1.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
2.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
3.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
4.
DrugBank
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The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a resource, DrugBank combines detailed drug data with comprehensive drug target information. Because of its scope, comprehensive referencing and unusually detailed data descriptions. As a result, links to DrugBank are maintained for nearly all drugs listed in Wikipedia, DrugBank is widely used by the drug industry, medicinal chemists, pharmacists, physicians, students and the general public. Its extensive drug and drug-target data has enabled the discovery and repurposing of a number of existing drugs to treat rare, the latest release of the database contains 8227 drug entries including 2003 FDA-approved small molecule drugs,221 FDA-approved biotech drugs,93 nutraceuticals and over 6000 experimental drugs. Additionally,4270 non-redundant protein sequences are linked to these drug entries, each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Four additional databases, HMDB, T3DB, SMPDB and FooDB are also part of a suite of metabolomic/cheminformatic databases. The first version of DrugBank was released in 2006 and this early release contained relatively modest information about 841 FDA-approved small molecule drugs and 113 biotech drugs. It also included information on 2133 drug targets, the second version of DrugBank was released in 2009. This greatly expanded and improved version of the database included 1344 approved small molecule drugs and 123 biotech drugs as well as 3037 unique drug targets. Version 2.0 also included, for the first time, withdrawn drugs and illicit drugs, version 3.0 was released in 2011. This version contained 1424 approved small molecule drugs and 132 biotech drugs as well as >4000 unique drug targets, version 3.0 also included drug transporter data, drug pathway data, drug pricing, patent and manufacturing data as well as data on >5000 experimental drugs. Version 4.0 was released in 2014 and this version included 1558 FDA-approved small molecule drugs,155 biotech drugs and 4200 unique drug targets. Version 4.0 also incorporated information on drug metabolites, drug taxonomy, drug spectra, drug binding constants. Table 1 provides a complete statistical summary of the history of DrugBank’s development. All data in DrugBank is non-proprietary or is derived from a non-proprietary source and it is freely accessible and available to anyone. In addition, nearly every item is fully traceable and explicitly referenced to the original source. DrugBank data is available through a web interface and downloads
5.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks 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 commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling 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, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is 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 export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and 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 officially identified in the EU as being of very 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 then move to another list
6.
IUPHAR/BPS
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The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology and the British Pharmacological Society and this replaces and expands upon the original 2009 IUPHAR Database. The information featured includes pharmacological data, target and gene nomenclature, overviews and commentaries on each target family are included, with links to key references. The Guide to PHARMACOLOGY was initially made available online in December 2011 with additional material released in July 2012 and its network of over 700 specialist advisors contribute expertise and data. The current PI and Grant holder of the GtoPdb project is Prof. Jamie A. Davies, the development and release of the first version of the GtoPdb in 2012 was described in an editorial published in the British Journal of Pharmacology entitled Guide to Pharmacology. org- an update. The IUPHAR-DB is no longer being developed and all the contained within this site is now available through the Guide to PHARMACOLOGY. A complete list of all the approved drugs included on the website is available via the ligand list. The Guide to PHARMACOLOGY is being expanded to include information on targets and ligands. Search features on the website include quick and advanced search options, other features include Hot topic news items and a recent receptor-ligand pairing list. A hard copy summary of the database is published as The Concise Guide to Pharmacology 2015/2016 as a series of papers as a bi-annual supplement to the British Journal of Pharmacology. The Guide to PHARMACOLOGY includes links to other relevant resources via target, many of these resources maintain reciprocal links with the relevant Guide to PHARMACOLOGY pages. As of November 2015 the Wellcome Trust is supporting a new project to develop the Guide to Immumopharmacology, the latter continues to be supported by the British Pharmacological Society
7.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
8.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
9.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in 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 modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a 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 generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally 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, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently 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, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
10.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
11.
Odor
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An odor or odour or fragrance is caused by one or more volatilized chemical compounds, generally at a very low concentration, that humans or other animals perceive by the sense of olfaction. Odors are also commonly called scents, which can refer to both pleasant and unpleasant odors, the terms fragrance and aroma are used primarily by the food and cosmetic industry to describe a pleasant odor, and are sometimes used to refer to perfumes, and to describe floral scent. In contrast, malodor, stench, reek, and stink are used specifically to describe unpleasant odor, the term smell is used for both pleasant and unpleasant odors. In the United Kingdom, odour refers to scents in general, the sense of smell gives rise to the perception of odors, mediated by the olfactory nerve. The olfactory receptor cells are present in the olfactory epithelium. There are millions of olfactory receptor neurons that act as sensory signaling cells, each neuron has cilia in direct contact with air. The olfactory nerve is considered the smell mediator, the axon connects the brain to the external air, odorous molecules act as a chemical stimulus. Molecules bind to receptor proteins extended from cilia, initiating an electric signal, thus, by using a chemical that binds to copper in the mouse nose, so that copper wasn’t available to the receptors, the authors showed that the mice couldnt detect the thiols. However, these also found that MOR244-3 lacks the specific metal ion binding site suggested by Suslick. When the signal reaches a threshold, the fires, sending a signal traveling along the axon to the olfactory bulb. Interpretation of the begins, relating the smell to past experiences. The olfactory bulb acts as a station connecting the nose to the olfactory cortex in the brain. Olfactory information is processed and projected through a pathway to the central nervous system. Odor sensation usually depends on the concentration available to the olfactory receptors, the olfactory system does not interpret a single compound, but instead the whole odorous mix, not necessarily corresponding to concentration or intensity of any single constituent. The widest range of odors consists of compounds, although some simple compounds not containing carbon, such as hydrogen sulfide. The perception of an effect is a two-step process. First, there is the part, the detection of stimuli by receptors in the nose. The stimuli are processed by the region of the brain which is responsible for olfaction
12.
Piperidine
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Piperidine is an organic compound with the molecular formula 5NH. This heterocyclic amine consists of a ring containing five methylene bridges. It is a liquid with an odor described as objectionable. The name comes from the genus name Piper, which is the Latin word for pepper, although, piperidine is a common organic compound, it is best known as a representative structure element within many pharmaceuticals and alkaloids. Piperidine was first reported in 1850 by the Scottish chemist Thomas Anderson and again, independently, in 1852 by the French chemist Auguste Cahours, both men obtained piperidine by reacting piperine with nitric acid. Piperidine itself has been obtained from black pepper, from Psilocaulon absimile, the piperidine structural motif is present in numerous natural alkaloids. These include piperine, which gives black pepper its spicy taste and this gave the compound its name. Piperidine prefers a chair conformation, similar to cyclohexane, unlike cyclohexane, piperidine has two distinguishable chair conformations, one with the N–H bond in an axial position, and the other in an equatorial position. After much controversy during the 1950s–1970s, the equatorial conformation was found to be stable by 0.72 kcal/mol in the gas phase. In nonpolar solvents, a range between 0.2 and 0.6 kcal/mol has been estimated, but in polar solvents the axial conformer may be more stable. In the case of N-methylpiperidine, the conformation is preferred by 3.16 kcal/mol. Piperidine is a widely used secondary amine and it is widely used to convert ketones to enamines. Enamines derived from piperidine can be used in the Stork enamine alkylation reaction, Piperidine can be converted to the chloramine C5H10NCl with calcium hypochlorite. The resulting chloramine undergoes dehydrohalogenation to afford the cyclic imine, 13C NMR,47.27.2,25.2 1H NMR,2.79,2.19,1.51 Piperidine is used as a solvent and as a base. A significant industrial application of piperidine is for the production of dipiperidinyl dithiuram tetrasulfide, Piperidine and its derivatives are ubiquitous building blocks in the synthesis of pharmaceuticals and fine chemicals. Piperidine is also used as a base for the deprotection of Fmoc-amino acids used in solid-phase peptide synthesis
13.
Density
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The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
14.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
15.
Boiling point
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The boiling point of a substance is the temperature at which the vapor pressure of the liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the environmental pressure. A liquid in a vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a boiling point than when that liquid is at atmospheric pressure. For a given pressure, different liquids boil at different temperatures, for example, water boils at 100 °C at sea level, but at 93.4 °C at 2,000 metres altitude. The normal boiling point of a liquid is the case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level,1 atmosphere. At that temperature, the pressure of the liquid becomes sufficient to overcome atmospheric pressure. The standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar, the heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation, evaporation is a surface phenomenon in which molecules located near the liquids edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, a saturated liquid contains as much thermal energy as it can without boiling. The saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase, the liquid can be said to be saturated with thermal energy. Any addition of energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed, similarly, a liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the pressure of the liquid equals the surrounding environmental pressure. Thus, the point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, at higher elevations, where the atmospheric pressure is much lower, the boiling point is also lower. The boiling point increases with increased pressure up to the critical point, the boiling point cannot be increased beyond the critical point. Likewise, the point decreases with decreasing pressure until the triple point is reached
16.
Aqueous solution
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An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending to the relevant chemical formula, for example, a solution of table salt, or sodium chloride, in water would be represented as Na+ + Cl−. The word aqueous means pertaining to, related to, similar to, as water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry. Substances that are hydrophobic often do not dissolve well in water, an example of a hydrophilic substance is sodium chloride. Acids and bases are aqueous solutions, as part of their Arrhenius definitions, the ability of a substance to dissolve in water is determined by whether the substance can match or exceed the strong attractive forces that water molecules generate between themselves. If the substance lacks the ability to dissolve in water the molecules form a precipitate, reactions in aqueous solutions are usually metathesis reactions. Metathesis reactions are another term for double-displacement, that is, when a cation displaces to form a bond with the other anion. The cation bonded with the latter anion will dissociate and bond with the other anion, aqueous solutions that conduct electric current efficiently contain strong electrolytes, while ones that conduct poorly are considered to have weak electrolytes. Those strong electrolytes are substances that are ionized in water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity, examples include sugar, urea, glycerol, and methylsulfonylmethane. When writing the equations of reactions, it is essential to determine the precipitate. To determine the precipitate, one must consult a chart of solubility, soluble compounds are aqueous, while insoluble compounds are the precipitate. Remember that there may not always be a precipitate, when performing calculations regarding the reacting of one or more aqueous solutions, in general one must know the concentration, or molarity, of the aqueous solutions. Solution concentration is given in terms of the form of the prior to it dissolving. Metal ions in aqueous solution Solubility Dissociation Acid-base reaction theories Properties of water Zumdahl S.1997, 4th ed. Boston, Houghton Mifflin Company
17.
Partition coefficient
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In the physical sciences, a partition-coefficient or distribution-coefficient is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium. This ratio is therefore a measure of the difference in solubility of the compound in two phases. In the chemical and pharmaceutical sciences, both phases usually are solvents, most commonly, one of the solvents is water while the second is hydrophobic such as 1-octanol. Hence the partition coefficient measures how hydrophilic or hydrophobic a chemical substance is, partition coefficients are useful in estimating the distribution of drugs within the body. Hydrophobic drugs with high octanol/water partition coefficients are distributed to hydrophobic areas such as lipid bilayers of cells. Conversely hydrophilic drugs are primarily in aqueous regions such as blood serum. If one of the solvents is a gas and the other a liquid, for example, the blood/gas partition coefficient of a general anesthetic measures how easily the anesthetic passes from gas to blood. Partition coefficients can also be defined one of the phases is solid, for instance, when one phase is a molten metal. The partitioning of a substance into a solid results in a solid solution, partition coefficients can be measured experimentally in various ways or estimated via calculation based on a variety of methods. Despite formal recommendation to the contrary, the partition coefficient remains the predominantly used term in the scientific literature. In contrast, the IUPAC recommends that the term no longer be used, rather. When one of the solvents is water and the other is a non-polar solvent, for measurements of distribution coefficients, the pH of the aqueous phase is buffered to a specific value such that the pH is not significantly perturbed by the introduction of the compound. In addition, since log D is pH-dependent, the pH at which the log D was measured must be specified. In areas such as drug discovery—areas involving partition phenomena in systems such as the human body—the log D at the physiologic pH,7.4, is of particular interest. It is often convenient to express the log D in terms of P I, defined above, the values in the following table are from the Dortmund Data Bank. They are sorted by the coefficient, smallest to largest. Values for other compounds may be found in a variety of available reviews, critical discussions of the challenges of measurement of log P, and related computation of its estimated values, appear in several reviews. Hence, the log P of a molecule is one used in decision-making by medicinal chemists in pre-clinical drug discovery, for example
18.
Vapor pressure
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Vapor pressure or equilibrium vapor pressure is defined as the pressure exerted by a vapor in thermodynamic equilibrium with its condensed phases at a given temperature in a closed system. The equilibrium vapor pressure is an indication of a liquids evaporation rate and it relates to the tendency of particles to escape from the liquid. A substance with a vapor pressure at normal temperatures is often referred to as volatile. The pressure exhibited by vapor present above a surface is known as vapor pressure. As the temperature of a liquid increases, the energy of its molecules also increases. As the kinetic energy of the molecules increases, the number of molecules transitioning into a vapor also increases, the vapor pressure of any substance increases non-linearly with temperature according to the Clausius–Clapeyron relation. The atmospheric pressure boiling point of a liquid is the temperature at which the pressure equals the ambient atmospheric pressure. With any incremental increase in temperature, the vapor pressure becomes sufficient to overcome atmospheric pressure. Bubble formation deeper in the liquid requires a pressure, and therefore higher temperature. More important at shallow depths, is the temperature required to start bubble formation. The surface tension of the wall lead to an overpressure in the very small initial bubbles. Thus, thermometer calibration should not rely on the temperature in boiling water, the vapor pressure that a single component in a mixture contributes to the total pressure in the system is called partial pressure. Vapor pressure is measured in the units of pressure. The International System of Units recognizes pressure as a unit with the dimension of force per area. One pascal is one newton per square meter, experimental measurement of vapor pressure is a simple procedure for common pressures between 1 and 200 kPa. Most accurate results are obtained near the point of substances. Better accuracy is achieved when care is taken to ensure that the entire substance and this is often done, as with the use of an isoteniscope, by submerging the containment area in a liquid bath. Very low vapor pressures of solids can be measured using the Knudsen effusion cell method, the Antoine equation is a mathematical expression of the relation between the vapor pressure and the temperature of pure liquid or solid substances
19.
Refractive index
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In optics, the refractive index or index of refraction n of a material is a dimensionless number that describes how light propagates through that medium. It is defined as n = c v, where c is the speed of light in vacuum, for example, the refractive index of water is 1.333, meaning that light travels 1.333 times faster in a vacuum than it does in water. The refractive index determines how light is bent, or refracted. The refractive indices also determine the amount of light that is reflected when reaching the interface, as well as the angle for total internal reflection. This implies that vacuum has a index of 1. The refractive index varies with the wavelength of light and this is called dispersion and causes the splitting of white light into its constituent colors in prisms and rainbows, and chromatic aberration in lenses. Light propagation in absorbing materials can be described using a refractive index. The imaginary part then handles the attenuation, while the real part accounts for refraction, the concept of refractive index is widely used within the full electromagnetic spectrum, from X-rays to radio waves. It can also be used with wave phenomena such as sound, in this case the speed of sound is used instead of that of light and a reference medium other than vacuum must be chosen. Thomas Young was presumably the person who first used, and invented, at the same time he changed this value of refractive power into a single number, instead of the traditional ratio of two numbers. The ratio had the disadvantage of different appearances, newton, who called it the proportion of the sines of incidence and refraction, wrote it as a ratio of two numbers, like 529 to 396. Hauksbee, who called it the ratio of refraction, wrote it as a ratio with a fixed numerator, hutton wrote it as a ratio with a fixed denominator, like 1.3358 to 1. Young did not use a symbol for the index of refraction, in the next years, others started using different symbols, n, m, and µ. For visible light most transparent media have refractive indices between 1 and 2, a few examples are given in the adjacent table. These values are measured at the yellow doublet D-line of sodium, with a wavelength of 589 nanometers, gases at atmospheric pressure have refractive indices close to 1 because of their low density. Almost all solids and liquids have refractive indices above 1.3, aerogel is a very low density solid that can be produced with refractive index in the range from 1.002 to 1.265. Moissanite lies at the end of the range with a refractive index as high as 2.65. Most plastics have refractive indices in the range from 1.3 to 1.7, for infrared light refractive indices can be considerably higher
20.
GHS hazard pictograms
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Hazard pictograms form part of the international Globally Harmonized System of Classification and Labelling of Chemicals. Two sets of pictograms are included within the GHS, one for the labelling of containers and for workplace hazard warnings, either one or the other is chosen, depending on the target audience, but the two are not used together. The two sets of use the same symbols for the same hazards, although certain symbols are not required for transport pictograms. Transport pictograms come in variety of colors and may contain additional information such as a subcategory number. It has still to be implemented by the European Union in 2009, the following pictograms are included in the Worldwide Model Using but have not been incorporated into the GHS, ICZ and Catwallsh Hazcom Labelling because of the nature of the hazards. Globally Harmonized System of Classification and Labelling of Chemicals, New York and Geneva, United Nations,2007, ISBN 978-92-1-116957-7, ST/SG/AC. 10/30/Rev. Model Regulations, New York and Geneva, United Nations,2007, ISBN 978-92-1-139120-6, manual of Tests and Criteria, New York and Geneva, United Nations,2002, ISBN 92-1-139087-7, ST/SG/AC. 10/11/Rev.4 GHS pictogram gallery from the United Nations Economic Commission for Europe
21.
Flash point
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The flash point is the lowest temperature at which vapours of a volatile material will ignite, when given an ignition source. The flash point may sometimes be confused with the autoignition temperature, the fire point is the lowest temperature at which the vapor will keep burning after being ignited and the ignition source removed. The fire point is higher than the point, because at the flash point the vapor may be reliably expected to cease burning when the ignition source is removed. The flash point is a characteristic that is used to distinguish between flammable liquids, such as petrol, and combustible liquids, such as diesel. It is also used to characterize the fire hazards of liquids, all liquids have a specific vapor pressure, which is a function of that liquids temperature and is subject to Boyles 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 liquid in the air. The flash point is the lowest temperature at which there will be enough flammable vapor to induce ignition when a source is applied. There are two types of flash point measurement, open cup and closed cup. In open cup devices, the sample is contained in a cup which is heated and, at intervals. The measured flash point will vary with the height of the flame above the liquid surface and, at sufficient height. The best-known example is the Cleveland open cup, in both these types, the cups are sealed with a lid through which the ignition source can be introduced. Closed cup testers normally give lower values for the 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 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, 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, ISO2719, DIN51758, 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 ISO3679 and 3680, cEN/TR15138 Guide to Flash Point Testing and ISO TR29662 Guidance for Flash Point Testing cover the key aspects of flash point testing. Gasoline is a used in a spark-ignition engine
22.
Propylamine
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Propylamine, also known as n-propylamine, is an amine with the chemical formula C2H5CH2NH2. It is a volatile liquid. Propyl amine hydrochloride can be prepared by reacting 1-propanol with ammonium chloride at high temperature and pressure using a Lewis acid catalyst such as ferric chloride
23.
Sec-Butylamine
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Sec-Butylamine is an organic chemical compound with the formula CH3CH2CHCH3, and occurs as a colorless liquid. Sec-Butylamine is one of the four isomeric amines of butane, the others being n-butylamine, tert-butylamine and isobutylamine and it is very harmful to aquatic organisms. Sec-Butylamine is used as a fungicide and is considered a production volume chemical. It is undergoing comprehensive review by the American Chemistry Councils Amines Panel as part of the Primary Amines Category, sec-Butylamine is one of the isomers of butylamine. It is chiral and therefore can exist in either of two enantiomeric forms and this compound is moderately toxic, as well as flammable and corrosive
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