Organic chemistry calculations

HBF4 is a useful reagent, especially in organic chemistry. Calculate the mass of HF required to make 125 g of HBF4 by the following reaction ... 

Jorgenson W 1989 Free energy calculations a breakthrough in modeling organic chemistry in solution Accounts Chem. Res. 22 184... 

Take the Final Function Value of TINKER as the steric energy for this calculation. Compare the results with each other and with a standard value from a good elementar-y organic chemistry text (e.g., Ege, 1994). Calculate for the reaction cis trans and compare it with a standard text and with Kistiakowsky s original value. Kistiakowsky s original work was carried out at 355 K, but the temperature difference between 298 K and 355 K cancels for this isomerization. 

Because of its severe approximations, in using the Huckel method (1932) one ignores most of the real problems of molecular orbital theory. This is not because Huckel, a first-rate mathematician, did not see them clearly they were simply beyond the power of primitive mechanical calculators of his day. Huckel theory provided the foundation and stimulus for a generation s research, most notably in organic chemistry. Then, about 1960, digital computers became widely available to the scientific community. 

The regioselectivity benefits from the increased polarisation of the alkene moiety, reflected in the increased difference in the orbital coefficients on carbon 1 and 2. The increase in endo-exo selectivity is a result of an increased secondary orbital interaction that can be attributed to the increased orbital coefficient on the carbonyl carbon ". Also increased dipolar interactions, as a result of an increased polarisation, will contribute. Interestingly, Yamamoto has demonstrated that by usirg a very bulky catalyst the endo-pathway can be blocked and an excess of exo product can be obtained The increased di as tereo facial selectivity has been attributed to a more compact transition state for the catalysed reaction as a result of more efficient primary and secondary orbital interactions as well as conformational changes in the complexed dienophile" . Calculations show that, with the polarisation of the dienophile, the extent of asynchronicity in the activated complex increases . Some authors even report a zwitteriorric character of the activated complex of the Lewis-acid catalysed reaction " . Currently, Lewis-acid catalysis of Diels-Alder reactions is everyday practice in synthetic organic chemistry. 

Semiempirical calculations have been very successful in the description of organic chemistry, where there are only a few elements used extensively and the molecules are of moderate size. Some semiempirical methods have been devised specifically for the description of inorganic chemistry as well. The following are some of the most commonly used semiempirical methods. 

Organic molecule calculations can be done routinely to good accuracy on workstation-class hardware. It is advisable to examine tabulations of results in order to choose a method with acceptable accuracy and computational time for the property of interest. The trend toward having microcomputer versions of computational chemistry codes is making calculations on small organic molecules even more readily accessible. 

Acids and bases are a big part of organic chemistry but the emphasis is much different from what you may be familiar with from your general chemistry course Most of the atten tion m general chemistry is given to numerical calculations pH percent loniza tion buffer problems and so on Some of this returns m organic chemistry but mostly we are concerned with the roles that acids and bases play as reactants products and catalysts m chemical reactions We 11 start by reviewing some general ideas about acids and bases... 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

Several methods of quantitative description of molecular structure based on the concepts of valence bond theory have been developed. These methods employ orbitals similar to localized valence bond orbitals, but permitting modest delocalization. These orbitals allow many fewer structures to be considered and remove the need for incorporating many ionic structures, in agreement with chemical intuition. To date, these methods have not been as widely applied in organic chemistry as MO calculations. They have, however, been successfully applied to fundamental structural issues. For example, successful quantitative treatments of the structure and energy of benzene and its heterocyclic analogs have been developed. It remains to be seen whether computations based on DFT and modem valence bond theory will come to rival the widely used MO programs in analysis and interpretation of stmcture and reactivity. 

H. B. Schlegel and M. J. Frisch, Computational Bottlenecks in Molecular Orbital Calculations, in Theoretical and Computational Models for Organic Chemistry, ed. S. J. Formosinho et. al. (Kluwer Academic Pubs., NATO-ASI Series C 339, The Netherlands, 1991), 5-33. 

In semi-empirical methods, complicated integrals are set equal to parameters that provide the best fit to experimental data, such as enthalpies of formation. Semi-empirical methods are applicable to a wide range of molecules with a virtually limitless number of atoms, and are widely popular. The quality of results is very dependent on using a reasonable set of experimental parameters that have the same values across structures, and so this kind of calculation has been very successful in organic chemistry, where there are just a few different elements and molecular geometries. 

For the method for calculating these and similar results given in this chapter, see Higasi, K. Baba, H. Rembaum, A. Quantum Organic Chemistry Interscience NY, 1965. For values of calculated orbital energies and bond orders for many conjugated molecules, see Couison, C.A. Streitwieser Jr., A. Dictionary ofn Electron Calculations W.H. Freeman San Francisco, 1965. 

Study, the students are taught the basic concepts of chemistry such as the kinetic theory of matter, atomic stmcture, chemical bonding, stoichiometry and chemical calculations, kinetics, energetics, oxidation-reduction, electrochemistry, as well as introductory inorgarric and organic chemistry. They also acquire basic laboratory skills as they carry out simple experiments on rates of reaction and heat of reaction, as well as volrrmetric analysis and qualitative analysis in their laboratory sessions. 

Englman R (1981) Vibrations in Interaction with Impurities. 43 113-158 Epstein IR, Kustin K (1984) Design of Inorganic Chemical Oscillators. 56 1-33 firmer O (1976) Calculations of Molecular Properties Using Force Fields. Applications in Organic Chemistry. 27 161-211... 

The atom economy for this process is 86.5% (100 X 116/134), which is reasonable. To calculate the E-factor and EMY further information is needed. From published literature (Vogel s Practical Organic Chemistry ), a standard procedure is to mix butanol (37 g) with glacial acetic acid (60 g), and a small amount of sulfuric acid catalyst (ignored in all calculations). Following completion of the reaction the mixture is added to water (250 g). The crude ester is washed further with water (100 g), then saturated sodium bicarbonate solution (25 g) and finally water (25 g). After drying over 5 g of anhydrous sodium sulfate the crude ester is distilled to give product (40 g) in a yield of 69%. 

Ermer, O. Calculations of Molecular Properties Using Force Fields. Applications in Organic Chemistry. Vol. 27, pp. 161-211. 

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