Molecules drawing 3-dimensional

Remember that the structural formula does not accurately show the three-dimensional shape of the molecule. Three-dimensional shape is depicted with drawings or models, as shown for ethanol in Figure 1.4. 

There are a number of different ways that the molecular graph can be conununicated between the computer and the end-user. One common representation is the connection table, of which there are various flavours, but most provide information about the atoms present in the molecule and their connectivity. The most basic connection tables simply indicate the atomic number of each atom and which atoms form each bond others may include information about the atom hybridisation state and the bond order. Hydrogens may be included or they may be imphed. In addition, information about the atomic coordinates (for the standard two-dimensional chemical drawing or for the three-dimensional conformation) can be included. The connection table for acetic acid in one of the most popular formats, the Molecular Design mol format [Dalby et al. 1992], is shown in Figure 12.3. 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Sawhorse formula (Section 3 1) A representation of the three dimensional arrangement of bonds in a molecule by a draw mg of the type shown... 

Stereochemistry deals with the three-dimensional ariangement of a molecule s atoms, and we have attempted to show stereochemistry with wedge-and-dash drawings and computergenerated models. It is possible, however, to convey stereochemical information in an abbreviated form using a method devised by the German chemist Emil Fischer. 

So, consider a typical molecule such as aspirin (acetylsalicylic acid), shown in Figure 1.11. Such two-dimensional drawings can be made using ChemDraw or ISlSDraw, but all the features needed to construct a molecular mechanics force field are apparent. 

Make three-dimensional drawings of the following molecules, and predict whether each has a dipole moment. If you expect a dipole moment, show its direction. 

Drawing the Three-Dimensional Structure of a Chiral Molecule... 

The Lewis structure of chlorine trifluoride is treated in Example. Determine the molecular geometry and draw a three-dimensional picture of the molecule. 

C09-0103. How many different structural isomers are there for octahedral molecules with the general formula A Xz Draw three-dimensional structures of each. 

Although these projections of organic molecules on surfaces deemphasize the stereochemistry of the adsorbed species, they are easy to draw and properly reveal the relative sizes and locations of surface atoms and organic species. When greater stereochemistry is desired, three-dimensional drawings may be made as shown in Scheme 1.3. 

The potential energy of water molecule is a function of three parameters, i.e. ru r2 and angle 0. A plot of the complete potential energy surface of a water molecule, therefore, will be four dimensional. Since we are limited to three dimensions for plotting functions, we cannot draw the entire potential... 

These two-dimensional, formula-like diagrams help you count and keep track of valence electrons, and communicate essential information about the placement and bonding of atoms or ions in a molecule. Chemists often draw Lewis structures in a way that suggests the shape of a molecule. However, this is not their function. It is important to remember that Lewis structures do not communicate any information about a molecule s shape. To represent the shapes of real molecules, you need a model that depicts them in three-dimensions. 

Note how we have resorted to another form of representation of the ethane, ethylene, and acetylene molecules here, representations that are probably familiar to you (see Section 1.1). These line drawings are simpler, much easier to draw, and clearly show how the atoms are bonded - we use a line to indicate the bonding molecular orbital. They do not show the difference between a and rr bonds, however. We also introduce here the way in which we can represent the tetrahedral array of bonds around carbon in a two-dimensional drawing. This is to use wedges and dots for bonds instead of lines. By convention, the wedge means the bond is coming towards you, out of the plane of the paper. The dotted bond means it is going away from you, behind the plane of the paper. We shall discuss stereochemical representations in more detail later (see Section 3.1). 

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