A chemical structure determination includes a
chemist's specifying the
molecular geometry and, when feasible and necessary, the
electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of
atoms in a
molecule and the
chemical bonds that hold the atoms together, and can be represented using
structural formulae and by
molecular models; complete electronic structure descriptions include specifying the occupation of a molecule's
molecular orbitals. Structure determination can be applied to a range of targets from very simple molecules (e.g.,
diatomic oxygen or
nitrogen), to very complex ones (e.g., such as
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
or
DNA).
Background
Theories of chemical structure were first developed by
August Kekulé,
Archibald Scott Couper
Archibald Scott Couper (; 31 March 1831 – 11 March 1892) was a Scottish chemist who proposed an early theory of chemical structure and bonding. He developed the concepts of tetravalent carbon atoms linking together to form large molecules ...
, and
Aleksandr Butlerov, among others, from about 1858. These theories were first to state that chemical compounds are not a random cluster of atoms and functional groups, but rather had a definite order defined by the
valency of the
atoms composing the molecule, giving the molecules a three dimensional structure that could be determined or solved.
Concerning chemical structure one has to distinguish between pure connectivity of the atoms within a molecule (chemical constitution), a description of a three-dimensional arrangement (
molecular configuration, includes e.g. information on
chirality) and the precise determination of bond lengths, angles and torsion angles, i.e. a full representation of the (relative) atomic coordinates.
In determining structures of
chemical compounds, one generally aims to obtain, first and minimally, the pattern and degree of bonding between all atoms in the molecule; when possible, one seeks the three dimensional spatial coordinates of the atoms in the molecule (or other solid).
The methods by which one can elucidate the structure of a molecule include:
* concerning only connectivity of the atoms:
spectroscopies such as
nuclear magnetic resonance (
proton and
carbon-13 NMR Carbon-13 (C13) nuclear magnetic resonance (most commonly known as carbon-13 NMR spectroscopy or 13C NMR spectroscopy or sometimes simply referred to as carbon NMR) is the application of nuclear magnetic resonance (NMR) spectroscopy to carbon. It ...
), various methods of
mass spectrometry (to give overall molecular mass, as well as fragment masses).Techniques such as
absorption spectroscopy and the
vibrational spectroscopies,
infrared and
Raman, provide, respectively, important supporting information about the numbers and adjacencies of multiple bonds, and about the types of functional groups (whose internal bonding gives vibrational signatures); further inferential studies that give insight into the contributing electronic structure of molecules include
cyclic voltammetry
Cyclic voltammetry (CV) is a type of potentiodynamic electrochemical measurement. In a cyclic voltammetry experiment, the working electrode potential is ramped linearly versus time. Unlike in linear sweep voltammetry, after the set potential is r ...
and
X-ray photoelectron spectroscopy.
* concerning precise metric three-dimensional information: can be obtained for gases by
gas electron diffraction and
microwave (rotational) spectroscopy (and other rotationally resolved spectroscopy) and for the crystalline solid state by
X-ray crystallography or neutron diffraction. These technique can produce three-dimensional models at atomic-scale
resolution, typically to a precision of 0.001 Å for distances and 0.1° for angles (in unusual cases even better).
Additional sources of information are: When a molecule has an unpaired electron spin in a
functional group of its structure,
ENDOR Endor or Ein Dor may refer to:
Places
* Endor (village), from the Hebrew Bible, a Canaanite village where the Witch of Endor lived
* Indur, a Palestinian village depopulated during the 1948 Arab-Israeli war
* Ein Dor, a Kibbutz in modern Israel
F ...
and
electron-spin resonance spectroscopes may also be performed. These latter techniques become all the more important when the molecules contain metal atoms, and when the crystals required by crystallography or the specific atom types that are required by NMR are unavailable to exploit in the structure determination. Finally, more specialized methods such as
electron microscopy are also applicable in some cases.
See also
*
Structural chemistry
Structural chemistry is a part of chemistry and deals with spatial structures of molecules (in the gaseous, liquid or solid state) and solids (with extended structures that cannot be subdivided into molecules).
The main tasks are:
* The formulat ...
*
Chemical structure diagram
*
Crystallographic database
MOGADOCA data base for experimental structures determined in the gas phase
*
Pauli exclusion principle
In quantum mechanics, the Pauli exclusion principle states that two or more identical particles with half-integer spins (i.e. fermions) cannot occupy the same quantum state within a quantum system simultaneously. This principle was formula ...
*
Chemical graph generator
A chemical graph generator is a software package to generate computer representations of chemical structures adhering to certain boundary conditions. The development of such software packages is a research topic of cheminformatics. Chemical graph g ...
References
Further reading
*
* {{Cite book , last1=Ward , first1=S. C. , url=https://journals.iucr.org/b/issues/2016/02/00/bm5086/index.html#BB59 , title=The Cambridge Structural Database , last2=Lightfoot , first2=M. P. , last3=Bruno , first3=I. J. , last4=Groom , first4=C. R. , date=2016-04-01 , work=Acta Crystallographica Section B , volume=72 , pages=171–179 , language=en , doi=10.1107/S2052520616003954 , issn=2052-5206 , pmc=4822653 , pmid=27048719 , doi-access=free , issue=2
Analytical chemistry