Organic molecules geometry

Table B3.5.1 Number of cycles to converge for geometry optimizations of some typical organic molecules usmg Cartesian, Z-matrix and delocalized internal coordinates. ...

The Merck molecular force field (MMFF) is one of the more recently published force fields in the literature. It is a general-purpose method, particularly popular for organic molecules. MMFF94 was originally intended for molecular dynamics simulations, but has also seen much use for geometry optimization. It uses five valence terms, one of which is an electrostatic term, and one cross tenn. 

A somewhat dilferent way to define a molecule is as a simplified molecular input line entry specification (SMILES) structure. It is a way of writing a single text string that defines the atoms and connectivity. It does not define the exact bond lengths, and so forth. Valid SMILES structures for ethane are CC, C2, and H3C-CH3. SMILES is used because it is a very convenient way to describe molecular geometry when large databases of compounds must be maintained. There is also a very minimal version for organic molecules called SSMILES. 

Organic molecules are generally composed of covalent bonded atoms with several well-defined hybridization states tending to have well-understood preferred geometries. This makes them an ideal case for molecular mechanics parameterization. Likewise, organic molecules are the ideal case for semiempirical parameterization. 

Our reviewer felt the molecule builder was easy to use. It is set up for organic molecules. Specialized building modes are available for peptides, nucleotides, and carbohydrates. It is also possible to impose constraints on the molecular geometry. Functions are accessed via a separate window with buttons labeled with abbreviated names. This layout is convenient to use, but not completely self-explanatory. The program is capable of good-quality rendering. At the time of this book s publication, a new three-dimensional graphic user interface called Maestro was under development. 

Conjugation is crucial not only for the colors we see in organic molecules but also for the light-sensitive molecules on which our visual system is based. The key substance for vision is dietary /3-carotene, which is converted to vitamin A by enzymes in the liver, oxidized to an aldehyde called 11-frans-retinal, and then isomerized by a change in geometry of the C11-C12 double bond to produce 11-cis-retinal. 

The n molecular orbitals described so far involve two atoms, so the orbital pictures look the same for the localized bonding model applied to ethylene and the MO approach applied to molecular oxygen. In the organic molecules described in the introduction to this chapter, however, orbitals spread over three or more atoms. Such delocalized n orbitals can form when more than two p orbitals overlap in the appropriate geometry. In this section, we develop a molecular orbital description for three-atom n systems. In the following sections, we apply the results to larger molecules. 

Many techniques are available for the determination of the geometry of organic molecules in their ground states, such as microwave spectroscopy, infrared and Raman spectroscopy, and electron and x-ray diffraction. 

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