PSU CHEM 408 - Parameterization Validation & Uses of MM FFs

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CHEM 408 – Sp06 2/6/2006 1Worksheet #4 – Parameterization, Validation, & Uses of MM FFs Team #: _______ Manager: _____________________________________ Class Period: 2/8/06 Recorder: _____________________________________ Resources: Cramer 2.5 Speaker: _____________________________________ Jensen 2.3-2.4, 2.6-2.8 Liljefors ’04 article Analyst: _____________________________________ 1. Explain why complete specification of all force field parameters is virtually impossible for a force field with 50 or more atom types. 2. What can be done if, as is often the case, one or more parameters needed for a given calculation is not present in the force field of choice?CHEM 408 – Sp06 2/6/2006 2 3. Why is it that inorganic systems are treated using completely different force fields (and usually different programs) than are organic systems? 4. What sorts of questions about isolated molecules or small collections of molecules should MM type methods to be able to answer reliably? (Give three or more examples.) 5. For what sorts of questions does one expect that the answers provided by MM methods to be unreliable? (Give three or more examples.)CHEM 408 – Sp06 2/6/2006 3 6. Use the results tabulated in the Appendix of the Liljefors article (attached for your convenience) to draw some conclusions concerning the relative accuracy of the various force fields for predicting conformational energies. Keep in mind that the errors in many of the experimental values are not negligible compared to the calculation errors. To help in your thinking, I’ve provided an alternative version of the table which lists the differences between the calculations and the experiments rather than the values themselves. Also included in the last row of the table are the mean absolute deviations between the various calculations and the MP2//B3LYP calculations, which are assumed to be the most accurate. Notes: “Macromodel”, “Cerius2”, “Jaguar”, and “Gaussian” refer to computational programs. The columns labeled “MM2*” to “CFF99” are molecular mechanics calculations, the columns to the right are various electronic structure calculations.CHEM 408 – Sp06 2/6/2006 4 7. The mean absolute errors in the force field calculations range between about 0.5 to 1.0 kcal/mol (2.0 – 4.4 kJ/mol). What do these errors mean in terms of the errors in the equilibrium constants that would be predicted by assuming that ΔEFF is an adequate estimator for ΔG in the relation GRTKeqΔ−= ln ? 8. How can one determine the accuracy of MM methods for a specific problem of interest?CHEM 408 – Sp06 2/6/2006 5CHEM 408 – Sp06 2/6/2006 6 Liljefors Appendix: Updated MM & Newly Determined QM Energies in kcal/molDifferences wrt ExperimentExpt MM2* MM3* Amber* MMFF OPLS CFF99 HF B3LYP HF B3LYP MP2/H MP2/BEthane, TS-GS 2.9 -0.2 -0.5 -0.1 0.3 -0.1 -0.3 0.1 -0.1 0.1 -0.1 0.3 0.3Propene, TS-GS 2.0 0.1 -0.3 -0.4 0.0 -0.1 -0.3 0.1 0.1 0.1 0.1 -0.1 -0.1Isoprene, TS-GS 2.7 0.2 -1.9 -1.3 0.4 -1.7 -0.1 0.2 -0.2 0.2 -0.2 0.0 0.0Ethylbenzene, TS-GS 1.7 -0.2 0.1 -1.3 -0.5 -0.3 0.0 -0.3 -0.6 -0.3 -0.6 -0.2 -0.1Trimethylisopropyl benzne TS-GS 12.8 -1.8 -1.9 -2.4 0.1 0.5 -1.7 2.0 0.0 1.8 -0.1 -0.6 -0.5Styrene, TS-GS 1.8 -0.1 1.5 0.6 -0.8 1.2 -0.7 1.1 2.6 1.1 2.6 0.4 0.0Butane, g-a 1.0 -0.1 -0.2 -0.5 -0.2 -0.2 -0.1 0.0 -0.2 0.0 -0.2 -0.3 -0.32,3-Dirnethylbutane, g--a 0.1 0.0 0.3 -0.2 -0.3 -0.3 0.4 -0.2 0.0 -0.2 -0.1 0.0 0.01,3,5-Trineopentylbenzene,twosyn-a1.0 -0.2-0.6-0.7-0.5-0.3-0.5-1.2-1.1-1.2-1.1-0.8-0.9Methyl acetate c/t C=O 8.0 -2.4 -1.0 -1.6 0.3 1.0 0.7 1.4 -0.2 1.4 -0.2 0.6 0.62-Butanone, skew-ecl2.0 -0.4-0.4-0.4-1.2-2.0-0.6-0.5-0.5-0.5-2.0-1.0-2.0Ethyl methyl ether g-a 1.5 0.2 0.0 -0.1 0.0 0.0 0.0 0.2 -0.1 0.2 -0.1 -0.1 -0.12-Methoxy-THP, q-axb 1.0 -0.5 -0.1 0.4 0.8 2.2 0.9 0.0 -0.2 0.1 -0.1 0.3 0.4Ethanol CO g-a 0.7 -0.1 -0.3 -0.5 -0.5 -0.6 -0.3 -0.6 -1.0 -0.6 -1.0 -0.5 -0.6Propanol CC g-a -0.30.60.70.10.60.20.60.20.20.20.20.00.0 Ethyl amine CN g-a 0.7 -0.8 -0.8 -0.8 -1.1 -0.7 -0.9 -0.8 -0.3 -0.8 -0.3 -0.9 -0.9N-Methylaoetamide, E,.Z 2.4 -0.5 0.2 -0.5 -0.2 -0.1 0.7 0.1 -0.5 0.1 0.1 0.0 -0.3N-Methylpiperidine, ax--eq 3.2 -0.7 -0.9 -1.9 0.1 -1.1 0.1 0.4 0.2 0.4 0.2 0.7 0.72-Methylpiperidine, ax-eq 2.5 -0.4 -0.2 -1.3 -0.1 -0.2 -0.1 0.6 0.5 0.6 0.4 0.6 0.63-Methylpiperidine, ax-eq 1.6 0.0 -0.1 -1.1 -0.5 0.7 -0.2 0.0 0.0 0.0 0.0 -0.3 -0.34-Methyipiperidine, ax-eq 1.9 -0.2 -0.2 -0.8 -0.5 0.6 -0.1 0.6 0.5 0.5 0.5 0.4 0.4Cydohexane, twist-cha5.5 -0.1 1.0 0.3 0.4 1.5 1.6 1.3 1.0 1.3 1.0 1.1 1.1Phenylzyclohexane, ax--eqb 2.9 1.0 1.4 -0.9 -0.6 1.1 1.0 1.3 0.7 1.3 0.7 0.7 0.6Methylcyclohexane, ax-eq 1.8 0.0 0.0 -0.8 -0.4 0.0 0.0 0.5 0.4 0.5 0.4 0.2 0.2Aminocyclohexarte, ax--eqb 1.5 -0.1 -0.3 -1.8 -0.7 1.0 -1.1 -0.4 -0.1 -0.4 -0.1 -0.4 -0.5N,N-Dimethylamino-cyclohax--eqb 1.3 -0.3 -0.1 -0.1 0.1 4.2 -0.3 0.8 0.5 0.8 0.5 -0.9 -0.9trans-1,2-dimethylcyclohexax-eq.eq 2.6 -0.2 0.0 -1.3 -0.8 -0.3 0.1 0.6 0.5 0.6 0.5 0.2 0.1c/s-1,3-dimethylcyclohexanax,ax-eq.5.5 -0.2 0.2 -1.1 -0.4 -0.1 -0.1 1.1 0.5 1.0 0.4 0.3 0.2FCH2CH2F, g-a -0.80.20.21.60.20.22.41.30.41.30.40.30.3PrCl, g-a -0.20.40.50.40.2-0.11.20.60.30.60.40.30.3CICH2CH2CI, g-a 1.1 -0.7 0.3 -0.4 0.1 -0.3 0.1 0.8 0.6 0.8 0.6 0.4 0.3CICH2CH2CH2CI, g,a-g,g 1.1 -0.8 -1.1 -1.3 -0.7 -1.3 -2.0 -0.7 -0.4 -0.7 -0.4 -0.4 -0.4CICH2CH2CH2CI, a,a-g,g 1.5 -0.7 -1.3 -1.6 -0.4 -1.6 -3.4 -0.7 -0.2 -0.7 -0.2 -0.2 -0.2F, ax-eq 0.2 0.0 0.0 0.1 -0.6 0.1 1.4 -0.5 -0.4 -0.5 -0.4 -0.4 -0.3CI, ax-eq 0.5 -0.1 0.1 0.0 -0.8 -0.7 1.2 0.5 0.3 0.5 0.3 0.4 0.5Br, ax---eq 0.7 -0.2 -0.1 0.1 -0.7 -0.4 1.4 0.2 0.0 -0.7 -0.9 -0.5 -0.5trans-l,2-diF, ax,ax-eq,0.6 0.2 0.3 -0.9 -0.8 0.8 1.1 -2.0 -1.4 -2.0 -1.4 -1.4 -1.4trans-l,2-diCl, ax,ax-eq,-0.9 1.8 0.5 1.0 -1.1 -1.3 3.1 0.5 0.3 0.5 0.4 0.7 0.8trans-1,2diBr ax,ax-eq,-1.5 0.8 1.1 2.2 -0.2 -0.8 3.2 -0.5 -0.6 -1.0 -1.0 -1.7 -1.5trans-l,4-diF ax,ax-eq,-1.1 0.6 0.8 0.9 -1.5 0.6 3.8 -0.6 -0.4 -0.6 -0.4 -0.8 -0.8trans-1,4-diCl ax,ax-eq,-0.8 1.1 1.5 0.9 -1.2 0.3 4.2 1.6 1.1 1.6 1.1 1.4 1.4trans-l,4-diBr, ax,ax-eq,-0.9 1.5 1.8 2.1 0.1 0.3 4.0 1.3 0.8 -0.5 -0.9 -0.1 -0.1Butadiene, s-ci#s-tra2.5 0.2 -0.8 0.7 0.9 1.1 0.4 0.6 1.4 0.5 1.0 0.1 0.3Acrolein, s-cis--s-tr1.7 -0.1 0.2 0.7 0.3 0.9 0.1 0.0 0.0 0.0 0.0 0.2 0.3Root mean square error (RMS) 0 0.72 0.80 1.07 0.61 1.07 1.58 0.84 0.69 0.82 0.75 0.62 0.67Mean absolute error (MAE) 0 0.48 0.59 0.87 0.50 0.75 1.06 0.66 0.49 0.65 0.54 0.48 0.50MA deviation from


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PSU CHEM 408 - Parameterization Validation & Uses of MM FFs

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