Structure determination of ferrocene derivatives

PhD thesis

Veronika Kudar

Eötvös Loránd University, Faculty of Science

Chemistry Doctorate School

School Leader: Prof. György Inzelt

Theoretical and Physical Chemistry, Structural Chemistry

Program Leader: Prof. Péter Surján

Supervisors: Prof. Pál Sohár, Prof. Kálmán Simon

2007.

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Introduction

Fifty years ago, the first reports of the remarkably stable compound bis(cyclopenta-

dienyl)iron, later to become known as ferrocene, touched off a flurry of research activity that

led to the development of the modern field of organometallic chemistry. This discovery was

seminal because it evoked new concepts of structure and bonding that served as a basis for the

synthesis and structure determination of a wide range of new compounds and materials.

The unique sandwich structure, the special bond system and the numerous fields of

applicability of ferrocene make it in itself interesting for science. The different heteroatomic

rings and the variance of the substituents can be an attractive task to both the preparative and

structural chemists. The two building blocks themselves show biological activity and the

collective application in pharmacological studies can be promising.

Recently, ferrocene got again into the centre of interest. Numerous research groups in

nearly all areas of science deal with the preparation, the properties, analysis or the

adaptabilities of different derivatives of ferrocene. In the modern science the structure of a

new material or any material before use must be accurately described. To solve this problem

we commonly use different structure analysis – generally spectroscopic and diffraction –

methods. The most often used technique is the combination of nuclear magnetic resonance

(NMR) and x-ray diffraction methods. The molecular structure sometimes differs in liquid

and crystalline state so these two techniques can supplement each other in sophisticated

structure determination.

Applied methods

We studied the ferrocene derivatives by nuclear magnetic resonance (NMR)

spectroscopic and single crystal x-ray diffraction methods. 1H and 13C NMR spectra were recorded in CDCl3 or DMSO[D6] solution in 5 mm

tubes at room temperature on a Bruker DRX 500 spectrometer at 500 (1H) or 125 (13C) MHz,

using TMS as internal reference with the deuterium signal of the solvent as the lock. DEPT

spectra were run in a standard manner, using only the = 135° pulse to separate CH/CH3 and

CH2 lines phased “up” and “down”, respectively. 2D-HMQC and 2D-HMBC spectra were

obtained by using the standard Bruker pulse programs.

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The X-ray measurements of two compound were made on an Enraf Nonius Kappa

CCD or on a Rigaku R-Axis Rapid diffractometer with graphite-monochromated Mo-K

radiation ( = 0.71073 Å). The measurements of all other compounds were made on a Rigaku

AFC6S diffractometer with graphite monochromated Cu K radiation. The crystals were

mounted on a glass fibre and data were collected at a temperature of 293 K. Cell constants

and an orientation matrix for data collection, obtained from a least-squares refinement using

the setting angles of carefully centred reflections. The data were collected using the -2 scan

technique. The intensities of three representative reflections were measured after every 150

reflections. No decay correction was applied. An empirical absorption correction was applied.

The data were corrected for Lorentz and polarization effects. Data processing was carried out

using the software supplied with the diffractometer. The structure was solved by direct

methods and expanded using Fourier techniques. The non-hydrogen atoms were refined

anisotropically. Hydrogen atoms were generated based upon geometric evidence and their

positions were refined by the riding model. All calculations were performed using the teXsan

crystallographic software package of Molecular Structure Corporation except for refinement,

which was performed using SHELXL-97 with full matrix least squares method on F2.

Thesis

1. We have determined the structure of six heterocyclic and three macrocyclic compounds

in liquid phase by NMR spectroscopic methods and in crystalline phase by single crystal

x-ray diffraction studies.

2. In the case of reactions leading to different products the analysis could clarify

unambiguously the structures of the resulted compounds.

3. In the crystals of a pirazole derivative we found that a chiral lattice was built up from

the achiral molecules due to the cease of the conformational movement during

crystallization, a phenomenon observed relatively rare.

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4. The two similar sulphur containing compounds – an imidazole and an analogue

pirimidine derivative – found to be isostructural. The unit cells are nearly the same, the

cell similarity index is 0.001. The space group is the same and packing landscape has

realized.

Figure 1. The crystal structure of the two isostructural compounds view against the a axis

5. The macrocyclic compounds incorporated of two azine groups (2,3-diaza-1,3-

butadienes) and two ferrocene units show both staggered and eclipsed conformation.

The symmetry properties of macrocycles depend on the mutual orientation of the

cyclopentadienyl rings and the binding chains and their flexibility.

6. In the crystals of macrocyclic compounds the high molecular symmetry overlaps the

crystallographic symmetry in only one case.

7. In the palladium complex the torsion of the macrocyclic system can be seen due to the

palladium coordination.

Conclusions

The structure determination of a new compound is important and useful. The materials

may show unexpected molecule or crystal structures that can cause interesting or strange

comparisons. The knowledge of the structure of the products of a reaction mainly helps the

understanding and systematization of the experimental results and the explanation of the

mechanism.

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Own publications in the subject of the dissertation

A. Csámpai, Gy. Túrós, V. Kudar, K. Simon, H. Oeynhausen, H. Wamhoff and P. Sohár,

Ethyl -(Triphenylphosphoranylidene)amino- -ferrocenylacrylate as a Starting Material for

[2_2] Cycloadditions, Including the Aza-Wittig Reaction,

Eur. J. Org. Chem., 2004, 4, 717-723.

A. Csámpai, Á Abrán, V. Kudar, Gy. Túrós, H. Wamhoff, P. Sohár, Synthesis, NMR, IR

spectroscopic and X-ray study of novel [pyridazin-3(2H)-one-6-yl]ferrocenes and related

ferrocenophane derivatives. Study on ferrocenes. Part 14,

J. Organomet. Chem. 2005, 690, 802–810.

V. Kudar, V. Zsoldos-Mády, K. Simon, A. Csámpai, P. Sohár, Synthesis, IR-, NMR- and X-

ray investigations on some novel N-hetaryl-dihydro-pyrazolyl ferrocenes. Study on

ferrocenes, part 16,

J. Organomet. Chem., 2005, 690, 4018–4026.

P. Sohár, A. Csámpai, Á. Abrán, Gy. Túrós, E. Vass, V. Kudar, K. Újszászy, B. Fábián,

Macrocyclic double ferrocenes, their stereostructure, and an IR and NMR spectroscopic, X-

ray crystallographic, and conformational and dynamic investigation,

Eur. J. Org. Chem. 2005, 1659–1664.

V. Kudar, Gy. Túrós, V. Zsoldos-Mády, A. Csámpai, M. Hanusz, P. Sohár, K. Simon,

Synthesis and crystal structure of ferrocene derivatives,

22nd European Crystallographic Meeting, Budapest, 2004. augusztus 26-31.

Acta Cryst. 2004,. A60, s288

Kudar V., Simon K., Sohár P., Ferrocén-származékok vizsgálata röntgendiffrakcióval.

Anyag- és Molekulaszerkezeti Bizottság ülése, Budapest, 2005, május 27.

Kudar V., Ferrocének szerkezetének felderítése röntgendiffrakcióval

Fiatal analitikusok 20. el adói napja, 2005. november 9.