Bioinorganic systems

Bertini, I. Rosato, A. In Molecular Modeling and Dynamics of Bioinorganic Systems Banci, L., Comba, P. Eds. Kluwer Academic Publishers Dordrecht, 1997, 1. 

Piquemal J-P (2004) Evaluation of molecular interactions in bioinorganic systems from ab initio computations to polarizable force fields. PhD Thesis, UPMC number 2004PA066267, Universite Pierre et Marie Curie, Paris, France... 

The applications of polarized x-ray absorption spectroscopy (PXAS) for structure determination in inorganic and bioinorganic systems are discussed. PXAS studies of oriented samples add angular detail to the information obtained from x-ray absorption edges and from EXAFS. In some cases, PXAS can be used to determine molecular orientation. In other cases, PXAS can be used to infer the details of electronic structure or of chemical bonding. Some of the potential future applications of PXAS are discussed. 

Elizondo-Riojas, M.-A., Gonnet, F., Auge-Barrere-Mazouat, P., Allain, F., Ber-ges, J., Attias, R., Chottard, J.-C. and Kozelka J., in Band, L. and Comba, P. (eds.), Molecular Modeling and Dynamics of Bioinorganic Systems, Kluver Academic Publishers, 1997, p. 131. 

For I > 1/2, nuclei also possess an electric quadrupole moment, Q. Quadrupolar nuclei exchange energy with electric fields in the rest of the molecule in which they are located causing profound effects on NMR spectra. Table 3.3 lists properties for some nuclei found in bioinorganic systems. 

As the preceding discussion of nitrogenase metal-sulfur clusters indicate, analysis of complex bioinorganic systems requires the use of multiple analytical techniques and the cooperative exchange of data and ideas of many researchers. The descriptions in this chapter have attempted to give students some idea of the scope and complexity of instrumental techniques available to the bioinorganic chemist. It has not been intended to be either comprehensive or theoretical in presentation. Students are encouraged to acquaint themselves further with the theory and practice of instrumental techniques, especially those that are important to their particular research interests. 

Chemists considering the design of model compounds for bioinorganic systems usually take one of two approaches ... 

Introduce instrumental techniques used in analysis of the bioinorganic systems I will lecture on (Chapter 3 Instrumental and Computer-Based Methods). Typically, these would be electron paramagnetic resonance (EPR) and Mossbauer spectroscopies not often covered in undergraduate instrumental analysis courses plus X-ray diffraction and NMR techniques used for structural analyses of metalloproteins and their small molecule model compounds. 

The range of redox potentials for hem derivatives given on the right illustrates the possibilities involved in bioinorganic systems. 

Electron transfer reactions and theory have been highlighted in this Conference. It is apparent that detailed characterization of the electron tranfer process both in the ground and excited states will be continued. The empirical and theoretical correlations of redox rate parameters with known properties of the donor and acceptor centers, the intersite distance for electron travel, and the nature of the medium (51) will continue to be amassed. Such results have been, and promise to be, important ingredients for success with bioinorganic systems (52-55). 

The preceding brief review of inorganic chemistry has been oriented toward questions that will arise in subsequent discussion of bioinorganic systems. The... 

Kenneth Suslick has written several pertinent statements about the study of metalloproteins and their model compounds. This paradigm will guide the study of the varied bioinorganic systems described in this chapter. Additions to Suslick s statement in point 2 stress the importance of modern structural analysis (X-ray crystallography, EXAFS, EPR, and two- and three-dimensional high-held NMR) of the purihed metalloproteins and their model compounds. As paraphrased from reference 19, the following statements outline the steps involved in the study of metalloproteins ... 

Whereas in many metalloprotein redox systems the oxidation states +2, +3, and +4 are involved, horseradish peroxidase catalysis appears to involve five oxidation states. The interest to coordination chemists of this study goes well beyond bioinorganic systems, for here, as in several cases reported earlier, the X-rays used to obtain the high-resolution structures induced chemical changes during structure determination. The X-rays liberate electrons, which may change the oxidation state of the metal. ... 

J. Li, P. Beroza, L. Noodleman, D. A. Case. In L. Banci P. Comba, editors. Molecular modeling and dynamics of bioinorganic systems, page 279, Dordrecht, 1997. Proceedings of NATO ASI workshop, Klnwer. 

Toward the calculations of bioinorganic systems from ab initio molecular dynamics simulations and static quantum chemistry... 

In recent years the fast increasing computing power has allowed a much more reliable insight into bioinorganic systems by computational approaches. Mostly, static quantum chemistry... 

One solution to such problems is provided by ab initio molecular dynamics (AIMD) simulations (11,53-57). These are still very expensive, but they include dynamical aspects and they are thus one of the most powerful tools to investigate bioinorganic systems if many conformations and unexpected events play a role. A necessary prerequisite will always be that inexpensive electronic structure methods such as DFT can be applied to the bioinorganic system of interest. 

Within our review we would like to highlight some selected research protocols for possible AIMD studies of bioinorganic systems, see Section II. In Section II.A we give a very brief introduction to the method as well as some references to useful reviews of the methodology. Next we introduce the research protocols (Section II.B) and after this we show the outcome of such protocols at two selected examples, see Section II.C. Additionally, we shortly introduce at selected examples solvation... 

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