Computations in the gas-phase

3 Computations in the gas-phase Theoretical modeling is typically performed by organometallic chemists using the framework of pervasive density functional theory (DFT). The vast majority of these quantum chemical calculations are traditionally performed in the gas-phase (vacuum) and quite frequently by using simplified molecular models. The most typical motivation for this is to reduce computational time.  

On the other hand, it is well-known experimentally that even slight simplifications of catalyst structure can result in significant losses in activity, enantioface selectivity and other parameters. Therefore the use cf gas-phase computations or simplified models in order to reduce computational time should be avoided by all means, since very different mechanisms may be in operation in the presence and absence of solvent and for different catalysts.  

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In other words, since for solvents with H-bonding ability (methanol and water) the aN of the nitroxide radical is shifted to higher values because of the influence of one or more hydrogen bonds between the solute and the solvent, it becomes necessary to build a model in which nonspecific effects are described in terms of continuum polarizable medium with a dielectric constant typical of the protic solvent under study, whereas specific effects are taken into account through an explicit hydrogen-bonded complex between the radical and some solvent molecules. Figure 2.6 reports the aN values for the complexes formed by TEMPO with phenol, methanol, and water measured experimentally at room temperature, and computed in the gas phase and in solution. The values computed in solution fit the experimental data quite well. 

Fig. 10.10. Alternate transition structures for Diels-Alder reaction of isoprene with propenal (a) structure without formyl hydrogen bond (b) structure with formyl hydrogen bond. Dimensions are from B3LYP/6-31G( f) computations in the gas phase and in PMC with s = 4.335 (shown in parentheses). Adapted from Org. Lett., 5, 649 (2003), by permission of the American Chemical Society.

Computation in the gas phase did not locate a concerted TS, but indicated instead that the reactions proceed by dissociation-reassociation. The reassociation process has no barrier, whereas the dissociation has a very small one (2.4-2.6 kcal/mol). For the oxy anion, inclusion of a Li+ counterion resulted in a concerted process with a barrier of about 12 kcal/mol. Since this more closely approximates solution conditions, it suggests that a concerted mechanism is feasible in solution. The dissociation mechanism is favored for both nitrogen and carbon. 

In addition, there are munerous polynitrogen species that have been computed in the gas phase (Fig. 5) [24-30], however, none of these compounds has yet been prepared in the laboratory, not even on a milligram scale. 

Computer simulation techniques offer the ability to study the potential energy surfaces of chemical reactions to a high degree of quantitative accuracy [4]. Theoretical studies of chemical reactions in the gas phase are a major field and can provide detailed insights into a variety of processes of fundamental interest in atmospheric and combustion chemistry. In the past decade theoretical methods were extended to the study of reaction processes in mesoscopic systems such as enzymatic reactions in solution, albeit to a more approximate level than the most accurate gas-phase studies. 

Procedures to compute acidities are essentially similar to those for the basicities discussed in the previous section. The acidities in the gas phase and in solution can be calculated as the free energy changes AG and AG" upon proton release of the isolated and solvated molecules, respectively. To discuss the relative strengths of acidity in the gas and aqueous solution phases, we only need the magnitude of —AG and — AG" for haloacetic acids relative to those for acetic acids. Thus the free energy calculations for acetic acid, haloacetic acids, and each conjugate base are carried out in the gas phase and in aqueous solution. 

Compute the frequency associated with carbonyl stretch in solution with acetonitrUe for the carbonyl systems we looked at in the gas phase in Chapter 4. Run your calculations using RHF/6-31+G(d) with the Onsager SCRF model. Discuss the substituent effect on the predicted solvent effects. 

Computations can be carried out on systems in the gas phase or in solution, and in their ground state or in an excited state. Gaussian can serve as a powerful tool for exploring areas of chemical interest like substituent effects, reaction mechanisms, potential energy surfaces, and excitation energies. 

Owing to the increasing efficiency of computational methods, it has become possible to investigate base pairs in the gas phase and solution simulated by super-molecular approaches with up to six water molecules [98IJQ37, 98JPC(A) 10374, 98JPC(B)9109, 99JST107]. In the cytosine-isocytosine Watson-Crick base pair. 

Finally, metalated epoxides undergo isomerization processes characteristic of traditional carbenoids (Scheme 5.2, Path C). The structure of a metalated epoxide is intermediate in nature between the structures 2a and 2b (Scheme 5.2). The existence of this intermediacy is supported by computational studies, which have shown that the a-C-O bond of oxirane elongates by -12% on a-lithiation [2], Furthermore, experimentally, the a-lithiooxycarbene 4a (Scheme 5.3) returned cydo-pentene oxide 7 among its decomposition products indeed, computational studies of singlet 4a suggest it possesses a structure in the gas phase that is intennediate in nature between an a-lithiocarbene and the lithiated epoxide 4b [3],... 

Figure 3.11 illustrates the mass transfer coefficient for batch-grown R. rubrum and was computed with various acetate concentrations at 200 rpm agitation speed, 500 lux light intensity, and 30 °C. As the experiment progressed, there was an increase in the rate of carbon monoxide uptake in the gas phase and a gradual decrease in die partial pressure of carbon monoxide. Also, a decrease in the partial pressure of carbon monoxide was affected by acetate concentration in the culture media. The value of the slope of the straight line increased with the decrease in acetate concentrations, i.e. 2.5 to 1 g-l. The maximum mass transfer coefficient was obtained for 1 g-l 1 acetate concentration (KLa = 4.3-h 1). The decrease in mass transfer coefficient was observed with the increase in acetate concentration. This was due to acetate inhibition on the microbial cell population as acetate concentration increased in the culture media. The minimum KLa was 1.2h 1 at 3g l 1 acetate concentration. 

P the total pressure, aHj the mole fraction of hydrogen in the gas phase, and vHj the stoichiometric coefficient of hydrogen. It is assumed that the hydrogen concentration at the catalyst surface is in equilibrium with the hydrogen concentration in the liquid and is related to this through a Freundlich isotherm with the exponent a. The quantity Hj is related to co by stoichiometry, and Eg and Ag are related to - co because the reaction is accompanied by reduction of the gas-phase volume. The corresponding relationships are introduced into Eqs. (7)-(9), and these equations are solved by analog computation. 

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