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.
Sulfinamide is a functional group in organosulfur chemistry with the formula RSNR'2. With a sulfur-oxygen double bond as well as S-C and S-N single bonds, the compounds are chiral. Sulfinamides are amides of sulfinic acid. Tert-Butanesulfinamide, p-toluenesulfinamide, 2,4,6-trimethylbenzenesulfinamide have been obtained in optically pure form, they are used in asymmetric synthesis. Sulfinamides arise in nature by the addition of thiols to nitroxyl: RSH + HNO → RSNH2
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, phase of matter, color and biological activity; the angles between bonds that an atom forms depend only weakly on the rest of molecule, i.e. they can be understood as local and hence transferable properties. The molecular geometry can be determined by diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density.
Gas electron diffraction can be used for small molecules in the gas phase. NMR and FRET methods can be used to determine complementary information including relative distances, dihedral angles and connectivity. Molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries. Larger molecules exist in multiple stable geometries that are close in energy on the potential energy surface. Geometries can be computed by ab initio quantum chemistry methods to high accuracy; the molecular geometry can be different as a solid, in solution, as a gas. The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms; the molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, torsion angles of three consecutive bonds. Since the motions of the atoms in a molecule are determined by quantum mechanics, one must define "motion" in a quantum mechanical way.
The overall quantum mechanical motions translation and rotation hardly change the geometry of the molecule. In addition to translation and rotation, a third type of motion is molecular vibration, which corresponds to internal motions of the atoms such as bond stretching and bond angle variation; the molecular vibrations are harmonic, the atoms oscillate about their equilibrium positions at the absolute zero of temperature. At absolute zero all atoms are in their vibrational ground state and show zero point quantum mechanical motion, so that the wavefunction of a single vibrational mode is not a sharp peak, but an exponential of finite width. At higher temperatures the vibrational modes may be thermally excited, but they oscillate still around the recognizable geometry of the molecule. To get a feeling for the probability that the vibration of molecule may be thermally excited, we inspect the Boltzmann factor β ≡ exp , where Δ E is the excitation energy of the vibrational mode, k the Boltzmann constant and T the absolute temperature.
At 298 K, typical values for the Boltzmann factor β are: β = 0.089 for ΔE = 500 cm−1. When an excitation energy is 500 cm−1 about 8.9 percent of the molecules are thermally excited at room temperature. To put this in perspective: the lowest excitation vibrational energy in water is the bending mode. Thus, at room temperature less than 0.07 percent of all the molecules of a given amount of water will vibrate faster than at absolute zero. As stated above, rotation hardly influences the molecular geometry. But, as a quantum mechanical motion, it is thermally excited at low temperatures. From a classical point of view it can be stated that at higher temperatures more molecules will rotate faster, which implies that they have higher angular velocity and angular momentum. In quantum mechanical language: more eigenstates of higher angular momentum become thermally populated with rising temperatures. Typical rotational excitation energies are on the order of a few cm−1; the results of many spectroscopic experiments are broadened because they involve an averaging over rotational states.
It is difficult to extract geometries from spectra at high temperatures, because the number of rotational states probed in the experimental averaging increases with increasing temperature. Thus, many spectroscopic observations can only be expected to yield reliable molecular geometries at temperatures close to absolute zero, because at higher temperatures too many higher rotational states are thermally populated. Molecules, by definition, are most held together with covalent bonds involving single, and/or triple bonds, where a "bond
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
Accounts of Chemical Research
Accounts of Chemical Research is a monthly peer-reviewed scientific journal published by the American Chemical Society containing overviews of basic research and applications in chemistry and biochemistry. It was established in 1968 and the editor-in-chief is Cynthia J. Burrows; the journal is abstracted and indexed in: According to the Journal Citation Reports, the journal has a 2017 impact factor of 20.955. Official website
Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a reduction process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions; the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in simple terms: Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion. Reduction is a decrease in oxidation state by a molecule, atom, or ion; as an example, during the combustion of wood, oxygen from the air is reduced, gaining electrons from carbon, oxidized. Although oxidation reactions are associated with the formation of oxides from oxygen molecules, oxygen is not included in such reactions, as other chemical species can serve the same function; the reaction can occur slowly, as with the formation of rust, or more in the case of fire.
There are simple redox processes, such as the oxidation of carbon to yield carbon dioxide or the reduction of carbon by hydrogen to yield methane, more complex processes such as the oxidation of glucose in the human body. "Redox" is a portmanteau of the words "reduction" and "oxidation". The word oxidation implied reaction with oxygen to form an oxide, since dioxygen was the first recognized oxidizing agent; the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions. The meaning was generalized to include all processes involving loss of electrons; the word reduction referred to the loss in weight upon heating a metallic ore such as a metal oxide to extract the metal. In other words, ore was "reduced" to metal. Antoine Lavoisier showed. Scientists realized that the metal atom gains electrons in this process; the meaning of reduction became generalized to include all processes involving a gain of electrons. Though "reduction" seems counter-intuitive when speaking of the gain of electrons, it might help to think of reduction as the loss of oxygen, its historical meaning.
Since electrons are negatively charged, it is helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes when they occur at electrodes; these words are analogous to protonation and deprotonation, but they have not been adopted by chemists worldwide. The term "hydrogenation" could be used instead of reduction, since hydrogen is the reducing agent in a large number of reactions in organic chemistry and biochemistry. But, unlike oxidation, generalized beyond its root element, hydrogenation has maintained its specific connection to reactions that add hydrogen to another substance; the word "redox" was first used in 1928. The processes of oxidation and reduction occur and cannot happen independently of one another, similar to the acid–base reaction; the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction.
When writing half-reactions, the gained or lost electrons are included explicitly in order that the half-reaction be balanced with respect to electric charge. Though sufficient for many purposes, these general descriptions are not correct. Although oxidation and reduction properly refer to a change in oxidation state — the actual transfer of electrons may never occur; the oxidation state of an atom is the fictitious charge that an atom would have if all bonds between atoms of different elements were 100% ionic. Thus, oxidation is best defined as an increase in oxidation state, reduction as a decrease in oxidation state. In practice, the transfer of electrons will always cause a change in oxidation state, but there are many reactions that are classed as "redox" though no electron transfer occurs. In redox processes, the reductant transfers electrons to the oxidant. Thus, in the reaction, the reductant or reducing agent loses electrons and is oxidized, the oxidant or oxidizing agent gains electrons and is reduced.
The pair of an oxidizing and reducing agent that are involved in a particular reaction is called a redox pair. A redox couple is a reducing species and its corresponding oxidizing form, e.g. Fe2+/Fe3+ Substances that have the ability to oxidize other substances are said to be oxidative or oxidizing and are known as oxidizing agents, oxidants, or oxidizers; that is, the oxidant removes electrons from another substance, is thus itself reduced. And, because it "accepts" electrons, the oxidizing agent is called an electron acceptor. Oxygen is the quintessential oxidizer. Oxidants are chemical substances with elements in high oxidation states, or else electronegative elements that can gain extra electrons by oxidizing another substance. Substances that have the ability to reduce other substances are said to be reductive or reducing and are known as
Acetic acid, systematically named ethanoic acid, is a colourless liquid organic compound with the chemical formula CH3COOH. When undiluted, it is sometimes called glacial acetic acid. Vinegar is no less than 4% acetic acid by volume, making acetic acid the main component of vinegar apart from water. Acetic acid has pungent smell. In addition to household vinegar, it is produced as a precursor to polyvinyl acetate and cellulose acetate, it is classified as a weak acid since it only dissociates in solution, but concentrated acetic acid is corrosive and can attack the skin. Acetic acid is the second simplest carboxylic acid, it consists of a methyl group attached to a carboxyl group. It is an important chemical reagent and industrial chemical, used in the production of cellulose acetate for photographic film, polyvinyl acetate for wood glue, synthetic fibres and fabrics. In households, diluted acetic acid is used in descaling agents. In the food industry, acetic acid is controlled by the food additive code E260 as an acidity regulator and as a condiment.
In biochemistry, the acetyl group, derived from acetic acid, is fundamental to all forms of life. When bound to coenzyme A, it is central to the metabolism of fats; the global demand for acetic acid is about 6.5 million metric tons per year, of which 1.5 Mt/a is met by recycling. Vinegar is dilute acetic acid produced by fermentation and subsequent oxidation of ethanol; the trivial name acetic acid is the most used and preferred IUPAC name. The systematic name ethanoic acid, a valid IUPAC name, is constructed according to the substitutive nomenclature; the name acetic acid derives from acetum, the Latin word for vinegar, is related to the word acid itself. Glacial acetic acid is a name for water-free acetic acid. Similar to the German name Eisessig, the name comes from the ice-like crystals that form below room temperature at 16.6 °C. A common symbol for acetic acid is AcOH, where Ac is the pseudoelement symbol representing the acetyl group CH3−C−. To better reflect its structure, acetic acid is written as CH3–COH, CH3−COH, CH3COOH, CH3CO2H.
In the context of acid-base reactions, the abbreviation HAc is sometimes used, where Ac in this case is a symbol for acetate. Acetate is the ion resulting from loss of H+ from acetic acid; the name acetate can refer to a salt containing this anion, or an ester of acetic acid. The hydrogen centre in the carboxyl group in carboxylic acids such as acetic acid can separate from the molecule by ionization: CH3CO2H ⇌ CH3CO2− + H+Because of this release of the proton, acetic acid has acidic character. Acetic acid is a weak monoprotic acid. In aqueous solution, it has a pKa value of 4.76. Its conjugate base is acetate. A 1.0 M solution has a pH of 2.4, indicating that 0.4% of the acetic acid molecules are dissociated. However, in dilute solution acetic acid is >90% dissociated. In solid acetic acid, the molecules form chains, individual molecules being interconnected by hydrogen bonds. In the vapour at 120 °C, dimers can be detected. Dimers occur in the liquid phase in dilute solutions in non-hydrogen-bonding solvents, a certain extent in pure acetic acid, but are disrupted by hydrogen-bonding solvents.
The dissociation enthalpy of the dimer is estimated at 65.0–66.0 kJ/mol, the dissociation entropy at 154–157 J mol−1 K−1. Other carboxylic acids engage in similar intermolecular hydrogen bonding interactions. Liquid acetic acid is a hydrophilic protic similar to ethanol and water. With a moderate relative static permittivity of 6.2, it dissolves not only polar compounds such as inorganic salts and sugars, but non-polar compounds such as oils as well as polar solutes. It is miscible with polar and non-polar solvents such as water and hexane. With higher alkanes, acetic acid is not miscible, its miscibility declines with longer n-alkanes; the solvent and miscibility properties of acetic acid make it a useful industrial chemical, for example, as a solvent in the production of dimethyl terephthalate. At physiological pHs, acetic acid is fully ionised to acetate; the acetyl group, formally derived from acetic acid, is fundamental to all forms of life. When bound to coenzyme A, it is central to the metabolism of fats.
Unlike longer-chain carboxylic acids, acetic acid does not occur in natural triglycerides. However, the artificial triglyceride triacetin is a common food additive and is found in cosmetics and topical medicines. Acetic acid is produced and excreted by acetic acid bacteria, notably the genus Acetobacter and Clostridium acetobutylicum; these bacteria are found universally in foodstuffs and soil, acetic acid is produced as fruits and other foods spoil. Acetic acid is a component of the vaginal lubrication of humans and other primates, where it appears to serve as a mild antibacterial agent. Acetic acid is produced industrially both synthetically and by bacterial fermentation. About 75% of acetic acid made for use in the chemical industry is made by the carbonylation of methanol, explained below; the biological route accounts for only a