Supramolecular Chemistry: Computer-Assisted Instruction in

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Supramolecular Chemistry Computer-Assisted Instruction in Undergraduate and Graduate Chemistry Courses Alexandre A. Varnek,* Bernard Dietrich, Georges Wipff, and Jean-Marie Lehn Institut de Chimie, Université Louis Pasteur, 67000 Strasbourg, France; *[email protected] Elena V. Boldyreva Division Solid-State Chemistry, Novosibirsk State University, Russia

Supramolecular chemistry is a highly interdisciplinary field of science involving chemical species assembled from smaller molecular fragments, which are held together and organized by means of intermolecular (noncovalent) binding interactions (1). The field has its roots in synthetic organic chemistry, the metal ion–ligand complexes of coordination chemistry, the physical chemistry of molecular interactions, the binding and recognition of biological substrates, materials science, and the mechanical properties of solids (1). As the unifying power of supramolecular chemistry has become more apparent, a large number of research groups worldwide have begun to work in this field, as evidenced by the broad range of books, journals, meetings, and symposia devoted entirely to supramolecular chemistry. Despite the rapid expansion of the supramolecular field, its concepts are only slowly being adopted by the university chemistry curriculum, and supramolecular chemistry is not included as a keyword in this Journal (2). Although many monographs and reviews on supramolecular chemistry are now available for specialists (see ref 1 and references therein), including a multivolume edition (3), there is still no comprehensive textbook aimed at advanced undergraduate or graduate students. Modern computing facilities provide a unique opportunity to develop flexible courses that are applicable to undergraduate and graduate teaching. Different options of a given software package (representing various aspects of the topic of interest) can be used separately or in various combinations, allowing adoption of the same “electronic textbook” for teaching different courses at different levels. An interactive computerassisted course can be used for demonstrations, self-education, training, and testing. It permits the visualization of complex structures and the performance of some modest calculations while concomitantly reading the text itself. Finally, a computerassisted course is easy to update, which is especially important for rapidly expanding and developing fields. Recently, a number of such courses have appeared: see for example the interactive electronic version (4a) of Fundamentals of Crystallography, edited by C. Giacovazzo (4b), or the Web-derived instructional tool developed by Leon et al. (5) for the structural analysis and modeling of proteins. Videos can be used to illustrate the many facets of supramolecular systems, but they do not allow for the interactive study of the topic (6 ). At the University of Louis Pasteur in Strasbourg (France) and at the Novosibirsk State University (Russia) we have been developing a comprehensive interactive electronic textbook on supramolecular chemistry, hereafter referred to as SC-WEB, 222

based on the monograph by Lehn (1). The book (1) is mostly oriented toward experienced chemists, but its electronic version has been especially adapted for educational purposes and can be used for teaching numerous facets of supramolecular chemistry. Moreover, it can be used in courses in related disciplines, for example, organic chemistry, inorganic and coordination chemistry, physical chemistry, or biochemistry. The present version of SC-WEB focuses on the structural features of supramolecular species and assemblies, but extensions involving, for example, thermodynamic properties or physical properties can be added using a similar approach. Software and Computing Facilities Required; Availability of SC-WEB SC-WEB uses two types of programs. One reads files in PDF format (Acrobat Reader) and the other, WebLab Viewer Lite (7 ) (which can be downloaded free via the Internet [http://www.msi.com/weblab]), is used for the visualization and manipulation of structures. SC-WEB can run on any PC (W95/NT4.0) computer. A reduced version of SC-WEB is available (http://crypt.u-strasbg.fr/varnek/SC-WEB.html).1 It contains about 100 interactive structures, their 2-D formula, entry points into the related book (1), and related explanations. SC-WEB is a user-friendly program and no instruction is needed to run it. An expanded version also containing the text of ref 1 will be available from VCH as a supplement to a new edition of this book. General Description of SC-WEB SC-WEB includes the text of the monograph (1) with additional notes in HTML format that are specially adapted for educational purposes. It also contains solid-state structures for the molecules and supermolecules described in the monograph. In some cases several conformers or analogues are presented. The list includes about 100 structures retrieved from the Cambridge Structural Database (CSD) (8). The structural data can be retrieved from SC-WEB in two ways. The first option is clicking the mouse on the highlighted name directly in the text, as done when retrieving data from the Internet. The second option is to choose the compound from a list, independent of the text. The choice can be made by formula, chemical name, the number in the monograph, the reference code in the CSD, or the chemical class to which the compound belongs (see the list of chemical classes in Box 1). For each structure included in SC-WEB, a full reference to the primary literature is available and the list can be easily updated. For comparison of “solid-state” and “solution” structures of the same compounds, we have also included in SC-WEB

Journal of Chemical Education • Vol. 77 No. 2 February 2000 • JChemEd.chem.wisc.edu


Box 1. Classes of Chemical Compounds Included in SC-WEB I. Solid-state structures 1. Monocycles 1.1. Valinomycin 1.2. 18-Crown-6 and its analogues 1.3. Substituted crown ethers 1.4. α-Cyclodextrin 2. Polycycles 2.1. Cryptands [2.1.1], [2.2.1], and [2.2.2] 2.2. Spherands 2.3. Cryptospherands 2.4. Calixarenes 2.5. Cryptophanes 2.6. Cyclophanes and their analogues 2.7. Carcerands 2.8. Tricycles 2.9. Polyheterocycles 3. Electrides and alkalides 4. Helicates 5. Multicomponent self-assemblies 5.1. Grids 5.2. Catenands 5.3. Knots 6. Self-assemblies by hydrogen bonding 7. Inorganic cryptates II. Structures in water and in acetonitrile solution obtained in molecular dynamics simulations. 1. 18-crown-6 (Ci, D3d and C1 forms). 2. Cryptand [2.2.2.] (K and II forms) 3. Complex K+.t -butyl-calix[4]arenetetraamide

Box 2. Some Possible Applications of SC-WEB for Teaching CRYSTALLOGRAPHY; SOLID-STATE CHEMISTRY Retrieve the X-ray structural data, transform the crystallographic coordinates into cartesian ones. Calculate intramolecular bond distances and angles, calculate intermolecular distances, analyze the possibility of the formation of hydrogen bonds and of other noncovalent interactions in the system. Compare the conformations of selected fragments in related structures. Describe the packing of the molecules in the crystal structure. Consider the coordination of the selected species in the crystal structure.

ENVIRONMENTAL CHEMISTRY Retrieve data on the supramolecular complexes involving selected ions to be removed from waste waters. Describe the structures of the complexes, analyze which factors and interactions account for the selectivity of ionic binding. Visualize the results of molecular simulations of cation binding in solution in order to interpret the effect of solvent on selective binding.

BIOCHEMISTRY Retrieve data on compounds of biological importance. Consider the role of substrate–receptor recognition and selective binding in various biochemical processes, such as membrane transfer, gene transfer, RNA and DNA cleavage, transport of ATP, and cell signaling, replication, templating.

MATERIALS SCIENCE Retrieve data on compounds that can be used in various devices or as materials with interesting properties. Consider the molecular structures, and try to correlate the structures with properties. Which of the properties can characterize the assembly as a whole, but not individual molecules in it? Which of the molecular properties are modified, and how, by including the molecule in the assembly?

the structures of 18-crown-6, cryptand [2.2.2.], and t-butylcalix[4]arenetetraamide obtained from molecular dynamics simulations in water and in acetonitrile solutions (9–11). Retrieval of a structure opens an extra window containing the structural model of the compound (Fig. 1). Structures can be represented in a line, ball-and-stick, stick, CPK, or polyhedron mode, depending on the user’s preference. They

Figure 1. SC-WEB: three windows representing the text of the book (1), the list of structures (containing chemical formulas and bibliographic references), and three-dimensional structures of molecules, visualized with the WebLab View program.

can be rotated and translated on the screen along any chosen axis. Any atoms can be selected, highlighted, or hidden. It is possible to monitor the interatomic distances, bond angles, or dihedral angles between any selected atoms. Hydrogen bonds can be also visualized. Usage SC-WEB for Teaching Supramolecular Chemistry and Related Disciplines SC-WEB can be used for teaching supramolecular chemistry at undergraduate and graduate levels. It also allows for the introduction of some concepts and problems relating to supramolecular chemistry in, for example, advanced inorganic chemistry, solid-state chemistry, and biochemistry courses taken by graduate students and advanced undergraduates. Some ideas of how this can be effectively done are summarized in Box 2. To illustrate the abilities of SC-WEB, we present several examples based on the material of Chapters 2 and 4 of the monograph (1). They involve the binding of alkali cations by organic receptors, the binding of R–NH3+ cations by organic receptors, and alkali cation binding by inorganic receptors. This allows one to introduce the following important concepts of supramolecular chemistry: molecular recognition, receptor, substrate, complementarity, multiple interaction sites, medium effects, and the lock-and-key principle. Various aspects of cation recognition by macrocyclic ligands can be treated: (i) spherical recognition and binding selectivity as a function of the size of the macrocyclic cavity, (ii) the conformational flexibility of the macrocycles, (iii) the thermodynamics of substrate–receptor interactions in solution, or, more specifically, solvent effects on binding selectivity, and (iv) the effect of the receptor-type on cation binding by crown ethers and cryptands. In addition, in order to introduce the concepts of the double complementarity principle, interactional complementarity, endo- and exo-receptors, we consider: (v) the role of hydrogen bond formation in the recognition of nonspherical (for example, R–NH3+) cations, and (vi) binding of cations by inorganic receptors.

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Table 1. Some Ionic and van der Waals Radii Ionic Radius/Å Li

Na

+

+

0.68

0.97

K+

Rb+

Cs+

1.33

1.47

1.67

van der Waals Radius/Å O

N

C

H

1.40

1.50

1.85

1.20

NOTE: Values for ionic radii are from ref 29. Values for van der Waals radii are from ref 30.

18-Crown-6 in the Solid State: Demonstration of the Steric Fit Approach One of the simplest approaches to the problem of selectivity of the cation binding by macrocyclic receptors is the steric fit approximation. The idea is that binding of the alkali metal cations by macrocycles is driven by spherical recognition. This means that the interactions of the cation with the walls of the macrocyclic cavity are isotropic, and the binding selectivity is a function of the size complementarity between the cation and the cavity of the receptor. In this section we show how, following a straightforward procedure, one can use SC-WEB to find an alkali cation that best fits the cavity of the classic receptor, 18-crown-6 (1).

Figure 2. Conformations of 18-crown-6 in the solid state (orthogonal views).

Figure 3. Interaction site complementarity and linear recognition: complexes of primary ammonium cations with (a) tetra-tartaro-18crown-6 and (b) cylindrical cryptand. 1

2

3

Some macrocyclic receptors and their complexes

Many macrocyclic receptors are conformationally mobile and can adopt different conformations in their complexes. In the solid state, uncomplexed 18-crown-6 has an elongated shape of Ci symmetry with two weak intramolecular hydrogen C–H…O bonds and only four oxygens pointing into the interior of the cavity (Figure 2). This conformer differs from that observed for complexed ligands in which all oxygens are pointed into the cavity and are coordinated to the cation. Two typical forms of complexed 18-crown-6 are found in the solid state: D3d (in the complex with K+) and C1 (in the complex with Na+) (Fig. 2). According to molecular mechanics (12, 13) and quantum mechanical (14 ) calculations, the C1 conformer is substantially more strained than the D3d one. The distances between cation and oxygen atoms in the 18-crown-6⭈K+ (D3d) complex (2.77 Å) are close to the sum of the van der Waals radius of an oxygen atom (RO = 1.40 Å) and the ionic radius of the K+ cation (RM+ = 1.33 Å, see Table 1). Large Rb+ (R M+ = 1.47 Å) and Cs+ (R M+ = 1.67 Å) cations are not accommodated in the cavity of 18-crown-6 (D3d). The smaller Na+ cation does not fit the macrocyclic cavity well. In fact, only two of six Na+–O distances (2.45 and 2.47 Å) are close to the sum RO + R M+ = 2.37 Å (Table 1); others are significantly larger (2.55–2.62 Å). From these estimates, it 224

becomes clear that the K+ cation presents the best steric fit for the crown-ether. This analysis predicts that 18-crown-6 should bind K + more tightly than other alkali cations. However, as we shall see later, the complexation selectivity of ionophores in solution is a function of many variables, and cannot be explained solely by the steric fit approach.

Interaction Site Complementarity and Linear Recognition When “nonspherical” cations such as NH4+ or R–NH3+ are bound, size complementarity and interaction site complementarity play essential role in the molecular recognition process. Several structural examples of complexes between primary ammonium cations and substituted crown-ethers are included in SC-WEB, to illustrate this effect. In the complex of NH3+–C2H4–NH3+ with tetra-tartaro-18-crown-6 (15) (2), the binding sites of the substrate perfectly fit those of the receptor; that is, the R–NH3+ cation forms three strong linear hydrogen NH…O bonds (1.80 Å) with the oxygens of the macrocyclic cavity (Fig. 3a). Another interesting example is complex 3, where the NH3+–(CH2)5 –NH3+ substrate is located in the central molecular cavity of the host molecule and is anchored by its two NH3+ groups to the macrocyclic binding sites (16 ) (Fig. 3b). The length of the –(CH2)5– spacer of the substrate is complementary to the molecular “length” of the receptor (linear recognition).



and in acetonitrile) the ionophore adopts a D3d conformation. However, both in water and in acetonitrile, the D3d form is the most populated, making the crown-ether apparently more suitable for complexation with metal cations. On the other hand, the calculated solvation pattern strongly suggests that in polar solvents, solvation of the preorganized conformer prevents rather than facilitates the cation capture. Another example of solvent-induced preorganization has been reported for the [2.2.2] cryptand (9). Solvent Effects on the Complexation Selectivity in Solution Figure 4. 18-crown-6 in water and in acetonitrile solutions. Snapshots after 100 ps of molecular dynamics simulations.

Relationship between Molecular Structures in the Solid State and in Solution Molecular dynamics simulations allow one to gain microscopic insights into conformational equilibria of ionophores in solution. Calculations performed on 18-crown-6 in aqueous vs nonaqueous solvent (10, 11, 18) using the AMBER4.1 program (17 ) demonstrate a remarkable solvent effect on the populations of different conformers of this molecule. As explained in detail in ref 18, in aqueous solution, the D3d conformer is the best hydrated one (Esolvation = ᎑55.8 kcal/ mol) because of a very specific hydration pattern. On each face of the macrocycle, one water molecule bridges two opposite oxygen atoms by hydrogen bonds, whereas the second H2O molecule links the oxygen atom of the first water molecule and one of the oxygens of the ionophore (Fig. 4). On the other hand, the Ci conformer, which is most stable in the gas phase, is poorly hydrated (᎑35.3 kcal/mol). It is able to form only weak linear hydrogen bonds with water molecules, because their H–O dipoles are aligned so that they repulse each other (Fig. 4) (18). In acetonitrile, the different conformers of the crownether are stabilized by dipole–dipole and van der Waals interactions (10). Again, the D3d conformer (᎑37.2 kcal/mol) is solvated better than the Ci conformer (᎑29.7 kcal/mol). Schematically, in its first solvation shell, the D3d form has two acetonitrile molecules perpendicular to the ring with the methyl groups pointed towards the macrocycle (Fig. 4). The Ci conformer forms van der Waals contacts with acetonitrile molecules, which lie more or less parallel to the ring. From the molecular dynamics simulations it follows that the conformational state of 18-crown-6 depends on its environment. In the solid state, the uncomplexed crown is found only in its Ci form. In aqueous solution, this conformer is virtually absent, whereas in acetonitrile it has a significant population (10, 19). Solvent-Induced Preorganization According to Cram’s definition of the principle of preorganization (which is in fact a reformulation of the lock and key principle of Emil Fischer), “the smaller the changes in organization of host, guest and solvent required for complexation, the stronger will be the binding” (20). Based on the solid-state structures, it is clear that the Ci conformer of 18-crown-6 is not preorganized for complexation, because in its complex with K+ (the best recognized guest in water

In solution, the interaction of both the cation and the macrocyclic host with solvent should be taken into account. In fact, the selectivity of an ionophore (L) with respect to different cations may even be inverted when changing the solvent. For example, 18-crown-6, with a cavity perfectly suited for K+, selectively binds this cation in water and in methanol (21), but prefers Na+ in 4:1 THF:CHCl3 solvent (22). There are many other examples when complexation selectivity of L in solution does not follow the steric fit approach. In fact, the molecular recognition process in host-guest complexes can be defined by the relative free energies ∆∆Gc of binding of two guests, M1 and M2, to the same host L in solution (sol). According to the thermodynamic cycle (23), ∆G1 (L + M1+)sol → (LM1+)sol ↓ ∆G3 ↓ ∆G4 (L + M2+)sol → (LM2+)sol ∆G2 ∆∆Gc = ∆G1 – ∆G2 = ∆G3 – ∆G4, where ∆G1 and ∆G2 are the free energies of complexation of M1+ and M2+ to L, ∆G3 is the difference between desolvation free energies of M1+ and M2+, and ∆G4 is the free energy difference between LM1+ and LM2+ complexes. Free energy calculations coupled with molecular dynamics simulations (using the GROMOS program [24 ]) on uncomplexed Na+ and K+ cations and on their complexes with 18-crown-6 in water (25) show that the ligand intrinsically interacts more strongly with the smaller Na+ cation (∆G4 [Na+ → K+] = 20.5 kcal/mol). However, the dehydration energy of Na+ is larger than that of K+ (∆G3 [Na+ → K+] = 22.4 kcal/mol. Thus, the binding selectivity for K+ results from a compromise between the relative desolvation energy of the cations (∆G3) and relative interaction energies with the host (∆G4) in solution.

Inorganic exo and endo Receptors The inorganic receptors of alkali cations are less often reviewed in the traditional literature on supramolecular chemistry than are organic host molecules, even though they are materials of great practical importance (26, 27). In SC-WEB we consider the inorganic matrix γ-Al(OH)3 (gibbsite) (Fig. 5a), which complexes exclusively Li+ in an endo fashion and different anions in an exo fashion (Fig. 5b) (28). In the intercalate, cations occupy the cavities formed by the six oxygens of neighboring Al(OH)3 fragments; interestingly, the octahedral coordination pattern of Li+ in this matrix is not the same as that observed in [Li+ 傺 2.1.1.] cryptate. Bound anions are located between layers of [Li+⭈Al(OH)3]n.


225


Literature Cited

Figure 5. (a) The γ-Al(OH)3 matrix and (b) its intercalate with LiCl.

One may compare the crystal structure of uncomplexed

γ-Al(OH)3 (Fig. 5a) with one of its Li+ intercalates. Complex-

ation with the inorganic guest perturbs the hydrogen bonding network in the structure of γ-Al(OH)3 and leads to a dramatic increase of the interlayer Al–Al distances in the starting inorganic matrix from 4.82 Å to 7.15 Å (Fig. 5b). Large anions, such as C6H5(CH=CH)COO᎑, NH2C6H4COO᎑, and some other species cannot intercalate directly into γ-Al(OH)3, but they can replace Cl᎑ from the LiCl/γ-Al(OH)3 intercalate (26, 27). Conclusion In this contribution we have briefly discussed selected applications of the SC-WEB computer program in order to introduce and illustrate some concepts of supramolecular chemistry. Many other topics could be developed using the present version of SC-WEB, for example, the analysis of the topological features of cryptands, spherands, and cryptospherands; analysis of the coordination patterns of transition metals in multicomponent systems (e.g., helicates, grids, catenates); analysis of the structure of polynuclear cryptates; or analysis of the complementarity of hydrogen bonds in selfassembled supramolecular polymers. The interactive electronic version of the monograph (1) makes it possible to use the same material very flexibly, so that every teacher can develop his or her own examples, which best fit the interests and background of the audience. The preparation of a detailed tutorial guide with further applications of SC-WEB for educational purposes is now in progress. Note 1. SC-WEBuses two programs. The first program reads files in PDF format (Acrobat Reader available at http://www.adobe.com/ acrobat/). The second program, WebLab Viewer Lite, is used for the visualization and manipulation of structures and can be downloaded free from http://www.msi.com/weblab/. These two programs should be installed before running SC-WEB (start.pdf file).

Acknowledgments We are grateful to K. Merz for linguistic help and to T. Volkova for technical assistance. EVB gratefully acknowledges the opportunity to spend a term in 1997-1998 as an Invited Professor at Strasbourg University with J.-M. Lehn and G. Wipff. 226

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