The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
In chemistry, an alcohol is any organic compound in which the hydroxyl functional group is bound to a carbon. The term alcohol referred to the primary alcohol ethanol, used as a drug and is the main alcohol present in alcoholic beverages. An important class of alcohols, of which methanol and ethanol are the simplest members, includes all compounds for which the general formula is CnH2n+1OH, it is these simple monoalcohols. The suffix -ol appears in the IUPAC chemical name of all substances where the hydroxyl group is the functional group with the highest priority; when a higher priority group is present in the compound, the prefix hydroxy- is used in its IUPAC name. The suffix -ol in non-IUPAC names typically indicates that the substance is an alcohol. However, many substances that contain hydroxyl functional groups have names which include neither the suffix -ol, nor the prefix hydroxy-. Alcohol distillation originated in India. During 2000 BCE, people of India used. Alcohol distillation was known to Islamic chemists as early as the eighth century.
The Arab chemist, al-Kindi, unambiguously described the distillation of wine in a treatise titled as "The Book of the chemistry of Perfume and Distillations". The Persian physician, alchemist and philosopher Rhazes is credited with the discovery of ethanol; the word "alcohol" is from a powder used as an eyeliner. Al- is the Arabic definite article, equivalent to the in English. Alcohol was used for the fine powder produced by the sublimation of the natural mineral stibnite to form antimony trisulfide Sb2S3, it was considered to be the essence or "spirit" of this mineral. It was used as an antiseptic and cosmetic; the meaning of alcohol was extended to distilled substances in general, narrowed to ethanol, when "spirits" was a synonym for hard liquor. Bartholomew Traheron, in his 1543 translation of John of Vigo, introduces the word as a term used by "barbarous" authors for "fine powder." Vigo wrote: "the barbarous auctours use alcohol, or alcofoll, for moost fine poudre."The 1657 Lexicon Chymicum, by William Johnson glosses the word as "antimonium sive stibium."
By extension, the word came to refer to any fluid obtained by distillation, including "alcohol of wine," the distilled essence of wine. Libavius in Alchymia refers to "vini alcohol vel vinum alcalisatum". Johnson glosses alcohol vini as "quando omnis superfluitas vini a vino separatur, ita ut accensum ardeat donec totum consumatur, nihilque fæcum aut phlegmatis in fundo remaneat." The word's meaning became restricted to "spirit of wine" in the 18th century and was extended to the class of substances so-called as "alcohols" in modern chemistry after 1850. The term ethanol was invented 1892, combining the word ethane with the "-ol" ending of "alcohol". IUPAC nomenclature is used in scientific publications and where precise identification of the substance is important in cases where the relative complexity of the molecule does not make such a systematic name unwieldy. In naming simple alcohols, the name of the alkane chain loses the terminal e and adds the suffix -ol, e.g. as in "ethanol" from the alkane chain name "ethane".
When necessary, the position of the hydroxyl group is indicated by a number between the alkane name and the -ol: propan-1-ol for CH3CH2CH2OH, propan-2-ol for CH3CHCH3. If a higher priority group is present the prefix hydroxy-is used, e.g. as in 1-hydroxy-2-propanone. In cases where the OH functional group is bonded to an sp2 carbon on an aromatic ring the molecule is known as a phenol, is named using the IUPAC rules for naming phenols. In other less formal contexts, an alcohol is called with the name of the corresponding alkyl group followed by the word "alcohol", e.g. methyl alcohol, ethyl alcohol. Propyl alcohol may be n-propyl alcohol or isopropyl alcohol, depending on whether the hydroxyl group is bonded to the end or middle carbon on the straight propane chain; as described under systematic naming, if another group on the molecule takes priority, the alcohol moiety is indicated using the "hydroxy-" prefix. Alcohols are classified into primary and tertiary, based upon the number of carbon atoms connected to the carbon atom that bears the hydroxyl functional group.
The primary alcohols have general formulas RCH2OH. The simplest primary alcohol is methanol, for which R=H, the next is ethanol, for which R=CH3, the methyl group. Secondary alcohols are those of the form RR'CHOH, the simplest of, 2-propanol. For the tertiary alcohols the general form is RR'R"COH; the simplest example is tert-butanol, for which each of R, R', R" is CH3. In these shorthands, R, R', R" represent substituents, alkyl or other attached organic groups. In archaic nomenclature, alcohols can be named as derivatives of methanol using "-carbinol" as the ending. For instance, 3COH can be named trimethylcarbinol. Alcohols have a long history of myriad uses. For simple mono-alcohols, the focus on this article, the following are most important industrial alcohols: methanol for the production of formaldehyde and as a fuel additive ethanol for alcoholic beverages, fuel additive, solvent 1-propanol, 1-butanol, isobutyl alcohol for use as a solvent a
Organic chemistry is a subdiscipline of chemistry that studies the structure and reactions of organic compounds, which contain carbon in covalent bonding. Study of structure determines their chemical formula. Study of properties includes physical and chemical properties, evaluation of chemical reactivity to understand their behavior; the study of organic reactions includes the chemical synthesis of natural products and polymers, study of individual organic molecules in the laboratory and via theoretical study. The range of chemicals studied in organic chemistry includes hydrocarbons as well as compounds based on carbon, but containing other elements oxygen, sulfur and the halogens. Organometallic chemistry is the study of compounds containing carbon–metal bonds. In addition, contemporary research focuses on organic chemistry involving other organometallics including the lanthanides, but the transition metals zinc, palladium, cobalt and chromium. Organic compounds constitute the majority of known chemicals.
The bonding patterns of carbon, with its valence of four—formal single and triple bonds, plus structures with delocalized electrons—make the array of organic compounds structurally diverse, their range of applications enormous. They form the basis of, or are constituents of, many commercial products including pharmaceuticals; the study of organic chemistry overlaps organometallic chemistry and biochemistry, but with medicinal chemistry, polymer chemistry, materials science. Before the nineteenth century, chemists believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds. According to the concept of vitalism, organic matter was endowed with a "vital force". During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various alkalis, he separated the different acids. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats, producing new compounds, without "vital force".
In 1828 Friedrich Wöhler produced the organic chemical urea, a constituent of urine, from inorganic starting materials, in what is now called the Wöhler synthesis. Although Wöhler himself was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological starting materials; the event is now accepted as indeed disproving the doctrine of vitalism. In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkin's mauve, his discovery, made known through its financial success increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper. Both researchers suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions.
The era of the pharmaceutical industry began in the last decade of the 19th century when the manufacturing of acetylsalicylic acid—more referred to as aspirin—in Germany was started by Bayer. By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine, as the first effective medicinal treatment of syphilis, thereby initiated the medical practice of chemotherapy. Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies, his laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums. Early examples of organic reactions and applications were found because of a combination of luck and preparation for unexpected observations; the latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative; the production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer.
In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals. In the early part of the 20th century and enzymes were shown to be large organic molecules, petroleum was shown to be of biological origin; the multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to terpineol. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12; the discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into different types of compounds by various chemical processes led to organic reactions enabling a broad range of
Acid dissociation constant
An acid dissociation constant, Ka, is a quantitative measure of the strength of an acid in solution. It is the equilibrium constant for a chemical reaction known as dissociation in the context of acid–base reactions. K a =; the chemical species HA, A−, H+ are said to be in equilibrium when their concentrations do not change with the passing of time, because both forward and backward reactions are occurring at the same fast rate. The chemical equation for acid dissociation can be written symbolically as: HA ↽ − − ⇀ A − + H + where HA is a generic acid that dissociates into A−, the conjugate base of the acid and a hydrogen ion, H+, it is implicit in this definition that the quotient of activity coefficients, Γ, Γ = γ A − γ H + γ A H is a constant that can be ignored in a given set of experimental conditions. For many practical purposes it is more convenient to discuss the logarithmic constant, pKa p K a = − log 10 The more positive the value of pKa, the smaller the extent of dissociation at any given pH —that is, the weaker the acid.
A weak acid has a pKa value in the approximate range −2 to 12 in water. For a buffer solution consisting of a weak acid and its conjugate base, pKa can be expressed as: p K a = pH − log 10 The pKa for a weak monoprotic acid is conveniently determined by potentiometric titration with a strong base to the equivalence point and taking the pH value measured at one-half this volume as being equal to pKa; that is because at this half equivalence point, the number of moles of strong base added is one-half the number of moles of weak acid present, while the concentrations of the conjugate base and the remaining weak acid are the same. Acids with a pKa value of less than about −2 are said to be strong acids. In water, the dissociation of a strong acid in dilute solutions is complete such that the final concentration of the undissociated acid final is low. Consider a strong monoprotic acid, such as HCl; because of their 1:1 ratio, the final concentration of the conjugate base, final, is taken to be equal to the concentration of the hydronium ion, which can be directly measured by a pH meter.
For strong monoprotic acids like HCl, final and are both nearly equal to the initial concentration of initial placed into solution. With conventional acid-base titration methods it is difficult to measure the pH of a strong acid solution and, hence, to determine the or final, with a sufficient number of significant figures to and compute the low values encountered for final, which can be as low as 10-9 mol per liter for some strong acids. Furthermore, if 100% dissociation is assumed, final is zero and the fraction within parenthesis in the equation above becomes undefined; because the second expression on the right-hand side of the above equation is therefore indeterminable by conventional titration methods, the entire equation is not as useful a means of experimentally measuring pKa for strong acids as it is for weak acids. However, pKa and/or Ka values for strong acids can be estimated by theoretical means, such as computing gas phase dissociation constants and using Gibbs free energies of solvation for the molecular anions.
It is possible to use spectroscopy in some cases to determine the ratio of the concentrations of the conjugate base produced and the undissociated acid. For example, the Raman spectra of dilute nitric acid solutions contain signals of the nitrate ion and as the solutions become more concentrated signals of undissociated nitric acid molecules emerge; the acid dissociation constant for an acid is a direct consequence of the underlying thermodynamics of the dissociation reaction. The value of the pKa changes with temperature and can be understood qualitatively based on Le Châtelier's principle: when the reaction is endothermic, Ka increases and pKa decreases with
Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules; the original SMILES specification was initiated in the 1980s. It has since been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other'linear' notations include the Wiswesser Line Notation, ROSDAL and SLN. In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol. Algorithms have been developed to generate the same SMILES string for a given molecule; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.
The public domain consists of all the creative works to which no exclusive intellectual property rights apply. Those rights may have been forfeited, expressly waived, or may be inapplicable; the works of William Shakespeare and Beethoven, most early silent films, are in the public domain either by virtue of their having been created before copyright existed, or by their copyright term having expired. Some works are not covered by copyright, are therefore in the public domain—among them the formulae of Newtonian physics, cooking recipes, all computer software created prior to 1974. Other works are dedicated by their authors to the public domain; the term public domain is not applied to situations where the creator of a work retains residual rights, in which case use of the work is referred to as "under license" or "with permission". As rights vary by country and jurisdiction, a work may be subject to rights in one country and be in the public domain in another; some rights depend on registrations on a country-by-country basis, the absence of registration in a particular country, if required, gives rise to public-domain status for a work in that country.
The term public domain may be interchangeably used with other imprecise or undefined terms such as the "public sphere" or "commons", including concepts such as the "commons of the mind", the "intellectual commons", the "information commons". Although the term "domain" did not come into use until the mid-18th century, the concept "can be traced back to the ancient Roman Law, as a preset system included in the property right system." The Romans had a large proprietary rights system where they defined "many things that cannot be owned" as res nullius, res communes, res publicae and res universitatis. The term res nullius was defined as things not yet appropriated; the term res communes was defined as "things that could be enjoyed by mankind, such as air and ocean." The term res publicae referred to things that were shared by all citizens, the term res universitatis meant things that were owned by the municipalities of Rome. When looking at it from a historical perspective, one could say the construction of the idea of "public domain" sprouted from the concepts of res communes, res publicae, res universitatis in early Roman law.
When the first early copyright law was first established in Britain with the Statute of Anne in 1710, public domain did not appear. However, similar concepts were developed by French jurists in the 18th century. Instead of "public domain", they used terms such as publici juris or propriété publique to describe works that were not covered by copyright law; the phrase "fall in the public domain" can be traced to mid-19th century France to describe the end of copyright term. The French poet Alfred de Vigny equated the expiration of copyright with a work falling "into the sink hole of public domain" and if the public domain receives any attention from intellectual property lawyers it is still treated as little more than that, left when intellectual property rights, such as copyright and trademarks, expire or are abandoned. In this historical context Paul Torremans describes copyright as a, "little coral reef of private right jutting up from the ocean of the public domain." Copyright law differs by country, the American legal scholar Pamela Samuelson has described the public domain as being "different sizes at different times in different countries".
Definitions of the boundaries of the public domain in relation to copyright, or intellectual property more regard the public domain as a negative space. According to James Boyle this definition underlines common usage of the term public domain and equates the public domain to public property and works in copyright to private property. However, the usage of the term public domain can be more granular, including for example uses of works in copyright permitted by copyright exceptions; such a definition regards work in copyright as private property subject to fair-use rights and limitation on ownership. A conceptual definition comes from Lange, who focused on what the public domain should be: "it should be a place of sanctuary for individual creative expression, a sanctuary conferring affirmative protection against the forces of private appropriation that threatened such expression". Patterson and Lindberg described the public domain not as a "territory", but rather as a concept: "here are certain materials – the air we breathe, rain, life, thoughts, ideas, numbers – not subject to private ownership.
The materials that compose our cultural heritage must be free for all living to use no less than matter necessary for biological survival." The term public domain may be interchangeably used with other imprecise or undefined terms such as the "public sphere" or "commons", including concepts such as the "commons of the mind", the "intellectual commons", the "information commons". A public-domain book is a book with no copyright, a book, created without a license, or a book where its copyrights expired or have been forfeited. In most countries the term of protection of copyright lasts until January first, 70 years after the death of the latest living author; the longest copyright term is in Mexico, which has life plus 100 years for all deaths since July 1928. A notable exception is the United States, where every book and tale published prior to 1924 is in the public domain.
European Chemicals Agency
The European Chemicals Agency is an agency of the European Union which manages the technical and administrative aspects of the implementation of the European Union regulation called Registration, Evaluation and Restriction of Chemicals. ECHA is the driving force among regulatory authorities in implementing the EU's chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and addresses chemicals of concern, it is located in Finland. The agency headed by Executive Director Bjorn Hansen, started working on 1 June 2007; the REACH Regulation requires companies to provide information on the hazards and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most used substances have been registered; the information is technical but gives detail on the impact of each chemical on people and the environment.
This gives European consumers the right to ask retailers whether the goods they buy contain dangerous substances. The Classification and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU; this worldwide system makes it easier for workers and consumers to know the effects of chemicals and how to use products safely because the labels on products are now the same throughout the world. Companies need to notify ECHA of the labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100 000 substances; the information is available on their website. Consumers can check chemicals in the products. Biocidal products include, for example, insect disinfectants used in hospitals; the Biocidal Products Regulation ensures that there is enough information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation; the law on Prior Informed Consent sets guidelines for the import of hazardous chemicals.
Through this mechanism, countries due to receive hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have serious effects on human health and the environment are identified as Substances of Very High Concern 1; these are substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment and do not break down. Other substances considered. Companies manufacturing or importing articles containing these substances in a concentration above 0,1% weight of the article, have legal obligations, they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy. Once a substance has been identified in the EU as being of high concern, it will be added to a list; this list is available on ECHA's website and shows consumers and industry which chemicals are identified as SVHCs.
Substances placed on the Candidate List can move to another list. This means that, after a given date, companies will not be allowed to place the substance on the market or to use it, unless they have been given prior authorisation to do so by ECHA. One of the main aims of this listing process is to phase out SVHCs where possible. In its 2018 substance evaluation progress report, ECHA said chemical companies failed to provide “important safety information” in nearly three quarters of cases checked that year. "The numbers show a similar picture to previous years" the report said. The agency noted that member states need to develop risk management measures to control unsafe commercial use of chemicals in 71% of the substances checked. Executive Director Bjorn Hansen called non-compliance with REACH a "worry". Industry group CEFIC acknowledged the problem; the European Environmental Bureau called for faster enforcement to minimise chemical exposure. European Chemicals Bureau Official website