The Basics of Molecular Geometry

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Chemical reactivity, especially in biochemical processes, is often related to the three-dimensional arrangement of atoms in the molecule relative to one another. Methods of describing and predicting the shape of a chemical substance are very important components of many introductory chemistry courses.

Molecular geometry is typically described relative to a central atom. For instance, carbon tetrachloride is viewed as a carbon atom with four chlorine atoms surrounding it in some precise arrangement. In a chemical formula, it is common convention to list the central atom first. The simplest approach to describing molecular geometry is the Valence Shell Electron Pair Repulsion theory (VSEPR). VSEPR draws on the concept of Lewis electron dot diagrams. In Lewis diagrams, the number of valance electron groups (single, double, or triple bonds and unshared electron pairs) around the central atom is determined by a set of rules.

VSEPR theory simply states that the electron groups will distribute themselves around the central atom in such as way as to minimize their electrostatic repulsions by maximizing their separations. For a system with two "groups" of valence electrons, this is accomplished by orienting the electron groups on opposite sides of the central atom. If both groups are bonding electrons, then the three atoms in the molecule will lie along a straight line and the molecular geometry is said to be linear.

For the case of three electron groups, separation is maximized by a planar arrangement with the electron pairs oriented toward the corners of a triangle. If all three pairs are bonding, the terminal atoms will lie at the corners of the imaginary triangle with the central atom in the center. This molecular geometry is known as trigonal planar. It could be that one of the electron groups is non-bonding. For instance, tin (II) chloride has a Lewis structure with two single bonding pairs and one non-bonding pair on the central tin atom. The three electron pairs, according to VSEPR theory, will adopt a trigonal planar separation in space. If we consider the impact on the atoms, this dictates a Cl-Sn-Cl bond angle of about 120 degrees, or a molecular geometry referred to as bent (or non-linear).

Note that the arrangement of the valence electron pairs (the electronic geometry) is the fundamental geometry and that the molecular geometry is derived from it. There are characteristic electronic geometries for different numbers of valence groups. In each case, the central atom lies at the center of an imaginary structure with electron pairs oriented towards the vertices of the structure. These include: tetrahedral (four electron groups); trigonal bipyramidal (five electron groups) and octahedral (six electron groups). Any general chemistry textbook will have a section describing these electronic geometries and the corresponding related molecular geometries.

Geometries of larger molecules such as ethanol cannot be described relative to a single central atom. None the less, an overall view of the shape of the molecule can be determined by drawing a Lewis structure for the molecule and describing the geometry relative to each atom.

Explaining these geometries is the realm of bonding theory. The simplest approach, Linus Pauling's Valence Bond Theory, rationalized the geometries as an overlapping of mixed (hybridized) atomic orbitals. While this approach works well for many cases, it has some shortcomings. It is a localized model and so cannot account for resonance, and it is non-predictive. In other words, it can rationalize an observed geometry but can not predict an unknown one. Molecular orbital theory takes the existing set of valence atomic orbitals and combines them into a new set of molecular orbitals. These orbitals are not necessarily localized and can thus account for resonance delocalization. Molecular orbital theory also allows accurate prediction of bond strengths and so, while a conceptually more difficult model, is a more realistic model than VB theory.

Molecular geometry plays a key role in many biological processes. In the case of a tetrahedral molecule having the general formula MABCD (where A, B, C, and D are different terminal atoms) there are two possible arrangements. These arrangements are asymmetric nonsuperimposable mirror images of each other in the same way that human hands are. (Different structural arrangements of the same chemical formula are called isomers) This phenomenon is responsible for optical activity. If the mixture of two mirror image isomers can be separated, it is found that they interact with light in different ways. A beam of plane polarized light will be rotated one way by one isomer and the opposite way by the second isomer. For this reason, isomers of this type are called optical isomers. Many biological processes occur selectively with one optical isomer. This is one reason the costs to develop new pharmaceutical materials are so high, as often only one of the two possible isomeric products are viable.

Sometimes there is more than one possible arrangement for the atoms in a molecule. For instance, a compound with two carbon atoms double bonded to each other of the general formula ABC=CAB (where A and B are terminal atoms) can have two arrangements: one where the atoms of type A are on the same side of the double bond (cis isomerism) or one where they are on opposite sides (trans isomerism). This is an example of geometric isomerism. Unlike optical isomers, geometric isomers are chemically distinct, having different physical and chemical properties. The larger the number of atoms in a molecule, the larger the number of geometric isomers possible.

In conclusion, molecular geometry is an important tool for visualizing chemical structure in three dimensions and using this model to better understand chemical processes. This allows better control of synthetic design and leads to better understanding of chemical and biochemical processes.

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