Skeletal structures representations

The following molecular model is a representation of para-aminobenzoic acid (PABA), the active ingredient in many sunscreens. Indicate the positions of the multiple bonds, and draw a skeletal structure (gray = C, red = O, blue = N, ivory - H). 

Figure 1 Schematic representation of the facially amphiphilic and asymmetric structure of a bile acid, a skeletal structure which can be likened to the body of a turtle.

Pig. Representive skeletal structures of linear and non-linear polymers. 

Drawing organic molecules presents a special challenge. Because they often contain many atoms, we need shorthand methods to simplify their structures. The two main types of shorthand representations used for organic compounds are condensed structures and skeletal structures. 

Skeletal structure (Section 1.7B) A shorthand representation of the stmcture of an organic compound in which carbon atoms and the hydrogen atoms bonded to them are omitted. All heteroatoms and the hydrogens bonded to them are drawn in. Carbon atoms are assumed to be at the junction of any two lines or at the end of a line. 

Figure 3.18 The Watson-Crick double helical structure of DNA illustrated by the crystal structure of an oligonucleotide. (a) Skeletal model representation, in stereo (note the tilting of the base pairs in certain cases this is responsible for causing the DNA double helix to coil up, for example, into the nucleosome, a key component of the chromosome). (b) Space filling representation, in stereo, (c) Beevers molecular model. Figures kindly provided by Dr W. N. Hunter with permission.

Figure 16.3 Four representations of the structure of 2-methylbutane (a) structural formula, (b) abbreviated structural formula, (c) skeletal structure,...

Although informative, the structural formula is time-consuming to draw. Therefore, chemists have devised ways to simplify the representation. Figure 16.3(b) is an abbreviated version, and the structure shown in Figure 16.3(c) is called the skeletal structure in which all the C and H letters are omitted. A carbon atom is assumed to be at each intersection of two lines (bond) and at the end of each line. Because every C atom forms four bonds, we can always deduce the number of H atoms bonded to any C atom. The element symbols for substituent atoms in the skeletal structure are always shown explicitly, such as in l-bromo-3-chlorobutane [C4H8BrCl] ... 

Let us suppose it is possible to treat the nuclear subsystem in a molecule classically and electronic subsystem quantum mechanically. This type of theoretical framework is called a mixed quantum-classical representation. Such a mixed representation can find many applications in science. For instance, a fast mode such as the proton dynamics in a protein should be considered as a quantum subsystem, while the rest of the skeletal structure can be treated as a classical subsystem [3, 484, 485]. It is quite important in this context to establish the correct equations of motion for each of the subsystems and to ask what are their rigorous solutions and how the quantum effects penetrate into the classical subsystems. By studying the quantum-electron and classical-nucleus nonadiabatic dynamics as deeply as possible, we will see how such rigorous solutions, if any, look like qualitatively and quantitatively. This is one of the main aims of this book. 

If you have access to a set of molecular models, converting between perspective formulas, Fischer projections, and skeletal structures is rather straightforward. If, however, you are interconverting these three-dimensional structures on a two-dimensional piece of paper, it is easy to make a mistake, particularly if you are not good at visualizing structures in three dimensions. Fortunately, there is a relatively foolproof method for these interconversions. All you need to know is how to determine whether an asymmetric center has the / or the 5 configuration (Sections 4.7 and 4.14). Look at the following examples to learn how easy it is to interconvert the various stractural representations. 

Quetiapine, marketed as Seroquel, is a heavily prescribed antipsychotic drug used in the treatment of schizophrenia and bipolar disorder. Convert the following representation into a skeletal structure, and give the molecular formula of quetiapine. 

In this chapter ball and stick models are used from time to time to depict the skeletal structures of polyhedral boron hydrides. No attempt is made to portray these structures in terms of two- and three-center bonds since the author wishes to avoid the problems associated with the valence bond structural ellipsis (50,51) implied even by a sophisticated representation (17). 

There is a special and very important feature of the anticipated open nido twelve-vertex structures in Fig. 12 repetition of single Lipscomb dsd rearrangements (denoted by the two-headed arrows) monotonically allows the six skeletal atoms about the open face to rotate about the second tier of five skeletal atoms (two-tier dsd rotation). Each dsd rearrangement [85, 163) (valence bond tautomerism) recreates the same configuration and involves only the motion of two skeletal atoms (in the ball-and-stick representation) and would allow carbons, if located in different tiers, to migrate apart. Such wholesale valence bond tautomerism is known to accompany the presence of seven-coordinate BH groups, e.g., and CBjoHu 142,155). 

Figure 2. Representation of the three dimensional structure of skeletal muscle.

The hydrides HM(PF3)4, M = Co, Rh, Ir, possess a structure simUar to that of HCo(CO)4. In C3v skeletal symmetry the filled metal orbitals are of symmetry e(2), the Rh-H a bond transforms as a, and the metal-phosphorus a bonds span the irreducible representations a,(2) + e. Three low-energy peaks (Table XXIX) (169, 227) have been detected in the UPS of HCo(PF3)4, and overlapping of ionization occurs with the Rh and Ir compounds (Fig. 28). While the assignments cannot be regarded as definitive at the present time, the first two peaks in the UPS of HCo(PF3)4 probably correspond to the two 2E ionic states of predominant metal character. 

Figure 8.7 Skeletal representation and crystallographic structure of the (tmtaa)CrCl catalyst for the copolymerization of epoxides and C02.

Figure 8.71 Skeletal representations of face-to-face stacking in the X-ray crystal structures of some typical charge transfer complex co-crystals (a) naphthalene-TCNE, (b) skatole-trinitrobenzene, (c) perylene-fluoroanil (d) anthracene-trinitrobenzene and (e) TCNQ-TMPD.

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