Periodic Structures and

Crystal Chemistry...
aka
the Topological Approach
to Crystal Chemistry
 based on a topological approach
Reticular Chemistry Scale Chemistry

O.M.Yaghi, M. OKeeffe 2003 J. Frey 2003

 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

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
Topological approach to Crystal Chemistry

Analysis of Periodic Structures:

simplification and rationalization nets

nets

topological classification/analysis of nets

single/entangled/catenated/knotted
enumeration of nets
tiling theory
surfaces
 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...
Why interest in nets? MOF
structures reported in the CSD
Doubling time 3.6 yrs compared with 9.3 yrs for all CSD!
 Simplifications:
Keep only atoms with cooordination/connectivity > 2
Nodes/Vertex of the Net

Simplification of polydentate O
groups with centres of the N N
same coord/conn N
 A Net,
et 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
 A Net is a periodic connected simple graph
hence and INFINITE GRAPH

1991

Any mention of
infinite graphs
... or 3D nets?
NO
 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 2D honeycomb layer

63-hcb

brick wall parquet

SbCl3(p-diacetylbenzene)
 pcu dia
SbCl3(p-diacetylbenzene)
 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-conn

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.
 Analysis of Periodic Structures:

simplification and rationalization nets

A brief history of the

topological approach to crystal chemistry...
through the story of a net...
ICSD Inorganic Chemistry Structural Database
 CdSO4
(1963,1980)
 CdSO4 Net la
(1963,1980) Wells

simplification
 CdSO4 Net la ???
(1963,1980) Wells

simplification distortion
1954
1956

A.F. Wells
1954
1956

A.F. Wells
1954
1956

A.F. Wells
1954
1956

A.F. Wells

inorganic
organic (H-bond supramolecular)
interpenetration of coordination polymers
1954
1954
1954

2 points in repeat unit ...

and this is not permessible
 1977

J.V. Smith
1974 M. OKeeffe
1980 1984
W. E. Klee
infinite (periodic) graphs as crystal structures

1980 1984
W. E. Klee
Examples of Nets with 1 or 2 nodes in the
repeating unit (topological, cell)

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

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

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

march 1991... cds is still unknown

1991 M. OKeeffe

CdSO4 as Net
 1991 M. OKeeffe
cds

non bonded contacts 1.000

... not a SP
 1991 M. OKeeffe
cds

non bonded contacts 1.000

non bonded
... not a SP
contacts 1.118
Sphere Packing!
W. Fischer, E. Koch, A. Sowa
(1970) 1991 2004/2005
Sphere Packing 4/6/t4 is cds

1991
 W. Fischer, E. Koch, A. Sowa
(1970) 1991 2004/2005
Sphere Packing 4/6/t4 is cds

2004 1991

2005
 W. Fischer, E. Koch, A. Sowa
(1970) 1991 2004/2005
Sphere Packing 4/6/t4 is cds
1.118
2005 1.015
2004 1991

2005

2004
early 90 Crystal Engineering
Crystal Design

Infinite Polymeric Frameworks

Coordination Polymers

Organic/Inorganic Hybrid Materials

Metal Organic Frameworks

Supramolecular Architectures
R. Robson 1989

Polymeric
Frameworks

Scaffolding-Like
Materials
R. Robson 1989

Polymeric
Frameworks

Scaffolding-Like
Materials

T. Iwamoto
1966 - ...
7/2008

9/2007
 R. Robson
1991
the 1 example of cds in
Polymeric Network
3D [(Pdtpyp)(Cd(NO33)22)22] 1991
1991 R.
R. Robson
Robson
3D [(Pdtpyp)(Cd(NO33)22)22] 1991
1991 R.
R. Robson
Robson
3D [(Pdtpyp)(Cd(NO33)22)22] 1991
1991 R.
R. Robson
Robson
3D [(Pdtpyp)(Cd(NO33)22)22] 1991
1991 R.
R. Robson
Robson
3D single cds [(Mtpyp)(MX)22]

cds ideal cds-a

#########################################
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 1 0.5000 -0.5000 1.0000 ( 0-1 1) 19.905A
Pd 1 -1.0000 0.0000 -1.5000 (-1 0-2) 17.126A
Pd 1 1.0000 0.0000 1.5000 ( 1 0 1) 17.126A
Pd 1 -0.5000 0.5000 -1.0000 (-1 0-1) 19.905A
-------------------------
Structure consists of 3D framework with Pd (SINGLE NET)

Coordination sequences
----------------------
Pd1: 1 2 3 4 5 6 7 8 9 10
Num 4 12 30 58 94 138 190 250 318 394
Cum 5 17 47 105 199 337 527 777 1095 1489
----------------------
TOPOS OUTPUT
Vertex symbols for selected sublattice
------------------- -------------------

65.8-cds
Pd1 Point/Schlafli symbol:{6^5;8}
With circuits:[6.6.6.6.6(2).8(2)]
With rings: [6.6.6.6.6(2).*]
--------------------------------------
Total Point/Schlafli symbol: {6^5;8}

4-c net; uninodal net

Classification of the topological type: cds/CdSO4 {6^5;8} - VS [6.6.6.6.6(2).*]
1991 - 1996
M. OKeeffe
1991 - 1996
M. OKeeffe
1992
International School of Crystallography, Erice (Sicily, Italy)
MODERN PERSPECTIVES IN INORGANIC CRYSTAL CHEMISTRY
May 29 to June 7, 1992
Director : Erwin Parth, Geneva
Speakers: OKeeffe
partecipants:
O.M. Yaghi
J. Long
D.M. Proserpio, A. Sironi
 ..\libro_braga\figure\asufig.jpg
...and what happened to cds ???
 O.M. Yaghi, H. Li, M. O'Keeffe
Mater. Res. Soc. Symp. Proc. 1997, 453, 127
Ag2htmn(NO3)2 single cds

refcode FABMAX
but ...no coordinates
are available in CSD
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
S. R. Batten & R. Robson 1998

S. R. Batten
web page on interpenetration
 Carlucci, Ciani &
Proserpio 1994-2003
 Carlucci, Ciani &
Proserpio 1994-2003
...and what about interpenetrated cds ???

S. R. Batten &
R. Robson
1998
interpenetrated
nbo or cds??
...

supramolecular H-Bonded nets

Stainton, Harries, Howie Chem. Commun 1991,
1991 1781
 ...and covalent bonded
..\libro_braga\figure\asufig.jpg
interpenetrated cds ???
 The first examples
of 2-fold cds
Chem. Commun. 1998 PUJQEQ - SIPZEW

cds/nbo confusion
 The first examples
of 2-fold cds
Chem. Commun. 1998 PUJQEQ - SIPZEW

not named and interpenetration

missed in the first report
two Chem. Mater. 1998

cds/nbo confusion
 The first examples
of 2-fold cds
Chem. Commun. 1998 PUJQEQ - SIPZEW

not named and interpenetration

missed in the first report
two Chem. Mater. 1998

... need of a database/software

for identification

cds/nbo confusion
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
M.M Treacy
1997

http://www.hypotheticalzeolites.net

Zeolite

Deem & Earl

1999
Reticular Chemistry Structure Resource
rcsr.anu.edu.au
 S.J. Ramsden, V. Robins, S.T. Hyde
3D Euclidean Nets from 2D Hyperbolic Tilings
cds = sqc5
 ...end of the nineties

2000
1998 IF 4.18 IF 4.16

Crystal Engineering / Crystal Design

Infinite Polymeric Frameworks
Coordination Polymers
Organic/Inorganic Hybrid Materials
Metal Organic Frameworks
Supramolecular Architectures
 H. Li, M Eddaoudi, M. O'Keeffe, O.M. Yaghi
...endNature
of the 199
nineties
9
MOF-5 2000
1998 IF 4.18 IF 4.16

Crystal Engineering / Crystal Design

Infinite Polymeric Frameworks
Coordination Polymers
Organic/Inorganic Hybrid Materials
Metal Organic Frameworks
Supramolecular Architectures
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

 S. Hyde
1984 - 1988 - 1997
Minimal Surfaces & more
 S. Hyde
1984 - 1988 - 1997
Minimal Surfaces & more
 B. Chen, M. Eddaoudi,
S.T. Hyde, M. O'Keeffe, O.M. Yaghi
Science 2001

MOF-14

2001
minimal surfaces
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
 M. OKeeffe &
O. Delgado-Friedrichs
1999

a whole new approach

to the Taxonomy of Nets
 OKeffe & Delgado-Friedrichs

3dt

2002

SyStRe

2003

Symmetry Structure Realization

one can determine without
ambiguity whether two nets are
isomorphic or not
SyStRe
 3dt
3D Tiling
 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
 NSF Workshop on Reticular Chemistry 2003
US Grant Hotel, San Diego
Organized by: OKeeffe &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"
... database/software
Vanessa Robins "From hyperbolic patterns to euclidean structures"
Robert Connelly "Embedding graphs in Euclidean space"
Michael OKeeffe "The taxonomy of reticulations"
for identification??
Michael Thorpe Flexibility in 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"
 1999

Blatov &
Proserpio Samara
2003 2004
Volga river
 1999

Blatov &
Proserpio
2003
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
Graph Theory
XX Congress IUCr August 2005

J.-G. Eon
1998
Hyde Eon Blatov Koch Batten OKeeffe Proserpio
Lyon 2007
Topological approach to Crystal Chemistry in textbook ...

2007

2005

2007
2007

...and software

2003
... were is..\libro_braga\figure\asufig.jpg
cds ???
 2003
65.8-usf

2006
65.8-dmp

2008
65.8-cds
unrecognized
 2003
65.8-usf

12 Nets with Point Symbol (65.8) :

cds usf dmp mok 2006
ict, uni, unl, unm, uns, 4/6/t7 sqc2077, 4/6/h14,
65.84/6/h6
-dmp

2008
65.8-cds
unrecognized
 how many cds nets in CSD ?

14 HB
Organic
Interp.
1999 65.8-cds 4fold unnamed, recognized by Batten
2001 65.8-cds 4fold fully recognized
ODAHIK

XEBGEQ

2000 65.8-cds 4fold

not reported as such
(long weak
interactions)
but JOLSAE (1991) is not in the list... why ???
... with different H-bond analysis is Not Interpenetrated
... but a Single (3,4)-c Net ! (new and with collision)

B
 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. 3-28
http://www.hyle.org/journal/issues/3/hoffman.htm
 Topological approach
Helices to
areCrystal Chemistry
everywhere...
2007
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. 3-28
http://www.hyle.org/journal/issues/3/hoffman.htm