Pre-lab 6.4.a Introduction to Molecular

In Chapters 3 and 4 we learned about ab initio and semi-empirical calculations. In this chapter, we make use of empirical calculations, which are particularly valuable when the molecular system of interest is too large to treat practically with other approaches and quantum effects are expected to play a very minor role. Molecular mechanics (MM) calculations, also known as empirical force-field calculations, are commonly employed in such cases. 

Good results from MM calculations, then, rely on a suitable force. Force fields for is-platin binding to DNA have been aggressively developed over the past 15 years. Parameter refinements include the deviation of the Pt-N7 bond from the plane of the coordinated purine, planarity of the platinum moiety, the van der Waal radius, and charges of the Pt atom. The combination of structural information from techniques such as two-dimensional NMR spectroscopy and X-ray crystallography with MM calculations are now providing valuable insight into the role of cw-platin. 

Procedure 6.4 Molecular Mechanics Calculations on the C/s-platin-Oligonucleotide Interactions20 

Double click on the Spartan shortcut icon on the desktop. This should open the Spartan program and you should have a blank, workspace window in front of you. 

Select New under File on the top toolbar. Your building tools should appear on the right hand of the screen. 

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