A chemical structure determination includes a

chemist A chemist (from Greek ''chēm(ía)'' alchemy; replacing ''chymist'' from Medieval Latin ''alchemist'') is a scientist trained in the study of chemistry. Chemists study the composition of matter and its properties. Chemists carefully describe t ...

's specifying the

molecular geometry Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that dete ...

and, when feasible and necessary, the

electronic structure In quantum chemistry, electronic structure is the state of motion of electrons in an electrostatic field created by stationary nuclei. The term encompasses both the wave functions of the electrons and the energies associated with them. Electr ...

of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of

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, ...

s in 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 bioche ...

and 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 that hold the atoms together, and can be represented using structural formulae and by

molecular model A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecu ...

s; complete electronic structure descriptions include specifying the occupation of a molecule's

molecular orbital In chemistry, a molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of findin ...

s. Structure determination can be applied to a range of targets from very simple molecules (e.g., diatomic

oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as ...

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...

), 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 Friedrich August Kekulé, later Friedrich August Kekule von Stradonitz ( , ; 7 September 1829 – 13 July 1896), was a German organic chemist. From the 1850s until his death, Kekulé was one of the most prominent chemists in Europe, especially ...

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 Alexander Mikhaylovich Butlerov (Алекса́ндр Миха́йлович Бу́тлеров; 15 September 1828 – 17 August 1886) was a Russian chemist, one of the principal creators of the theory of chemical structure (1857–186 ...

, 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

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 The molecular configuration of a molecule is the ''permanent'' geometry that results from the spatial arrangement of its bonds. The ability of the same set of atoms to form two or more molecules with different configurations is stereoisomerism. ...

, 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 compound A chemical compound is a chemical substance composed of many identical molecules (or molecular entities) containing atoms from more than one chemical element held together by chemical bonds. A molecule consisting of atoms of only one element ...

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). 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 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 ...

( proton and carbon-13 NMR), various methods of mass spectrometry (to give overall molecular mass, as well as fragment masses).Techniques such as

absorption spectroscopy Absorption spectroscopy refers to spectroscopic techniques that measure the absorption of radiation, as a function of frequency or wavelength, due to its interaction with a sample. The sample absorbs energy, i.e., photons, from the radiating fi ...

and the vibrational spectroscopies,

infrared Infrared (IR), sometimes called infrared light, is electromagnetic radiation (EMR) with wavelengths longer than those of visible light. It is therefore invisible to the human eye. IR is generally understood to encompass wavelengths from around ...

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 X-ray photoelectron spectroscopy (XPS) is a surface-sensitive quantitative spectroscopic technique based on the photoelectric effect that can identify the elements that exist within a material (elemental composition) or are covering its surface, ...

. * 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 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 ...

or neutron diffraction. These technique can produce three-dimensional models at atomic-scale

resolution Resolution(s) may refer to: Common meanings * Resolution (debate), the statement which is debated in policy debate * Resolution (law), a written motion adopted by a deliberative body * New Year's resolution, a commitment that an individual mak ...

, 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 In organic chemistry, a functional group is a substituent or moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions regardless of the re ...

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 Electron paramagnetic resonance (EPR) or electron spin resonance (ESR) spectroscopy is a method for studying materials that have unpaired electrons. The basic concepts of EPR are analogous to those of nuclear magnetic resonance (NMR), but the spin ...

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.

Background

See also

References

Further reading