Molecular geometry importance

How is the geometry of a molecule defined and why is the study of molecular geometry important ... 

Why is molecular geometry important Cite some examples. 

Sketch the molecules on graph paper to help in determining the atomic coordinates. This is the first use of molecular geometry, a property that will become increasingly important as we go on. At this stage, the geometries are approximate the difference, for example, between cis and trans isomer s is ignored. 

Some properties, such as the molecular size, can be computed directly from the molecular geometry. This is particularly important, because these properties are accessible from molecular mechanics calculations. Many descriptors for quantitative structure activity or property relationship calculations can be computed from the geometry only. 

Molden (we tested Version 3.6) is a molecular display program. It can display molecular geometries read from a number of molecular file formats. Various views of the wave function can be displayed from the output of the Gaussian and GAMESS programs. Some functionality is available from MOP AC and AMP AC files. Conversion programs are available to import wave functions from ADF, MOLPRO, ACES II, MOLCAS, DALTON, Jaguar, and HONDO. 

In addition to molecular geometry, the most important quantity to come out of molecular modeling is the energy. Energy can be used to reveal which of several isomers is most stable, to determine whether a particular chemical reaction will have a thermodynamic driving force (an exothermic reaction) or be thermodynamically uphill (an endothermic reaction), and to ascertain how fast a reaction is likely to proceed. Other molecular properties, such as the dipole moment, are also important, but the energy plays a special role. 

There are phenomena such as the Renner and the Jahn-Teller effects where the Bom-Oppenheimer approximation breaks down, hut for the vast majority of chemical applications the Born-Oppenheimer approximation is a vital one. It has a great conceptual importance in chemistry without it we could not speak of a molecular geometry. 

A comprehensive and critical compilation has been published relatively recently on gas-phase molecular geometries of sulfur compounds including sulfoxides and sulfones5. This book covers the literature up to about 1980 and contains virtually all structures determined experimentally, up to that date, either by electron diffraction or microwave spectroscopy. Here we shall highlight only some of the most important observations from that source5 and shall discuss recent results in more detail. 

The most important approximations of the HMO method are, the consideration of only the it-electrons, the neglect of the interaction between them and the neglect of all atom-atom-interactions, if the atoms are not neighbouring. Contrary to the other methods, the molecular geometry does not play a role in the HMO method because only the topologic connection of the atoms in the molecule is considered. In spite of these drastic approximations, the HMO method proved its worth as the first semiempirical procedure with a wide field of applications as well as in the theoretical interpretation of many chemical phenomenons. The method was broadly used in the field of cationic polymerizations in the 60-70 years too (see 2)). 

The E-state is based solely on atom connectivity information obtained from the molecular graph, without any input from the molecular geometry or sophisticated quantum calculations. We start this chapter with a brief presentation of the relevant notions of graph theory and continue with the definitions of a couple of important graph matrices. Then the molecular connectivity indices are mentioned... 

This is a good discussion of the importance of intraatomic interactions in determining molecular geometry. 

---