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Molecular geometry is the
three-dimensional Three-dimensional space (also: 3D space, 3-space or, rarely, tri-dimensional space) is a geometric setting in which three values (called '' parameters'') are required to determine the position of an element (i.e., point). This is the inform ...
arrangement of the
atom Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons. Every solid, liquid, gas, a ...
s that constitute a
molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and b ...
. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter,
color Color (American English) or colour (British English) is the visual perceptual property deriving from the spectrum of light interacting with the photoreceptor cells of the eyes. Color categories and physical specifications of color are associ ...
,
magnetism Magnetism is the class of physical attributes that are mediated by a magnetic field, which refers to the capacity to induce attractive and repulsive phenomena in other entities. Electric currents and the magnetic moments of elementary particles ...
and
biological activity In pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or ...
. 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.


Determination

The molecular geometry can be determined by various spectroscopic methods and
diffraction Diffraction is defined as the interference or bending of waves around the corners of an obstacle or through an aperture into the region of geometrical shadow of the obstacle/aperture. The diffracting object or aperture effectively becomes a s ...
methods. IR,
microwave Microwave is a form of electromagnetic radiation with wavelengths ranging from about one meter to one millimeter corresponding to frequencies between 300 MHz and 300 GHz respectively. Different sources define different frequency ra ...
and
Raman spectroscopy Raman spectroscopy () (named after Indian physicist C. V. Raman) is a spectroscopic technique typically used to determine vibrational modes of molecules, although rotational and other low-frequency modes of systems may also be observed. Raman ...
can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques.
X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
neutron diffraction Neutron diffraction or elastic neutron scattering is the application of neutron scattering to the determination of the atomic and/or magnetic structure of a material. A sample to be examined is placed in a beam of thermal or cold neutrons to ob ...
and
electron diffraction Electron diffraction refers to the bending of electron beams around atomic structures. This behaviour, typical for waves, is applicable to electrons due to the wave–particle duality stating that electrons behave as both particles and waves. S ...
can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density.
Gas electron diffraction Gas electron diffraction (GED) is one of the applications of electron diffraction techniques. The target of this method is the determination of the structure of gaseous molecules, i.e., the geometrical arrangement of the atoms from which a molec ...
can be used for small molecules in the gas phase. NMR and
FRET A fret is any of the thin strips of material, usually metal wire, inserted laterally at specific positions along the neck or fretboard of a stringed instrument. Frets usually extend across the full width of the neck. On some historical instru ...
methods can be used to determine complementary information including relative distances, dihedral angles, angles, and connectivity. Molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries (see next section). Larger molecules often exist in multiple stable geometries (
conformational isomerism In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a mo ...
) that are close in energy on the potential energy surface. Geometries can also be computed by ab initio quantum chemistry methods to high accuracy. The molecular geometry can be different as a solid, in solution, and as a gas. The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, and torsion angles (
dihedral angle A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the un ...
s) of three
consecutive {{Short pages monitor * Octahedral: ''Octa-'' signifies eight, and ''-hedral'' relates to a face of a solid, so " octahedral" means "having eight faces". The bond angle is 90 degrees. For example,
sulfur hexafluoride Sulfur hexafluoride or sulphur hexafluoride (British spelling) is an inorganic compound with the formula SF6. It is a colorless, odorless, non- flammable, and non-toxic gas. has an octahedral geometry, consisting of six fluorine atoms attach ...
(SF6) is an octahedral molecule. *
Trigonal pyramidal In chemistry, a trigonal pyramid is a molecular geometry with one atom at the apex and three atoms at the corners of a trigonal base, resembling a tetrahedron (not to be confused with the tetrahedral geometry). When all three atoms at the corne ...
: 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.Miessler G.L. and Tarr D.A. ''Inorganic Chemistry'' (2nd ed., Prentice-Hall 1999), pp.57-58 For example,
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous ...
(NH3).


VSEPR table

The bond angles in the table below are ideal angles from the simple VSEPR theory (pronounced "Vesper Theory"), followed by the actual angle for the example given in the following column where this differs. For many cases, such as trigonal pyramidal and bent, the actual angle for the example differs from the ideal angle, and examples differ by different amounts. For example, the angle in H2S (92°) differs from the tetrahedral angle by much more than the angle for H2O (104.48°) does.


3D representations

* Line or stick – atomic nuclei are not represented, just the bonds as sticks or lines. As in 2D molecular structures of this type, atoms are implied at each vertex. * Electron density plot – shows the electron density determined either crystallographically or using
quantum mechanics Quantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistry, ...
rather than distinct atoms or bonds. * Ball and stick – atomic nuclei are represented by spheres (balls) and the bonds as sticks. * Spacefilling models or
CPK model In chemistry, a space-filling model, also known as a ''calotte model'', is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-t ...
s (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, and alpha helices are represented diagrammatically and no atoms or bonds are explicitly represented (e.g. the protein backbone is represented as a smooth pipe). The greater the amount of lone pairs contained in a molecule, the smaller the angles between the atoms of that molecule. The VSEPR theory predicts that lone pairs repel each other, thus pushing the different atoms away from them.


See also

* Jemmis mno rules *
Lewis structure Lewis structures, also known as Lewis dot formulas, Lewis dot structures, electron dot structures, or Lewis electron dot structures (LEDS), are diagrams that show the bonding between atoms of a molecule, as well as the lone pairs of electrons ...
* Molecular design software * Molecular graphics * Molecular mechanics *
Molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...
*
Molecular symmetry Molecular symmetry in chemistry describes the symmetry present in molecules and the classification of these molecules according to their symmetry. Molecular symmetry is a fundamental concept in chemistry, as it can be used to predict or explain m ...
* Molecule editor * Polyhedral skeletal electron pair theory *
Quantum chemistry Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions ...
* Topology (chemistry)


References


External links


Molecular Geometry & Polarity Tutorial
3D visualization of molecules to determine polarity.

3D structure visualization of molecules using Crystallography. {{DEFAULTSORT:Molecular Geometry