Molecular geometry in organic chemistry

This discussion points up the important fact that models in science are not reality but rather are our attempts to describe aspects of reality that we have been able to measure, such as bond distances, bond energies, molecular geometries, and so on. A model may work well up to a certain point but not beyond it, as with the idea of hybrid orbitals. The hybrid orbital model for period 2 elements has proven very useful and is an essential part of any modern discussion of bonding and molecular geometry in organic chemistry. When it comes to substances such as SFg, however, we encounter the limitations of the model. 

The hybrid orbital model is widely used to explain molecular geometries in organic chemistry, and for those molecules its predictions are generally consistent with calculations based on molecular orbital theory. The most common application is the construction of sp, sp, and sp hybrid orbitals at carbon, nitrogen, and oxygen atoms, and we will confine the discussion here to those cases. ... 

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. 

In spite of the lack of a unique and precise definition, aromaticity is one of the most frequently used concepts in (organic) chemistry. This phenomenon, which is classically associated with a cyclic tt-electron delocalization, results in a stabilization of the molecular system considered. Benzene is the archetype of the phenomenon of aromaticity. Thus, a question of interest is to what extent the amino substituent influences the electron delocalization in the ring. There are several criteria to evaluate the aromaticity, including the geometry-based (HOMA), energy-based (ASE), magnetism-based (NICS) and electronic delocalization (PDI) models. Recent theoretical evaluations65 of these parameters... 

The concept of cis-trans (Z-E) isomerism, originally used for the description of the relative geometry of olefins, has been extended to many other functions which feature a double bond character (pseudo double bonds), such as amides, as well as single bonds with a partial or complete limited rotation due to steric or stereoelec-tronic effects. Cis-trans isomerization (CTI) therefore exists in non-re-bonded or overcrowded molecules that switch from a given stable conformational state to another. This is the case of biaryl compounds which have been utilized in organic chemistry as the basis of molecular switches and rotors [1,2]. Nature has also exploited CTI of single bonds to increasing molecular diversity, in particular with the bulky thyroxin, a thyroid hormone, and the well-known disulfide bond which plays a critical role in the structure of peptides and in the conformation of proteins. 

DFT computations can be done with less computer time than the most advanced ab initio MO methods. As a result, there has been extensive use of B3LYP and other DFT methods in organic chemistry. As with MO calculations, the minimum energy geometry and total energy are calculated. Other properties that depend on electronic distribution, such as molecular dipoles, can also be calculated. 

The three-dimensional shape of a molecule, that is, its molecular geometry, is particularly important in organic chemistry. This is because the molecular geometry... 

This will preserve the reaction mechanism. We cannot do such changes in chemistry. However, we may think of some other molecular systems, which have similar geometry but opposite overall charge pattern ( counter pattern ). The new reaction has a chance to run in a similar direction as before. This concept is parallel to the idea of Umpolung functioning in organic chemistry. It seems that nolxxfy has looked, from that point of view, at all known reaction mechanisms. ... 

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