Molecule

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. However, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions.

In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are monatomic molecules.[9]

A molecule may be homonuclear, that is, it consists of atoms of one chemical element, as with oxygen (O2); or it may be heteronuclear, a chemical compound composed of more than one element, as with water (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 in organic substances (and therefore biochemistry). They also make up most of the oceans and atmosphere. However, the majority of familiar solid substances on Earth, including most of the minerals that make up the crust, mantle, and core of the Earth, contain many chemical bonds, but are not made of identifiable molecules. Also, no typical molecule can be defined for ionic crystals (salts) and covalent crystals (network solids), although these are often composed of repeating unit cells that extend either in a plane (such as in graphene) or three-dimensionally (such as in diamond, quartz, or sodium chloride). The theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses (solids that exist in a vitreous disordered state), atoms may also be held together by chemical bonds with no presence of any definable molecule, nor any of the regularity of repeating units that characterizes crystals.

PTCDA AFM
Atomic force microscopy (AFM) image of a PTCDA molecule, in which the five six-carbon rings are visible.[1]
Pentacene on Ni(111) STM
A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings.[2]
TOAT AFM
AFM image of 1,5,9-trioxo-13-azatriangulene and its chemical structure.[3]

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.

  • Molecule (1794) – "extremely minute particle", from French molécule (1678), from New Latin molecula, diminutive of Latin moles "mass, barrier". A vague meaning at first; the vogue for the word (used until the late 18th century only in Latin form) can be traced to the philosophy of Descartes.[11][12]

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

Covalent bond hydrogen
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

NaF
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−. Basically, an ionic bond is the transfer of electrons from a metal to a non-metal for both atoms to obtain a full valence shell.

Molecular size

Most molecules are far too small to be seen with the naked eye, but there are exceptions. DNA, a macromolecule, can reach macroscopic sizes, as can molecules of many polymers. 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 ethyl alcohol or ethanol 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 (12C isotope) atom. For network solids, the term formula unit is used in stoichiometric calculations.

Structural formula

Atisane3
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

Cyanostar STM
Structure and STM image of a "cyanostar" dendrimer molecule.[22]

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

Dehydrogenation of H2TPP by STM
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.[23]

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

References

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  3. ^ Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; Van Der Heijden, Nadine J.; Ondráček, Martin; Van Der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel (2016). "Mapping the electrostatic force field of single molecules from high-resolution scanning probe images". Nature Communications. 7: 11560. Bibcode:2016NatCo...711560H. doi:10.1038/ncomms11560. PMC 4894979. PMID 27230940.
  4. ^ a b IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version:  (2006–) "Molecule". doi:10.1351/goldbook.M04002
  5. ^ Ebbin, Darrell D. (1990). General Chemistry (3rd ed.). Boston: Houghton Mifflin Co. ISBN 978-0-395-43302-7.
  6. ^ Brown, T.L.; Kenneth C. Kemp; Theodore L. Brown; Harold Eugene LeMay; Bruce Edward Bursten (2003). Chemistry – the Central Science (9th ed.). New Jersey: Prentice Hall. ISBN 978-0-13-066997-1.
  7. ^ Chang, Raymond (1998). Chemistry (6th ed.). New York: McGraw Hill. ISBN 978-0-07-115221-1.
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  10. ^ "Molecule". Encyclopædia Britannica. 22 January 2016. Retrieved 23 February 2016.
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  12. ^ "molecule". Merriam-Webster. Retrieved 22 February 2016.
  13. ^ Molecule Definition (Frostburg State University)
  14. ^ The Hutchinson unabridged encyclopedia with atlas and weather guide. Oxford, England. OCLC 696918830.
  15. ^ Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life. Boston: Pearson Prentice Hall. ISBN 978-0-13-250882-7. Retrieved 5 February 2012.
  16. ^ Campbell, Flake C. (2008). Elements of Metallurgy and Engineering Alloys. ASM International. ISBN 978-1-61503-058-3.
  17. ^ Roger L. DeKock; Harry B. Gray; Harry B. Gray (1989). Chemical structure and bonding. University Science Books. p. 199. ISBN 978-0-935702-61-3.
  18. ^ Chang RL; Deen WM; Robertson CR; Brenner BM (1975). "Permselectivity of the glomerular capillary wall: III. Restricted transport of polyanions". Kidney Int. 8 (4): 212–218. doi:10.1038/ki.1975.104. PMID 1202253.
  19. ^ Chang RL; Ueki IF; Troy JL; Deen WM; Robertson CR; Brenner BM (1975). "Permselectivity of the glomerular capillary wall to macromolecules. II. Experimental studies in rats using neutral dextran". Biophys. J. 15 (9): 887–906. Bibcode:1975BpJ....15..887C. doi:10.1016/S0006-3495(75)85863-2. PMC 1334749. PMID 1182263.
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  22. ^ Hirsch, Brandon E.; Lee, Semin; Qiao, Bo; Chen, Chun-Hsing; McDonald, Kevin P.; Tait, Steven L.; Flood, Amar H. (2014). "Anion-induced dimerization of 5-fold symmetric cyanostars in 3D crystalline solids and 2D self-assembled crystals". Chemical Communications. 50 (69): 9827–30. doi:10.1039/C4CC03725A. PMID 25080328.
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External links

Aromaticity

In organic chemistry, the term aromaticity is used to describe a cyclic (ring-shaped), planar (flat) molecule with a ring of resonance bonds that exhibits more stability than other geometric or connective arrangements with the same set of atoms. Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, but only aromatic rings have special stability (low reactivity).

Since the most common aromatic compounds are derivatives of benzene (an aromatic hydrocarbon common in petroleum and its distillates), the word aromatic occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many non-benzene aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the double-ringed bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group.

The earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of benzene compounds, many of which have odors (aromas), unlike pure saturated hydrocarbons. Aromaticity as a chemical property bears no general relationship with the olfactory properties of such compounds (how they smell), although in 1855, before the structure of benzene or organic compounds was understood, chemists like Hofmann were beginning to understand that odiferous molecules from plants, such as terpenes, had chemical properties that we recognize today are similar to unsaturated petroleum hydrocarbons like benzene.

In terms of the electronic nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the molecule's pi system to be delocalized around the ring, increasing the molecule's stability. The molecule cannot be represented by one structure, but rather a resonance hybrid of different structures, such as with the two resonance structures of benzene. These molecules cannot be found in either one of these representations, with the longer single bonds in one location and the shorter double bond in another (see Theory below). Rather, the molecule exhibits bond lengths in between those of single and double bonds. This commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds (cyclohexatriene), was developed by August Kekulé (see History below). The model for benzene consists of two resonance forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a more stable molecule than would be expected without accounting for charge delocalization.

Cell signaling

Cell signaling (cell signalling in British English) is part of any communication process that governs basic activities of cells and coordinates all cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity, as well as normal tissue homeostasis. Errors in signaling interactions and cellular information processing are responsible for diseases such as cancer, autoimmunity, and diabetes. By understanding cell signaling, diseases may be treated more effectively and, theoretically, artificial tissues may be created.Systems biology studies the underlying structure of cell signaling networks and how changes in these networks may affect the transmission and flow of information (signal transduction). Such networks are complex systems in their organization and may exhibit a number of emergent properties including bistability and ultrasensitivity. Analysis of cell signaling networks requires a combination of experimental and theoretical approaches including the development and analysis of simulations and modeling. Long-range allostery is often a significant component of cell signaling events.

Cellular respiration

Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy in the process, as weak so-called "high-energy" bonds are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. Cellular respiration is considered an exothermic redox reaction which releases heat. The overall reaction occurs in a series of biochemical steps, most of which are redox reactions themselves. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow release of energy from the series of reactions.

Nutrients that are commonly used by animal and plant cells in respiration include sugar, amino acids and fatty acids, and the most common oxidizing agent (electron acceptor) is molecular oxygen (O2). The chemical energy stored in ATP (its third phosphate group is weakly bonded to the rest of the molecule and is cheaply broken allowing stronger bonds to form, thereby transferring energy for use by the cell) can then be used to drive processes requiring energy, including biosynthesis, locomotion or transportation of molecules across cell membranes.

Chemical formula

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 formulas 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 formulas.

The simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the simple numbers of each type of atom in a molecule, with no information on structure. For example, the empirical formula for glucose is CH2O (twice as many hydrogen atoms as carbon and oxygen), while its molecular formula is C6H12O6 (12 hydrogen atoms, six carbon and oxygen atoms).

Sometimes a chemical formula is complicated by being written as a condensed formula (or condensed molecular formula, occasionally called a "semi-structural formula"), which conveys additional information about the particular ways in which the atoms are chemically bonded together, either in covalent bonds, ionic bonds, or various combinations of these types. This is possible if the relevant bonding is easy to show in one dimension. An example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. However, even a condensed chemical formula is necessarily limited in its ability to show complex bonding relationships between atoms, especially atoms that have bonds to four or more different substituents.

Since a chemical formula must be expressed as a single line of chemical element symbols, it often cannot be as informative as a true structural formula, which is a graphical representation of the spatial relationship between atoms in chemical compounds (see for example the figure for butane structural and chemical formulas, at right). For reasons of structural complexity, there is no condensed chemical formula (or semi-structural formula) that specifies glucose (and there exist many different molecules, for example fructose and mannose, that have the same molecular formula C6H12O6 as glucose). Linear equivalent chemical names exist that can and do specify any complex structural formula (see chemical nomenclature), but such names must use many terms (words), rather than the simple element symbols, numbers, and simple typographical symbols that define a chemical formula.

Chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. While, as noted, chemical formulas do not have the full power of structural formulas to show chemical relationships between atoms, they are sufficient to keep track of numbers of atoms and numbers of electrical charges in chemical reactions, thus balancing chemical equations so that these equations can be used in chemical problems involving conservation of atoms, and conservation of electric charge.

Chemical polarity

In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end.

Polar molecules must contain polar bonds due to a difference in electronegativity between the bonded atoms. A polar molecule with two or more polar bonds must have a geometry which is asymmetric in at least one direction, so that the bond dipoles do not cancel each other.

Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. Polarity underlies a number of physical properties including surface tension, solubility, and melting and boiling points.

Chirality (chemistry)

Chirality is a geometric property of some molecules and ions. A chiral molecule/ion is non-superposable on its mirror image. The presence of an asymmetric carbon center is one of several structural features that induce chirality in organic and inorganic molecules. The term chirality is derived from the Ancient Greek word for hand, χεῖρ (kheir).

The mirror images of a chiral molecule or ion are called enantiomers or optical isomers. Individual enantiomers are often designated as either right-handed or left-handed. Chirality is an essential consideration when discussing the stereochemistry in organic and inorganic chemistry. The concept is of great practical importance because most biomolecules and pharmaceuticals are chiral.

Chiral molecules and ions are described by various ways of designating their absolute configuration, which codify either the entity's geometry or its ability to rotate plane-polarized light, a common technique in studying chirality.

Diatomic molecule

Diatomic molecules are molecules composed of only two atoms, of the same or different chemical elements. The prefix di- is of Greek origin, meaning "two". If a diatomic molecule consists of two atoms of the same element, such as hydrogen (H2) or oxygen (O2), then it is said to be homonuclear. Otherwise, if a diatomic molecule consists of two different atoms, such as carbon monoxide (CO) or nitric oxide (NO), the molecule is said to be heteronuclear.

The only chemical elements that form stable homonuclear diatomic molecules at standard temperature and pressure (STP) (or typical laboratory conditions of 1 bar and 25 °C) are the gases hydrogen (H2), nitrogen (N2), oxygen (O2), fluorine (F2), and chlorine (Cl2).The noble gases (helium, neon, argon, krypton, xenon, and radon) are also gases at STP, but they are monatomic. The homonuclear diatomic gases and noble gases together are called "elemental gases" or "molecular gases", to distinguish them from other gases that are chemical compounds.At slightly elevated temperatures, the halogens bromine (Br2) and iodine (I2) also form diatomic gases. All halogens have been observed as diatomic molecules, except for astatine, which is uncertain.

The mnemonics BrINClHOF, pronounced "Brinklehof", and HONClBrIF, pronounced "Honkelbrif", and HOFBrINCl (pronounced as Hofbrinkle) have been coined to aid recall of the list of diatomic elements.

Other elements form diatomic molecules when evaporated, but these diatomic species repolymerize when cooled. Heating ("cracking") elemental phosphorus gives diphosphorus, P2. Sulfur vapor is mostly disulfur (S2). Dilithium (Li2) is known in the gas phase. Ditungsten (W2) and dimolybdenum (Mo2) form with sextuple bonds in the gas phase. The bond in a homonuclear diatomic molecule is non-polar. Dirubidium (Rb2) is diatomic.

Hydrolysis

Hydrolysis (; from Ancient Greek hydro-, meaning 'water', and lysis, meaning 'to unbind') is a term used for both an electro-chemical process and a biological one. The hydrolysis of water is the separation of water molecules into hydrogen and oxygen atoms (water splitting) using electricity (electrolysis).

Biological hydrolysis is the cleavage of biomolecules where a water molecule is consumed to effect the separation of a larger molecule into component parts. When a carbohydrate is broken into its component sugar molecules by hydrolysis (e.g. sucrose being broken down into glucose and fructose), this is termed saccharification. Generally, hydrolysis or saccharification is a step in the degradation of a substance.

Hydrolysis can be the reverse of a condensation reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water and any other solvents. Some hydration reactions are hydrolysis.

Macromolecule

A macromolecule is a very large molecule, such as protein, commonly created by the polymerization of smaller subunits (monomers). They are typically composed of thousands of atoms or more. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, carbohydrates and lipids) and large non-polymeric molecules (such as lipids and macrocycles). Synthetic macromolecules include common plastics and synthetic fibers as well as experimental materials such as carbon nanotubes.

Mole (unit)

The mole is the base unit of amount of substance in the International System of Units (SI). Effective 20 May 2019, the mole is defined as the amount of a chemical substance that contains exactly 6.02214076×1023 (Avogadro constant) constitutive particles, e.g., atoms, molecules, ions or electrons.This definition was adopted in November 2018, revising its old definition based on the number of atoms in 12 grams of carbon-12 (12C) (the isotope of carbon with relative atomic mass 12 Da by definition). The mole is an SI base unit, with the unit symbol mol.

The mole is widely used in chemistry as a convenient way to express amounts of reactants and products of chemical reactions. For example, the chemical equation 2H2 + O2 → 2H2O can be interpreted to mean that 2 mol dihydrogen (H2) and 1 mol dioxygen (O2) react to form 2 mol water (H2O). The mole may also be used to represent the number of atoms, ions, or other entities in a given sample of a substance. The concentration of a solution is commonly expressed by its molarity, defined as the amount of dissolved substance per unit volume of solution, for which the unit typically used is moles per litre (mol/l), commonly abbreviated M.

The term gram-molecule was formerly used for essentially the same concept. The term gram-atom has been used for a related but distinct concept, namely a quantity of a substance that contains an Avogadro's number of atoms, whether isolated or combined in molecules. Thus, for example, 1 mole of MgBr2 is 1 gram-molecule of MgBr2 but 3 gram-atoms of MgBr2.

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 determine the position of each atom.

Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.e. they can be understood as approximately local and hence transferable properties.

Molecule Man

Molecule Man (Owen Reece) is a fictional character appearing in American comic books published by Marvel Comics. He first appeared in Fantastic Four #20 in November 1963 and was created by Stan Lee and Jack Kirby.

He is often portrayed as a supervillain, but sometimes takes the role of a reformed outlaw or reluctant hero.

Monomer

A monomer ( MON-ə-mər; mono-, "one" + -mer, "part") is a molecule that "can undergo polymerization thereby contributing constitutional units to the essential structure of a macromolecule". Large numbers of monomers combine to form polymers in a process called polymerization.

Organic compound

In chemistry, an organic compound is generally any chemical compound that contains carbon. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. Study of the properties and synthesis of organic compounds is the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds (e.g., carbonates and cyanides), along with a handful of other exceptions (e.g., carbon dioxide), are not classified as organic compounds and are considered inorganic. No consensus exists among chemists on precisely which carbon-containing compounds are excluded, making the definition of an organic compound elusive.Although organic compounds make up only a small percentage of the Earth's crust, they are of central importance because all known life is based on organic compounds. Living things incorporate inorganic carbon into organic compounds through a network of processes (the carbon cycle) that begins with the conversion of carbon dioxide and a hydrogen source like water into simple sugars and other organic molecules by autotrophic organisms using light (photosynthesis) or other sources of energy. Most synthetically produced organic compounds are ultimately derived from petrochemicals consisting mainly of hydrocarbons, which are themselves formed from the high pressure and temperature degradation of organic matter underground over geological timescales. This ultimate derivation notwithstanding, organic compounds are no longer defined as compounds originating in living things, as they were historically.

In chemical nomenclature, an organyl group, frequently represented by the letter R, refers to any monovalent substituent whose open valence is on a carbon atom.

Polymer

A polymer (; Greek poly-, "many" + -mer, "part") is a large molecule, or macromolecule, composed of many repeated subunits. Due to their broad range of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass relative to small molecule compounds produces unique physical properties, including toughness, viscoelasticity, and a tendency to form glasses and semicrystalline structures rather than crystals. The terms polymer and resin are often synonymous with plastic.

The term "polymer" derives from the Greek word πολύς (polus, meaning "many, much") and μέρος (meros, meaning "part"), and refers to a molecule whose structure is composed of multiple repeating units, from which originates a characteristic of high relative molecular mass and attendant properties. The units composing polymers derive, actually or conceptually, from molecules of low relative molecular mass. The term was coined in 1833 by Jöns Jacob Berzelius, though with a definition distinct from the modern IUPAC definition. The modern concept of polymers as covalently bonded macromolecular structures was proposed in 1920 by Hermann Staudinger, who spent the next decade finding experimental evidence for this hypothesis.Polymers are studied in the fields of biophysics and macromolecular science, and polymer science (which includes polymer chemistry and polymer physics). Historically, products arising from the linkage of repeating units by covalent chemical bonds have been the primary focus of polymer science; emerging important areas of the science now focus on non-covalent links. Polyisoprene of latex rubber is an example of a natural/biological polymer, and the polystyrene of styrofoam is an example of a synthetic polymer. In biological contexts, essentially all biological macromolecules—i.e., proteins (polyamides), nucleic acids (polynucleotides), and polysaccharides—are purely polymeric, or are composed in large part of polymeric components—e.g., isoprenylated/lipid-modified glycoproteins, where small lipidic molecules and oligosaccharide modifications occur on the polyamide backbone of the protein.The simplest theoretical models for polymers are ideal chains.

Properties of water

Water (H2O) is a polar inorganic compound that is at room temperature a tasteless and odorless liquid, which is nearly colorless apart from an inherent hint of blue. It is by far the most studied chemical compound and is described as the "universal solvent" and the "solvent of life". It is the most abundant substance on Earth and the only common substance to exist as a solid, liquid, and gas on Earth's surface. It is also the third most abundant molecule in the universe.Water molecules form hydrogen bonds with each other and are strongly polar. This polarity allows it to dissociate ions in salts and bond to other polar substances such as alcohols and acids, thus dissolving them. Its hydrogen bonding causes its many unique properties, such as having a solid form less dense than its liquid form, a relatively high boiling point of 100 °C for its molar mass, and a high heat capacity.

Water is amphoteric, meaning that it can exhibit properties of an acid or a base, depending on the pH of the solution that it is in; it readily produces both H+ and OH− ions. Related to its amphoteric character, it undergoes self-ionization. The product of the activities, or approximately, the concentrations of H+ and OH− is a constant, so their respective concentrations are inversely proportional to each other.

Receptor (biochemistry)

In biochemistry and pharmacology, receptors are chemical structures, composed of protein, that receive and transduce signals that may be integrated into biological systems. These signals are typically chemical messengers, which bind to a receptor, they cause some form of cellular/tissue response, e.g. a change in the electrical activity of a cell. There are three main ways the action of the receptor can be classified: relay of signal, amplification, or integration. Relaying sends the signal onward, amplification increases the effect of a single ligand, and integration allows the signal to be incorporated into another biochemical pathway. In this sense, a receptor is a protein-molecule that recognizes and responds to endogenous chemical signals. For example, an acetylcholine receptor recognizes and responds to its endogenous ligand, acetylcholine. However, sometimes in pharmacology, the term is also used to include other proteins that are drug targets, such as enzymes, transporters, and ion channels.Receptor proteins can be classified by their location. Transmembrane receptors include ion channel-linked (ionotropic) receptors, G protein-linked (metabotropic) hormone receptors, and enzyme-linked hormone receptors. Intracellular receptors are those found inside the cell, and include cytoplasmic receptors and nuclear receptors. A molecule that binds to a receptor is called a ligand, and can be a protein or peptide (short protein), or another small molecule such as a neurotransmitter, hormone, pharmaceutical drug, toxin, or parts of the outside of a virus or microbe. The endogenously designated -molecule for a particular receptor is referred to as its endogenous ligand. E.g. the endogenous ligand for the nicotinic acetylcholine receptor is acetylcholine but the receptor can also be activated by nicotine and blocked by curare. Receptors of a particular type are linked to a specific cellular biochemical pathways that correspond to the signal. While numerous receptors are found in most cells, each receptor will only bind with ligands of a particular structure. This has been analogously compared to how locks will only accept specifically shaped keys. When a ligand binds to a corresponding receptor, it activates or inhibits the receptor's associated biochemical pathway.

Substrate (chemistry)

In chemistry, a substrate is typically the chemical species being observed in a chemical reaction, which reacts with a reagent to generate a product. In synthetic and organic chemistry, the substrate is the chemical of interest that is being modified. In biochemistry, an enzyme substrate is the material upon which an enzyme acts. When referring to Le Chatelier's principle, the substrate is the reagent whose concentration is changed. The term substrate is highly context-dependent. It essentially refers to the part of the molecule that is precursor to a product.

VCAM-1

Vascular cell adhesion protein 1 also known as vascular cell adhesion molecule 1 (VCAM-1) or cluster of differentiation 106 (CD106) is a protein that in humans is encoded by the VCAM1 gene. VCAM-1 functions as a cell adhesion molecule.

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