Editing Chemical structure

{{Short description|Organized way in which molecules are ordered and sorted}}
{{Use mdy dates|date=February 2021}}
[[File:Phosphorus-pentoxide-2D-dimensions.svg|class=skin-invert-image|thumb|300px|[[Phosphorus pentoxide]] chemical structure in 2D]]
A '''chemical structure''' of a [[molecule]] is a spatial arrangement of its [[atom]]s and their chemical bonds. Its 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 [[atom]]s in a [[molecule]] and the [[chemical bond]]s that hold the atoms together and can be represented using [[structural formula]]e and by [[molecular model]]s;<ref>{{cite book |last=Haaland |first=Arne |title=Molecules and Models: The Molecular Structures of Main Group Element Compounds |date=2008 |publisher=Oxford University Press |isbn=978-0-19-923535-3 |location=Oxford |oclc=173809048 |url=https://search.worldcat.org/title/173809048}}</ref> complete electronic structure descriptions include specifying the occupation of a molecule's [[molecular orbital]]s.<ref>{{cite book |last1=Weinhold |first1=Frank |title=Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective |date=2005 |publisher=Cambridge University Press |last2=Landis |first2=Clark R. |isbn=0-521-83128-8 |location=Cambridge, UK |oclc=59712377 |url=https://search.worldcat.org/title/59712377}}</ref><ref>{{cite book |last1=Gillespie |first1=Ronald J. |title=Chemical Bonding and Molecular Geometry: From Lewis to Electron Densities |date=2001 |publisher=Oxford University Press |last2=Popelier |first2=Paul L. A. |isbn=0-19-510495-1 |location=New York |oclc=43552798 |url=https://search.worldcat.org/title/43552798}}</ref> 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]] or [[DNA]]).

==Background==
Theories of chemical structure were first developed by [[August Kekulé]], [[Archibald Scott Couper]], and [[Aleksandr Butlerov]], among others, from about 1858.<ref>36th congress of the German physicians and scientists 1861</ref> 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 (chemistry)|valency]] of the [[atom]]s 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 (chemistry)|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 compound]]s, 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).<ref>{{cite book |last=Wells |first=A. F. |author-link=Alexander F. Wells |title=Structural inorganic chemistry |edition=Fifth |date=July 12, 2012 |isbn=978-0-19-965763-6 |publisher=Clarendon Press |location=Oxford |oclc=801026482 |url=https://search.worldcat.org/title/801026482}}</ref>

===Structural elucidation===
The methods by which one can determine the structure of a molecule is called ''structural elucidation''. These methods include:

* concerning only connectivity of the atoms: [[spectroscopy|spectroscopies]] such as [[nuclear magnetic resonance]] ([[proton NMR|proton]] and [[carbon-13 NMR]]), and various methods of [[mass spectrometry]] (to give overall molecular mass, as well as fragment masses). Techniques such as [[absorption spectroscopy]] and the [[vibrational spectroscopy|vibrational spectroscopies]], [[infrared spectroscopy|infrared]], and [[Raman spectroscopy|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]] and [[X-ray photoelectron spectroscopy]].
* concerning precise metric three-dimensional information: can be obtained for gases by [[gas electron diffraction]] and [[rotational spectroscopy|microwave (rotational) spectroscopy]] (and other rotationally resolved spectroscopy) and for the crystalline solid state by [[X-ray crystallography]]<ref name=":0">{{cite book |last=Rankin, David W. H. |title=Structural methods in molecular inorganic chemistry |others=Morrison, Carole A., 1972-, Mitzel, Norbert W., 1966- |date=January 2, 2013 |publisher=Wiley |location=Chichester, West Sussex, United Kingdom |isbn=978-1-118-46288-1 |oclc=810442747 |url=https://search.worldcat.org/title/810442747}}</ref> or [[neutron diffraction]]. These technique can produce three-dimensional models at atomic-scale [[optical resolution|resolution]], typically to a precision of 0.001 Å for distances and 0.1° for angles (in unusual cases even better).<ref>{{cite book |last=Glusker, Jenny Pickworth |title=Crystal structure analysis for chemists and biologists |date=1994 |publisher=VCH |others=Lewis, Mitchell; Rossi, Miriam |isbn=0-89573-273-4 |location=New York |oclc=25412161 |url=https://search.worldcat.org/title/25412161}}</ref><ref name=":0"/>

Additional sources of information are: When a molecule has an unpaired electron spin in a [[functional group]] of its structure, [[ENDOR]] 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.

==TeX for chemical structures==
{{See also|Comparison of TeX editors}}
[[Chemfig]] and [[tikz]] are package add-ons for [[LaTeX]] for chemical structures.<ref>{{cite web | url=https://emleddin.github.io/comp-chem-website/Otherguide-chemistry-latex.html | title=Helpful LaTeX Packages for Chemistry &#124; Computational Chemistry Resources }}</ref>

==See also==
* [[ChemDraw]] - software for chemical structure diagrams
* [[Chemical graph generator]]
* [[Crystallographic database]]
* [[Pauli exclusion principle]]
* [[Structural chemistry]]
* [[Structural formula]]

==References==
{{Reflist}}

==Further reading==
*{{cite book |last=Gallagher |first=Warren |chapter=Lecture 7: Structure Determination by X-ray Crystallography |title=Chem 406: Biophysical Chemistry |publisher=University of Wisconsin-Eau Claire, Department of Chemistry |year=2006 |location=Eau Claire, WI, USA |type=self-published course notes |url=http://www.chem.uwec.edu/Chem406_F06/Pages/lecture_notes/lect07/C406-lect07-notes.pdf |access-date=2014-07-02}}
*{{cite journal |last1=Ward |first1=S. C. |title=The Cambridge Structural Database |last2=Lightfoot |first2=M. P. |last3=Bruno |first3=I. J. |last4=Groom |first4=C. R. |date=2016-04-01 |journal=Acta Crystallographica Section B |volume=72 |pages=171–179 |language=en |issn=2052-5206 |issue=2 |pmid=27048719 |doi=10.1107/S2052520616003954 |doi-access=free |pmc=4822653 |bibcode=2016AcCrB..72..171G }}

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[[Category:Chemical structures| ]]