A
chemical structure includes
molecular geometryMolecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule. It determines several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism, and biological activity.- Molecular geometry determination...
, electronic structure and
crystal structureIn mineralogy and crystallography, crystal structure is a unique arrangement of atoms or molecules in a crystalline liquid or solid. A crystal structure is composed of a pattern, a set of atoms arranged in a particular way, and a lattice exhibiting long-range order and symmetry...
of
moleculeA molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s. Molecular geometry refers to the spatial arrangement of
atomThe atom is a basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons...
s in a
moleculeA molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
and the
chemical bondA chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...
s that hold the atoms together. Molecular geometry can range from the very simple, such as
diatomicDiatomic molecules are molecules composed only of two atoms, of either the same or different chemical elements. The prefix di- means two in Greek. Common diatomic molecules are hydrogen , nitrogen , oxygen , and carbon monoxide . Seven elements exist in the diatomic state in the liquid and solid...
oxygenOxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
or
nitrogenNitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
molecules, to the very complex, such as
proteinProteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
or
DNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
molecules. Molecular geometry can be roughly represented using a
structural formulaThe structural formula of a chemical compound is a graphical representation of the molecular structure, showing how the atoms are arranged. The chemical bonding within the molecule is also shown, either explicitly or implicitly...
. Electronic structure describes the occupation of a molecule's
molecular orbitalIn chemistry, a molecular orbital is a mathematical function describing the 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 finding an electron in any specific region. The term "orbital" was first...
s.
The theory of chemical structure was first developed by
Aleksandr ButlerovAleksandr Mikhailovich Butlerov was a Russian chemist, one of the principal creators of the theory of chemical structure , the first to incorporate double bonds into structural formulas, the discoverer of hexamine , and the discoverer of the formose reaction.The...
, which stated that the chemical compounds are not a random cluster of atoms and functional groups but structures with definite order formed according the valency of the composing atoms.
Structure determination
Structural determination in
chemistryChemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
is the process of determining the chemical structure of molecules. Practically, the end result of such process is the obtainment of the coordinates of the atoms in a molecule. The methods by which one can determine the structure of a molecule include
spectroscopySpectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...
, such as
nuclear magnetic resonanceNuclear magnetic resonance is a physical phenomenon in which magnetic nuclei in a magnetic field absorb and re-emit electromagnetic radiation...
(NMR),
infrared spectroscopyInfrared spectroscopy is the spectroscopy that deals with the infrared region of the electromagnetic spectrum, that is light with a longer wavelength and lower frequency than visible light. It covers a range of techniques, mostly based on absorption spectroscopy. As with all spectroscopic...
and
Raman spectroscopyRaman spectroscopy is a spectroscopic technique used to study vibrational, rotational, and other low-frequency modes in a system.It relies on inelastic scattering, or Raman scattering, of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range...
, electron microscopy, and
x-ray crystallographyX-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
(x-ray diffraction). The last technique can produce three-dimensional models at atomic-scale
resolutionOptical resolution describes the ability of an imaging system to resolve detail in the object that is being imaged.An imaging system may have many individual components including a lens and recording and display components...
, as long as
crystalA crystal or crystalline solid is a solid material whose constituent atoms, molecules, or ions are arranged in an orderly repeating pattern extending in all three spatial dimensions. The scientific study of crystals and crystal formation is known as crystallography...
s are available, as x-ray diffraction needs numerous copies of the molecule being studied that must also be arranged in an organised way.
The following are common methods for determining the chemical structure (
Structural elucidationStructural elucidation is the determination of the chemical structure of chemically uncharacterised substances such as natural products. It is preceded by the extraction and isolation steps. It makes use of various chromatography techniques as well as spectrometric techniques...
) :
- X-ray diffraction
- Proton NMR
Proton NMR is the application of nuclear magnetic resonance in NMR spectroscopy with respect to hydrogen-1 nuclei within the molecules of a substance, in order to determine the structure of its molecules. In samples where natural hydrogen is used, practically all of the hydrogen consists of the...
- Carbon-13 NMR
Carbon-13 NMR is the application of nuclear magnetic resonance spectroscopy to carbon. It is analogous to proton NMR and allows the identification of carbon atoms in an organic molecule just as proton NMR identifies hydrogen atoms...
- Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
- Infrared spectroscopy
Infrared spectroscopy is the spectroscopy that deals with the infrared region of the electromagnetic spectrum, that is light with a longer wavelength and lower frequency than visible light. It covers a range of techniques, mostly based on absorption spectroscopy. As with all spectroscopic...
The following are common methods for determining the electronic structure:
- Electron-spin resonance
- Cyclic voltammetry
Cyclic voltammetry or CV is a type of potentiodynamic electrochemical measurement. In a cyclic voltammetry experiment the working electrode potential is ramped linearly versus time like linear sweep voltammetry. Cyclic voltammetry takes the experiment a step further than linear sweep voltammetry...
- Electron absorption spectroscopy
- X-ray photoelectron spectroscopy
X-ray photoelectron spectroscopy is a quantitative spectroscopic technique that measures the elemental composition, empirical formula, chemical state and electronic state of the elements that exist within a material...
See also
- Pauli exclusion principle
The Pauli exclusion principle is the quantum mechanical principle that no two identical fermions may occupy the same quantum state simultaneously. A more rigorous statement is that the total wave function for two identical fermions is anti-symmetric with respect to exchange of the particles...
- Lipinski's Rule of Five
Lipinski's Rule of Five is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has properties that would make it a likely orally active drug in humans. The rule was formulated by Christopher A...
, describing molecular properties of drugs
- QSAR, quantitative structure-affinity relationship
- Chemical property
A chemical property is any of a material's properties that becomes evident during a chemical reaction; that is, any quality that can be established only by changing a substance's chemical identity...
- Molecular property
Molecular properties include the chemical properties, physical properties, and structural properties of molecules, including drugs. Molecular properties typically do not include pharmacological or biological properties of a chemical compound.- See also :...
- Physical property
A physical property is any property that is measurable whose value describes a physical system's state. The changes in the physical properties of a system can be used to describe its transformations ....
- Crystallographic database
A crystallographic database is a database specifically designed to store information about crystals and crystal structures. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology,...