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
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, and ...
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 bioch ...
. It includes the general shape of the molecule as well as
bond length
In molecular geometry, bond length or bond distance is defined as the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed types, relatively independent of the rest of ...
s, bond angles,
torsional 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 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 ord ...
,
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 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
Applied spectroscopy is the application of various spectroscopic methods for the detection and identification of different elements or compounds to solve problems in fields like forensics, medicine, the oil industry, atmospheric chemistry, and ...
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 ...
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 ran ...
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 sp ...
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 o ...
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 ...
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 instrume ...
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 mole ...
) 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 exci ...
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 of ...
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 length
In molecular geometry, bond length or bond distance is defined as the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed types, relatively independent of the rest of ...
s of two joined atoms, bond angles of three connected atoms, and
torsion angles
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 ...
(
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 ...
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
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 corner ...
: 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 was ...
(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 theo ...
(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 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-to ...
s or CPK models (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
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 theo ...
predicts that lone pairs repel each other, thus pushing the different atoms away from them.
See also
*
Jemmis mno rules
In chemistry, the Jemmis ''mno'' rules represent a unified rule for predicting and systematizing structures of compounds, usually clusters. The rules involve electron counting. They were formulated by Eluvathingal Devassy Jemmis to explain the s ...
*
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 chemical bonding, bonding between atoms of a molecule, as well as the lone pairs ...
*
Molecular design software Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''.
In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemis ...
*
Molecular graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekul ...
*
Molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Mo ...
*
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
A molecule editor is a computer program for creating and modifying representations of chemical structures.
Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ...
*
Polyhedral skeletal electron pair theory
In chemistry the polyhedral skeletal electron pair theory (PSEPT) provides electron counting rules useful for predicting the structures of clusters such as borane and carborane clusters. The electron counting rules were originally formulated by ...
*
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) In chemistry, topology provides a way of describing and predicting the molecular structure within the constraints of three-dimensional (3-D) space. Given the determinants of chemical bonding and the chemical properties of the atoms, topology provid ...
References
External links
Molecular Geometry & Polarity Tutorial 3D visualization of molecules to determine polarity.
3D structure visualization of molecules using Crystallography.
{{DEFAULTSORT:Molecular Geometry