Lesson 1 Química Supramolecular Introducction

Lesson 1_Química Supramolecular.pptx

1. DECANATO DE POSGRADO DECANATO DE POSGRADO Maestría en: Ciencias Químicas Asignatura: Química Inorgánica Avanzada ESCUELA SUPERIOR POLITÉCNICA DE CHIMBORAZO ESCUELA SUPERIOR POLITÉCNICA DE CHIMBORAZO

2. History of Supramolecular Chemistry Prof. Ximena Jaramillo Fierro

3. Chronological representation of the main concepts of chemistry supramolecular

4. Chronological representation of the main concepts of chemistry supramolecular

5. Chronological representation of the main concepts of chemistry supramolecular

6. Supramolecular Chemistry Overview Supramolecular chemistry can be divided into three overlapping areas:

7. Supramolecular Chemistry Overview Molecular Recognition, Catalysis, and Transport: Focuses on designing supramolecular entities with photoactive and electroactive units. These entities store, process, and transfer matter, signals, and information. Applied as drugs and sensors.

8. Supramolecular Chemistry Overview Self-Organizing Systems: Explores systems that spontaneously generate well-defined functional supramolecular architectures through self-assembly. This phase bridges supramolecular chemistry with nanoscience and nanotechnology. Produces nanoscale, molecularly functional architectures, offering alternatives to nanofabrication and nanomanipulation.

9. Supramolecular Chemistry Overview Dynamic Combinatorial Chemistry: Introduces reversible bonds in molecular entities, allowing continuous structural changes through exchange and reorganization of constituents. Positions supramolecular chemistry as an emerging, adaptive, and evolving field.

10. https://www.youtube.com/watch?v=ssr9OOtzgyg

11. Nanofabrication Preparation of nanomaterials is commonly referred as Nanofabrication . Two approaches used for fabricating to nano scale particles are Top-down nanofabrication and Bottom-up nanofabrication . Top-down method involves carving bulk to desired size. Techniques used to perform this method are Precision Engineering and Lithography . The bottom-up method involves building up of materials atom by atom or molecule by molecule. Positional assembly and Self-assembly , are the techniques.

12. Supramolecular Chemistry

13. Supramolecular Interactions Prof. Ximena Jaramillo Fierro

14. According to Dr. Lehn, who invented the term, a supermolecule formed by the association of two or more chemical species linked by intermolecular forces , and not by chemical bonds . Molecular interactions

15. Dipole Interaction The partial positive and negative ends of the molecules hold the molecules together.

16. Hydrogen Bonding H O H O H H O H H

17. Some simple models for assembled by π-π interaction: Cation–π interaction (Benzene and a Na cation). Polar π interaction (Water molecule and benzene) π - π interaction ( e - rich benzene and e - poor hexafluorobenzene )

18. London Dispersion Forces (LDF) Instantaneous dipole–induced dipole forces These forces are induced dipoles caused by temporary rearrangement of the electron cloud.

19. Metal- Ligand bonds

20. Solvated host Solvated guest Complex

21. Self Assembly Prof. Ximena Jaramillo Fierro

22. Molecular Self Assembly – Building Supermolecules Supramolecular assemblies- The supermolecules result from self-assembling (or self-organizing) processes. Molecular Self Assembly – Building Supermolecules fuzzy molecular interaction. programmed assembly (precisely defined recognition) Molecular Self Assembly

23. Supramolecular Assembly via Fuzzy Interactions Supramolecular assemblies based on less precise recognition processes sometimes produce more flexible, sensitive and adaptable functionality. Cell membranes , are best example of a natural supramolecular assembly based on fuzzy molecular interactions. fuzzy (unclear or un-precise) Other examples are micelles, liposomes, vesicles, cast films etc ….

24. Programmed Supramolecular Assembly “Precisely programmed” structural information in the unit structure. For example, the three-dimensional structures of proteins are defined by their amino acid sequences; or, the structure of a protein is programmed in its amino acid sequence.

25. For example, exact DNA replication relies upon complementary hydrogen bonding between nucleobases. In programmed systems, the structural information in the units must be transferred precisely to the assembly. Lessons from nature DNA bound by base pairs

26. Lessons from nature DNA bound by base pairs

27. The formation of shape-defined supermolecules requires direction-specific molecular interactions . E.g. Hydrogen-bonds H-bond is an important interaction for precise recognition because it requires a specific geometry for the pair of interacting components. Lessons from nature DNA bound by base pairs

28. P. J. Stang, Chem. Eur. J. , 1998, 4, 19-27

29. Molecular recognition Prof. Ximena Jaramillo Fierro

30. What supramolecules look like?

31. Supramolecular Chemistry Chemistry of molecular recognition Chemistry associated with a molecule recognizing a partner molecule Chemistry of molecules assembly to specific shapes Chemistry of molecular associations from numerous molecules “lock and key” host–guest chemistry Molecular recognition chemistry ( host–guest chemistry ) + chemistry of molecular assemblies + chemistry of molecular associations  “ Supramolecular Chemistry ” [Amphiphilic molecules – micelles, lipids...] [Rotaxane, catenane , Dendrimers, Fullerene, CNTs...] [Crown ether, Polyamines, Cyclodextrin, calixarne ...]

32. Host - Guest chemistry is an example of supramolecular chemistry. Molecular assembly!? Human made DNA  Host-guest chemistry

33. Host-guest chemistry

34. Host-guest chemistry “lock and key”

35. “lock and key” Host-guest chemistry

36. Endoreceptors and Exoreceptors According to Lehn’s definition, host molecules that have binding sites inside their molecular structures (cavities) are called endoreceptors . For example, enzymes are generally endoreceptors , because they recognize the guest substrate in a reaction pocket located inside the enzyme. Host molecules with guest binding sites on their surfaces are defined as exoreceptors . For example, antibodies are classified as the exoreceptors because they recognize antigen on the terminal surface.

37. "enthalpy-entropy compensation"

38. Supramolecular Ligands Receptors of cations, anions and neutral molecules Prof. Ximena Jaramillo Fierro

39. Natural Host Molecules

40. Artificial Host Molecules

41. Crown ethers were the first artificial host molecules discovered. They were accidentally found as a byproduct of an organic reaction. When Pedersen synthesized bisphenol, contaminations from impurities led to the production of a small amount (0.4%) of a cyclic hexaether .

42. Pedersen called the cyclic compound a crown ether , because the cyclic host “wears” the ion guest like a crown . The oxygen atom, which has a high electronegativity, can act as a binding site for metal ions and ammonium ions through dipole–ion interactions .

43. Crown ethers are classified by structural types: Noncyclic hosts are known as podands . Monocyclic hosts including crown ethers are called coronands . Oligocyclic hosts are termed cryptands , which have a motion-restricted cyclic structure; they can accommodate only strictly size-matched guest molecules.

44. K⁺

45. Chlorophyll a Heme

46. Replacing the oxygen atoms in the crown ethers by nitrogen atoms - macrocyclic polyamines . Strong basic nature of the amine group results in unique host properties. Thioether-type crown compounds (crown ethers with sulfur atoms instead of oxygen atoms) are called as thiacrowns .

47. Calixarenes are macrocyclic host molecules made from phenol units linked through methylene bridges. Name “calixarene” reflects the structures of these molecules, since a calix is a chalice (trophy). Calix[n]arene Calix[4]arene

48. Calix[4]arene Calix[8]arene Calix[6]arene

49. Different views of calix[4]arene ~ 3-7 Å width

50. The isomers vary in terms of the orientations of their phenol groups: has a cone structure with all of the phenols pointing to the same direction; (b) has a partial cone structure with one phenol pointing in a different direction to the others; (c) has a 1,3-alternate structure with neighboring phenols pointing in opposite directions. Confirmation isomers of Calix[4]arene

51. The calix[8]arene depicted in Fig. can bind fullerenes Binding of fullerene by Calix[8]arene The calix[8]arene has a cavity with an inner diameter of ∼1nm, which is therefore suitable for C 60 , since it has a diameter of ∼0.7nm. So in the figure 10 we can see the fullerene “soccer ball” is trapped in the calix.

52. Cyclodextrins can be obtained from starch (polysaccharide with an α 1–4 linkage of glucose) via certain enzymes. The enzyme changes this polysaccharide into a cyclic oligomer with an appropriate number of glycopyranoside units. 6,7,8 glycopyranside units (are called α -, β - and γ -cyclodextrin, respectively)

53. Structural design : Primary hydroxyl groups are located at the side of a narrow inlet, while secondary hydroxyl groups are found on the reverse side (at the side of a wide inlet). Therefore, no hydroxyl groups exist on the wall, and so the cavity of the cyclodextrin is hydrophobic . Cyclodextrins dissolved in an aqueous phase can accommodate hydrophobic guests such as aromatic hydrocarbons (benzene), inorganic ions & gas molecules in their cavities.

54. Structure of a cyclodextrin and some pore diameters

55. Dimer naphthalene formation results in stronger emission Inclusion of a guest inside the cavity of a cyclodextrin induces light emission

56. Hydrolysis of phenyl acetate by cyclodextrin to phenol & acetate Artificial enzyme, where a cyclodextrin cavity works as a hydrophobic binding site and hydroxyl groups play the role of a catalytic residue.

57. Cyclophanos Cyclophanes are cyclic hosts made from aromatic rings that recognize hydrophobic guest molecules. Three dimensional cavities can be constructed by attaching tails, walls and caps to the cyclic hosts.

58. Fullerenes One example is the Buckminsterfullerene (Buckyball) It has a formula C 60 It is a black solid Dissolves in petrol to make a red solution Free moving electrons so conducts electricity They are spheres of only carbon atoms and are also allotropes of carbon

59. Buckminsterfullerene C 60 , also known as the buckyball, is the smallest member of the fullerene family. Metal-doped fullerene can therefore be regarded as a “superatom”. Doped fullerenes are also known to exhibit superconductivity. C 60 Metal-doped fullerene

60. Iijima, 1991 Carbon Nanotubes

61. Nano tubes are tiny tubes of carbon about 10,000 times thinner than human hair. These consist of rolled up sheets of multi layer carbon atoms in hexagon shape. They conduct electricity better than copper and are stronger than steel wire. Carbon nanotubes can store huge volumes of gas Carbon nanotubes can also be used as tips in probe microscopy.

62. Single wall Nanotubes Multi wall Nanotubes

63. Dendrimers – Molecular Trees Dendrimers have systematic branching structures and they are built in a stepwise manner. The word “dendrimer” contains “dendr-”, which means tree. So it can be treated as a molecular trees or they are nano sized polymers. Dendrimers are constructed by stepwise connection of several parts ( divergent method and convergent method ).

64. Porphyrin unit immobilized in a dendrimer Dendrimer Porphyrin

65. Star-shaped dendrimers can also be synthesized, using stepwise dendrimer growth and subsequent linear polymerization

66. Rotaxanes and Catenanos Catenano

67. Rotaxanes and Catenanos

68. Rotaxanes and Catenanos

69. Rotaxanes –Threading Molecular Rings Rotaxanes are obtained by threading linear polymers through molecular rings such as cyclodextrins, crown ethers and cyclophanes. The word “rotaxane” means wheel axle (rota = wheel, axis = axle). Structurally, they consist of molecular rings threaded by molecular wires that have stoppers at both ends to keep the rings in place. When more than one ring is threaded by a single wire, the structure is called a polyrotaxane . Sometimes we encounter a rotaxane with no stoppers; these molecules are called pseudo-rotaxanes .

70. These structures occur in naturally-occurring systems (some DNA enzymes are ring-shaped, and the DNA chain passes through the enzyme ring). In 1960s researchers discovered artificial rotaxane structures by stepwise process Cyclodextrin-based rotaxane

71. Catenanes – Complex Molecular Associations Catenanes consist of two or more interlocked rings. (Latin word “catena”, means linked chains.) Although the interlocked rings in catenanes are not bonded together by covalent bonds, they cannot be separated from each other. Strategies for catenane synthesis

72. Cell Membranes Assembly of mainly lipids and proteins. ( eg. lipid bilayer structure). The structure of the cell membrane comprises lipids that form a double-layer structure containing floating proteins. The major driving force for lipid bilayer formation is hydrophobic interaction. A lipid molecule consists of a hydrophilic head and hydrophobic tail. Conceptual structure of an amphiphile

73. Simplified illustration of a cell membrane The structure of the cell membrane comprises lipids that form a double-layer structure containing floating proteins.

74. Amphiphiles - Molecules that have affinities for both hydrophilic and hydrophobic media. Many kinds of artificial amphiphiles are reported to form membrane-like structures in aqueous media. When amphiphilic molecules are dispersed in water, the polar part of the amphiphile tends to expose itself to bulk water while the hydrophobic part shields itself from the aqueous phase, forming an assembly through hydrophobic interactions. Cell Membranes

75. Micelles The simplest kind of supramolecular assembly formed by amphiphiles is the micelle surfactants or detergents . Such molecules show relatively high solubility and easily disperse in water up to a certain concentration level, above which they form micelles. This concentration is called the critical micelle concentration (CMC).

76. Liposomes, Vesicles and Cast Films Amphiphilic molecules or lipid molecules sometimes form double-layer structures . This structure is called a bilayer structure , and it can be used to model a cell membrane. Liposome-like structures formed from various kinds of amphiphiles are sometimes called “ vesicles ”, while the term “ liposome ” is sometimes limited to assemblies from phospholipids. The lipid bilayer structure, is the fundamental structural unit of liposomes and vesicles .

77. Liposomes are lipid bilayer structure extends two-dimensionally and forms the “ skin ” of a closed sphere that has a water pool inside. This capsule-like structure can be thought of as a simplified model of a cell. Liposome or vesicle with a lipid bilayer membrane

78. Lipid bilayer behaves as a thermotropic liquid crystal The gel (or crystalline) to liquid-crystalline transition temperature at which the change in state occurs is called the gel (or crystalline)–liquid crystalline phase transition temperature.

79. Thin films of bilayer forming amphiphiles are called cast films , has a multilayered lipid bilayer structure. It is prepared by gradual evaporating water from a solution of aqueous vesicles on a solid support. Cast film with a multibilayer structure

80. The cast film has a structurally anisotropic nature . It can provide an anisotropic medium for material syntheses. Using cast film as a template , structurally anisotropic materials can be synthesized. Formation of an anisotropic polymer in the interlayer spaces of lipid bilayers

81. Supramolecular chemistry - Applications Prof. Ximena Jaramillo Fierro

82. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts

83. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts

84. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts

85. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts

86. Crown-anthracene system: a fluorescent sensor system i ) Receptor (Host) : crown ether, ii ) Substrate ( Guest ) : K+, iii) Signalling unit : anthracene iv) Spacer : –CH2-.

87. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts

88. Phase transfer agents Drug delivery Separation of mixtures Molecular sensors Swithces and molecular machinery Catalysts