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
Azide is the anion with the formula N−3. It is the conjugate base of hydrazoic acid. N−3 is a linear anion, isoelectronic with CO2, NCO−, N2O, NO+2 and NCF. Per valence bond theory, azide can be described by several resonance structures. Azide is a functional group in organic chemistry, RN3; the dominant application of azides is as a propellant in air bags. Sodium azide is made industrially by the reaction of nitrous oxide, N2O with sodium amide in liquid ammonia as solvent: N2O + 2 NaNH2 → NaN3 + NaOH + NH3Many inorganic azides can be prepared directly or indirectly from sodium azide. For example, lead azide, used in detonators, may be prepared from the metathesis reaction between lead nitrate and sodium azide. An alternative route is direct reaction of the metal with silver azide dissolved in liquid ammonia; some azides are produced by treating the carbonate salts with hydrazoic acid. The principal source of the azide moiety is sodium azide; as a pseudohalogen compound, sodium azide displaces an appropriate leaving group to give the azido compound.
Aryl azides may be prepared by displacement of the appropriate diazonium salt with sodium azide, or trimethylsilyl azide. Anilines and aromatic hydrazines undergo diazotization, as do alkyl hydrazines. Appropriately functionalized aliphatic compounds undergo nucleophilic substitution with sodium azide. Aliphatic alcohols give azides via a variant of the Mitsunobu reaction, with the use of hydrazoic acid. Hydrazines may form azides by reaction with sodium nitrite: PhNHNH2 → PhN3Alkyl or aryl acyl chlorides react with sodium azide in aqueous solution to give acyl azides, which give isocyanates in the Curtius rearrangement; the azo-transfer compounds, trifluoromethanesulfonyl azide and imidazole-1-sulfonyl azide, are prepared from sodium azide as well. They react with amines to give the corresponding azides: RNH2 → RN3 A classic method for the synthesis of azides is the Dutt–Wormall reaction in which a diazonium salt reacts with a sulfonamide first to a diazoaminosulfinate and on hydrolysis the azide and a sulfinic acid.
Azide salts can decompose with release of nitrogen gas. The decomposition temperatures of the alkali metal azides are: NaN3, KN3, RbN3, CsN3; this method is used to produce ultrapure alkali metals. Protonation of azide salts gives toxic hydrazoic acid in the presence of strong acids: H+ + N−3 → HN3Azide salts may react with heavy metals or heavy metal compounds to give the corresponding azides, which are more shock sensitive than sodium azide alone, they decompose with sodium nitrite. This is a method of destroying residual azides, prior to disposal. 2 NaN3 + 2 HNO2 → 3 N2 + 2 NO + 2 NaOHMany inorganic covalent azides have been described. The azide anion behaves as a nucleophile, it reacts with epoxides. Azides can be used as precursors of the metal nitrido complexes. Azide complexes thus is induced to release N2, generating a metal complex in unusual oxidation states. Organic azides engage in useful organic reactions; the terminal nitrogen is mildly nucleophilic. Azides extrude diatomic nitrogen, a tendency, exploited in many reactions such as the Staudinger ligation or the Curtius rearrangement or for example in the synthesis of γ-imino-β-enamino esters.
Azides may be reduced with a phosphine in the Staudinger reaction. This reaction allows azides to serve as protected -NH2 synthons, as illustrated by the synthesis of 1,1,1-trisethane: 3 H2 + CH3C3 → CH3C3 + 3 N2In the azide alkyne Huisgen cycloaddition, organic azides react as 1,3-dipoles, reacting with alkynes to give substituted 1,2,3-triazoles; this reaction is popular in click chemistry. Another azide regular is tosyl azide here in reaction with norbornadiene in a nitrogen insertion reaction: About 250 tons of azide-containing compounds are produced annually, the main product being sodium azide. Sodium azide is the propellant in automobile airbags, it decomposes on heating to give nitrogen gas, used to expand the air bag: 2 NaN3 → 2 Na + 3 N2Heavy metal salts, such as lead azide, Pb2, are shock-sensitive detonators which decompose to the corresponding metal and nitrogen, for example: Pb2 → Pb + 3 N2Silver and barium salts are used similarly. Some organic azides are an example being 2-dimethylaminoethylazide.
Because of the hazards associated with their use, few azides are used commercially although they exhibit interesting reactivity for researchers. Low molecular weight azides are considered hazardous and are avoided. In the research laboratory, azides are precursors to amines, they are popular for their participation in the "click reaction" and in Staudinger ligation. These two reactions are quite reliable, lending themselves to combinatorial chemistry; the antiviral drug zidovudine contains an azido group. Some azides are valuable as bioorthogonal chemical reporters. Azides are toxins. Sodium azide can be absorbed through the skin, it decomposes explosively upon heating to above 275 °C and reac
The Buchner–Curtius–Schlotterbeck reaction is the reaction of aldehydes or ketones with aliphatic diazoalkanes to form homologated ketones. It was first described by Eduard Buchner and Theodor Curtius in 1885 and by Fritz Schlotterbeck in 1907. Two German chemists preceded Schlotterbeck in discovery of the reaction, Hans von Pechmann in 1895 and Viktor Meyer in 1905; the reaction has since been extended to the synthesis of β-keto esters from the condensation between aldehydes and diazo esters. The general reaction scheme is as follows: The reaction yields two possible carbonyl compounds along with an epoxide; the ratio of the products is determined by the reaction conditions. The general mechanism is shown below; the resonating arrow shows a resonance contributor of the diazo compound with a lone pair of electrons on the carbon adjacent to the nitrogen. The diazo compound does a nucleophilic attack on the carbonyl-containing compound, producing a tetrahedral intermediate; this intermediate decomposes by the evolution of nitrogen gas forming the tertiary carbocation intermediate.
The reaction is completed either by the reformation of the carbonyl through an 1,2-rearrangement or by the formation of the epoxide. There are two possible carbonyl products: one formed by migration of R1 and the other by migration of R2; the relative yield of each possible carbonyl is determined by the migratory preferences of the R-groups. The epoxide product is formed by an intramolecular addition reaction in which a lone pair from the oxygen attacks the carbocation; this reaction is exothermic due to the stability of nitrogen gas and the carbonyl containing compounds. This specific mechanism is supported by several observations. First, kinetic studies of reactions between diazomethane and various ketones have shown that the overall reaction follows second order kinetics. Additionally, the reactivity of two series of ketones are in the orders Cl3CCOCH3 > CH3COCH3 > C6H5COCH3 and cyclohexanone > cyclopentanone > cycloheptanone > cyclooctanone. These orders of reactivity are the same as those observed for reactions that are well established as proceeding through nucleophilic attack on a carbonyl group.
The reaction was carried out in diethyl ether and generated high yields due to the inherent irreversibly of the reaction caused by the formation of nitrogen gas. Though these reactions can be carried out at room temperature, the rate does increase at higher temperatures; the reaction is carried out at less than refluxing temperatures. The optimal reaction temperature is determined by the specific diazoalkane used. Reactions involving diazomethanes with alkyl or aryl substituents are exothermic at or below room temperature. Reactions involving diazomethanes with acyl or aroyl substituents require higher temperatures; the reaction has since been modified to proceed in the presence of Lewis acids and common organic solvents such as THF and dichloromethane. Reactions run at room temperature for about an hour, the yield ranges from 70%-80% based on the choice of Lewis acid and solvent. Steric effects of the alkyl substituents on the carbonyl reactant have been shown to affect both the rates and yields of Büchner–Curtius–Schlotterbeck reaction.
Table 1 shows the percent yield of the ketone and epoxide products as well as the relative rates of reaction for the reactions between several methyl alkyl ketones and diazomethane. The observed decrease in rate and increase in epoxide yield as the size of the alkyl group becomes larger indicates a steric effect. Ketones and aldehydes with electron-withdrawing substituents react more with diazoalkanes than those bearing electron-donating substituents. In addition to accelerating the reaction, electron-withdrawing substituents increase the amount of epoxide produced; the effects of substituents on the diazoalkanes is reversed relative to the carbonyl reactants: electron-withdrawing substituents decrease the rate of reaction while electron-donating substituents accelerate it. For example, diazomethane is more reactive than ethyl diazoacetate, though less reactive than its higher alkyl homologs. Reaction conditions may affect the yields of carbonyl product and epoxide product. In the reactions of o-nitrobenzaldehyde, p-nitrobenzaldehyde, phenylacetaldehyde with diazomethane, the ratio of epoxide to carbonyl is increased by the inclusion of methanol in the reaction mixture.
The opposite influence has been observed in the reaction of piperonal with diazomethane, which exhibits increased carbonyl yield in the presence of methanol. The ratio of the two possible carbonyl products obtained is determined by the relative migratory abilities of the carbonyl substituents. In general, the R-group most capable of stabilizing the partial positive charge formed during the rearrangement migrates preferentially. A prominent exception to this general rule is hydride shifting; the migratory preferences of the carbonyl R-groups can be influenced by solvent and diazoalkane choice. For example, methanol has been shown to promote aryl migration; as shown below, if the reaction of piperanol with diazomethane is carried out in the absence of methanol, the ketone obtained though a hydride shift is the major product. If methanol is the solvent, an aryl shift occurs to form the aldehyde, which cannot be isolated as it continues to react to form the ketone and the epoxide products; the diazoalkane employed can determine relative yields of products by influencing migratory preferences, as conveyed by the reactions of o-nitropiperonal with diazomethane and diazoethane.
In the reactio
Diethyl ether, or ether, is an organic compound in the ether class with the formula 2O, sometimes abbreviated as Et2O. It is a colorless volatile flammable liquid, it is used as a solvent in laboratories and as a starting fluid for some engines. It was used as a general anesthetic, until non-flammable drugs were developed, such as halothane, it has been used as a recreational drug to cause intoxication. Most diethyl ether is produced as a byproduct of the vapor-phase hydration of ethylene to make ethanol; this process uses solid-supported phosphoric acid catalysts and can be adjusted to make more ether if the need arises. Vapor-phase dehydration of ethanol over some alumina catalysts can give diethyl ether yields of up to 95%. Diethyl ether can be prepared both in laboratories and on an industrial scale by the acid ether synthesis. Ethanol is mixed with a strong acid sulfuric acid, H2SO4; the acid dissociates in the aqueous environment producing hydronium ions, H3O+. A hydrogen ion protonates the electronegative oxygen atom of the ethanol, giving the ethanol molecule a positive charge: CH3CH2OH + H3O+ → CH3CH2OH2+ + H2OA nucleophilic oxygen atom of unprotonated ethanol displaces a water molecule from the protonated ethanol molecule, producing water, a hydrogen ion and diethyl ether.
CH3CH2OH2+ + CH3CH2OH → H2O + H+ + CH3CH2OCH2CH3This reaction must be carried out at temperatures lower than 150 °C in order to ensure that an elimination product is not a product of the reaction. At higher temperatures, ethanol will dehydrate to form ethylene; the reaction to make diethyl ether is reversible, so an equilibrium between reactants and products is achieved. Getting a good yield of ether requires that ether be distilled out of the reaction mixture before it reverts to ethanol, taking advantage of Le Chatelier's principle. Another reaction that can be used for the preparation of ethers is the Williamson ether synthesis, in which an alkoxide performs a nucleophilic substitution upon an alkyl halide, it is important as a solvent in the production of cellulose plastics such as cellulose acetate. Diethyl ether has a high cetane number of 85–96 and is used as a starting fluid, in combination with petroleum distillates for gasoline and Diesel engines because of its high volatility and low flash point.
Ether starting fluid is sold and used in countries with cold climates, as it can help with cold starting an engine at sub-zero temperatures. For the same reason it is used as a component of the fuel mixture for carbureted compression ignition model engines. In this way diethyl ether is similar to one of its precursors, ethanol. Diethyl ether is a common laboratory aprotic solvent, it has limited solubility in water and dissolves 1.5 g/100 g water at 25 °C. This, coupled with its high volatility, makes it ideal for use as the non-polar solvent in liquid-liquid extraction; when used with an aqueous solution, the diethyl ether layer is on top as it has a lower density than the water. It is a common solvent for the Grignard reaction in addition to other reactions involving organometallic reagents. Due to its application in the manufacturing of illicit substances, it is listed in the Table II precursor under the United Nations Convention Against Illicit Traffic in Narcotic Drugs and Psychotropic Substances as well as substances such as acetone and sulfuric acid.
William T. G. Morton participated in a public demonstration of ether anesthesia on October 16, 1846 at the Ether Dome in Boston, Massachusetts. However, Crawford Williamson Long, is now known to have demonstrated its use as a general anesthetic in surgery to officials in Georgia, as early as March 30, 1842, Long publicly demonstrated ether's use as a surgical anesthetic on six occasions before the Boston demonstration. British doctors were aware of the anesthetic properties of ether as early as 1840 where it was prescribed in conjunction with opium. Diethyl ether supplanted the use of chloroform as a general anesthetic due to ether's more favorable therapeutic index, that is, a greater difference between an effective dose and a toxic dose. Diethyl ether increases tracheobronchial secretions. Diethyl ether could be mixed with other anesthetic agents such as chloroform to make C. E. mixture, or chloroform and alcohol to make A. C. E. Mixture. In the 21st century, ether is used; the use of flammable ether was displaced by nonflammable fluorinated hydrocarbon anesthetics.
Halothane was the first such anesthetic developed and other used inhaled anesthetics, such as isoflurane and sevoflurane, are halogenated ethers. Diethyl ether was found to have undesirable side effects, such as post-anesthetic nausea and vomiting. Modern anesthetic agents reduce these side effects. Prior to 2005 it was on the World Health Organization's List of Essential Medicines for use as an anesthetic. Ether was once used in pharmaceutical formulations. A mixture of alcohol and ether, one part of diethyl ether and three parts of ethanol, was known as "Spirit of ether", Hoffman's Anodyne or Hoffman's Drops. In the United States this concoction was removed from the Pharmacopeia at some point prior to June 1917, as a study published by William Procter, Jr. in the American Journal of Pharmacy as early as 1852 showed that there were differences in formulation to be found between commercial manufacturers, between international pharmacopoeia, from Hoffman's original recipe. The anesthetic and intoxicating effects of ether have made it a recreational drug.
Diethyl ether in anesthetic dosage is an inhalant which has a long history
Occupational safety and health
Occupational safety and health commonly referred to as occupational health and safety, occupational health, or workplace health and safety, is a multidisciplinary field concerned with the safety and welfare of people at work. These terms refer to the goals of this field, so their use in the sense of this article was an abbreviation of occupational safety and health program/department etc; the goals of occupational safety and health programs include to foster a safe and healthy work environment. OSH may protect co-workers, family members, employers and many others who might be affected by the workplace environment. In the United States, the term occupational health and safety is referred to as occupational health and occupational and non-occupational safety and includes safety for activities outside of work. In common-law jurisdictions, employers have a common law duty to take reasonable care of the safety of their employees. Statute law may in addition impose other general duties, introduce specific duties, create government bodies with powers to regulate workplace safety issues: details of this vary from jurisdiction to jurisdiction.
As defined by the World Health Organization "occupational health deals with all aspects of health and safety in the workplace and has a strong focus on primary prevention of hazards." Health has been defined as "a state of complete physical and social well-being and not the absence of disease or infirmity." Occupational health is a multidisciplinary field of healthcare concerned with enabling an individual to undertake their occupation, in the way that causes least harm to their health. Health has been defined as It contrasts, for example, with the promotion of health and safety at work, concerned with preventing harm from any incidental hazards, arising in the workplace. Since 1950, the International Labour Organization and the World Health Organization have shared a common definition of occupational health, it was adopted by the Joint ILO/WHO Committee on Occupational Health at its first session in 1950 and revised at its twelfth session in 1995. The definition reads: "The main focus in occupational health is on three different objectives: the maintenance and promotion of workers’ health and working capacity.
The concept of working culture is intended in this context to mean a reflection of the essential value systems adopted by the undertaking concerned. Such a culture is reflected in practice in the managerial systems, personnel policy, principles for participation, training policies and quality management of the undertaking." Those in the field of occupational health come from a wide range of disciplines and professions including medicine, epidemiology and rehabilitation, occupational therapy, occupational medicine, human factors and ergonomics, many others. Professionals advise on a broad range of occupational health matters; these include how to avoid particular pre-existing conditions causing a problem in the occupation, correct posture for the work, frequency of rest breaks, preventative action that can be undertaken, so forth. "Occupational health should aim at: the promotion and maintenance of the highest degree of physical and social well-being of workers in all occupations. The research and regulation of occupational safety and health are a recent phenomenon.
As labor movements arose in response to worker concerns in the wake of the industrial revolution, worker's health entered consideration as a labor-related issue. In the United Kingdom, the Factory Acts of the early nineteenth century arose out of concerns about the poor health of children working in cotton mills: the Act of 1833 created a dedicated professional Factory Inspectorate; the initial remit of the Inspectorate was to police restrictions on the working hours in the textile industry of children and young persons. However, on the urging of the Factory Inspectorate, a further Act in 1844 giving similar restrictions on working hours for women in the textile industry introduced a requirement for machinery guarding. In 1840 a Royal Commission published its findings on the state of conditions for the workers of the mining industry that documented the appallingly dangerous environment that they had to work in and the high frequency of accidents; the commission sparked public outrage which resulted in the Mines Act of 1842.
The act set up an inspectorate for mines and collieries which resulted in many prosecutions and safety improvements, by 1850, inspectors were able to enter and inspect premises at their discretion. Otto von Bismarck inaugurated the first social insurance legislation in 1883 and the first worker's compensation law in 1884 – the first of their kind in the Western world. Similar acts followed in other countries
The boiling point of a substance is the temperature at which the vapor pressure of a liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the surrounding environmental pressure. A liquid in a partial vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a higher boiling point than when that liquid is at atmospheric pressure. For example, water at 93.4 °C at 1,905 metres altitude. For a given pressure, different liquids will boil at different temperatures; the normal boiling point of a liquid is the special case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level, 1 atmosphere. At that temperature, the vapor pressure of the liquid becomes sufficient to overcome atmospheric pressure and allow bubbles of vapor to form inside the bulk of the liquid; 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 liquid's 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, resulting in the formation of vapor bubbles within the liquid. A saturated liquid contains as much thermal energy. Saturation temperature means boiling point; 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 thermal 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.
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 vapor pressure of the liquid equals the surrounding environmental pressure. Thus, the boiling point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, or the IUPAC standard pressure of 100.000 kPa. At higher elevations, where the atmospheric pressure is much lower, the boiling point is lower; the boiling point increases with increased pressure up to the critical point, where the gas and liquid properties become identical. The boiling point cannot be increased beyond the critical point; the boiling point decreases with decreasing pressure until the triple point is reached. The boiling point cannot be reduced below the triple point. If the heat of vaporization and the vapor pressure of a liquid at a certain temperature are known, the boiling point can be calculated by using the Clausius–Clapeyron equation, thus: T B = − 1, where: T B is the boiling point at the pressure of interest, R is the ideal gas constant, P is the vapour pressure of the liquid at the pressure of interest, P 0 is some pressure where the corresponding T 0 is known, Δ H vap is the heat of vaporization of the liquid, T 0 is the boiling temperature, ln is the natural logarithm.
Saturation pressure is the pressure for a corresponding saturation temperature at which a liquid boils into its vapor phase. Saturation pressure and saturation temperature have a direct relationship: as saturation pressure is increased, so is saturation temperature. If the temperature in a system remains constant, vapor at saturation pressure and temperature will begin to condense into its liquid phase as the system pressure is increased. A liquid at saturation pressure and temperature will tend to flash into its vapor phase as system pressure is decreased. There are two conventions regarding the standard boiling point of water: The normal boiling point is 99.97 °C at a pressure of 1 atm. The IUPAC recommended standard boiling point of water at a standard pressure of 100 kPa is 99.61 °C. For comparison, on top of Mount Everest, at 8,848 m elevation, the pressure is about 34 kPa and the boiling point of water is 71 °C; the Celsius temperature scale was defined until 1954 by two points: 0 °C being defined by the wate
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.