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Three-component reactions leading to metal-organic frameworks and hydrogen-bonded organic networks

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Three-component reactions leading to metal-organic frameworks and hydrogen-bonded organic networks
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Shafer, Nicole Marie
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English
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ix, 145 leaves : ; 28 cm

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Coordination polymers ( lcsh )
Organometallic chemistry ( lcsh )
Ligands ( lcsh )
Coordination polymers ( fast )
Ligands ( fast )
Organometallic chemistry ( fast )
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bibliography ( marcgt )
theses ( marcgt )
non-fiction ( marcgt )

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Bibliography:
Includes bibliographical references (leaves 141-145).
Thesis:
Department of Chemistry
Statement of Responsibility:
Nicole Marie Shaker.

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|University of Colorado Denver
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Full Text
THREE-COMPONENT REACTIONS LEADING TO METAL-ORGANIC
FRAMEWORKS AND HYDROGEN-BONDED
ORGANIC NETWORKS
by
Nicole Marie Shafer
B.S., Colorado School of Mines, 2008
A thesis submitted to the
University of Colorado Denver
in partial fulfillment
of the requirements for the degree of
Masters of Science
Chemistry
2011


This thesis for the Masters of Chemistry
degree by
Nicole Marie Shafer
has been approved
by
Xaiotai Wang
Hai Lin
Date


Shafer, Nicole Marie (M.S. Chemistry)
Three-Component Reactions Leading to Metal-Organic Frameworks and Hydrogen-
Bonded Organic Networks
Thesis directed by Associate Professor Xiaotai Wang
ABSTRACT
Metal-organic coordination polymers, also known as metal-organic frameworks
(MOFs), have attracted intense research interest recently. In this work, five novel
MOFs and three hydrogen-bonded organic networks have been synthesized from
three-component reactions of the form of M + LI + L2. The five MOFs have the
empirical formulas [Zn3(bpy)(bpc)3] (1), [Cu(bpy)i/2(bdc-N02)(H20)] (2),
[Ni(bpy)(pdp)] (3), [Cu(bpy)i/2(cdc)] (4) and [Cu3(bpy)2(cdc)3] (5), where bpy =
4,4-bipyridne, bpc = 4,4-biphenylenedicarboxylate, bdc-N02 = 2-nitro-l,4-
benzenedicarboxylate, pdp = 1,4-phenylenedipropanoate and cdc = 1,4-
cyclohexanedicarboxylate. The three hydrogen-bonded networks are [(3-
aminobenzoate)(Hbpy+)] (6), [(H2bdc-NH2)(bpy)] (7) and [(H2cdc)(bpy)] (8), where
H2bdc-NH2= 5-amino-1,3-benzenedicarboxylic acid. These compounds have been
characterized by a combination of IR, TGA (for 2, 7 and 8) and X-ray
crystallography. Compounds 1, 4, and 5 show 3D interpenetrated coordination
networks, while 2 and 3 are 2D MOFs arising from infinite metal-carboxylate ribbons
cross-linked via the bpy ligands. Compounds 6 and 7 display 2D interweaving
hydrogen-bonded networks, while 8 displays a 1D hydrogen-bonded ribbon.
This abstract accurately represents the content of the candidates thesis. I
recommend its publication
Signed
Xiaotai Wang


ACKNOWLEDGEMENT
I would like to thank my advisor, Dr. Xiaotia Wang, for his guidance and support
over the past three years. I would also like to thank Dr. Xiao-ying Huang who ran all
of the crystal data as well as solving all of the disorder problems that were occurring.
A special thanks to Maddie Torres, Long San and Huong Nguyen for getting me
started in Dr. Wangs lab. Thank you to Dr. Douglas Dyckes and Dr. Hai Lin for
being on my committee. Thank you to Cathy Rathbun for not only being an amazing
lab coordinator but for being my friend. Thank you to my mom and my sister for
your support during my academic career, and last but not least a very special thanks
to Mike Shoup for standing by me while I was writing this thesis.


TABLE OF CONTENTS
List of Abbreviations........................................................vi
List of Figures.............................................................vii
Chapter
1. Introduction...............................................................1
1.1 MOFs Based on Coordination Chemistry......................................1
1.2 Synthetic Methods........................................................4
1.3 Applications of MOFs.....................................................5
2. Review of Recent Literature...............................................8
3. Experimental.............................................................21
3.1 Materials and Methods...................................................21
3.2 Synthesis of Metal-Organic Frameworks...................................21
3.3 Formation of Hydrogen-Bonded Networks...................................24
4. Results and Discussion...................................................26
4.1 Synthesis and Characterization by IR and TGA............................26
4.2 Crystal Structures......................................................28
5. Conclusions..............................................................49
Appendix
A. IR Spectra, TGA Data and Space-Filling Models............................50
B. Crystallographic Information Files.......................................58
References..................................................................141
v


LIST OF ABBREVIATIONS
Abbreviations
MOFs ................................................Metal-Organic Frameworks
bpy...............................................................4,4-bipyridine
bpc....................................................4,4-biphenyldicarboxylate
bdc-N02...........................................2-nitro-1,4-benzenedicarboxylate
pdp.....................................................1,4-phenylenedipropanoate
cdc............................................trans-1,4-cyclohexanedicarboxylate
H2bdc-NH2..................................5-amino-1,3-benzenedicarboxylic acid
H2cdc......................................rrarcs-l,4-cyclohexanedicarboxylic acid
bdc......................................................1,4-benzenedicarboxylate
btc...............................................1,2,4,5-benzenetetracarboxylate
bpe......................................................l,2-bis(4-pyridyl)ethane
bpp......................................................l,3-bis(4-pyridyl)propane
dabco.................................................4-diazabicyclo[2.2.2]octane
dpa.................................................................diphenylamine
pyz......................................................................pyrazine
lac.......................................................................lactate
TGA .................................................Thermal Gravimetric Analysis
vi


LIST OF FIGURES
Figure
1.1 Organic Ligands Used in This Work...................................3
1.2 Porous MOF Channels..................................................5
2.1 Coordination Environment of Cobalt..................................8
2.2 Double Helix of Compound C.........................................9
2.3 Luminescence Spectra of Complexes F-1..............................10
2.4 N2 and H2 Gas Sorption Isotherms
of M-Q and R Measured at 78 K....................................12
2.5 Chromatograms of Alkane Mixtures
Separated on a Zn(bdc)(bpy)o.5 Column............................15
2.6 Three-Dimensional MOF Structure with
the Ni4(dpa)4 Macrocyclic Unit...................................16
2.7 Luminescence Spectroscopy of the Five Compounds
Synthesized by Ma and Others.....................................18
2.8 Temporal Evolution of UV/vis Absorption Spectra
for the Delivery of 12...........................................19
4.1 ORTEP Drawing Displaying Compound 1.................................29
4.2 Secondary Building Unit of 1.......................................29
4.3 Compound 1 Square Channel..........................................30
4.4 Interpenetration of compound 1.....................................31
4.5 Expansion of Compound 1............................................31
4.6 ORTEP Drawing of 2.................................................32
4.7 Linear Ribbon of Compound 2........................................33
vii


4.8 Compound 2 Ladder Structure
Showing bpy Linkers in the yz Plane...............................34
4.9 The Wave Formation in the Ladder Structure
Found in 2........................................................34
4.10 Expansion of Compound 2 Displaying the
Waves Interacting Through the y Axis..............................35
4.11 ORTEP of 3.........................................................35
4.12 Secondary Building Unit of 3.......................................36
4.13 Two-Dimensional Wave of Compound 3.................................37
4.14 The Two-Dimensional Plane of 3.....................................37
4.15 Expansion of Compound 3............................................38
4.16 ORTEP Drawing of 4.................................................38
4.17 Infinite Structure of Compound 4...................................39
4.18 Interpenetration of 4..............................................40
4.19 Expansion of compound 4............................................40
4.20 ORTEP Drawing of 5.................................................41
4.21 One-Dimensional Ribbon of 5........................................42
4.22 Compound 5 Expanded into the y and z-Axis..........................42
4.23 Display of the Channels Through the y-axis of 5....................43
4.24 The Two-Fold Interpenetration of 5.................................44
4.25 Secondary Building Unit of 6.......................................44
4.26 Basic Crystallographic Unit of 6...................................45
4.27 Expansion of Network 6.............................................45
4.28 One-Dimensional Hydrogen-Bonded
Network of 7......................................................46
4.29 The Non-Planar Hydrogen Bonds of 7.................................46
4.30 Expansion of 7.....................................................47
4.31 Basic Unit of compound 8...........................................47
viii


4.32 Expansion of Network 8.....................................48
A.l IR ofl......................................................50
A.2 IR of 2.....................................................50
A.3 IR of 3.....................................................51
A.4 IR of 4 and 5...............................................51
A.5 IR of 6.....................................................52
A.6 IR of 7.....................................................52
A.7 IR of 8.....................................................53
A.8TGA Data for 2...............................................54
A.9TGA Data for 7...............................................54
A.10TGA Data for 8..............................................55
A.l 1 Space Filling Model of Compound 1.........................56
A. 12 Expanded space filling model of compound 1................56
A. 13 Expanded space filling model of compound 4................57
A. 14 Expanded space filling model of compound 5................57
IX


1. Introduction
1.1 MOFs Based on Coordination Chemistry
Coordination chemistry is the study of compounds formed between metal ions and
other neutral molecules or negatively charged ions known as ligands, which has long
dominated the chemistry of transition metal elements. Metal-organic coordination
polymers, also known as metal-organic frameworks (MOFs), consists of repeating
units of metal ions and one or more multitopic organic ligands.1 The organic ligands
can be formally thought of as donating electron pairs to the metal centers, and in
some cases MOFs can also incorporate counter-ions and solvent molecules.1,2 One-
dimensional MOFs are crystal structures that expand in one direction generating
ribbons or helixes, two-dimensional MOFs expand into two directions and create
planes or layers and three-dimensional MOFs expand in three directions creating
paddle-wheels and other three-dimensional structures. Porous MOFs have open
channels where the guest species can be removed and reintroduced without collapse
of the framework. The MOFs described in this work have more condensed
frameworks, consisting of interpenetrated three-dimensional coordination networks
or two-dimensional layers packed by weak intermolecular forces.
In recent years MOFs have attracted intense research interest because such
supramolecular assemblies have interesting structures as well as potential
1


applications in smart optoelectronic, magnetic and porous applications.1'3 The
synthesis of MOFs, which is based upon the methodology of coordination chemistry,
occurs under relatively mild, low-energy conditions as opposed to the high-
temperature, high-energy preparations of classical solid state compounds.1 MOF
design takes into account such factors as the coordination nature of the metal ion, the
structural characteristics of the polydentate organic ligand, the metal to ligand ratio
and possible counter-ion influence. A subtle change in any of these factors can lead
to new extended network structures. Thus, a great variety of supramolecular
architectures have been constructed, some of which exhibit useful properties.
The majority of MOFs are made from two-component reactions that involve a
metal ion node (M) and an organic connector ligand (L), and in some cases ancillary
modules such as donor solvent molecules and counterions.1 Charge-neutral
connector ligands, such as 4,4-bipyridine, will result in cationic MOFs balanced by
counter-ions. Anionic connector ligands, such as 1,4-benzenedicarboxylate, will
balance the charge on the metal center and therefore support charge-neutral MOFs.
Besides robustness, such neutral MOFs exclude uncoordinated counter-ions that
could occupy and block any open channels, therefore being favored for porous
applications such as size- and shape-selective separations and catalysis.1
There have been an increasing number of reports of MOFs made from three-
component reactions in the form of M + LI + L2 (Figure 1.1), and this approach
offers an even wider variety for MOF synthesis, which provides more functionality
2


and design.1,4 Reactions of this type with two neutral ligands will result in cationic
MOFs balanced by counter-ions, similar to what is seen in M + L methodologies.
Neutral ligands, generally derivatives of bipyridine, predominate MOFs with
rectangular pores.1 Three-component reactions in which one ligand is anionic and
the other is neutral are considerably more common due to the fact that the charge of
the metal center is balanced by the anionic ligand.1 The most common combination
of neutral/anionic ligands are bipyridine and multicarboxylates. This work
explores three-component reactions involving 4,4-bipyridine, dicarboxylates of
varying flexibility, and zinc(II), copper(II) or nickel(II) salts.
4,4-bipyridine
1,4-phenylenepropanoic acid /ra/w-cyclohexanc-1,4-dicarboxylic acid
Figure 1.1: Organic ligands used in this work to synthesize MOFs using the methodology M + LI +
3


1.2 Synthetic Methods
As discussed above, MOFs are synthesized under relatively mild conditions. There
are several synthetic methods reported in the literature and choosing the correct
synthetic method can be challenging due to changes in the overall structure based
upon the method.6 Methods such as microwave heating, ultrasonic synthesis and
microemulsions are less common, but do allow for control of the framework
crystal. The most common methods for synthesis of MOFs are diffusion and
solvothermolysis. The two methods each have their advantages in crystal design and
each can lead to different structures from the same starting metals and ligands.2,6
This work takes advantage of solvothermal synthesis.
Solvothermolysis is the most widely used technique for the synthesis of MOFs,
which involves heating the metal and ligand sources in a sealed vessel at a range of
temperatures from 60 to 180 C. Choosing the correct solvent is important since both
inorganic and organic starting materials are present.2 Polar solvents, such as N,N-
dimethylformamide, are advantageous because the polarity can disassociate metal
salts. These solvents are also slightly basic which can deprotonate carboxylic acids,
affording anionic COO for better coordination to metal ions. Mixtures of
immiscible solvents are also useful for synthesis because crystals can form at the
solvent interface.2,6 Solvothermal synthesis also allows for structure control by
changing reaction conditions, specifically concentration and temperature.
4


1.3 Applications of MOFs
MOFs are highly desirable because synthesis can be controlled and networks can be
designed to specific qualifications.13 Porous MOFs have applications in gas storage
and transport, and condensed MOFs have uses in magnetic and optoelectronic
materials. In order for porous frameworks to be useful, the guest solvent molecules
must be removed without destroying the framework.1'3 This activation process is
generally achieved by gentle heating of the MOF.3
1.3.1 Gas Storage
Porous MOFs are ideal for gas storage applications (Figure 1.2) due to low densities,
high porosities and pore
sizes that can be tailored
a) Dots (OD cavity)
b) Channels (ID space)
c) Layers (2D space)
d) Intersecting channels (3D space)
z
z


for specific adsorption
properties.I'3,6,8 Hydrogen
and methane are of
particular interest due to
need for clean energy
options. Hydrogen has
been difficult to work with
due to the small size of the
Figure 1.2: Porous MOF channels that can be used for gas storage.1 molecule.8 There has
been successful uptake of hydrogen at 77 K at standard pressures, but at standard
5


temperature, higher pressures must be implemented in order to saturate the MOF with
Q
hydrogen.
Methane is also of interest as a clean energy fuel because of ease of
combustion, it is simple to refine, deposits are globally found and combustion
byproducts are carbon dioxide and water.8 A limited number of MOFs have been
synthesized that can adsorb methane. Methane requires a high surface area and
functional pores in order for usable storage to be obtained.8 Currently more research
is needed in order to optimize porous MOFs for use in hydrogen and methane
storage.1,6,8
Porous MOFs have also been shown to adsorb other gases such as nitrogen
and carbon dioxide, which has applications in gas transportation.1 Nitrogen and
argon have been used to evaluate the ability of the pore to uptake gases once the
guest molecules have been removed, which is an important step to determine the
dynamic behavior of the pore.1 MOF storage of carbon dioxide has also been tested
Q
for potential uses for capture. Carbon dioxide capture can be improved by
incorporating alkylamine functional groups to the ligands as both a pre- and post-
synthetic modification.8 By enhancing carbon dioxide adsorption, the greenhouse gas
can be sequestered away without harm to the environment.
1.3.2 Separations and Catalysis
Using porous MOFs for separations is mechanistically very similar to storage
because the pore site is selecting only one species.2 MOFs for separation have uses
6


in size-exclusion chromatography, where compounds such as methane are adsorbed
onto the stationary phase and impurities are passed through the column.9'11
Preliminary studies show promising use of MOFs as the stationary phase for large
molecule separations.10,11
There have been some studies of using MOFs as catalysts.2 These MOFs are
post-synthetically treated to become catalytically active by removing all guest species
and any ancillary ligands to activate the Lewis acid metal sites. MOFs as catalysts
have certain advantages over zeolites in that their size and shape selectivity toward
the substrates can be synthetically talored.
1.3.4 Other Uses
MOFs have also shown potential in areas of optics, magnets, drug delivery, nano-
sized templates, and thin films. Optics is one of the more studied areas since many
2 6 12
MOFs show fluorescent properties. Interest in the area of optics for MOFs is due
y
to the fact that the material can be tuned to the needs of potential fluorescent probes.
Nonlinear optical materials synthesized from MOFs are also of research interest and
can be specifically engineered. MOFs are also being considered for molecular
magnets because several frameworks display ferromagnetic and ferrimagnetic
behavior.2,6 Beyond the categories described above, many of the proposed uses for
MOFs need further exploration in order to determine if these applications are viable.
7


2. Review of Recent Literature
The synthesis of metal-organic frameworks has been well documented in the
literature and has an extensive scope well outside of what is presented in this work.
The following review is most relevant to this work, which discusses recent literature
on three-component reactions leading to MOFs containing dicarboxylates and
bipyridine derivatives with various transition metal centers.
Figure 2.1: Coordination environment of cobalt of the three complexes were all very
from research by Tao and others in 2000.13
similar in which 1,4-benzenedicarboxylate acts as a chelating and a bridging ligand,
while 4,4-bipyridine acts as a linker to build subunits into three dimensions (Figure
In 2001 Sun and others reported five new structures with cobalt, capper, zinc,
manganese, and cadmium with the ligands 1,4-benzenedicarboxylic acid and 1,10-
In 2000, Tao and others reported
three new structures of 1,4-
benzenedicarboxylic acid and 4,4-
bipyridine with cobalt, cadmium or zinc,
all of which show twofold
interpenetrating three-dimensional
coordination networks.13 The structures
8


phenanthroline.14 The 1,4-benzenedicarboxylic acid unit was hydrolyzed from 1,4-
cyanobenzene due to the authors having problems creating stable MOFs from 1,4-
benzenedicarboxylate salts. Structures of complexes with cobalt, copper and zinc are
similar with one-dimensional zigzag chains. The compounds with manganese and
cadmium possess a three-dimensional network structure with the metal center in a
distorted octahedron geometry. The manganese complex shows antiferromagnetic
interactions, the cobalt and copper complexes show some magnetic activity but it
decreases as temperature decreases.
In 2002 Chen and Liu
reported five copper frameworks
that were specifically synthesized
to be helical in shape.
15
Structures A-D were successful in
Figure 2.2: Double helix of compound C from Chen and
this endeavor; one-dimensional Lius 2002 report.15
helical chains were synthesized with no flexible dicarboxylates and bipyridine
derivatives. Structure E was a flexuous chain due to the dicarboylate ligand being
longer. Structure C (Figure 2.2), copper coordinated with 4,4-oxybis(benzoate) and
1,10-phenanthroline, is of particular interest because the ligands were of correct
orientation to allow for n interactions of the aromatic rings. Structure E, copper
coordinated with ethylenedi(4-oxybenzoate) and 1,10-phenanthroline, also showed
interesting structure because the flexibility allows for a zipper effect.
9


In 2003 Zhang and others reported four one-dimensional coordination
polymers.16 In structures F and G, cadmium and zinc ions are respectively
coordinated with 1,3-benzenedicarboxylic acid and 1,10-phenanthroline. These
structures are one-dimensional helical ribbons that are then packed with ji
interactions. In structures H and I, zinc and cadmium ions are respectively
coordinated with 1,3-benzenedicarboxylic acid and 2,2-bipyridine. These structures
show different properties due to the fact that there is no n interaction between the
one-dimensional ribbons. Instead these structures zip up to make larger super
structures. Compounds F and G show intense blue photoluminescence which is
assigned as ligand-to-metal charge transfer. Complexes H and I show similar
behavior to F and G, but there is also emission from the 2,2-bipyridine ligand
observed (Figure 2.3).
Figure 2.3: Luminescence spectra of complexes F-I from Zhangs research, (a) represents
compounds F (solid line) and G (dashed line), (b) represents compounds I (solid line) and H (dashed
line).16
Sun and others reported three new structures that are constructed based upon
coordination bonds of silver with 4,4-bipyridine and dicarboxylate ligands, as well
10


as hydrogen bonds, n interactions and weak coordinative interactions.17 Structure J
shows a ladder like chain where silver is coordinated to 4,4-bipyridine as the sides of
the ladder with 4,4-bipyridine and carboxylate acting as the rungs. Structure K
shows similar silver/4,4-bipyridine bridging, but the carboxylate groups act as
hydrogen-bond donor/acceptor, affording a zigzag stack. Structure L has two
crystallographically independent silver atoms that form similar 4,4-bipyridine
coordination found in J and K as well as carboxylate group bridging across the
network in a similar fashion to these compounds as well.
In 2004, Ruiz-Perez and others successfully synthesized two compounds
Mn(Hbta)(Hbpy)(H20)2 and H2bpy[Co(bta)(bpy)(H20)2] each with the
benzenetetracarboxylic acid ligand which has interesting characteristics for MOF
development and more complex crystal structures.18 Dai and others successfully
synthesized four new cadmium compounds with benzenedicarboxylate derivatives
and bipyridine derivatives.19 Two of the compounds show twofold interpenetration
topology, the third structure shows fourfold interpenetration and the forth structure
has a three-dimensional spiral pipe-like structure. All compounds display strong
fluorescent emissions in solid state at room temperature which implies that these
compounds could be useful potential photoactive materials. The fluorescent
emissions are attributed to ligand-to-metal charge transfer transitions. Yang and
others synthesized two independent [Cu2(mellitate)(bpy)(H20)2] three-dimensional
polymers with helical substructures that were interwoven in double-stranded helical
11


tubes with host one-dimensional linear polymers of [Cu(bpy)(H20)4]2+.20 Ionic
interactions along with n and alkane-7t interactions between the two different 4,4-
bipyridine moieties from the helical and linear polymer retains the structure.
In 2005 Chun and others synthesized seven new compounds based upon
Zn2(bdc)2(dabco) in order to maximize gas adsorption; specifically hydrogen.21
Compound R (zinc coordinated with 2,3,5,6-tetramethyl-l,4-benzenedicarboxylic
acid and 4,4-bipyridine) displayed permanent porosity. The adsorption of
compounds M-Q and R were all studied with N2 at 78 K as well as hydrogen gas
under the same conditions, which correlates with most zeolites. Compound N (zinc
coordinated with 2,3,5,6-tetramethyl-l,4-benzenedicarboxylic acid and 4-
diazabicyclo[2.2.2]octane) has shown the highest affinity to hydrogen, allowing the
authors to propose that shape and size of the framework is important for hydrogen
adsorption more so then the ligands.
Figure 2.4: N2 (left) and H2 (right) gas sorption isotherms of M-Q and R measured at 78 K. Data for
1 are shown for comparison. Solid lines in H2 isotherms are visual aids. Notice compound N (in blue)
has highest hydrogen adsorption.21
He, Zu and Ng report of the successful synthesis of Cu2(C8H3N03)2(CioH8N2)-
(H20)2, that has one unique Cu atom, water molecule and bipyridine in a mirror plane
*
S
fi-
x'
00 01 02 03 04 06 06 07 08 06 10 0.0 01 03 03 04 OS 06 07 08 06 10
Pi atm
12


with 2-nitro-l,4-benzenedicarboxylic acid lying in on a twofold axis which leads to a
two dimensional network. Manna and others reported the synthesis of three new
complexes; Co(bpp)(bdc)(H20)2, Mn(bpds)(bdc)(H20)2(bpds) and
Mn(bpy)(H20)(bdc). The first structure shows a two-dimensional corrugated layer
with a square mesh composition in which both ligands are bridging. The second
structure contains a two-dimensional undulating sheets that fills a square grid. In the
third complex, hydrated manganese units are bridged by 4,4-bipyridine to give a
one-dimensional polymer with the 1,4-benzenedicarboxylate sandwiched between the
one-dimensional layers. Magnetic data were collected on the first two compounds
based on the fact there is a pseudo-one-dimensional structure formed by Co(II) and
Mn(II), the third complex with a sandwiched 1,4-benzenedicarboxylate would be
antiferromagnetic.
Also in 2005, Ma, Mulfort and Hupp synthesized five mixed-ligand
frameworks of the formula Zn2L2L where L is the dicarboxylic acid and L is one of
several bipyridine derivatives.24 All MOFs displayed the dicarboxylates acting as
terminating units on the Zn ions with the bipyridine derivatives acting as struts.
Compounds S-V were subjected to adsorption tests with N2 gas and confirmed
permanent microporosity for compounds T and V. Zheng and others report four new
structures with lanthanide series metals with 1,4-naphthlenedicarboxylic acid and
4,4-bipyridine.25 Lanthanide frameworks are of interest due to their light emitting
and other properties. Compounds W and X have a similar structure; a binuclear
13


asymmetric unit with two crystallographically unique metal centers. Compound Y is
similar but bipyridine ligands are also acting as neutral linkers throughout the system.
Compounds W, X and Y are all nine coordinate around the metal center. Compound
Z has two independent ytterbium ions that are eight coordinate. Compound X
displays magnetic properties. Wang and others synthesized two new copper
frameworks with 1,2,4-benzenetricarboxylic acid and 4,4-bipyridine, which show
two-dimensional neutral frameworks.26 The magnetic susceptibility of the
compounds were then studied, which show a dominate ferromagnetic exchange
between the Cu(II) ions.
In 2006 Chen and others reported the synthesis of Zn(bdc)(bpy)o.5 that was
specifically designed to have a cubic framework and one-dimensional pores.9 This is
ideal for alkane separation which is useful in the petroleum industry. The original
synthesis included guest molecules of N,N-dimethylformamide and water which can
be easily removed, and resolvated, without deforming the crystal structure. The
authors did several gas chromatography studies to determine retentions of natural gas
as well as n-pentane and n-hexane isomers (Figure 2.5).
14


Figure 2.5: Chromatograms of alkane mixtures separated on a Zn(bdc)(bpy)0 5 column: a) separation
of n-pentane and n-hexane, b) separation of 2-methylbutane and n-pentane, c) separation of 2,2-
dimethylbutane, 2-methylpentane, and n-hexane, and d) separation of an alkane mixture containing 2-
methylbutane (1), n-pentane (2), 2,2-dimethylbutane (3), 2-methylpentane (4), and n-hexane (5).
S=thermal conductivity detector response.9
In 2007 Manna and others reported the synthesis of three new cobalt
complexes with 4,4-dipyridyl N,N-dioxide and various dicarboxylate ligands.27
Structure AA is a covalently bonded two-dimensional layered structure. Structure
AB is also a two-dimensional layered structure will parallel crystal planes with 4,4-
dipyridyl N,N-dioxide and fumerate acting like bis-monodentate spacers connected
Co(H20)2 units. Structure AC has two structurally independent cobalt atoms set up
as a one-dimensional coordination polymer with uncoordinated 1,4-
benzenedicarboxylate and water molecules in the pores. The magnetic properties of
all three structures were tested and all showed antiferromagnetic coupling consistent
with literature values of similar species. Wang and others reported the synthesis of
two new frameworks of cadmium and zinc with croconate and 1,2-bis-(4-
pyridyl)ethylene that have two-dimensional structures. Three-dimensional
superstructures are achieved through n interactions of the aromatic rings. Zhao and
others synthesized two new frameworks that were based on heterometallic metal
centers of neodymium or gadolinium with colbalt.29 The two compounds are
15


structurally isomorphous and only differentiate based upon lattice water molecules.
The two crystal structures show an adsorption of radical compounds, tested with the
radical NIT4Py. The molecules can also adsorb methanol upon the loss of
uncoordinated water molecules. Hu and others prepared the compound
Ni6(dpa)4(pyz)4(H20)8*l IH2O which upon dehydration shows permanent
microporosity and dynamic structural transformation triggered by
in
removal/readsorption of guest molecules (Figure 2.6). There are two unique Ni(II)
atoms in the crystal structure in which each is in an octahedral coordination
environment. The authors then further showed that water, methanol, carbon dioxide,
and acetone could all be adsorbed and released from the desolvated compound.
Figure 2.6: Three-dimensional MOF structure with the Ni4(dpa)4 macrocyclic unit from Hus work
(a) and topological network (b) viewed along the c axis of 1. The guest water molecules in the
channels are highlighted in blue spheres. The dpa and pyz ligands are represented by red and blue
lines, respectively.30
In 2008, Ren and others reported a new coordination polymer, Cu2(p-SC>4)(p-
bpy)2*H2bdc, which displays a three-dimensional framework containing three-
coordinate copper centers.31 The copper centers reduced to an oxidation state of 1 +
16


during synthesis. This structure is also interesting because the 4,4-bipyrdine ligands
act as struts with the sulfate bridging two copper atoms. 1,4-benzenedicarboxylic
acid is sandwiched between two such setups and is hydrogen bonding with the free
oxygen on the sulfate. This compound shows photoluminescent properties and has
two emission bands; one corresponding to the n-n* transition of
benzenedicarboxylate, the other is attributed to the metal-to-ligand charge transfer
from Cu to bipyridine. Xaio and others synthesized a new zinc framework which
shows an interesting two-dimensional structure with Zn/bipyridne chains that are
bridged by 1,4-naphthlenedicarboxylate units.32 Thermogravametric analysis data
shows that water is lost by 200 C and final loss of ligands occur at 400 C,
displaying the stability of the framework.
In 2009, Zhang and others reported the systematic changes in temperature and
concentration to control the noninterpentrated form of the framework
[Cd(bpy)(bdc)]3DMFH20.33 The experiments were repeated at a higher
temperature which proved to cause the interpenetrated compound. Overall the
authors proved that changes in temperature have a higher influence on
interpenetration than changes in concentration, though the larger the concentration
the lower the temperature needs to be to cause interpenetration.
In 2010, Peng and others synthesized six new heterometallic frameworks of
lanthanide series metals with copper and silver.34 Systematic architecture variations
from one-dimensional to three-dimensional supramolecular frameworks were
17


attempted with oxalate and lH-benzimidazole-5-carboxylic acid ligands. The authors
then investigated thermal stability, it interactions, hydrogen bonding and the optical
properties of each of the structures. Ma and others described the synthesis and
crystal structure of five new frameworks based upon Zn and Cd. The structures
showed.37 The authors explored luminescent properties that were not based upon
metal-to-ligand or ligand-to metal charge transfer but were instead attributed to
deprotonated effect of the carboxylic acid and coordination interactions (Figure 2.7).
Hu and others successfully synthesized five new frameworks based upon zinc, cobalt
and cadmium that show the diversity of complexes that can be achieved based up on
the flexibility of the ligands the photochemical properties of the complexes and found
that compounds AD-AF and AH all showed emission that is similar to the free
ligands. Complex AG has an
intense 7t->Remission and d-d
transitions due to two different Co
environments.
Also in 2010, Zeng and
others discussed the successful
Wavelength |nm|
Figure 2.7: Luminescence spectroscopy of the five
compounds synthesized by Ma and others.35
synthesis of Zn3(oL-
lac)2(pybz)2*2.5DMF (AI) and
desolvation that opens the pores to activity (AI).37 The structure is built upon
18


{[Zn3(DL-lac]2+}n infinite pillars. The three zinc atoms are independent with evidence
of pseudosymmetry element through an inversion center on Zn2. Each formula unit
has 2.5 guest DMF molecules which were removed by soaking the crystals in
methanol which resulted in only a slight deformation of the framework. The
framework is stable up to 400 C based upon thermalgravimetric studies, which could
be ideal for frequent loading and unloading of guests. The adsorption of N2 was
tested at 77 K, followed by testing with I2 in a cyclohexane or benzene solution. The
I2 was shown to be easily removed with ethanol as a solvent under continuous stirring
at room temperature. Overall the I2 has shown donor-acceptor interaction that is
cooperative by anisotropic electrical conductivity (Figure 2.8).
Figure 2.8: Temporal evolution of UV/vis absorption spectra for the delivery of I2 from AId3I2.
Inset: fit curves of the controlled delivery of I2 ([I2] )Kt) in the first 1 h.37
Jiang and others prepared nonporous to microporous frameworks by controlled
interpenetration.10 The interpenetration was controlled by decreasing reactant
concentrations and reaction times. Three frameworks were formed, Cd(2-
19


NH2BDC)(bpy), Cd(2-NH2BDC)(bpy)-4H202.5DMF and Cd(2-
NH2BDC)(bpy)4.5H203DMF. The fundamental difference is the size of the pores
due to the amount of guest molecules and orientation of the ligands about the Cd(II)
atom. The third listed compound is not stable under air and will spontaneously turn
to the second compound upon the removal of the solvent molecules. These
frameworks show promising luminescent probe capabilities and as well as liquid
chromatography stationary phase uses. Xu and others are focused on creating new
frameworks that are flexible and exhibit breathing effects towards guest species.11
The authors report four new manganese species in which compound AL was
investigated for absorption and separation of aromatic compounds up to eight
carbons. Compounds AJ-AL show no pores with both x-ray diffraction and N2
absorption.
In 2011 Lan and others reported the synthesis of two new frameworks with
dinickel-dicarboxylate secondary building units connected by bipyridine derivative
spacers.4 The magnetic characterization observes antiferromagnetic coupling
between the Ni(II) ions in both compounds. This brief review of three-component
reactions leading to metal-organic frameworks all show novel and interesting
framework stabilities as well as magnetic and photoluminescent properties.
20


3. Experimental
3.1 Materials and Methods
All chemicals were obtained from commercial suppliers and were used without
further purification. Infrared spectroscopy was recorded neat on a Thermo Nicolet
Avatar 360 FT-IR from 4000 to 400 cm'1. Thermogravimetric analysis (TGA) was
performed on a TGA-Q50 under a flow of nitrogen gas at a rate of 5 C/min for the
MOFs and 20 C/min for the hydrogen-bonded networks.
Several crystals of each compound were indexed on a Bruker SMART CCD
diffractometer using 40 frames with an exposure time of 20 seconds per frame. One
crystal of each compound with good reflection quality was chosen for data collection.
The exposure time was 20 seconds for each frame. The reflections were collected in
the hemisphere of the reciprocal lattice of the triclinic cell to ensure enough
redundancy. An empirical absorption correction using the program SADABS was
applied to all observed reflections.38 The structure was solved with direct methods
using the SHELXTL program. Full matrix least-squares refinement on F was
->o
carried out using the SHELXTL program.
3.2 Synthesis of Metal-Organic Frameworks
Synthesis of [Zn3(bpy)(bpc)3] (1): A mixture of Zn(N03)2'6H20 (59.0 mg, 0.198
mmol), 4,4-bipyridine (31.0 mg, 0.198 mmol) and 4,4-biphenyldicarboxylic
21


acid (48.0 mg, 0.198 mmol) was placed in a Teflon lined autoclave with 5 mL of
N, N-dimethylformamide. The reaction vessel was sealed and then placed in a 150
C oven for 3 days. The oven was turned off and the autoclave was allowed to come
to room temperature overnight. The colorless block shaped crystals were removed
from the autoclave to a beaker where the mother liquor was removed by Pasteur
pipet. The crystals were allowed to dry overnight to give a final mass of 49.2 mg
(23.2 % from Zn2+). Main IR adsorption bands are (cm1): 1670.83 (s), 1593.19 (s),
1535.98 (m), 1384.79 (s), 1094.67 (m), 841.32 (m), 771.85 (s), 677.87 (m).
Synthesis of [Cu(bpy)i/2(bdc-N02)(H2C))] (2): A mixture of
Cu(N03)2-2.5H20 (46.8 mg, 0.201 mmol), 4,4-bipyridine (31.3 mg, 0.200 mmol), 2-
nitro-1,4-benzenedicarboxylic acid (42.3 mg, 0.175 mmol) were placed in a Teflon
lined autoclave with 5 mL of H2O. The reaction vessel was sealed then placed in a
150 C oven for 3 days. The oven was turned off and the autoclave was allowed to
come to room temperature overnight. The dark blue crystals were transferred to a
beaker and the mother liquor was removed with a Pasteur pipet. The crystals dried
overnight to give a final mass of 31.6 mg (42.5 % from Cu2+). Main IR adsorption
bands are (cm1): 3117.37(w), 1609.53 (s) 1519.64 (s), 1360.27 (s), 1070.15 (s),
808.63 (s), 767.76 (s), 718.73 (m), 645.18 (s).
Synthesis of [Ni(bpy)(pdp)] (3): A mixture of Ni(N03)2-6H20 (58.3 mg,
O. 200 mmol), 4,4-bipyridine (31.0 mg, 0.198 mmol), 1,4-phenylenedipropanoic acid
(44.5 mg, 0.200 mmol) were placed in a Teflon lined autoclave with 5 mL of H20.
22


The vessel was sealed and placed in a 160 C oven for 3 days. The oven was turned
off and the autoclave was allowed to cool to room temperature overnight. The light
green needle like crystals were transferred to a beaker and the mother liquor was
removed by Pasteur pipet. The crystals dried overnight to give a final mass of 46.8
mg (54 % by Ni2+). Main IR adsorption bands are (cm'1): 3056.07 (w), 1695.35 (s),
1601.36 (s), 1405.22 (s), 1315.32 (s), 1204.99 (s), 1066.06 (s), 1000.68 (s), 804.54
(s), 620.66 (s).
Synthesis of [Cu(bpy)i/2(cdc)] (4) and [Cu3(bpy)2(cdc)3] (5):
Cu(N03)22.5H20 (46.8 mg, 0.201 mmol), 4,4-bipyridine (30.9 mg, 0.198 mmol),
4,4-cyclohexanedicarboxylic acid (34.6 mg, 0.201 mmol) were placed in a Teflon
lined autoclave with 5 mL of H2O. The vessel was sealed and placed in a 160 C
oven for 3 days. The oven was turned off and the autoclave was allowed to cool to
room temperature overnight. The fine blue crystals were transferred to a beaker and
the mother liquor was removed by Pasteur pipet. The crystals dried overnight to give
a final mass of 25.2 mg. Main IR adsorption bands are (cm1): 3072.42 (w), 2933.48
(w), 2851.76 (w), 1621.79 (m), 1556.41 (s), 1388.88 (s), 1282.63 (m), 1221.34 (m),
1086.49 (m), 928.04 (w), 829.06 (s), 726.90 (m), 649.26 (m). The crystals were
actually a mixture of 4 and 5, as revealed by X-ray crystallography, and separation
was not possible.
23


3.3 Formation of Hydrogen-Bonded Organic Networks
Synthesis of [(3-aminobenzoate)(Hbpy+)] (6): Zn(N03)2-6H20 (59.6 mg, 0.200
mmol), 4,4-bipyridine (31.3 mg, 0.199 mmol), 2-amino-1,4 benzenedicarboxylic
acid (36.2 mg, 0.200 mmol) were added to a Teflon lined autoclave with 5 mL of
H20. The vessel was sealed and placed in a 150 C oven for 3 days. The oven was
turned off and the autoclave was allowed to cool to room temperature overnight. The
orange needle crystals were then transferred to a beaker and the mother liquor was
removed by Pasteur pipet. The crystals dried overnight to give a final mass of 30.1
mg (to 2-amino-1,4 benzenedicarboxylic acid 25.7 %). The main IR adsorption
bands are (cm'1): 3415.66 (w), 3293.08 (w), 3199.09 (w), 1689.09 (w), 1589.10 (s),
1405.22 (m), 1327.58 (m), 1258.12 (m), 1208.08 (m), 1066.06 (w), 992.51 (w),
804.54 (s), 751.42 (s), 616.57 (s).
Synthesis of [(H2bdc-NH2)(bpy)] (7): Zn(N03)2-6H20 (59.0 mg, 0.198
mmol), 4,4-bipyridine (31.3 mg, 0.200 mmol), 5-amino-1,3-benzenedicarboxylic
acid (36.2 mg, 0.200 mmol) were added to a Teflon lined autoclave with 5 mL of
H20. The vessel was sealed and placed in a 150 C oven for 3 days. The oven was
turned off and the autoclave was allowed to cool to room temperature overnight. The
orange needle like crystals were then transferred to a beaker and the mother liquor
was removed by Pasteur pipet. The crystals dried overnight to give a final mass of
30.9 mg (to 5-amino-1,3-benzenedicarboxylic acid 26.4 %). The main IR adsorption
bands are (cm1): 3456.53 (w), 3366.33 (w), 1691.26 (m), 1597.29 (m), 1401.14 (m),
24


1335.75 (m), 1262.20 (m), 1204.99 (m), 1057.89 (m), 996.59 (m), 800.45 (s), 759.59
(s), 624.74 (s).
Synthesis of [(H2cdc)(bpy)] (8): Zn(NC>3)2-6H2C) (59.1 mg, 0.199 mmol),
4,4-bipyridine (31.4 mg, 0.201 mmol), 1, 4-cyclohexanedicarboxylic acid (34.1 mg,
0.198 mmol) were added to a Teflon lined autoclave with 5 mL of H20. The vessel
was sealed and placed in a 160 C oven for 3 days. The oven was turned off and the
autoclave was allowed to cool to room temperature. The orange needle crystals were
then transferred from the autoclave to a beaker, the mother liquor was removed by
Pasteur pipet. The crystals dried overnight to give a final mass of 23.3 mg (to 1, 4-
cyclohexanedicarboxylic acid 35.9 %). The main IR adsorption bands are (cm1):
3051.99 (w), 2958.00 (w), 2929.40 (w), 1691.26 (m), 1597.28 (s), 1405.22 (s),
1254.23 (s), 1200.91 (s), 1074.23 (s), 996.59 (m), 902.61 (m), 808.63 (s), 747.63 (m),
620.66 (s).
25


4. Results and Discussion
4.1 Synthesis and Characterization by IR and TGA
The coordination compounds described by this work have been synthesized from
three-component solvothermal reactions of the form M(N03)i/bpy/H00C-C00H.
The crystalline MOFs are insoluble in water and common organic solvents. IR
spectroscopy was used to determine coordination of the carboxylate groups (COO),
which shows shifts in the C=0 stretching band from that of the carboxyl group
(COOH). No definitive evidence of coordination of bpy ligand can be determined by
IR because changes in the bipyridyl stretches are minimal.40 IR spectroscopy of 1
shows a small shift to lower wavenumbers of the C=0 stretch from 1690 cm'1 to 1671
cm'1 and a small shift to higher wavenumbers of the CO stretch form 1300 cm'1 to
1384 cm'1, from reported F^bpc, which is indicative of a bridging or a unidentate
carboxylate. Further evidence of coordination is supported by the fact that the
COOH stretch from 3300 cm'1 to 2400 cm'1 is not present.40
IR spectroscopy of 2 shows a significant shift to lower wavenumbers of the
C=0 stretch from 1710 cm'1 to 1610 cm'1 and a small shift to lower wavenumbers of
the CO stretch from 1367 cm'1 to 1360 cm'1, from reported ^bdc-NCF, which is
indicative of a bridging or a unidentate carboxylate. Further evidence of coordination
is supported by the fact that the COOH stretch from 3097 cm'1 to 2676 cm'1 is not
26


present, and is replaced by evidence of a coordinated water molecule.40 The
coordinated water molecule is supported by a weak, wide band from 3117 cm'1 to
2892 cm'1.40 TGA data of 2 shows a sharp loss of mass at 316 C that is attributed to
the loss of the coordinated water molecule as well as decomposition of bdc-NC>2
releasing two molecules of CO2 and NO2. Following this drop is slow decomposition
of the rest of the structure.
IR spectroscopy of 3 shows two shifts to lower wavenumbers of C=0
stretching from 1701 cm1 to 1695 cm'1 and 1601 cm'1 and a significant shift to
higher wavenumbers of CO stretching from 1224 cm'1 to 1315 cm1, from reported
H2PDP, which is indicative of bridging and chelating ligands. Further evidence of
coordination is supported by the fact that the COOH stretch from 3200 cm"1 to 2500
cm 1 is not present40 IR spectroscopy of the mixture of 4 and 5 shows two shifts to
lower wavenumbers of the C=0 stretch from 1695 cm'1 to 1622 cm'1 and 1556 cm1,
and a small shift to higher wavenumbers of CO from 1321 cm'1 to 1388 cm1, from
reported H2cdc, which is indicative of bridging and chelating ligands. Further
evidence supporting coordination is the fact that the COOH stretch from 2958 cm'1 to
2728 cm"1 is not present.40
The hydrogen-bonded organic networks 6-8 were isolated from the three-
component hydrothermal reactions that had been intended to synthesize MOFs, and it
is yet to be understood why these reactions form 6-8 rather than MOFs. The crystals
of 6-8 were all needle-like and red-brown in color. IR spectroscopy of 6 reveals
27


characteristic NH stretching at 3415.66 cm"1, 3293.08 cm'1 and 3199.09 cm"1. The
O-H and C=0 stretching bands in the carboxyl group (COOH) of H2bdc-NH2 are
both shifted to lower wavenumbers, indicating hydrogen bonding. IR spectroscopy
of 7 reveals two NH stretching bands at 3456.53 cm"1 and 3366.63 cm"1, which is
shifted slightly to lower wavenumbers from what is reported in the literature,
indicating hydrogen bonding. The O-H and C=0 stretching bands in the carboxyl
group (COOH) are both shifted to lower wavenumbers, also indicating hydrogen
bonding. TGA data of 7 shows a slow stepwise decomposition from room
temperature to 600 C. The loss of CO2 and NH3 is observed at 254 C, followed by
another CO2 molecule at 371 C. The remaining network slowly decomposes up to
600 C. IR spectroscopy of 8 reveals sp and sp CH stretching followed by
evidence of extensive carboxylic acid hydrogen bonding. The carbonyl stretch has
shifted to 1597 cm"1 from 1695 cm"1 from un-coordinated H2cdc. TGA data shows
complete decomposition of the structure at 276 C.
4.2 Crystal Structures
4.2.1 Metal-Organic Frameworks
Single crystal X-ray analysis of 1 displayed an orthorhombic system of Pbcn. The
framework has two crystallographically independent Zn(II) atoms that are bridged by
three independent bpc ligands. Zn(II)l has a bpy cap, acting like a strut creating a
larger three-dimensional network. Figure 4.1 shows the ORTEP drawing of the basic
crystallographic unit displaying the two independent Zn(II) ions.
28


C44
Figure 4.1: ORTEP drawing displaying compound 1 basic crystallographic unit. Symmetry codes:
#1 = 0.5+x, 0.5+y, 0.5-z; #2 = 1-x, y, 0.5-z.
The two Zn(II) ions are separated by a distance of 3.5 A. The secondary
building unit of 1, shown in Figure 4.2, is made up of a ZnyOi2 unit with N caps.
Zn(II)2 center is six-coordinate octahedral geometry by six bridging O atoms (028,
028#1, 046, 046#1, 047, 047#2). Zn(ll)l is four coordinate tetrahedral geometry
with three bridging O atoms (048, 045, 029#1) with an axial N (N11). The overall
o o
ZnO bond lengths range from 1.9 2.1 A, and ZnN bond length of 2.1 A.
Figure 4.2: Secondary building unit of 1. Zn is turquoise, N is blue, O is red and C is grey.
Symmetry Code: #2 = 1-x, y, 0.5-z.
29


The infinite structure of 1 shows bpc linking subunits in the xy plane while bpy
linkers connect subunits in the z direction creating a three-dimensional MOF with
rectangular channels. The effective dimensions of the channels are estimated from
the Van der Waal contact surfaces of a space filling model (Figure A.l 1 in Appendix)
o o
to be 7.5 A from adjacent bpy units and 12.8 A from adjacent bdc units (Figure 4.3).
V, ,* ^ V jT C% L KXX'S
A f! A A v A A V i
/ t * i y-' -V > \ > V X
i *
i
Figure 4.3: Compound 1 square channel. Zn is turquoise, N is blue, O is red and C is grey, hydrogen
atoms are omitted for clarity.
The structure overall has two fold interpenetration from the same rectangular
unit. The bpy and the Zn3Oi2 secondary building unit run parallel to each other while
the bpc weaves through the channels creating the interpenetration (Figure 4.4).
30


Figure 4.4: Interpenetration of compound 1. Zn is turquoise, N is blue, O is red and C is grey,
hydrogen atoms omitted for clarity.
The structure grows infinitely to show hexagonal channels cross liked by
o
interpenetrated bpc moieties. The effective channel size is 4.6 A across the y-axis
o
and 6.2 A across the x-axis (Figure 4.5), as estimated from a space-filling model
(Figure A. 12 in Appendix).
Figure 4.5: Extended view of compound 1. Zn is turquoise, N is blue, O is red and C is grey,
hydrogen atoms omitted for clarity.
31


Single X-ray crystal of 2 revealed an orthorhombic system of Cmca. The
framework has one independent Cu(II) that is coordinated with one bdc-N02 anion,
half bpy and one water molecule. Figure 4.6 shows the ORTEP drawing of 2
displaying the independent Cu(II) ion.
Figure 4.6: ORTEP drawing of 2 displaying the basic crystallographic unit. Symmetry code: #1 = 1-
x, 1.5-y, -0.5+z.
Cu(II) displays a planar geometry in which one carboxylate oxygen from two
bdc-NC>2 molecules (01, 01#1) coordinate trans to each other. The other trans sites
are occupied by nitrogen from bpy (N1) and the oxygen from water (03w). CuO
bond lengths measure to 1.9 A for Cu(II)l01 and 1.9 A for Cu(II)l03w and
Cu(II)lN1 bond length measures to 2.0 A. The second uncoordinated carboxylate
oxygen atoms (02, 02#1) extend above the planar Cu(II) coordination sites. The
basic subunit expands along the x axis to form a one-dimensional ribbon of repeating
Cu(II) bdc-N02 moieties (Figure 4.7).
32




I"
tx 11
Figure 4.7: Linear ribbon of compound 2. Cu is turquoise, N is blue, O is red and C is grey.
Hydrogen atoms (excluding water) are omitted for clarity.
Separate ribbons are connected by bpy ligands to form a two-dimensional ladder
structure. The metal center is rotated approximately 90 every bdc-NC>2 molecule,
which changes the direction of the bpy linkers (Figure 4.8). The 90 rotation of the
metal centers causes the ladder structure to buckle into a wave formation in the xz
plane (Figure 4.9).
Figure 4.8: Compound 2 ladder structure showing bpy linkers in the yz plane. Cu is turquoise, N is
blue, O is red and C is grey. Ligands moving in and out of the plane and hydrogen atoms (excluding
water) are omitted for clarity.
33


*-
Figure 4.9: The wave formation in the ladder structure found in 2. Cu is turquoise, N is blue, O is red
and C is grey, hydrogen atoms are omitted for clarity.
The extended view of compound 2 shows that the two-dimensional waves are
packed by weak intermolecular forces (Figure 4.10).
Figure 4.10: Extended view compound 2 displaying the waves interacting through the y axis. Cu is
turquoise, N is blue, O is red and C is grey. Hydrogen atoms omitted for clarity.
Single X-ray crystal analysis of compound 3 displayed a triclinic system of
PL The framework consists of one crystallographically independent Ni(II) ion which
34


is coordinated by one chelating pdp carboxylate and two bridging oxygens from pdp
carboxylate (02, 03, 024, 032). Figure 4.11 displays the ORTEP drawing of 3.
Figure 4.11: ORTEP of 3 drawing displaying the basic crystal structure.
The coordinating oxygen atom are in equatorial positions with bpy nitrogen (N4, N5)
in axial positions. The NiO bond lengths were found to be between 1.9 2.3 A and
the NiN bond lengths were found to be 2.1 A for N4 and N5. The bond angles for
the chelating pdp ligands are 120 for 02-C6-03.
The secondary building unit of 3, made up of Ni2C>8, shows that 032 (Figure
4.11) acts as both a bridge between the two Ni(II) centers and a chelator with 033.
The distance between the two Ni(II) ions is 3.8 A. The angle for the Ni(II)032
Ni(II) bridge is 133, and the carboxylate bridge 024C31023 has an angle of
126. Figure 4.12 displays the secondary building unit of 3 with N in axial positions
on each Ni(II) ion.
35


Figure 4.12: Secondary building unit of 3. Ni is turquoise, N is blue, O is red and C is grey.
The Ni2C>8 secondary building unit expands into a one-dimensional helix due to the
flexibility of the pdp ligand (Figure 4.13).
Figure 4.13: One-dimensional helix of compound 3. Ni is turquoise, N is blue, O is red and C is
grey. Hydrogen atoms and bpy ligands are omitted for clarity.
The two-dimensional layer of 3 expands from bpy linkers through the xz
plane infinitely connecting the secondary building units (Figure 4.14).
36


Figure 4.14: Two-dimensional layer of 3 displaying secondary building unit connectivity. Ni is
turquoise, N is blue, O is red and C is grey. Hydrogen atoms are omitted for clarity.
The extended view of 3 shows that the two-dimensional layers are packed by weak
intermolecular forces (Figure 4.15).
(b)
*- '

K
_ > > V *
' 4
* \ N ; /
< ^
^ ...' - -m
Figure 4.15: Expanded view of compound 3. Ni is turquoise, N is blue, O is red and C is grey.
Hydrogen atoms are omitted for clarity, (a) displays how units line up across the y-axis, (b) displays
the view through the xz-plane.
Single X-ray crystal analysis of 4 displayed a triclinic system of PI. The
framework consist of two crystallographically independent Cu(II) ions that are
bridged by four carboxylate groups from cdc (Ol, 02, 07#8, 08#8, 081, 082,
091#8, 092#8). The C^Og secondary building unit is then capped by nitrogen from


two bpy ligands (N115 and N116). Figure 4.16 displays the ORTEP drawing of the
two independent Cu(II) ions.
C3
Figure 4.16: ORTEP drawing of 4 displaying the two independent Cu(II) ions. Symmetry code: #8
= -1+x, y, z.
The coordinating oxygen atoms are equatorial with nitrogen in the axial positions.
Each independent Cu(II) ion displays a distorted octahedral geometry with a Cu(II)
Cu(II) bond distance of 2.6 A. The Cu(II)O bond distance measures to 2.0 A and
the Cu(II)N bond distance is 2.2 A for N115 and N116.
Compound 4 shows diamond shaped channels grown from the connections of
the cdc ligands between the secondary building units that expand through the xy
plane. The bpy linkers connect C^Og subunits through the z axis (Figure 4.17).
38


(a)
(b)
a A
v y y
s

Figure 4.17: Infinite structure of 4. Cu is turquoise, N is blue, O is red and C is grey. Hydrogen
atoms are omitted for clarity, (a) shows the diamond shaped channels (bpy omitted for clarity), (b)
displays the bpy linkers.
The overall structure has two-fold interpenetration of the same unit. The
CU2O8 subunit runs parallel to the bpy units through the z axis (Figure 4.18).
Figure 4.18: Interpenetration of compound 4. Cu is turquoise, N is blue, O is red and C is grey.
Hydrogen atoms are omitted for clarity, (a) shows the interpenetration through diamond shaped pores,
(b) displays the parallel nature of the bpy linkers and the Cu208 subunit.
Expansion of the framework reveals rectangular channels whose effective dimensions
are estimated from the Van der Waal contact surfaces of a space filling model (Figure
A. 13 in Appendix) to be 4.4 A across the adjacent bpy units and 2.5 A across the
39


adjacent cdc units (Figure 4.19). Though the diamond channel is obscured by the
interpenetration, the rectangular channel opens up into the xy plane.
Figure 4.19: Expansion of compound 4. Cu is turquoise, N is blue, O is red and C is grey. Hydrogen
atoms are omitted for clarity.
Single X-ray crystal analysis of 5 displayed a triclinic system of PI. The
framework consists of three crystallographically independent Cu(II) ions that are
bridged by four carboxylate groups from cdc (067, 068, Ol 13, Ol 14, 0238, 0239,
0240, 0241). The terminating Cu(II) ions each have a chelating carboxylate group
(066#4, 0112#4, 0176, 0177), as well as extending bpy linkers that expand through
the z axis and the y axis(N4, N138, N242, N243). Figure 4.20 displays the ORTEP
drawing of the basic crystallographic unit of 5.
40


C118
Figure 4.20: ORTEP drawing of 5 displaying the basic crystallographic unit. Symmetry code: #4 =
-1+x, y, z.
The coordinating oxygen atoms are in both axial and equatorial positions with
each Cu(II) ion displaying an overall distorted trigional bipyramidal geometry. The
coordinating nitrogen atoms are in axial positions of the terminating Cu(II) ions. The
Cu(II)O bond length measures between 1.9 2.5 A. The Cu(II)N bond length
measures to 2.0 A. The two chelating carboxylate groups have an angle of 120 for
Ol 12#4C246#4066#4 and 125 for 0176Cl840177. 0239 acts as both a
bridge and chelator with 0238 creating Cu2350239Cul73 bond angle of 78,
the carboxylate bridge from Cu235 to Cul73 has an 0240C2500241 bond angle
of 126. The distance between Cu234 and Cu235 and Cu235 and Cul73 measures to
3.3 A.
The framework increases infinitely through the x-axis with repeating CU3O12
units connected by chelating cdc moieties creating a one-dimensional ribbon (Figure
4.21).
41


Figure 4.21: One-dimensional ribbon of 5. Cu is turquoise, N is blue, O is red and C is grey.
Hydrogen atoms are omitted for clarity.
Expanding the framework through the y and z-axis reveals a three-dimensional
structure with cdc and bpy linkers (Figure 4.22).
Figure 4.22: Compound 5 expanded into the y and z-axis. Cu is turquoise, N is blue, O is red and C
is grey. Hydrogen atoms are omitted for clarity.
The linkers line up parallel to each other revealing rectangular channels where the
space between cdc moieties along the x-axis is 5.2 A and the seperation between cdc
and bpy moieties along the z-axis is 9.3 A (Figure 4.23). These are effective
distances estimated from a Van der Waal space filling model (Figure A. 14 in
Appendix).
42


Figure 4.23: Display of the channels through the y-axis of 5. Cu is turquoise, N is blue, O is red and
C is grey. Hydrogen atoms are omitted for clarity.
The structure overall has two-fold interpenetration of the same three-
dimensional MOF. The ribbon structure runs parallel to each other through the x-axis
while the bpy and cdc linkers grow through the channels in the y and z axis (Figure
4.24). The interpenetration completely obscures the channels and no pore or channel
opens up upon further expansion.
Figure 4.24: The two-fold interpenetration of 5. Cu is turquoise, N is blue, O is red and C is grey.
Hydrogen atoms are omitted for clarity.
43


4.2.2 Hydrogen-Bonded Organic Networks
Single X-ray crystal analysis of 6 reveals a triclinic system of PI. The basic subunit
suggests an ionic pair of Hbpy+ and [3-amino-benzoate] The ionic pair can be
considered a secondary building unit with an intramolecular hydrogen bond (Figure
4.25).
Figure 4.25: Secondary Building Unit of 6. N is blue, O is red, C is grey, and H is white.
The secondary building unit of compound 6 is then interlaced into a two-dimensional
network by two equivalent hydrogen bonds (Figure 4.26).
r1
9
Figure 4.26: Basic crystallographic unit of 6. N is blue, O is red, C is grey, and H is white.
44


Hbpy+ stacks in the x direction with the ionic nitrogen alternating direction through
the z axis. 3-amino-benzoate stacks along the yz plane alternating direction through
the x axis. Expansion reveals that the two-dimensional networks stack along the x-
axis by weak intermolecular forces (Figure 4.27).
Figure 4.27: Expansion of 6 displaying the tight stacking. N is blue, O is red, C is grey, and H is
white.
Single X-ray crystal analysis of 7 reveals an orthorhombic system of Pbca.
The basic subunit shows an extended two-dimensional hydrogen-bonded network
that expands into the yz plane via hydrogen bonds between the H21,3bdc-NH3 and
bpy subunits. There are four groups of equivalent hydrogen bonds which are
displayed in Figure 4.28.
45


Figure 4.28: Hydrogen-bonded network of 7. N is blue, O is red, C is grey, and H is white.
Figure 4.29 shows that the hydrogen bonds between the two H2l,3-bdc-NH2
molecules are not in the same plane.
Figure 4.29: The non-planar hydrogen bonds of 7. N is blue, O is red, C is grey, and H is white.
Expanding the network shows that the overall three-dimensional structure is held
together by intermolecular forces (Figure 4.30).
46


X
Figure 4.30: Expansion of 7 showing the condensed stacking. N is blue, O is red, C is grey, and H is
white.
Single X-ray crystal analysis of 8 revealed a triclinic system of PI. The basic
subunit shows a one-dimensional linear hydrogen-bonded network between H2cdc
and bpy, with a hydrogen bond distance of 1.7 A. Figure 4.31 shows the basic
hydrogen-bonded subunit of 8.
Figure 4.31: Basic unit of network 8. N is blue, O is red, C is grey, and H is white.
47


Expanding the structure reveals that linear subunits stack through the xy plane as well
as the yz plane. Figure 4.32 displays the crystal packing diagram showing the one-
dimensional chains packed together by weak intermolecular forces.
48


5. Conclusions
This work has led to the successful synthesis and characterization of five MOFs,
[Zn3(bpy)(bpc)3] (1), [Cu(bpy)1/2(bdc-N02)(H20)] (2), [Ni(bpy)(pdp)] (3),
[Cu(bpy)i/2(cdc)J (4) and [Cu3(bpy>2(cdc)3] (5), via three-component reactions. It
has also resulted in the formation and characterization of three hydrogen-bonded
networks: [(3-aminobenzoate')2(Hbpy+)2] (6), [(H2bdc-NH2)(bpy)] (7) and
[(H2cdc)(bpy)] (8). These compounds have been characterized by a combination of
IR, TGA (for 2, 7 and 8) and X-ray crystallography. Compounds 1, 4, and 5 show
three-dimensional interpenetrated coordination networks, while 2 and 3 are two-
dimensional MOFs arising from infinite metal-carboxylate ribbons cross-linked via
the bpy ligands. Compounds 6 and 7 display two-dimensional interweaving
hydrogen-bonded networks, while 8 displays a one-dimensional hydrogen-bonded
ribbon.
Further investigation could be made internally or in collaboration with
external groups. It could involve exploring more flexible derivatives of bipyridine as
ligands, considering that only flexible dicarboxylic acids have been utilized in this
work. In addition, adjusting reaction conditions could prevent framework
interpenetration in 1, 4 and 5, which could lead to more porous MOFs. Furthermore,
with multiple paramagnetic metal centers in a secondary building unit, MOFs 5 could
be tested for possible magnetic coupling properties.
49


APPENDIX
Appendix A. IR Spectra, TGA Data, and
Space-Filling Models
Figure A.l: IRofl
Figure A.2: IR of 2
50


ire A.4: IR of 4 and 5
jure A.3: IR of 3




%Transmttance


120
Figure A.8: TGA data for 2
Temperature (*C)
Figure A.9: TGA data for 7
54


55


Hydrogen atoms were omitted from the space-filling models for 4 and 5 due to the
disorder problems
Figure A.ll: Space filling model of compound 1 with unit cell. Zn is turquoise, N is blue, O is red
and C is grey, hydrogen is white.
Figure A.12: Expanded space filling model of compound 1 with unit cell. Zn is turquoise, N is blue,
O is red and C is grey, hydrogen is white.
56


Figure A.13: Expanded space filling model of compound 4 with unit cell. Cu is turquoise, N is blue,
O is red and C is grey.
Figure A.13: Expanded space filling model of compound 5 with unit cell. Cu is turquoise, N is blue,
O is red and C is grey.
57


Appendix B. Crystallographic Information Files
B.l Compound 1
data_xw30a
_audit_creation_method
_chemical_name_systematic
t
7
/
_chemical_name_common
_chemical_melting_point
_chemical_formula_moiety
_chemical_formula_sum
'C52 H32 N2 012 Zn3'
_chemical_formula_weight
SHELXL-9 7
7
7
7
1072.91
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
orthorhombic
' P b c n'
loop_
_at om_t ype_s ymbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
'C' 'C' 0.0033 0.0016
'International Tables Vol C Tables
'N' 'N' 0.0061 0.0033
'International Tables Vol C Tables
'O' 'O' 0.0106 0.0060
'International Tables Vol C Tables
'Zn' 'Zn' 0.2839 1.4301
'International Tables Vol C Tables 4.2
'H' 'H' 0.0000 0.0000
'International Tables Vol C Tables
_symmetry_cell_setting
_symmetry_space_group_name_H-M
loop_
_s ymmet r y_equ i v_po s_a s_xy z
'x, y, z'
'-x+1/2, -y+1/2, z+1/2'
'x+1/2, -y+1/2, -z'
'-x, y, -z+1/2'
'-x, -y, -z'
'x-1/2, y-1/2, -z-1/2'
'-x-1/2, y-1/2, z
58


'x, -y, z-1/2'
_cell_length_a
_cell_length_b
_cell_length_c
_cell_angle_alpha
_cell_angle_beta
_cell_angle_ganuna
_cell_volume
_cell_formula_units_Z
_cell_measurement_temperature
_cell_measurement_reflns_used
_cell_measurement_theta_min
_cell_measurement_theta_max
_exptl_crystal_description
_exptl_crystal_colour
_exptX_crystal_size_max
_exptl_crystal_size_mid
_exptl_crystal_size_min
_exptl_crystal_density_meas
_exptl_crystal_density_diffrn
_exptl_crystal_density_method
_exptl_crystal_F_000
_exptl_absorpt_coefficient_mu
_exptl_absorpt_correction_type
_exptl_absorpt_correction_T_min
_exptl_absorpt_correction_T_max
_exptl_absorpt_process_details
_exptl_special_details
.diffrn_ambient_temperature
_diffrn_radiation_wavelength
.diffrn_radiation_type
.diffrn_radiation_source
.diffrn_radiation_monochromator
.diffrn_measurement_device_type
.diffrn_measurement_method
diffrn_detector_area_resol_mean
.diffrn_standards_number
diffrn_standards_interval_count
diffrn_standards_interval_time
,diffrn_standards_decay_%
.diffrn_reflns_number
.diffrn_reflns_av_R_equivalents
14.5443(11)
24.9938(19)
18.1214(14)
90.00
90.00
90.00
6587.4(9)
4
293(2)
342
-14
14
fragment
colorless
0.10
0.08
0.08
j
1.082
'not measured'
2176
1.131
multi-scan
0.2049
0.2644
'SADABS (Sheldrick, 2000) '
293(2)
0.71073
MoK\a
'fine-focus sealed tube'
graphite
'Bruker SMART CCD PLATFORM'
'\w scans'
0
0
0
0
0
47436
0.0545
59


_diffrn_reflns_av_sigmal/netl
_diffrn_reflns_limit_h_min
_d i f f rn_re f1n s_limi t_h_max
_diffrn_reflns_limit_k_min
_diffrn_reflns_limi t_k_ma x
_d iffrn_reflns_limi t_l_mi n
_d i f f r n_r eflns_limi t_l_ma x
_diffrn_reflns_theta_min
_diffrn_reflns_theta_max
_r e f 1 n s_n umbe r _t o t a 1
_reflns_number_gt
_reflns_threshold_expression
_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_publication_material
0.0306
-17
17
-29
29
-21
21
1.62
25.00
5817
5305
>2sigma(I)
'SMART (Bruker, 1999)'
'SMART and SAINT (Bruker, 1999)'
'SAINT (Bruker, 1999)'
'SIR97 (Altomare et al., 1999)'
'SHELXTL (Sheldrick, 1997)'
'SHELXTL (Sheldrick, 1997)'
'SHELXTL (Sheldrick, 1997)'
_publ_section_references
;Altomare, A., Burla, M.C., Camalli, M.,
Cascarano, G.L., Giacovazzo, C.,
Guagliardi, A., Moliterni, A.G.G.,
Polidori, G. & Spagna, R. (1999) .
J. Appl. Cryst. 32, 115-119.
Bruker (1999) SMART and SAINT. Data Collection
and Reduction Software
for the SMART System. Bruker Analytical X-ray
Instruments Inc., Madison, Wisconsin, USA.
Flack, H. D. (1983). Acta Cryst. A39, 876-881.
Sheldrick, G.M. (2000). SADABS. Program for
Empirical Absorption Correction of Area Detector
Data. University of G\"ottingen, Germany.
Sheldrick, G.M. (1997). SHELXTL. Version 5.1.
Bruker Analytical X-Ray Systems, Madison,
Wisconsin, USA.
.refine_special_details
Refinement of FA2A against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on FA2A, conventional R-factors R are based
on F, with F set to zero for negative FA2A. The threshold expression of
60


FA2A > 2sigma(FA2A) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on FA2A are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.
_refine_ls_structure_factor_coef Fsqd
_refine_ls_matrix_type full
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
'calc w=l/[\sA2A(FoA2A)+(0.2000P)A2A+O.OOOOP] where P=(FoA2A+2FcA2A)/3'
_atom_sites_solution_primary direct
_atom_sites_solution_secondary difmap
_atom_sites_solution_hydrogens geom
_refine_ls_hydrogen_treatment constr
_refine_ls_extinction_method SHELXL
_refine_ls_extinction_coef 0.110(12)
_refine_ls_extinction_expression
1FcA *A=kFc[l+0.001xFcA2A\lA3A/sin(2\q)]A-1/4A'
_refine_ls_number_refIns 5817
_refine_ls_number_parameters 313
_refine_ls_number_restraints 0
_refine_ls_R_factor_all 0.2089
_refine_ls_R_factor_gt 0.2015
_refine_ls_wR_factor_ref 0.4880
_refine_ls_wR_factor_gt 0.4837
_refine_ls_goodness_of_fit_ref 2.205
_refine_ls_restrained_S_all 2.205
_refine_ls_shift/su_max 0.553
_refine_ls_shift/su_mean 0.105
loop_
_at om_s ite_label
_atom_site_type_symbol
_a t om_s i t e_fr act_x
_atom_site_fract_y
_atom_site_fract_z
_a t om_s i t e_U_i s o_o r_e qu i v
_atom_site_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_at om_s i t e_re f i nement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
Znl Zn 0.53516(9) 0.64808(4) 0.44268(6) 0.0486(7) Uani lid...
Zn2 Zn 0.5000 0.64918(6) 0.2500 0.0452(7) Uani 1 2 d S .
Nil N 0.5252(9) 0.6481(3) 0.5586(5) 0.064(3) Uani lid...
C12 C 0.5490(9) 0.6904(5) 0.5957(6) 0.069(3) Uani lid...
61


H12 H 0.5730 0.7197 0.5706 0.083 Uiso 1 1 calc R .
C13 C 0.5399(12) 0.6929(6) 0.6701(8) 0.095(5) Uani lid.
H13 H 0.5578 0.7237 0.6949 0.114 Uiso 1 1 calc R .
C14 C 0.5037(9) 0.6494(4) 0.7105(7) 0.059(3) Uani lid.
C15 C 0.4839(10) 0.6034(5) 0.6697(7) 0.076(4) Uani lid.
H15 H 0.4659 0.5719 0.6930 0.091 Uiso 1 1 calc R .
C16 C 0.4919(8) 0.6060(5) 0.5917(5) 0.059(3) Uani lid.
H16 H 0.4730 0.5769 0.5635 0.071 Uiso 1 1 calc R .
C21 C 0.2244(7) 0.6555(5) 0.1774(7) 0.064(3) Uani lid.
C22 C 0.2100(10) 0.6557(10) 0.2543(8) 0.161(12) Uani lid
H22 H 0.2601 0.6559 0.2862 0.194 Uiso 1 1 calc R .
C23 C 0.1234(9) 0.6555(7) 0.2820(10) 0.115(7) Uani lid.
H23 H 0.1152 0.6539 0.3328 0.138 Uiso 1 1 calc R .
C24 C 0.0439(9) 0.6577(5) 0.2349(7) 0.068(3) Uani lid.
C25 C 0.0624(9) 0.6627(7) 0.1603(8) 0.087(4) Uani lid.
H25 H 0.0135 0.6683 0.1282 0.104 Uiso 1 1 calc R .
C26 C 0.1502(11) 0.6599(8) 0.1312(7) 0.108(6) Uani lid.
H26 H 0.1589 0.6609 0.0804 0.129 Uiso 1 1 calc R .
C27 C 0.3203(9) 0.6499(5) 0.1463(7) 0.069(3) Uani lid.
028 0 0.3836(7) 0.6432(8) 0.1865(9) 0.198(10) Uani lid.
029 0 0.3309(7) 0.6508(4) 0.0793(6) 0.091(3) Uani lid.
C31 C 0.3451(9) 0.4951(5) 0.4334(6) 0.069(3) Uani lid.
H31 H 0.3621 0.5099 0.4785 0.083 Uiso 1 1 calc R .
C32 C 0.2979(10) 0.4491(4) 0.4326(7) 0.072(3) Uani lid.
H32 H 0.2929 0.4296 0.4761 0.086 Uiso 1 1 calc R .
C33 C 0.2554(10) 0.4292(5) 0.3681(6) 0.077(4) Uani lid.
C34 C 0.2075(9) 0.3789(5) 0.3621(6) 0.069(3) Uani lid.
C35 C 0.171(2) 0.3580(9) 0.4229(8) 0.210(17) Uani lid.
H35 H 0.1824 0.3755 0.4672 0.252 Uiso 1 1 calc R .
C36 C 0.1154(14) 0.3113(6) 0.4260(7) 0.110(6) Uani lid.
H36 H 0.0858 0.3011 0.4692 0.132 Uiso 1 1 calc R .
C37 C 0.1078(9) 0.2831(5) 0.3649(7) 0.075(3) Uani lid.
C38 C 0.173(2) 0.2936(10) 0.3083(14) 0.235(18) Uani lid
H38 H 0.1812 0.2695 0.2697 0.282 Uiso 1 1 calc R .
C39 C 0.2223(14) 0.3384(9) 0.3114(13) 0.134(8) Uani lid
H39 H 0.2697 0.3427 0.2775 0.161 Uiso 1 1 calc R .
C40 C 0.2873(9) 0.4529(5) 0.2968(6) 0.076(4) Uani lid.
H40 H 0.2729 0.4377 0.2514 0.092 Uiso 1 1 calc R .
C41 C 0.3446(10) 0.5034(5) 0.3034(7) 0.084(4) Uani lid.
H41 H 0.3620 0.5215 0.2608 0.101 Uiso 1 1 calc R .
C42 C 0.3701(7) 0.5222(4) 0.3672(5) 0.053(2) Uani lid.
C43 C 0.4282(10) 0.5699(6) 0.3675(7) 0.084(4) Uani lid.
C44 C 0.0595(11) 0.2292(5) 0.3680(7) 0.078(4) Uani lid.
045 O 0.4659(6) 0.5830(3) 0.4285(4) 0.066(2) Uani lid.
046 0 0.4446(16) 0.5934(8) 0.3131(8) 0.246(13) Uani lid
047 0 0.072(2) 0.1955(7) 0.3194(9) 0.289(16) Uani lid.
048 0 0.0294(6) 0.2156(3) 0.4261(5) 0.070(2) Uani lid.
loop_
62


_a t om_s i t e_a niso_label
_atom_sit e_a n i s o_U_l1
_at om_s i t e_a n i s o_U_2 2
_at om_s i t e_a n i s o_U_3 3
_atom_site_aniso_U_23
_a t om_s i t e_a n i s o_U_l 3
_atom_sit e_a n i s o_U_l2
Znl 0.0499(10) 0.0517(10) 0.0442(9) -0.0002(5) 0.0039(5) -0.0019(4)
Zn2 0.0495(13) 0.0445(11) 0.0415(11) 0.000 0.0015(7) 0.000
Nil 0.096(9) 0.063(7) 0.032(5) -0.002(4) 0.006(4) 0.006(5)
C12 0.103(10) 0.062(7) 0.041(6) -0.006(5) 0.002(6) -0.031(6)
C13 0.157(15) 0.070(9) 0.058(8) 0.005(7) 0.004(8) -0.020(9)
C14 0.058(7) 0.076(8) 0.044(6) -0.003(5) 0.001(5) 0.003(5)
C15 0.119(11) 0.047(7) 0.062(7) 0.018(6) 0.012(7) 0.010(6)
C16 0.080(8) 0.065(7) 0.033(5) -0.001(5) 0.016(5) -0.016(6)
C21 0.027(5) 0.095(8) 0.070(7) -0.011(6) 0.000(5) -0.010(5)
C22 0.048(8) 0.38(4) 0.056(9) 0.064(13) -0.005(6) -0.030(12)
C23 0.044(7) 0.23(2) 0.075(9) -0.036(10) -0.004(7) -0.005(9)
C24 0.076(8) 0.077(8) 0.050(7) -0.005(5) -0.001(5) -0.007(6)
C25 0.042(6) 0.131(12) 0.088(10) -0.007(8) -0.019(7) 0.029(7)
C26 0.081(10) 0.205(18) 0.037(6) -0.013(8) 0.012(6) -0.006(10)
C27 0.048(7) 0.084(9) 0.073(9) 0.015(6) 0.004(6) 0.018(5)
028 0.033(5) 0.44(3) 0.118(11) -0.006(12) 0.013(7) 0.026(9)
029 0.050(5) 0.149(9) 0.076(6) -0.013(5) 0.022(5) 0.030(5)
C31 0.082(8) 0.078(8) 0.048(6) 0.008(5) 0.003(5) -0.028(6)
C32 0.096(9) 0.051(6) 0.068(7) 0.013(5) 0.009(6) 0.002(6)
C33 0.108(10) 0.079(8) 0.044(6) -0.012(6) -0.019(6) -0.023(7)
C34 0.084(8) 0.068(7) 0.056(6) -0.009(5) -0.002(6) -0.030(6)
C35 0.36(4) 0.23(2) 0.044(7) -0.041(10) 0.045(13) -0.26(3)
C36 0.203(18) 0.083(9) 0.045(6) -0.011(6) 0.011(8) -0.074(11)
C37 0.068(7) 0.083(8) 0.073(7) -0.005(6) 0.006(6) -0.022(7)
C38 0.37(4) 0.19(2) 0.15(2) -0.067(18) 0.12(3) -0.18(3)
C39 0.103(14) 0.166(18) 0.133(16) -0.008(14) 0.071(13) -0.040(13)
C40 0.109(10) 0.065(7) 0.055(7) 0.016(5) -0.009(6) -0.026(7)
C41 0.100(10) 0.082(8) 0.070(8) 0.023(7) -0.005(7) -0.045(7)
C42 0.051(6) 0.063(6) 0.046(5) 0.000(5) 0.010(4) -0.007(5)
C43 0.083(9) 0.103(10) 0.064(7) 0.014(7) 0.006(7) -0.026(8)
C44 0.108(10) 0.062(7) 0.065(7) -0.017(6) 0.028(7) -0.022(7)
045 0.098(6) 0.067(5) 0.033(4) 0.002(3) -0.011(3) -0.024(4)
046 0.39(3) 0.246(19) 0.099(9) 0.077(12) -0.063(14) -0.26(2)
047 0.54(4) 0.191(16) 0.133(11) -0.097(12) 0.188(19) -0.22(2)
048 0.080(6) 0.061(5) 0.068(5) -0.006(4) -0.018(4) -0.018(4)
_geom_special_details
All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
63


used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
loop_
_geom_bond_atom_site_label_l
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_s ite_symmetry_2
_geom_bond_publ_flag
Znl 045 1.930(8) ?
Znl 048 1.955(8) 7_665 ?
Znl 029 1.989(9) 4_655 ?
Znl Nil 2.106(8) 7
Zn2 046 1.974(11) 4_655
Zn2 046 1.974(11) 7
Zn2 028 2.054(14) 4_655
Zn2 028 2.054(14) 7
Zn2 047 2.007(19) 6_666
Zn2 047 2.007(19) 7_665
Nil C16 1.304(14) 7
Nil C12 1.300(13) 7
C12 C13 1.355(17) 7
C13 C14 1.412(17) 7
C14 C15 1.398(17) 7
C14 C14 1.43(2) 4 _656 ?
C15 C16 1.420(15) 7
C21 C26 1.37(2) . 7
C21 C22 1.41(2) . 7
C21 C27 1.511(17) 7
C22 C23 1.36(2) . 7
C23 C24 1.438(19) 7
C24 C24 1.39(3) 4 7
C24 C25 1.384(19) 7
C25 C26 1.38(2) . 7
C27 028 1.185(18) 7
C27 029 1.223(16) 7
029 Znl 1.989(9) 4_655 ?
C31 C32 1.339(16) 7
C31 C42 1.424(15) 7
C32 C33 1.413(16) 7
C33 C34 1.441(17) 7
C33 C40 1.495(16) 7
C34 C35 1.333 (18) 7
C34 C39 1.38(2) . 7
C35 C36 1.418(18) 7
C36 C37 1.317(17) 7
C37 C38 1.42(2) . 7
C37 C44 1.522(17) 7
64


C38 C39 1.33(2) ?
C40 C41 1.519(15) ?
C41 C42 1.301(16) ?
C42 C43 1.460(17) ?
C43 046 1.173(16) ?
C43 045 1.277(14) ?
C44 048 1.189(13) ?
C44 047 1.232(18) ?
047 Zn2 2.007(19) 6_556 ?
048 Znl 1.955(8) 7_655 ?
loop_
_geom_angle_atom_site_label_l
_ge om_a ngle_atom_site_label_2
_ge om_a ngle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_l
_ge om_a ng 1 e_s i t e_s ymme t r y_3
_geom_angle_publ_flag
045 Znl 048 117 -2(4) . 7_665 7
045 Znl 029 120 .9(4) . 4_655 7
048 Znl 029 114 2(4) 7 ' 6 6 5 4 _655 ?
045 Znl Nil 95. 6(3) . 7
048 Znl Nil 96. 9(4) 7_ .665 . 7
029 Znl Nil 105 .5(5) 4 :_655 . 7
046 Zn2 046 90. 2(15) 4 _655 . 7
046 Zn2 028 86. 4(7) 4_ 655 4_ 655 ?
046 Zn2 028 87. 7(7) . 4_655 7
046 Zn2 028 87. 7(7) 4_ 655 . 7
046 Zn2 028 86. 4(7) . 7
028 Zn2 028 171 .6(11) 4_655 7
046 Zn2 047 80. 3(12) 4 _655 6 _666 ?
046 Zn2 047 169 .7(10) . 6_666 ?
028 Zn2 04 7 87. 8(7) 4_ .655 6_ .666 ?
028 Zn2 047 97. 1(7) . 6_666 7
046 Zn2 047 169 .7(10) 4_655 7_665
046 Zn2 047 80. 3(12) . 7_665 7
028 Zn2 047 97. 1(7) 4_ .655 7_ .665 ?
028 Zn2 047 87. 8(7) . 7_665 7
047 Zn2 047 109 .5(16) 6_666 7_665
C16 Nil C12 121 .1(9) . 7
C16 Nil Znl 119 .0(7) . 7
C12 Nil Znl 119 .8(8) . 7
Nil C12 C13 121 .7(11) ?
C12 C13 Cl 4 121 .1(12) ?
C13 C14 C15 115 .8(12) ?
C13 C14 C14 123 .0(9) . 4_656 7
C15 C14 C14 120 .8(8) . 4_656 7
Cl 4 C15 C16 118 .2(11) ?
65


Nil C16 C15 121.7(10) ?
C26 C21 C22 119.2(12) ?
C26 C21 C27 120.4(12) ?
C22 C21 C27 120.4(12) ?
C23 C22 C21 120.2(13) ?
C22 C23 C24 121.8(15) ?
C24 C24 C25 124.3(15) 4 ?
C24 C24 C23 120.3(15) 4 ?
C25 C24 C23 115.3(12) ?
C26 C25 C24 123.1(13) ?
C21 C26 C25 119.9(12) ?
028 C27 029 120.9(13) ?
028 C27 C21 120.0(13) ?
029 C27 C21 119.0(12) ?
C27 028 Zn2 167.0(16) ?
C27 029 Znl 108.8(9) . 4_655
C32 C31 C42 122.0(11) ?
C31 C32 C33 122.4(11) ?
C32 C33 C34 125.6(11) ?
C32 C33 C40 116.1(11) ?
C34 C33 C40 115.4(9) ?
C35 C34 C39 108.8(14) ?
C35 C34 C33 118.3(10) ?
C39 C34 C33 127.9(13) ?
C34 C35 C36 125.7(12) ?
C37 C36 C35 117.0(12) ?
C36 C37 C38 116.9(15) ?
C36 C37 C44 118.8(11) ?
C38 C37 C44 119.9(14) ?
C39 C38 C37 118.9(19) ?
C38 C39 C34 124.1(17) ?
C33 C40 C41 115.5(10) ?
C42 C41 C40 121.8(10) ?
C41 C42 C31 120.3(10) ?
C41 C42 C43 117.5(10) ?
C31 C42 C43 122.2(10) ?
046 C43 045 120.7(13) ?
046 C43 C42 121.6(13) ?
045 C43 C42 117.4(11) ?
048 C44 047 119.7(13) ?
048 C44 C37 117.0(11) ?
047 C44 C37 120.5(13) ?
C43 045 Znl 123.8(8) ?
C43 046 Zn2 157.5(12) ?
C44 047 Zn2 140(2) . 6_556 ?
C44 048 Znl 123.9(8) . 7_655
.diffrn_measured_fraction_theta_max 1.000
diffrn_reflns_theta_full 25.00
66


1.000
_diffrn_measured_fraction_theta_full
_refine_diff_density_max 4.044
_refine_diff_density_min -1.168
_refine_diff_density_rms 0.606
B.2 Compound 6
data_pl
_audit_creation_method
_chemical_name_systematic
SHELXL-9 7
5
_chemical_name_common ?
_chemical_melting_point ?
_chemical_formula_moiety ?
_chemi cal_formula_s um
'C34 H30 N6 04'
_chemical_formula_weight 586.64
loop_
_at om_t ype_s ymbo1
_atom_type_description
_atom_type_scat_dispersion_real
_atom_t ype_s cat_di spers ion_imag
_atom_type_scat_source
'C' 'C' 0.0033 0.0016
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'H' 'H' 0.0000 0.0000
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'N' 'N' 0.0061 0.0033
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'O' 'O' 0.0106 0.0060
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
_symmetry_cell_setting ?
_syiranetry_space_group_name_H-M ?
loop_
_symmetry_equiv_pos_as_xyz
cell_angle_alpha
cell_length_a
,cell_length_b
,cell_length_c
8.2524(17)
10.004(2)
10.004(2)
116.40(3)
67


_cell_angle_beta 90.12(3)
_cell_angle_gamma 90.12(3)
_cell_volume 739.8(3)
_cell_formula_units_Z 1
_cell_measurement_temperature 293 (2)
_cell_measurement_reflns_used ?
_cell_measureinent_theta_min ?
_cell_measurement_theta_max ?
_exptl_crystal_description
_exptl_crystal_colour
_exptl_crystal_size_max
_exptl_crystal_size_mid
_exptl_crystal_size_min
_exptl_crystal_density_meas
_exptl_crystal_density_diffrn
_exptl_crystal_density_method
_exptl_crystal_F_000
_exptl_absorpt_coefficient_mu
_exptl_absorpt_correction_type
_exptl_absorpt_correct ion_T_min
_exptl_absorpt_correction_T_max
_exptl_absorpt_process_details
?
7
7
7
7
7
1.317
'not measured'
308
0.089
7
7
7
p
exptl_special_details
5
_diffrn_ambient_temperature
_diffrn_radiation_wavelength
_diffrn_radiation_type
_diffrn_radiation_source
_diffrn_radiation_monochromator
_diffrn_measurement_device_type
_diffrn_measurement_method
_diffrn_detector_area_resol_mean
_diffrn_standards_number
_diffrn_standards_interval_count
_d i f f r n_s t andar ds_i nt er va l_t ime
_diffrn_standards_decay_%
_diffrn_reflns_number
_diffrn_reflns_av_R_equivalents
_diffrn_reflns_av_sigmal/netl
_diffrn_reflns_limit_h_min
_diffrn_reflns_limi t_h_ma x
_diffrn_reflns_limit_k_min
_diffrn_reflns_limit_k_max
_diffrn_reflns_limit_l_min
173(2)
0.71073
MoK\a
'fine-focus sealed tube'
graphite
7
7
7
7
7
7
7
1820
0.0000
0.0522
-3
9
-11
11
-11
68


_diffrn_reflns_limit_l_max
_diffrn_reflns_theta_min
_diffrn_reflns_theta_max
_reflns_number_total
_reflns_number_gt
_reflns_threshold_expression
_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_ref inement
_computing_molecular_graphics
_computing_publication_material
10
2.27
25.05
1820
966
>2sigma(I)
7
7
7
'SHELXS-97 (Sheldrick, 1990)'
'SHELXL-97 (Sheldrick, 1997)
7
_refine_special_details
Refinement of FA2A against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on FA2A, conventional R-factors R are based
on F, with F set to zero for negative FA2A. The threshold expression of
FA2A > 2sigma(FA2A) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on FA2A are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.
.refine_ls_structure_factor_coef Fsqd
refine_ls_matrix_type full
.refine_ls_weighting_scheme calc
.refine_ls_weighting_details
'calc w=l/[\sA2A(FoA2A)+(0.089OP)A2A+0.9459P]
,atom_sites_solution_primary direct
,atom_sites_solution_secondary difmap
atom_sites_solution_hydrogens geom
refine_ls_hydrogen_treatment mixed
refine_ls_extinction_method none
.refine_ls_extinction_coef ?
.refine_ls_number_refIns 1820
refine_ls_number_parameters 201
.refine_ls_number_restraints 0
.refine_ls_R_factor_all 0.1707
.refine_ls_R_factor_gt 0.0939
.refine_ls_wR_factor_ref 0.2525
refine_ls_wR_factor_gt 0.2163
.refine_ls_goodness_of_fit_ref 1.088
refine_ls_restrained_S_all 1.088
refine_ls_shift/su_max 0.000
.refine_ls_shift/su_mean 0.000
where P=(Foa2a+2Fca2a)/3'
69


loop_
_at om_s i t e_labe1
_a t om_s i t e_t ype_symbol
_atom_site_fract_x
_at om_s ite_fract_y
_atom_site_fract_z
_at om_s i t e_U_i s o_o r_e qu i v
_atom_site_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_at om_s i t e_d i s order_gr oup
01 0 0.3397(9) 0.3596(10) 0.3291(7) 0.134(3) Uani lid..
02 0 0.1124(9) 0.2396(8) 0.2928(8) 0.095(2) Uani lid..
N1 N 0.4103(11) 0.6387(10) 0.8917(10) 0.109(3) Uani lid.
H1A H 0.3943 0.6780 0.9886 0.131 Uiso 1 1 calc R .
H1B H 0.5036 0.6520 0.8567 0.131 Uiso 1 1 calc R .
N2 N 0.6729(11) 0.2024(10) 0.7779(9) 0.101(3) Uani lid.
-0.1163(12) -0.0012(9) 0.103(3) Uani lid
N3 N 0.8071(10)
Cl C 0.2204(14)
C2 C 0.1836(13)
C3 C 0.0433(11)
H3B H -0.0396 0,
C4 C 0.0219(15)
H4A H -0.0786 0,
C5 C 0.1430(15)
0.3330(13) 0.3787(12) 0.082(3) Uani lid
0.4047(11) 0.5448(12) 0.080(3) Uani lid
0.3830(10) 0.5998(11) 0.080(3) Uani lid
3223 0.5352 0.096 Uiso 1 1 calc R .
0.4514(13) 0.7535(13) 0.100(4) Uani lid
4399 0.7934 0.120 Uiso 1 1 calc R .
0.5356(12) 0.8498(12) 0.090(3) Uani lid
H5A H 0.1264 0.5798 0.9547 0.108 Uiso
C6 C 0.2875(14) 0.5550(12) 0.7930(12)
C7 C 0.3095(12) 0.4877(11)
H7A H 0.4090 0.4990 0.5952
C8 C 0.6152(12) 0.2630(12)
H8A H 0.5597 0.3553 0.7444
C9 C 0.6292(11) 0.2024(11)
H9A H 0.5813 0.2518 0.4894
CIO C 0.7107(11
Cll C 0.7770(12
0.6368(11)
0.101 Uiso
0.6951(13)
0.124 Uiso
0.5416(12)
0.113 Uiso
0.0732(10) 0.4652(10) 0.074(3) Uani
0.0125(11) 0.5519(11) 0.093(3) Uani
1 1 calc R .
0.082(3) Uani
0.084(3)
1 1 calc
0.103(3)
1 1 calc
0.094(3)
1 1 calc
Uani
R .
Uani
R .
Uani
R .
lid
lid
HI1A H 0.8400 -0.0758 0.5069 0.111 Uiso 1 1 calc R .
C12 C 0.7523(14) 0.0794(12) 0.7041(12) 0.110(4) Uani
H12A H 0.7969 0.0317 0.7593 0.132 Uiso 1 1 calc R .
C13 C 0.7412(11) 0.0087(12) 0.3050(11) 0.080(3) Uani
C14 C 0.7418(16) 0.0878(11) 0.2235(11) 0.122(4) Uani
H14A H 0.7218 0.1920 0.2735 0.146 Uiso 1 1 calc R .
C15 C 0.7698(19) 0.0242(16) 0.0743(13) 0.150(6)
H15A H 0.7619 0.0843 0.0230 0.180 Uiso 1 1 calc
lid
Uani
R .
lid
C16 C 0.8010(14) -0.1976(12) 0.0728(13) 0.110(4) Uani lid
H16A H 0.8200 -0.3018 0.0195 0.132 Uiso 1 1 calc R .
C17 C 0.7685(13) -0.1394(14) 0.2224(12) 0.104(4) Uani lid
70


H17A H 0.7651 -0.2038 0.2692 0.125 Uiso 1 1 calc R .
H2A H 0.1719 0.1683 0.1513 0.22(6) Uiso 1 1 d R .
loop_
_atom_site_aniso_label
_atom_site_aniso_U_ll
_atom_site_aniso_U_22
_at om_s i t e_an i s o_U_3 3
_atom_site_aniso_U_23
_atom_site_anis o_U_l3
_atom_site_aniso_U_12
01 0. .108 (6) 0. .178 (8) 0 .076 (5) 0. .022 (6) 0. .024 (4) 0.029(5)
02 0. .109 (5) 0. .087 (6) 0 .078 (6) 0. .026 (5) 0. .006 (4) 1 0.007(4)
N1 0. ,110 (6) 0. .125 (8) 0 .076 (7) 0. .029 (7) 0. .012 (5) 0 .001 (6)
N2 0. .140 (8) 0. .088 (7) 0 .059 (6) 0. .019 (6) 0. .016 (5) 0 .017 (6)
N3 0. .123 (7) 0. .104 (8) 0 .075 (7) 0. .032 (7) 0. .028 (5) 0 .029 (6)
Cl 0. .078 (7) 0. .083 (9) 0 .080 (9) 0. .031 (8) 0. .020 (6) 0 .008 (6)
C2 0. .089 (7) 0. .080 (8) 0 .086 (8) 0. .050 (7) 0. .029 (7) 0 .030 (6)
C3 0. .081 (6) 0. .065 (7) 0 .094 (9) 0. .034 (7) 0. .008 (6) 0 .012 (5)
C4 0. .126 (9) 0. .103 (10) I 0.081(10) 0.049 (! 3) 0.048(1 3) 0.040(8
C5 0. .132 (9) 0, .070 (8) 0 .058 (8) 0. .020 (8) 0. .014 (7) 0 .022 (7)
C6 0. .105 (8) 0. .076 (8) 0 .075 (8) 0. .043 (8) 0. .038 (7) 0 .039 (6)
C7 0. .075 (6) 0. .107 (9) 0 .084 (8) 0. .056 (8) 0. .029 (6) 0 .027 (6)
C8 0. .121 (8) 0. .092 (9) 0 .064 (8) 0. ,005 (8) 0. ,029 (6) 0 .021 (7)
C9 0. .095 (7) 0. ,089 (8) 0 .096 (9) 0. .039 (7) 0. ,012 (6) 0 .035 (6)
CIO 0.091(6) 0.074(7) 0.052(6) 0.024(6) 0.006(5) 0.009(5)
Cll 0.124(8) 0.074(7) 0.069(8) 0.023(7) 0.022(6) 0.029(6)
C12 0.169(11) 0.085(9) 0.077(9) 0.035(8) 0.027(7) 0.038(8)
C13 0.100(7) 0.059(8) 0.061(8) 0.010(8) 0.004(6) 0.003(6)
C14 0.222(13) 0.073(8) 0.064(8) 0.025(8) 0.019(8) 0.027(8)
C15 0.260(16) 0.116(12) 0.080(10) 0.050(10) 0.042(10) 0.071(12)
C16 0.143(9) 0.080(8) 0.101(10) 0.034(8) 0.013(7) 0.036(7)
C17 0.143(9) 0.101(11) 0.056(8) 0.023(8) 0.024(6) 0.017(8)
_geom_special_detai1s
t
All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
loop_
_geom_bond_atom_site_label_l
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_s i t e_s ymmet ry_2
71


_geom_bond_publ_flag
01 Cl 1. 185(10) ?
02 Cl 1. 299(11) ?
02 H2A 1 .3636 ?
N1 C6 1. 400(12) ?
N1 H1A 0 .8800 ?
N1 H1B 0 .8800 ?
N2 C12 1 .299(11) ?
N2 C8 1. 314(12) ?
N3 C15 1 .303(12) ?
N3 C16 1 .322(11) ?
Cl C2 1. 520(12) ?
C2 C3 1. 341(12) ?
C2 C7 1. 389(13) ?
C3 C4 1. 389(12) ?
C3 H3B 0 .9500 ?
C4 C5 1. 381(13) ?
C4 H4A 0 .9500 ?
C5 C6 1. 372(13) ?
C5 H5A 0 .9500 ?
C6 C7 1. 413(12) ?
C7 H7A 0 .9500 ?
o 00 C9 1. 383(12) ?
C8 H8A 0 .9500 ?
C9 CIO 1 .355(11) ?
C9 H9A 0 .9500 ?
CIO Cll 1.375(11) ?
CIO C13 1.460(12) ?
Cll C12 1.379(12) ?
Cll H11A 0.9500 ?
C12 H12A 0.9500 ?
C13 C17 1.357(12) ?
C13 C14 1.365(11) ?
C14 C15 1.358(12) ?
C14 H14A 0.9500 ?
C15 H15A 0.9500 ?
C16 C17 1.371(12) ?
C16 H16A 0.9500 ?
C17 H17A 0.9500 ?
loop_
_geom_angle_atom_site_label_l
_ge om_a ng1e_atom_s ite_label_2
_ge om_ang1e_atom_s ite_label_3
_geom_angle
_georn_angle_site_symmetry_l
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
Cl 02 H2A 109.2 . ?
72


C6 N1 H1A 120.0 . ?
C6 N1 H1B 120.0 . ?
H1A N1 H1B 120.0 . 9
C12 N2 C8 114.3(9) 9
C15 N3 C16 116.1(9) .
01 Cl 02 121.3(10) 9
01 Cl C2 122.8(12) 9
02 Cl C2 115.8(10) ?
C3 C2 Cl 122.0(10) ?
C3 C2 Cl 122.7(12) ?
Cl C2 Cl 115.1(10) 9
C2 C3 C4 118.5(10) 9
C2 C3 H3B 120.8 . 9
C4 C3 H3B 120.8 . 9
C5 C4 C3 121.7(11) 9
C5 C4 H4A 119.1 . 9
C3 C4 H4A 119.1 . 9
C6 C5 C4 119.5(11) 9
C6 C5 H5A 120.2 . 9
C4 C5 H5A 120.2 . 9
C5 C6 N1 119.1(10) 9
C5 C6 Cl 119.2(12) 9
N1 C6 Cl 121.8(10) 9
C2 Cl C6 119.0(10) . . 9
C2 Cl H7A 120.5 . 9
C6 Cl H7A 120.5 . 9
N2 C8 C9 124.8(9) . ?
N2 C8 H8A 117.6 . 9
C9 C8 H8A 117.6 . 9
CIO C9 C8 120.5(9) . ?
CIO C9 H9A 119.7 . ?
C8 C9 H9A 119.7 . ?
C9 CIO Cll 114.9(8) . ?
C9 CIO C13 123.5(9) . ?
Cll CIO C13 121.3(8) . . ?
CIO Cll C12 120.2(8) . . ?
CIO Cll HI1A 119.9 . . ?
C12 Cll HI1A 119.9 . . ?
N2 C12 Cll 125.2(9) . ?
N2 C12 H12A 117.4 . ?
Cll C12 H12A 117.4 . ?
Cl7 C13 Cl4 113.7(9) . . ?
C17 C13 CIO 121.9(9) . . ?
Cl4 C13 CIO 124.4(10) . . ?
C15 C14 C13 123.0(10) . . ?
C15 C14 H14A 118.5 . . ?
C13 C14 H14A 118.5 . . ?
N3 C15 C14 122.4(10) . ?
N3 C15 H15A 118.8 . ?
73


C14 C15 H15A 118.8 . ?
N3 C16 Cl7 123.4(10) . ?
N3 C16 H16A 118.3 . ?
Cl7 C16 H16A 118.3 . ?
C13 C17 C16 121.1(10) . ?
C13 C17 H17A 119.4 . ?
C16 C17 H17A 119.4 . ?
loop_
_geom_torsion_atom_site_label_l
_ge om_t o r s i o n_a t om_s ite_label_2
_geom_t or s ion_a t om_s i t e_label_3
_geom_t or s i on_at om_s i t e_labe 1_4
_geom_torsion
_geom_t orsion_site_s ymme t r y_l
_geom_t orsion_site_symmetry_2
_ge om_t orsion_site_s ymme t r y_3
_geom_torsion_site_symmetry_4
_geom_tor s ion_publ_flag
01 Cl C2 C3 174.9(9) . 9
02 Cl C2 C3 -5.1(12) . 9
01 Cl C2 Cl -8.7(13) . 9
02 Cl C2 Cl 171.3(8) . 9
C7 C2 C3 C4 2.8(13) . 9
Cl C2 C3 C4 178.9(8) . 9
C2 C3 C4 C5 -2.4(14) . 9
C3 C4 C5 C6 1.2(15) . 9
C4 C5 C6 N1 -179.0(9) . 9
C4 C5 C6 Cl -0.3(13) . 9
C3 C2 C7 C6 -1.9(13) . 9
Cl C2 C7 C6 -178.3(7) . 9
C5 C6 C7 C2 0.6(12) . 9
N1 C6 C7 C2 179.3(8) . 9
C12 N2 C8 C9 2.4 (16) . .
N2 C8 C9 CIO -1.8(17) .
C8 C9 CIO Cll -0.9(15) .
C8 C9 CIO C13 -175.1(9) .
C9 CIO Cll C12 2.8(15) .
C13 CIO Cll C12 177.1(10)
C8 N2 C12 Cll -0.3(17) .
CIO Cll C12 N2 -2.3(19) .
C9 CIO C13 Cl7 -155.9(11)
Cll CIO C13 C17 30.2(15) .
C9 CIO C13 C14 22.6(17) .
Cll CIO C13 C14 -151.2(11)
C17 C13 C14 C15 -1.0(19) .
CIO C13 C14 C15 -179.6(12)
C16 N3 C15 Cl4 6(2) . .
C13 C14 C15 N3 -4(2) . .
74


C15 N3 C16 C17 -4.3(18) . . ?
C14 C13 C17 C16 2.9(16) ... ?
CIO C13 C17 C16 -178.4(10) ... ?
N3 C16 C17 C13 -0.4(19) . . ?
loop_
_geom_hbo nd_at om_s i t e_labe1_D
_ge om_hbo nd_a t om_s i t e_labe1_H
_geom_hbo nd_at om_s i t e_labe1_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbo nd_s i t e_s yiranetr y_A
N1 H1A N2 0.88 2.17 3.044(12) 170.9 2_667
N1 H1B 01 0.88 2.23 3.030(11) 151.7 2_666
_diffrn_measured_fraction_theta_max
_diffrn_reflns_theta_full
_diffrn_measured_fraction_theta_full
_refine_diff_density_max 0.175
_refine_diff_density_min -0.172
_refine_diff_density_rms 0.039
0.697
25.05
0.697
B.3 Compound 7
data_xw29
_audit_creation_method SHELXL-97
_chemical_name_systematic
i
7
r
_chemical_name_common ?
_chemical_melting_point ?
_chemical_formula_moiety ?
_chemical_formula_sum
'C18 H15 N3 04'
_chemical_formula_weight 337.33
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C' 'C' 0.0033 0.0016
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
75


N' 'N' 0.0061 0.0033
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4
'O' 'O' 0.0106 0.0060
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4
'H' 'H' 0.0000 0.0000
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4
_symmetry_cell_setting Orthorhombic
_symmetry_space_group_name_H-M loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, -y, z+1/2' 'x+1/2, -y+1/2, -z' '-x, y+1/2, -z+1/2' '-x, -y, -z' 'x-1/2, y, -z-1/2' '-x-1/2, y-1/2, z' 'x, -y-1/2, z-1/2' ' P b c a'
_cell_length_a _cell_length_b _cell_length_c _cell_angle_alpha _cell_angle_beta _cell_angle_gamma 7.1743(8) 14.0233(15) 31.277(3) 90.00 90.00 90.00
_cell_volume _ce1l_formu1a_un i t s_Z _cell_measurement_temperature _cell_measurement_reflns_used 3146.7(6) 8 293(2) 470
_cell_measurement_theta_min -14
_cell_measurement_theta_max 14
_exptl_crystal_description column
_exptl_crystal_colour _exptl_crystal_siz e_ma x orange 0.80
_exptl_crystal_size_mid _exptl_crystal_size_min 0.50 0.20
_exptl_crystal_density_meas
_exptl_crystal_density_diffrn 1.424
_exptl_crystal_density_method _exptl_crystal_F_000 _exptl_absorpt_coefficient_mu 'not measured' 1408 0.103
_expt l_absorpt_corr ect ion_t ype _exptl_absorpt_correction_T_min _exptl_absorpt_correction_T_max _exptl_absorpt_process_details multi-scan 0.1993 0.2643 'SADABS (Sheldrick, 2000)
76


_exptl_special_details
t
9
_diffrn_ambient_temperature
_diffrn_radiation_wavelength
_diffrn_radiation_type
_diffrn_radiation_source
_diffrn_radiation_monochromator
_diffrn_measurement_device_type
_diffrn_measurement_method
_diffrn_detector_area_resol_mean
_diffrn_standards_number
_diffrn_standards_interval_count
_diffrn_standards_interval_time
_diffrn_standards_decay_%
_diffrn_reflns_number
_diffrn_reflns_av_R_equivalents
_diffrn_reflns_av_sigmal/netl
_diffrn_reflns_limit_h_min
_diffrn_reflns_limit_h_max
_diffrn_reflns_limit_k_min
_diffrn_reflns_limit_k_max
_diffrn_reflns_limit_l_min
_diffrn_reflns_limit_l_max
_diffrn_reflns_theta_min
_diffrn_reflns_theta_max
_reflns_number_total
_reflns_number_gt
_reflns_threshold_expression
_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_publication_material
293(2)
0.71073
MoK\a
'fine-focus sealed tube'
graphite
'Bruker SMART CCD PLATFORM'
'\w scans'
7
?
7
7
7
21801
0.0384
0.0236
-8
8
-16
16
-37
36
2.60
25.00
2779
2599
>2sigma(I)
'SMART (Bruker, 1999)'
'SMART and SAINT (Bruker, 1999)
'SAINT (Bruker, 1999)'
'SIR97 (Altomare et al., 1999)'
'SHELXTL (Sheldrick, 1997)'
'SHELXTL (Sheldrick, 1997)'
'SHELXTL (Sheldrick, 1997)'
_publ_section_references
;Altomare, A., Burla, M.C., Camalli, M.,
Cascarano, G.L., Giacovazzo, C.,
Guagliardi, A., Moliterni, A.G.G.,
Polidori, G. & Spagna, R. (1999).
J. Appl. Cryst. 32, 115-119.
Bruker (1999). SMART and SAINT. Data Collection
and Reduction Software
77


for the SMART System. Bruker Analytical X-ray
Instruments Inc., Madison, Wisconsin, USA.
Flack, H. D. (1983). Acta Cryst. A39, 876-881.
Sheldrick, G.M. (2000). SADABS. Program for
Empirical Absorption Correction of Area Detector
Data. University of G\"ottingen, Germany.
Sheldrick, G.M. (1997). SHELXTL. Version 5.1.
Bruker Analytical X-Ray Systems, Madison,
Wisconsin, USA.
refine_special_details
Refinement of FA2A against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on FA2A, conventional R-factors R are based
on F, with F set to zero for negative FA2A. The threshold expression of
FA2A > 2sigma(FA2A) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on fa2a are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.
refine_ls_structure_factor_coef Fsqd
refine_ls_matrix_type full
refine_ls_weighting_scheme calc
refine_ls_weighting_details
'calc w=l/[\sA2A(FoA2A)+(0.0742P)A2A+2.1128P] where P=(FoA2A+2FcA2A)/3'
atom_sites_solution_primary direct
,atom_sites_solution_secondary difmap
,atom_sites_solution_hydrogens geom
.refine_ls_hydrogen_treatment mixed
refine_ls_extinction_method none
refine_ls_extinction_coef ?
refine_ls_number_refIns 2779
.refine_ls_number_parameters 232
.refine_ls_number_restraints 0
.refine_ls_R_factor_all 0.1041
.refine_ls_R_factor_gt 0.0964
.refine_ls_wR_factor_ref 0.2179
.refine_ls_wR_factor_gt 0.2131
.refine_ls_goodness_of_fit_ref 1.364
.refine_ls_restrained_S_all 1.364
.refine_ls_shift/su_max 0.000
.refine_ls_shift/su_mean 0.000
loop_
78


_a t om_s i t e_labe1
_atom_site_type_symbo1
_atom_site_fract_x
_atom_sit e_fract_y
_atom_site_fract_z
_at om_s i t e_U_i s o_o r_equ iv
_atom_s it e_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
Cll C 0.1421(5) -0.0071(2) 0.62741(10) 0.0492(8) Uani lid
C12 C 0.1339(5) 0.0433(2) 0.58937(10) 0.0548(9) Uani lid.
H12 H 0.1357 0.1110 0.5895 0.066 Uiso 1 1 calc R .
C13 C 0.1229(5) -0.0057(3) 0.55144(11) 0.0586(9) Uani lid
H13 H 0.1203 0.0301 0.5257 0.070 Uiso 1 1 calc R .
N14 N 0.1158(4) -0.1003(2) 0.54865(9) 0.0569(8) Uani lid.
C15 C 0.1252(6) -0.1487(3) 0.58539(11) 0.0633(10) Uani lid
H15 H 0.1221 -0.2163 0.5843 0.076 Uiso 1 1 calc R .
C16 C 0.1393(6) -0.1055(2) 0.62461(11) 0.0594(9) Uani lid
H16 H 0.1472 -0.1431 0.6498 0.071 Uiso 1 1 calc R .
Cl7 C 0.1545(5) 0.0426 (2) 0.66931 (10) 0.0514(8) Uani lid.
C18 C 0.0923(6) -0.0007(3) 0.70658(11) 0.0660(11) Uani lid
H18 H 0.0410 -0.0631 0.7057 0.079 Uiso 1 1 calc R .
C19 C 0.1054(6) 0.0475(3) 0.74491(11) 0.0685(11) Uani lid
H19 H 0.0610 0.0168 0.7700 0.082 Uiso 1 1 calc R .
N20 N 0.1767(5) 0.1345(2) 0.74866(9) 0.0645(9) Uani lid.
C21 C 0.2338(6) 0.1764(3) 0.71307(11) 0.0689(11) Uani lid
H21 H 0.2833 0.2391 0.7149 0.083 Uiso 1 1 calc R .
C22 C 0.2250(6) 0.1338(3) 0.67339(11) 0.0671(11) Uani lid
H22 H 0.2675 0.1672 0.6488 0.081 Uiso 1 1 calc R .
C31 C 0.1072(5) 0.6578(2) 0.43886(9) 0.0476(8) Uani lid.
C32 C 0.1365(5) 0.7055(2) 0.40052(9) 0.0490(8) Uani lid.
H32 H 0.1420 0.7732 0.3999 0.059 Uiso 1 1 calc R .
C33 C 0.1577(5) 0.6534(2) 0.36315(9) 0.0473(8) Uani lid.
C34 C 0.1440(5) 0.5550(2) 0.36429(10) 0.0509(8) Uani lid.
H34 H 0.1569 0.5199 0.3385 0.061 Uiso 1 1 calc R .
C35 C 0.1119(5) 0.5061(2) 0.40222(9) 0.0492(8) Uani lid.
C36 C 0.0953(5) 0.5594(2) 0.43964(10) 0.0501(8) Uani lid.
H36 H 0.0754 0.5277 0.4661 0.060 Uiso 1 1 calc R .
C311 C 0.0930(5) 0.7111(2) 0.48002(10) 0.0519(8) Uani lid
0311 O 0.0776(5) 0.67221(18) 0.51423(7) 0.0798(9) Uani lid
0312 0 0.1022(4) 0.80377(17) 0.47573(7) 0.0697(8) Uani lid
H312 H 0.099(7) 0.836(3) 0.5041(15) 0.105 Uiso lid. .
C331 C 0.1996(6) 0.7000(2) 0.32124(10) 0.0580(9) Uani lid
0331 0 0.2567(5) 0.78897(18) 0.32429(7) 0.0741(9) Uani lid
H331 H 0.282(7) 0.810(3) 0.2965(15) 0.111 Uiso lid. .
79


0332 0 0.1860(6) 0.65932(19) 0.28766(8) 0.0980(12) Uani lid...
N351 N 0.0935(5) 0.4084(2) 0.40275(9) 0.0664(9) Uani lid. .
H35A H 0.1021 0.3758 0.3788 0.080 Uiso 1 1 calc R .
H35B H 0.0732 0.3785 0.4271 0.080 Uiso 1 1 calc R .
loop_
_at om_s i t e_a niso_label
_atom_site_aniso_U_ll
_at om_s i t e_a n i s o_U_2 2
_at om_s i te_an i so_U_3 3
_atom_s it e_ani s o_U_2 3
_a t om_s i t e_an i s o_U_l3
_atom_site_aniso_U_12
Cll 0.054(2)
C12 0.071(2)
C13 0.075(3)
N14 0.066(2)
C15 0.088(3)
C16 0.086(3)
C17 0.063(2)
C18 0.095(3)
C19 0.097(3)
N20 0.093(2)
C21 0.104(3)
C22 0.101(3)
C31 0.053(2)
C32 0.059(2)
C33 0.058(2)
C34 0.063(2)
C35 0.058(2)
C36 0.062(2)
C311 0.065(2)
0311 0.139(3)
0312 0.121(2)
C331 0.084(3)
0331 0.125(3)
0332 0.193(4)
N351 0.106(3)
0.0499(19)
0.0470(19)
0.059(2) 0
0.0568(18)
0.048(2) 0
0.0473(19)
0.051(2) 0
0.055(2) 0
0.064(2) 0
0.0564(18)
0.054(2) 0
0.054(2) 0
0.0521(19)
0.0443(17)
0.0459(18)
0.0495(19)
0.0478(18)
0.0509(19)
0.051(2)
0.0616(16
0.0474(15
0.049(2)
0.0565(16
0.0604(17
0.0441(16
0.0434(17) -0.0027(14) -0.0002(14) -0.0001(15)
0.0463(18) -0.0032(15) -0.0080(17) 0.0019(17)
.0417(17) -0.0050(16) -0.0085(17) 0.0026(19)
0.0474(16) -0.0097(14) -0.0021(13) 0.0001(15)
.054(2) -0.0103(16) 0.0050(19) -0.0036(19)
0.0446(18) 0.0012(15) 0.0016(17) -0.0009(18)
.0401(17) -0.0020(14) -0.0013(15) 0.0020(16)
.0483(19) -0.0050(16) -0.0012(19) -0.009(2)
.0436(19) 0.0017(17) 0.0016(19) -0.005(2)
0.0447(15) -0.0070(14) -0.0035(15) -0.0014(17)
.048(2) -0.0051(16) -0.002(2) -0.009(2)
.0468(19) -0.0017(16) -0.001(2) -0.011(2)
0.0375(16) 0.0014(14) 0.0038(14) -0.0011(15)
0.0036(15) -0.0007(15)
0.0438(17) 0.0016(14
0.0379(16)
0.0399(17)
0.0020(13) 0.0031(14)
-0.0037(14) 0.0027(15)
0.0414(17) 0.0021(14)
0.0380(17) 0.0069(14)
0.0003(15)
0.0023(16)
0.0018(15) 0.0059(16)
0.0044(15) 0.0030(16)
0.0401(17) 0.0021(15) 0.0044(15) -0.0022(17)
) 0.0394(13) 0.0021(11) 0.0147(15) -0.0058(17)
) 0.0403(13) -0.0035(10) 0.0016(13) 0.0038(14)
0.0410(18) 0.0030(15) 0.0050(17) -0.0001(19)
) 0.0405(13) 0.0054(11) 0.0083(15) -0.0206(16)
) 0.0408(14) -0.0031(12) 0.0101(18) -0.018(2)
) 0.0487(16) 0.0021(13) 0.0075(16) 0.0030(17)
,geom_special_details
All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
80


loop_
_geom_bond_atom_site_label_l
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Cll C16 1.382(5) . 7
Cll C12 1.385(5) . 7
Cll C17 1.487(4) . 7
C12 C13 1.373(4) . 7
C12 H12 0.9500 ?
C13 N14 1.330(4) . 7
C13 H13 0.9500 ?
N14 C15 1.336(4) . 7
C15 C16 1.372(5) . 7
C15 H15 0.9500 ?
C16 H16 0.9500 ?
C17 C22 1.381(5) . 7
C17 C18 1.388(5) . 7
C18 C19 1.379(5) . 7
C18 H18 0.9500 ?
C19 N20 1.329(5) . 7
C19 H19 0.9500 ?
N20 C21 1.324(5) . 7
C21 C22 1.379(5) . 7
C21 H21 0.9500 ?
C22 H22 0.9500 ?
C31 C36 1.382(4) . 7
C31 C32 1.389(4) . 7
C31 C311 1.492(4) 7
C32 C33 1.387(4) . 7
C32 H32 0.9500 ?
C33 C34 1.384(4) . 7
C33 C331 1.495(4) 7
C34 C35 1.389(4) . 7
C34 H34 0.9500 ?
C35 N351 1.377(4) 7
C35 C36 1.394(4) . 7
C36 H36 0.9500 ?
C311 0311 1.206(4) 7
C311 0312 1.308(4) 7
0312 H312 1.00(5) 7
C331 0332 1.199(4) 7
C331 0331 1.317(4) 7
0331 H331 0.93(5) 7
N351 H35A 0.8800 . 7
N351 H35B 0.8800 . 7


_geom_angle_atom_site_label_l
_geom_a n g1e_atom_s ite_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_l
_geom_ang1e_site_symmetry_3
_geom_angle_publ_flag
C16 Cll C12 117.0(3) 7
C16 Cll C17 121.6(3) 7
C12 Cll Cl 7 121.3(3) 7
C13 C12 Cll 119.3(3) 7
C13 C12 H12 120.4 . 7
Cll C12 H12 120.4 . 7
N14 C13 C12 123.9(3) 7
N14 C13 H13 118.0 . 7
C12 C13 H13 118.0 . 7
C13 N14 C15 116.6(3) 7
N14 C15 C16 123.3(3) 7
N14 C15 H15 118.4 . 7
C16 C15 H15 118.4 . 7
C15 C16 Cll 119.9(3) 7
C15 C16 H16 120.1 . 7
Cll C16 H16 120.1 . 7
C22 C17 C18 116.4(3) 7
C22 C17 Cll 122.5(3) 7
C18 C17 Cll 121.1(3) 7
C19 C18 C17 119.6(3) 7
C19 C18 H18 120.2 . 7
Cl 7 C18 HI 8 120.2 . 7
N20 C19 C18 123.6 (3) 7
N20 C19 H19 118.2 . 7
C18 C19 H19 118.2 . 7
C21 N20 C19 116.9(3) 7
N20 C21 C22 123.4(4) . . 7
N20 C21 H21 118.3 . 7
C22 C21 H21 118.3 . 7
C21 C22 Cl 7 120.1(3) 7
C21 C22 H22 119.9 . 7
C17 C22 H22 119.9 . 7
C36 C31 C32 120.3(3) . 7
C36 C31 C311 118.7(3) .
C32 C31 C311 120.9(3) .
C33 C32 C31 119.4(3) . . 7
C33 C32 H32 120.3 . 7
C31 C32 H32 120.3 . 7
C34 C33 C32 119.7(3) 7
C34 C33 C331 118.2(3)
C32 C33 C331 122.0(3)
C33 C34 C35 121.7(3) 7
82


C33 C34 H34 119.2 . . ?
C35 C34 H34 119.2 . . ?
N351 C35 C34 121.1(3) . ?
N351 C35 C36 121.0(3) . ?
C34 C35 C36 117.8(3) . . ?
C31 C36 C35 121.0(3) . . ?
C31 C36 H36 119.5 . . ?
C35 C36 H36 119.5 . . ?
0311 C311 0312 123.0(3) . ?
0311 C311 C31 123.0(3) . . ?
0312 C311 C31 113.9(3) . . ?
C311 0312 H312 111(3) . ?
0332 C331 0331 122.7(3) . ?
0332 C331 C33 122.9(3) . . ?
0331 C331 C33 114.4(3) . . ?
C331 0331 H331 107(3) . ?
C35 N351 H35A 120.0 . ?
C35 N351 H35B 120.0 . ?
H35A N351 H35B 120.0 . ?
loop_
_geom_hbond_atom_site_labe1_D
_geoin_hbo nd_a t om_s i t e_labe 1_H
_geom_hbo nd_atom_si t e_labe1_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbo nd_s i t e_s ynune t r y_A
0312 H312 N14 1.00(5) 1.66(5) 2.650(3) 172(4)
0331 H331 N20 0.93(5) 1.71(5) 2.641(4) 171(4)
N351 H35A 0331 0.88 2.33 3.159(4) 157.9 7_655
N351 H35B 0311 0.88 2.25 3.087(4) 159.5 5_566
.diffrn_measured_fraction_theta_max 0.999
diffrn_reflns_theta_full 25.00
.diffrn_measured_fraction_theta_full 0.999
.refine_diff_density_max 0.245
.refine_diff_density_min -0.177
.refine_diff_density_rms 0.049
B.4 Compound 2
data_x
_audit_creation_method SHELXL-97
_chemical_name_systematic
,_565
!_5 6 4
83


>
_chemical_name_common ?
_chemical_melting_point ?
_chemical_formula_moiety 'C13 H9 Cu N2 07'
_chemical_formula_sum
'C13 H9 Cu N2 07'
_chemical_formula_weight 368.76
loop_
_at om_t ype_s ymbo 1
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
'C' 'C' 0.0033 0.0016
'International Tables Vol C Tables
'H' 'H' 0.0000 0.0000
'International Tables Vol C Tables
'N' 'N' 0.0061 0.0033
'International Tables Vol C Tables
'O' 'O' 0.0106 0.0060
'International Tables Vol C Tables
'Cu' 'Cu' 0.3201 1.2651
'International Tables Vol C Tables
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
4.2.6.8 and 6.1.1.4'
.symmetry_cell_setting orthorhombic
symmetry_space_group_name_H-M 'C m c a'
,symmetry_space_group_name_Hall '-C 2bc 2'
loop_
_s ymme t r y_equ i v_po s_a s_x y z
'x, y, z'
'-x, -y+1/2, z+1/2'
'-x, y+1/2, -z+1/2'
'x, -y, -z
'x+1/2, y+1/2, z'
'-x+1/2, -y+1, z+1/2'
'-x+1/2, y+1, -z+1/2'
'x+1/2, -y+1/2, -z'
'-x, -y, -z'
'x, y-1/2, -z-1/2'
'x, -y-1/2, z-1/2'
'-x, y, z'
'-x+1/2, -y+1/2, -z
'x+1/2, y, -z-1/2'
'x+1/2, -y, z-1/2'
'-x+1/2, y+1/2, z'
84


_cell_length_a
_cell_length_b
_cell_length_c
_cell_angle_alpha
_cell_angle_beta
_c e1l_ang1e_gamma
_cell_volume
_ce1l_formu1a_un i t s_Z
_cell_measurement_temperature
_cell_measurement_reflns_used
_cell_measurement_theta_min
_cell_measurement_theta_max
21.6974(16)
16.7364(15)
7.4067(5)
90.00
90.00
90.00
2689.6(4)
8
293(2)
2353
2.4339
27.4701
_exptl_crystal_description
_exptl_crystal_colour
_exptl_crystal_size_max
_exptl_crystal_size_mid
_exptl_crystal_size_min
_exptl_crystal_density_meas
_exptl_crystal_density_diffrn
_exptl_crystal_density_method
_exptl_crystal_F_000
_exptl_absorpt_coefficient_mu
_exptl_absorpt_correction_type
_expt l_absorpt_corr ect ion_T_min
_exptl_absorpt_correction_T_max
_exptl_absorpt_process_details
sheet
blue
0.18
0.14
0.03
7
1.821
'not measured'
1488
1.666
'Multi-scan'
0.8961
1.0000
'CrystalClear (Rigaku/MSC Inc., 2005)'
,exptl_special_details
>
.diffrn_ambient_temperature
.diffrn_radiation_wavelength
diffrn_radiation_type
.diffrn_radiation_source
.diffrn_radiation_monochromator
.diffrn_measurement_device_type
.diffrn_measurement_method
diffrn_detector_area_resol_mean
.diffrn_standards_number
.diffrn_standards_interval_count
.diffrn_standards_interval_time
.diffrn_standards_decay_%
.diffrn_reflns_number
.diffrn_reflns_av_R_equivalents
.diffrn_reflns_av_sigmal/netl
293(2)
0.71073
MoK\a
'fine-focus sealed tube'
graphite
'Saturn724 (2x2 bin mode)'
'CCD_Profile_fitting'
7
7
7
7
7
9850
0.0497
0.0357
85


_diffrn_reflns_limit_h_min
_diffrn_reflns_limit_h_max
_diffrn_reflns_limit_k_min
_diffrn_ref lns_limit_k_max
_diffrn_reflns_limit_l_min
_diffrn_reflns_limit_l_max
_diffrn_reflns_theta_min
_diffrn_reflns_theta_max
_reflns_number_total
_reflns_number_gt
_reflns_threshold_expression
_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_publication_material
-28
28
-21
21
-9
9
2.43
27.47
1585
1381
>2sigma(I)
'CrystalClear (Rigaku Inc., 2005)'
'CrystalClear (Rigaku Inc., 2005)'
'CrystalClear (Rigaku Inc., 2005)'
'SHELXS-97 (Sheldrick, 1990)'
'SHELXL-97 (Sheldrick, 1997)'
y
_refine_special_details
I
Refinement of FA2A against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on FA2A, conventional R-factors R are based
on F, with F set to zero for negative FA2A. The threshold expression of
FA2A > 2sigma(FA2A) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on FA2A are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.
.refine_ls_structure_factor_coef Fsqd
.refine_ls_matrix_type full
.refine_ls_weighting_scheme calc
.refine_ls_weighting_details
'calc w=l/[\sA2A(FoA2A)+(0.0300P)A2A+10.0000P] where P=(FoA2A+2FcA2A)/3'
atom_sites_solution_primary direct
,atom_sites_solution_secondary difmap
.atom_sites_solution_hydrogens geom
.refine_ls_hydrogen_treatment constr
.refine_ls_extinction_method none
.refine_ls_extinction_coef ?
.refine_ls_number_refIns 1585
.refine_ls_number_parameters 152
.refine_ls_number_restraints 126
.refine_ls_R_factor_all 0.0589
.refine_ls_R_factor_gt 0.0485
refine_ls_wR_factor_ref 0.1014
.refine_ls_wR_factor_gt 0.0956
86


_refine_ls_goodness_of_fit_ref
_refine_ls_restrained_S_all
_refine_ls_shift/su_max
_refine_ls_shift/su_mean
1.073
1.041
0.000
0.000
loop_
_a t om_s ite_label
_atom_site_type_symbol
_a t om_s ite_fract_x
_a t om_s ite_fract_y
_atom_site_fract_z
_a t om_s i t e_U_i s o_o r_e qu i v
_atom_s i t e_adp_t ype
_atom_site_occupancy
_atom_site_symetry_multiplicity
_atom_site_ca1c_f1ag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
Cul Cu 0.5000 0.65038(3) 0.33321(8) 0.03593(19) Uani 1 2 d S . .
01 0 0.41086(9) 0.64640(15) 0.3135(3) 0.0474(6) Uani lid. . .
02 0 0.40150(11) 0.7727(2) 0.4014(4) 0.0688(9) Uani lid. . .
03 0 0.5000 0.7005(2) 0.0990(5) 0.0509(9) Uani 1 2 d S .
H3 H 0.5343 0.7050 0.0446 0.076 Uiso 1 1 d R . .
N1 N 0.5000 0.5963(2) 0.5744(5) 0.0353(9) Uani 1 2 d S .
Cl C 0.38052(14) 0.7101(3) 0.3413(4) 0.0431(9) Uani lid. . .
C2 C 0.31281(13) 0.7077(2) 0.2946(4) 0.0370(7) Uani lid. . .
C3 C 0.28107(13) 0.7784(2) 0.2733(5) 0.0383(8) Uani lid. . .
H3A H 0.3022 0.8282 0.2902 0.046 Uiso 1 1 d R .
C4 C 0.28099(16) 0.6377(2) 0.2725(6) 0.0542(10) Uani 1 1 d U .
H4A H 0.3021 0.5878 0.2880 0.065 Uiso 0.50 1 d PR A 1
N2 N 0.2997(8) 0.5539(11) 0.329(5) 0.070(6) Uani 0.310(13) 1 d PU 2
04 0 0.3181(6) 0.5446(9) 0.494(3) 0.084(5) Uani 0.310(13) 1 d PU 2
05 0 0.2984(7) 0.5035(10) 0.220(5) 0.110(7) Uani 0.310(13) 1 d PU . 2
N2B N 0.3052(13) 0.563(2) 0.222(7) 0.081(8) Uani 0.190(13) 1 d PU . 3
04B 0 0.3142(13) 0.523(2) 0.368(6) 0.086(10) Uani 0.190(13) 1 d PU 3
05B 0 0.3128(10) 0.5326(17) 0.071(5) 0.102(8) Uani 0.190(13) 1 d PU . 3
C5 C 0.44813(14) 0.5770(3) 0.6581(5) 0.0579(12) Uani lid. . .
H5A H 0.4109 0.5896 0.6025 0.069 Uiso 1 1 calc R .
C6 C 0.44649(16) 0.5393(3) 0.8225(5) 0.0629(13) Uani lid...
H6A H 0.4087 0.5270 0.8748 0.075 Uiso 1 1 calc R .
Cl C 0.5000 0.5197(3) 0.9108(6) 0.0362(10) Uani 1 2 d S .
atom_site_aniso_label
a t om_s i t e_a n i s o_U_l1
a t om_s i t e_a n i s o_U_2 2
.a t om_s i t e_a n i s o_U_3 3
a t om_s i t e_a n i s o_U_2 3
loop.
87


_a t om_s i t e_a n i s o_U_l3
_at om_s i t e_an i s o_U_l2
Cul 0.0133(2) 0.0521(3) 0.0424(3) 0.0171(3) 0.000 0.000
01 0.0154(10) 0.0698(16) 0.0570(16) 0.0283(13) -0.0009(10) 0.0020(11)
02 0.0272(12) 0.106(2) 0.073(2) -0.0285(18) -0.0147(13) -0.0053(14)
03 0.0174(14) 0.087(3) 0.048(2) 0.0257(19) 0.000 0.000
N1 0.0196(16) 0.047(2) 0.040(2) 0.0114(18) 0.000 0.000
Cl 0.0167(13) 0.082(3) 0.0308(17) 0.0087(17) -0.0018(13) -0.0024(16)
C2 0.0165(13) 0.063(2) 0.0312(17) 0.0021(15) -0.0023(12) -0.0004(14)
C3 0.0245(15) 0.0535(19) 0.0369(18) -0.0034(15) -0.0003(13) -0.0064(14)
C4 0.0325(18) 0.048(2) 0.082(3) 0.002(2) -0.0075(19) 0.0083(16)
N2 0.018(6) 0.049(8) 0.144(18) 0.016(12) -0.013(10) -0.004(6)
04 0.038(5) 0.081(8) 0.134(13) 0.055(9) 0.001(8) 0.000(5)
05 0.065(8) 0.053(8) 0.21(2) -0.030(11) -0.044(12) 0.023(7)
N2B 0.031(10) 0.089(17) 0.12(2) 0.025(17) 0.009(14) -0.003(11)
04B 0.048(14) 0.09(2) 0.12(2) 0.05(2) 0.013(17) 0.007(13)
05B 0.054(10) 0.096(14) 0.156(19) -0.046(14) -0.023(12) 0.025(10)
C5 0.0191(16) 0.101(3) 0.054(2) 0.036(2) -0.0024(15) 0.0005(17)
C6 0.0255(17) 0.110(3) 0.053(2) 0.042(2) 0.0030(16) -0.0035(19)
C7 0.026(2) 0.047(3) 0.036(2) 0.010(2) 0.000 0.000
_ge om_sp e c i a l_de t a i 1 s
All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
loop_
_geom_bond_atom_site_label_l
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Cul 03 1.926(3) ?
Cul 01 1.941(2) ?
Cul 01 1.941(2) 12_655 ?
Cul N1 2.003(4) . ?
01 Cl 1.270(4) ?
02 Cl 1.226(4) ?
03 H3 0.8501 ?
N1 C5 1.325(4) ?
N1 C5 1.325(4) 12_655 ?
Cl C2 1.510(4) ?
C2 C4 1.369(5) ?
C2 C3 1.378(5) ?
88


C3 C3 1.392(6) 7_545 ?
C3 H3A 0.9598 ?
C4 C4 1.385(7) 7_545 ?
C4 N2B 1.40(4) ?
C4 N2 1.52(2) ?
C4 H4A 0.9600 ?
N2 05 1.17(3) ?
N2 04 1.29(3) ?
04 04 1.49(3) 4_566 ?
N2B 05B 1.24(5) . ?
N2B 04B 1.28(5) ?
C5 C6 1.372(5) ?
C5 H5A 0.9300 ?
C6 C7 1.373(4) ?
C6 H6A 0.9300 ?
C7 C6 1.373(4) 12_655 ?
C7 C7 1.476(9) 9_667 ?
loop_
_geom_angle_atom_site_label_l
_geom_angle_atom_site_label_2
_geom_angle_atom_site_labe1_3
_geom_angle
_geom_a ngle_site_s yitune t r y_l
_ge om_a ngle_site_symmetry_3
_geom_angle_publ_flag
03 Cul 01 86.96(7) . ?
03 Cul 01 86.96(7) 12_655 ?
01 Cul 01 170.49(16) 12_655 ?
03 Cul N1 178.92(16) . ?
01 Cul N1 92.97(7) . ?
01 Cul N1 92.97(7) 12_655 ?
Cl 01 Cul 118.4(2) . ?
Cul 03 H3 117.8 . ?
C5 N1 C5 116.3(4) 12_655 ?
C5 N1 Cul 121.8(2) . ?
C5 N1 Cul 121.8(2) 12_655 ?
02 Cl 01 125.7(3) . . ?
02 Cl C2 117.8(3) . . ?
01 Cl C2 116.4(3) . . ?
C4 C2 C3 117.9(3) . . ?
C4 C2 Cl 122.7(3) . . ?
C3 C2 Cl 119.3(3) . . ?
C2 C3 C3 120.84(18) 7_545 ?
C2 C3 H3A 119.5 . ?
C3 C3 H3A 119.6 7_545 ?
C2 C4 C4 121.22(19) 7_545 ?
C2 C4 N2B 127.1(13) . ?
C4 C4 N2B 107.4(14) 7_545 ?
89


C2 C4 N2 128.4(7)
C4 C4 N2 109.0(6)
C2 C4 H4A 119.4 .
C4 C4 H4A 119.4 7_
05 N2 04 125(2) .
05 N2 C4 118(3) .
04 N2 C4 117.0(18)
05 N2 H4A 108.0 .
04 N2 H4A 121.8 .
05B N2B 04B 121(4)
05B N2B C4 131(4)
04B N2B C4 108(4)
N1 C5 C6 123.3(3)
N1 C5 H5A 118.3 .
C6 C5 H5A 118.3 .
C5 C6 C7 120.8(3)
C5 C6 H6A 119.6 .
C7 C6 H6A 119.6 .
C6 C7 C6 115.5(4)
C6 C7 C7 122.2(2)
C6 C7 Cl 122.2(2)
545
_545
>
12_655 ?
9_667 ?
12 655 9 667 ?
loop_
_geom_t or s i on_at om_s i t e_labe1_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
03 Cul N1 C5
01 Cul N1 C5
_geom_torsion_site_symmetry_l
_geom_torsion_site_symmetry_2
_geom_t orsion_site_s ymme t r y_3
_ge om_t orsion_site_s y mme t r y_4
_geom_torsion_publ_f1ag
03 Cul 01 Cl -77.2(3) . . . . ?
01 Cul 01 Cl -127.6(8) 12_655 ... 7
N1 Cul 01 Cl 103.8(3) . . . . ?
-89.6(4) . . . . ?
-3.3(4) . . ?
01 Cul N1 C5 -175.9(4) 12_655 . ?
03 Cul N1 C5 89.6(4) . 12_655 ?
01 Cul N1 C5 175.9(4) . 12_655 ?
01 Cul N1 C5 3.3(4) 12_655 . 12_655
-9.5(5) . . ?
170.2(2) . . . . ?
-162.4(4) . . . . ?
17.9(5) . . . . ?
17.5(5) . . . . ?
-162.2(3) . . . . ?
Cul 01 Cl 02
Cul 01 Cl C2
02 Cl C2 C4 -
01 Cl C2 C4
02 Cl C2 C3
01 Cl C2 C3
C4 C2 C3 C3 -1.4(6)
7_545 ?
90


Cl C2 C3 C3 178.6(4) . . . 7_545 ?
C3 C2 C4 C4 0.9(8) . . 7_545 ?
Cl C2 C4 C4 -179.2(5) . 7_545 ?
C3 C2 C4 N2B 155(3) . ... 7
Cl C2 C4 N2B -25(3) . ... 7
C3 C2 C4 N2 -164.5(16) . ... 7
Cl C2 C4 N2 15.5(17) . . . ?
C2 C4 N2 05 -127.5(15) . . . ?
C4 C4 N2 05 66(2) 7_545 ... 7
N2B C4 N2 05 -27(3) . ... 7
C2 C4 N2 04 50(2) ... 7
C4 C4 N2 04 -116.6(13) 7_545 ... 7
05 N2 04 04 -15(2) . 4_566 ?
C4 N2 04 04 167.9(14) . . 4_566 ?
C5 N1 C5 C6 0.3(8) 12_655 . . . ?
Cul N1 C5 C6 179.5(4) ... 7
N1 C5 C6 C7 0.2(8) . . ?
C5 C6 C7 C6 -0.7(9) . 12_655 ?
C5 C6 C7 C7 179.0(5) . 9_667 ?
loop_
_geom_hbond_atom_site_labe1_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
03 H3 02 0.85 1.79 2.629(3) 168.8 2_664
_diffrn_measured_fraction_theta_max 0.997
_diffrn_reflns_theta_full 27.47
_diffrn_measured_fraction_theta_full 0.997
_refine_diff_density_max 0.393
_refine_diff_density_min -0.573
_refine_diff_density_rms 0.070
B.5 Compound 3
data_x
_audit_creation_date
_audit_creation_method
_symmetry_space_group_name_H-M
_symmetry_Int_Tables_number
_symmetry_cell_setting
loop_
_symmet ry_equiv_po s_as_xy z
2011-04-07
'Materials Studio'
PI.
1
triclinic
91