Chains, layers, channels, and more: Supramolecular chemistry of potent diphosphonic tectons with tuned flexibility. the generation of pseudopolymorphs, polymorphs, and adducts

Article abstract of DOI:10.1021/cg400859e

Naphthalene-1,5-diphosphonic acid [C₁₀H₆(PO ₃H₂)₂, H₄NDP(1,5), 1] and its more flexible counterpart, naphthalene-1,5-bis(methylphosphonic) acid [C ₁₀H₆(CH₂PO₃H₂) ₂, H₄NDP(1C,5C), 2], have been synthesized, characterized, and used as building blocks in supramolecular assemblies with 4-(N,N-dimethylamino)pyridine (DMAP) and morpholine. The two acids generate two distinct solvatomorphs each, with and without dimethyl sulfoxide (DMSO) molecules. The two adducts of H₄NDP(1,5) with DMAP (3A and 3B) reveal conformational polymorphism caused by the rotation of phosphonic groups. The two adducts of H₄NDP(1C,5C) show unexpected structural diversity, generating a symmetric hydrogen bond and creating a layered structure, 4A, or a channel structure, 4B. The adducts of both acids with morpholine (5A and 5B) allow for observing the influence of the conformational flexibility of the acids on the dimensionality of a final hydrogen bond network, which is in general higher for H₄NDP(1C,5C). The structural motifs and trends are analyzed in terms of the geometric criteria of these interactions. For the first time, Hirshfeld surface analysis has also been applied for the investigation of supramolecular interactions of phosphonic acids in different protonation states.

Full text of DOI:10.1021/cg400859e

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Article
Chains, layers, channels and more - supramolecular chemistry
of potent diphosphonic tectons with tuned flexibility. The
generation of pseudopolymorphs, polymorphs, and adducts
Micha# Jacek Bia#ek, Jan Kazimierz Zar#ba, Jan Janczak, and Jerzy Zon
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/cg400859e • Publication Date (Web): 01 Aug 2013
Downloaded from http://pubs.acs.org on August 11, 2013
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Chains, layers, channels and more – supramolecular chemistry of potent
diphosphonic tectons with tuned flexibility. The generation of pseudopolymorphs,
polymorphs, and adducts
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Michał J. Białek,a,b,* Jan K. Zaręba,a Jan Janczak,c Jerzy Zońa,d*
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a) Faculty of Chemistry, Wrocław University of Technology, 27 Wybrzeze Wyspianskiego Street, 50ꢀ370 Wrocław,
Poland
b) Department of Chemistry, University of Wrocław, 14 F. JoilotꢀCurie Street, 50ꢀ383 Wrocław, Poland
c) Institute of Low Temperature and Structural Research, Polish Academy of Sciences, 2 Okolna Street, P.O. Box
1410, 50ꢀ950 Wrocław, Poland
d) Faculty of Mechanical and Power Engineering, Wrocław University of Technology, 27 Wybrzeze Wyspianskiego
Street, 50ꢀ370 Wrocław, Poland
* (M.J.B.) michal.bialek@chem.uni.wroc.pl
* (J.Z.) jerzy.zon@pwr.wroc.pl
ABSTRACT
Naphthaleneꢀ1,5ꢀdiphosphonic acid [C10H6(PO3H2)2, H4NDP(1,5), 1] and its more flexible
counterpart – naphthaleneꢀ1,5ꢀbis(methylphosphonic) acid [C10H6(CH2PO3H2)2, H4NDP(1C,5C),
2] – have been synthesized, characterized and used as building blocks in supramolecular
assemblies with 4ꢀ(N,Nꢀdimethylamino)pyridine (DMAP) and morpholine. The two acids
generate two distinct solvatomorphs each, which all contain dimethyl sulfoxide (DMSO)
molecules. The two adducts of H4NDP(1,5) with DMAP (3A and 3B) reveal conformational
polymorphism caused by the rotation of phosphonic groups. The two adducts of H4NDP(1C,5C)
show unexpected structural diversity, generating a symmetric hydrogen bond and creating
a layered structure 4A or a channel structure 4B. The adducts of both acids with morpholine (5A
and 5B) allow for observing the influence of the conformational flexibility of the acids on the
dimensionality of a final hydrogen bond network, which is in general higher for H4NDP(1C,5C).
The structural motifs and trends are analyzed in terms of the geometric criteria of these
interactions. For the first time, Hirshfeld surface analysis has also been applied for the
investigation of supramolecular interactions of phosphonic acids in different protonation states.
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Chains, layers, channels and more – supramolecular
chemistry of potent diphosphonic tectons with tuned
flexibility. The generation of pseudopolymorphs,
polymorphs, and adducts
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Michał J. Białek,a,b,* Jan K. Zaręba,a Jan Janczak,c Jerzy Zońa,d*
a) Department of Chemistry, Wrocław University of Technology, 27 WybrzeŜe Wyspiańskiego
Street, 50ꢀ370 Wrocław, Poland
b) Department of Chemistry, University of Wrocław, 14 F. JoilotꢀCurie Street, 50ꢀ383 Wrocław,
Poland
c) Institute of Low Temperature and Structural Research, Polish Academy of Sciences, 2 Okólna
Street, P.O. Box 1410, 50ꢀ950 Wrocław, Poland
d) Faculty of Mechanical and Power Engineering, Wrocław University of Technology, 27
WybrzeŜe Wyspiańskiego Street, 50ꢀ370 Wrocław, Poland
* (M.J.B.) michal.bialek@chem.uni.wroc.pl
* (J.Z.) jerzy.zon@pwr.wroc.pl
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ABSTRACT
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Naphthaleneꢀ1,5ꢀdiphosphonic acid [C10H6(PO3H2)2, H4NDP(1,5), 1] and its more flexible
counterpart – naphthaleneꢀ1,5ꢀbis(methylphosphonic) acid [C10H6(CH2PO3H2)2, H4NDP(1C,5C),
2] – have been synthesized, characterized and used as building blocks in supramolecular
assemblies with 4ꢀ(N,Nꢀdimethylamino)pyridine (DMAP) and morpholine. The two acids
generate two distinct solvatomorphs each, which all contain dimethyl sulfoxide (DMSO)
molecules. The two adducts of H4NDP(1,5) with DMAP (3A and 3B) reveal conformational
polymorphism caused by the rotation of phosphonic groups. The two adducts of H4NDP(1C,5C)
show unexpected structural diversity, generating a symmetric hydrogen bond and creating a
layered structure 4A or a channel structure 4B. The adducts of both acids with morpholine (5A
and 5B) allow for observing the influence of the conformational flexibility of the acids on the
dimensionality of a final hydrogen bond network, which is in general higher for H4NDP(1C,5C).
The structural motifs and trends are analyzed in terms of the geometric criteria of these
interactions. For the first time, Hirshfeld surface analysis has also been applied for the
investigation of supramolecular interactions of phosphonic acids in different protonation states.
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INTRODUCTION
Crystal engineering is an already wellꢀestablished but continuously developing branch of
material science.1,2 Nevertheless, the accurate prediction of a structure and the properties of a
product from the structures of basic substrates, which can be considered a designing process,
remains the ultimate goal.2,3 The exploration of new crystal structures and interactions
responsible for such an arrangement brings a lot of useful information concerning factors
important in structure formation, which enables drawing more general conclusions, helpful in the
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design process.4,5 Geometrical criteria are usually used in the analysis of intermolecular
interactions. Recently, Hirshfeld surface (HS) analysis has also become a potent tool for
structural investigations.6,7
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It should, however, be noted that supramolecular assemblies are vulnerable to environmental
changes. From the same building blocks, one can obtain different supramolecular products,
depending on the kind of interactions that prevail in the applied conditions. Such supramolecular
isomers, with the same chemical composition but different structural arrangements, constitute a
group of polymorphs.8,9 If the composition is variable only due to the presence of solvent
molecules, one is dealing with the pseudopolymorphism (also known as solvatomorphism)
phenomenon.10ꢀ12 Both polymorphism and pseudopolymorphism are significant in terms of the
modulation of the physicochemical properties of materials, which manifests itself, for example,
in pharmacy.11ꢀ16
Nonetheless, an important step in crystal structure design is the careful selection of building
blocks that will constitute the final solid. Selected units need to contain functional groups that are
able to create intermolecular bonding with prefixed directionality. When organic solids are
considered, hydrogen bonding is the most important and the most widely studied interaction,17
which can be supported, for example, by less directional but still influential πꢀπ aromatic
interactions.18,19 Due to this fact, organic acids containing aromatics in their scaffold are
frequently utilized in the synthesis of new materials. Such versatile molecules provide a great
opportunity for the introduction of a design factor to the final product structure.
A naphthalene ring is one of the most important aromatic platforms for organic functional
ligands. It is usually divergently substituted with functional groups accessible for intermolecular
interactions, i.e. coordination or hydrogen bonding. This platform is successfully applied in a
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number of novel structures. If a functional group is considered, the most widely explored one,
especially in the context of MetalꢀOrganic Frameworks, is the carboxylic group. 1,4ꢀ and 2,6ꢀ
disubstituted naphthalenes perform an important role as linear, rigid linkers between metal
centres.20,21 In this context, naphthaleneꢀ1,5ꢀdicarboxylic acid is prevalent in patent literature.22ꢀ25
It is quite the opposite case when the sulfonic function (ꢀSO3H) is applied.26,27 Naphthaleneꢀ
1,5ꢀdisulfonic acid [H2NDS(1,5)] is frequently used as an organic building unit for
supramolecular assemblies,28ꢀ33 and in coordination chemistry – as a counter ion34,35 or
coordination polymer linker.36ꢀ43 The CSD search44 provided 194 structures into which NDS(1,5)
moiety is incorporated. In general, sulfonic acids have quite different properties from carboxylic
acids. They are much more acidic, thus remain ionized in a wide pH range and are more soluble.
The sulfonic group is tetrahedral due to an additional oxygen atom bonded to a central sulfur
atom, which introduces some additional conformational flexibility in comparison to the
carboxylic group.
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Following this approach, substitution of the sulfonic group by a geometrically similar
phosphonic one, i.e. ꢀPO3H2, should give new potent phosphonic tectons,45,46 also with some
advantages over sulfonated molecules: 1) phosphonic acids are more stable in a free state,
whereas sulfonic acids are usually handled as sodium salts; 2) coordination structures of
phosphonic acids are less labile and often have high thermal stability; 3) phosphonic acids are
also a little less acidic and have two deprotonation states. Especially this last fact enriches the
supramolecular chemistry of the phosphonic function in terms of hydrogen bond network
generation, as well as providing a better control of accessibility to lone electron pairs due to
gradual deprotonation of the group. Such a tecton opens new paths to obtaining novel organic
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solids and metal phosphonates, which have already grown into a potent family of hybrid
materials.27,47ꢀ50
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Scheme 1. Representation of potent organic tectons based on a 1,5ꢀnaphthalene scaffold:
dicarboxylic (NDC), disulfonic (NDS), and diphosphonic (NDP) acids.
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In view of the fact that naphthaleneꢀ1,5ꢀdisulfonic acid is an important tecton, we have
obtained its phosphonic analogue, namely naphthaleneꢀ1,5ꢀdiphosphonic acid, [H4NDP(1,5)],
which had previously remained a missing link in the series of 1,5ꢀdisubstituted naphthalenes
(Scheme 1). To enable the study of the conformational flexibility issue, we have also obtained its
flexible counterpart – naphthaleneꢀ1,5ꢀbis(methylphosphonic) acid, [H4NDP(1C,5C)], with
methylene groups introduced between the ring and each group. This facilitates the
accommodation of the groups to the requirements of engineered networks, especially
coordination ones. We have discussed this behavior in our recent paper concerning the first
diphosphonic acids based on a naphthalene ring.10 There, two 1,4ꢀdisubstituted acids proved to
be useful in the synthesis of crystalline lanthanum phosphonates with the evident influence of pH
and the flexibility of the ligand on the final hybrid structures. Herein, we present two easily
obtainable 1,5ꢀdiacids (1 and 2) as potent supramolecular building units, exploring their abilities
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to generate pseudopolymorphs (1Aꢀ2B), polymorphs and adducts with 4ꢀ(N,Nꢀ
dimethylamino)pyridine (3Aꢀ4B), and morpholine (5A, 5B) (see Scheme 2). We also apply
geometrical criteria for interaction analysis assisted by Hirshfeld surface analysis of phosphonic
tectons in such diverse environments.
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Scheme 2. The building units used in this article and the symbols of the structures.
EXPERIMENTAL SECTION
Synthesis of phosphonic acids. Both compounds (1 and 2) were obtained in accordance with
wellꢀknown methods51,52 with high yield and simple workup (see Electronic Supporting
Information (ESI) for detailed description and characterization). During the phosphonylation step
of the process (the transformation of compound b to c in Scheme 3), nickelꢀcatalyzed crossꢀ
coupling53,54 was applied for 1 and the Arbuzov reaction55 for 2. Scheme 3 summarizes the
synthetic route for both diphosphonic acids. Their DMSO solvatomorphs were obtained through
the slow cooling of saturated DMSO/water solutions (see ESI for details).
Scheme 3. Synthesis of phosphonic acids: a) naphthaleneꢀ1,5ꢀdiphosphonic acid [1,
H4NDP(1,5)]; and b) naphthaleneꢀ1,5ꢀbis(methylphosphonic) acid [2, H4NDP(1C,5C)].
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Synthesis of acid-base adducts. The general procedure is as follows:
0.10 mmol of acid [0.0288g of H4NDP(1,5) or 0.0316 g of H4NDP(1C,5C)] were mixed with a
few cm3 of solvent and one equivalent [for 4A – C10H6(CH2PO3H)2(C7H11N2)2 ꢁ 2H2O and for 4B
– C10H6(CH2PO3H)(CH2PO3H2)(C7H11N2) ꢁ H2O] or two equivalents [for 3A and 3B –
C10H6(PO3H)2(C7H11N2)2] of 4ꢀ(N,Nꢀdimethylamino)pyridine (DMAP). The mixtures were
filtered (and also refluxed for 3A and 3B) and left for slow evaporation at room temperature.
After a few weeks, colorless crystals were obtained with yields ranging from 20 to 60 %. The
adducts of both acids with morpholine [5A – C10H6(PO3H)2(C4H8ONH2)2 and 5B ꢀ
C10H6(CH2PO3H)2(C4H8ONH2)2] were obtained from appropriate mixtures with an excess of
amine (detailed description in ESI).
X-ray crystallography. All the obtained single crystals were used for data collection on a
fourꢀcircle KUMA KM4 diffractometer equipped with a twoꢀdimensional CCD area detector.
Graphite monochromatized MoKα radiation (λ = 0.71073 Å) and the ωꢀscan technique (ꢀω = 1º)
were also used for data collection, while additional data collection and reduction, along with
absorption correction, were performed using the CrysAlis software package.56 The structures
were solved by direct methods using SHELXSꢀ97,57 revealing the positions of almost all nonꢀ
hydrogen atoms. The remaining atoms were located as a result of subsequent difference Fourier
syntheses. The structures were refined using SHELXLꢀ9757 with anisotropic displacement
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parameters. Details of the data collection parameters, crystallographic data and final agreement
parameters are listed in Table S1, while selected geometrical parameters can be found in Table
S2. The geometry of the hydrogen bonds is listed in Table S3. Visualisation of the structures was
conducted using the Diamond program,58 while a topological simplification of HB networks was
performed with the Topos package.59 Some geometrical features of intermolecular interactions
were determined with the help of Platon software,60 while the Hirshfeld surface and 2D
fingerprint calculations61 were performed using the Crystal Explorer package.62
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Hirshfeld surface analysis. Hirshfeld surface analysis is a method with a different philosophy
than traditional structure viewing: it treats molecular interactions as being a whole.63 Such an
analysis provides information about all existing interactions in the structure, not only about those
that arbitrarily seem to be important for a crystal engineer. Information about interactions is
conveyed by the use of colorꢀcoding the surface properties (i.e. dnorm, shape index, and
curvedness functions) onto the surface,64 thus the localization of contacts of interest is achieved
using color differentiation. HS analysis is almost always connected with considerations of 2D
Fingerprint Plots (FP).65,66 In such plots, relative areas of points, which can be attributed to
certain close contacts, are identified and their percentage share is provided. This quantification of
molecular interactions enables an objective comparison of crystal structures. The visual
breakdown of the HS and FP into selected contacts (decomposed HSs and FPs) allows for
selective viewing and analyzing of a particular type of interactions. HS analysis is also a helpful
tool in the comparison of very similar polymorph structures.8,67
RESULTS AND DISCUSSION
The synthesis of phosphonic acids. The synthesis of acids (1 and 2) from commercially
available substrates proceeds in three steps, with good to excellent yields. The main step is a
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phosphonylation reaction of appropriate dihalides [catalyzed with NiBr2 for H4NDP(1,5)]. The
dihalides can be dibromide as well as diiodide, but variants of the reactions presented in Scheme
3 appear to be the easiest to access. The molecular structures of obtained esters have been
confirmed by spectroscopic examinations as well as single crystal Xꢀray diffraction studies (6A
and 6B) (Fig. S7). Although ester 2c is mentioned in the available literature, no detailed synthetic
and physicochemical descriptions are provided.68,69 After a simple workup, the obtained
tetraesters can be subjected to an acidic hydrolysis reaction in order to obtain final acids as white
solids. Free phosphonic acids are usually utilized as organic building blocks, especially in
coordination polymer synthesis. Nonetheless, esters can be hydrolyzed in situ in appropriate
conditions, providing interesting metal phosphonate structures.70,71
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Pseudopolymorphism observed for the structures of acids
Despite the enormous interest in metal phosphonate chemistry, less pronounced investigations
of the structures of free phosphonic acids in their solid state have been conducted thus far.
However, the examination of such structures can provide valuable information about a given
organic building unit and its preferences concerning supramolecular network generation.10,72ꢀ80
In the case of both acids, 1 and 2, we describe such structures together with their
solvatomorphs (unsolvated – 1A and 2A; and solvated – 1B and 2B). The majority of organic
molecular crystal structures do not contain incorporated organic solvents, but if such solvent
molecules are present, DMSO is one of the most frequently occurring,81 and this is also the case
here, which allows for an exploration of the solvent’s effects on these systems.
Naphthalene-1,5-diphopshonic acid, NDP(1,5) (1A) and its DMSO solvate (1B). The
pseudopolymorphs of H4NDP(1,5) show to what extent the presence of solvent molecules can
affect a final superstructure. The free acid crystallizes in the Pbca space group. Due to the
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internal Ci symmetry, the molecule lies at the inversion centre, thus the asymmetric unit is
comprised of half of the molecule (Fig. S1). All molecules in 1A are arranged in a wellꢀknown
motif in phosphonate chemistry, where phosphonic groups constitute hydrogenꢀbonded layers
and are interconnected in the third dimension by organic linkers, in this case – 1,5ꢀdisubstituted
naphthalenes (Fig. 1). The separation of HB layers is ca. 0.5 Å higher for such a linker than for
the analogous 1,4ꢀdisubstituted naphthalene (6.95 Å vs. 6.40 Å from one terminal phosphorous
atom to the other).10
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The predominant force responsible for the arrangement of the molecules is hydrogen bonding.
A hydrogen bond network is two dimensional (Fig. 2), parallel to the ab plane and is built from
two crystallographically independent OꢀHꢁꢁꢁO hydrogen bonds (Table S3). Hydroxyl oxygen
atoms are single donors, while a phosphoryl oxygen atom is a double acceptor of HBs. This leads
to a motif that can be described, according to the graph set theory,82 as a secondꢀorder ꢀꢁꢂꢃ14ꢄ
ring motif. The complete network is constructed by the multiplication of the motif using aꢀ and
bꢀglide planes. From another point of view, this network can be rebuilt from two firstꢀorder
chains C(4) constituted by each hydrogen bond. The first one, O1ꢀP1ꢀO3ꢀH3O, is propagated
along [100] (light blue), and the second, O1ꢀP1ꢀO2ꢀH2O, runs along [010] (dark blue). The
connection of HB layers in the third direction by naphthalene linkers results in the generation of
a 3D network.
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Figure 1. Projections of the crystal structures of solvatomorphs a) 1A and b) 1B together with
their topological simplifications.
Acceptor sites are visible on the shape index surface (Fig. S8) as slightly elongated red
depressions of the HS above the naphthalene fused ring. Complementary donor sites of these
interactions are marked blue around the aromatic hydrogen atoms.
The supramolecular structure of the second pseudopolymorph, 1B, is drastically different from
ꢅ
1A: the typical layered structure is broken (Fig. 1). The crystal’s symmetry is reduced to the P1
space group. The asymmetric unit (Fig. S1) consists of half of the acid molecule and one DMSO
molecule. Thus, there are two DMSO molecules per one H4NDP(1,5) moiety. Each solvent
molecule is therefore connected via an O5ꢁꢁꢁH3ꢀO3 hydrogen bond to the one phosphonic group.
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Another intermolecular hydrogen bonding, (O2ꢀH2ꢁꢁꢁO1), connects adjacent phosphonic groups
providing a strong ꢀꢆꢆꢃ8ꢄ motif. This synthon holds together the acid molecules, generating a
supramolecular chain which runs along the c axis (Fig. 2).
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Figure 2. Isolated hydrogenꢀbonded networks for a) 1A and b) 1B. Dashed lines symbolize
hydrogen bonds.
DMSO molecules act as pendants in these chains. They also participate in the interactions that
hold the whole crystal together in the two other directions. In Figure S8, DMSO molecule
interactions with the acid molecule are presented using the shape index surface of 1B. Along the
a and c axes, mainly van der Waals and H2CꢀHꢁꢁꢁO interactions can be observed. The latter ones
appear as red spots around the phosphonic group, as well as being present in the 2D fingerprint
plot (Table S4) with de = 1.12 Å and di = 1.42 Å. Along the b axis, one can distinguish CꢀHꢁꢁꢁCg
interactions between one methyl group and the naphthalene ring.
Naphthalene-1,5-bis(methylphosphonic) acid, NDP(1C,5C) (2A) and its DMSO solvate,
2B. H4NDP(1C,5C) molecules undergo a selfꢀassembly process providing a layered structure,
similarly to 1A. Crystal 2A belongs to the monoclinic crystal system with the P21/c space group.
The asymmetric unit of 2A is, analogically to 1A, comprised of half of the acid molecule (Fig.
S1). The organization of the molecules in the crystal is shown in Figure 3. Layers are arranged in
an ABAB fashion and are parallel to the bc plane. The HB layers are connected by 1,5ꢀ
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dimethylenenaphthalene fragments, in which the PꢀP distance is about 1.7 Å higher than for
NDP(1,5) (8.67 Å vs. 6.95 Å). This value depends on the conformation of this molecule and is
slightly smaller in structure 2B (ca. 8.55 Å).
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Figure 3. Projections of the crystal structures of solvatomorphs a) 2A and b) 2B together with
their topological simplifications.
An isolated hydrogenꢀbonded layer is presented in Figure 4. Another similarity to the 1A
structure can be seen due to the presence of two independent hydrogen bonds (Table S3).
Nonetheless, they contribute to the generation of two secondꢀorder supramolecular motifs:
ꢀꢁꢆꢃ12ꢄ and ꢀꢁꢁꢃ16ꢄ. The inversion centre lies at the centre of both motifs. The network can also
be considered an assemblage of two firstꢀorder graph set motifs. Each hydrogen bond creates one
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C(4) motif, developing the network along the b and c axis (O1ꢀP1ꢀO3ꢀH3 – dark blue, and O1ꢀ
5
6
P1ꢀO2ꢀH2 – light blue, respectively).
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Figure 4. Isolated hydrogenꢀbonded networks for a) 2A and b) 2B. Dashed lines symbolize
hydrogen bonds.
The solvent molecules interact with H4NDP(1C,5C) molecules in a different manner than with
H4NDP(1,5). It may be due to the higher conformational flexibility of the acid molecule, which
enables better accommodation of the supramolecular system to external stimuli (DMSO
molecules). In the solvated structure 2B, one deals with the insertion of solvent molecules into
the HB layer (Fig. 3). This results in the reduction of the overall dimensionality from 3D to 2D,
as well as in the more pronounced separation of the layers, and in the increase of the cell
constant a from 9.613 to 13.345 Å (b and c remain almost untouched). Also the β angle is much
closer to 90°, but the overall crystal symmetry remains unaffected (Table S1). When analyzing
only strong HBs, one can see a chain parallel to [001], composed of O1ꢀP1ꢀO2ꢀH2 atoms. Such
chains are joined by organic links along [010] creating a wavy 2D layer. However, DMSO
molecules have a substantial influence on the intermolecular interactions present in the crystal. In
turn, if the weak CꢀHꢁꢁꢁO bonds donated by DMSO are also explored, one can notice that 4
independent hydrogen bonds create 2 HB motifs much the same as in the case of 2A (Fig. 4).
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The HB motifs thus constructed are ꢀꢁꢆꢃ10ꢄ and ꢀꢁꢁꢃ16ꢄ, which provides a topology of the HB
layers very similar to 2A. The most pronounced difference is that both these motifs are fourthꢀ
order, thus they include all 4 HBs, two of which are donated by the methyl group from the
DMSO molecules. The second CH3 group is directed beyond the layer plane and interacts with
the inversionꢀrelated second layer through van der Waals and weak CꢀHꢁꢁꢁO interactions between
the DMSO molecules (the unique CꢁꢁꢁO distances amount to: 3.34, 3.36, and 3.73 Å). HꢁꢁꢁH
contacts (the main contributors of vdW) constitute 33.3 % of the acid’s HS (Fig. 13).
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Supramolecular adducts with 4ꢀ(N,Nꢀdimethylamino)pyridine (DMAP)
Phosphonic acids are used in the synthesis of engineered organic solids with substantial
success.73,76,83ꢀ89 The reactions of acids with a substituted pyridine base (DMAP) allow for an
exploration of the rich supramolecular chemistry of such systems, where interactions can occur
due to the presence of a protonated pyridine nitrogen atom, an aromatic ring or a bulky ꢀN(CH3)2
substituent.86,90 The naphthaleneꢀ1,5ꢀdiphosphonic acid provides two polymorphic structures, 3A
and 3B, where subtle conformational changes of the phosphonic group relative to the
naphthalene ring introduce a different arrangement of the molecules. These differences can be
derived from nucleation processes, in which slightly different crystallization systems are applied.
This fact shows the significance of the solvent system on the supramolecular level.91 The second
acid, H4NDP(1C,5C), gives two kinds of adducts, one of which contains acid and base molecules
in a 1:2 ratio (4A), similarly to polymorphs 3A and 3B, while the second – in a 1:1 ratio (4B).
These different compositions introduce large structural changes to the final superstructures.
Polymorphs 3A and 3B. The polymorphic adducts of naphthaleneꢀ1,5ꢀdiphosphonic acid
ꢅ
crystallize in the P1 space group (acid as a dianion with two base molecules per one acid
molecule). The asymmetric unit consists of half of the acid molecule and one base molecule (Fig.
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S3). The pyridine nitrogen atom in a DMAP molecule is protonated, which is also confirmed by
an almost 120° CꢀNꢀC angle. When analyzing distances for the PꢀO bond that (nearly) lies in a
naphthalene plane, one can clearly observe that for 3A there is a bond with the protonated
oxygen atom PꢀOH (1.53 Å), and the electron density of the two remaining bonds is delocalized
(1.50 and 1.51 Å). For 3B, the bond in the plane is ascribed to PꢀOꢀ (1.51 Å), and the electron
density is localized (1.58 Å for PꢀOH and 1.48 Å for P=O). Both these conformations can be
seen in Figure S3. The foregoing observation has clear consequences on the geometrical features
of both structures, despite the similar (or even the same – in the case of a low level of detail)
topology of supramolecular units.
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Figure 5. Projections of crystal structures of polymorphs a) 3A and b) 3B together with
topological simplifications of the HB networks.
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When analyzing only phosphonic acid molecules, hydrogenꢀbonded chains run along [111] for
3A and [010] for 3B (Fig. 5). Monodeprotonated phosphonic groups tend to generate dimeric
ꢀꢆꢆꢃ8ꢄ ring motifs, and this is the case in 3A and 3B. Strong hydrogen bonds are readily visible
on the dnorm surface as red spots; while engagement of the phosphonic group of both adducts into
a ring motif is visible as a set of two red spots that lie in a coplanar relation to each other. Base
molecules serve as important supramolecular tectons in these networks. They are connected
through a pyridinium nitrogen atom with the oxygen atom that is (for 3B) or is not (for 3A)
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ꢆꢃ ꢄ
involved in the ꢀꢆ 8 ring motif, providing NꢀHꢁꢁꢁO bonds (Table S3). The different acceptor
sites of NꢀHꢁꢁꢁO hydrogen bonding are one of the most distinctive differences while viewing
dnorm polymorph surfaces. In both structures, there is also one significantly stronger interaction,
C10ꢀH10ꢁꢁꢁO1, donated by a carbon atom connected directly to the N+ pyridinium atom (which
results in the activation of the CꢀH donor).92 Thus, other centrosymmetric motifs are generated:
ꢀꢁꢆꢃ10ꢄ for 3A and ꢀꢁꢁꢃ14ꢄ for 3B (Fig. 6). The resulting 2D hydrogenꢀbonded layers are parallel
ꢅ
to (110) and (100), respectively.
The pyridine ring plays an important role in the stabilization of the structure, also due to
extensive πꢁꢁꢁπ and CꢀHꢁꢁꢁπ interactions (Fig. S4 and Fig. 7 for the HS). A pair of inversionꢀ
related Py rings is arranged in an offset faceꢀtoꢀface manner. This pair is offset to the others and
stacked along the a axis. The Py rings interact with the naphthalene ones as a result of an edgeꢀ
toꢀface arrangement, which is confirmed by the inclination angle of ring planes and also the
apparent CꢀHꢁꢁꢁπ interaction (Table 1). Besides the interactions between the rings, the base
molecules contribute to the structure’s stabilization through CꢀHꢁꢁꢁO hydrogen bonds and van der
Waals forces, mainly from the N,Nꢀdimethylamino group. Such an edgeꢀtoꢀface arrangement of
the base molecules in both structures (3A and 3B) finds its reflection in the shape index surfaces
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as a set of red spots above the acid’s naphthalene ring. (Fig. 7). Additionally, the structures vary
in the number of intramolecular CꢀHꢁꢁꢁOꢀP interactions within the H4NDP(1,5) molecule, which
stabilize the conformation of the phosphonic group (Fig. S3). In 3B, one can find weaker Cꢀ
HꢁꢁꢁO bonds donated by the naphthalene ring (C5) and a methyl group (C11) (Table S3 and Fig.
S4). The higher number of CꢀHꢁꢁꢁO interactions in structure 3B is reflected on the dnorm surface as
lighter red spots in the phosphonic group’s surroundings.
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Figure 6. Isolated hydrogenꢀbonded networks for polymorphs a) 3A and b) 3B. Dashed lines
symbolize hydrogen bonds. DMAP fragments are partially transparent for clarity.
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Figure 7. Hirshfeld surfaces and 2D fingerprint plots for polymorphs a) 3A and b) 3B.
Phosphonic tectons are mapped with their shape index (left) and dnorm (centre) functions. Specific
short contacts are labeled.
The application of the geometrical criterion, i.e. a comparison of DꢀA distances and DꢀHꢀA
angles, for HB strength leads to the conclusion that structure 3A has a more optimized geometry
with a slightly stronger hydrogen bond network. Additionally, an edgeꢀtoꢀface ring arrangement
is closer to the optimal one for 3A (~90°) than for 3B (about 78°).
Table 1. A comparison of geometrical parameters for aromatic interactions in polymorphs 3A
and 3B. Py – pyridinium ring, Naph – naphthalene ring.
Py to Py
inclination
Py to Py slippage
(offset shift
angle)
Interacting
Py rings
Py to Py
distance
angle
3A
0
pair
between
3.5364(8)
3.5748(8)
2.173 (31.57)
2.634 (36.39)
0
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3B
pair
3.5350(8)
3.5604(8)
0
0
1.431 (22.04)
1.813 (26.99)
between
Py to Naph
inclination
angle
C-H···Cg
distance
C···Cg
distance
C-H···Cg angle
3A
3.833(2)
3B
3.589(2)
9
C9ꢀH9
2.99
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89.71(9)
77.73(8)
151
137
C7ꢀH7
2.86
Adducts 4A and 4B. The structures of salts with H4NDP(1C,5C) provide an opportunity to
examine the impact of an acid to base molecules ratio on a final supramolecular arrangement.
ꢇ
Adduct 4A, which has a 1:2 acid to base ratio, crystallizes in the triclinic P1 space group. It
presents a structure converging in many ways to structures 3A and 3B. The asymmetric unit is
composed of half a molecule of acid, one protonated DMAP molecule and, additionally, one
water molecule (Fig. S3). The arrangement of molecules (Fig. 8) is primarily governed by a set
of HB motifs known from naphthaleneꢀ1,5ꢀdiphosphonic acid salts. The monodeprotonated
ꢆꢃ ꢄ
phosphonic groups mounted on flexible ꢀCH2ꢀ links create the expected ꢀꢆ 8 motifs. The
described synthon connects the acid molecules into supramolecular chains running along the
ꢅ
[110] direction. Due to the presence of water molecules (the O4 atom), these chains are bridged
by relatively weak HBs along the a axis (Fig. 9). This results in the generation of a hydrogenꢀ
bonded layer parallel to the (001) plane, a topological simplification of which is depicted in
Figure 8. When one introduces the DMAP molecules under consideration, it should be noted that
they donate a hydrogen bond from the protonated nitrogen atom to an oxygen atom that is not
ꢆꢃ ꢄ
involved in the ꢀꢆ 8 motif (analogy to polymorph 3A). Deeper exploration shows additional
C11ꢀH11ꢁꢁꢁO4 bonding provided by the ortoꢀcarbon atom from the pyridine ring donated to the
water oxygen atom. On the other side of the NH+ group, there is another weakly donating carbon
atom which generates C7ꢀH7ꢁꢁꢁO3 interaction with the protonated oxygen atom. These
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interactions are weaker than the corresponding CꢀHꢁꢁꢁO interaction in polymorphs (Table S3).
Nevertheless, the former interaction creates centrosymmetric ꢀꢈꢁꢃ14ꢄ motif with the NꢀHꢁꢁꢁO
bond. The latter gives [ꢀꢆꢆꢃ7ꢄ] and contributes to the stabilization of the crystal in the [001]
direction, as well as to CꢀHꢁꢁꢁπ interactions between the pyridine and naphthalene rings.
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Figure 8. Projections of crystal structures of adducts a) 4A and b) 4B together with topological
simplifications of the HB networks.
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Figure 9. Isolated hydrogenꢀbonded networks for adducts a) 4A and b) 4B. Dashed lines
symbolize hydrogen bonds. The DMAP fragments and water molecules are partially transparent
for clarity.
The reduction of the number of base (and water) molecules per acid molecule to a 1:1 ratio in
4B leads to a structure with a monoclinic symmetry and has enormous structural consequences.
The asymmetric unit consists of halves of acid, base and water molecules (Fig. S3). One DMAP
molecule can accept only one proton; therefore, the second group should have two hydrogen
atoms unaffected. However, due to the internal Ci symmetry of the acid molecule, both groups
have to be the same, thus one hydroxyl group remains intact and the second proton lies at the
inversion centre and is shared by two inversionꢀrelated phosphonic groups, constituting a strong
symmetric hydrogen bond with the OꢁꢁꢁO distance of 2.468(3) Å (Table S3). In general, the
formation of the symmetric HB, even ten times stronger than the typical ones, is rare. The
phosphonic group, as a strong donor and acceptor, sometimes allows for the observation of such
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a type of bonding.74,93 The second HB is generated by a free hydroxyl group with cꢀglide related
3
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8
ꢁꢃ
ꢄ
groups. Together, four phosphonic groups create a strong ꢀꢁ 16 motif (Fig. 9). The
supramolecular chain formed from this motif is oriented along the c axis. This chain is also
connected with four other such chains through naphthalene linkers, which provides a 3D
hydrogenꢀbonded anionic network. As one can see in Figure 8, this network contains 9 x 13 Å
supramolecular channels running along the c axis. The channels are filled with DMAP and water
molecules. These two species interact through a linear NꢀHꢁꢁꢁO hydrogen bond, but they only
interact weakly with the phosphonic acid framework through uncommonly weak interactions
donated by the water molecule. The C7ꢀH7ꢁꢁꢁCg and C10ꢀH10BꢁꢁꢁCg interactions between
pyridine and naphthalene rings also help in stabilizing the guests inside the channels. Aromatic
interactions are rather scarce due to the strong directionality of the HB network. Interestingly
enough, the significant differences in composition and bonding between structures 4A and 4B
lead to a quite similar participation of all interactions in the Hirshfeld surface.94
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Adducts with morpholine: 5A and 5B. The two last structures provide an opportunity for the
direct comparison of the different influences of phosphonic tectons with varying conformational
flexibility on the final supramolecular adduct structure. In addition to the structures with 4ꢀ(N,Nꢀ
dimethylamino)pyridine, we have obtained, for both phosphonic acids, adducts with morpholine
in a 1:2 ratio. They crystallize in the P21/c space group. Asymmetric units for 5A and 5B
consisting of half an acid and one base molecules can be seen in Figure S5. Crystal packing,
shown in Figure 10, is represented by layered structures in both cases. Nonetheless, for
H4NDP(1,5) in 5A, there is a regular arrangement of the acid molecules in layers separated by
protonated morpholine molecules along the a axis.
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Figure 10. Crystal structure projections of a) 5A and b) 5B along the b axis together with
topological simplifications of the HB networks.
The morpholine molecules are more than pendants. Both protons from the NHꢆꢉ group force
ꢂꢃ
ꢄ
the generation of a ꢀꢂ 10 motif with deprotonated oxygen atoms, which, however, remains in
ꢆꢃ ꢄ
close resemblance to the typical ꢀꢆ 8 motif. The glideꢀrelated hydrogenꢀbonded rings produce
a supramolecular chain along the c axis (Fig. 11). These chains are connected by naphthalene
linkers to give wavy 2D layers, similarly as in the case of structure 2B. The CꢀHꢁꢁꢁO bonds again
play an important role in crystal packing in the two remaining directions. The HB chains are
interconnected mainly by a C9ꢀH9BꢁꢁꢁO1 interaction and along the a axis by a C6ꢀH6AꢁꢁꢁO4
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bonding (Table S3). The CꢀHꢁꢁꢁO bonds are constituted not only by an aliphatic CꢀH, but also by
an aromatic hydrogen atom (C5ꢀH5ꢁꢁꢁO1). This is the shortest CꢀHꢁꢁꢁO contact in this structure
with de = 1.10 Å and di = 1.43 Å.
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Figure 11. Isolated hydrogenꢀbonded networks for adducts a) 5A and b) 5B. Dashed lines
symbolize hydrogen bonds. The morpholine molecules are partially transparent for clarity.
The morpholine adduct of H4NDP(1C,5C) (5B) also shows a layered structure, where the
hydrogenꢀbonded 2D network parallel to the (100) plane is linked in the [100] direction by
naphthalene joints spaced by the base molecules (Fig. 10). This less regular arrangement is
clearly a result of the higher flexibility of the phosphonic tecton and is connected with a higher
amount of more optimized interactions. An isolated HB layer is shown in Figure 11. The
monodeprotonated phosphonic groups generate a dimeric ꢀꢆꢆꢃ8ꢄ synthon, whereas the protonated
morpholine nitrogen atom bridges two screwꢀrelated phosphonic acid molecules. An additional
ring motif [ꢀꢆꢆꢃ7ꢄ] is provided by the C10ꢀH10BꢁꢁꢁO2 bond. Also here, a carbon donor is
activated by the proximity to N+.
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2D fingerprints of phosphonic acids, their adducts and quantitative remarks
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Strong hydrogen bonds, e.g. OꢀHꢁꢁꢁO contacts, are readily visible in a 2D fingerprint plot and
are referred to in the available literature (mainly in the context of carboxylic acids) as two long
narrow spikes pointing toward the bottom left of the plot.6 This kind of interaction is also present
for herein described systems, but as can be seen from their 2D fingerprint plots, the spikes are
not as narrow. In fact, beginning from the tip, they significantly broaden with increasing di and de
values. This is the result of the presence of a tetrahedral phosphonic group having three oxygen
atoms; each of them with a different local environment which provides a larger library of
possible HBs. So far, only one other phosphonic system, i.e. polyphosphonylated calixarene, was
investigated using HS and FP analysis, showing similar patterns to what has been described
above.95,96
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For the herein reported compounds, the shortest OꢁꢁꢁH contact, described by its di + de value, is
in a range between 1.50 and 1.65 Å (for 3A and 2A, respectively). Other hydrogen bond
acceptors are engaged in more distant contacts, which results in the wider distribution of points
in the 2D fingerprint plots. This is apparent on the upper spike, corresponding to the hydrogen
bond donor sites. The lower spike, corresponding to the acceptor sites of the HBs, represents not
only strong hydrogen bonding, but also, at higher di and de values, shows a contribution from
weak CꢀHꢁꢁꢁO bonding.
It is interesting how the fingerprint plot of a protonated acid differs from the fingerprint plot of
a monodeprotonated moiety. To examine this, we compared OꢁꢁꢁH decomposed 2D fingerprint
plots of acid structures with respective adducts, along with their dnorm surfaces. For selected
examples (1A and 5A), see Figure 12, and for all OꢁꢁꢁH decomposed 2D fingerprint plots, see
Table S4. Generally, FPs of adducts reflect changes in the protonation state of the acid molecule.
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A special feature of their plots is a slightly narrowed upper spike while the lower spike is
broadened. This observation is explained by the fact that when phosphonic acid forms salt, then
the transfer of the proton from the acid to the base molecules occurs. Such a transferred proton is
no longer inside the Hirshfeld surface, which results in a decrease in the donor contacts of acid
moiety and in an increase of the acceptor ones. The dnorm surfaces of acids and
monodeprotonated molecules (Fig. 12) are similar, with 4 red spots which are located around the
phosphonic group. However, the ratio of acceptor and donor sites differentiates two protonation
forms of the phosphonic group. For structure 1A, one can observe 2 accepting sites and 2 donor
sites of OꢀHꢁꢁꢁO interactions around the PO3H2 group. When an adduct structure is considered
(5A), for the PO3Hꢀ group there are 3 accepting sites (two deriving from the NꢀHꢁꢁꢁO interaction
and one from the OꢀHꢁꢁꢁO) and one donor site, which remains in agreement with the presented
fingerprint plots.
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Figure 12. Hirshfeld surfaces and 2D fingerprint plots for a) 1A and b) 5A. Phosphonic tectons
are mapped with dnorm functions. The features of the diagrams coming from accepting and
donating interactions are labeled.
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In all structures (1Aꢀ5B), the biggest part of the HS is covered by OꢁꢁꢁH contacts (44 % on
average). The total percentage share of OꢁꢁꢁH contacts is not dependent on the protonation state
of the phosphonic group, and also there is no correlation with the acid structure. This cannot be
said about the CꢁꢁꢁH interactions that, according to Figure 13, cover less of the Hirshfeld surface
for structures containing flexible tectons. Here, the exception is structure 2B that has a greater
participation of these contacts than its analogue 1B (22.2 % and 16.6 %, respectively). HꢁꢁꢁH
dispersion forces are the second most abundant type of interactions in structures 1Aꢀ5B. The
structures based on H4NDP(1C,5C) have a systematically bigger contribution from HꢁꢁꢁH
contacts. For characteristic arrays of points in CꢁꢁꢁH and HꢁꢁꢁH decomposed fingerprint plots,
please see Table S5 and Table S6, respectively.
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Figure 13. The percentage contribution of specific close contacts to the Hirshfeld surfaces for all
structures. For 1A, 2A, 2B, 5A, and 5B, CꢁꢁꢁC contributions amount to 2.4, 0.9, 0.4, 2.4, and 1.9
%, respectively. Other contacts are as follows: CꢁꢁꢁO, SꢁꢁꢁH, SꢁꢁꢁO.
Potentiometric studies
Potentiometric measurements reveal that H4NDP(1C,5C) is slightly less acidic than
H4NDP(1,5). This is manifested by the absence of the monodeprotonated form H3NDP(1,5)ꢀ in
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