Molecule

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Atomic force microscopy (AFM) image of a PTCDA molecule, in which the five six-carbon rings are visible. PTCDA AFM.jpg
Atomic force microscopy (AFM) image of a PTCDA molecule, in which the five six-carbon rings are visible.
A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. Pentacene on Ni(111) STM.jpg
A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings.
AFM image of 1,5,9-trioxo-13-azatriangulene and its chemical structure. TOAT AFM.png
AFM image of 1,5,9-trioxo-13-azatriangulene and its chemical structure.

A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. [4] [5] [6] [7] [8] Molecules are distinguished from ions by their lack of electrical charge.

Contents

In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions.

In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of its composition. This violates the definition that a molecule contain two or more atoms, since the noble gases are individual atoms. [9]

A molecule may be homonuclear, that is, it consists of atoms of one chemical element, as with two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, as with water (two hydrogen atoms and one oxygen atom; H2O).

Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considered single molecules. [10]

Molecules as components of matter are common. They also make up most of the oceans and atmosphere. Most organic substances are molecules. The substances of life are molecules, e.g. proteins, the amino acids they are made of, the nucleic acids (DNA & RNA), sugars, carbohydrates, fats, and vitamins. The nutrient minerals ordinarily are not molecules, e.g. iron sulfate.

However, the majority of familiar solid substances on Earth are not made of molecules. Including all of the minerals that make up the substance of the Earth, soil, dirt, sand, clay, pebbles, rocks, boulders, bedrock, the molten interior, the core of the Earth. All of these, contain many chemical bonds, but are not made of identifiable molecules.

No typical molecule can be defined for salts nor for covalent crystals, although these are often composed of repeating unit cells that extend either in a plane, e.g. graphene; or three-dimensionally e.g. diamond, quartz, sodium chloride. The theme of repeated unit-cellular-structure also holds for most metals which are condensed phases with metallic bonding. Thus solid metals are not made of molecules.

In glasses, which are solids that exist in a vitreous disordered state, the atoms are held together by chemical bonds with no presence of any definable molecule, nor any of the regularity of repeating unit-cellular-structure that characterizes salts, covalent crystals, and metals.

Molecular science

The science of molecules is called molecular chemistry or molecular physics , depending on whether the focus is on chemistry or physics. Molecular chemistry deals with the laws governing the interaction between molecules that results in the formation and breakage of chemical bonds, while molecular physics deals with the laws governing their structure and properties. In practice, however, this distinction is vague. In molecular sciences, a molecule consists of a stable system (bound state) composed of two or more atoms. Polyatomic ions may sometimes be usefully thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i.e., short-lived assemblies (resonances) of electrons and nuclei, such as radicals, molecular ions, Rydberg molecules, transition states, van der Waals complexes, or systems of colliding atoms as in Bose–Einstein condensate.

History and etymology

According to Merriam-Webster and the Online Etymology Dictionary, the word "molecule" derives from the Latin "moles" or small unit of mass.

The definition of the molecule has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. [13] This definition often breaks down since many substances in ordinary experience, such as rocks, salts, and metals, are composed of large crystalline networks of chemically bonded atoms or ions, but are not made of discrete molecules.

Bonding

Molecules are held together by either covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment. For example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements. [14]

Covalent

A covalent bond forming H2 (right) where two hydrogen atoms share the two electrons Covalent bond hydrogen.svg
A covalent bond forming H2 (right) where two hydrogen atoms share the two electrons

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are termed shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is termed covalent bonding. [15]

Ionic

Sodium and fluorine undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. NaF.gif
Sodium and fluorine undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically.

Ionic bonding is a type of chemical bond that involves the electrostatic attraction between oppositely charged ions, and is the primary interaction occurring in ionic compounds. The ions are atoms that have lost one or more electrons (termed cations) and atoms that have gained one or more electrons (termed anions). [16] This transfer of electrons is termed electrovalence in contrast to covalence. In the simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of a more complicated nature, e.g. molecular ions like NH4+ or SO42−.

Molecular size

Most molecules are far too small to be seen with the naked eye, although molecules of many polymers can reach macroscopic sizes, including biopolymers such as DNA. Molecules commonly used as building blocks for organic synthesis have a dimension of a few angstroms (Å) to several dozen Å, or around one billionth of a meter. Single molecules cannot usually be observed by light (as noted above), but small molecules and even the outlines of individual atoms may be traced in some circumstances by use of an atomic force microscope. Some of the largest molecules are macromolecules or supermolecules.

The smallest molecule is the diatomic hydrogen (H2), with a bond length of 0.74 Å. [17]

Effective molecular radius is the size a molecule displays in solution. [18] [19] The table of permselectivity for different substances contains examples.

Molecular formulas

Chemical formula types

The chemical formula for a molecule uses one line of chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, and plus (+) and minus (−) signs. These are limited to one typographic line of symbols, which may include subscripts and superscripts.

A compound's empirical formula is a very simple type of chemical formula. [20] It is the simplest integer ratio of the chemical elements that constitute it. [21] For example, water is always composed of a 2:1 ratio of hydrogen to oxygen atoms, and ethanol (ethyl alcohol) is always composed of carbon, hydrogen, and oxygen in a 2:6:1 ratio. However, this does not determine the kind of molecule uniquely dimethyl ether has the same ratios as ethanol, for instance. Molecules with the same atoms in different arrangements are called isomers. Also carbohydrates, for example, have the same ratio (carbon:hydrogen:oxygen= 1:2:1) (and thus the same empirical formula) but different total numbers of atoms in the molecule.

The molecular formula reflects the exact number of atoms that compose the molecule and so characterizes different molecules. However different isomers can have the same atomic composition while being different molecules.

The empirical formula is often the same as the molecular formula but not always. For example, the molecule acetylene has molecular formula C2H2, but the simplest integer ratio of elements is CH.

The molecular mass can be calculated from the chemical formula and is expressed in conventional atomic mass units equal to 1/12 of the mass of a neutral carbon-12 (12 C isotope) atom. For network solids, the term formula unit is used in stoichiometric calculations.

Structural formula

3D (left and center) and 2D (right) representations of the terpenoid molecule atisane Atisane3.png
3D (left and center) and 2D (right) representations of the terpenoid molecule atisane

For molecules with a complicated 3-dimensional structure, especially involving atoms bonded to four different substituents, a simple molecular formula or even semi-structural chemical formula may not be enough to completely specify the molecule. In this case, a graphical type of formula called a structural formula may be needed. Structural formulas may in turn be represented with a one-dimensional chemical name, but such chemical nomenclature requires many words and terms which are not part of chemical formulas.

Molecular geometry

Structure and STM image of a "cyanostar" dendrimer molecule. Cyanostar STM.png
Structure and STM image of a "cyanostar" dendrimer molecule.

Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the same average geometrical structure. The chemical formula and the structure of a molecule are the two important factors that determine its properties, particularly its reactivity. Isomers share a chemical formula but normally have very different properties because of their different structures. Stereoisomers, a particular type of isomer, may have very similar physico-chemical properties and at the same time different biochemical activities.

Molecular spectroscopy

Hydrogen can be removed from individual H2TPP molecules by applying excess voltage to the tip of a scanning tunneling microscope (STM, a); this removal alters the current-voltage (I-V) curves of TPP molecules, measured using the same STM tip, from diode like (red curve in b) to resistor like (green curve). Image (c) shows a row of TPP, H2TPP and TPP molecules. While scanning image (d), excess voltage was applied to H2TPP at the black dot, which instantly removed hydrogen, as shown in the bottom part of (d) and in the rescan image (e). Such manipulations can be used in single-molecule electronics. Dehydrogenation of H2TPP by STM.jpg
Hydrogen can be removed from individual H2TPP molecules by applying excess voltage to the tip of a scanning tunneling microscope (STM, a); this removal alters the current-voltage (I-V) curves of TPP molecules, measured using the same STM tip, from diode like (red curve in b) to resistor like (green curve). Image (c) shows a row of TPP, H2TPP and TPP molecules. While scanning image (d), excess voltage was applied to H2TPP at the black dot, which instantly removed hydrogen, as shown in the bottom part of (d) and in the rescan image (e). Such manipulations can be used in single-molecule electronics.

Molecular spectroscopy deals with the response (spectrum) of molecules interacting with probing signals of known energy (or frequency, according to Planck's formula). Molecules have quantized energy levels that can be analyzed by detecting the molecule's energy exchange through absorbance or emission. [24] Spectroscopy does not generally refer to diffraction studies where particles such as neutrons, electrons, or high energy X-rays interact with a regular arrangement of molecules (as in a crystal).

Microwave spectroscopy commonly measures changes in the rotation of molecules, and can be used to identify molecules in outer space. Infrared spectroscopy measures the vibration of molecules, including stretching, bending or twisting motions. It is commonly used to identify the kinds of bonds or functional groups in molecules. Changes in the arrangements of electrons yield absorption or emission lines in ultraviolet, visible or near infrared light, and result in colour. Nuclear resonance spectroscopy measures the environment of particular nuclei in the molecule, and can be used to characterise the numbers of atoms in different positions in a molecule.

Theoretical aspects

The study of molecules by molecular physics and theoretical chemistry is largely based on quantum mechanics and is essential for the understanding of the chemical bond. The simplest of molecules is the hydrogen molecule-ion, H2+, and the simplest of all the chemical bonds is the one-electron bond. H2+ is composed of two positively charged protons and one negatively charged electron, which means that the Schrödinger equation for the system can be solved more easily due to the lack of electron–electron repulsion. With the development of fast digital computers, approximate solutions for more complicated molecules became possible and are one of the main aspects of computational chemistry.

When trying to define rigorously whether an arrangement of atoms is sufficiently stable to be considered a molecule, IUPAC suggests that it "must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state". [4] This definition does not depend on the nature of the interaction between the atoms, but only on the strength of the interaction. In fact, it includes weakly bound species that would not traditionally be considered molecules, such as the helium dimer, He2, which has one vibrational bound state [25] and is so loosely bound that it is only likely to be observed at very low temperatures.

Whether or not an arrangement of atoms is sufficiently stable to be considered a molecule is inherently an operational definition. Philosophically, therefore, a molecule is not a fundamental entity (in contrast, for instance, to an elementary particle); rather, the concept of a molecule is the chemist's way of making a useful statement about the strengths of atomic-scale interactions in the world that we observe.

See also

Related Research Articles

Chemistry scientific discipline

Chemistry is the scientific discipline involved with elements and compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo during a reaction with other substances.

Chemical bond Lasting attraction between atoms that enables the formation of chemical compounds

A chemical bond is a lasting attraction between atoms, ions or molecules that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between oppositely charged ions as in ionic bonds or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force and hydrogen bonding.

Covalent bond Chemical bond that involves the sharing of electron pairs between atoms

A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonds are much more common than ionic bonds.

A chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, commas and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulae can fully specify the structure of only the simplest of molecules and chemical substances, and are generally more limited in power than are chemical names and structural formulae.

Coordination complex molecule or ion containing ligands covalently bonded to a central atom

A coordination complex consists of a central atom or ion, which is usually metallic and is called the coordination centre, and a surrounding array of bound molecules or ions, that are in turn known as ligands or complexing agents. Many metal-containing compounds, especially those of transition metals, are coordination complexes. A coordination complex whose centre is a metal atom is called a metal complex of d block element.

Electronegativity, symbol χ, measures the tendency of an atom to attract a shared pair of electrons. An atom's electronegativity is affected by both its atomic number and the distance at which its valence electrons reside from the charged nucleus. The higher the associated electronegativity, the more an atom or a substituent group attracts electrons.

Hydrogen bond Partial intermolecular bonding interaction

A hydrogen bond is a partial intermolecular bonding interaction between a lone pair on an electron rich donor atom, particularly the second-row elements nitrogen (N), oxygen (O), or fluorine (F), and the antibonding molecular orbital of a bond between hydrogen (H) and a more electronegative atom or group. Such an interacting system is generally denoted Dn–H···Ac, where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The use of three centered dots for the hydrogen bond is specifically recommended by the IUPAC. While hydrogen bonding has both covalent and electrostatic contributions, and the degrees to which they contribute are currently debated, the present evidence strongly implies that the primary contribution is covalent.

Ionic bonding Chemical bonding involving attraction between ions

Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, and is the primary interaction occurring in ionic compounds. It is one of the main types of bonding along with covalent bonding and metallic bonding. Ions are atoms with an electrostatic charge. Atoms that gain electrons make negatively charged ions. Atoms that lose electrons make positively charged ions. This transfer of electrons is known as electrovalence in contrast to covalence. In the simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of a more complex nature, e.g. molecular ions like NH+
4
or SO2−
4
. In simpler words, an ionic bond results from the transfer of electrons from a metal to a non-metal in order to obtain a full valence shell for both atoms.

Atomic radius size Is directly proportional to radius.

The atomic radius of a chemical element is a measure of the size of its atoms, usually the mean or typical distance from the center of the nucleus to the boundary of the surrounding shells of electrons. Since the boundary is not a well-defined physical entity, there are various non-equivalent definitions of atomic radius. Three widely used definitions of atomic radius are: Van der Waals radius, ionic radius, and covalent radius.

Lewis structures, also known as Lewis dot diagrams, Lewis dot formulas,Lewis dot structures, electron dot structures, or Lewis electron dot structures (LEDS), are diagrams that show the bonding between atoms of a molecule and the lone pairs of electrons that may exist in the molecule. A Lewis structure can be drawn for any covalently bonded molecule, as well as coordination compounds. The Lewis structure was named after Gilbert N. Lewis, who introduced it in his 1916 article The Atom and the Molecule. Lewis structures extend the concept of the electron dot diagram by adding lines between atoms to represent shared pairs in a chemical bond.

In chemistry, valence bond (VB) theory is one of the two basic theories, along with molecular orbital (MO) theory, that were developed to use the methods of quantum mechanics to explain chemical bonding. It focuses on how the atomic orbitals of the dissociated atoms combine to give individual chemical bonds when a molecule is formed. In contrast, molecular orbital theory has orbitals that cover the whole molecule.

Molecular geometry Study of the 3D shapes of molecules

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 determine the position of each atom.

In chemistry, the valence or valency of an element is a measure of its combining power with other atoms when it forms chemical compounds or molecules.

A non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol (1000–5000 calories per 6.02 × 1023 molecules). Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.

The quantum theory of atoms in molecules (QTAIM) is a model of molecular and condensed matter electronic systems in which the principal objects of molecular structure - atoms and bonds - are natural expressions of a system's observable electron density distribution function. An electron density distribution of a molecule is a probability distribution that describes the average manner in which the electronic charge is distributed throughout real space in the attractive field exerted by the nuclei. According to QTAIM, molecular structure is revealed by the stationary points of the electron density together with the gradient paths of the electron density that originate and terminate at these points. QTAIM was primarily developed by Professor Richard Bader and his research group at McMaster University over the course of decades, beginning with analyses of theoretically calculated electron densities of simple molecules in the early 1960s and culminating with analyses of both theoretically and experimentally measured electron densities of crystals in the 90s. The development of QTAIM was driven by the assumption that, since the concepts of atoms and bonds have been and continue to be so ubiquitously useful in interpreting, classifying, predicting and communicating chemistry, they should have a well-defined physical basis.

History of molecular theory

In chemistry, the history of molecular theory traces the origins of the concept or idea of the existence of strong chemical bonds between two or more atoms.

This glossary of chemistry terms is a list of terms and definitions relevant to chemistry, including chemical laws, diagrams and formulae, laboratory tools, glassware, and equipment. Chemistry is a physical science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions; it features an extensive vocabulary and a significant amount of jargon.

Mass spectral interpretation

Mass spectral interpretation is the method employed to identify the chemical formula, characteristic fragment patterns and possible fragment ions from the mass spectra. Mass spectra is a plot of relative abundance against mass-to-charge ratio. It is commonly used for the identification of organic compounds from electron ionization mass spectrometry. Organic chemists obtain mass spectra of chemical compounds as part of structure elucidation and the analysis is part of many organic chemistry curricula.

Chemical compound Substance composed of multiple elements

A chemical compound is a chemical substance composed of many identical molecules composed of atoms from more than one element held together by chemical bonds. A molecule consisting of atoms of only one element is therefore not a compound.

Argon compounds, the chemical compounds that contain the element argon, are rarely encountered due to the inertness of the argon atom. However, compounds of argon have been detected in inert gas matrix isolation, cold gases, and plasmas, and molecular ions containing argon have been made and also detected in space. One solid interstitial compound of argon, Ar1C60 is stable at room temperature. Ar1C60 was discovered by the CSIRO.

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