Periodic Structures and Crystal Chemistry... aka the Topological Approach to Crystal Chemistry

Transcription

1 Periodic Structures and Crystal Chemistry... aka the Topological Approach to Crystal Chemistry

2 based on a topological approach Reticular Chemistry Scale Chemistry O.M.Yaghi, M. O Keeffe 2003 J. Férey 2003

3 Periodic Structures and Crystal Chemistry n-periodic Structures structures (as nets) that have translational symmetry in exactly n independent directions. Any crystalline material is a 3D ordered arrangement of atoms any crystal is a 3D supramolecular entity depending on the interactions considered we may see chains 1-periodic, layers 2-periodic or 3-periodic netwoks Double-layers are 3D 2-periodic

4 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled/catenated/knotted enumeration of nets tiling theory surfaces

5 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled/catenated/knotted enumeration of nets tiling theory surfaces

6 Coordination Polymers/Networks - Metal-Organic Frameworks MOF and Supramolecular networks node Ligand or H-bond... or weaker interactions... Different frameworks could be obtained on changing the coordination/h-bond geometry of the nodes...

7 Why interest in nets? Why interest in nets? MOF structures reported in the CSD Doubling time 3.6 yrs compared with 9.3 yrs for all CSD!

8 Simplifications: Keep only atoms with cooordination/connectivity > 2 Nodes/Vertex of the Net N Simplification of polydentate groups with centres of the same coord/conn N N O N

9 A Net, as used in solid state chemistry, is a periodic connected simple graph n-periodic = has translational symmetry in n-independent directions connected = there is a continuous path between every pair of vertices simple = contains only simple edges 2-p 2D 3-p 3D

10 A Net is a periodic connected simple graph hence and INFINITE GRAPH 1991 Any mention of infinite graphs... or 3D nets? NO

11 simplification and rationalization... Topology is the theory of shapes which are allowed to stretch, compress, flex and bend, but without tearing or gluing 2-p p 2D honeycomb layer 6 3 -hcb brick wall parquet

12 SbCl 3 (p-diacetylbenzene)

13 SbCl 3 (p-diacetylbenzene) pcu dia

14 n-periodic = has translational symmetry in n-independent directions connected = there is a continuous path between every pair of vertices n-coordinated = vertex/node degree 3-c 6-c 6-coord but 4-conn4 In a more rigorous graph-theoretical approach we should use the term n- coordinated for the vertex/node degree, instead of n-connected, but we keep here the word n-connected to indicated what is clear to chemists: for example, a metal could be 6-coordinated but give only a 4-connected net if two coordination sites are occupied by ligands that are not links of the network.

15 Analysis of Periodic Structures: simplification and rationalization nets A brief history of the topological approach to crystal chemistry... through the story of a net...

16 ICSD Inorganic Chemistry Structural Database

17 CdSO 4 (1963,1980)

18 CdSO 4 (1963,1980) Net à la Wells simplification

19 CdSO 4 (1963,1980) Net à la Wells??? simplification distortion

20 A.F. Wells

21 A.F. Wells

22 A.F. Wells

23 A.F. Wells inorganic organic (H-bond supramolecular) interpenetration of coordination polymers

24 1954

25 1954

26 points in repeat unit... and this is not permessible

27 1977 J.V. Smith

28 1974 M. O KeeffeO

29 W. E. Klee

30 infinite (periodic) graphs as crystal structures W. E. Klee

31 Examples of Nets with 1 or 2 nodes in the repeating unit (topological, cell) pcu

32 Examples of Nets with 1 or 2 nodes in the repeating unit (topological, cell) pcu dia

33 Examples of Nets with 1 or 2 nodes in the repeating unit (topological, cell) pcu dia cds

34 Examples of Nets with 1 or 2 nodes in the repeating unit (topological, cell) march cds is still unknown

35 1991 M. O KeeffeO CdSO 4 as Net

36 1991 M. O KeeffeO cds non bonded contacts not a SP

37 1991 M. O KeeffeO cds non bonded contacts not a SP non bonded contacts Sphere Packing!

38 W. Fischer, E. Koch, A. Sowa (1970) /2005 cds Sphere Packing 4/6/t4 is cds 1991

39 W. Fischer, E. Koch, A. Sowa (1970) /2005 cds Sphere Packing 4/6/t4 is cds

40 W. Fischer, E. Koch, A. Sowa (1970) /2005 cds Sphere Packing 4/6/t4 is cds

41 early 90 Crystal Engineering Crystal Design Infinite Polymeric Frameworks Coordination Polymers Organic/Inorganic Hybrid Materials Metal Organic Frameworks Supramolecular Architectures

42 R. Robson 1989 Polymeric Frameworks Scaffolding-Like Materials

43 R. Robson 1989 Polymeric Frameworks Scaffolding-Like Materials T. Iwamoto

44 7/2008 9/2007

45 R. Robson 1991 the 1 1 example of cds in Polymeric Network

46

47 3D [(Pdtpyp)(Cd(NO 3 ) 2 ) 2 ] 1991 R. Robson

48 3D [(Pdtpyp)(Cd(NO 3 ) 2 ) 2 ] 1991 R. Robson

49 3D [(Pdtpyp)(Cd(NO 3 ) 2 ) 2 ] 1991 R. Robson

50 3D [(Pdtpyp)(Cd(NO 3 ) 2 ) 2 ] 1991 R. Robson

51 3D single cds [(Mtpyp)(M X) 2 ] cds ideal cds-a

52

53 ######################################### 12;RefCode:SOBTUY:C40 H42 Cd2 N12 O21 Pd1 Author(s): Abrahams B.F.,Hoskins B.F.,Robson R. Journal: J.AM.CHEM.SOC. Year: 1991 Volume: 113 Number: Pages: 3606 ######################################### Atom Pd1 links with R(A-A) Pd ( 0-1 1) A Pd (-1 0-2) A Pd ( 1 0 1) A Pd (-1 0-1) A Structure consists of 3D framework with Pd (SINGLE NET) Coordination sequences Pd1: Num Cum Vertex symbols for selected sublattice Pd1 Point/Schlafli symbol:{6^5;8} With circuits:[ (2).8(2)] With rings: [ (2).*] Total Point/Schlafli symbol: {6^5;8} TOPOS OUTPUT cds 4-c net; uninodal net Classification of the topological type: cds/cdso4 {6^5;8} - VS [ (2).*]

54 M. O KeeffeO

55 M. O KeeffeO

56 1992 International School of Crystallography, Erice (Sicily, Italy) MODERN PERSPECTIVES IN INORGANIC CRYSTAL CHEMISTRY May 29 to June 7, 1992 Director : Erwin Parthé, Geneva Speakers: O KeeffeO partecipants: O.M. Yaghi J. Long D.M. Proserpio, A. Sironi

57

58 ..\libro_braga\figure\asufig.jpg...and what happened to cds???

59 O.M. Yaghi,, H. Li, M. O'Keeffe Mater. Res. Soc. Symp. Proc. 1997,, 453, 127 Ag 2 htmn(no 3 ) 2 single cds refcode FABMAX but...no coordinates are available in CSD

60 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled : interpenetration & polycatenation enumeration of nets tiling theory surfaces

61 S. R. Batten & R. Robson 1998 S. R. Batten web page on interpenetration

62 Carlucci, Ciani & Proserpio

63 Carlucci, Ciani & Proserpio

64 ...and what about interpenetrated cds??? S. R. Batten & R. Robson 1998 interpenetrated nbo or cds??... supramolecular H-Bonded H nets Stainton, Harries, Howie Chem. Commun 1991, 1781

65 ...and covalent bonded interpenetrated cds???..\libro_braga\figure\asufig.jpg

66 Chem. Commun The first examples of 2-fold cds PUJQEQ - SIPZEW cds/nbo confusion

67 Chem. Commun The first examples of 2-fold cds PUJQEQ - SIPZEW not named and interpenetration missed in the first report two Chem. Mater cds/nbo confusion

68 Chem. Commun The first examples of 2-fold cds PUJQEQ - SIPZEW not named and interpenetration missed in the first report two Chem. Mater need of a database/software for identification cds/nbo confusion

69 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled enumeration of nets, identification tiling theory surfaces

70 M.M Treacy 1997 Zeolite Deem & Earl 1999

71 Reticular Chemistry Structure Resource rcsr.anu.edu.au

72

73

74 S.J. Ramsden, V. Robins, S.T. Hyde 3D Euclidean Nets from 2D Hyperbolic Tilings

75 cds = sqc5

76 ...end of the nineties 1998 IF 4.18 Crystal Engineering / Crystal Design Infinite Polymeric Frameworks Coordination Polymers Organic/Inorganic Hybrid Materials Metal Organic Frameworks Supramolecular Architectures 2000 IF 4.16

77 1998 IF 4.18 H. Li, M Eddaoudi, M. O'Keeffe, O.M. Yaghi...end Nature of the 1999 nineties MOF-5 Crystal Engineering / Crystal Design Infinite Polymeric Frameworks Coordination Polymers Organic/Inorganic Hybrid Materials Metal Organic Frameworks Supramolecular Architectures 2000 IF 4.16

78 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled enumeration of nets tiling theory minimal surfaces & structures

79 S. Hyde Minimal Surfaces & more

80 S. Hyde Minimal Surfaces & more

81 B. Chen, M. Eddaoudi, S.T. Hyde, M. O'Keeffe, O.M. Yaghi Science 2001 MOF minimal surfaces

82 Topological approach to Crystal Chemistry Analysis of Periodic Structures: simplification and rationalization nets topological classification/analysis of nets single/entangled enumeration of nets tiling theory: Natural Tiles & Nets surfaces

83 M. O Keeffe O & O. Delgado-Friedrichs 1999 a whole new approach to the Taxonomy of Nets

84 O Keffe & Delgado-Friedrichs 3dt 2002 SyStRe 2003 Symmetry Structure Realization one can determine without ambiguity whether two nets are isomorphic or not

85 SyStRe

86 3dt 3D Tiling

87 2003 Reticular Chemistry Reticular is defined in OED as Resembling a net in appearance or construction; consisting of closely interwoven fibres or filaments; net-like: also, Resembling a net in effect or operation; intricate, entangled

88 NSF Workshop on Reticular Chemistry 2003 US Grant Hotel, San Diego Organized by: O Keeffe &Yaghi Walter Klemperer Disorderly conduct in reticular chemistry Omar Yaghi Reticular synthesis of MOFs Kim Dunbar "Building block approaches to magnetic materials" Michael Ward Hydrogen-bonded networks in organic crystals, architectural isomerism, and symmetry transcending length scale Davide M. Proserpio "Polycatenation, polythreading and polyknotting in metal-organic frameworks" Erica Flapan "Topological approaches to chirality" Vanessa Robins "From... database/software hyperbolic patterns to euclidean structures" Robert Connelly "Embedding graphs in Euclidean space" Michael O Keeffe "The taxonomy of reticulations" Michael Thorpe Flexibility for in identification?? glasses and proteins Tianwei Lin "Structural exploitation of an icosahedral virus for nanochemistry and nanomaterials" Stefano Leoni "Modelling structural intermediates with topology and molecular dynamics Jerry Atwood Weak interactions may lead to robust 3D structures Olaf Delgado-Friedrichs,"Barycentric coordinates, symmetry and canonical forms for 3- periodic nets" Jeff R. Long "Cluster-expanded metal-cyanide frameworks: a strategy for assembling functional microporous materials" Pingyung Feng "Supertetrahedral clusters as building blocks for open framework materials - structures, properties and applications" Walter Whiteley "Rigidity and design of molecular structures: counting degrees of freedom"

89 1999 Blatov & Proserpio 2003 Samara 2004 Volga river

90 1999 Blatov & Proserpio 2003

91 Graph Theory J.-G. Eon 1998 Eon, J.-G., Klee, W. E. Souvigner B & Rutherford, J. In preparation Graph Theory in Crystallography and Crystal Chemistry IUCr/Oxford University Press

92 Graph Theory XX Congress IUCr August 2005 J.-G. Eon Hyde Eon Blatov Koch Batten O Keeffe O Proserpio

93 Lyon 2007

94 Topological approach to Crystal Chemistry in textbook and software 2003

95 ..\libro_braga\figure\asufig.jpg... were is cds???

96 usfusf dmpdmp cdscds 6 5. unrecognized

97 usfusf Nets with Point Symbol (6 5. 8) : cds usf dmp mok ict, uni, unl, unm, uns, 4/6/t7 sqc dmpdmp 4/6/t7 sqc2077, 4/6/h14, 4/6/h cdscds 6 5. unrecognized

98 14 HB Organic Interp. how many cds nets in CSD?

99 cds cds 4fold unnamed, recognized by Batten

100 cds cds 4fold fully recognized ODAHIK XEBGEQ cds cds 4fold not reported as such (long weak interactions)

101 but JOLSAE (1991) is not in the list... why???

102 ... with different H-bond analysis is Not Interpenetrated

103 ... but a Single (3,4)-c c Net! (new and with collision) A B

104 Topological approach to Crystal Chemistry simplification and rationalization of nets topological classification/analysis of nets Ockham's Razor Principle of Parsimony It is futile to do with more what can be done with fewer. [Frustra fit per plura quod potest fieri per pauciora.] Plurality should not be assumed without necessity. [Pluralitas non est ponenda sine necessitate.] Hoffmann, R., V.I. Minkin, and B.K. Carpenter, HYLE--International Journal for Philosophy of Chemistry, Vol. 3 (1997), pp

105 Topological approach Helices to are Crystal Chemistry everywhere... simplification and rationalization of nets 2007 topological classification/analysis of nets Ockham's Razor Principle of Parsimony It is futile to do with more what can be done with fewer. [Frustra fit per plura quod potest fieri per pauciora.] Plurality should not be assumed without necessity. [Pluralitas non est ponenda sine necessitate.] Hoffmann, R., V.I. Minkin, and B.K. Carpenter, HYLE--International Journal for Philosophy of Chemistry, Vol. 3 (1997), pp

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