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Molecular Shape

The Shape of Molecules

The three dimensional shape or configuration of a molecule is an important characteristic. This shape is dependent on the preferred spatial orientation of covalent bonds to atoms having two or more bonding partners. Three dimensional configurations are best viewed with the aid of models.

In order to represent such configurations on a two-dimensional surface (paper, blackboard or screen), we often use perspective drawings in which the direction of a bond is specified by the line connecting the bonded atoms.

In most cases the focus of configuration is a carbon atom so the lines specifying bond directions will originate there. As defined in the diagram on the right, a simple straight line represents a bond lying approximately in the surface plane. The two bonds to substituents A in the structure on the left are of this kind. A wedge shaped bond is directed in front of this plane (thick end toward the viewer), as shown by the bond to substituent B; and a hatched bond is directed in back of the plane (away from the viewer), as shown by the bond to substituent D. Some texts and other sources may use a dashed bond in the same manner as we have defined the hatched bond, but this can be confusing because the dashed bond is often used to represent a partial bond (i.e. a covalent bond that is partially formed or partially broken). The following examples make use of this notation, and also illustrate the importance of including non-bonding valence shell electron pairs (colored blue) when viewing such configurations .

Methane		Ammonia		Water

Bonding configurations are readily predicted by valence-shell electron-pair repulsion theory, commonly referred to as VSEPR in most introductory chemistry texts. This simple model is based on the fact that electrons repel each other, and that it is reasonable to expect that the bonds and non-bonding valence electron pairs associated with a given atom will prefer to be as far apart as possible. The bonding configurations of carbon are easy to remember, since there are only three categories.

Configuration	Bonding Partners	Bond Angles
Tetrahedral	4	109.5º
Trigonal	3	120º
Linear	2	180º

In the three examples shown above, the central atom (carbon) does not have any non-bonding valence electrons; consequently the configuration may be estimated from the number of bonding partners alone. For molecules of water and ammonia, however, the non-bonding electrons must be included in the calculation. In each case there are four regions of electron density associated with the valence shell so that a tetrahedral bond angle is expected. The measured bond angles of these compounds (H₂O 104.5º & NH₃ 107.3º) show that they are closer to being tetrahedral than trigonal or linear. Of course, it is the configuration of atoms (not electrons) that defines the the shape of a molecule, and in this sense ammonia is said to be pyramidal (not tetrahedral). The compound boron trifluoride, BF₃, does not have non-bonding valence electrons and the configuration of its atoms is trigonal.

One way in which the shapes of molecules manifest themselves experimentally is through molecular dipole moments. A molecule which has one or more polar covalent bonds may have a dipole moment as a result of the accumulated bond dipoles. In the case of water, we know that the O-H covalent bond is polar, due to the different electronegativities of hydrogen and oxygen. Since there are two O-H bonds in water, their bond dipoles will interact and may result in a molecular dipole which can be measured. The following diagram shows four possible orientations of the O-H bonds.

The bond dipoles are colored magenta and the resulting molecular dipole is colored blue. In the linear configuration (bond angle 180º) the bond dipoles cancel, and the molecular dipole is zero. For other bond angles (120 to 90º) the molecular dipole would vary in size, being largest for the 90º configuration. In a similar manner the configurations of methane (CH₄) and carbon dioxide (CO₂) may be deduced from their zero molecular dipole moments. Since the bond dipoles have canceled, the configurations of these molecules must be tetrahedral (or square-planar) and linear respectively.
The case of methane provides insight to other arguments that have been used to confirm its tetrahedral configuration. For purposes of discussion we shall consider three other configurations for CH₄, square-planar, square-pyramidal and triangular-pyramidal

Substitution of one hydrogen by a chlorine atom gives a CH₃Cl compound. Since the tetrahedral, square-planar and square-pyramidal configurations have structurally equivalent hydrogen atoms, they would each give a single substitution product. However, in the trigonal-pyramidal configuration one hydrogen (the apex) is structurally different from the other three (the pyramid base). Substitution in this case should give two different CH₃Cl compounds if all the hydrogens react. In the case of disubstitution, the tetrahedral configuration of methane would lead to a single CH₂Cl₂ product, but the other configurations would give two different CH₂Cl₂ compounds. These substitution possibilities are shown in the above Chime insert.

Isomers

Isomers

Structural Formulas
It is necessary to draw structural formulas for organic compounds because in most cases a molecular formula does not uniquely represent a single compound. Different compounds having the same molecular formula are called isomers, and the prevalence of organic isomers reflects the extraordinary versatility of carbon in forming strong bonds to itself and to other elements.
When the group of atoms that make up the molecules of different isomers are bonded together in fundamentally different ways, we refer to such compounds as constitutional isomers. There are seven constitutional isomers of C₄H₁₀O, and structural formulas for these are drawn in the following table. These formulas represent all known and possible C₄H₁₀O compounds, and display a common structural feature. There are no double or triple bonds and no rings in any of these structures.

Structural Formulas for C₄H₁₀O Isomers
Kekulé Formula	Condensed Formula	Shorthand Formula

Simplification of structural formulas may be achieved without any loss of the information they convey. In condensed structural formulas the bonds to each carbon are omitted, but each distinct structural unit (group) is written with subscript numbers designating multiple substituents, including the hydrogens. Shorthand (line) formulas omit the symbols for carbon and hydrogen entirely. Each straight line segment represents a bond, the ends and intersections of the lines are carbon atoms, and the correct number of hydrogens is calculated from the tetravalency of carbon. Non-bonding valence shell electrons are omitted in these formulas.
Developing the ability to visualize a three-dimensional structure from two-dimensional formulas requires practice, and in most cases the aid of molecular models

Distinguishing Carbon Atoms
When discussing structural formulas, it is often useful to distinguish different groups of carbon atoms by their structural characteristics. A primary carbon (1º) is one that is bonded to no more than one other carbon atom. A secondary carbon (2º) is bonded to two other carbon atoms, and tertiary (3º) and quaternary (4º) carbon atoms are bonded respectively to three and four other carbons. The three C₅H₁₂ isomers shown below illustrate these terms.

Structural differences may occur within these four groups, depending on the molecular constitution. In the formula on the right all four 1º-carbons are structurally equivalent (remember the tetrahedral configuration of tetravalent carbon); however the central formula has two equivalent 1º-carbons (bonded to the 3º carbon on the left end) and a single, structurally different 1º-carbon (bonded to the 2º-carbon) at the right end. Similarly, the left-most formula has two structurally equivalent 2º-carbons (next to the ends of the chain), and a structurally different 2º-carbon in the middle of the chain. A consideration of molecular symmetry helps to distinguish structurally equivalent from nonequivalent atoms and groups. The ability to distinguish structural differences of this kind is an essential part of mastering organic chemistry. It will come with practice and experience.

Formula Analysis

Analysis of Molecular Formulas

Although structural formulas are essential to the unique description of organic compounds, it is interesting and instructive to evaluate the information that may be obtained from a molecular formula alone. Three useful rules may be listed:

For stable organic compounds the total number of odd-valenced atoms is even. Thus, when even-valenced atoms such as carbon and oxygen are bonded together in any number and in any manner, the number of remaining unoccupied bonding sites must be even. If these sites are occupied by univalent atoms such as H, F, Cl, etc. their total number will necessarily be even. Nitrogen is also an odd-valenced atom (3), and if it occupies a bonding site on carbon it adds two additional bonding sites, thus maintaining the even/odd parity.

Some Plausible
Molecular Formulas C₄H₄Cl₂, C₅H₉OBr, C₅H₁₁NO₂, C₁₂H₁₈N₂FCl

Some Impossible
Molecular Formulas C₅H₉O₂, C₄H₅ClBr, C₆H₁₁N₂O, C₁₀H₁₈NCl₂
The number of hydrogen atoms that can be bonded to a given number of carbon atoms is limited by the valence of carbon. For compounds of carbon and hydrogen (hydrocarbons) the maximum number of hydrogen atoms that can be bonded to n carbons is 2n + 2 (n is an integer). Consider CH₄, n=1 & 2n + 2 = 4. In a chain of carbon atoms the middle carbons will have two hydrogens each and the two end carbons have three hydrogens each. For a six-carbon chain (n = 6) we have H-(CH₂)₆-H, and the total hydrogen count is (2 x 6) + 2 = 14. The presence of oxygen (valence = 2) does not change this relationship; however, each nitrogen atom (valence = 3) increases the maximum number of hydrogens by one.

Some Plausible
Molecular Formulas C₇H₁₆O₃, C₉H₁₈, C₁₅H₂₈O₃, C₆H₁₆N₂

Some Impossible
Molecular Formulas C₈H₂₀O₆, C₂₃H₅₀, C₅H₁₀Cl₄, C₄H₁₂NO
The number of hydrogen atoms in stable compounds of carbon, hydrogen & oxygen reflects the number of double bonds and rings in their structural formulas. Consider a hydrocarbon with a molecular structure consisting of a simple chain of four carbon atoms, CH₃CH₂CH₂CH₃. The molecular formula is C₄H₁₀ (maximum number of bonded hydrogens). If the four carbon atoms form a ring, two hydrogens must be lost. Similarly, the introduction of a double bond entails the loss of two hydrogens, and a triple bond the loss of four hydrogens. The presence of one or more nitrogen atoms requires a modified analysis.

From the above discussion and examples it should be clear that the molecular formula of a hydrocarbon (C_nH_m) provides information about the number of rings and/or double bonds that must be present in its structural formula. A triple bond is counted as two double bonds.
This formula may be extended beyond hydrocarbons by a few simple corrections:
- Each nitrogen in the formula must be replaced by a CH moiety.

Community Contributions - Articles by goIITians

Molecular Shape

The Shape of Molecules

Isomers

Isomers

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Formula Analysis

Analysis of Molecular Formulas

Structural Formulas for C₄H₁₀O Isomers