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 flash point of a volatile material is the lowest temperature at which vapours of the material will ignite, when given an ignition source. The flash point is sometimes confused with the autoignition temperature, the temperature that results in spontaneous autoignition; the fire point is the lowest temperature at which vapors of the material will keep burning after the ignition source is removed. The fire point is higher than the flash point, because at the flash point more vapor may not be produced enough to sustain combustion. Neither flash point nor fire point depends directly on the ignition source temperature, but ignition source temperature is far higher than either the flash or fire point; the flash point is a descriptive characteristic, used to distinguish between flammable fuels, such as petrol, combustible fuels, such as diesel. It is used to characterize the fire hazards of fuels. Fuels which have a flash point less than 37.8 °C are called flammable, whereas fuels having a flash point above that temperature are called combustible.
All liquids have a specific vapor pressure, a function of that liquid's temperature and is subject to Boyle's Law. As temperature increases, vapor pressure increases; as vapor pressure increases, the concentration of vapor of a flammable or combustible liquid in the air increases. Hence, temperature determines the concentration of vapor of the flammable liquid in the air. A certain concentration of a flammable or combustible vapor is necessary to sustain combustion in air, the lower flammable limit, that concentration is different and is specific to each flammable or combustible liquid; the flash point is the lowest temperature at which there will be enough flammable vapor to induce ignition when an ignition source is applied There are two basic types of flash point measurement: open cup and closed cup. In open cup devices, the sample is contained in an open cup, heated and, at intervals, a flame brought over the surface; the measured flash point will vary with the height of the flame above the liquid surface and, at sufficient height, the measured flash point temperature will coincide with the fire point.
The best-known example is the Cleveland open cup. There are two types of closed cup testers: non-equilibrial, such as Pensky-Martens, where the vapours above the liquid are not in temperature equilibrium with the liquid, equilibrial, such as Small Scale, where the vapours are deemed to be in temperature equilibrium with the liquid. In both these types, the cups are sealed with a lid through which the ignition source can be introduced. Closed cup testers give lower values for the flash point than open cup and are a better approximation to the temperature at which the vapour pressure reaches the lower flammable limit; the flash point is an empirical measurement rather than a fundamental physical parameter. The measured value will vary with equipment and test protocol variations, including temperature ramp rate, time allowed for the sample to equilibrate, sample volume and whether the sample is stirred. Methods for determining the flash point of a liquid are specified in many standards. For example, testing by the Pensky-Martens closed cup method is detailed in ASTM D93, IP34, ISO 2719, DIN 51758, JIS K2265 and AFNOR M07-019.
Determination of flash point by the Small Scale closed cup method is detailed in ASTM D3828 and D3278, EN ISO 3679 and 3680, IP 523 and 524. CEN/TR 15138 Guide to Flash Point Testing and ISO TR 29662 Guidance for Flash Point Testing cover the key aspects of flash point testing. Gasoline is a fuel used in a spark-ignition engine; the fuel is mixed with air within its flammable limits and heated by compression and subject to Boyle's Law above its flash point ignited by the spark plug. To ignite, the fuel must have a low flash point, but in order to avoid preignition caused by residual heat in a hot combustion chamber, the fuel must have a high autoignition temperature. Diesel fuel flash points vary between 52 and 96 °C. Diesel is suitable for use in a compression-ignition engine. Air is compressed until it has been heated above the autoignition temperature of the fuel, injected as a high-pressure spray, keeping the fuel–air mix within flammable limits. In a diesel-fueled engine, there is no ignition source.
Diesel fuel must have a high flash point and a low autoignition temperature. Jet fuel flash points vary with the composition of the fuel. Both Jet A and Jet A-1 have flash points between 38 and 66 °C, close to that of off-the-shelf kerosene, yet both Jet B and JP-4 have flash points between −23 and −1 °C. Flash points of substances are measured according to standard test methods described and defined in a 1938 publication by T. L. Ainsley of South Shields entitled "Sea Transport of Petroleum"; the test methodology defines the apparatus required to carry out the measurement, key test parameters, the procedure for the operator or automated apparatus to follow, the precision of the test method. Standard test methods are written and controlled by a number of national and international committees and organizations; the three main bodies are the CEN / ISO Joint Working Group on Flash Point, ASTM D02.8B Flammability Section and the Energy Institute's TMS SC-B-4 Flammability Panel. Autoignition temperature Fire point Safety data sheet
A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different elements as members of its ring. Heterocyclic chemistry is the branch of organic chemistry dealing with the synthesis and applications of these heterocycles. Examples of heterocyclic compounds include all of the nucleic acids, the majority of drugs, most biomass, many natural and synthetic dyes. Although heterocyclic chemical compounds may be inorganic compounds or organic compounds, most contain at least one carbon. While atoms that are neither carbon nor hydrogen are referred to in organic chemistry as heteroatoms, this is in comparison to the all-carbon backbone, but this does not prevent a compound such as borazine from being labelled "heterocyclic". IUPAC recommends the Hantzsch-Widman nomenclature for naming heterocyclic compounds. Heterocyclic compounds can be usefully classified based on their electronic structure; the saturated heterocycles behave like the acyclic derivatives. Thus and tetrahydrofuran are conventional amines and ethers, with modified steric profiles.
Therefore, the study of heterocyclic chemistry focuses on unsaturated derivatives, the preponderance of work and applications involves unstrained 5- and 6-membered rings. Included are pyridine, thiophene and furan. Another large class of heterocycles are fused to benzene rings, which for pyridine, thiophene and furan are quinoline, benzothiophene and benzofuran, respectively. Fusion of two benzene rings gives rise to a third large family of compounds the acridine, dibenzothiophene and dibenzofuran; the unsaturated rings can be classified according to the participation of the heteroatom in the conjugated system, pi system. Heterocycles with three atoms in the ring are more reactive because of ring strain; those containing one heteroatom are, in general, stable. Those with two heteroatoms are more to occur as reactive intermediates. Common 3-membered heterocycles with one heteroatom are: Those with two heteroatoms include: Compounds with one heteroatom: Compounds with two heteroatoms: With heterocycles containing five atoms, the unsaturated compounds are more stable because of aromaticity.
The 5-membered ring compounds containing two heteroatoms, at least one of, nitrogen, are collectively called the azoles. Thiazoles and isothiazoles contain a nitrogen atom in the ring. Dithiolanes have two sulfur atoms. A large group of 5-membered ring compounds with three heteroatoms exists. One example is dithiazoles that contain a nitrogen atom. Six-membered rings with a single heteroatom: With two heteroatoms: With three heteroatoms: With four heteroatoms: With five heteroatoms: The hypothetical compound with six nitrogen heteroatoms would be hexazine. With 7-membered rings, the heteroatom must be able to provide an empty pi orbital for "normal" aromatic stabilization to be available. Compounds with one heteroatom include: Those with two heteroatoms include: Names in italics are retained by IUPAC and they do not follow the Hantzsch-Widman nomenclature Heterocyclic rings systems that are formally derived by fusion with other rings, either carbocyclic or heterocyclic, have a variety of common and systematic names.
For example, with the benzo-fused unsaturated nitrogen heterocycles, pyrrole provides indole or isoindole depending on the orientation. The pyridine analog is isoquinoline. For azepine, benzazepine is the preferred name; the compounds with two benzene rings fused to the central heterocycle are carbazole and dibenzoazepine. Thienothiophene are the fusion of two thiophene rings. Phosphaphenalenes are a tricyclic phosphorus-containing heterocyclic system derived from the carbocycle phenalene; the history of heterocyclic chemistry began in the 1800s, in step with the development of organic chemistry. Some noteworthy developments: 1818: Brugnatelli isolates alloxan from uric acid 1832: Dobereiner produces furfural by treating starch with sulfuric acid 1834: Runge obtains pyrrole by dry distillation of bones 1906: Friedlander synthesizes indigo dye, allowing synthetic chemistry to displace a large agricultural industry 1936: Treibs isolates chlorophyl derivatives from crude oil, explaining the biological origin of petroleum.
1951: Chargaff's rules are described, highlighting the role of heterocyclic compounds in the genetic code. Heterocyclic compounds are pervasive in many areas of technology. Many drugs are heterocyclic compounds. Hantzsch-Widman nomenclature, IUPAC Heterocyclic amines in cooked meat, US CDC List of known and probable carcinogens, American Cancer Society List of known carcinogens by the State of California, Proposition 65
Safety data sheet
A safety data sheet, material safety data sheet, or product safety data sheet is a document that lists information relating to occupational safety and health for the use of various substances and products. SDSs are a used system for cataloging information on chemicals, chemical compounds, chemical mixtures. SDS information may include instructions for the safe use and potential hazards associated with a particular material or product, along with spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements. A SDS for a substance is not intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. There is a duty to properly label substances on the basis of physico-chemical, health or environmental risk. Labels can include hazard symbols such as the European Union standard symbols; the same product can have different formulations in different countries. The formulation and hazard of a product using a generic name may vary between manufacturers in the same country.
The Globally Harmonized System of Classification and Labelling of Chemicals contains a standard specification for safety data sheets. The SDS follows a 16 section format, internationally agreed and for substances the SDS should be followed with an Annex which contains the exposure scenarios of this particular substance; the 16 sections are: SECTION 1: Identification of the substance/mixture and of the company/undertaking 1.1. Product identifier 1.2. Relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4. Emergency telephone number SECTION 2: Hazards identification 2.1. Classification of the substance or mixture 2.2. Label elements 2.3. Other hazards SECTION 3: Composition/information on ingredients 3.1. Substances 3.2. Mixtures SECTION 4: First aid measures 4.1. Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3. Indication of any immediate medical attention and special treatment needed SECTION 5: Firefighting measures 5.1.
Extinguishing media 5.2. Special hazards arising from the substance or mixture 5.3. Advice for firefighters SECTION 6: Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2. Environmental precautions 6.3. Methods and material for containment and cleaning up 6.4. Reference to other sections SECTION 7: Handling and storage 7.1. Precautions for safe handling 7.2. Conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION 8: Exposure controls/personal protection 8.1. Control parameters 8.2. Exposure controls SECTION 9: Physical and chemical properties 9.1. Information on basic physical and chemical properties 9.2. Other information SECTION 10: Stability and reactivity 10.1. Reactivity 10.2. Chemical stability 10.3. Possibility of hazardous reactions 10.4. Conditions to avoid 10.5. Incompatible materials 10.6. Hazardous decomposition products SECTION 11: Toxicological information 11.1. Information on toxicological effects SECTION 12: Ecological information 12.1.
Toxicity 12.2. Persistence and degradability 12.3. Bioaccumulative potential 12.4. Mobility in soil 12.5. Results of PBT and vPvB assessment 12.6. Other adverse effects SECTION 13: Disposal considerations 13.1. Waste treatment methods SECTION 14: Transport information 14.1. UN number 14.2. UN proper shipping name 14.3. Transport hazard class 14.4. Packing group 14.5. Environmental hazards 14.6. Special precautions for user 14.7. Transport in bulk according to Annex II of MARPOL73/78 and the IBC Code SECTION 15: Regulatory information 15.1. Safety and environmental regulations/legislation specific for the substance or mixture 15.2. Chemical safety assessment SECTION 16: Other information 16.2. Date of the latest revision of the SDS In Canada, the program known as the Workplace Hazardous Materials Information System establishes the requirements for SDSs in workplaces and is administered federally by Health Canada under the Hazardous Products Act, Part II, the Controlled Products Regulations. Safety data sheets have been made an integral part of the system of Regulation No 1907/2006.
The original requirements of REACH for SDSs have been further adapted to take into account the rules for safety data sheets of the Global Harmonised System and the implementation of other elements of the GHS into EU legislation that were introduced by Regulation No 1272/2008 via an update to Annex II of REACH. The SDS must be supplied in an official language of the Member State where the substance or mixture is placed on the market, unless the Member State concerned provide otherwise; the European Chemicals Agency has published a guidance document on the compilation of safety data sheets. The German Federal Water Management Act requires that substances be evaluated for negative influence on the physical, chemical or biological characteristics of water; these are classified into numeric water hazard classes. WGK nwg: Non-water polluting substance WGK 1: Slightly water polluting substance WGK 2: Water polluting substance WGK 3: Highly water polluting substance This section contributes to a better understanding of the regulations governing SDS within the South African framework.
As regulations may change, it is the responsibility of the reader to verify the validity of the regulations mentioned in text. As globalisation increased and countries engaged in cross-border trade, the quantity of hazardous material crossing international borders a
Alkaloids are a class of occurring organic compounds that contain basic nitrogen atoms. This group includes some related compounds with neutral and weakly acidic properties; some synthetic compounds of similar structure may be termed alkaloids. In addition to carbon and nitrogen, alkaloids may contain oxygen, sulfur and, more other elements such as chlorine and phosphorus. Alkaloids are produced by a large variety of organisms including bacteria, fungi and animals, they can be purified from crude extracts of these organisms by acid-base extraction. Alkaloids have a wide range of pharmacological activities including antimalarial, anticancer, vasodilatory, analgesic and antihyperglycemic activities. Many have found use as starting points for drug discovery. Other alkaloids possess psychotropic and stimulant activities, have been used in entheogenic rituals or as recreational drugs. Alkaloids can be toxic too. Although alkaloids act on a diversity of metabolic systems in humans and other animals, they uniformly evoke a bitter taste.
The boundary between alkaloids and other nitrogen-containing natural compounds is not clear-cut. Compounds like amino acid peptides, nucleotides, nucleic acid and antibiotics are not called alkaloids. Natural compounds containing nitrogen in the exocyclic position are classified as amines rather than as alkaloids; some authors, consider alkaloids a special case of amines. The name "alkaloids" was introduced in 1819 by the German chemist Carl Friedrich Wilhelm Meißner, is derived from late Latin root alkali and the suffix -οειδής – "like". However, the term came into wide use only after the publication of a review article by Oscar Jacobsen in the chemical dictionary of Albert Ladenburg in the 1880s. There is no unique method of naming alkaloids. Many individual names are formed by adding the suffix "ine" to the genus name. For example, atropine is isolated from the plant Atropa belladonna. Where several alkaloids are extracted from one plant their names are distinguished by variations in the suffix: "idine", "anine", "aline", "inine" etc.
There are at least 86 alkaloids whose names contain the root "vin" because they are extracted from vinca plants such as Vinca rosea. Alkaloid-containing plants have been used by humans since ancient times for therapeutic and recreational purposes. For example, medicinal plants have been known in the Mesopotamia at least around 2000 BC; the Odyssey of Homer referred to a gift given to Helen by the Egyptian queen, a drug bringing oblivion. It is believed. A Chinese book on houseplants written in 1st–3rd centuries BC mentioned a medical use of Ephedra and opium poppies. Coca leaves have been used by South American Indians since ancient times. Extracts from plants containing toxic alkaloids, such as aconitine and tubocurarine, were used since antiquity for poisoning arrows. Studies of alkaloids began in the 19th century. In 1804, the German chemist Friedrich Sertürner isolated from opium a "soporific principle", which he called "morphium" in honor of Morpheus, the Greek god of dreams; the term "morphine", used in English and French, was given by the French physicist Joseph Louis Gay-Lussac.
A significant contribution to the chemistry of alkaloids in the early years of its development was made by the French researchers Pierre Joseph Pelletier and Joseph Bienaimé Caventou, who discovered quinine and strychnine. Several other alkaloids were discovered around that time, including xanthine, caffeine, nicotine, colchicine and cocaine; the development of the chemistry of alkaloids was accelerated by the emergence of spectroscopic and chromatographic methods in the 20th century, so that by 2008 more than 12,000 alkaloids had been identified. The first complete synthesis of an alkaloid was achieved in 1886 by the German chemist Albert Ladenburg, he produced coniine by reacting 2-methylpyridine with acetaldehyde and reducing the resulting 2-propenyl pyridine with sodium. Compared with most other classes of natural compounds, alkaloids are characterized by a great structural diversity. There is no uniform classification; when knowledge of chemical structures was lacking, botanical classification of the source plants was relied on.
This classification is now considered obsolete. More recent classifications are based on similarity of the carbon biochemical precursor. However, they require compromises in borderline cases. Alkaloids are divided into the following major groups: "True alkaloids" contain nitrogen in the heterocycle and originate from amino acids, their characteristic examples are atropine and morphine. This group a
Arthur Rudolf Hantzsch
Arthur Rudolf Hantzsch was a German chemist. Hantzsch studied chemistry in Dresden and graduated at the University of Würzburg under Johannes Wislicenus; as a professor, he taught at the Universities of Würzburg und Leipzig. The Hantzsch pyridine synthesis, a multi-component organic reaction, is named after him, as is the Hantzsch pyrrole synthesis, his surname is pronounced /Haːntʃ/
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