Sunday, October 31, 2010

Better Detection for Diagnostics and Biochemical Defense

ScienceDaily (Oct. 29, 2010) — Current detection methods for chemical and biological molecules involve using tiny, molecular "labels," typically fluorescent or radioactive entities, which can be a time-consuming and expensive process. A University of Michigan research team headed by Associate Professor Xudong (Sherman) Fan, recently developed a system for detecting chemical and biological molecules without labels, and they expect the technology to have broad applications ranging from clinical diagnostics to drug development, as well as homeland security and environmental monitoring for biological and chemical weapons.

According to Fan, the new method has the additional benefit of not altering the molecules of interest. "We just measure the molecules directly," he says, adding that labeling "is a time-consuming and costly process... and may affect the biological functions of the molecule" being examined.
Fan and his colleagues built their system by adapting an optical sensing device known as a ring resonator, which has greater sensitivity than traditional optical fiber or waveguide sensors. The team partnered the ring device with a capillary-based fluidic system, creating a "unique integration of capillary fluidics with ring resonator technology," according to Fan.
The capillary system can be used for the introduction of either liquid or gas to the sensor, giving the new device a broad spectrum of potential applications. In a clinical diagnostic setting, for example, body fluids such as blood and saliva can be used. Alternatively, vapor analysis can also be performed on exhaled breath for early and non-invasive diagnosis of diseases such as cancers. For homeland security and environmental monitoring purposes, volatile organic compounds, such as explosives, are typically of interest. Particularly for gaseous compounds, most current systems suffer from a lack of specificity. The combined device developed by Fan's group, however, can be built into a so-called "micro GC" (gas chromatography), which enables highly specific identification of compounds.
The talk, "Optical Ring Resonator Based Biological and Chemical Sensors," took place on Oct. 26 at the Frontiers in Optics (FiO) 2010/Laser Science XXVI -- the 94th annual meeting of the Optical Society (OSA), which was held together with the annual meeting of the American Physical Society (APS) Division of Laser Science at the Rochester Riverside Convention Center in Rochester, N.Y., from Oct. 24-28.

Saturday, October 30, 2010

Halogen



Halogen
From Wikipedia, the free encyclopedia
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This article is about the chemical series. For other uses, see Halogen (disambiguation).
The halogens or halogen elements are a series of nonmetal elements from Group 17 IUPAC Style (formerly: VII, VIIA) of the periodic table, comprising fluorine (F), chlorine (Cl), bromine (Br), iodine (I), and astatine (At). The artificially created element 117, provisionally referred to by the systematic name ununseptium, may also be a halogen.
The group of halogens is the only periodic table group which contains elements in all three familiar states of matter at standard temperature and pressure.

 Abundance

Owing to their high reactivity, the halogens are found in the environment only in compounds or as ions. Halide ions and oxoanions such as iodate (IO3) can be found in many minerals and in seawater. Halogenated organic compounds can also be found as natural products in living organisms. In their elemental forms, the halogens exist as diatomic molecules, but these only have a fleeting existence in nature and are much more common in the laboratory and in industry. At room temperature and pressure, fluorine and chlorine are gases, bromine is a liquid and iodine and astatine are solids; Group 17 is therefore the only periodic table group exhibiting all three states of matter at room temperature.
 Etymology
The Swedish chemist Baron Jöns Jakob Berzelius coined the term "halogen" – λς (háls), "salt" or "sea", and γεν- (gen-), from γίγνομαι (gnomai), "come to be" – for an element that produces a salt when it forms a compound with a metal.[1]
 Properties

Fluorine, (F); chlorine, (Cl); bromine, (Br); iodine, (I) at room temperature. The first two are gaseous, the third is liquid and the fourth is solid

















http://bits.wikimedia.org/skins-1.5/common/images/magnify-clip.png
Fluorine, (F); chlorine, (Cl); bromine, (Br); iodine, (I) at room temperature. The first two are gaseous, the third is liquid and the fourth is solid.
Like other groups, the candidates of this family show patterns in its electron configuration, especially the outermost shells resulting in trends in chemical behavior:
9
fluorine
2, 7
17
chlorine
2, 8, 7
35
bromine
2, 8, 18, 7
53
iodine
2, 8, 18, 18, 7
85
astatine
2, 8, 18, 32, 18, 7
The halogens show a series of trends when moving down the group—for instance, decreasing electronegativity and reactivity, and increasing melting and boiling point.
Halogen
Standard Atomic Weight (u)
Melting Point (K)
Boiling Point (K)
Electronegativity (Pauling)
18.998
53.53
85.03
3.98
35.453
171.60
239.11
3.16
79.904
265.80
332.00
2.96
126.904
386.85
457.40
2.66
(210)
575
610 (?)
2.20
 Diatomic halogen molecules
halogen molecule structure model d(X−X) / pm
(gas phase)
d(X−X) / pm
(solid phase)


fluorine


F2


Difluorine-2D-dimensions.png


Fluorine-3D-vdW.png


143


149


chlorine


Cl2


Dichlorine-2D-dimensions.png


Chlorine-3D-vdW.png


199


198


bromine


Br2


Dibromine-2D-dimensions.png


Bromine-3D-vdW.png


228


227


iodine


I2


Diiodine-2D-dimensions.png


Iodine-3D-vdW.png


266


272





























The elements become less reactive and have higher melting points as the atomic number increases.
 Chemistry
 Reactivity
Halogens are highly reactive, and as such can be harmful or lethal to biological organisms in sufficient quantities. This high reactivity is due to the atoms being highly electronegative due to their high effective nuclear charge. They can gain an electron by reacting with atoms of other elements. Fluorine is one of the most reactive elements in existence, attacking otherwise inert materials such as glass, and forming compounds with the heavier noble gases. It is a corrosive and highly toxic gas. The reactivity of fluorine is such that if used or stored in laboratory glassware, it can react with glass in the presence of small amounts of water to form silicon tetrafluoride (SiF4). Thus fluorine must be handled with substances such as Teflon (which is itself an organofluorine compound), extremely dry glass, or metals such as copper or steel which form a protective layer of fluoride on their surface.
The high reactivity of fluorine means that once it does react with something, it bonds with it so strongly that the resulting molecule is very inert and non-reactive to anything else. For example, Teflon is fluorine bonded with carbon.
Both chlorine and bromine are used as disinfectants for drinking water, swimming pools, fresh wounds, spas, dishes, and surfaces. They kill bacteria and other potentially harmful microorganisms through a process known as sterilization. Their reactivity is also put to use in bleaching. Sodium hypochlorite, which is produced from chlorine, is the active ingredient of most fabric bleaches and chlorine-derived bleaches are used in the production of some paper products.
 Hydrogen halides
The halogens all form binary compounds with hydrogen known as the hydrogen halides (HF, HCl, HBr, HI, and HAt), a series of particularly strong acids. When in aqueous solution, the hydrogen halides are known as hydrohalic acids. HAt, or "hydroastatic acid", should also qualify, but it is not typically included in discussions of hydrohalic acid due to astatine's extreme instability toward alpha decay.
 Interhalogen compounds
Main article: Interhalogen
The halogens react with each other to form interhalogen compounds. Diatomic interhalogen compounds such as BrF, ICl, and ClF bear resemblance to the pure halogens in some respects. The properties and behaviour of a diatomic interhalogen compound tend to be intermediate between those of its parent halogens. Some properties, however, are found in neither parent halogen. For example, Cl2 and I2 are soluble in CCl4, but ICl is not since it is a polar molecule due to the relatively large electronegativity difference between I and Cl.
 Organohalogen compounds
Many synthetic organic compounds such as plastic polymers, and a few natural ones, contain halogen atoms; these are known as halogenated compounds or organic halides. Chlorine is by far the most abundant of the halogens, and the only one needed in relatively large amounts (as chloride ions) by humans. For example, chloride ions play a key role in brain function by mediating the action of the inhibitory transmitter GABA and are also used by the body to produce stomach acid. Iodine is needed in trace amounts for the production of thyroid hormones such as thyroxine. On the other hand, neither fluorine nor bromine are believed to be essential for humans.
 Polyhalogenated compounds
Polyhalogenated compounds are industrially created compounds substituted with multiple halogens. Many of them are very toxic and bioaccumulate in humans, and have a very wide application range. They include the much maligned PCB's, PBDE's, and PFC's as well as numerous other compounds.
 Drug discovery
In drug discovery, the incorporation of halogen atoms into a lead drug candidate results in analogues that are usually more lipophilic and less water soluble.[2] Consequently, halogen atoms are used to improve penetration through lipid membranes and tissues. Consequently, there is a tendency for some halogenated drugs to accumulate in adipose tissue.
The chemical reactivity of halogen atoms depends on both their point of attachment to the lead and the nature of the halogen. Aromatic halogen groups are far less reactive than aliphatic halogen groups, which can exhibit considerable chemical reactivity. For aliphatic carbon-halogen bonds the C-F bond is the strongest and usually less chemically reactive than aliphatic C-H bonds. The other aliphatic-halogen bonds are weaker, their reactivity increasing down the periodic table. They are usually more chemically reactive than aliphatic C-H bonds. Consequently, the most common halogen substitutions are the less reactive aromatic fluorine and chlorine groups.
Reactivity with water
Fluorine reacts vigorously with water to produce oxygen (O2) and hydrogen fluoride (HF):[3]
2 F2(g) + 2 H2O(l) → O2(g) + 4 HF(aq)
Chlorine has minimal solubility of 0.7g Cl2 per kg of water at ambient temperature (21oC).[4] Dissolved chlorine reacts to form hydrochloric acid (HCl) and hypochlorous acid, a solution that can be used as a disinfectant or bleach:
Cl2(g) + H2O(l) → HCl(aq) + HClO(aq)
Bromine has a solubility of 3.41 g per 100 g of water,[5] but it slowly reacts to form hydrogen bromide (HBr) and hypobromous acid (HBrO):
Br2(g) + H2O(l) → HBr(aq) + HBrO(aq)
Iodine, however, is minimally soluble in water (0.03 g/100 g water @ 20 °C) and does not react with it.[6] However, iodine will form an aqueous solution in the presence of iodide ion, such as by addition of potassium iodide (KI), because the triiodide ion is formed.

From wikipedia

Wednesday, October 27, 2010

Make Sodium Acetate "Hot Ice" with vinegar and baking soda (pt1)

Sodium and Water in a 40 gallon trash can

Chemistry experiment 2. - Coloured flask.

Chemistry

From Wikipedia, the free encyclopedia
Jump to: navigation, search
Chemistry is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions.
Chemistry is the study of interactions of chemical substances with one another and energy.
Chemistry (the etymology of the word has been much disputed[1]) is the science of matter and the changes it undergoes. The science of matter is also addressed by physics, but while physics takes a more general and fundamental approach, chemistry is more specialized, being concerned with the composition, behavior, structure, and properties of matter, as well as the changes it undergoes during chemical reactions.[2] It is a physical science which studies of various atoms, molecules, crystals and other aggregates of matter whether in isolation or combination, which incorporates the concepts of energy and entropy in relation to the spontaneity of chemical processes.
Disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study of organic (carbon based) matter; biochemistry, the study of substances found in biological organisms; physical chemistry, the study of chemical processes using physical concepts such as thermodynamics and quantum mechanics; and analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system (see subdisciplines).

Summary

Chemistry is the scientific study of interaction of chemical substances[3] that are constituted of atoms or the subatomic particles: protons, electrons and neutrons.[4] Atoms combine to produce molecules or crystals. Chemistry is often called "the central science" because it connects the other natural sciences such as astronomy, physics, material science, biology and geology.[5][6]
The genesis of chemistry can be traced to certain practices, known as alchemy, which had been practiced for several millennia in various parts of the world, particularly the Middle East.[7]
The structure of objects we commonly use and the properties of the matter we commonly interact with are a consequence of the properties of chemical substances and their interactions. For example, steel is harder than iron because its atoms are bound together in a more rigid crystalline lattice; wood burns or undergoes rapid oxidation because it can react spontaneously with oxygen in a chemical reaction above a certain temperature; sugar and salt dissolve in water because their molecular/ionic properties are such that dissolution is preferred under the ambient conditions.
The transformations that are studied in chemistry are a result of interaction either between different chemical substances or between matter and energy. Traditional chemistry involves study of interactions between substances in a chemistry laboratory using various forms of laboratory glassware.
Laboratory, Institute of Biochemistry, University of Cologne
A chemical reaction is a transformation of some substances into one or more other substances.[8] It can be symbolically depicted through a chemical equation. The number of atoms on the left and the right in the equation for a chemical transformation is most often equal. The nature of chemical reactions a substance may undergo and the energy changes that may accompany it are constrained by certain basic rules, known as chemical laws.
Energy and entropy considerations are invariably important in almost all chemical studies. Chemical substances are classified in terms of their structure, phase as well as their chemical compositions. They can be analyzed using the tools of chemical analysis, e.g. spectroscopy and chromatography. Scientists engaged in chemical research are known as chemists.[9] Most chemists specialize in one or more sub-disciplines.

History

Ancient Egyptians pioneered the art of synthetic "wet" chemistry up to 4,000 years ago.[10] By 1000 BC ancient civilizations were using technologies that formed the basis of the various branches of chemistry such as; extracting metal from their ores, making pottery and glazes, fermenting beer and wine, making pigments for cosmetics and painting, extracting chemicals from plants for medicine and perfume, making cheese, dying cloth, tanning leather, rendering fat into soap, making glass, and making alloys like bronze.
Democritus' atomist philosophy was later adopted by Epicurus (341–270 BCE).
The genesis of chemistry can be traced to the widely observed phenomenon of burning that led to metallurgy—the art and science of processing ores to get metals (e.g. metallurgy in ancient India). The greed for gold led to the discovery of the process for its purification, even though the underlying principles were not well understood—it was thought to be a transformation rather than purification. Many scholars in those days thought it reasonable to believe that there exist means for transforming cheaper (base) metals into gold. This gave way to alchemy and the search for the Philosopher's Stone which was believed to bring about such a transformation by mere touch.[11]
Greek atomism dates back to 440 BC, as what might be indicated by the book De Rerum Natura (The Nature of Things)[12] written by the Roman Lucretius[13] in 50 BC. Much of the early development of purification methods is described by Pliny the Elder in his Naturalis Historia.
A tentative outline is as follows:
  1. Egyptian alchemy [3,000 BCE – 400 BCE], formulate early "element" theories such as the Ogdoad.
  2. Greek alchemy [332 BCE – 642 CE], the Greek king Alexander the Great conquers Egypt and founds Alexandria, having the world's largest library, where scholars and wise men gather to study.
  3. Arab alchemy [642 CE – 1200], the Muslim conquest of Egypt (primarily Alexandria); development of the Scientific Method by Alhazen and Jābir ibn Hayyān revolutionise the field of Chemistry. Jābir (Latin name Geber) accepted many of the ideas of Aristotle but also modified Aristotle's ideas.[14]
  4. The House of Wisdom (Arabic: بيت الحكمة‎; Bait al-Hikma), Al-Andalus (Arabic: الأندلس‎) and Alexandria (Arabic: الإسكندرية) become the world leading institutions where scientists of all religious and ethnic backgrounds worked together in harmony expanding the reaches of Chemistry in a time known as the Islamic Golden Age.
  5. Arabs and Persians continue to dominate the field of Chemistry, mastering it and expanding the boundaries of knowledge and experimentation. Besides technical advances in processes and apparatus, the Arabs had developed and improved the purity of substances such as alcohols, acids, and gunpowder, which were not available to the Europeans.[14]
  6. European alchemy [1300 – present], Pseudo-Geber builds on Arabic chemistry.[citation needed] From the 12th century, major advances in the chemical arts shifted from Arab lands to western Europe.[14]
  7. Chemistry [1661], Boyle writes his classic chemistry text The Sceptical Chymist.
  8. Chemistry [1787], Lavoisier writes his classic Elements of Chemistry.
  9. Chemistry [1803], Dalton publishes his Atomic Theory.
  10. Chemistry [1869], Dmitry Mendeleev presented his Periodic Table being the framework of the modern chemistry
The earliest pioneers of Chemistry, and inventors of the modern scientific method,[15] were medieval Arab and Persian scholars. They introduced precise observation and controlled experimentation into the field and discovered numerous Chemical substances.[16][verification needed]
"Chemistry as a science was almost created by the Muslims; for in this field, where the Greeks (so far as we know) were confined to industrial experience and vague hypothesis, the Saracens introduced precise observation, controlled experiment, and careful records. They invented and named the alembic (al-anbiq), chemically analyzed innumerable substances, composed lapidaries, distinguished alkalis and acids, investigated their affinities, studied and manufactured hundreds of drugs. Alchemy, which the Muslims inherited from Egypt, contributed to chemistry by a thousand incidental discoveries, and by its method, which was the most scientific of all medieval operations."
[16]
The most influential Muslim chemists were Jābir ibn Hayyān (Geber, d. 815), al-Kindi (d. 873), al-Razi (d. 925), al-Biruni (d. 1048) and Alhazen (d. 1039).[17] The works of Jābir became more widely known in Europe through Latin translations by a pseudo-Geber in 14th century Spain, who also wrote some of his own books under the pen name "Geber". The contribution of Indian alchemists and metallurgists in the development of chemistry was also quite significant.[18]
The emergence of chemistry in Europe was primarily due to the recurrent incidence of the plague and blights there during the so called Dark Ages.[citation needed] This gave rise to a need for medicines. It was thought that there exists a universal medicine called the Elixir of Life that can cure all diseases[citation needed], but like the Philosopher's Stone, it was never found.
Antoine-Laurent de Lavoisier is considered the "Father of Modern Chemistry".[19]
For some practitioners, alchemy was an intellectual pursuit, over time, they got better at it. Paracelsus (1493–1541), for example, rejected the 4-elemental theory and with only a vague understanding of his chemicals and medicines, formed a hybrid of alchemy and science in what was to be called iatrochemistry. Similarly, the influences of philosophers such as Sir Francis Bacon (1561–1626) and René Descartes (1596–1650), who demanded more rigor in mathematics and in removing bias from scientific observations, led to a scientific revolution. In chemistry, this began with Robert Boyle (1627–1691), who came up with an equation known as Boyle's Law about the characteristics of gaseous state.[20]
Chemistry indeed came of age when Antoine Lavoisier (1743–1794), developed the theory of Conservation of mass in 1783; and the development of the Atomic Theory by John Dalton around 1800. The Law of Conservation of Mass resulted in the reformulation of chemistry based on this law[citation needed] and the oxygen theory of combustion, which was largely based on the work of Lavoisier. Lavoisier's fundamental contributions to chemistry were a result of a conscious effort[citation needed] to fit all experiments into the framework of a single theory. He established the consistent use of the chemical balance, used oxygen to overthrow the phlogiston theory, and developed a new system of chemical nomenclature and made contribution to the modern metric system. Lavoisier also worked to translate the archaic and technical language of chemistry into something that could be easily understood by the largely uneducated masses, leading to an increased public interest in chemistry. All these advances in chemistry led to what is usually called the chemical revolution. The contributions of Lavoisier led to what is now called modern chemistry—the chemistry that is studied in educational institutions all over the world. It is because of these and other contributions that Antoine Lavoisier is often celebrated as the "Father of Modern Chemistry".[21] The later discovery of Friedrich Wöhler that many natural substances, organic compounds, can indeed be synthesized in a chemistry laboratory also helped the modern chemistry to mature from its infancy.[22]
The discovery of the chemical elements has a long history from the days of alchemy and culminating in the discovery of the periodic table of the chemical elements by Dmitri Mendeleev (1834–1907)[23] and later discoveries of some synthetic elements.

Etymology

The word chemistry comes from the earlier study of alchemy, which is a set of practices that encompasses elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism and medicine. Alchemy in turn is derived from the Arabic word "كيمياء" meaning "value", it is commonly thought of as the quest to turn lead or another common starting material into gold.[24] This linguistic relation between the pursuit of value and alchemy is thought to have Egyptian origins. Many believe that the Arabic word "alchemy" is derived from the word Chemi or Kimi, which is the ancient name of Egypt in Egyptian.[25][26][27] The word was subsequently borrowed by the Greeks, and from the Greeks by the Arabs when they occupied Alexandria (Egypt) in the 7th century. The Arabs added the Arabic definite article "al" to the word, resulting in the word "الكيمياء" (al-kīmiyā). Thus, an alchemist was called a 'chemist' in popular speech, and later the suffix "-ry" was added to this to describe the art of the chemist as "chemistry".

Definitions

In retrospect, the definition of chemistry seems to invariably change per decade, as new discoveries and theories add to the functionality of the science. Shown below are some of the standard definitions used by various noted chemists:
  • Alchemy (330) – the study of the composition of waters, movement, growth, embodying, disembodying, drawing the spirits from bodies and bonding the spirits within bodies (Zosimos).[28]
  • Chymistry (1661) – the subject of the material principles of mixt bodies (Boyle).[29]
  • Chymistry (1663) – a scientific art, by which one learns to dissolve bodies, and draw from them the different substances on their composition, and how to unite them again, and exalt them to a higher perfection (Glaser).[30]
  • Chemistry (1730) – the art of resolving mixt, compound, or aggregate bodies into their principles; and of composing such bodies from those principles (Stahl).[31]
  • Chemistry (1837) – the science concerned with the laws and effects of molecular forces (Dumas).[32]
  • Chemistry (1947) – the science of substances: their structure, their properties, and the reactions that change them into other substances (Pauling).[33]
  • Chemistry (1998) – the study of matter and the changes it undergoes (Chang).[34]

Basic concepts

Several concepts are essential for the study of chemistry; some of them are:[35]

Atom

An atom is the basic unit of chemistry. It consists of a positively charged core (the atomic nucleus) which contains protons and neutrons, and which maintains a number of electrons to balance the positive charge in the nucleus. The atom is also the smallest entity that can be envisaged to retain some of the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state(s), coordination number, and preferred types of bonds to form (e.g., metallic, ionic, covalent).

Element

The concept of chemical element is related to that of chemical substance. A chemical element is specifically a substance which is composed of a single type of atom. A chemical element is characterized by a particular number of protons in the nuclei of its atoms. This number is known as the atomic number of the element. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, and all atoms with 92 protons in their nuclei are atoms of the element uranium. 94 different chemical elements or types of atoms based on the number of protons exist naturally. A further 18 have been recognised by IUPAC as existing artificially only. Although all the nuclei of all atoms belonging to one element will have the same number of protons, they may not necessarily have the same number of neutrons, such atoms are termed isotopes. In fact several isotopes of an element may exist.
The most convenient presentation of the chemical elements is in the periodic table of the chemical elements, which groups elements by atomic number. Due to its ingenious arrangement, groups, or columns, and periods, or rows, of elements in the table either share several chemical properties, or follow a certain trend in characteristics such as atomic radius, electronegativity, etc. Lists of the elements by name, by symbol, and by atomic number are also available.

Compound

A compound is a substance with a particular ratio of atoms of particular chemical elements which determines its composition, and a particular organization which determines chemical properties. For example, water is a compound containing hydrogen and oxygen in the ratio of two to one, with the oxygen atom between the two hydrogen atoms, and an angle of 104.5° between them. Compounds are formed and interconverted by chemical reactions.

Substance

A chemical substance is a kind of matter with a definite composition and set of properties.[36] Strictly speaking, a mixture of compounds, elements or compounds and elements is not a chemical substance, but it may be called a chemical. Most of the substances we encounter in our daily life are some kind of mixture; for example: air, alloys, biomass, etc.
Nomenclature of substances is a critical part of the language of chemistry. Generally it refers to a system for naming chemical compounds. Earlier in the history of chemistry substances were given name by their discoverer, which often led to some confusion and difficulty. However, today the IUPAC system of chemical nomenclature allows chemists to specify by name specific compounds amongst the vast variety of possible chemicals. The standard nomenclature of chemical substances is set by the International Union of Pure and Applied Chemistry (IUPAC). There are well-defined systems in place for naming chemical species. Organic compounds are named according to the organic nomenclature system.[37] Inorganic compounds are named according to the inorganic nomenclature system.[38] In addition the Chemical Abstracts Service has devised a method to index chemical substance. In this scheme each chemical substance is identifiable by a number known as CAS registry number.

Molecule

A molecule is the smallest indivisible portion of a pure chemical substance that has its unique set of chemical properties, that is, its potential to undergo a certain set of chemical reactions with other substances. Molecules can exist as electrically neutral units unlike ions. Molecules are typically a set of atoms bound together by covalent bonds, such that the structure is electrically neutral and all valence electrons are paired with other electrons either in bonds or in lone pairs.
A molecular structure depicts the bonds and relative positions of atoms in a molecule such as that in Paclitaxel shown here
Not all substances consist of discrete molecules. Most chemical elements are composed of lone atoms as their smallest discrete unit. Other types of substances, such as ionic compounds and network solids, are organized in such a way as to lack the existence of identifiable molecules per se. Instead, these substances are discussed in terms of formula units or unit cells as the smallest repeating structure within the substance; as they lack identifiable molecules.
One of the main characteristic of a molecule is its geometry often called its structure. While the structure of diatomic, triatomic or tetra atomic molecules may be trivial, (linear, angular pyramidal etc.) the structure of polyatomic molecules, that are constituted of more than six atoms (of several elements) can be crucial for its chemical nature.

Mole and amount of substance

Mole is a unit to measure amount of substance (also called chemical amount). A mole is the amount of a substance that contains as many elementary entities (atoms, molecules or ions) as there are atoms in 0.012 kilogram (or 12 grams) of carbon-12, where the carbon-12 atoms are unbound, at rest and in their ground state.[39] The number of entities per mole is known as the Avogadro constant, and is determined empirically. The currently accepted value is 6.02214179(30) × 1023 mol−1 (2007 CODATA). One way to understand the meaning of the term "mole" is to compare and contrast it to terms such as dozen. Just as one dozen eggs contains 12 individual eggs, one mole contains 6.02214179(30) × 1023 atoms, molecules or other particles. The term is used because it is much easier to say, for example, 1 mole of carbon, than it is to say 6.02214179(30) × 1023 carbon atoms, and because moles of chemicals represent a scale that is easy to experience.
The amount of substance of a solute per volume of solution is known as amount of substance concentration, or molarity for short. Molarity is the quantity most commonly used to express the concentration of a solution in the chemical laboratory. The most commonly used units for molarity are mol/L (the official SI units are mol/m3).

Ions and salts

An ion is a charged species, an atom or a molecule, that has lost or gained one or more electrons. Positively charged cations (e.g. sodium cation Na+) and negatively charged anions (e.g. chloride Cl) can form a crystalline lattice of neutral salts (e.g. sodium chloride NaCl). Examples of polyatomic ions that do not split up during acid-base reactions are hydroxide (OH) and phosphate (PO43−).
Ions in the gaseous phase are often known as plasma.

Acidity and basicity

A substance can often be classified as an acid or a base. There are several different theories which explain acid-base behavior. The simplest is Arrhenius theory, which states than an acid is a substance that produces hydronium ions when it is dissolved in water, and a base is one that produces hydroxide ions when dissolved in water. According to Brønsted–Lowry acid-base theory, acids are substances that donate a positive hydrogen ion to another substance in a chemical reaction; by extension, a base is the substance which receives that hydrogen ion. A third common theory is Lewis acid-base theory, which is based on the formation of new chemical bonds. Lewis theory explains that an acid is a substance which is capable of accepting a pair of electrons from another substance during the process of bond formation, while a base is a substance which can provide a pair of electrons to form a new bond. According to concept as per Lewis, the crucial things being exchanged are charges.[40][unreliable source?] There are several other ways in which a substance may be classified as an acid or a base, as is evident in the history of this concept [41]
Acid strength is commonly measured by two methods. One measurement, based on the Arrhenius definition of acidity, is pH, which is a measurement of the hydronium ion concentration in a solution, as expressed on a negative logarithmic scale. Thus, solutions that have a low pH have a high hydronium ion concentration, and can be said to be more acidic. The other measurement, based on the Brønsted–Lowry definition, is the acid dissociation constant (Ka), which measure the relative ability of a substance to act as an acid under the Brønsted–Lowry definition of an acid. That is, substances with a higher Ka are more likely to donate hydrogen ions in chemical reactions than those with lower Ka values.

Phase

In addition to the specific chemical properties that distinguish different chemical classifications chemicals can exist in several phases. For the most part, the chemical classifications are independent of these bulk phase classifications; however, some more exotic phases are incompatible with certain chemical properties. A phase is a set of states of a chemical system that have similar bulk structural properties, over a range of conditions, such as pressure or temperature. Physical properties, such as density and refractive index tend to fall within values characteristic of the phase. The phase of matter is defined by the phase transition, which is when energy put into or taken out of the system goes into rearranging the structure of the system, instead of changing the bulk conditions.
Sometimes the distinction between phases can be continuous instead of having a discrete boundary, in this case the matter is considered to be in a supercritical state. When three states meet based on the conditions, it is known as a triple point and since this is invariant, it is a convenient way to define a set of conditions.
The most familiar examples of phases are solids, liquids, and gases. Many substances exhibit multiple solid phases. For example, there are three phases of solid iron (alpha, gamma, and delta) that vary based on temperature and pressure. A principal difference between solid phases is the crystal structure, or arrangement, of the atoms. Another phase commonly encountered in the study of chemistry is the aqueous phase, which is the state of substances dissolved in aqueous solution (that is, in water). Less familiar phases include plasmas, Bose-Einstein condensates and fermionic condensates and the paramagnetic and ferromagnetic phases of magnetic materials. While most familiar phases deal with three-dimensional systems, it is also possible to define analogs in two-dimensional systems, which has received attention for its relevance to systems in biology.

Redox

It is a concept related to the ability of atoms of various substances to lose or gain electrons. Substances that have the ability to oxidize other substances are said to be oxidative and are known as oxidizing agents, oxidants or oxidizers. An oxidant removes electrons from another substance. Similarly, substances that have the ability to reduce other substances are said to be reductive and are known as reducing agents, reductants, or reducers. A reductant transfers electrons to another substance, and is thus oxidized itself. And because it "donates" electrons it is also called an electron donor. Oxidation and reduction properly refer to a change in oxidation number—the actual transfer of electrons may never occur. Thus, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number.

Bonding

Electron atomic and molecular orbitals
Atoms sticking together in molecules or crystals are said to be bonded with one another. A chemical bond may be visualized as the multipole balance between the positive charges in the nuclei and the negative charges oscillating about them.[42] More than simple attraction and repulsion, the energies and distributions characterize the availability of an electron to bond to another atom.
A chemical bond can be a covalent bond, an ionic bond, a hydrogen bond or just because of Van der Waals force. Each of these kind of bond is ascribed to some potential. These potentials create the interactions which hold atoms together in molecules or crystals. In many simple compounds, Valence Bond Theory, the Valence Shell Electron Pair Repulsion model (VSEPR), and the concept of oxidation number can be used to explain molecular structure and composition. Similarly, theories from classical physics can be used to predict many ionic structures. With more complicated compounds, such as metal complexes, valence bond theory is less applicable and alternative approaches, such as the molecular orbital theory, are generally used. See diagram on electronic orbitals.

Reaction

When a chemical substance is transformed as a result of its interaction with another or energy, a chemical reaction is said to have occurred. Chemical reaction is therefore a concept related to the 'reaction' of a substance when it comes in close contact with another, whether as a mixture or a solution; exposure to some form of energy, or both. It results in some energy exchange between the constituents of the reaction as well with the system environment which may be a designed vessels which are often laboratory glassware. Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more smaller molecules, or rearrangement of atoms within or across molecules. Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions.
A chemical reaction can be symbolically depicted through a chemical equation. While in a non-nuclear chemical reaction the number and kind of atoms on both sides of the equation are equal, for a nuclear reaction this holds true only for the nuclear particles viz. protons and neutrons.[43]
The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is called its mechanism. A chemical reaction can be envisioned to take place in a number of steps, each of which may have a different speed. Many reaction intermediates with variable stability can thus be envisaged during the course of a reaction. Reaction mechanisms are proposed to explain the kinetics and the relative product mix of a reaction. Many physical chemists specialize in exploring and proposing the mechanisms of various chemical reactions. Several empirical rules, like the Woodward-Hoffmann rules often come handy while proposing a mechanism for a chemical reaction.
According to the IUPAC gold book a chemical reaction is a process that results in the interconversion of chemical species".[44] Accordingly, a chemical reaction may be an elementary reaction or a stepwise reaction. An additional caveat is made, in that this definition includes cases where the interconversion of conformers is experimentally observable. Such detectable chemical reactions normally involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use the term also for changes involving single molecular entities (i.e. 'microscopic chemical events').

Equilibrium

Although the concept of equilibrium is widely used across sciences, in the context of chemistry, it arises whenever a number of different states of the chemical composition are possible. For example, in a mixture of several chemical compounds that can react with one another, or when a substance can be present in more than one kind of phase. A system of chemical substances at equilibrium even though having an unchanging composition is most often not static; molecules of the substances continue to react with one another thus giving rise to a dynamic equilibrium. Thus the concept describes the state in which the parameters such as chemical composition remain unchanged over time. Chemicals present in biological systems are invariably not at equilibrium; rather they are far from equilibrium.

Energy

In the context of chemistry, energy is an attribute of a substance as a consequence of its atomic, molecular or aggregate structure. Since a chemical transformation is accompanied by a change in one or more of these kinds of structure, it is invariably accompanied by an increase or decrease of energy of the substances involved. Some energy is transferred between the surroundings and the reactants of the reaction in the form of heat or light; thus the products of a reaction may have more or less energy than the reactants. A reaction is said to be exergonic if the final state is lower on the energy scale than the initial state; in the case of endergonic reactions the situation is the reverse. A reaction is said to be exothermic if the reaction releases heat to the surroundings; in the case of endothermic reactions, the reaction absorbs heat from the surroundings.
Chemical reactions are invariably not possible unless the reactants surmount an energy barrier known as the activation energy. The speed of a chemical reaction (at given temperature T) is related to the activation energy E, by the Boltzmann's population factor e E / kT - that is the probability of molecule to have energy greater than or equal to E at the given temperature T. This exponential dependence of a reaction rate on temperature is known as the Arrhenius equation. The activation energy necessary for a chemical reaction can be in the form of heat, light, electricity or mechanical force in the form of ultrasound.[45]
A related concept free energy, which also incorporates entropy considerations, is a very useful means for predicting the feasibility of a reaction and determining the state of equilibrium of a chemical reaction, in chemical thermodynamics. A reaction is feasible only if the total change in the Gibbs free energy is negative,  \Delta G \le 0 \,; if it is equal to zero the chemical reaction is said to be at equilibrium.
There exist only limited possible states of energy for electrons, atoms and molecules. These are determined by the rules of quantum mechanics, which require quantization of energy of a bound system. The atoms/molecules in a higher energy state are said to be excited. The molecules/atoms of substance in an excited energy state are often much more reactive; that is, more amenable to chemical reactions.
The phase of a substance is invariably determined by its energy and the energy of its surroundings. When the intermolecular forces of a substance are such that the energy of the surroundings is not sufficient to overcome them, it occurs in a more ordered phase like liquid or solid as is the case with water (H2O); a liquid at room temperature because its molecules are bound by hydrogen bonds.[46] Whereas hydrogen sulfide (H2S) is a gas at room temperature and standard pressure, as its molecules are bound by weaker dipole-dipole interactions.
The transfer of energy from one chemical substance to another depends on the size of energy quanta emitted from one substance. However, heat energy is often transferred more easily from almost any substance to another because the phonons responsible for vibrational and rotational energy levels in a substance have much less energy than photons invoked for the electronic energy transfer. Thus, because vibrational and rotational energy levels are more closely spaced than electronic energy levels, heat is more easily transferred between substances relative to light or other forms of electronic energy. For example, ultraviolet electromagnetic radiation is not transferred with as much efficacy from one substance to another as thermal or electrical energy.
The existence of characteristic energy levels for different chemical substances is useful for their identification by the analysis of spectral lines. Different kinds of spectra are often used in chemical spectroscopy, e.g. IR, microwave, NMR, ESR, etc. Spectroscopy is also used to identify the composition of remote objects - like stars and distant galaxies - by analyzing their radiation spectra.
Emission spectrum of iron
The term chemical energy is often used to indicate the potential of a chemical substance to undergo a transformation through a chemical reaction or to transform other chemical substances.

Chemical laws

Chemical reactions are governed by certain laws, which have become fundamental concepts in chemistry. Some of them are:

Subdisciplines

Chemistry is typically divided into several major sub-disciplines. There are also several main cross-disciplinary and more specialized fields of chemistry.[47]
  • Analytical chemistry is the analysis of material samples to gain an understanding of their chemical composition and structure. Analytical chemistry incorporates standardized experimental methods in chemistry. These methods may be used in all subdisciplines of chemistry, excluding purely theoretical chemistry.
  • Inorganic chemistry is the study of the properties and reactions of inorganic compounds. The distinction between organic and inorganic disciplines is not absolute and there is much overlap, most importantly in the sub-discipline of organometallic chemistry.
  • Materials chemistry is the preparation, characterization, and understanding of substances with a useful function. The field is a new breadth of study in graduate programs, and it integrates elements from all classical areas of chemistry with a focus on fundamental issues that are unique to materials. Primary systems of study include the chemistry of condensed phases (solids, liquids, polymers) and interfaces between different phases.
  • Neurochemistry is the study of neurochemicals; including transmitters, peptides, proteins, lipids, sugars, and nucleic acids; their interactions, and the roles they play in forming, maintaining, and modifying the nervous system.
Other fields include agrochemistry, astrochemistry (and cosmochemistry), atmospheric chemistry, chemical engineering, chemical biology, chemo-informatics, electrochemistry, environmental chemistry, femtochemistry, flavor chemistry, flow chemistry, geochemistry, green chemistry, histochemistry, history of chemistry, hydrogenation chemistry, immunochemistry, marine chemistry, materials science, mathematical chemistry, mechanochemistry, medicinal chemistry, molecular biology, molecular mechanics, nanotechnology, natural product chemistry, oenology, organometallic chemistry, petrochemistry, pharmacology, photochemistry, physical organic chemistry, phytochemistry, polymer chemistry, radiochemistry, solid-state chemistry, sonochemistry, supramolecular chemistry, surface chemistry, synthetic chemistry, thermochemistry, and many others.

Chemical industry

The chemical industry represents an important economic activity. The global top 50 chemical producers in 2004 had sales of 587 billion US dollars with a profit margin of 8.1% and research and development spending of 2.1% of total chemical sales.




From Wikipedia