Computational studies calculations

Pyridinethiol is in equilibrium with 2-pyridinethione and it is been previously thought that the thiol is more stable in nonpolar solvents while the thione is more stable in polar solvents. Recent variable temperature Fourier transform IR experiments and computational studies calculated at the B3LYP/6-311 level of theory indicate that the thione is more thermodynamically stable than the thiol in nonpolar solvents and that tautomerism occurs via the dimer <2002JOC9061> (Equation 82). 

Several theoretical studies have considered LiH addition as a model for the more computationally difficult L1A1H4 and NaBH4 [45]. However, reaction of aldehydes and ketones with LiH seldom if ever leads to reduction [46]. AIH3, while less commonly used than the complex boron and aluminium hydrides, is useful for reducing carbonyls [47] and therefore is a suitable model for computational study. Calculations [2, 5] show that gas-phase reduction of formaldehyde by AIH3 occurs by formation of complex 1, which rearranges via a four-centre transition state to form an aluminium methoxide product. Two conformational isomers of... 

Using MMd. calculate A H and. V leading to ATT and t his reaction has been the subject of computational studies (Kar, Len/ and Vaughan, 1994) and experimental studies by Akimoto et al, (Akimoto, Sprung, and Pitts. 1972) and by Kapej n et al, (Kapeijn, van der Steen, and Mol, 198.V), Quantum mechanical systems, including the quantum harmonic oscillator, will be treated in more detail in later chapters. 

Polymers can be crystalline, but may not be easy to crystallize. Computational studies can be used to predict whether a polymer is likely to crystallize readily. One reason polymers fail to crystallize is that there may be many conformers with similar energies and thus little thermodynamic driving force toward an ordered conformation. Calculations of possible conformations of a short oligomer can be used to determine the difference in energy between the most stable conformer and other low-energy conformers. 

Further support for this approach is provided by modern computer studies of molecular dynamics, which show that much smaller translations than the average inter-nuclear distance play an important role in liquid state atom movement. These observations have conhrmed Swalin s approach to liquid state diffusion as being very similar to the calculation of the Brownian motion of suspended particles in a liquid. The classical analysis for this phenomenon was based on the assumption that the resistance to movement of suspended particles in a liquid could be calculated by using the viscosity as the frictional force in the Stokes equation... 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

A recent paper by Singh et al. summarized the mechanism of the pyrazole formation via the Knorr reaction between diketones and monosubstituted hydrazines. The diketone is in equilibrium with its enolate forms 28a and 28b and NMR studies have shown the carbonyl group to react faster than its enolate forms.Computational studies were done to show that the product distribution ratio depended on the rates of dehydration of the 3,5-dihydroxy pyrazolidine intermediates of the two isomeric pathways for an unsymmetrical diketone 28. The affect of the hydrazine substituent R on the dehydration of the dihydroxy intermediates 19 and 22 was studied using semi-empirical calculations. ... 

Many computational studies in heterocyclic chemistry deal with proton transfer reactions between different tautomeric structures. Activation energies of these reactions obtained from quantum chemical calculations need further corrections, since tunneling effects may lower the effective barriers considerably. These effects can either be estimated by simple models or computed more precisely via the determination of the transmission coefficients within the framework of variational transition state calculations [92CPC235, 93JA2408]. 

The deprotonation of 132 is favored at Ni and the coordination of 135 occurs preferentially at 82- A second entity of 135 coordinates at N3. A computational study of thiouracil derivatives of the tungsten(O) hexacarbonyl shows that the sulfur-bound thiouracil is serving as a ir-donor during the CO dissociation (Scheme 91) [99IC4715]. DFT calculations show that 137 is significantly stabilized with respect to the alternative reaction product 138. 

In a combined experimental/computational study, the vibrational spectra of the N9H and N7H tautomers of the parent purine have been investigated [99SA(A) 2329]. Solvent effects were estimated by SCRF calculations. Vertical transitions, transition dipole moments, and permanent dipole moments of several low-lying valence states of 2-aminopurine 146 were computed using the CIS and CASSCF methods [98JPC(A)526, 00JPC(A)1930]. While the first excited state of adenine is characterized by an n n transition, it is the transition for 146. The... 

Palladium(II) complexes provide convenient access into this class of catalysts. Some examples of complexes which have been found to be successful catalysts are shown in Scheme 11. They were able to get reasonable turnover numbers in the Heck reaction of aryl bromides and even aryl chlorides [22,190-195]. Mechanistic studies concentrated on the Heck reaction [195] or separated steps like the oxidative addition and reductive elimination [196-199]. Computational studies by DFT calculations indicated that the mechanism for NHC complexes is most likely the same as that for phosphine ligands [169], but also in this case there is a need for more data before a definitive answer can be given on the mechanism. 

Apart from the question whether the 14-electron species 12-B is a relevant intermediate, computational studies have been conducted in order to shed light on other aspects of the mechanism. Stereochemical issues, for instance, have not yet been investigated by experiment. DFT calculations suggest that attack of the alkene to 12-B occurs trans, because cis attack is associated with a rather high barrier [30b]. 

There have a number of computational studies of hypothetical RMMR species [10-13, 40, 411. The simplest compounds are the hydrides HMMH. Some calculated structural parameters and energies of the linear and trans-bent metal-metal bonded forms of the hydrides are given in Table 1. It can be seen that in each case the frans-bent structure is lower in energy than the linear configuration. However, these structures represent stationary points on the potential energy surface, and are not the most stable forms. There also exist mono-bridged, vinylidene or doubly bridged isomers as shown in Fig. 2... 

A thorough computational study of this process has been carried out using B3LYP/ONIOM calculations.31 The rate-determining step is found to be the formation of the rhodium hydride intermediate. The barrier for this step is smaller for the minor complex than for the major one. Additional details on this study can be found at ... 

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