Chemical structure

Chemical structure

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A chemical structure includes molecular geometry
Molecular geometry
Molecular 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 structure
Crystal structure
In 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 molecule
Molecule
A 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 atom
Atom
The 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 molecule
Molecule
A 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 bond
Chemical bond
A 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 diatomic
Diatomic
Diatomic 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...

 oxygen
Oxygen
Oxygen 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 nitrogen
Nitrogen
Nitrogen 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 protein
Protein
Proteins 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 DNA
DNA
Deoxyribonucleic 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 formula
Structural formula
The 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 orbital
Molecular orbital
In 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 Butlerov
Aleksandr Butlerov
Aleksandr 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 chemistry
Chemistry
Chemistry 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 spectroscopy
Spectroscopy
Spectroscopy 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 resonance
Nuclear magnetic resonance
Nuclear magnetic resonance is a physical phenomenon in which magnetic nuclei in a magnetic field absorb and re-emit electromagnetic radiation...

 (NMR), infrared spectroscopy
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...

 and Raman spectroscopy
Raman spectroscopy
Raman 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 crystallography
X-ray crystallography
X-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 resolution
Optical resolution
Optical 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 crystal
Crystal
A 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 elucidation
Structural elucidation
Structural 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
    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
    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
    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
    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
    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
    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
    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
    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
    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 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
    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
    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,...