Coordination chemistry molecular mechanics

Molecular mechanics calculations in coordination chemistry, G. R, Brubaker and D. W. Johnson,... 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

This section would not be complete without a brief mention of the use of molecular mechanics calculations in coordination chemistry, as these have been applied mainly to amine complexes 46,47 While most calculations relate to complexes of Co111, these are now being extended to complexes with other metal centres, e.g. Ni11.48... 

The parameterization can be based on any type of experimental data that are directly related to the results available from molecular mechanics calculations, i. e., nuclear coordinates, nuclear vibrations, or strain energies. Most of the force fields available, and this is certainly true for force fields used in coordination chemistry are at least partially based on structural data. The Consistent Force Field (CFF)[43,49,601 is an... 

The pioneering applications of molecular mechanics to coordination compounds were conformational analyses127,281. Recent applications involving the computation of conformer equilibria discussed in this chapter are studies of solution structure refinements126,29 1, racemate separations131 3il and the evaluation of reaction pathways11 1,34,3S1. The importance of conformer equilibria in the areas of electron transfer rates and redox potentials is discussed in Chapter 10, and many examples discussed in the other chapters of Part II indicate how important the prediction of conformational equilibria is in various areas of coordination chemistry. 

Cucurbit [6] uril and increasingly its higher homologues have been used extensively in a variety of host-guest chemistry and nanostructure assemblies. Of particular appeal are rotaxanes and molecular necklaces, mechanically interlocked assemblies of molecules based on CB [6]. Efficient synthesis of ID, 2D and 3D polyrotaxanes and molecular necklaces (cucurbituril beads linked by a macrocyclic molecule string ) has been achieved by a combination of self-assembly and coordination chemistry. We discuss rotaxanes and molecular necklaces in Section 10.7, and cucurbil-based systems are summarised in a recent review.23... 

Sellmann, D. Sutter, J. Biological N2 fixation Molecular mechanism of the nitrogen-ase catalyzed N2 dependent HD-formation, the N2 fixation inhibition and the open-side FeMoco model, Perspectives in Coordination Chemistry , Vol. 5 Eds. Trzeciak, A. M. Sobota, D. Ziolkowski, J. University of Wroclaw Poland, 2000. 

Molecular-mechanics calculations on platinum-oligonucleotide adducts have to deal with problems related to nucleic acids as well as with those arising from the platinum coordination chemistry. 

Molecular mechanics calculations as a tool in coordination chemistry . 

---