Molecular GeometryPrepared by

Glenn Szobotka

Geometry of the water molecule

Molecular Geometry

is the three-dimensional arrangement of the atoms that

constitute a molecule. It determines several properties

of a substance including its reactivity, polarity, phase

of matter, color, magnetism, and biological activity. The

angles between bonds that an atom forms depend only

weakly on the rest of molecule, i.e. they can be

understood as approximately local and

hence transferable properties.

Molecular geometry determination

The molecular geometry can be determined by various spectroscopicmethods and diffraction methods. IR, microwave and Raman spectroscopy cangive information about the molecule geometry from the details of thevibrational and rotational absorbance detected by these techniques.Geometries can also be computed by ab initio quantum chemistry methods tohigh accuracy. The molecular geometry can be different as a solid, insolution, and as a gas.The position of each atom is determined by the nature of the chemicalbonds by which it is connected to its neighboring atoms. The moleculargeometry can be described by the positions of these atoms in space,evoking bond lengths of two joined atoms, bond angles of three connectedatoms, and torsion angles (dihedral angles) of three consecutivebonds.

The influence of thermal excitation

Since the motions of the atoms in a molecule are determined by quantum mechanics, one must define “motion” in a quantum mechanical way. The overall (external) quantum mechanical motions translation and rotation hardly change the geometry of the molecule. (To some extent rotation influences the geometry via Coriolis forces and centrifugal distortion, but this is negligible for the present discussion.) In addition to translation and rotation, a third type of motion is molecular vibration, which corresponds to internal motions of the atoms such as bond stretching and bond angle variation. The molecular vibrations are harmonic (at least to good approximation), and the atoms oscillate about their equilibrium positions, even at the absolute zero of temperature. At absolute zero all atoms are in their vibrational ground state and show zero point quantum mechanical motion, so that the wavefunction of a single vibrational mode is not a sharp peak, but an exponential of finite width (the wavefunction for n = 0 depicted in the article on thequantum harmonic oscillator). At higher temperatures the vibrational modes may be thermally excited (in a classical interpretation one expresses this by stating that “the molecules will vibrate faster”), but they oscillate still around the recognizable geometry of the molecule.

BondingMolecules, by definition, are most often held together with covalent bonds involving single, double, and/or triple bonds, where a "bond" is a shared pair of electrons (the other method of bonding between atoms is called ionic bonding and involves a positive cation and a negative anion).

Molecular geometries can be specified in terms of bond lengths, bond angles and torsional angles. The bond length is defined to be the average distance between the nuclei of two atoms bonded together in any given molecule. A bond angle is the angle formed between three atoms across at least two bonds. For four atoms bonded together in a chain, the torsional angle is the angle between the plane formed by the first three atoms and the plane formed by the last three atoms.

Molecular geometry is determined by the quantum mechanical behavior of the electrons. Using the valence bond approximation this can be understood by the type of bonds between the atoms that make up the molecule. When atoms interact to form a chemical bond, the atomic orbitals of each atom are said to combine in a process called orbital hybridisation. The two most common types of bonds are sigma bonds (usually formed by hybrid orbitals) and pi bonds (formed by unhybridized p orbitals for atoms of main group elements). The geometry can also be understood by molecular orbital theory where the electrons are delocalised.

An understanding of the wavelike behavior of electrons in atoms and molecules is the subject of quantum chemistry.

IsomersIsomers are types of molecules that share a chemical formula but have different geometries, resulting in very different properties:

A pure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure).

Structural isomers have the same chemical formula but different physical arrangements, often forming alternate molecular geometries with very different properties. The atoms are not bonded (connected) together in the same orders. Functional isomers are special kinds of structural isomers, where certain groups of atoms exhibit

a special kind of behavior, such as an ether or an alcohol. Stereoisomers may have many similar physicochemical properties (melting point, boiling point) and at the

same time very different biochemical activities. This is because they exhibit a handedness that is commonly found in living systems. One manifestation of this chirality or handedness is that they have the ability to rotate polarized light in different directions.

Protein folding concerns the complex geometries and different isomers that proteins can take.

Types of molecular structureSome common shapes of simple molecules include:

Linear: In a linear model, atoms are connected in a straight line. The bond angles are set at 180°. A bond angle is very simply the geometric angle between two adj acent bonds. For example, carbon dioxide and nitric oxide have a linear molecular shape.

Trigonal planar: Just from its name, it can easily be said that molecules with the trigonal planar shape are somewhat triangular and in one plane (flat). Consequently, the bond angles are set at 120°. An example of this is boron trifluoride.

Bent: Bent or angular molecules have a non-linear shape. A good example is water, or H2O, which has an angle of about 105°. A water molecule has two pairs of bonded electrons and two unshared lone pairs.

Tetrahedral: Tetra- signifies four, and -hedral relates to a face of a solid, so "tetrahedral" literally means "having four faces". This shape is found when there are four bonds all on one central atom, with no extra unshared electron pairs. In accordance with the VSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds are arccos(−1/3) = 109.47°. An example of a tetrahedral molecule is methane (CH4).

Octahedral: Octa- signifies eight, and -hedral relates to a face of a solid, so "octahedral" literally means "having eight faces". The bond angle is 90 degrees. An example of an octahedral molecule is sulfur hexafluoride (SF6).

Trigonal pyramidal: A trigonal pyramidal molecule has a pyramid-like shape with a triangular base. Unlike the linear and trigonal planar shapes but similar to the tetrahedral orientation, pyramidal shapes require three dimensions in order to fully separate the electrons. Here, there are only three pairs of bonded electrons, leaving one unshared lone pair. Lone pair – bond pair repulsions change the bond angle from the tetrahedral angle to a slightly lower value.[8] An example is NH3 (ammonia).

3D representations

Line or stickatomic nuclei are not represented, j ust the bonds as sticks or lines. As in 2D molecular structures of this type, atoms are implied at each vertex.

Electron density plotshows the electron density determined either crystallographically or using quantum mechanics rather than distinct atoms or bonds

Ball and stick atomic nuclei are

represented by spheres (balls) and the bonds as sticks

Spacefilling models or CPKmodels (also an atomic coloring scheme in representations)

the molecule is represented by overlapping spheres

representing the atoms

Cartoon a representation used for proteins where loops, beta sheets, alpha helices are represented diagrammatically and no atoms or bonds are represented explicitly just the protein backbone as a smooth pipe

The End