Structure of Crown Ethers

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Jabir ibn Hayyan, born in 721 AD, is considered as the father of Chemistry. ... Abdullah bin Abdul-Aziz Al Saud became the King of Saudi Arabia. I myself, at ...
Structure of Crown Ethers A. A. El-Azhary, N. Al-Jallal, A. Al-Kahtani, N. Al-Badri, K. Al-Farhan, and M. Al-Qunaibit Department of Chemistry, Faculty of Science, King Saud University, P.O.Box 2455, Riyadh, 11451, Kingdom of Saudi Arabia Abstract. We use the combined conformational and vibrational analysis methodology to predict in what conformation different crown ethers and some of their complexes exist. Comparison between the structure of some of the low and high energy conformations allows the prediction of the factors that affects the conformational stability of the studied crown ether. Using the conformational analysis, it was predicted that 12-crown-4 (12c4) and 18-crown-6 (18c6) have S4 and S6 conformations, respectively, as the gas phase ground state structure. This was rationalized since in both of the S4 and S6 conformations there is one hydrogen bond for each oxygen atom and at distances shorter than any other predicted conformation of either molecule. This suggests that crown ethers adopt the conformation that maximizes the hydrogen bond rather than to have an endodentate structure. Using vibrational analysis, it was concluded that both of 12c4 and 18c6 have Ci conformation in the solid phase. Using the combined conformation and vibrational analysis, it was concluded that 12-thiacrown-4 (12t4) exists in the D4 conformation in the gas and solid phases. Conformational analysis of 18-thiacrown-6 (18t6) predicted a new C2 conformation as the ground state gas phase conformation which is lower by 4.67 kcal/mol at the MP2/6-311G** level than the solid state structure. The ground state C2 conformation of 18t6, and also the D4 conformation of 12t4 have all the SCCS angles adopt an exodentate structure without any exception. It is concluded that for the stability of thiacrown ethers a SCCS dihedral angle of 180º requirement is more important than a gauche CSCC dihedral angle requirement.

Keywords: Crown ethers, conformational analysis, vibrational analysis, structure of crown ethers, ab initio. PACS: 33.15.-e

IMPORTANCE OF CROWN ETHERS Pedersen while working in DuPont discovered the outstanding binding properties of crown ethers.1,2 Thus he was awarded the Nobel Prize in 1967 while he was only a M.Sc. degree holder.

12-crown-4 (12c4)

18-crown-6 (18c6)

Due to the selective binding properties of crown ethers, crown ethers have wide applications. For example, they are used in cancer treatment,3 treatment of nuclear waste,4 treatment of contaminated water,5 catalysis,6 ion transport systems,7 macrocyclic liquid crystals8 and zeolite synthesis.9 In addition, a new field in chemistry called molecular design10 has developed with a large variety of molecules, e.g. cavitands, cryptands, cyclidenes, cryptophanes, etc.

THEORETICAL AND EXPERIMENTAL DETAILS Crown ethers are large ring flexible molecules with large number of possible conformations. We use the combined conformational and vibrational analysis methodology to predict in what conformation crown ethers and their complexes exit. To predict the possible conformations of a given crown ether, conformational search is done using the efficient CONFLEX11 method of conformational search of cyclic molecules. To predict the gas phase ground state conformation, computations are performed at different levels of the ab initio theory as the B3LYP and MP2 levels. Comparison between the structure of some of the low and high energy conformations allows the prediction of the factors that affects the conformational stability of the studied crown ether. Comparison between the calculated and experimental vibrational spectra, usually solid and solution phases, makes it possible to predict in what conformation the considered crown ether exists.

FREE 12C4 AND ITS COMPLEXES Conformational analysis followed by ab initio computations at the MP2/6-31+G* level for 12c4 predicted, in agreement with the previous studies,12 that the S4 conformation is the ground state conformation, Figure 1.13 It was concluded that the S4 conformation is the ground state conformation of 12c4 since it has one hydrogen bond per oxygen atom and at distances shorter than any other predicted conformation of 12c4. However, a vibrational study of 12c4 showed that IR active modes are Raman inactive and IR inactive modes are Raman active, Figure 2.14 This led to the conclusion that 12c4 in the considered phases exits in the Ci conformation. Conformational and vibrational analysis of the 12c4 alkali metal cation complexes concluded that these complexes exist in the C4 conformation, Figures 3–4.15,16 This is with the exception of the Li+ complex which may exist in the C4 or Cs conformation. These reported structures of the 12c4 alkali metal cation complexes were confirmed later by gas phase IR predissociation spectroscopy study.17 Notice that in the C4 conformation of the 12c4 complexes, Figure 4, since the metal cation is larger than the ring cavity, the metal cation is displaced out of the ring plane, thus allowing the existence of optically active enantiomers.

12c4 Ci

S4

18c6

S6

Ci

Theoretical

Experimental

FIGURE 1. Comparison between the gas phase and experimental, usually solid and solution phases, conformations of 12c4 and 18c6.

FIGURE 2. Vibrational spectra of 12c4, showing that IR active modes are Raman inactive and IR inactive modes are Raman active.

FIGURE 3. Left: IR and Right: Raman, spectra of the solid phase of the 12c4 alkali metal cation complexes. No Raman spectrum could be obtained for the 12c4–Rb+ and Cs+ complexes. The Figure shows a shift of the position of some of the bands of the 12c4–Li+ complex compared to the corresponding bands of the other 12c4 alkali metal cation complexes, especially in the 1300–800 cm–1 region.

(a)

(b)

FIGURE 4. (a) Structure of the C4 conformation of the 12c4 alkali metal cation complexes, (b) Structure of the D3d conformation of some of the 18c6 alkali metal cation complexes.

FREE 18C6 ANS ITS COMPLEXES It is known by X-ray18 that 18c6 in the solid phase exists in the Ci conformation, Figure 1, which was also confirmed by us using vibrational spectroscopy.19 However, conformational analysis of 18c6 concluded that a new S6 conformation is the ground state conformation of 18c6. 19,20 This is quite interesting since the case now is similar to that of 12c4, as both of 12c4 and 18c6 have similar S4 and S6 conformations, respectively, as the ground state structure, and the similar Ci conformation in the solid state. Similar to the S4 conformation of 12c4, it was rationalized that the reason behind the stability of the S6 conformation of 18c6 is that it has one hydrogen bond per oxygen atom and at distances shorter than any other predicted conformation of 18c6. This indicates that the hydrogen bond is what controls the structure of crown ethers. This is contrary to the original irrational statement which is based on solid phase structure that crown ethers have endodentate structure. Assuming that crown ether

have endodentate structure, they would have a structure similar to that found in their complexes, Figure 4. A more accurate statement is that crown ethers, due to the hydrogen bond, have an endodentate-like structure. Conformational analysis of the 18c6 alkali metal cation complexes predicted C1, D3d, D3d, C3v and C3v conformations for the 18c6–Li+, Na+, K+, Rb+ and Cs+ complexes, respectively,19 Figures 4 and 5. The vibrational analysis concluded that the 18c6–Li+ complex exists in the C2 or D2 conformation, the Na+, K+, Rb+ and Cs+ complexes exist in the D3d, D3d, C3v and C3v conformations, respectively. This is in agreement with the structure determined by X-ray for the 18c6–Na+, K+, Rb+ and Cs+ complexes, although a C1 structure was also reported for the Na + complex.21-25 This is also in agreement with the combined gas phase infrared multiple photon dissociation spectra and quantum mechanical calculations which was published later which predicted C1 and D3d structures for the 18c6–Na+ complex, and D2, D3d, C3v and C3v structures for the 18c6–Li+, K+, Rb+ and Cs+ complexes, respectively.26

FIGURE 5. Left: IR and Right: Raman, spectra of the 18c6 alkali metal cation complexes. The 18c6–Na+ complex was obtained in an emulsified form, thus the poor Raman spectrum. Notice the similarity between the 18c6–K+, Rb+ and Cs+ spectra. Notice that the 18c6–Li+ spectra are different especially in the 750-850 and 1200–1300 cm–1 regions in the IR and 500-600 cm–1 region in the Raman.

FREE 12T4 AND ITS COMPLEXES Conformational and vibrational analysis of free 12t4 predicted that 12t4 exists in the D4 conformation, Figure 6.27,28 This is in agreement with the X-ray results29 and the previous conformational studies.30 Comparison between the dihedral angles of some of the low and high energy conformations concluded that for the stability of 12t4, a SCCS dihedral angle of 180º requirement is more important than a gauche CSCC dihedral angle requirement. Conformational analysis of the 12t4 complexes predicted C4, C4, C4, C2v and C4 conformations for the 12t4–Ag+, Bi3+, Cd2+, Cu+ and Sb3+ complexes, respectively, to be ground state conformations. This is in agreement with the experimental X-ray data for the 12t4–Ag+31 and Cd2+32 complexes but experimentally, by X-ray, the 12t4–Bi33 and Cu+34,35 complexes have Cs and C4 structures, respectively. To the best of our knowledge, there is no experimental geometry available for the 12t4–Sb3+ complex. Notice that, except for the 12t4–Cu+ complex, similar to the 12c4 alkali metal cation complexes, all of the 12t4 complexes have a C4 structure, Figure 4. Synthesis and measurement of the vibrational spectra of 12t4 complexes is currently underway in our Lab. 28

FREE 18T6 AND ITS COMPLEXES Conformational analysis of free 18t636 predicted a new C2 conformation to be the ground state conformation, Figure 6. At the MP2/6-311G** level this new C2 conformation is more stable by 4.67 kcal/mol than the experimentally known C2 conformation of 18t6.37 It is known that crown ethers adopt endodentate structure, as was mentioned above, and thiacrown ethers adopt exodentate structure and that in 18t6 two of the sulphur atoms violate this rule.26 A problem with this definition, for either crown ethers or thiacrown ethers, is that it is based on crystal structure where crystal packing forces may affect the molecular structure while the structure of molecules has to be judged by that of the gas phase. Since computations correspond to gas phase isolated molecule, the reported predicted ground state conformation of free 18t6 in Ref. 36 has all of the SCCS dihedral angles, without any exception, adopt exodentate structure. It was also concluded, similar to 12t4, for the stability of 18t6 a linear SCCS angle requirement is more important than a gauche angle requirement. Vibrational analysis of 18t6 in the solid state28 predicted the same C2 conformation as that determined by X-ray37. Conformational analysis of the 18t6–Ag+, Co2+, Cu+ and Ni2+ complexes predicted C2, Ci, C1 and C2 structures for these four complexes, respectively.36 However, X-ray studies indicate C2h,38 S639 and C140 structures for the 18t6–Ag+ complex, Ci structure for the 18t6–

Co2+ complex,41 C142 and Ci43 structure for the 18t6–Cu+ complex and Ci structure for the 18t6–Ni2+ complex.44 Vibrational analysis of these complexes is underway in our Lab. 28

12t4

D4

D4

18t6

C2

C2 Theoretical

Experimental

FIGURE 6. Comparison between the gas phase and experimental, solid phase, conformations of 12t4 and 18t6.

ACKNOWLEDGEMENT Supported by NPST program by King Saud University, Project Number: ADV400-02, King Abdul Aziz City of Science and Technology, Project number: AR 21-45 and Research Centre at the Faculty of Science, King Saud University, Project numbers: Chem/24-25/09 and Chem/27/06.

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16. Al-Rusaese, S.; Al-Kahtani, A. A.; El-Azhary A. A. J. Phys. Chem. A, 2006, 110, 8676. 17. Rodriguez, J. D.; Kim, D.; Tarakeshwar, P.; Lisy, J. M. J. Phys. Chem. A, 2010, 114, 1514. 18. Maverick, E.; Seiler, P.; Schweizer, W. B.; Dunitz, J. D. Acta Crystallogr. B 1980, 36, 615. 19. A. Al-Jallal, Ph.D. thesis "Structural and vibrational study of free 18-crown-6 and some of its complexes, King Saud University, 2006. 20. Al-Jallal, N. A.; Al-Kahtani, A. A.; El-Azhary, A. A. J. Phys. Chem. A 2005, 109, 3694. 21. Bailey, S. I.; Engehardt, L. M.; Leurg, W. P.; Raston, C. L.; Ritchie, I. M.;White, A. H. J.Chem.Soc. Dalton Trans. 1985, 1747. 22. Dolber, M.; Dunitz, J. D.; Seiler, P. Acta Cryst. B 1974, 2741. 23. Dolber, M.; Phizackerley, R. P. Acta Cryst. B 1974, 2746. 24. Dolber, M.; Phizackerley, R. P. Acta Cryst. B 1974, 2748. 25. Seiler, P.; Dolber, M.; Dunitz, J. D. Acta Cryst. B 1974, 2744. 26. Martínez-Haya, B.; Hurtado, P; Hortal, A. R., Hamad, S.; Steill, J. D.; Oomens, J. Phys. Chem. A, 2010, 114, 7048. 27. Al-Badri, N. I.; Al-Jallal, N. A.; El-Azhary, A. A. Theor. Chem. Acc., 2011, 130, 919. 28. Al-Badri, N. I.; Al-Jallal, N. A.; El-Azhary, A. A., K. Al-Farhan, and M. Al-Qunaibit, to be submitted for publication. 29. Wolf, R. E.; Hartman, J. R.; Storey, J. M. E.; Foxman, B. M.; Cooper, S. R. J. Am. Chem. Soc. 1987, 109, 4328. 30. Bultinck, P.; Huyghebaert, A.; Van Alsenoy, C.; Goeminne, A. J. Phys. Chem. A 2001, 105, 11266. 31. Helm, M. L.; Hill, L. L.; Lee, J. P.; Van Derveer, D. G.; Grant, G. J. Dalton Trans, 2006, 3534. 32. Baker, P. K.; Harris, S. D.; Durrant, M. C.; Hughes, D. L.; Richards, R.L. Acta Crystallogr., Sect. C: Cryst. 33. Blake, A. J.; Holder, A. J.; Reid, G.; Schroder, M. J. Chem. Soc., Dalton Trans. 1994, 627. 34. Robinson, G. H.; Sangokoya, S. A. J.Am.Chem. Soc. 1988, 110, 1494. Struct. Commun. 1995, 51, 697. 35. Blake, A. J.; Wan-Sheung Li; Lippolis, V.; Parsons, S.; Schroder, M. Acta Crystallogr., Sect. B: Struct. Sci. 2007, 63, 81. 36. El-Azhary, A. A., in preparation. 37. Hartman, J. R.; Wolf, R. E.; Foxman, B. M.; Cooper, S. R. J. Amer. Chem. Soc. 1983, 105, 131. 38. A.J.Blake, R.O.Gould, S.Parsons, C.Radek, M.Schroder (1995) Angew. Chem., Int. Ed., 34, 2374. 39. A.J.Blake, R.O.Gould, Wan-Sheung Li, V.Lippolis, S.Parsons, C.Radek, M. Schroder (1998) Inorg. Chem., 37,5070. 40. J.Pickardt, L.von Chrzanowski, R.Steudel, M.Borowski (2004) Z. Naturforsch., B:Chem. Sci., 59, 1077. 41. J.R.Hartman, E.J.Hintsa, S.R.Cooper (1984) Chem.Commun. ,386. 42. J.R.Hartman, S.R.Cooper (1986) J.Am.Chem.Soc. ,108, 1202. 43. A.J.Blake, R.O.Gould, A.J.Holder, A.J.Lavery, M.Schroder (1990) Polyhedron, 9, 2919. 44. E.J.Hintsa, J.A.R.Hartman, S.R.Cooper (1983) J.Am.Chem.Soc. ,105, 3738.

Special Appendix

Chemistry in Egypt and in the Arabian Gulf Countries Trying to Catch the West up Due to the recent developments in the Middle East after the amazing revolutions, which is known as the Arab Spring, I have been kindly invited by Prof. Clementi to attend this international conference and to give a talk about my research work and about Chemistry and especially Quantum Chemistry in Egypt and the in Arabian Gulf area. It is too tough to talk about Chemistry in Egypt and in the Arabian Gulf area in this short space. However, few points can be made. Firstly, in terms of history, the word corresponding to “Chemistry” in the English language is quite similar to that in the Arabic language “Al Chemeia”. The origin of the word “Chemistry” or “Al Chemeia” is Greek, first appeared in the fourth century as “chemeia”. It is believed that this name was given to Egypt due to the black soil of the Nile Valley. Jabir ibn Hayyan, born in 721 AD, is considered as the father of Chemistry. He is the first to establish the notation that science, including chemistry, is based on experimental research rather than being based on theory. Secondly, to give a short idea about Chemistry in Egypt and in the Arabian Gulf area, this can be divided into three parts. 1. Undergraduate. In fact, most of the contents of all Chemistry subjects are known for a quite long time and more or less the same textbooks are available and taught everywhere in the Globe. In addition, most of the Universities is the area have now been through the process of Academic Accreditation. However, a major problem in the Middle East is that the system of home work and teaching assistant is hardly being followed. As a result students depends mainly on memorizing rather than thinking. 2.

Graduate. This area is suffering the most. There are several problems which cannot be discussed in this short space. It is simply can be stated, as an example, that none of the Universities in the Middle East has a library, with the needed journals, as that in an average University in Europe or USA.

3.

Advanced academic institutions. There are probably three. These were made in an effort to close the gap with the West or even precede it. These are the “Qatar Foundation” in Qatar, “King Abdullah University of Science and Technology (KAUST )” in Saudi Arabia and “Zewail City of Science and Technology” in Egypt.

I have to add here that I am proud of being Egyptian, my wife is Syrian while I am working in the Kingdom of Saudi Arabia. Thus in a way, I represent the Arab Unity. While I am working at King Saud University (KSU), King Abdullah bin Abdul-Aziz Al Saud became the King of Saudi Arabia. I myself, at least, consider him a man of wisdom. King Abdullah set three goals, concerning Education, Economy and the country Infrastructure. Concerning Education, as an example, the budget of KSU increased from about one Billion to two billion dollars. It is a nice picture to see labs which were rarely opened now full of researchers and research equipments. As a result, the number of publications of the University increased from 412 to 1112 publications. I hope that there will be better chance to present these points in more detail during the Conference.