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Three-Dimensional Arrangement of Atoms in a Molecule
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By
Anne Marie Helmenstine, Ph.D.
Anne Marie Helmenstine, Ph.D.
Chemistry Expert
- Ph.D., Biomedical Sciences, University of Tennessee at Knoxville
- B.A., Physics and Mathematics, Hastings College
Dr. Helmenstine holds a Ph.D. in biomedical sciences and is a science writer, educator, and consultant. She has taught science courses at the high school, college, and graduate levels.
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Updated on November 04, 2019
Molecular geometry or molecular structure is the three-dimensional arrangement of atoms within a molecule. It is important to be able to predict and understand the molecular structure of a molecule because many of the properties of a substance are determined by its geometry. Examples of these properties include polarity, magnetism, phase, color, and chemical reactivity. Molecular geometry may also be used to predict biological activity, to design drugs or decipher the function of a molecule.
The Valence Shell, Bonding Pairs, and VSEPR Model
The three-dimensional structure of a molecule is determined by its valence electrons, not its nucleus or the other electrons in the atoms. The outermost electrons of an atom are its valence electrons. The valence electrons are the electrons that are most often involved in forming bonds and making molecules.
Pairs of electrons are shared between atoms in a molecule and hold the atoms together. These pairs are called "bonding pairs".
One way to predict the way electrons within atoms will repel each other is to apply the VSEPR (valence-shell electron-pair repulsion) model. VSEPR can be used to determine a molecule's general geometry.
Predicting Molecular Geometry
Here is a chart that describes the usual geometry for molecules based on their bonding behavior. To use this key, first draw out the Lewis structure for a molecule. Count how many electron pairs are present, including both bonding pairs and lone pairs. Treat both double and triple bonds as if they were single electron pairs. A is used to represent the central atom. B indicates atoms surrounding A. E indicates the number of lone electron pairs. Bond angles are predicted in the following order:
lone pair versus lone pair repulsion > lone pair versus bonding pair repulsion > bonding pair versus bonding pair repulsion
Molecular GeometryExample
There are two electron pairs around the central atom in a molecule with linear molecular geometry, 2 bonding electron pairs and 0 lone pairs. The ideal bond angle is 180°.
| Geometry | Type | # of Electron Pairs | Ideal Bond Angle | Examples |
| linear | AB2 | 2 | 180° | BeCl2 |
| trigonal planar | AB3 | 3 | 120° | BF3 |
| tetrahedral | AB4 | 4 | 109.5° | CH4 |
| trigonal bipyramidal | AB5 | 5 | 90°, 120° | PCl5 |
| octohedral | AB6 | 6 | 90° | SF6 |
| bent | AB2E | 3 | 120° (119°) | SO2 |
| trigonal pyramidal | AB3E | 4 | 109.5° (107.5°) | NH3 |
| bent | AB2E2 | 4 | 109.5° (104.5°) | H2O |
| seesaw | AB4E | 5 | 180°,120° (173.1°,101.6°) | SF4 |
| T-shape | AB3E2 | 5 | 90°,180° (87.5°,<180°) | ClF3 |
| linear | AB2E3 | 5 | 180° | XeF2 |
| square pyramidal | AB5E | 6 | 90° (84.8°) | BrF5 |
| square planar | AB4E2 | 6 | 90° | XeF4 |
Isomers in Molecular Geometry
Molecules with the same chemical formula may have atoms arranged differently. The molecules are called isomers. Isomers may have very different properties from each other. There are different types of isomers:
- Constitutional or structural isomers have the same formulas, but the atoms are not connected to each other the same water.
- Stereoisomers have the same formulas, with the atoms bonded in the same order, but groups of atoms rotate around a bond differently to yield chirality or handedness. Stereoisomers polarize light differently from each other. In biochemistry, they tend to display different biological activity.
Experimental Determination of Molecular Geometry
You can use Lewis structures to predict molecular geometry, but it's best to verify these predictions experimentally. Several analytical methods can be used to image molecules and learn about their vibrational and rotational absorbance. Examples include x-ray crystallography, neutron diffraction, infrared (IR) spectroscopy, Raman spectroscopy, electron diffraction, and microwave spectroscopy. The best determination of a structure is made at low temperature because increasing the temperature gives the molecules more energy, which can lead to conformation changes. The molecular geometry of a substance may be different depending on whether the sample is a solid, liquid, gas, or part of a solution.
Molecular Geometry Key Takeaways
- Molecular geometry describes the three-dimensional arrangement of atoms in a molecule.
- Data that may be obtained from a molecule's geometry includes the relative position of each atom, bond lengths, bond angles, and torsional angles.
- Predicting a molecule's geometry makes it possible to predict its reactivity, color, phase of matter, polarity, biological activity, and magnetism.
- Molecular geometry may be predicted using VSEPR and Lewis structures and verified using spectroscopy and diffraction.
References
- Cotton, F. Albert; Wilkinson, Geoffrey; Murillo, Carlos A.; Bochmann, Manfred (1999), Advanced Inorganic Chemistry (6th ed.), New York: Wiley-Interscience, ISBN 0-471-19957-5.
- McMurry, John E. (1992), Organic Chemistry (3rd ed.), Belmont: Wadsworth, ISBN 0-534-16218-5.
- Miessler G.L. and Tarr D.A.Inorganic Chemistry(2nd ed., Prentice-Hall 1999), pp. 57-58.
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Helmenstine, Anne Marie, Ph.D. "Molecular Geometry Introduction." ThoughtCo, Apr. 5, 2023, thoughtco.com/introduction-to-molecular-geometry-603800.Helmenstine, Anne Marie, Ph.D. (2023, April 5). Molecular Geometry Introduction. Retrieved from https://www.thoughtco.com/introduction-to-molecular-geometry-603800Helmenstine, Anne Marie, Ph.D. "Molecular Geometry Introduction." ThoughtCo. https://www.thoughtco.com/introduction-to-molecular-geometry-603800 (accessed June 8, 2024).
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