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 informal ...

arrangement of the atoms 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 bioch ...

. 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 Polarity may refer to: Science *Electrical polarity, direction of electrical current * Polarity (mutual inductance), the relationship between components such as transformer windings * Polarity (projective geometry), in mathematics, a duality of or ...

phase of matter In the physical sciences, a phase is a region of space (a thermodynamic system), throughout which all physical properties of a material are essentially uniform. Examples of physical properties include density, index of refraction, magnetizati ...

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 associa ...

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 p ...

. 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 rang ...

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 s ...

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 angle ...

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. Si ...

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 Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...

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 instrum ...

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 m ...

) that are close in energy on the

potential energy surface A potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates ...

. Geometries can also be computed by

ab initio quantum chemistry methods ''Ab initio'' quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excit ...

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 bond A chemical bond is a lasting attraction between atoms or ions that enables the formation of molecules and crystals. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds, or through the sharing o ...

s 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 uni ...

s) of three

consecutive {{Short pages monitor *

Octahedral In geometry, an octahedron (plural: octahedra, octahedrons) is a polyhedron with eight faces. The term is most commonly used to refer to the regular octahedron, a Platonic solid composed of eight equilateral triangles, four of which meet at ea ...

: ''Octa-'' signifies eight, and ''-hedral'' relates to a face of a solid, so "

octahedral In geometry, an octahedron (plural: octahedra, octahedrons) is a polyhedron with eight faces. The term is most commonly used to refer to the regular octahedron, a Platonic solid composed of eight equilateral triangles, four of which meet at ea ...

" 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 attached ...

(SF₆) is an octahedral molecule. * 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.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 wa ...

(NH₃).

VSEPR table

The bond angles in the table below are ideal angles from the simple

VSEPR theory Valence shell electron pair repulsion (VSEPR) theory ( , ), is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. It is also named the Gillespie-Nyholm th ...

(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, qu ...

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

predicts that lone pairs repel each other, thus pushing the different atoms away from them.

References

External links

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

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

Determination

VSEPR table

3D representations

See also

References

External links