 Graphical abstract
  11. ^ Novel molecular drug carrier: encapsulation of oxaliplatin in cucurbit[7]uril and its effects on stability and reactivity of the drug Young Jin Jeon, Soo-Young Kim, Young Ho Ko, Shigeru Sakamoto, Kentaro Yamaguchi and Kimoon Kim Organic & Biomolecular Chemistry, 2005, 3(11), 2122 - 2125 Abstract
  12. ^ A facile, stereoselective [2 + 2] photoreaction mediated by cucurbit[8]uril Sang Yong Jon, Young Ho Ko, Sang Hyun Park, Hee-Joon Kim and Kimoon Kim Chemical Communications, 2001, (19), 1938 - 1939 DOI Abstract
  13. ^ Template directed photodimerization of trans-1,2-bis(n-pyridyl)ethylenes and stilbazoles in water Mahesh Pattabiraman, Arunkumar Natarajan, Raja Kaliappan, Joel T. Chemical Communications, known as ChemComm, is a peer-reviewed Scientific journal. Chemical Communications, known as ChemComm, is a peer-reviewed Scientific journal. Mague and V. Ramamurthy Chemical Communications, 2005, (36), 4542 - 4544 DOI Abstract Full Article
  14. ^ The Inverted Cucurbit[n]uril Family Isaacs, L. Chemical Communications, known as ChemComm, is a peer-reviewed Scientific journal. ; Park, S. -K. ; Liu, S. ; Ko, Y. H. ; Selvapalam, N. ; Kim, Y. ; Kim, H. ; Zavalij, P. Y. ; Kim, G. -H. ; Lee, H. -S. ; Kim, K. J. Am. Chem. Soc.; (Communication); 2005; 127(51); 18000-18001. The Journal of the American Chemical Society (usually abbreviated as J DOI: 10. 1021/ja056988k Abstract
  15. ^ Mono-, Oligo- und Polyrotaxane mit Cucurbituril und gemischte Polyrotaxane mit Cucurbituril und alpha-Cyclodextrin mittels Selbstorganisation Claudia Meschke 1999 Online German language

Dictionary

cucurbituril

-noun

  1. (organic chemistry) Any of a class of macrocyclic molecules consisting of glycoluril repeat units.
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