XRAY CRYSTALLOGRAPHY
A THESIS SUBMITTED TO THE UNIVERSITY OF MANCHESTER FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
2017
Organisation of thesis 11
General features of halogen bonding 14
The σ-hole and origin of halogen bonding 15
Brief history of halogen bonding 18
Halogen bonding in crystal engineering 20
One dimensional (1D) architectures 20
Two and Three-dimensional (2D and 3D) Architectures 14
Crystal structures 29
Crystallographic methods 31
X-rays 33
Slow evaporation 38
Vapour diffusion 38
Solvent layering 39
Step four: structure solution and refinement 42
X-ray powder diffraction (XRPD) 45
Conclusion 46
tetrafluoroethaneand 1,4-diazabicyclo[2.2.2]octane.
DABCO adducts.
1,4-diazabicyclo[2.2.2]octane.
alkanes and DABCO.
Chapter
8
4
Halogen X
Halogen bonding type (I) C-X…X-C
Halogen bonding type (II) C-X…B
Halogen X-
Crystallographic Information File CIF
X-ray powder diffraction XRPD
Differential scanning calorimetry DSC
6
Abstract
This thesis describes work conducted on a series of halogen-bonded adducts derived from a
series of fluoro-alkyl and -aryl bromides and iodides with 1,4-diazabicyclo[2.2.2]octane
(DABCO). Vapour-phase diffusion of DABCO with 1,2-dibromotetrafluoroethane results in
the formation of crystals of a 1:1 adduct of formula C2Br2F4.C6H12N2. This forms an infinite
one-dimensional polymeric structure linked by intermolecular N…Br halogen bonds. These
are characterised by d = 2.829 (3) Å, which is 0.57 Å shorter than the sum of the van der
Waals radii and an N…Br-C angle of 175.6(1)°. Extending this work to the longer chained
dibromo-perfluoroalkyl compounds BrCF2(CF2)nCF2Br (n = 2, 4, 6) gives rise to colourless
crystals of Br2C4F8•C6H12N2, Br2C6F12•C6H12N2 and Br2C8F16•C6H12N2, each of which form
one-dimensional halogen-bonded networks. All three adducts exhibit N···Br halogen bonds
with N-Br. The shortest N…Br distances were observed in Br2C4F8•C6H12N2, 2.809 (3) and
2.818 (3) Å, which are 0.58 and 0.59 Å shorter than the sum of the van der Waals radii and
the shortest N···Br halogen bond distance reported to date between a bromoperfluorocarbon
and a nitrogen base.
The X-ray structure of the second ever adduct based on an aromatic bromofluoroalkane and
DABCO, is reported from the vapour phase diffusion of DABCO and 1-
bromoperfluorobenzene. The near-linear N…Br halogen bond (C-Br···N = 167.8 (2) to
169.3 (3) ) exhibits a N…Br bond distance of 2.814 (7) Å, which is 0.58 Å shorter than the
sum of van der Waals radii.
An investigation of the halogen bonded adducts formed from the vapour phase between four
iodoperfluoroalkanes with DABCO resulted in the formation of one-dimensional structures
of the formula CF3(CF2)nCF2I•C6H12N2 (n = 2, 4 and 6) with N…I distances ranging from
2.685 (6) to 2.799 (3) Å. Disorder was observed in structures of the longer chained adducts.
When crystals were regrown from a dichloromethane solution of I(CF2)4I and DABCO
single crystals containing (ClCH2 +DABCO)I(CF2)4ICl-I(CF2)4ICl-
I(CF2)4I(DABCO+CH2Cl) resulted, arising from mono-quaternisation of DABCO and the
formation of a structure based on a mixture of N...I and I…Cl halogen bond interactions.
The interaction between volatile perfluoroalkyl iodides, such as C3F7I, C4F9I, C6F13I and
PPh3 in the vapour phase in glass containers results in the formation of crystals identified as
F2PPh3 on the basis of single-crystal diffraction studies and NMR data. The mechanism of
this reaction is not known, but in the absence of light the rate of reaction was shown to slow
down, while the presence of glass was found to give rise to a number of silicon-containing
decomposition products including (C6H5)3PO…HOP(C6H5)3.SiF5 and Ph3POSiF4OPPh3
consistent with the attack of the glass by Ph3PF2, or its hydrolysis products.
7
Declaration
No portion of the work referred to in this thesis has been submitted in support of an
application for another degree or qualification of this or any another university or other
institute of learning.
Copyright Statement
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any copyright in it (the “Copyright”) and s/he has given The University of Manchester the
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restriction declarations deposited in the University Library, The University Library’s
regulations (see http://www.manchester.ac.uk/library/aboutus/regulations) and in The
University’s policy on Presentation of Theses.
9
Acknowledgements and Messages
Finally, the time is here to say a huge “thank you” to everyone who have been so much a
part of the interesting journey of this PhD. Furthermore, this thesis would not have been
possible without the co-operation and assistance, offering by the staff members and lab
technicians of the chemistry school at the University of Manchester.
My gratitude is endless to Dr Alan Brisdon, my main supervisor, for his support,
encouragement, help and advice. He has not only been my supervisor, but also a true friend.
I am very grateful to my Co-supervisor, Dr Robin Pritchard, for willing offering idea,
expertise and guidance on crystallography. Robin has been wonderful.
I appreciate all the support and advice from Dr Inigo Vitorica-yrezabal, one of the most
helpful people in the X-ray lab. I offer my blessing and regards to all colleagues and friends
in fluorine and crystallography groups, who assisted me with any respect to complete my
project.
Enormous thanks are due to my Mom, Dad, brothers and sisters for all their support, love
and prayers. You are fantastic and I love you all.
Nobody has been more important to me in the pursuit of this project than my three wonderful
children, Adnan, Ghassan and Wejdan, whose love and patient are with me in whatever I
pursue. Most importantly, I express my immense gratitude to my loving and supportive
husband, Abdulbaset, who selflessness and dignity inspired me throughout.
10
Rational for alternative format thesis
This thesis is presented in the University of Manchester’s permitted “alternative format”,
that is the results and discussion chapters consist of papers that have either been published
or accepted for publication and chapters written in manuscript format ready for submission.
The work described in this thesis is suitable for this format because it contains a number of
well-defined sections, albeit all related to the topic of halogen-bonded structures. This area
of chemistry is rapidly evolving and so publication throughout the progress of the studies
was warrented and delaying publication might considerably diminish the importance of this
work. Thus, chapter three corresponds to a paper that has already been published, and the
extension of this work to longer chained molecules described in chapter four has been
accepted for publication. Chapters five and six describe complete pieces of work which are
written and ready for submission, while chapter seven describes an extension to the work on
halogen bonding of nitrogen systems to related phosphorus systems and although a little
more speculative is written in an appropriate style for a journal manuscript.
Organisation of thesis
Chapter Two is a general introduction and a review to halogen bonding and crystallography.
Chapters Three, Four, Five, Six and Seven are original research papers published, submitted
or in the form of journal articles. Chapter Eight is further work and conclusions.
Contributing authors
Chapter 3, Paper 1, “Halogen-bonded adduct of 1,2-dibromo-1,1,2,2-tetrafluoroethaneand
1,4-diazabicyclo[2.2.2]octane ” is an original research article written by the thesis author.
Crystallization and X-ray crystallography were performed by the thesis author. IR
measurements and analysis were performed by the thesis author. The Manuscript was written
by Dr. Alan Brisdon with the assistance from the other authors.
Chapter 4, Paper 2, “Halogen bonding in three Di-bromoperfluoroalkane-DABCO adducts”
is an original research article written by the thesis author. The thesis author synthesized all
adducts and performed X-ray crystallographic measurements and structure solution. IR
12
measurements were performed by the thesis author. The paper was written by the thesis
author (with the assistance from Dr Alan Brisdon and Dr Robin Pritchard).
Chapter 5, Paper 3, “Halogen-bonded adduct of 1-bromoperfluorobenzene and 1,4-
diazabicyclo[2.2.2]octane” is an original research article written by the thesis author.
Crystallization and X-ray crystallography were performed by the thesis author. The
manuscript was written by the thesis author.
Chapter 6, Paper 4, “Halogen bonding in some adducts of iodo-perfluorinated alkanes and
DABCO” is an original research article written by the thesis author. The thesis author
synthesized all adducts and performed all the physical measurements. X-ray crystallography
and analysis were performed by the thesis author and Dr Robin Pritchard. The paper was
written by the thesis author.
Chapter7, Paper 5, “The interaction of phosphines with perfluoroalkylioides” is an original
research article written by the thesis author. Synthesis and Crystallization were performed
by the thesis author. X-ray crystallography and NMR measurements were performed by the
thesis author. Theoretical analysis for NMR data were performed by the thesis author and
Dr Alan Brisdon. The manuscript was written by the thesis author (with contributions from
Dr Alan Brisdon).
14
What is halogen bonding
Halogen bonding, in many aspects comparable to the better known hydrogen bonding, is
widely defined as an interaction in which a halogen atom instead of a hydrogen atom is the
acceptor for a Lewis base. According to the recommendations of the International Union of
Pure and Applied Chemistry (IUPAC), a halogen bond is a non-covalent attractive
interaction between a positive region on a halogen atom (X) in a molecule or a fragment (R-
X) and a negative region of (B) in the same, or a different molecule [1] (Fig.1).
Figure. 1 Schematic Representation of Halogen Bond (XB). R = Organic Fragment(s); X = Cl, Br, I; B =
Rich Electron Density Atom.
Where R-X is the halogen bond donor, with X being a halogen atom with an electron-poor
(electrophilic) region, that is covalently bonded to another atom or molecule, R. B is the
halogen bond acceptor, and is usually a molecule with an electron rich (nucleophilic) region.
Several common donors and acceptors for halogen bonding are summarized in Table 1.
Table 1: Some common halogen bond donors and acceptors.
Halogen bond donors (R-X) Halogen bond acceptors (B)
Haloalkanes Lone Pair atoms
Halogen bonding is typically characterised by high directionality and strength, as well as a
greater versatility in the atoms involved than hydrogen bonding. In the study of Primagi [2],
15
a comparison was made between halogen bonding and the better known hydrogen bonding,
in this it was concluded that a halogen bond is more directional than a hydrogen bond, and
its strength is potentially easier to tune making it a useful interaction to design smart
functional materials. This observation is supported by an earlier study by Metrangolo, in
2008 [3], which found that the high strength and particularly high directionality means that
halogen bonds can be used as a general system to drive the self-assembly processes in the
solid phase. According to spectral and crystallographic data in theoretical and experimental
studies of typical halogen-bonded adducts (R-X…B), the following generalizations may be
made:
1. Halogen bonding distances between a halogen atom (X) and an electron donor atom
(B) tend to be less than the sum of their van der Waals radii (∑vdW).
2. When the acceptor (B) approaches the halogen atom (X) along the extension of the
covalent (R-X bond, the angle (R-X…B) tends to be nearly linear (approximately
180°).
3. The short (X…B) distances indicate strong and highly directional halogen bonding.
4. Halogen bonding is an electrostatic interaction, for that reason when a halogen atom
(X) is bound to (R) a more electronegative atom(s), it becomes a better halogen bond
donor.
5. The covalent bond length (R-X) generally rises relative to the unbound distance.
6. The tendency of (XB) acceptors to form halogen bonding increases as the Lewis
basicity on the B molecule increases.
7. The strength of the halogen bond increases as the ability of (R) to withdraw electrons
increases.
8. The strength of the halogen bond interaction increases in the order Cl < Br < I.
The σ-hole and origin of halogen bonding
If we restrict this work to covalently carbon-bound halogen atoms, then halogen bond
interactions can be separated into two major groups (i) C-X…X-C interactions (X and X =
Cl, Br or I), and (ii) C-X…B where B is an electron pair donor. In these cases, halogen bonds
are indicated by X… X or X…B distances shorter than the sum of van der Waals radii and
the angles of their approach. For the X… X interactions two different geometries are
possible, labelled as type (I) and type (II), and illustrated in Fig. 2, while C-X interactions
with a Lewis base B gives rise to only one geometry that is identified by its near linearity
(Fig.2).
16
Figure. 2 Geometric information for halogen bond interactions. Type (I) 1 = 2 = ~120°; Type (II) 1 =
90° and 2 = ~180°; Lewis base interaction = 180°. Modified From Published Data in Reference [8].
It is generally agreed that electrostatic factors are responsible for halogen bonding [4], even
if charge-transfer and dispersion forces might also contribute to the detected structure
patterns. Statistical studies of XB interactions in crystal structures have revealed that halogen
atoms can be defined by two different radii instead of a single van der Waals radius, a smaller
radius along the C-X axis and a longer radius perpendicular to it, a feature called “polar
flattening” [5]. Experimental analysis and theoretical studies [6, 7] have pointed out the
anisotropic distribution of the electron density around a bound halogen atom, with the
concentration of charge in the equatorial area, and depletion of charge along the polar C-X
axis, known as a σ-hole (see Fig. 3).
Figure. 3 Electron density around a halogen atom, X. Green colour indicates σ-Hole; Read colour shows
electrophile approach.
B
B
B
17
As is shown in Fig. 3, the term σ-hole indicates the positive electrostatic potential, which is
centred on the C-X axis and is surrounded by a negative electrostatic region. The R-C bond
is formed due to the interaction between the half-filled pz orbital of a halogen atom with a
hybrid orbital of a carbon atom. While the remaining electrons in s2 px 2 and py
2, orbitals are
not involved, since the px and py orbitals are perpendicular to the C-X axis, a negative belt
is formed around the halogen atom at 90° to the C-X direction. As a consequence of this, a
halogen atom acts as a nucleophile at its equator and as an electrophile at its pole.
The occurrence and magnitude of a σ-hole depends upon the nature of the halogen atom,
and the ease with which it can be polarised as is demonstrated in (Fig.4) which shows the
formation of a more positive σ-hole in the compounds CF3X on moving from X = fluorine
to iodine. [7].
Figure. 4 Molecular surfaces of CF4, CF3Cl, CF3Br and CF3I. Red colours represent positive portions (σ-
Hole); Yellow are neutral regions; blue colours indicate negative portions. Sourced from Data Published in
Reference [7].
The strength of a halogen bond interaction also varies with the hybridization of the carbon
atom in the order C≡CI > C=CI > R3CI and is activated by the existence of electron
withdrawing groups such as in the fluorocarbons CnF2n+1I [9]. The σ-hole is a very important
issue to understand in X…B interactions. In fact, the σ-hole concept is not limited to
halogens, it is also recognized for bonded atoms of group IV, V and VI elements. A
phosphorus atom, with three half-filled p-type orbitals participating in covalent contacts, has
three σ holes on the extension of each contact; any or all may be positive, depending on the
other partner in the interaction [10]. These can offer important applications in crystal
engineering to prepare and design new crystalline solids through σ-hole bonding.
CF4 CF3Br CF3I CF3Cl
Brief history of the halogen bonding
The first observations of X…B interactions were in the nineteenth century, when I2, Br2 and
Cl2 formed complexes with ammonia (NH3) and methylamines (CH3NH2) [11, 12]. These
interactions were sometimes described as “electron-pair donor/acceptor” or “charge-
transfer” interactions. Later Mulliken [13] and Flurry [14] developed detailed theoretical
formalisms to describe them. Finally, it was pointed out that many organic halides can also
form such complexes via X…B interactions [15]. The similarities between these interactions
and conventional hydrogen bonding, where halogen or hydrogen atoms act as electron-pair
acceptors, were presented and studied by Bent [15] and by Hassel [16]. The crystallographic
work of Hassel was an essential advance in understanding the non-covalent halogen bond.
He first showed that the X…B interaction is a powerful tool to drive the formation of
crystalline solids. He and his groups studied the X-ray structures of different addition
compounds and concluded that the X…B distance was much less than the sum of van der
Waals radii, which indicated a very strong contact between halogen atoms and electron-pair
donors. Consequently, the short distances of X…B interactions were recognized through the
analysis of many crystals from the Cambridge Structural Database (CSD) [17, 18].
Over the last decades, the number of publications concerned with halogen bonding has
grown almost exponentially (Fig. 5), especially after the paper entitled “Halogen Bonding:
A Paradigm in Supramolecular Chemistry” was published in 2001 by Metrangolo and
Resnati [19]. This paper boosted the interest of scientists in the topic and has thereby drawn
widespread interest in three major fields related to halogen bonding: computational
chemistry, such as the published work by Politzer et. al. [7,20-23] and of Auffinger et. al.
[24], biological chemistry also by Auffinger et. al. [24] and material science such as the
seminal work by Pan, Metrangolo and Resnati et al., [19,25-32].
Computational studies have shed light on the electrostatic behaviour of the halogen atoms
[7, 20, 22 - 24, 33 - 38]. This was particularly the case for the work of J. S. Murrary and P.
Politzer , which were essentially important as they showed the anisotropic distribution of the
charge on halogens involved in forming C-X covalent bonds to give rise to the “σ-hole”
definition [39 -41]. The electropositive σ-hole enables halogen atoms to behave in a similar
way to hydrogen in hydrogen bonding. Indeed, the similarity between halogen bonding and
hydrogen bonding offers the prospect to exploit halogen bond interactions in drug design
and biological engineering [24, 42 -48].
19
Recently, Voth et. al highlighted the competition between halogen bonding and hydrogen
bonding in DNA Halliday junctions utilising brominated uracil [42]. They showed that the
stability of the DNA construct with a halogen bond interaction increases by approximately
2 Kcal/mol compared with the hydrogen bond construct. The specific properties of the X…B
interaction make it a reliable and effective tool in different fields for preparing and designing
new crystalline solids [49, 50]. This type of interaction can be significant for molecular
recognition and binding developments, potentially offering a powerful tool to improve the
binding selectivity and the binding affinity in recognition processes of biological molecules
[51, 52]. For example, the halogen bond interaction has been utilised to design new drugs in
biological applications for cancer treatment [53]. Furthermore, a better understanding of
halogen bond interaction in biological systems and how halogenated molecules bind to
biological systems could open up new ways to develop drugs for future therapeutic
treatments and could help to rationalize the adverse biological effects of several halogenated
chemicals to which human are commonly exposed.
Figure. 5 Number of publications containing the concept halogen bonding. Data obtained from the SciFinder
until June 20th, 2017.
At the present time, however there are some questions that are being highlighted by the larger
communities of chemists, crystallographers and solid state researchers. Such as, while we
know about the structure of a molecule, and we can determine many small structures, we
still do not know much about the crystallization mechanism of a molecular solid and the
relationship between molecular structures and the properties of crystal structures. This
perspective might offer a brief introduction to the potential role of halogen bonds in crystal
engineering.
0
200
400
600
800
1000
1200
Halogen bonding in crystal engineering
When discussing the significant role that halogen bonding has to offer in different areas such
as medicinal chemistry, biochemistry and material science it is important to point out that
strong and directional halogen bonding has been successfully employed in crystal
engineering. The strategy for crystal engineering involves the understanding of crystal
structures in terms of intermolecular interactions and then utilization of such knowledge to
design new solids with specific physical and chemical properties. Traditional hydrogen bond
interactions have been used in such applications, but the halogen bond interaction has
properties that parallel those of a hydrogen bonding interaction in terms of strength and
directionality. Moreover, the typical strength of hydrogen bonding is approximately 4-60
kJ/mol [54], while halogen bonding is reported to range between 5-180 kJ/mol [25].
Accordingly, halogen bonding interactions can be used as reliable and robust tools to control
the self-assembly of organic molecules as building blocks (tectons) in solids. Additionally,
the high directionality of halogen bonds from iodine/bromine atoms, which have an
electropositive crown (σ-hole) in their polar regions activated by electron-withdrawing
neighbouring groups, should effectively direct molecular aggregation during the
crystallization process. As a result, it is possible to predict crystal structures from the
molecular structures of their starting compounds. Thus, the geometries of molecules
involved in halogen bonding can be related to the geometries of the supramolecular
architectures. This observation is supported by a study of Metrangolo et al in 2008, who
showed how halogen–bonding can give rise to supramolecular architectures in 1D, 2D and
3D networks as can be seen below [3]. For the purpose of this project, one-dimensional
architecture will be considered in more details than the other two types.
One-dimensional (1D) architectures
The angles formed along the C-X axis to the halogen bonding donor and the axis of the lone
pair on the halogen bonding acceptor determine the geometry of the halogen-bonded
molecules. For instance, the interaction between 1,4diazabicyclo[2.2.2]octane (DABCO)
and 1,2-dibromotetrafluoroethane results in the formation of crystals that adopt a one-
dimensional polymeric structure linked by intermolecular N…Br halogen [55]. In addition,
when bidentate X…B acceptors (HCs = hydrocarbons compounds) interact with bidentate
X…B donors (RfI = perfluorinated carbons), an intermolecular X…B interaction is formed
and repeated at each end of the molecule. Liantonio et al (2002) in his study reported the
21
formation of one-dimensional linear chain by the presence of N…I interactions between
N,N,N,N–tetramethyl-1,4-phenylenediamine and 1,4-diiodotetrafluorobenzene (Fig. 6) [56].
Figure. 6 1D infinite chain of the co-crystal formed by N,N,N,N–tetramethyl-1,4-phenylenediamine and 1, 4-
diiodotetrafluorobenzene.
In that study, the N…I interaction organises the HC and Rf-I molecules into the 1-D linear
networks [56]. The N…I bond length is 2.935(2) Å, significantly shorter than the sum of the
van der Waals radii (3.53 Å), and the C-I…N angle, at 174.04(7)°, is approximately linear,
in agreement with the general characteristics of halogen bonds. Moreover, the formation of
this bond results in an extension to the covalent C-I bond length from 2.075 Å in pure 1,4-
diiodotetrafluorobenzene [57] to 2.091 Å in the co-crystal [56] (although the significance of
these numbers cannot be accurately assessed because error values are not given in the
published papers). In the crystal packing, a clear segregation is observed due to the low
affinity between HCs and RfI layers that are alternate and held together via the attractive
N…I interaction [56] (Fig. 7). Using the same design principles and based on the geometry
of the tectons used, different one-dimensional chains were generated in the study by
Metrangolo, et al in 2008 [3], see Figure 8 and Figure 9.
Figure. 7 Crystal packing of the co-crystal formed by N,N,N,N–tetramethyl-1,4-phenylenediamine and 1, 4-
diiodotetrafluorobenzene.
22
Figure 8. Several examples of halogen bonds showing N…I Interactions. (I) Linear 1D infinite chains.
(II) Stepped (Linear) 1D infinite chains. Copied from data published in reference [3].
(I)
(II)
23
Figure 9. Non-linear 1D infinite chains and several examples of halogen bonds showing N…I interactions.
Sourced from data published in reference [3].
24
As can be seen from Figures 8 and 9, 1D architectures can be classified into 3 types
depending on the geometric arrangement of halogen-bonded molecules. Linear chains are
generated when linear, monodentate or bidentate X…B acceptors and/or donors interact with
each other on the same or different molecules. Whereas, non-linear chains such as stepped
and zig-zag chains are formed when molecules with non-linear angles between halogen bond
donor or acceptor sites are involved in the halogen bond interactions. Furthermore, the angle
along zig-zag chains mainly depends upon the angle between B…X acceptors and donors.
For instance in Figure 9, the halogen-bonded acceptors and/or donors that have 120° or 60°
angles between their sites result in the formation of zig-zag chains with 120° or 60° angles,
respectively.
When halogen-bonding donors and/or acceptors are tridentate molecules, two dimensional
architectures can be obtained. Furthermore, these networks are usually formed on self-
assembly of tridentate XB acceptors (which sit at the network nodes) with bi- or tridentate
XB donors (which form the network sides) [58]. Such architectures are shown in the trigonal
molecule 1,3,5-tris[(4-iodophenoxy)-carbonyl] benzene that crystallised from chloroform
to yield a 2-dimensional supramolecular architecture (Figure 10 ) [59]. In addition, a non-
covalent X…B interaction is not only an effective tool in the generation of 1D and 2D
networks (Figure 11) , but also in 3D architectures, using tetradentate XB modules (See
Figure 12).
Figure 10. Tridentate Halogen-Bonding Acceptors and Donors in 2D networks. Sourced from
published data in Reference [59].
25
The study of 2D and 3D architectures in crystal engineering was previously highlighted by
Metrangolo et al. (2008) [3]. He suggested that different types of architectures can be formed
when one, or both, of the XB acceptors and donors are tetradentate molecules, see Figure 11
and Figure 12. For example, the use of tetrakis(4-pyridyl)pentaerythritol as a tetradentate
X…B acceptor with 1,4-diiodoperfluorooctane as a bidentate X…B donor or tetrakis(4-
iodotetrafluorophenyl)pentaerythritol as a tetradentate X…B donor, resulted in the
formation of two- and three-dimensional architectures [60]. The geometric information of
both compounds is summarised in Table 2 and indicates the presence of short and directional
N…I interactions in the crystal structures.
Table 2. Geometric Parameters of Tetrakis(4-pyridyl) Pentaerythritol-1,4-Diiodoperfluorooctyl , and
Tetrakis(4-Iodotetrafluorophenyl) Pentaerythritol. Taken from Published Data in Reference [60].
Compound
(4)
2.817 (5) 175.2 (1)
In these halogen-bonded systems the RfI and HCs molecules are connected by X…B
interactions into chains, while the chains might be joined by other interactions such as F…F
and F…H contacts. Moreover, the design for a crystal structure mainly depends on viewing
it as a combination of interactions of different types and strengths [61].
26
Figure 11. Formation of 2D Halogen-bonded Architectures. Copied from Published Data in Reference [3].
27
Figure 12. Formation of 3D Halogen-bonded Architectures. Sourced from Published Data in Reference [3,
60].
28
It is clear from the previous figures that halogen bonds are strong enough to overcome the
low affinity between Rf-I and HC compounds and drive their self-assembly into extended
structures. However, it is not so easy to use this knowledge predictively because of the
different factors that might influence the design of crystal structures and so influence their
predicted structures. For example, the steric and electronic effects involved in the halogen
bonding interaction cause a decrease in XB acceptor ability and subsequently the strength of
the halogen bond and the crystal packing. Research has shown that in a series of halogen
bonded nitrogen containing molecules with iodine acceptors that the strength of the N…I
interaction depends upon both the steric and electronic properties of the two molecules
involved [62]. For example, the N…I bond length in the 1:1 complex of 4,4-bipyridine (bpy)
and, 1,4-diiodotetrafluorobenzene (F4DIB) is shorter than that found between (bpy) and 1,4-
diiodobenzene (DIB). This is due to the increase in Lewis acidity of the iodine centre when
more fluorine atoms are present in the ring. The influence of the steric properties is shown
by the complex formed between hexamethylenetetramine (hmta) and 1,4-
diiodotetrafluorobenzene (F4DIB), which was only observed as a 1:1 complex, rather than
the anticipated 2:1 adduct, because of the steric demand of the amine.
There is also another argument to be made here; the N…I interaction is relatively well
established for the formation of halogen bonding in many crystal studies, but the non-
covalent interactions between N and Br atoms has attracted less attention by researchers.
Theoretical and experimental studies show that all four halogen atoms can be halogen
bonding donors, with iodine typically forming the strongest halogen bond interactions and
fluorine showing the least tendency to give halogen bonding due to the difficulty in
polarising its electron density.
Similarly, to date most of the halogen-bonded adducts have involved nitrogen-containing
compounds as the Lewis base, however phosphorus, which is in the same group as nitrogen,
might also be expected to bind to a halogen acceptor and form a halogen-bonded adduct.
Since both P and N atoms have the same electronic structure in their valance shells [s2p3]
they might be expected to form similar structures for their compounds. However, little
attention has been paid to the phosphorus atom as an electron donor atom in halogen
bonding, even less than that for oxygen and sulphur atoms. In fact, it is very rare to find
research using phosphorus compounds to produce halogen-bonded molecules. For these
reasons, the purpose of this project involves investigation of N…I, N…Br and P…I
interactions in order to hold halofluorocarbons in crystal structures.
29
Crystal structures
A single crystal is a precisely regular arrangement of atoms, molecules or ions in an ordered
array extending in three dimensions. The basic building unit of the ordered pattern in a
crystal is expressed by the term ‘‘unit cell’’. The asymmetric unit is the smallest unique
representation of contents within the unit cell of the crystal structure; it is transformed to the
unit cell using a suitable symmetry operation such as translation, rotation and reflection (Fig.
13) [63] and repeating the unit cell will result in the observed crystal packing.
Crystallographic symmetry operations, such as translations and reflections, are applied to
the arrangement of atoms in a crystal lattice and always leave these arrangements unchanged
after their performance. The main types of symmetry operations that happen in crystal
lattices are inversion, reflection, rotation, translation and rotation-inversion. The
combination between rotation or reflection and translation generates screw axes and glide
planes in the lattice of the structure [64, 65].
Figure 13. A simple example of the generation of a crystal from an asymmetric unit. Where the black dot
represents an inversion centre (or 2 fold rotational axis). The entire crystal is generate by translation of the
unit cell in three dimensions. Modified From Online Article in Reference [63].
When identical molecules pack together they form a crystal lattice. If each molecule is
presented by a single point, the result is a lattice of points. To define the repeat unit of this
lattice, a parallelogram of eight points is chosen. However, without rules, an infinite number
of unit cells are possible to describe the array. As a consequence, lattice symmetry which
refers to the size and shape of the unit cell is a very important condition to guide this choice.
30
Moreover, each primitive unit cell should contains the equivalent of one lattice point (one
repeat unit) [65].
A three-dimensional unit cell has three edges and the lengths of these edges are called a, b
and c, whereas the angles between them are known as α, β and γ as shown in Fig. 14. The
presence of reflection or rotation symmetry in the structure impose rules and special values
on the unit cell dimensions and as a result of this there are seven sorts of symmetries of
lattices, called crystal systems that exist. (Table 3) [66].
Figure. 14 Unit Cell Dimensions. a, b and c indicate vectors and α, β and γ are the angles.
Table 3. The Seven crystal systems and their different unit cell dimensions.
Crystal System
Lengths Angles
Hexagonal a = b ≠ c α = β = 90; γ = 120
In addition, these seven crystal systems have a further classification to fourteen crystal
lattices where sometimes the unit cell contains more than one lattice point. These 14 lattices
31
are called the Bravais lattices formed by the combination of the seven crystal systems and
centred unit cells (P, F, I). A primitive unit cell (P) has only one lattice point at its eight
corners. If there are extra lattice points in the centres of the faces of the unit cell, it is known
as a face-centred unit cell (F), whereas if there is an additional point in the centre of the body
of the unit cell it is called a body-centred unit cell (I). An extra point at the centre of one pair
of the unit cell faces (be that A, B or C) is referred to as centring on the A face, B face or C
face.
A space group is defined as a full collection of transformations for an infinitely repeating
array to leave a set of labelled points without any change. Furthermore, all space groups are
indicated by symbols starting with a lattice type, followed by a set of symmetry operations
in the three-dimensional unit cell. There are 230 space groups which are reported in standard
reference tables and books, but the most common one is the International Table for
Crystallography, Volume A [65].
Taking everything into consideration, it is possible to say that the unit cell is the building
block of any crystal structure, which in turn contains the asymmetric unit, which is the
smallest fraction of atoms, ions or molecules that in combination with symmetry can
generate the unit cell.
Crystallographic methods
Crystallography is the science of determining the atomic structure of crystals in order to
identify a compound and to understand how the molecules interact and pack. Raman,
Infrared and NMR spectroscopic methods can also be used to provide some structural
information, but none of these techniques can provide the same detail as crystallography.
The importance of crystallographic techniques is demonstrated by the large number of
crystal structures which have been determined by X-ray diffraction methods. These
techniques, particularly single crystal X-ray diffraction, are powerful tools utilised to
investigate novel crystals and produce a three-dimensional picture of the crystal under study,
including geometrical information such as bond distances and angles.
The eye and microscope analogy:
Objects are visible to human eyes because they scatter light which enters the eye, and this is
focused by the lens to produce a picture on the retina [65]. Light is composed of waves, and
32
each ray of scattered light has a particular intensity, I. These relative intensities, in turn,
identify the nature (shape/structure) of the picture produced in the eye and represent the
object being viewed. This means that the structural information of the object is carried in the
intensities of the scattered light waves and consequently, objects with various structures must
have various, individual scattering patterns.
Small objects might be examined under a microscope using more powerful lenses to generate
a larger picture. However, very small samples which have sizes less than the wavelength of
light, do not provide any significant scattering patterns. For this reason, X-rays, which have
wavelengths of a few Angstrom, are required to observe the structure of molecules instead
of visible light. On the other hand, the recombination of X-ray scattering patterns to give an
image cannot physically be performed, as the eye does for visible light, so it requires an
instrument to collect the scattered X-rays and a considerable amount of mathematical
calculations to generate a “picture” of the molecule under investigation. The method is called
crystal structure determination. It has two main parts, firstly to record the X-ray scattering
patterns either on photographic film or sensitive detector and then carry out the
recombination of scattered X-rays by mathematics on a computer, to generate a picture of
the molecule, see figure 15.
Figure 15. Diffraction pattern from (a) optical microscopy; (b) x-ray in a crystallographic experiment.
Modified from Reference [67].
33
X-rays:
X-rays are defined as a form of electromagnetic radiation that have wavelengths, λ, ranging
from 0.1 to 10 Å, and very high energy [64]. They are usually generated in X-ray tubes by
applying a high voltage between a filament (cathode) and a massive anode in a highly
evacuated glass tube. A schematic representation of a typical X-ray tube is shown in Figure
16. The voltage causes acceleration of the emitted electrons from the cathode to the anode
(a metal target such as copper and molybdenum) which suddenly decelerate when they hit
the target resulting in the emission of X-rays from the metal target. In this case, an electron
in an inner atomic orbital is ionised to create a hole and leaving the atom unstable. An
electron from an outer orbital can take its place. The drop in energy generates emission of a
characteristic X-ray of a definite frequency and wavelength, where E = hγ (E indicates
energy emitted, h is Planck’s constant and γ represents the frequency). The type of emission
depends on which atoms are involved in the transition, and occur as sharp spikes at a specific
position, see figure 17. In X-ray diffraction experiments, Kα is generally recognised as the
characteristic X-ray of copper and molybdenum, to provide X-ray of wavelengths 1.54184
and 0.71073 Å, respectively.
34
Figure 17. Electronic transitions in characteristic X-ray radiation. I = intensity; λ = wavelength
There are different types of instruments to record the scattered X-ray patterns of crystals,
whichever is used a good quality crystal always produces patterns of spots of different
intensities. These patterns have several properties, which can be related to the properties of
crystal structures. Furthermore, the pattern has a regular arrangement of spots as each spot
is produced at the detector by an individual scattered beam travelling in a certain direction
from the crystal. Moreover, the various intensities of spots have valuable information about
the atomic positions in the unit cell. Therefore, the measurement of an X-ray pattern gives
information on the geometry and symmetry of the unit cell in the crystal structure.
Diffraction by crystals
Whenever, a beam of electromagnetic radiation falls on a crystalline solid, each atom in this
solid absorbs a part of the energy and then it reflects beams in all directions [69]. Interference
can take place between these scattered X-rays in specific directions and this results in the
generation of X-ray patterns in those directions, which are known as diffraction patterns
[70]. When the scattered X-rays at one angle from an atomic plane reinforces those from
another plane then constructive interference occurs, which produces a bright spot in the
diffraction pattern (Figure 18). Conversely, destructive interferences will occur when
scattered waves are exactly out of phase. To simplify the calculations of a diffraction pattern,
crystal planes are defined as Miller indices. Furthermore, the points at which the crystal
planes intercept, a/h, b/k and c/l, the cell axes (a, b and c) are called as Miller indices. The
X-ray diffraction by crystal planes can be described by Bragg’s law.
35
(1)
(2)
Figure 18. Interference types. (1) shows constructive interference; and (2) displays destructive interference.
36
Bragg’s Law
Bragg, in 1913, introduced the first experiment using X-rays to study the structure of sodium
chloride crystals. It was based on the analogy between an optical microscopic and X-ray
diffraction for obtaining an image. Crystals can diffract X-rays and this is expressed in his
equation (Equation 1), which is commonly used as the basis for the geometry of X-ray
diffraction (XRD). This equation is used for all crystallographic methods to obtain the
geometric information of the unit cell from the X-ray diffraction pattern [65]. Furthermore,
Bragg considered X-ray diffraction as a series of reflections from successive planes of the
crystal lattice and that constructive interference will only occur when the following
conditions are satisfied:
1. The incidence angle and scattering angle, (), are equal.
2. The path difference must be equal to an integer number (n) of wavelengths (λ), see
figure 19.
nλ = 2dsin
Equation 1 Bragg’s Equation. n is an integer (n = 1, 2, 3, etc….), λ is the wavelength of X-rays, d is the
distance between planes and are angles of incidence and reflection.
Figure 19. A construction to illustrate the Bragg equation. The x-ray beam reflected from the lower layer
travels, 2dsin further distance than that beam reflected from the upper layer. Modified from published paper
in reference [71].
37
Single crystal X-ray diffraction (SXRD) is the most common and powerful technique for
detailed determinations of a crystal structure; it can provide accurate measurements of a
range of molecular dimensions. From single crystal diffraction data, the crystal structure of
a novel substance can be solved and refined. The possibility of success in this process is very
high and has increased recently as the experimental devices have improved and, refinement
and solution software have continued to develop [72, 73].
Crystal structure determination
There are main four steps to determine an X-ray crystal structure (Figure 20). 1. Crystal
growth, 2. X-ray measurements (Data collection), harvest reflection intensities for x-ray
images and correct for physical effects to give F2 values. 4. Solve and refine the structure,
More details about these steps will be given in the following sections.
Figure 20. Main steps to obtain an X-ray crystal structure. Sourced form [74]
38
Obtaining and selecting good quality crystals suitable for crystallographic analysis is the first
and most essential stage in solving a crystal structure. In 2011, Desiraju and his colleagues
pointed out that the quality of crystals is usually highlighted by characteristics such as size,
chemical and crystallographic purity [75]. For example, a single crystal of a suitable size is
a very important condition for a single X-ray diffraction analysis [76]. Moreover, a large
number of structural identifications have failed due to the lack of high quality crystals. A
good diffraction pattern requires good crystals with no cracks or other imperfections. In
addition, various factors such as the right solvent and time for growing crystals might have
an influence on the quality of a crystal and hence its structure. The crystallization process
can be considered as a chemical reaction of arranging atoms in a long-range order to build
up the full molecular structure [77]. Control over this process can allow one to produce
crystals with the required and reproducible properties [75]. Crystallisation might be one
simple step or might require multiple steps, as in pharmaceutical productions [77]. A range
of crystallisation methods are widely used [75, 76 and 77], but the most popular techniques
to grow crystals include vapour diffusion, solvent layering and slow evaporation; these will
be considered in the following section:
Slow evaporation: is the most common method used to crystallize organic and
organometallic compounds [75, 76, and 77]. It is based on preparation of a solution of the
compound in a suitable solvent which is placed in a covered container which is left in an
undisturbed state to let the solvent slowly evaporate (Figure 21). This procedure is very
simple and the growth ratio of crystals can be easily reduced either by slowing the
evaporation ratio of the solvent chosen or by cooling the solution.
Vapour diffraction: is the best crystallisation procedure to use according to the review of
Muller in 2009 [78]. It only requires milligram amounts of a compound and volatile solvents.
The sample is dissolved in a solvent (V1) into which the material is fully soluble in a small
vial, then placing the small vial in a larger vial that contains another solvent (V2) in which
the compound is insoluble. Vapour from the anti-solvent (V2) diffuses into the sample
solution in the small vial, causing the growth of crystals, see figure 22. These crystals,
usually, have more regular shapes than crystals obtained from the solvent evaporation
method [78].
39
Solvent layering: this process is based on the layering of one solvent (V1) in which the
material is soluble over the top of another solvent (V2) that the substance is insoluble. It is
carried out by preparing a solution of the sample using solvent (V1) in a small tube, and then
layering the second solvent (V2) very carefully. In order to succeed using this method the
density of the two solvents should be V2 < V1. However, crystals can be influenced by air
contamination or by solvent molecules which might be incorporated into the lattice of a
crystal. In fact, it is not easy to determine which crystallisation method might generate good
quality crystals, but one should attempt to define a reliable design process.
Figure 21. Crystals were grown by slow evaporation method.
Figure 22. Vapour diffusion method. Modified from [76]
40
Step two: Data collection
Once a suitable crystal for SXRD analysis has been obtained, an X-ray diffractometer is used
for collecting crystal data. This technique is designed to collect data by aiming an X-ray
beam through a crystal and record the diffracted intensity of each reflection. The X-ray
instrument consists a goniometer head, a beam stop, a detector, a video camera, a stream of
cooling N2 and an X-ray generator. A schematic of a diffractometer is given in Figure 23.
Figure 23. Schematic of a single crystal X-ray diffractometer. Obtained from [79]
The crystal is mounted on the X-ray instrument by picking it up on the tip of a thin glass
fibre, which fits into the adjustable goniometer of the diffractometer. It is usually that the
selected crystal is cooled via a stream of nitrogen gas in order to reduce the influence of
thermal motion on the data collected. An inert viscous oil is used to stick the crystal in
position on the goniometer, and to protect it from the atmosphere during the experiment. The
crystal is centred utilising a built-in telescope and by adjusting the x, y, z axes of the
goniometer head. Three of these circles (φ, x, ω) are applied to rotate the crystal and one
to move the detector round one axis. In the single crystal XRD method, very few reflections
are generated for a randomly orientated crystal in parallel X-ray beams, due to the limited
41
number of the lattice layers that are orientated at the correct angle for the Bragg equation
[65]. Accordingly, a rotation of the crystal in the X-ray beam and a variation of the angle
() must be carried out in order to increase the number of reflections and bring more lattice
layers into the correct position for a reflection. A small number of diffraction images are
recorded and processed, automatically, to determine the unit-cell dimensions and the crystal
class. This information is utilised to collect a full set of diffraction data, which has enough
images to produce an accurate molecular structure. The key step here is to assign the Miller
indices, hkl, to each refection as each spot is the sum result of the diffracted X-ray from a
Miller plane. The result of this process is a data file that contains refractions as h, k, l, a
measured intensity I and intensity associated with standard uncertainty σ(I).
Step three: Data reduction
Data reduction is a process to convert intensities I to observed structure amplitudes F.
Each spot in the X-ray diffraction pattern has an intensity, (Figure 24), which is proportional
to the square of the wave amplitude F2 [65].
Figure 24. An example of X-ray diffraction pattern. Modified from [79]
42
The measuring of these intensities might give useful information for calculating electron
density map. However several factors (both geometric and absorption) alter the observed
intensities, as a result geometrical and absorption corrections must be applied to the obtained
data from the images. Furthermore, the changes in the intensity of the incident X-ray beam
and the calculations of path lengths are examples for geometrical and absorption corrections,
respectively. A list of reflections, with h, k, l, F2, σ(F)2 are generated by the end of this
process. After abstracting the reflections from the images and applying geometrical and
absorption corrections to the observed intensities by data processing software, we turn now
to the following step.
Step four: structure solution and refinement
Solving and refining a structure from X-ray diffraction data involve a considerable amount
of mathematical work on a computer. Structure solution is the process used to obtain the
position of the atoms in the unit cell of a crystal structure from the data. An electron density
distribution at each point in the unit cell, Ρ(xyz), can be calculated from the X-ray diffraction
pattern by the following equation:
Ρ(xyz) = 1/V ∑all hklF(hkl). exp[i(hkl)] . exp[-2πi (hx + ky + lz)
Where V is the cell volume (Å3), is the phase, and F(hkl) is the structure amplitude
with Miller indices h, k, and l [65]. However, the relative phase for each reflection on the
recorded diffraction pattern is lost during the experiment. This is called the phase problem
and there are several methods used to overcome this problem. These days, direct methods
are the most popular and extensively used method in chemical crystallography. The idea of
these methods are based on selecting the most important reflections, determining the possible
relationship between their phases, then different possible phases are used to check how well
the observed relationship is satisfied [65]. Finally, calculations are performed and
recognizable molecular features are examined. If direct methods do not work, a different
method should be tried until one method is successful. The initial structural model can be
obtained by assigning atom types to the electron density map, this is done on the basis of
assigning the heaviest atoms first. The whole process of generating a satisfactory initial
solution can be made more difficult if there is disorder or weak diffraction data.
Structure refinement is a process that uses least-squares methods to obtain the simple
structural model. This is a process, whereby difference electron density maps are
superimposed on the molecular structure and any unusual structural features or unaccounted
43
for electron density identified and used to improve the model. It also provides the
crystallographer with a mathematical factor, the R-value to define the goodness of fit. Lower
values of the R-factor mean there is better matching between the molecular structure model
and the experimental data. Once the structure is fully refined, a crystallographic information
file (CIF) is generated. This file contains a full report of the structure and information such
as crystal data, bond lengths and packing. Finally, a check for any structures that are relevant
or related to the structure of interest is made in the Cambridge Crystallographic Database
(CSD) (See Figure 25).
44
Figure 25. Simple methodology followed to determine a crystal structure via X-ray
Crystallography.
X-ray powder diffraction (XRPD):
X-ray powder diffraction is a simple, rapid analytical technique which provides quantitative
and qualitative information about solid samples. It is based on the fact that each crystalline
material has a unique X-ray diffraction pattern, thus if there is an exact match between the
diffraction pattern of an unknown sample and an authentic material, then the unknown may
be identified.
When a homogenous crystalline powder sample is struck by an X-ray beam at an angle ,
and specific wavelength λ, a series of peaks, indicating diffraction from a particular set of
crystal layers, is produced, which is then detected. The powder diffraction pattern thus plots
various intensity lines, I, against 2 angles. The use of a powder diffraction pattern to
identify a species depends on the line positions and their relative intensities, see figure 26.
Moreover, the intensity of lines is based upon the kind and number of atomic scattering
centres in each series of layers.
Figure 26. An example of X-ray powder diffraction pattern
C4F9I
Operations: Background 0.021,1.000 | Import
C4F9I - File: C4FIPph3.raw - Type: 2Th/Th locked - Start: 5.000 ° - End: 59.995 ° - Step: 0.039 ° - Step time: 71.3 s - Temp.: 25 °C (Room) - Time Started: 12 s - 2-Theta: 5.000 ° - Theta: 2.500 ° - Chi: 0.00 ° - Ph
L in
I
2
46
The main advantages of the XRPD technique, over that of single crystal work, is the ease of
sample preparation, the rapidity of measurements, and the ability to identify the presence of
unknown phases, investigate phase changes and determine sample purity. Another important
advantage of this method is its ability to analyse mixed phases by measuring intensity peaks
arising from each component and comparing these with standard materials.
On the other hand, difficulty in measuring an accurate three-dimensional structure is the
main disadvantage of the powder diffraction technique, as much data is lost by the collapse
of the 3D single crystal diffraction pattern to the 1D diffraction pattern. The reduced
information available from a powder pattern often makes the process of trying to solve a
crystal structure difficult and ambiguous.
In fact, both X-ray powder diffraction and single crystal X-ray diffraction techniques can be
used for identification of new crystalline phases and new structures and both will be
employed in this investigation of halogen bonds in crystals.
Conclusion
The importance of having an effective tool to either store or destroy halocarbons arises from
the widespread use, naturally slow decomposition and bio-accumulation of heavily
fluorinated compounds, as such these compounds present a potential risk to human health.
Pollution from perfluoroalkyl compounds has been recorded by authors in different
environmental areas such as fish [80] and rivers [81]. Winterton [82] in his study points out
that approximately 200 cloro compounds are produced, transformed, transported and
accumulated by natural process in the environment. The identification of halogen bonding
by crystallography could signal a valuable method to trap and help reduce the emissions of
perfluorocarbons in nature.
Recently halogen bonding has become a valuable and reliable non-bonded interaction for
crystal engineering. It is a strong and directional intermolecular interaction which can be
used to synthesise and design new crystals with specific physical and chemical properties,
such as being able to control the dimensionality of the halogen-bonded adducts. Most of the
halogen-bonded interactions to date have focussed on N…I systems, demonstrating
distances that range from 2.715 – 3.452 Å [average distance is 2.932 Å] and with C-N…I
angles close to linearity.
47
Crystallography is an experimental science to identify the atomic and molecular structures
of crystals. It is an important technique to provide information on the non-covalent
intermolecular interactions between atoms and molecules. The importance of
crystallographic methods can be seen from the considerable development of our current
knowledge of supramolecular architectures which has been gained from X-ray diffraction
studies of crystals. The subsequent chapters demonstrate several investigations into N…I,
N…Br and P…I interactions for holding halofluorocarbons in the solid states.
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diazabicyclo[2.2.2]octane
Alan K. Brisdon, Abeer M. T. Muneer and Robin G. Pritchard, Acta Cryst., 2015, C71, 900–
902
Halogen-bonded adduct of 1,2-dibromo-1,1,2,2-tetrafluoroethane and 1,4-diazabicyclo[2.2.2]octane
Alan K. Brisdon, Abeer M. T. Muneer and Robin G. Pritchard
Acta Cryst. (2015). C71, 900–902
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Acta Cryst. (2015). C71, 900–902 Brisdon et al. · C2Br2F4·C6H12N2
Received 3 August 2015
Accepted 3 September 2015
England
1,4-diazabicyclo[2.2.2]octane; dibromotetra-
fluoroethane; extended structures; phase
change; one-dimensional polymeric structure;
supporting information at journals.iucr.org/c
Halogen-bonded adduct of 1,2-dibromo-1,1,2,2- tetrafluoroethane and 1,4-diazabicyclo[2.2.2]- octane
Alan K. Brisdon,* Abeer M. T. Muneer and Robin G. Pritchard
School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, England. *Correspondence e-mail:
alan.brisdon@manchester.ac.uk
Halogen bonding is an intermolecular interaction capable of being used to direct
extended structures. Typical halogen-bonding systems involve a noncovalent
interaction between a Lewis base, such as an amine, as an acceptor and a
halogen atom of a halofluorocarbon as a donor. Vapour-phase diffusion of 1,4-
diazabicyclo[2.2.2]octane (DABCO) with 1,2-dibromotetrafluoroethane results
in crystals of the 1:1 adduct, C2Br2F4C6H12N2, which crystallizes as an infinite
one-dimensional polymeric structure linked by intermolecular N Br halogen
bonds [2.829 (3) A], which are 0.57 A shorter than the sum of the van der Waals
radii.
molecular interaction, comparable to hydrogen bonding
(Metrangolo et al., 2005), capable of being used to direct
extended structures, and there are examples of its application
ranging from crystal engineering (Cavallo et al., 2010) to
organocatalysis (Kniep et al., 2013). Very recently, halogen
bonding has also been used as a method of converting highly
volatile organofluorine compounds, which are difficult to
handle, into a more easily handled form by halogen-bond
adduct formation (Aakeroy et al., 2015).
Prototypical halogen-bonding systems involve a noncova-
lent interaction between a Lewis base, such as an amine, as a
halogen-bond acceptor, and a halogen, most often iodine, of a
halofluorocarbon, which acts as a donor (Desiraju et al., 2013).
The halide of the fluorocarbon is able to act in this way
because of the distortion of the electron density of the Rf—X
bond (Rf is a perfluorinated organic group), caused by the
strongly electron-withdrawing Rf group, resulting in an area of
reduced electron density on the X atom opposite the C—X
bond, called a -hole. This linear, or near-linear, arrangement
is described as a type I halogen bond (Desiraju & Parthasar-
athy, 1989).
strength of the halogen-bond interaction is greater between
amines and iodine acceptors than it is in the bromo analogues,
and so, typically, C—I N halogen-bonded interactions are
frequently stronger than those in C—Br N systems.
ISSN 2053-2296
electronic reprint
trapping and holding small bromofluorocarbons that are
volatile and ozone-depleting substances. It was thus of interest
to investigate the halogen bonding in the 1:1 adduct, (I), of
1,4-diazabicyclo[2.2.2]octane (DABCO) with 1,2-dibromo-
tetrafluoroethane, the structure of which is reported here.
2. Experimental
from commercial sources and were used without further
purification.
Preparation of the title compound was by vapour diffusion
in a sealed system consisting of two concentric glass vials. In
the smaller inner vial was placed DABCO (0.1 g), with
BrCF2CF2Br (0.5 ml) in the outer vial. Crystals suitable for
X-ray diffraction studies formed within 24 h at room tem-
perature on the surface of the inner vial. IR (, cm1): 2934.9,
2871.0 (C—H), 1149.4, 1097.5 (C—F).
2.2. Refinement
details are summarized in Table 1. Adduct (I) crystallized in
the monoclinic space group I2/a, with half a molecule per
asymmetric unit. H atoms were visible in difference maps and
were allowed for as riding atoms, with C—H = 0.97 A and
Uiso(H) = 1.2Ueq(C).
3. Results and discussion
The asymmetric unit of the title adduct, (I), comprises half a
molecule of both DABCO and BrCF2CF2Br. Both the
DABCO and BrCF2CF2Br molecules possess crystallographic
C2 symmetry. The complete molecular structure of (I) is shown
in Fig. 1. The bond lengths and angles (Table 2) are largely as
expected. DABCO undergoes a phase change at 351 K under
atmospheric pressure (Chang & Westrum, 1960; Trowbridge &
Westrum, 1963). The low-temperature phase (Sauvajol, 1980),
i.e. phase II, data reports N—C and C—C bond lengths of
1.4834 and 1.5355 A, respectively, and C—N—C angles of
107.29, which compare with the corresponding average values
of 1.471 (5), 1.548 (5) A and 108.4 (3) in (I). Similarly, the
average parameters obtained for the BrCF2CF2Br unit here
[Br—C = 1.939 (4) A, C—C = 1.516 (8) A and C—F =
1.337 (5) A] are comparable to those obtained previously
from a neutron diffraction study (Pawley & Whitley, 1988).
The extended structure displays near-linear interactions
[N Br—C angle = 175.6 (1)] of the N atoms of the DABCO
research papers
Acta Cryst. (2015). C71, 900–902 Brisdon et al. C2Br2F4C6H12N2 901
Table 1 Experimental details.
Crystal data Chemical formula C2Br2F4C6H12N2
Mr 372.02 Crystal system, space group Monoclinic, I2/a Temperature (K) 150 a, b, c (A) 10.9815 (9), 10.8697 (10),
11.1525 (9) () 111.135 (9) V (A3) 1241.68 (19) Z 4 Radiation type Mo K (mm1) 6.55 Crystal size (mm) 0.20 0.13 0.07
Data collection Diffractometer Agilent SuperNova Single Source
diffractometer with an Eos detector
Absorption correction Multi-scan (CrysAlis PRO; Agilent, 2014)
Tmin, Tmax 0.159, 1.000 No. of measured, independent and
observed [I > 2(I)] reflections 2416, 1282, 1028
Rint 0.032 (sin /)max (A1) 0.627
Refinement R[F 2 > 2(F 2)], wR(F 2), S 0.037, 0.069, 1.03 No. of reflections 1282 No. of parameters 73 H-atom treatment H-atom parameters constrained max, min (e A3) 0.61, 0.64
Computer programs: CrysAlis PRO (Agilent, 2014), SHELXS87 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015) and OLEX2 (Dolomanov et al., 2009).
Table 2 Selected geometric parameters (A, ).
Br1—C4 1.939 (4) N1—C3 1.477 (5) F2—C4 1.336 (4) C4—C4i 1.516 (8) F1—C4 1.338 (5) C1—C1ii 1.535 (6) N1—C1 1.471 (5) C2—C3ii 1.553 (4) N1—C2 1.466 (5) C3—C2ii 1.553 (4)
C1—N1—C3 108.7 (3) F2—C4—Br1 109.2 (3) C2—N1—C1 108.8 (3) F2—C4—F1 107.6 (3) C2—N1—C3 107.6 (3) F1—C4—Br1 109.5 (3)
Symmetry codes: (i) xþ 1 2; y;zþ 1; (ii) x 1
2; y;z.
Figure 1 A view of the components of (I), showing the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. [Symmetry codes: (i) x + 1
2, y, z + 1; (ii) x 1 2, y, z.]
electronic reprint
molecule with the Br atoms of BrCF2CF2Br, resulting in an
extended one-dimensional polymeric structure based on the
formation of Br N contacts (Fig. 2). The N Br distance of
2.829 (3) A, is 0.57 A (16.8%) shorter than the sum of the van
der Waals radii for nitrogen and bromine (3.40 A). Taken
together, the short N Br distance and collinear allignment
indicate the presence of a type I halogen-bonding interaction.
This is further supported by a reduction in the C—F stretching
frequencies (max 1149.4 and 1097.5 cm1) in (I), compared
with the values 1158.6 and 1109.8 cm1 observed for
BrCF2CF2Br.
interactions in the structure of (I). There are no classical
hydrogen bonds formed, indeed the shortest intermolecular
H F distance is 2.66 A, and although some short F F and
F Br interactions are observed, these are intramolecular
rather than intermolecular in nature.
A search of the Cambridge Structural Database (CSD,
Version 5.36; Groom & Allen, 2014) was undertaken for
contacts between a tertiary N atom and an organic-bound Br
atom less than the sum of their van der Waals radii. Of the 37
hits returned, the C—N Br distances were found to lie
between 2.531 and 3.379 A, with the average being 3.138 A.
By comparison, searches carried out for the analogous iodine,
rather than bromine, system results in a slightly larger number
of hits (47), with C—N I distances in the range 2.715–
3.452 A, and a shorter average distance (2.932 A), which is
consistent with a greater degree of interaction for the more
polarizable iodine centre, in agreement with the current
understanding of halogen bonding.
It is noteworthy that of the crystallographically character-
ized C—N Br—C adducts, only two have DABCO as the
halogen-bond acceptor. In the structure of the adduct formed
between DABCO and 1,4-dibromotetrafluorobenzene (CSD
refcode DIVDUI; Cincic et al., 2008), a one-dimensional
polymeric arrangement is also formed, with C—N Br =
2.894 (2) and 2.910 (2) A. The shorter of these distances is still
significantly longer (20 ) than observed in (I), where the
halogen-bond distance is 2.829 (3) A. Whilst in the only
reported BrCF2CF2Br adducts of nitrogen-containing com-
pounds, namely Me2NCH2CH2NMe2 (REMBOB; Huang et
al., 2006) and 1,4-dimethylpiperizine (ULOJUA; Chu et al.,
2003), the C—N Br distances are remarkably similar at
2.864 (3) and 2.863 (5) A, respectively, but both distances are
longer than the equivalent interaction found in (I).
In conclusion, the adduct formed between DABCO and
BrCF2CF2Br results in a method of trapping the volatile (and
ozone-depleting) bromofluorocarbon. The resulting crystals
adopt a one-dimensional polymeric structure in which the C—
N Br halogen-bond length is shorter than the average for
related type I C—N Br—C halogen-bonded systems, and
shorter than found in the two other reported crystal structures
of related Br2C2F4 adducts.
We thank the Libyan Government for support of AM. We
acknowledge the EPSRC for support of the departmental
X-ray diffraction facilities (grant No. EP/K039547/1).
References
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research papers
902 Brisdon et al. C2Br2F4C6H12N2 Acta Cryst. (2015). C71, 900–902
Figure 2 A view of the intermolecular halogen bonds (dashed lines) in the crystal structure of (I).
electronic reprint
supporting information
supporting information
azabicyclo[2.2.2]octane
Alan K. Brisdon, Abeer M. T. Muneer and Robin G. Pritchard
Computing details
Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis
PRO (Agilent, 2014); program(s) used to solve structure: SHELXS87 (Sheldrick, 2008); program(s) used to refine
structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to
prepare material for publication: OLEX2 (Dolomanov et al., 2009).
1,2-Dibromo-1,1,2,2-tetrafluoroethane–1,4-diazabicyclo[2.2.2]octane (1/1)
Crystal data
C2Br2F4·C6H12N2
Mr = 372.02 Monoclinic, I2/a a = 10.9815 (9) Å b = 10.8697 (10) Å c = 11.1525 (9) Å β = 111.135 (9)° V = 1241.68 (19) Å3
Z = 4
F(000) = 720 Dx = 1.990 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 1070 reflections θ = 3.9–28.5° µ = 6.55 mm−1
T = 150 K Block, colourless 0.2 × 0.13 × 0.07 mm
Data collection
Radiation source: SuperNova (Mo) X-ray Source
Mirror monochromator Detector resolution: 8.0714 pixels mm-1
ω scans Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2014)
Tmin = 0.159, Tmax = 1.000 2416 measured reflections 1282 independent reflections 1028 reflections with I > 2σ(I) Rint = 0.032 θmax = 26.5°, θmin = 3.8° h = −8→13 k = −5→13 l = −13→13
Refinement
Refinement on F2
Least-squares matrix: full R[F2 > 2σ(F2)] = 0.037 wR(F2) = 0.069 S = 1.03 1282 reflections 73 parameters 0 restraints
Primary atom site location: structure-invariant direct methods
Hydrogen site location: inferred from neighbouring sites
H-atom parameters constrained w = 1/[σ2(Fo
2) + (0.0193P)2] where P = (Fo
2 + 2Fc 2)/3
Δρmax = 0.61 e Å−3 Δρmin = −0.63 e Å−3
Special details
Experimental. Absorption correction: CrysAlisPro, Agilent Technologies, Version 1.171.37.33 (release 27-03-2014 CrysAlis171 .NET) (compiled Mar 27 2014,17:12:48) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x y z Uiso*/Ueq
Br1 0.11014 (3) 0.89688 (4) 0.28496 (3) 0.02625 (16) F2 0.3393 (2) 0.8020 (3) 0.4401 (2) 0.0557 (9) F1 0.3359 (2) 1.0005 (3) 0.4381 (2) 0.0601 (9) N1 &