Comparing Crystallizations in Three Dimensions and Two Dimensions

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Comparing Crystallizations in 3D and 2D: Behavior of Isomers of [2,2'-Bipyridine]dicarbonitrile and [1,10-Phenanthroline]dicarbonitrile Aneeshma Peter, Midhun Mohan, Thierry Maris, James D. Wuest, and Adam Duong Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.7b00777 • Publication Date (Web): 14 Aug 2017 Downloaded from http://pubs.acs.org on August 15, 2017

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Crystal Growth & Design

Comparing Crystallizations in 3D and 2D: Behavior of Isomers of [2,2'-Bipyridine]dicarbonitrile and [1,10-Phenanthroline]dicarbonitrile

Aneeshma Peter,† Midhun Mohan,† Thierry Maris,‡ James D. Wuest,‡ and Adam Duong†*

†

Département de chimie, biochimie et physique, Université du Québec à Trois-

Rivières, 3351 boulevard des Forges, Trois-Rivières, Québec G9A 5H7, Canada

‡

Département de chimie, Université de Montréal, 2900 boulevard Édouard-

Montpetit, Montréal, Québec H3C 3J7, Canada

*To whom correspondence should be addressed. E-mail: [email protected]

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Abstract

Various

symmetric

isomers

of

[2,2'-bipyridine]dicarbonitrile

and

[1,10-

phenanthroline]dicarbonitrile were crystallized from solution and also deposited as monolayers adsorbed on graphite. The resulting 3D and 2D structures were studied by single-crystal X-ray diffraction (XRD) and scanning tunneling microscopy (STM), respectively. Previous comparisons of 3D and 2D structures have provided new understanding of molecular organization and have revealed that crystals and adlayers can have closely analogous structures despite the effects of the underlying surface, especially when organization is dominated by strong intermolecular interactions within a single plane. The present study extends previous work by showing that analogous 3D and 2D structures can be formed even when association is directed by weaker intermolecular forces, as exemplified by C-H···N interactions of nitriles.

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Introduction

Molecules containing atoms with potentially convergent lone pairs of electrons are widely used as ligands to chelate metals. 2,2'-Bipyridine, 1,10-phenanthroline, and related heteroaromatic compounds define particularly important classes of chelating ligands.1–6 Of special interest are derivatives functionalized with groups that can engage in additional strong intermolecular interactions, including hydrogen bonds or coordinative links to other metals. Such multiply substituted derivatives of 2,2'-bipyridine and 1,10-phenanthroline can serve as modular components for the programmed assembly of complex supramolecular structures.7–27

Because 2,2'-bipyridine and 1,10-phenanthroline have well-defined flattened structures,28 substituents that take part in additional interactions can be chosen to lie close to the average molecular plane. As a result, simple derivatives of 2,2'-bipyridine and 1,10-phenanthroline are well suited for the construction of sheets in which each molecule and its principal neighbors are approximately coplanar and held in positions determined by the strength and directional preferences of interactions governing the assembly. Earlier studies have confirmed that when 2,2'-bipyridines and 1,10-phenanthrolines incorporate groups able to engage in reliable patterns of hydrogen bonding, molecular organization in sheets is often favored.24

When compounds are engineered to associate in ways that place the strongest individual intermolecular interactions in a single plane, the 3D structures of their crystals, as determined by X-ray diffraction (XRD), are often closely analogous to the 2D structures of adlayers produced by adsorption on surfaces, as assessed by scanning tunneling microscopy (STM).29–36 Structural



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analogies in 3D and 2D can be expected to be closest when interactions with an underlying surface are strong enough to cause adsorption, yet are significantly weaker than interactions between the adsorbates themselves, which determine their relative positions. Families of compounds that are likely to associate in similar ways in 3D and 2D are rewarding subjects for detailed studies because unambiguous structural data derived from XRD can provide a reliable starting point for interpreting patterns of adsorption observed by STM, and details about crystalline defects and growth revealed at the molecular level by STM can offer complementary insights about the process of crystallization in 3D. In such ways, integrated studies of 3D and 2D crystallizations of families of related compounds have yielded deeper understanding of molecular organization, and they are a powerful tool for learning how to create new materials with predictable structures and properties.

Previous efforts to engineer 3D and 2D crystals derived from 2,2'-bipyridines, 1,10phenanthrolines, and related heteroaromatic compounds have focused on the behavior of derivatives with substituents that take part in strong hydrogen bonds. In such cases, intermolecular interactions will usually be more important than diffuse forces exerted by underlying surfaces as determinants of the patterns of association. We now report the results of a parallel study of the 3D and 2D crystallization of [2,2'-bipyridine]dicarbonitriles 1–3 and [1,10phenanthroline]dicarbonitriles 4–6, which cannot engage in specific in-plane noncovalent bonding other than relatively weak C-H···N interactions.37–40 Even under these circumstances, however, our observations show that patterns of association in 3D and 2D can still be closely analogous.


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Results and Discussion

Syntheses of Dicarbonitriles 1–6 and Analyses of Their Organization in 3D and 2D. Dicarbonitriles 1,41 2,24 3,42 4,24 5,24,43 and 624 were all synthesized by published procedures. Compounds 1, 3, 4, and 5 were crystallized from solution, and their structures were determined by XRD. STM was used to study the adsorption of compounds 1, 3, and 5 on highly-oriented pyrolytic graphite (HOPG) at the liquid-solid interface.

Structure of Crystals of [2,2'-Bipyridine]-6,6'-dicarbonitrile (1). Structural data at 120 K for compound 1 were deposited in the Cambridge Structural Database (refcode KOKBAP)44 but were never published and analyzed in detail. The structure we report here is similar, but with better refinement. Crystals grown from CHCl3/MeOH proved to belong to the monoclinic space group P21/c. Views of the structure are shown in Figure 1, and other crystallographic data are provided in Table 1. As expected,28 the molecules adopt flattened s-trans conformations with bond lengths and angles similar to those found in 2,2'-bipyridine itself and in 25 ACS Paragon Plus Environment


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pyridinecarbonitrile.45,46 The shortest intermolecular contacts are C-H···N interactions involving nitrile groups (H···N distance = 2.752 Å and C-H···N angle = 136°), which are similar to those found in other aromatic nitriles (Figure 1a).38 These interactions link the molecules into corrugated sheets (Figure 1a), which pack with offset π-π stacking (centroid-centroid distance = 3.814 Å) to give the observed structure (Figure 1b).

a

b

Figure 1. Representations of the structure of crystals of [2,2'-bipyridine]-6,6'-dicarbonitrile (1) grown from CHCl3/MeOH. (a) View along the a-axis showing a corrugated sheet of molecules linked by C-H···N interactions (broken lines). (c) Space-filling view of the packing of adjacent


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sheets, shown in red and blue. Unless stated otherwise, atoms of carbon appear in gray, atoms of hydrogen atoms in white, and atoms of nitrogen in blue.

Table 1. Crystallographic data for [2,2'-bipyridine]dicarbonitriles 1 and 3 and for [1,10phenanthroline]dicarbonitriles 4 and 5.

compound

1

3

4

5

crystallization medium

CHCl3/MeOH

CHCl3

CHCl3/MeOH

CHCl3

formula

C12H6N4

C12H6N4

C14H6N4

C14H6N4

crystal system

monoclinic

triclinic

monoclinic

orthorhombic

space group

P21/c

P1ത

P21/n

Pna21

a (Å)

3.8136(6)

3.7577(2)

10.4035(6)

6.9198(2)

b (Å)

10.0425(11)

5.8815(4)

15.7703(8)

14.7022(4)

c (Å)

12.9838(14)

10.9271(7)

13.5162(8)

10.7335(3)

α ( o)

90

94.985(4)

90

90

o

91.350(8)

94.575(4)

106.224(4)

90

o

γ( )

90

94.803(4)

90

90

V (Å3)

497.12(11)

238.82(3)

2129.2(2)

1091.99(5)

2

1

8

4

ρcalc (g cm )

1.378

1.434

1.436

1.400

T (K)

100

150

100

100

µ (mm )

0.714

0.477

0.734

0.716

measured reflections

7961

4672

31839

16726

independent reflections

803

784

3111

1973

Rint

0.0464

0.0785

0.0891

0.0588

observed reflections, I > 2σ

671

524

2137

1786

R1, I > 2σ

0.0349

0.0862

0.0745

0.0385

R1, all data

0.0420

0.1165

0.1023

0.0429

wR2, I > 2σ

0.0923

0.2564

0.1931

0.0963

wR2, all data

0.0982

0.2920

0.2222

0.1005

GoF

1.067

1.131

1.030

1.024

β( )

Z -3

-1



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Structure of Crystals of [2,2'-Bipyridinyl]-5,5'-dicarbonitrile (3). Crystals grown by slow evaporation of solutions in CHCl3 were found to belong to the triclinic space group P1ത. Views of the structure are provided in Figure 2, and other crystallographic data are summarized in Table 1. Again, the molecules have flattened s-trans conformations, and the bond lengths and angles are similar to those observed in 2,2'-bipyridine and in 3-pyridinecarbonitrile.45,46 The molecules are linked to form sheets held together by an elegant pattern of reciprocal C-H···N interactions involving nitrile groups and adjacent atoms of hydrogen (Figure 2a). In this way, each molecule participates in the formation of a total of eight intermolecular C-H···N interactions, with H···N distances (2.551 Å and 2.560 Å) and C-H···N angles (147 and 149°) similar to those observed in analogous cyclic motifs.38 Sheets pack with offset π-stacking (centroid-centroid distance = 3.758 Å) to produce the ultimate structure (Figure 2b).

a


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b

Figure 2. Representations of the structure of crystals of [2,2'-bipyridine]-5,5'-dicarbonitrile (3) grown from CHCl3. (a) View showing a sheet of molecules linked by reciprocal C-H···N interactions (broken lines). (b) Space-filling view showing packing of adjacent sheets in red and blue. Unless stated otherwise, atoms of carbon appear in gray, atoms of hydrogen in white, and atoms of nitrogen in blue.

Structure of Crystals of [1,10-Phenanthroline]-5,6-dicarbonitrile (4). Crystals grown from CHCl3/MeOH proved to belong to the monoclinic space group P21/n. Views of the structure are shown in Figure 3, and other crystallographic data are provided in Table 1. One of the molecules in the unit cell adopts a slightly bowed shape characteristic of phenanthroline itself,47–51 and bond lengths and angles are normal. Molecules of compound 4 are linked into tapes by intermolecular C-H···N interactions involving an atom of nitrogen in the phenanthroline core (H···N distance = 2.451 Å and C-H···N angle = 163°), and the tapes are connected by multiple C-H···N interactions (H···N distances = 2.610 Å, 2.718 Å, and 2.723 Å) involving nitrile groups (Figure 3a). Packing of the sheets is directed by π-stacking (Figure 3b), with closest neighbors in adjacent layers rotated relative to each other by 180° and with the centroids of their central aromatic rings separated by 3.621 Å.



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a

b

Figure 3. Representation of the structure of crystals of [1,10-phenanthroline]-5,6-dicarbonitrile (4) grown from CHCl3/MeOH. (a) View showing a sheet of molecules linked by various CH···N interactions (broken lines). (b) Space-filling view showing packing of adjacent sheets in red and blue. Unless stated otherwise, atoms of carbon appear in gray, atoms of hydrogen in white, and atoms of nitrogen in blue.

Structure of Crystals of [1,10-Phenanthroline]-4,7-dicarbonitrile (5). Crystals grown by slow evaporation of solutions in CHCl3 proved to belong to the orthorhombic space group Pna21. Figure 4 provides views of the structure, and Table 1 summarizes other crystallographic data. In the structure, molecules of compound 5 are virtually planar and have normal bond lengths and angles. The molecules can be considered to be linked into tapes by C-H···N interactions of nitrile 10 ACS Paragon Plus Environment

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groups (H···N distance = 2.493 Å and C-H···N angle = 145°), as shown in Figure 4a. Additional C-H···N interactions involving nitrile groups and atoms of nitrogen in the phenanthroline core (H···N distances = 2.557 Å, 2.656 Å, and 2.698 Å) join the tapes to form corrugated sheets (Figure 4a). Packing of the sheets is directed by π-stacking of parallel molecules of phenanthroline 5, with a separation of 3.463 Å between the centroids of the central aromatic rings of nearest neighbors in adjacent sheets (Figure 4b).

a

b

Figure 4. Representation of the structure of crystals of [1,10-phenanthroline-4,7-dicarbonitrile (5) grown from CHCl3. (a) View showing a sheet of molecules linked by various C-H···N interactions (broken lines). (b) Space-filling view showing packing of adjacent sheets in red and 11 ACS Paragon Plus Environment


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blue. Unless stated otherwise, atoms of carbon appear in gray, atoms of hydrogen in white, and atoms of nitrogen in blue.

Our structural studies of representative compounds 1, 3, 4, and 5 by XRD strongly support the conclusion

that

crystallization

of

[2,2'-bipyridine]dicarbonitriles

and

[1,10-

phenanthroline]dicarbonitriles in 3D is directed by four underlying principles: (1) The molecules adopt flattened conformations; (2) association is guided by multiple C-H···N interactions lying close to the average molecular planes; (3) association therefore favors the formation of sheets; and (4) packing of the sheets by π-stacking leads to the observed structures. These key features are observed in all four structures and can serve reliably as a basis for anticipating how related compounds will crystallize. The relative positions of neighboring molecules within sheets or in adjacent sheets are not easy to foresee because they depend on details of C-H···N bonding and other weak intermolecular interactions that are poorly directional. Nevertheless, our studies of 3D crystallization suggest that dinitriles 1-6 and related compounds are all predisposed to form sheets. As a result, they are ideally suited for testing the hypothesis that their 2D crystallization on surfaces should favor similar patterns of molecular organization, despite the lack of strong interactions between adsorbates.

Adsorption of [2,2'-Bipyridine]-6,6'-dicarbonitrile (1) on Graphite. A droplet of a solution of [2,2'-bipyridine]-6,6'-dicarbonitrile (1) in heptanoic acid (∼1 × 10-4 M) was placed on a sample of HOPG with a freshly exposed surface, and the liquid-solid interface was analyzed by STM. Representative images of the surface are provided in Figure 5, along with a superimposed unit


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cell and a model of the proposed molecular organization. The large well-ordered arrays shown in Figure 5a confirm that compound 1 has a strong affinity for the surface even though it lacks features such as long alkyl chains or other functional groups of the type conventionally used to facilitate adsorption on graphite. The observed high affinity presumably reflects the flattened topology of the adsorbate, its large aromatic surface, and the presence of electron-withdrawing nitrile substituents, rather than the incorporation of atoms of nitrogen in the bipyridyl core.52,53 Close examination of the periodic patterns of contrast (Figure 5b), combined with analysis of the unit cell parameters (a = 13.8 Å, b = 17.2 Å, and γ = 90 ± 2°), suggests that molecular organization in 2D closely resembles the motif observed in 3D (Figure 1a).

Adsorbed molecules of bipyridine 1 presumably adopt a flattened s-trans conformation like the one found in 3D crystals, and the pattern of adsorption appears to be determined by C-H···N interactions similar to those shown in Figure 1a. The preferred conformation of compound 1 has approximate C2h symmetry and is therefore chiral in 2D. The composition of the proposed assembly is racemic, and each molecule forms C-H···N interactions with four molecules of opposite handedness. In the sheets observed in 3D crystals, molecules of the same orientation are separated by a distance equal to the length of the unit cell along the b-axis (10.043 Å), which is similar to the separation of adsorbed molecules of the same configuration in 2D (13.8 Å). Small quantitative differences between the patterns of molecular organization observed in 3D and 2D can be attributed to the nonplanarity of sheets in the 3D structure of crystals and to efforts of adsorbed molecules to achieve registry with the underlying surface of graphite. The proposed model of 2D crystallization consists of molecules that appear to have an s-trans conformation and are efficiently packed, with no significant area of surface uncovered. These observations



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suggest that the adsorbed molecules correspond to the free basic form of bipyridine 1, not to a salt formed with heptanoic acid used in the deposition.

a

b

Figure 5. STM images of the adsorption of [2,2'-bipyridine]-6,6'-dicarbonitrile (1) on HOPG (deposition from heptanoic acid, with Vbias = - 0.51 V and Iset = 0.13 nA). (a) View of an area of 60 nm × 60 nm. (b) Enlarged view of an area of 10 nm × 10 nm. Superimposed on the image are the measured unit cell and a model of the proposed molecular organization to facilitate interpretation of the pattern of contrasts.

Adsorption of [2,2'-Bipyridine]-5,5'-dicarbonitrile (3) on Graphite. To extend our analysis of homology in 3D and 2D crystallization, we studied the adsorption of isomeric bipyridinedinitrile 3. A solution of compound 3 in heptanoic acid (∼1 × 10-4 M) was deposited on HOPG, and the liquid-solid interface was imaged by STM. Typical images of the surface appear in Figure 6,


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along with a superimposed unit cell and a model of the postulated molecular organization. Molecules are adsorbed with their long axes parallel, and the measured unit cell parameters are a = 13.1 Å, b = 13.1 Å, and γ = 33 ± 2°. The close similarity of the observed 2D pattern to the structure of sheets found in 3D crystals of compound 3 suggests that the adsorbed molecules adopt flattened s-trans conformations, are not protonated, and engage in multiple C-H···N interactions similar to those shown in Figure 2a. As in the case of isomeric bipyridine 1, the adsorbed molecules have approximate C2h symmetry and are chiral in 2D. In the postulated pattern of adsorption, all molecules in a single domain have the same handedness. The end-toend separation of adjacent molecules in the 3D structure (11.835 Å and 11.951 Å) is similar to the value observed in 2D by STM (13.1 Å). Small differences can be attributed to the nonplanarity of sheets observed in 3D and to the effect of the underlying surface of graphite on molecular adsorption in 2D.

a

b



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Figure 6. STM images of the adsorption of [2,2'-bipyridine]-5,5'-dicarbonitrile (3) on HOPG (deposition from heptanoic acid, with Vbias = - 0.51 V and Iset = 0.13 nA). (a) View of an area of 20 nm × 20 nm. (b) Enlarged view of an area of 10 nm × 10 nm. Superimposed on the image are the measured unit cell and a model of the proposed molecular organization to facilitate interpretation of the pattern of contrasts.

Adsorption of [1,10-Phenanthroline]-4,7-dicarbonitrile (5) on Graphite. Homology of 3D and 2D organization was further explored by studying the adsorption of phenanthroline 5. Droplets of solutions in heptanoic acid (∼1 × 10-4 M) were deposited on HOPG, and STM was used to analyze the liquid-solid interface. Representative images are shown in Figure 7, along with a superimposed unit cell and a model of the proposed molecular organization. The formation of large well-ordered arrays confirms that compound 5 has a strong affinity for the underlying surface (Figure 7a). Again, molecular organization in 3D and 2D appears to be closely analogous. The measured unit cell parameters for adsorption are a = 11.6 Å, b = 15.2 Å, and γ = 90 ± 2°, whereas the corresponding values determined by XRD for sheets observed in 3D crystals of phenanthroline 5 are 10.7335 Å, 14.7022 Å, and 90°. Again, coadsorption with heptanoic acid is not observed.


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a

b

Figure 7. STM images of the adsorption of [1,10-phenanthroline]-4,7-dicarbonitrile (3) on HOPG (deposition from heptanoic acid, with Vbias = - 0.55 V and Iset = 0.09 nA). (a) View of an area of 40 nm × 40 nm. (b) Enlarged view of an area of 10 nm × 10 nm. Superimposed on the image are the measured unit cell and a model of the proposed molecular organization to facilitate interpretation of the pattern of contrasts.

Conclusions

Various isomers of [2,2'-bipyridine]dicarbonitrile and [1,10-phenanthroline]dicarbonitrile have well-defined flattened heteroaromatic cores, as well as atoms of nitrogen that can be expected to take part in multiple C-H···N interactions close to the average molecular plane. As a result, the association of these families of compounds can be expected to favor the formation of sheets. This preference was confirmed by using XRD and STM to determine the 3D structure of crystals of selected isomers and the 2D organization of monolayers adsorbed on graphite. Molecular 17 ACS Paragon Plus Environment


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arrangements in sheets observed in 3D and 2D proved to be strikingly similar in all cases. Previous studies have established that structural homology in 3D and 2D can be attained when molecular components are designed to form sheets held together by strong directional intermolecular interactions such as hydrogen bonds.29–36 The present study extends this work by showing that weaker interactions can be sufficient for directing homologous assembly. In this way, our work provides deeper understanding of how the organization and properties of molecular materials can be controlled predictably.

Experimental Section

Crystallizations. All crystallizations were carried out at 25 °C. Crystals of compounds 1 and 4 were grown by exposing solutions in CHCl3 to vapors of MeOH in closed vessels. Crystals of compounds 3 and 5 were obtained by slow evaporation of saturated solutions in CHCl3.

Structural Analyses by XRD. Crystallographic data were collected at 150 K using a Bruker Venture Metaljet diffractometer with Ga Kα radiation for compound 3 and at 100 K using a Bruker Microstar diffractometer with Cu Κα radiation for the other compounds. The structures were solved by direct methods using SHELXT,54 and non-hydrogen atoms were refined anisotropically with SHELXL-2016/6.55 For all compounds, hydrogen atoms were first located from the difference Fourier map. They were fully refined for compound 1 and refined as riding atoms for compounds 3, 4, and 5.


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CCDC 1551998–1552001 contain the supplementary crystallographic data. These data can be obtained

free

of

charge

from

the

Cambridge

Crystallographic

Data

Centre

via

www.ccdc.cam.ac.uk/data_request/cif.

Studies of 2D Molecular Organization by STM. All STM experiments were performed at room temperature (20-25 °C) using a JEOL-5200 SPM instrument equipped with a narrow scanner. Platinum/iridium STM tips were mechanically cut from wire (Pt/Ir, 80%/20%, diameter = 0.25 mm). In typical experiments, the freshly cleaved basal surface of HOPG (Structure Probe, Inc., SPI-1 grade) was first imaged to determine the quality of the Pt/Ir tip and the smoothness of the graphite surface. Once this was determined, a droplet (~ 1 µL) of a solution of compounds 1– 6 in heptanoic acid (∼1 × 10-4 M) was applied. Only compounds 1, 3, and 5 were successfully imaged by STM. STM investigations were carried out at the liquid-solid interface in constantheight mode. STM imaging was performed by changing the tunneling parameters (voltage applied to the tip and the average tunneling current). Raw STM images were processed using a JEOL software package (WinSPM Data Processing System, Version 2.15, R. B. Leane, JEOL Ltd.) and a freeware (WSxM 5.0 Develop 1.2, Nanotec Electrónica S. L.).56

Acknowledgments. We are grateful to the Natural Sciences and Engineering Research Council of Canada, the Queen Elizabeth II Diamond Jubilee Scholarship, the Ministère de l'Éducation du Québec, the Canada Foundation for Innovation, the Canada Research Chairs Program, Université de Montréal, and Université du Québec à Trois-Rivières for financial support.



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Supporting Information Available. Supplementary STM images, analyses of unit cell parameters, and further crystallographic information, including ORTEP drawings and tables of structural data in CIF format. This material is available free of charge via the Internet at http://pubs.acs.org.

Notes and References

1)

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2)

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54) Sheldrick, G. M. Acta Crystallogr. 2015, A71, 3-8. 55) Sheldrick, G. M. Acta Crystallogr. 2015, C71, 3-8. 56) Horcas, I.; Fernández, R.; Gómez-Rodríguez, J.; Colchero, J.; Gómez-Herrero, J.; Baro, A. M. Rev. Sci. Instrum. 2007, 78, 013705.


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Table of Contents Graphic (For Table of Contents Use Only)

Comparing Crystallizations in 3D and 2D: Behavior of Isomers of [2,2'-Bipyridine]dicarbonitrile and [1,10-Phenanthroline]dicarbonitrile

Aneeshma Peter, Midhun Mohan, Thierry Maris, James D. Wuest, and Adam Duong

Table of Contents Synopsis

Nitrile-substituted 2,2'-bipyridines and 1,10-phenanthrolines are predisposed to associate in sheets because they have flattened conformations and can form multiple C-H···N interactions 25 ACS Paragon Plus Environment


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close to the average molecular plane. The structures of crystals and monolayers adsorbed on graphite were determined by XRD and STM. The observation of closely similar molecular arrangements shows that weak intermolecular interactions can be used to produce homologous 3D and 2D structures by design, despite the effects of the underlying surface.


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Comparing Crystallizations in Three Dimensions and Two Dimensions

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