# Chemical Compound - an overview (2023)

Chemical compounds (CC) are the main objects of chemical investigations.

From: Encyclopedia of Bioinformatics and Computational Biology, 2019

## Related terms:

• Pollutant
• Enzyme
• Protein
• DNA
• Toxicity
• Ligand
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## Liver Disease Caused by Anesthetics, Chemicals, Toxins, and Herbal and Dietary Supplements

Mark Feldman MD, in Sleisenger and Fordtran's Gastrointestinal and Liver Disease, 2021

### Miscellaneous Chemical Compounds

Dimethylformamide is a solvent used in the synthetic resin and leather industries that causes dose-related massive hepatic necrosis in animals78 and is capable of producing focal hepatic necrosis and microvesicular steatosis in humans.5 Most persons exposed for more than one year have symptomatic disease that slowly resolves when they are removed from the workplace.5 Disulfiram-like symptoms can occur.79 Alcohol use, HBV infection, and a high BMI are risk factors.80 Dimethylacetamide hepatotoxicity is well described in animals, with only rare reports after human exposure.81

Hydrazine and its derivatives used in jet and rocket fuel cells are also experimental hepatotoxins and carcinogens and have been reported to cause hepatic steatosis in animals2 and reversible injury in humans after inhalation.82 Bromoalkanes and iodoalkanes, used in insecticides and aircraft fuels, have rarely caused hepatic injury.5 Ethylene dibromide (dibromoethane) has led to zone 3 hepatic necrosis after ingestion in attempted suicide and to fatal hepatotoxicity associated with nephrotoxicity and cardiotoxicity following occupational exposure or inadvertent poisoning.83

## Chemoinformatics: From Chemical Art to Chemistry in Silico

Jaroslaw Polanski, in Encyclopedia of Bioinformatics and Computational Biology, 2019

### Teaching Computers Chemistry: From Molecular Data to Chemical Information and Chemical Ontology

The development of technology, in particular, scientific equipment capable of describing human environment by any type of records provided us with data, where data can be interpreted in the broadest sense as anything that is recorded, including metadata, i.e., data referring to other data. This can be both ordered and unordered collections of both nominal and numerical values, whereas the latter can be discrete numbers, intervals or ratios. Another type of data (binary large objects, BLOBs) is used to describe audio, video and graphic files (Maheshwari, 2014). With the enormous increase of data volume the so-called big data appeared recently. It is generally believed that big data brings new value and innovation. For example, Szlezak et al. cited the recent McKinsey research that suggests that the potential use of big data in US health care could reduce costs by \$300 billion a year (Szlezak et al., 2014). Current impact of big data for drug design is however far less noticeable that could be expected. The reason is that, first, this kind of information is much less clearly defined and messy. Accordingly, its analysis causes serious problems. Second, 120 million compounds were synthesized and registered in databases; however; this should be compared to 7 billion individuals in human society. Data gets bigger while going from chemistry to biology or economy (where humans are interacting). A single genome for a single individual can be interpreted as special type “big data”, e.g., already a structure of the genome is a large record. A phonotype yielded by the genome is a specific property. In comparison, a population of drugs or bioactive molecules is represented by much smaller data, in particular measured properties. Therefore, the generation of big data here must go by the increase of the number of properties registered for a single molecule, e.g., polypharmacology. Third, the availability of big data for drugs is limited because of the need to keep the secret during drug development. Therefore, in order to replace such data a library of building blocks is analyzed to probe big data behavior of the large molecular populations (Polanski et al., 2016). Formal classifications of big data and their analyses were discussed in Polanski (2017).

Science, in particular, chemistry is knowledge organized from data, that is, facts and numbers making up information. In turn, information develops chemical knowledge. Atoms, molecules, substances and their properties and transformations are the main objectives of chemistry. An unbelievably large number of molecules can be arranged from a matter available in the universe. The efficient data storage and management is needed for the control of this molecular representation, which indicates the next field of computer application in chemistry. Generally, a structure of chemical information is often chaotic which prevents its obvious transformation to in silico form. This can be illustrated by a fact that chemists often underlines chemistry is an art. This means that a human expert is needed for the efficient playing with uncertainty in the field. In turn, computer is an unsophisticated device for which uncertainty is a problem. Therefore, computer-understandable chemistry needed to be developed to store and process chemical data and information. Translating molecular data into a machine-readable and -processable structure is far from triviality. A problem is also the interaction between chemist and computer.

Chemical compounds (CC) are the main objects of chemical investigations. Surprisingly, although commonly used in chemistry a term chemical compound has never been defined by IUPAC. Historically, the ambiguity of the term CC can be related to the early term of mixts, a result of mixing different bodies (not necessarily in the contemporary chemical sense). Mixts was replaced in 18th century by composition or compounds (Bensaude-Vincent and Simon, 2012). What originally related to substances can be however also associated with molecules which are the combinations of chemical elements. Therefore, CC refers both to molecules and substances (chemical species). Actually, the meaning of the term CC is intuitively interpreted by a chemist and can indicate (Polanski and Gasteiger, 2016):

A synonym of a molecule (composed of at least two different atoms) representing a single chemical body for virtual needs (coding, in silico processing, visualization, etc.)

A molecule representing a single chemical body under measurement (e.g., a single DNA strand that can be observed, e.g., under microscopy).

A substance composed of a replicated but single molecular entity under measurement.

A chemical species under measurement when replicated is more than one molecule type.

However, a simplified meaning of a molecule is also a model-like representation that can refer both to a chemical compound that has been yet synthesized and described, or to a virtual structure (hypothetical compound) that is under design or speculation. Historical reasons decide that molecules belong to the domain of organic or inorganic chemistry. Although the organic vs. inorganic typology is more and more fuzzy the proportions of chemical compounds are approximately 1:200 in favor of organic chemistry, if we follow standard rules. The management of chemical compounds needs the efficient machine-searchable databases registering all virtual structures and real compounds that have been synthesized and described in chemical literature from the very early days to today. This problem of substantial importance for the organization of chemistry in silico is known under the term structure representation and searching (Willet, 2003) which basic concepts has been formulated as early as 1960s. Atomic composition given by molecular formulae is not sufficient to unambiguously identify a molecule. Therefore, in the broadest sense the structure of the chemical entity is defined by constitution and stereochemistry. What we mean by constitution is “the description of the identity and connectivity (and corresponding bond multiplicities) of the atoms in a molecular entity (omitting any distinction arising from their spatial arrangement, i.e., molecular stereochemistry”). Isomers are chemical entities of the same atomic composition but different constitution and/or stereochemistry or precisely isomers are “one of several species (or molecular entities) that have the same atomic composition (molecular formulae) but different line formulae or different stereochemical formulae and hence different physical and/or chemical properties.” In particular, a line formula is an example of molecular representation showing atoms that are “joined by lines representing single or multiple bonds, without any indication or implication concerning the spatial direction of bonds.”

We more and more understand in chemistry the importance of the precise shape of chemical formalism, typical for mathematics and physics. However, at the same time we would like to preserve the completeness of chemical information with its uncertainty. Therefore, we need an intelligent in silico system fitted to receive the soft chemical data without information reduction or deterioration. In this context chemical ontology is a recent solution of this problem (Hastings et al., 2011). It is a flexible dictionary like chemistry representation, a system capable of organizing the complete chemical information in silico. In other words, the strategy here is that the chaotic nature of chemical information is tamed not by the significant information reduction but by building a structure capable of accepting all variety of data and facts. The inspiration for the chemical ontology seems to be object-oriented programming where a processing of information attempts to imitate reality. We are defining here not only the data type of a data structure, but also the types of operations or functions that can be applied to the data structure. Therefore, data are structured by objects that includes both data and functions. Furthermore, relationships between the objects are defined. In particular a category of class is an extensible program-code-template for creating objects, providing initial values for state (member variables) and implementations of behavior (member functions or methods). Accordingly, let focus on chemical compound which can be defined as a class having a fixed ratio of defined atoms and a chemical structure that can be expressed by one connection table of non׳hydrogen atoms and one or more connection tables that include hydrogen atoms and bond orders as well, connected by OR logic. This allows, for example, to clearly classified all tautomeric forms of vitamin C as a single chemical compound (Bobach et al., 2012).

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## Hepatitis A Virus

John E. Bennett MD, in Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 2020

### Resistance to Physical and Chemical Agents

HAV is a relatively stable virus under a variety of environmental conditions. HAV is more resistant to heat than other picornaviruses and may not be completely inactivated (depending on the conditions) by exposure to 60°C for 10 to 12 hours.37–39 Complete inactivation in food requires heating to higher than 85°C for at least 1 minute.39 Outbreaks of hepatitis A have been reported after ingestion of steamed shellfish, suggesting that the internal temperature achieved by steaming sometimes may be insufficient to destroy the virus.40 However, HAV can be reliably inactivated by autoclaving (121°C for 30 minutes).41 Studies have also shown that HAV can be inactivated in shellfish by a nonthermal method using high hydrostatic pressure.42 The virus is resistant to most organic solvents and detergents and to a pH as low as 3.41,43 HAV can be inactivated by many common disinfecting chemicals including hypochlorite (bleach) and quaternary ammonium formulations containing 23% hydrochloric acid (HCl) (found in many toilet bowl cleaners).41 Currently licensed vaccines are inactivated by 1 : 4000 formalin at room temperature for at least 15 days to exceed complete inactivation by at least threefold. As a result of several outbreaks of hepatitis A in hemophiliacs who received factor VIII concentrates that had been treated by means of a solvent detergent method for inactivation of lipid-enveloped viruses, interest has focused on techniques capable of inactivating nonenveloped viruses without compromising the biologic activity of the product.44 Various manufacturers use different techniques to inactivate or remove HAV and human parvovirus B19. These include nanofiltration and other purification techniques, sensitive nucleic acid testing methods such as polymerase chain reaction (PCR) on minipools of source plasma, pasteurization at 60°C for 10 hours, and dry heat on lyophilized products.

## Risk assessment for metal exposures

Gunnar F. Nordberg, ... Bruce A. Fowler, in Handbook on the Toxicology of Metals (Fifth Edition), 2022

### 3.3.2 Availability of human data

Chemical substances in food and drinking water are supervised by national and international food agencies and national occupational health authorities regulate metals and their compounds occurring in workroom air. These organizations collect and use all available information in humans, in animals, and invitro as a basis for their assessments. Because the focus is on the safety of humans, epidemiological information, when available, is of special value. For metallic compounds such human data is often available (see below, Sections 3.3.33.3.6, and 6.2, Chapters 7, 16, and 17, Volume I).

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## Chemical Injuries

Ron M. Walls MD, in Rosen's Emergency Medicine: Concepts and Clinical Practice, 2018

### Chemical Agents

Chemical agents are classified as (1) nerve agents, (2) vesicants, (3) choking agents, or (4) cyanide and related toxins (Table 57.2). The first nerve agent documented was tabun, which was synthesized by German chemist Gerhard Schrader in 1937. Schrader developed tabun (military symbol: GA) while researching new insecticides. The following year, sarin (GB) was created. Other popular nerve agents include soman (GD) and VX. Although nerve agents were stockpiled for use during prior military conflicts, the first documented use in a war was in the 1980s during the Iran-Iraq War. The largest use of nerve agents by terrorists was by the Aum Shinrikyo cult of Japan, which produced both VX and sarin.

Vesicants, also known asblistering agents, are a class of drugs that produce blisters at the site of contact. Despite their discovery in the 1800s, their introduction to warfare did not occur until the 20th century. Since World War I, however, sulfur mustard (also known asmustard gas, mustard, orCAS No. 505-60-2) has remained a constant threat in modern warfare. Other vesicants include lewisite (dichloro-2-chlorovinylarsine), which is an organic arsenical, and phosgene (dichloroformoxime), which is a halogenated oxime. Although phosgene is often considered a vesicant, it technically is not, as the urticarial lesions that develop following contact are not fluid-filled.

Choking agents have been used in both military and civilian settings. Although there are many different agents and uses, the collective termchoking agent refers to a chemical that can potentially induce pulmonary edema. Phosgene and chlorine are two agents that were used in World War I. Although chlorine is no longer used as a warfare agent, it is still used widely in the industrial setting. Zinc-containing smoke is another choking agent that is used in conventional warfare. Other agents are used for riot control. These agents were discussed earlier in the Miscellaneous Gases section.

Cyanide agents, such as hydrogen cyanide or sodium azide, are cellular toxins. Cyanide was discovered in the 18th century by the Swedish chemist Carl Wilhelm Scheele. Today, hydrogen cyanide is one of the most toxic chemicals known.

## Main Characteristics of Relevance for the Assessment of Complex Inorganic Materials

Marnix Vangheluwe, ... Koen Oorts, in Risk Management of Complex Inorganic Materials, 2018

### 5.2.2 Importance of Solubility/Speciation in Complex Inorganic Materials

Depending on the solubility/speciation of the different mineral forms present in the complex inorganic material, different amounts of free metal ions will be released that may cause toxicity if the concentrations exceeds toxicological threshold values.

As indicated in Chapter 3, it is imperative for the assessment of metals and metal compounds to take into account that metals are naturally occurring and that (eco)toxicity is strongly driven by the amount of metal that is bioavailable.

For the environment, this fraction is a function of the physicochemical characteristics of the test media and the receiving environmental compartment. Extensive guidance on this topic can be found in the OECD guidance document “Guidance on the incorporation of bioavailability concepts for assessing the chemical ecological risk and/or environmental threshold values of metals and inorganic metal compounds” (OECD, 2016). For human health, more information can be found in Chapter 8.

Chemical species are specific forms of an element, defined in relation to their isotopic composition, electronic, or oxidation state, and/or complex mineral or molecular structure. Typically, inorganic UVCBs are chemically characterised by either their elemental composition and/or their speciation and/or mineralogical structure. Metal speciation includes the chemical form of the metal in solution or solid or gaseous phase, either as a free ion or complexed to a ligand. Speciation/mineralogical structure can be described on the basis of their characteristic constituting minerals, crystals, or other chemical species defining a mineralogical (crystallographic) profile. This refers to the speciation information, which is usually known for the major constituents and can be known or unknown (and often variable) for minor constituents. Chemical speciation or mineralogy may refer to the following forms:

Metallic speciation in the zero oxidation state: for example, Au, Cu, Cd, Ni, Pb, or Zn;

Soluble and sparingly soluble metal compounds: for example, CuSO4, AgCl, or PbSO4;

Minerals: for example, chalcopyrite, bornite, galena, gibbsite, and/or

Alloys: metallic speciation in the zero oxidation state.

In addition, each of the above speciation forms may be present as inclusions in other speciation forms (e.g. metallic inclusion in mineral structure) and various crystalline structures or matrices.

Models are able to predict the interactions of metals with the major (Cl, ${\text{SO}}_{4}{}^{2-}$, ${\text{HCO}}_{3}{}^{-}$, ${\text{CO}}_{3}{}^{2-}$, Br, F) and minor (OH, ${\text{H}}_{2}P{\text{O}}_{4}{}^{-}$, ${\text{HPO}}_{4}{}^{2-}$, ${\text{PO}}_{4}{}^{3-}$, HS) anions as a function of temperature, ionic strength, and pH (MINEQL+, MINTEQA2, PHREEQC, V) (Parkhurst and Appelo, 1999; Allison et al., 1991; Parker et al., 1995).

The importance of bioavailability in the environmental assessment of metals, classification, and development of environmental quality standards (EQS) has been demonstrated scientifically (Ankley et al., 1996; Allen and Hansen, 1996; Di Toro et al., 1991). The concepts and the scientific methods to assess bioavailability of metals have been proposed conceptually over a decade ago (Bergman and Dorward-King, 1996) and continue to gain recognition by regulatory authorities. Although the basic concepts defining divalent metal bioavailability were known widely by the mid-1970s, it was not until 1993 that the US EPA proposed basing water quality criteria for divalent metals on the dissolved phase (Prothro, 1993). This together with the work by Pagenkopf (1983) integrated the foregoing concepts about divalent metal speciation, bioavailability, and bioactivity into a ‘gill surface interaction modeĽ, the forerunner of the biotic ligand model (BLM) (Di Toro et al., 2001) for aquatic systems. A version of the original BLM copper model now exist for most divalent metals (multiple organisms) and accounts for the interaction of metal species complexation with organic and inorganic ligands as well as organism respiratory membranes (Schecher and McAvoy, 2001; Parkhurst and Appelo, 1999). It is also known that most divalent metals are complexed with organic ligands as described by Tipping and Hurley, (1992). The formation of metal ion-pairs or ion-complexes in natural waters can have a major effect on the rates of redox processes, mineral solubility and biochemical availability (Allen and Hansen, 1996). The form or speciation of a metal in natural waters can change its kinetic and thermodynamic properties. For example, Cu(II) in the free ionic form is toxic to phytoplankton, while copper complexed to organic ligands is non-toxic. The form of a metal in solution can also change its solubility, for example, Fe(II) is quite soluble in aqueous solutions while Fe(III) is nearly insoluble and precipitates rapidly out of solution as ferric hydroxide. Natural organic ligands interactions with Fe(III) can increase the solubility by 20-fold in seawater.

There is evidence to show that neither total nor dissolved aqueous metal concentrations are always good predictors of metal bioavailability and toxicity (Bergman and Dorward-King, 1996; Campbell, 1995).

Knowledge of the speciation/mineral composition offers several advantages as it provides toxicologists with the relevant metal speciation information needed for accurate UN GHS (United Nations Globally Harmonized System) classification as well as information for an informed environmental risk assessment. Most minerals and all elements have direct CAS numbers and for certain endpoints toxicological data are available. But most importantly, metal speciation information may illustrate that the constituents are tightly complexed in a natural mineral matrix, only slightly soluble and essentially nonbioavailable and nontoxic.

Metal speciation can be inferred from Eh–pH diagrams (Pourbaix, 1966), sequential extraction with metal analysis or it can be measured using appropriate analytical techniques. Mineralogical analyses provide information on the form in which each element is present in the UVCB (e.g. oxide, sulphide, silicate, etc.). Recent advances in analytical chemistry (e.g. microprobe assays, advanced X-ray crystallography, diffraction analysis, scanning electron microscopy/electron probe microanalysis, and synchrotron analyses) are available to define more precisely the structure and composition of the mineralogical form present in a UVCB. Frequently ion selective electrodes are used to measure free metal ions (i.e. Me++).

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## Rabies Therapeutics

Guillaume Castel, ... Noël Tordo, in Current Laboratory Techniques in Rabies Diagnosis, Research and Prevention, Volume 2, 2015

### 27.5.3 High-Throughput Screening in Infected Cells or Cell-Free Systems

Chemical compound libraries from public or private origins can be classically screened on RABV minireplicons or RABV-infected cells expressing reporter genes or on more sophisticated cell-free targets such as purified multiprotein complex (MPC). Recently, screening of interactions between newly synthesized HIV capsid proteins and their MPC host assembly machine has identified a compound (PAV-866) which is able to bind (directly or indirectly) to cellular ATP-binding cassette family E1 (ABCE1), a cellular protein playing a key role in HIV capsid formation. Interestingly, PAV-866 also inhibits RABV infection of cells in vitro.52

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## Isomers

Elaine M Aldred BSc (Hons), DC, Lic Ac, Dip Herb Med, Dip CHM, ... Kenneth Vall, in Pharmacology, 2009

### What Happens When a Compound has More Than One Chiral Centre?

Chemical compounds can have more than one chiral centre. Alpha tocopherol (Figure 6.7) is a good example of this. In this case, the nomenclature S or R is used to denote whether the methyl group is to the left (S) or right (L), respectively, counting from the aromatic end. The other notations of (+) or (−) can also be used for the various types of tocopherol (see Chapter 13 ‘Vitamins and minerals’, p. 107). All natural tocopherol is RRR. Synthetic tocopherol can have SRR, SSR, SRS, SSS, RSR, RRS, RSS and RRR forms, which is why nutritionists stress the use of natural tocopherol.

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## Chemistry/Trace/Firearm Discharge Residues

F.S. Romolo, in Encyclopedia of Forensic Sciences (Second Edition), 2013

### Vapor trapping

Chemical substances having high vapor pressure, such as NG, can be trapped by drawing a known volume of air through a trap. The trap can be a sampling tube containing a suitable material. The trapping material can be heated later, giving the trapped molecules the opportunity to return to the vapor phase and allowing chemical analysis. A special type of vapor trapping can be carried out using a fiber covered with a suitable phase (solid-phase microextraction, SPME). The SPME fiber can trap molecules in the vapor phase and release them later for analysis by heating. The item to be sampled by SPME must be closed in a sealed vessel (e.g., a piece of cloth in a multilayered bag, or a cartridge case in a vial). ‘Vapor trapping’ efficacy is increased with higher analyte vapor pressure.

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## Principles

J. Marshall Clark, Michael P. Kenna, in Handbook of Pesticide Toxicology (Second Edition), 2001

### 5.4.3 ALLELOPATHY

Chemical substances produced by some plants prevent or inhibit the growth of neighboring plants. For example, English walnut (Juglens sp.) are known to produce allelopathic substances. In Arkansas, 12 perennial ryegrasses that ranged from moderate to high stand density and 0–95% endophyte infection were evaluated for their ability to decrease crabgrass populations. Bermuda grass fairway plots were overseeded with new seed lots of the 12 cultivars in the fall of 1994 and 1995. Half of each plot was then overseeded with crabgrass each spring and evaluated for crabgrass suppression. No differences in crabgrass stand could be attributed to any of the 12 cultivars (King, 1998; King et al., 2000).

A basic laboratory evaluation for allelopathy using Lemna minor L. (duckweed) measured allelopathic effects of plant tissue extracts on the growth rate of duckweed fronds. Extracts from shoots were applied to duckweed cell plates at three concentrations. The amount of allelopathic inhibition (or stimulation) of duckweed varied with shoot tissue sample, season, and extract concentration. All cultivars affected duckweed growth, but inconsistently. Perhaps, eventually, selection of ryegrass cultivars for crabgrass inhibition may become an important part of IPM programs.

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