Force field selection

Working on a planet in another galaxy, where laboratory temperatures are 200 K, a scientist discovers a new force field selective for isotopes whose separation promises to fuel a bomb to blow an adjacent planet to smithereens. The maximum force exerted by this field on the two isotopes is 5.00 x 1010 dyn/mol. What is the lowest plate height the scientist can hope to achieve in an Sc-class separation In this field the velocity difference is 2% of the mean (which is remarkably selective for isotopes). What length separation tube is needed to separate the isotopes at unit resolution (Remember, lofty goals are worth the trouble.)... 

The OPLS force field is described in twtt papers, one discussing parameters for proteins W. L. Jorgensen and J. Tirado-Rives,/. Amer. (. hem. Soc., 110, 1557 (iy8K) and on e discii ssin g param eters for n iicleotide bases [J. Pranata, S. Wiersch ke, and W. L. Jorgen sen. , /.. Amer. Chem. Soc.. 117, 281(1 ( 1991)1. The force field uses the united atom concept ftir many, but not all. hydrttgens attached to carbons to allow faster calculation s on macromolecular systems. The amino and nucleic acid residue templates in HyperChein automatically switch to a united atom representation where appropriate when th e OPLS option is selected. 

Tine force field was then used to predict the results for fhe addition of the E and Z isomers c Ihe enol boronate of butanone (R = Me) to ethanol (R = Me). The relevant transitio. Iructures are shown in Figure 11.34. A Boltzmann distribution, calculated at the ten perature of the reaction (—78°C), predicted that the Z isomer would show almost complel syn selectivity syn anti = 99 1) and that the E isomer would be selective for the an product anti syn = 86 14). These results were in good agreement with the experunenti... 

If you are running an updated version (V 8.0) of PC Model, click on force fields mm3. Omit this step for older versions. Click on Analyze (or compute depending on the version of PCMODEL) to obtain a menu of options. Select minimize. The geometry changes can be seen on the screen and a sequence of numbers appears in the right panel of the CRT screen, ending in Hf, the enthalpy of formation. This is the PCMODEL-MM3 calculated value of for cis-2-... 

After selection of a force field simulation program which is appropriate to a given problem, the general procedure is as follows ... 

Knowledge of the approaches and target data used in the optimization of an empirical force field aids in the selection of the appropriate force field for a given study and acts... 

The second generation force fields for nucleic acids were designed to be used with an explicit solvent representation along with inclusion of the appropriate ions [28,29]. In addition, efforts were made to improve the representation of the conformational energetics of selected model compounds. Eor example, the availability of high level ab initio calculations on the conformational energetics of the model compound dimethylphosphate yielded... 

It should be clear that force field methods are models of the real quantum mechanical systems. The total neglect of electrons as individual particles forces the user to define explicitly the bonding present in the molecule prior to any calculations. The user must decide how to describe a given molecule in terms of the selected force field. The input to a calculation consists of three sets of information. 

Semi-empirical methods are zero-dimensional, just as force field mefhods are. There is no way of assessing the reliability of a given result within the method. This is due to the selection of a fixed (minimum) basis set. The only way of judging results is by comparing the accuracy of other calculations on similar systems with experimental data. 

The performance is (as expected) very good. MMX provides relative (and absolute) stabilities with a MAD of only 1.2 kcal/mol, which is better than the estimates from the combined theoretical methods in Table 11.31. Considering that force field calculations require a factor of 10 less computer time for these systems than the ab initio methods combined in Table 11.31, this clearly shows that knowledge of the strengths and weakness of different theoretical tools is important in selecting a proper model for answering a given question. 

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