query: what type of bonds are found in a molecule of octane

pos: Octane a place in modern English vernacular. Octane has 18 structural isomers (24 including stereoisomers): Octane Octane is a hydrocarbon and an alkane with the chemical formula CH, and the condensed structural formula CH(CH)CH. Octane has many structural isomers that differ by the amount and location of branching in the carbon chain. One of these isomers, 2,2,4-trimethylpentane (isooctane) is used as one of the standard values in the octane rating scale. Octane is a component of gasoline (petrol). As with all low-molecular-weight hydrocarbons, octane is volatile and very flammable. "Octane" is colloquially used as a short form of "octane rating" (an

pos: Alkane Alkane In organic chemistry, an alkane, or paraffin (a historical name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in which all the carbon–carbon bonds are single. Alkanes have the general chemical formula CH. The alkanes range in complexity from the simplest case of methane (CH), where "n" = 1 (sometimes called the parent molecule), to arbitrarily large and complex molecules, like pentacontane (CH) or 6-ethyl-2-methyl-5-(1-methylethyl)octane, an isomer of tetradecane (CH) IUPAC defines alkanes as "acyclic branched or unbranched hydrocarbons having the

pos: Energy-efficient driving States built since 1996 are equipped with OBD-II on-board diagnostics and most models will have knock sensors that will automatically adjust the timing if and when pinging is detected, so low octane fuel can be used in an engine designed for high octane, with some reduction in efficiency and performance. If the engine is designed for high octane then higher octane fuel will result in higher efficiency and performance under certain load and mixture conditions. The energy released during combustion of hydrocarbon fuel increases as the molecule chain length decreases, so gasoline fuels with higher ratios of the shorter chain

pos: Viologen that the molecule is, in effect, coplanar with slight nitrogen pyramidalization, and that the central carbon bonds are longer (144 pm) than what would be expected for a double bond (136 pm). Further research shows that the diradical exists as a mixture of triplets and singlets, although an ESR signal is absent. In this sense, the molecule resembles Tschischibabin's hydrocarbon, discovered during 1907. It also shares with this molecule a blue color in solution, and a metallic-green color as crystals. Compound 3 is a very strong reducing agent, with a redox potential of −1.48 V. Viologens with 2,2'-, 4,4'-, or

neg: Cross-conjugation chain is conjugated with the side group, but all parts are not conjugated together as strongly. Examples of cross-conjugation can be found in molecules such as benzophenone, divinylketones, "p"-quinones, dendralenes, radialenes, fullerene, and Indigo dye. The type of conjugation affects reactivity and molecular electronic transitions. Cross-conjugation Cross-conjugation is a special type of conjugation in a molecule, when in a set of three Pi bonds only two pi-bonds interact with each other by conjugation, the third one is excluded from interaction. Whereas a normal conjugated system such as a polyene typically has alternating single and double bonds along consecutive atoms, a

neg: Fullerene the type made of twenty hexagons and twelve pentagons, with a carbon atom at the vertices of each polygon and a bond along each polygon edge. The van der Waals diameter of a C molecule is about 1.1 nanometers (nm). The nucleus to nucleus diameter of a C molecule is about 0.71 nm. The C molecule has two bond lengths. The 6:6 ring bonds (between two hexagons) can be considered "double bonds" and are shorter than the 6:5 bonds (between a hexagon and a pentagon). Its average bond length is 1.4 angstroms. Silicon buckyballs have been created around metal ions.

neg: Bicyclic molecule bicyclo[1.1.0]butane is typically called simply bicyclobutane. The heterocyclic molecule DABCO has a total of 8 atoms in its bridged structure, hence the root name octane. Note that here the two bridgehead atoms are nitrogen instead of carbon atoms. Therefore, the official name gets the additional prefix "1,4-diaza" and the total name becomes 1,4-diazabicyclo[2.2.2]octane. Bicyclic molecule A bicyclic molecule ("bi" = two, "cycle" = ring) is a molecule that features two joined rings. Bicyclic structures occur widely, for example in many biologically important molecules like α-thujene and camphor. A bicyclic compound can be carbocyclic (all of the ring atoms are carbons),

neg: Erythrolitmin a shorter wavelength. This is what causes the molecule to appear red in the presence of an acid. Erythrolitmin Erythrolitmin (also called erythrolein) is the active ingredient extracted from the Litmus lichen, used in chemistry as a pH indicator. The erythrolitmin molecule is related to the orceins, and consists essentially of several phenoxazone and orcinol residues. The intense coloring of the molecule is generated by the absorption of specific wavelengths of light by the pi bonds. These bonds are ordinarily excited by light in the orange region of the spectrum, causing the molecule to appear blue. When the molecule interacts

neg: Ultra-high-molecular-weight polyethylene and increasingly in medical devices. UHMWPE is a type of polyolefin. It is made up of extremely long chains of polyethylene, which all align in the same direction. It derives its strength largely from the length of each individual molecule (chain). Van der Waals bonds between the molecules are relatively weak for each atom of overlap between the molecules, but because the molecules are very long, large overlaps can exist, adding up to the ability to carry larger shear forces from molecule to molecule. Each chain is bonded to the others with so many van der Waals bonds that the

neg: Phi bond example of a molecule purported to contain a phi bond (a U−U bond, in the molecule U). Phi bond In chemistry, phi bonds (φ bonds) are covalent chemical bonds, where six lobes of one involved atomic orbital overlap six lobes of the other involved atomic orbital. This overlap leads to the formation of a bonding molecular orbital with three nodal planes which contain the internuclear axis and go through both atoms. The Greek letter φ in their name refers to f orbitals, since the orbital symmetry of the φ bond is the same as that of the usual (6-lobed) type

neg: Sigma bond than 1 sigma bond between any two atoms. Molecules with rings have additional sigma bonds, such as benzene rings, which have 6 C−C sigma bonds within the ring for 6 carbon atoms. The anthracene molecule, CH, has three rings so that the rule gives the number of sigma bonds as 24 + 3 − 1 = 26. In this case there are 16 C−C sigma bonds and 10 C−H bonds. Sigma bond In chemistry, sigma bonds (σ bonds) are the strongest type of covalent chemical bond. They are formed by head-on overlapping between atomic orbitals. Sigma bonding is most simply

neg: Collagen, type III, alpha 1 Collagen, type III, alpha 1 Collagen alpha-1(III) chain also known as alpha 1 chain of type III collagen is a protein that in humans is encoded by the "COL3A1" gene. Three of these alpha 1 protein molecules, or chains, are required to form the type III collagen molecule which has a long triple-helical domain. Type III collagen is synthesized by cells as a pre-procollagen. The signal peptide is cleaved off producing a procollagen molecule. Three identical type III procollagen chains come together in the carboxy-terminal ends, and the structure is stabilized by the formation of disulphide bonds. Each individual chain

neg: Field effect (chemistry) were inductive the conformational position would not matter. Field effect (chemistry) A field effect is the polarization of a molecule through space. The effect is a result of an electric field produced by charge localization in a molecule. This field, which is substituent and conformation dependent, can influence structure and reactivity by manipulating the location of electron density in bonds and/or the overall molecule. The polarization of a molecule through its bonds is a separate phenomenon known as induction. Field effects are relatively weak, and diminish rapidly with distance, but have still been found to alter molecular properties such as

neg: Field effect (chemistry) Field effect (chemistry) A field effect is the polarization of a molecule through space. The effect is a result of an electric field produced by charge localization in a molecule. This field, which is substituent and conformation dependent, can influence structure and reactivity by manipulating the location of electron density in bonds and/or the overall molecule. The polarization of a molecule through its bonds is a separate phenomenon known as induction. Field effects are relatively weak, and diminish rapidly with distance, but have still been found to alter molecular properties such as acidity. Field effects can arise from the electric

neg: Hydrogen bond bonds of a water molecule is up to four. The number of hydrogen bonds formed by a molecule of liquid water fluctuates with time and temperature. From TIP4P liquid water simulations at 25 °C, it was estimated that each water molecule participates in an average of 3.59 hydrogen bonds. At 100 °C, this number decreases to 3.24 due to the increased molecular motion and decreased density, while at 0 °C, the average number of hydrogen bonds increases to 3.69. A more recent study found a much smaller number of hydrogen bonds: 2.357 at 25 °C. The differences may be due

neg: Quadruple bond to give a bond order of 2, meaning that there exists a double bond between the two carbons in a dicarbon (C) molecule. The molecular orbital diagram of diatomic carbon would show that there are two pi bonds and no sigma bonds. However, a recent paper by S. Shaik et al. has suggested that a quadruple bond exists in diatomic carbon. Quadruple bond A quadruple bond is a type of chemical bond between two atoms involving eight electrons. This bond is an extension of the more familiar types double bonds and triple bonds. Stable quadruple bonds are most common among

neg: Phosphorane Phosphorane A phosphorane (IUPAC name: λ-phosphane) is a functional group in organophosphorus chemistry with pentavalent phosphorus. It has the general formula PR. The parent hydride compound is the hypothetical molecule PH. The derivative pentaphenylphosphorane (PhP) is stable. Phosphoranes adopt a trigonal bipyramidal molecular geometry with the two apical bonds longer than the three equatorial bonds. Hypervalent bonding is described by inclusion of non-bonding MOs, as also invoked for the closely related molecule phosphorus pentafluoride. Phosphoranes of the type RP=CR are more common and more important. Phosphoranes are also considered to be one of the resonance structures of ylides, these compounds

neg: Neutral network (evolution) neutral) nucleotide substitution mutations of DNA must dominate. He computed that such mutations were occurring at the rate of roughly 0-5 per year per gamete. In later years, a new paradigm emerged, that placed RNA as a precursor molecule to DNA. A primordial molecule principle was put forth as early as 1968 by Crick, and lead to what is now known as The RNA World Hypothesis. DNA is found, predominantly, as fully base paired double helices, while biological RNA is single stranded and often exhibits complex base-pairing interactions. These are due to its increased ability to form hydrogen bonds, a

neg: Skeletal formula computer software. Hydrogen bonds are generally denoted by dotted or dashed lines. In other contexts, dashed lines may also represent partially formed or broken bonds in a transition state. Skeletal formula The skeletal formula, also called line-angle formula or shorthand formula, of an organic compound is a type of molecular structural formula that serves as a shorthand representation of a molecule's bonding and some details of its molecular geometry. A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule. It is represented in two dimensions, as

neg: Hypervalent molecule show an inverse correlation between bond length and bond overlap for all series. Pentacoordinated species are concluded to be more reactive because of their looser bonds as trigonal-bipyramidal structures. By calculating the energies for the addition and removal of a fluoride ion in various silicon and phosphorus species, several trends were found. In particular, the tetracoordinated species have much higher energy requirements for ligand removal than do pentacoordinated species. Further, silicon species have lower energy requirements for ligand removal than do phosphorus species, which is an indication of weaker bonds in silicon. Hypervalent molecule A hypervalent molecule (the phenomenon is

neg: Chemical polarity polar bonds at 120°. This results in no overall dipole in the molecule. Not every molecule with polar bonds is a polar molecule. Carbon dioxide (CO) has two polar C=O bonds, but the geometry of CO is linear so that the two bond dipole moments cancel and there is no net molecular dipole moment; the molecule is nonpolar. Examples of household nonpolar compounds include fats, oil, and petrol/gasoline. Therefore, most nonpolar molecules are water-insoluble (hydrophobic) at room temperature. Many nonpolar organic solvents, such as turpentine, are able to dissolve non-polar substances. In the methane molecule (CH) the four C−H bonds

neg: Compounds of fluorine molecules of the neighboring element oxygen, with two unpaired electrons per molecule, are paramagnetic (attracted to magnets). The fluorine–fluorine bond of the difluorine molecule is relatively weak when compared to the bonds of heavier dihalogen molecules. The bond energy is significantly weaker than those of Cl or Br molecules and similar to the easily cleaved oxygen–oxygen bonds of peroxides or nitrogen–nitrogen bonds of hydrazines. The covalent radius of fluorine of about 71 picometers found in F molecules is significantly larger than that in other compounds because of this weak bonding between the two fluorine atoms. This is a result of

neg: Homonuclear molecule Homonuclear molecule Homonuclear molecules, or homonuclear species, are molecules composed of only one type of element. Homonuclear molecules may consist of various numbers of atoms, depending on the element's properties. Some elements form molecules of more than one size. Noble gases rarely form bonds, so they only have one atom. The most familiar homonuclear molecules are diatomic, meaning they consist of two atoms, though not all diatomic molecules are homonuclear. Homonuclear diatomic molecules include hydrogen (H), oxygen (O), nitrogen (N) and all of the halogens. Ozone (O) is a common triatomic homonuclear molecule. Homonuclear tetratomic molecules include arsenic (As) and

neg: Organogels and B reactive sites are the same, then pp can be condensed to p and values for the fraction of all bonds at which an infinite network will form can be found. f and f are defined as above, where N are the number of moles of Ai containing f functional groups for each type of A functional molecule. Typically, gels are synthesized via sol-gel processing, a wet-chemical technique involving a colloidal solution (sol) that acts as the precursor for an integrated network (gel). There are two possible mechanisms whereby organogels form depending on the physical intermolecular inter-actions, namely the

neg: Heterocumulene Heterocumulene A heterocumulene is a molecule containing a chain of at least three double bonds between consecutive atoms, in which one or more atoms in the doubly bonded chain is a heteroatom. Such a molecule is analogous to a cumulene in which the chain of doubly bonded atoms contains only carbon, except that at least one carbon is replaced by a heteroatom. Some authors extend the definition to include molecules with chains of only two double bonds between consecutive atoms, also known as "heteroallenes". Heterocumulenes are commonly found in outer space or during combustion. Most of the longer ones are

neg: LEKTI LEKTI Lympho-epithelial Kazal-type-related inhibitor (LEKTI) also known as serine protease inhibitor Kazal-type 5 (SPINK5) is a protein that in humans is encoded by the "SPINK5" gene. LEKTI is a large multidomain serine protease inhibitor expressed in stratified epithelial tissue. It consists of 15 domains that are cleaved into smaller, functional fragments by the protease furin. Only two of these domains (2 and 15) contain 6 evenly spaced cysteines responsible for 3 intramolecular disulfide bonds characteristic of Kazal-type related inhibitors. The remaining domains contain 4 cysteines. These disulfide bonds force the molecule into a rigid conformation that enables the protein to

neg: Hypervalent molecule a hexacoordinate molecule such as sulfur hexafluoride, each of the six bonds is the same length. The rationalization described above can be applied to generate 15 resonance structures each with four covalent bonds and two ionic bonds, such that the ionic character is distributed equally across each of the sulfur-fluorine bonds. Spin-coupled valence bond theory has been applied to diazomethane and the resulting orbital analysis was interpreted in terms of a chemical structure in which the central nitrogen has five covalent bonds; This led the authors to the interesting conclusion that "Contrary to what we were all taught as undergraduates,

neg: Hypervalent molecule that are normally written with ionic bonds in order to conform to the octet rule, such as ozone O, nitrous oxide NNO, and trimethylamine N-oxide (CH)NO, are found to be genuinely hypervalent. Examples of γ calculations for phosphate PO (γ(P) = 2.6, non-hypervalent) and orthonitrate NO (γ(N) = 8.5, hypervalent) are shown below. Early considerations of the geometry of hypervalent molecules returned familiar arrangements that were well explained by the VSEPR model for atomic bonding. Accordingly, AB and AB type molecules would possess a trigonal bi-pyramidal and octahedral geometry, respectively. However, in order to account for the observed bond angles,

neg: Chromophore conformational change of the molecule when hit by light. In the conjugated chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds, often in aromatic systems. Common examples include retinal (used in the eye to detect light), various food colorings, fabric dyes (azo compounds), pH indicators, lycopene, β-carotene, and anthocyanins. Various factors in a chromophore's structure go into determining at what wavelength region in a spectrum the chromophore will absorb. Lengthening or extending a conjugated system with more unsaturated (multiple) bonds in a molecule will tend to shift

neg: Compounds of oxygen atoms, oxygen and hydrogen, with atoms of nearby water molecules. Hydrogen atoms are covalently bonded to oxygen in a water molecule but also have an additional attraction (about 23.3 kJ·mol per hydrogen atom) to an adjacent oxygen atom in a separate molecule. These hydrogen bonds between water molecules hold them approximately 15% closer than what would be expected in a simple liquid with just Van der Waals forces. Due to its electronegativity, oxygen forms chemical bonds with almost all other free elements at elevated temperatures to give corresponding oxides. However, some elements, such as iron which oxidises to iron oxide,

neg: TENM3 residues and is found immediately distal to the transmembrane domain. This is followed by eight phylogenetically conserved tenascin C-type EGF-like repeats, which features the uniquely conserved replacement of a single cysteine in repeats 2 and 5 in place of the original tyrosine and phenylalanine residues respectively. Since cysteines are susceptible to forming disulfide bonds, the single cysteines at the EGF-like repeats of a teneurin molecule can facilitate the homophilic and heterophilic dimerisation of teneurin family molecules. More distally is the globular domain consisting of a 700-800 amino acid residue region. There are 17 conserved cysteine residues, a region of NHL

neg: Polymorphism (materials science) a pyridinium salt. The review also questioned whether the polymorphs offered any advantages to the existing drug: something clearly demanded in a new patent. Acetylsalicylic acid has an elusive second polymorph that was first discovered by Vishweshwar et al.; fine structural details were given by Bond et al. A new crystal type was found after attempted co-crystallization of aspirin and levetiracetam from hot acetonitrile. In form I, two aspirin molecules form centrosymmetric dimers through the acetyl groups with the (acidic) methyl proton to carbonyl hydrogen bonds, and, in form II, each aspirin molecule forms the same hydrogen bonds, but then

neg: Octaazacubane Octaazacubane Octaazacubane is a hypothetical explosive allotrope of nitrogen with formula N, whose molecules have eight atoms arranged into a cube. (By comparison, nitrogen usually occurs as the diatomic molecule N.) It can be regarded as a cubane-type cluster, where all eight corners are nitrogen atoms bonded along the edges. It is predicted to be a metastable molecule, in which despite the thermodynamic instability caused by bond strain, and the high energy of the N–N single bonds, the molecule remains kinetically stable for reasons of orbital symmetry. Octaazacubane is predicted to have an energy density (assuming decomposition into N) of

neg: CGAS–STING cytosolic DNA sensing pathway Here they are stabilized through base stacking, hydrogen bonds, and divalent cations in order to catalyze phosphodiester bond formation to produce the cyclic dinucleotide cGAMP. Cyclic GMP-AMP (cGAMP) is a cyclic dinucleotide (CDN) and the first to be found in metazoans. Other CDNs (c-di-GMP and c-di-AMP) are commonly found in bacteria, archaea, and protozoa. As the name suggests, cGAMP is cyclic molecule composed of one Adenine monophosphate (AMP) and one Guanine monophosphate (GMP) connected by two phosphodiester bonds. However, cGAMP differs from other CDNs in that it contains a unique phosphodiester bonds between the 2’ OH of GMP and the

neg: Trisulfur Trisulfur The molecule or trisulfur or sulfur trimer or thiozone or triatomic sulfur is an allotrope of sulfur. It occurs as a mixture in liquid and gaseous sulfur and also at cryogenic temperatures as a solid. Under standard conditions it is unstable and self reacts to solid sulfur cyclooctasulfur. The molecule shape is similar to that of ozone. is found in sulfur vapour, comprising 10% of vapour species at and . It is cherry red in colour, with a bent structure, similar to ozone, . The bonds between the atoms are not full double bonds (as this would require two

neg: Conjugated system a lesser extent) are occupied by six electrons, while three destabilized orbitals of overall antibonding character remain unoccupied. The result is strong thermodynamic and kinetic aromatic stabilization. Both models describe rings of π electron density above and below the framework of C–C σ bonds. Not all compounds with alternating double and single bonds are aromatic. Cyclooctatetraene, for example, possesses alternating single and double bonds. The molecule typically adopts a "tub" conformation. Because the p orbitals of the molecule do not align themselves well in this non-planar molecule, the π bonds are essentially isolated and not conjugated. The lack of conjugation

neg: Bond energy selected typical chemical species containing that type of bond. Bond energy ("E") or bond enthalpy ("H") should not be confused with bond-dissociation energy. Bond energy is the average of all the bond-dissociation energies in a molecule, and will show a different value for a given bond than the bond-dissociation energy would. This is because the energy required to break a single bond in a specific molecule differs for each bond in that molecule. For example, methane has four C–H bonds and the bond-dissociation energies are 435 kJ/mol for "D"(CH–H), 444 kJ/mol for "D"(CH–H), 444 kJ/mol for "D"(CH–H) and 339 kJ/mol

neg: Chemical polarity "nonpolar covalent", or "ionic", this is often a relative term, with one molecule simply being "more polar" or "more nonpolar" than another. However, the following properties are typical of such molecules. A molecule is composed of one or more chemical bonds between molecular orbitals of different atoms. A molecule may be polar either as a result of polar bonds due to differences in electronegativity as described above, or as a result of an asymmetric arrangement of nonpolar covalent bonds and non-bonding pairs of electrons known as a full molecular orbital. A polar molecule has a net dipole as a result

neg: Carcerand imine bonds with sodium borohydride. Carcerand A carcerand is a host molecule that completely entraps its guest so that it will not escape even at high temperatures. This type of molecule was first described by Donald J. Cram in 1985 and is derived from the Latin "carcer", or prison. The complexes formed by a carcerand with permanently imprisoned guests are called carceplexes. In contrast hemicarcerands allow guests to enter and exit the cavity at high temperatures but will form stable complexes at ambient temperatures. The complexes formed by a hemicarcerand and a guest are called hemicarceplexes. Cram described the interior

neg: Conjugated system intensely red. The corrin unit has six conjugated double bonds but is not conjugated all the way around its macrocycle ring. Conjugated systems form the basis of chromophores, which are light-absorbing parts of a molecule that can cause a compound to be colored. Such chromophores are often present in various organic compounds and sometimes present in polymers that are colored or glow in the dark. Chromophores often consist of a series of conjugated bonds and/or ring systems, commonly aromatic, which can include C–C, C=C, C=O, or N=N bonds. Conjugated chromophores are found in many organic compounds including azo dyes (also

neg: Erythrolitmin Erythrolitmin Erythrolitmin (also called erythrolein) is the active ingredient extracted from the Litmus lichen, used in chemistry as a pH indicator. The erythrolitmin molecule is related to the orceins, and consists essentially of several phenoxazone and orcinol residues. The intense coloring of the molecule is generated by the absorption of specific wavelengths of light by the pi bonds. These bonds are ordinarily excited by light in the orange region of the spectrum, causing the molecule to appear blue. When the molecule interacts with protons from an acid the bonds become harder to excite and thus absorb green light which has

neg: Chemical bond the physical pictures of the valence bond and molecular orbital theories and is difficult to extend to larger molecules. Because atoms and molecules are three-dimensional, it is difficult to use a single method to indicate orbitals and bonds. In molecular formulas the chemical bonds (binding orbitals) between atoms are indicated in different ways depending on the type of discussion. Sometimes, some details are neglected. For example, in organic chemistry one is sometimes concerned only with the functional group of the molecule. Thus, the molecular formula of ethanol may be written in conformational form, three-dimensional form, full two-dimensional form (indicating every

neg: Sigma bond acetate. Organic molecules are often cyclic compounds containing one or more rings, such as benzene, and are often made up of many sigma bonds along with pi bonds. According to the sigma bond rule, the number of sigma bonds in a molecule is equivalent to the number of atoms plus the number of rings minus one. A molecule with no rings can be represented as a tree with a number of bonds equal to the number of atoms minus one (as in dihydrogen, H, with only one sigma bond, or ammonia, NH, with 3 sigma bonds). There is no more

neg: Yves Chauvin double bonds. One of the double bonds connects two parts of an organic molecule. The other double bond connects a metal-based catalyst to a fragment of an organic molecule. In metathesis, these two double bonds combine and split to make four single bonds. The single bonds form a ring that connects the metal catalyst, the organic fragment, and the two parts of the organic molecule. The metal catalyst then breaks off from the ring, carrying away part of the organic molecule. This process leaves the fragment attached to the remainder of the organic molecule with a double bond, forming a

neg: Functional group of one or more atoms of distinctive chemical properties no matter what they are attached to. The atoms of functional groups are linked to each other and to the rest of the molecule by covalent bonds. For repeating units of polymers, functional groups attach to their nonpolar core of carbon atoms and thus add chemical character to carbon chains. Functional groups can also be charged, e.g. in carboxylate salts (–COO), which turns the molecule into a polyatomic ion or a complex ion. Functional groups binding to a central atom in a coordination complex are called "ligands". Complexation and solvation are

neg: Ring strain compounds that is isolatable on a large scale; its strain energy is estimated at 63.9 kcal mol (267 kJ mol). The potential energy and unique bonding structure contained in the bonds of molecules with ring strain can be used to drive reactions in organic synthesis. Examples of such reactions are Ring opening metathesis polymerisation, photo-induced ring opening of cyclobutenes, and nucleophilic ring-opening of epoxides and aziridines. Ring strain In organic chemistry, ring strain is a type of instability that exists when bonds in a molecule form angles that are abnormal. Strain is most commonly discussed for small rings such as

neg: Td Molecular Orbitals representations found in the character table. Manipulation of reducible representations explain how many σ molecular orbitals and π molecular orbitals are found in the molecule. There are multiple methods utilizing reducible representations; two examples using methane are described below: Method one This method involves determining the reducible representations of the C-H bonds and the x, y, and z axes to determine the σ and π orbitals. 1. Considering C-H bonds (Γ) With this reducible representation for C-H bond, the following equation can be used for each irreducible representation in order to determine whether it composes Γ: n=1/h∑Nχχ In the above

neg: Cheletropic reaction orbital of the small molecule are pointed directly at the π-system. In the non-linear approach, the orbital approaches at a skew angle. The π-system's ability to rotate as the small molecule approaches is crucial in forming new bonds. The direction of rotation will be different depending on how many π-electrons are in the system. Shown below is a diagram of a two-electron fragment approaching a four-electron π-system using frontier molecular orbitals. The rotation will be disrotatory if the small molecule approaches linearly and conrotatory if the molecule approaches non-linearly. Disrotatory and conrotatory are sophisticated terms expressing how the bonds in

neg: Molecular geometry of two joined atoms, bond angles of three connected atoms, and torsion angles (dihedral 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 (external) quantum mechanical motions translation and rotation hardly change the geometry of the molecule. (To some extent rotation influences the geometry via Coriolis forces and centrifugal distortion, but this is negligible for the present discussion.) In addition to translation and rotation, a third type of motion is molecular vibration, which corresponds to internal motions of the

neg: Ketchup between the negatively charged oxygens on each molecule. The hydroxyls on each molecule will be able to form hydrogen bonds with the water in the product. The addition of salt will reduce the repulsive interactions between the negatively charged side chains of acetic acid and pectin within solution because they will create bonds with the dissociated sodium and chloride ions. The hydrogen bonds and electrostatic interactions will encourage leaching because the formation of bonds associated with the need for molecules to be in the lowest energy state are not always bonds that happen between different molecules and instead are formed

neg: Mitochondrial DNA genomes, classified by their structure (e.g. circular versus linear), size, presence of introns or plasmid like structures, and whether the genetic material is a singular molecule or collection of homogeneous or heterogeneous molecules. There is only one mitochondrial genome type found in animal cells. This genome usually contains one circular molecule with between 11–28 kbp of genetic material (type 1). There are three different genome types found in plants and fungi. The first type is a circular genome that has introns (type 2) and may range from 19 to 1000 kbp in length. The second genome type is a circular

neg: Gene silencing Hammerhead, hairpin, and hepatitis delta virus (HDV) ribozyme motifs are generally found in viruses or viroid RNAs. These motifs are able to self-cleave a specific phosphodiester bond on an mRNA molecule. Lower eukaryotes and a few bacteria contain group I and group II ribozymes. These motifs can self-splice by cleaving and joining together phosphodiester bonds. The last ribozyme motif, the RNase P ribozyme, is found in "Escherichia coli" and is known for its ability to cleave the phosphodiester bonds of several tRNA precursors when joined to a protein cofactor. The general catalytic mechanism used by ribozymes is similar to the

neg: Glycoside been developed that can form glycosidic bonds in excellent yield. There are many ways to chemically synthesize glycosidic bonds. Fischer glycosidation refers to the synthesis of glycosides by the reaction of unprotected monosaccharides with alcohols (usually as solvent) in the presence of a strong acid catalyst. The Koenigs-Knorr reaction is the condensation of glycosyl halides and alcohols in the presence of metal salts such as silver carbonate or mercuric oxide. Glycosides can be classified by the glycone, by the type of glycosidic bond, and by the aglycone. If the glycone group of a glycoside is glucose, then the molecule is

neg: Seesaw molecular geometry Seesaw molecular geometry Disphenoidal or Seesaw is a type of molecular geometry where there are four bonds to a central atom with overall C symmetry. The name "seesaw" comes from the observation that it looks like a playground seesaw. Most commonly, four bonds to a central atom result in tetrahedral or, less commonly, square planar geometry. The seesaw geometry, just like its name, is unusual. It occurs when a molecule has a steric number of 5, with the central atom being bonded to 4 other atoms and 1 lone pair (AXE in AXE notation). An atom bonded to 5 other

neg: Seesaw molecular geometry the disphenoidal molecular geometry (see image at upper right). The following compounds and ions have disphenoidal geometry: Seesaw molecular geometry Disphenoidal or Seesaw is a type of molecular geometry where there are four bonds to a central atom with overall C symmetry. The name "seesaw" comes from the observation that it looks like a playground seesaw. Most commonly, four bonds to a central atom result in tetrahedral or, less commonly, square planar geometry. The seesaw geometry, just like its name, is unusual. It occurs when a molecule has a steric number of 5, with the central atom being bonded to

neg: Dyotropic reaction reaction is concerted. Stepwise mechanisms in dyotropic reactions have also been investigated. In organic synthesis an important application is the conversion of 4-substituted-gamma-lactones to butyrolactones. Type I dyotropic rearrangements also occur around carbon-oxygen bonds, such as the thermal equilibration of RRSiRC-O-SiR to RRSiRC-O-SiR. The 1,2-Wittig rearrangement can also be considered an example of this reaction type. More dyotropic reactions are found involving N-O bonds and N-N bonds. Type II rearrangements often involve double hydrogen migration in a carbon skeleton. This reaction type can be found in certain transfer hydrogenations. An example is hydrogen transfer in syn-sesquinorbornene disulfones. Dyotropic reaction A

neg: Metal oxide adhesion to elastic-plastic debonding. This is due to a larger number of bonds being formed or an increase in strength of the bonds between the two materials. Elastic-plastic debonding is when local stresses are high enough to move dislocations or make new ones. When a gas molecule strikes a solid surface the molecule may either rebound or be adsorbed. The rate at which gas molecules strike the surface is a large factor in the overall kinetics of oxide growth. If there molecule is absorbed there are three potential outcomes. The surface interaction can be strong enough to dissociate the gas molecule

neg: Jet fuel defined by the requirements for the product, such as the freezing or smoke point. Kerosene-type jet fuel (including Jet A and Jet A-1) has a carbon number distribution between about 8 and 16 (carbon atoms per molecule); wide-cut or naphtha-type jet fuel (including Jet B), between about 5 and 15. Fuel for piston-engine powered aircraft (usually a high-octane gasoline known as avgas) has a high volatility to improve its carburetion characteristics and high autoignition temperature to prevent preignition in high compression aircraft engines. Turbine engines (like diesel engines) can operate with a wide range of fuels because fuel is injected

neg: Hydrate can form clathrate hydrates with water, especially under high pressure. Although there is no hydrogen bonding between water and guest molecules when methane is the guest molecule of the clathrate, guest-host hydrogen bonding often forms when the guest is a larger organic molecule such as tetrahydrofuran. In such cases the guest-host hydrogen bonds result in the formation of L-type Bjerrum defects in the clathrate lattice. The stability of hydrates is generally determined by the nature of the compounds, their temperature, and the relative humidity (if they are exposed to air). Hydrate In chemistry, a hydrate is a substance that contains

neg: Chemical compound covalent bonds, salts held together by ionic bonds, intermetallic compounds held together by metallic bonds, or the subset of chemical complexes that are held together by coordinate covalent bonds. Pure chemical elements are generally not considered chemical compounds, failing the two or more atom requirement, though they often consist of molecules composed of multiple atoms (such as in the diatomic molecule H, or the polyatomic molecule S, etc.). Many chemical compounds have a unique numerical identifier assigned by the Chemical Abstracts Service (CAS): its CAS number. There is varying and sometimes inconsistent nomenclature differentiating substances, which include truly non-stoichiometric examples,

neg: Jean-Marie Lehn premise for an entire new field in chemistry, sensors. Such mechanisms also play a great role in molecular biology. These cryptands, as Lehn dubbed them, became his main center of interest, and led to his definition of a new type of chemistry, "supramolecular chemistry", which instead of studying the bonds inside one molecule, looks at intermolecular attractions, and what would be later called "fragile objects", such as micelles, polymers, or clays. In 1980, he was elected to become a teacher at the prestigious Collège de France, and in 1987 was awarded the Nobel Prize, alongside Donald Cram and Charles Pedersen

neg: Hyperconjugation "...a method that uses only the pi orbitals of the interacting fragments in the geometry of the molecule for estimating pi interactions." For this type of analysis, the formation of bonds between various molecular moieties is a combination of three component terms. ΔE represents what Fernández and Frenking call a molecule’s “quasiclassical electrostatic attractions.” The second term, ΔE, represents the molecule’s Pauli repulsion. ΔE, the third term, represents stabilizing interactions between orbitals, and is defined as the sum of ΔE and ΔE. The total energy of interaction, ΔE, is the result of the sum of the 3 terms. A group

neg: Bredt's rule in the smaller ring system. An anti-bredt molecule is one that is found to exist and be stable (within certain parameters) despite this rule. A recent (2006) example of such a molecule is 2-quinuclidonium tetrafluoroborate. Bridgehead double bonds can be found in some natural products, discussed in a review by Mak, Pouwer and Williams, and an older review by Shea looked at bridgehead alkenes more generally. Bredt's rule Bredt's rule is an empirical observation in organic chemistry that states that a double bond cannot be placed at the bridgehead of a bridged ring system, unless the rings are large enough.

neg: 2,2'-Bis(2-indenyl) biphenyl 2,2'-Bis(2-indenyl) biphenyl 2,2'-Bis(2-indenyl) biphenyl is a ligand used to make organometallic complexes involving two aromatic-stabilized cyclopentadienyl-type carbocycle-to-metal atom bonds, complexes with distinct shapes and catalytic properties. The symmetry of the molecule--apparent in corresponding "top" and "bottom" halves of the molecule, connected together by a carbon-carbon bond between the two benzene rings (phenyl rings, see picture)--allows the two five-membered rings to participate in bonding on opposite sides of a metal atom, creating a type of sandwich compound. A prerequisite for the bonding is deprotonation of the cyclopentadiene-type five-membered ring to form the two anionic carbocycles that bind to the metal atom.

neg: Cross-conjugation Cross-conjugation Cross-conjugation is a special type of conjugation in a molecule, when in a set of three Pi bonds only two pi-bonds interact with each other by conjugation, the third one is excluded from interaction. Whereas a normal conjugated system such as a polyene typically has alternating single and double bonds along consecutive atoms, a cross-conjugated system has an alkene unit bonded to one of the middle atoms of another conjugated chain through a single bond. In classical terms, one of the double-bonds branches off rather than continuing consecutively: the main chain is conjugated, and part of that same main

neg: Buckminsterfullerene bond along each polygon edge. The van der Waals diameter of a molecule is about 1.01 nanometers (nm). The nucleus to nucleus diameter of a molecule is about 0.71 nm. The molecule has two bond lengths. The 6:6 ring bonds (between two hexagons) can be considered "double bonds" and are shorter than the 6:5 bonds (between a hexagon and a pentagon). Its average bond length is 0.14 nm. Each carbon atom in the structure is bonded covalently with 3 others. Buckminsterfullerene is the largest object observed to exhibit wave–particle duality; theoretically every object exhibits this behavior. The compound is stable,

neg: Oxygen 23.3 kJ/mol per hydrogen atom) to an adjacent oxygen atom in a separate molecule. These hydrogen bonds between water molecules hold them approximately 15% closer than what would be expected in a simple liquid with just van der Waals forces. Due to its electronegativity, oxygen forms chemical bonds with almost all other elements to give corresponding oxides. The surface of most metals, such as aluminium and titanium, are oxidized in the presence of air and become coated with a thin film of oxide that passivates the metal and slows further corrosion. Many oxides of the transition metals are non-stoichiometric compounds,

neg: Amylopectin Amylopectin Amylopectin is a water-insoluble polysaccharide and highly branched polymer of α-glucose units found in plants. It is one of the two components of starch, the other being amylose. Glucose units are linked in a linear way with α(1→4) glycosidic bonds. Branching takes place with α(1→6) bonds occurring every 24 to 30 glucose units, resulting in a soluble molecule that can be quickly degraded as it has many end points onto which enzymes can attach. In contrast, amylose contains very few α(1→6) bonds, or even none at all. This causes amylose to be hydrolyzed more slowly, but have higher density

neg: Metalation Metalation Metalation (Alt. Spelling: Metallation) is a chemical reaction which involves the bonding of a metal atom to what is typically an organic molecule to form a new compound. This reaction usually involves the replacement of a halogen atom in an organic molecule with a metal atom to form an organometallic compound. In the laboratory, metalation is commonly used to activate organic molecules during the formation of C—X bonds (where X is typically Carbon, Oxygen, or Nitrogen), which are necessary for the synthesis of many organic molecules. In synthesis, metallated reagents are typically involved in nucleophilic substitution, single-electron-transfer (SET), and

neg: Tennessine molecule. Such molecules are commonly bound via single sigma bonds between the atoms; these are different from pi bonds, which are divided into two parts, each shifted in a direction perpendicular to the line between the atoms, and opposite one another rather than being located directly between the atoms they bind. Sigma bonding has been calculated to show a great antibonding character in the At molecule and is not as favorable energetically. Tennessine is predicted to continue the trend; a strong pi character should be seen in the bonding of Ts. The molecule tennessine chloride (TsCl) is predicted to go

neg: Trisulfur are single. It is isoelectronic to sulfur dichloride. Trisulfur The molecule or trisulfur or sulfur trimer or thiozone or triatomic sulfur is an allotrope of sulfur. It occurs as a mixture in liquid and gaseous sulfur and also at cryogenic temperatures as a solid. Under standard conditions it is unstable and self reacts to solid sulfur cyclooctasulfur. The molecule shape is similar to that of ozone. is found in sulfur vapour, comprising 10% of vapour species at and . It is cherry red in colour, with a bent structure, similar to ozone, . The bonds between the atoms are not

neg: Elimination reaction 0.85 consistent with a S2 reaction because in this reaction type the C-H bonds tighten in the transition state. The KIE's for the ethyl (0.99) and isopropyl (1.72) analogues suggest competition between the two reaction modes. Elimination reaction In most organic elimination reactions, at least one hydrogen is lost to form the double bond: the unsaturation of the molecule increases. It is also possible that a molecule undergoes reductive elimination, by which the valence of an atom in the molecule decreases by two, though this is more common in inorganic chemistry. An important class of elimination reactions is those involving

neg: 2-sec-Butyl-4,5-dihydrothiazole 2-sec-Butyl-4,5-dihydrothiazole 2-"sec"-Butyl-4,5-dihydrothiazole (also known as SBT) is a thiazoline compound with the molecular formula CHNS. A volatile pheromone found in rodents such as mice and rats, SBT is excreted in the urine and promotes aggression amongst males while inducing synchronized estrus in females. Mouse major urinary proteins (MUPs) are responsible for binding to hydrophobic ligands such as the pheromone SBT. SBT binds within MUP-I's barrel-shaped active site, forming a hydrogen bond with a water molecule within the active site, which in turn is stabilized by forming hydrogen bonds with residue Phe56 and another water molecule; this second water molecule also

neg: Indigo dye The chemical formula of indigo is CHNO. The molecule absorbs light in the orange part of the spectrum (λ = 613 nm). The compound owes its deep color to the conjugation of the double bonds, i.e. the double bonds within the molecule are adjacent and the molecule is planar. In indigo white, the conjugation is interrupted because the molecule is nonplanar. Given its economic importance, indigo has been prepared by many methods. The Baeyer-Drewson indigo synthesis dates back to 1882. It involves an aldol condensation of o-nitrobenzaldehyde with acetone, followed by cyclization and oxidative dimerization to indigo. This route is

neg: Molecular modelling estimated using an empirical mathematical expression; these are termed "implicit solvation" simulations. Most force fields are distance-dependent, making the most convenient expression for these Cartesian coordinates. Yet the comparatively rigid nature of bonds which occur between specific atoms, and in essence, defines what is meant by the designation "molecule", make an internal coordinate system the most logical representation. In some fields the IC representation (bond length, angle between bonds, and twist angle of the bond as shown in the figure) is termed the Z-matrix or torsion angle representation. Unfortunately, continuous motions in Cartesian space often require discontinuous angular branches in

neg: Aircraft of the Battle of Britain "Department of Defence Co-Ordination", 'Proposals for securing adequate supplies of 100 octane fuel to meet war requirements', 23 December 1938, noted that there was a need to increase supplies of 100 octane fuel and discussed ways in which this could be achieved. A meeting was held on 16 March 1939 to consider the question of when the 100 octane fuel should be introduced to general use for all RAF aircraft, and what squadrons, number and type, were to be supplied. The decision taken was that there would be an initial delivery to 16 fighter and two twin-engined bomber squadrons by

neg: Octane rating may have octane ratings of 110 or significantly higher. Typical "octane booster" gasoline additives include MTBE, ETBE, isooctane and toluene. Lead in the form of tetraethyllead was once a common additive, but its use for fuels for road vehicles has been progressively phased-out worldwide, beginning in the 1970s. The most common type of octane rating worldwide is the Research Octane Number (RON). RON is determined by running the fuel in a test engine with a variable compression ratio under controlled conditions, and comparing the results with those for mixtures of iso-octane and n-heptane. Another type of octane rating, called Motor

neg: Conjugated system Each atomic orbital contributes one electron when the orbitals overlap pairwise to form two-electron σ bonds, or two electrons when the orbital constitutes a lone pair. These localized orbitals (bonding and non-bonding) are all located in the plane of the molecule, with σ bonds mainly localized between nuclei along the internuclear axis. "Pi (π) system or systems": Orthogonal to the σ framework described above, π bonding occurs above and below the plane of the molecule where σ bonding takes place. The π system(s) of the molecule are formed by the interaction of unhybridized p atomic orbitals on atoms employing sp-

neg: Hyalin component. One is filamentous, having flexible molecules containing a globular domain head at the end. Its conformation is retained mainly by disulfide bonds, as virtually all cysteine amino acids are found in the disulfide form, but also hydrophobic forces and salt linkages stabilize the molecule. The filament length is about 75 nm long, and the head being club-shaped with a diameter of 12 nm. An isoform of the molecule exists, having a longer filament of 125 nm instead. Both forms of these filaments often fold on themselves, making the protein heterogeneous, resulting in poorly resolved stains on a gel. This

neg: Localized molecular orbitals of the molecule. Localized orbitals may then be found as linear combinations of the delocalized orbitals, given by an appropriate unitary transformation. In the water molecule for example, ab initio calculations show bonding character primarily in two molecular orbitals, each with electron density equally distributed among the two O-H bonds. The localized orbital corresponding to one O-H bond is the sum of these two delocalized orbitals, and the localized orbital for the other O-H bond is their difference; as per Valence bond theory. For multiple bonds and lone pairs, different localization procedures give different orbitals. The Boys and Edmiston-Ruedenberg localization

neg: Intramolecular force charge separation. Covalent bonds are generally formed between two nonmetals. There are several types of covalent bonds: in polar covalent bonds, electrons are more likely to be found around one of the two atoms, whereas in nonpolar covalent bonds, electrons are evenly shared. Homonuclear diatomic molecules are purely covalent. The polarity of a covalent bond is determined by the electronegativities of each atom and thus a polar covalent bond has a dipole moment pointing from the partial positive end to the partial negative end. Polar covalent bonds represent an intermediate type in which the electrons are neither completely transferred from

neg: Rosalind Franklin a rarity. She in fact laughed at men who were embarrassed by the appointment of the first female professor Dorothy Garrod. Rosalind Franklin's first important contributions to the model popularised by Crick and Watson was her lecture at the seminar in November 1951, where she presented to those present, among them Watson, the two forms of the molecule, type A and type B, her position being that the phosphate units are located in the external part of the molecule. She also specified the amount of water to be found in the molecule in accordance with other parts of it, data

neg: Molecule Molecule A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge. However, in quantum physics, organic chemistry, and biochemistry, the term "molecule" is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the term "molecule" is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are monatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one chemical

neg: U.S. State Fuel Octane Standards offered for sale in most states. However 85 and 86 octane gasoline can still commonly be found in several rocky mountain states. The octane ratings below are the lowest allowed by law and may or may not reflect the actual levels offered for sale at most gas stations. Ethanol's effect on octane is not considered--these are ratings that are seen at the pump. U.S. State Fuel Octane Standards Most states do not mandate certain standard gasoline grade octane ratings. In the United States and Canada, octane ratings are in AKI, commonly shown as "(R+M)/2". All states require gas pump to

neg: Merlin (protein) animals, and the derivation of merlin is thought to be in early metazoa. Merlin is a member of the ERM family of proteins including ezrin, moesin, and radixin, which are in the protein 4.1 superfamily of proteins. Merlin is also known as "schwannomin", a name derived from the most common type of tumor in the NF2 patient phenotype, the schwannoma. Vertebrate merlin is a 70-kDa protein. There are 10 known isoforms of human merlin molecule (the full molecule being 595 amino acids in length). The two most common of these are also found in the mouse and are called "type

neg: Polyrotaxane Polyrotaxane A polyrotaxane is a type of mechanically interlocked molecule consisting of strings and rings, in which multiple rings are threaded onto a molecular axle and prevented from dethreading by two bulky end groups. As oligomeric or polymeric species of rotaxanes, polyrotaxanes are also capable of converting energy input to molecular movements because the ring motions can be controlled by external stimulus. Polyrotaxanes have attracted much attention for decades, because they can help build functional molecular machines with complicated molecular structure. Although there are no covalent bonds between the axes and rings, polyrotaxanes are stable due to the high free

neg: Chemical polarity more electronegative fluorine atom. Ammonia, NH, molecule the three N−H bonds have only a slight polarity (toward the more electronegative nitrogen atom). The molecule has two lone electrons in an orbital, that points towards the fourth apex of the approximate tetrahedron, (VSEPR). This orbital is not participating in covalent bonding; it is electron-rich, which results in a powerful dipole across the whole ammonia molecule. In ozone (O) molecules, the two O−O bonds are nonpolar (there is no electronegativity difference between atoms of the same element). However, the distribution of other electrons is unevensince the central atom has to share electrons

neg: Biochemistry Some are aromatic, while others are not. Some are flexible, while others are rigid. Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain). Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"),

neg: Methine group rest of the molecule by a triple bond) or to the methylidyne radical ⫶CH (the two atoms as a free molecule with dangling bonds). The name "methine" is also widely used in non-systematic nomenclature for the methanetriyl group (IUPAC): a carbon with four single bonds, where one bond is to a hydrogen (>CH−). Every carbon in this molecule is a methine carbon, "except" for three; two that are attached to the two nitrogens and not to any hydrogens, and the one attached to the nitrogen, which is attached to two hydrogens (far right). There is a five carbon poly-methine chain

neg: Quinacridone excellent color fastness and resistance to solvation. Another important modification is the β phase which provides a maroon shade that is also more weather resistant and light-fast. Both crystal modifications are more thermodynamically stable than the α crystal phase. The γ crystal modification is characterized by a criss-cross lattice where each quinacridone molecule hydrogen-bonds to four neighbors via single H-bonds. The β phase, meanwhile, consists of linear chains of molecules with double H-bonds between each quinacridone molecule and two neighbors. Basic modifications to the chemical structure of quinacridones include the addition of CH and Cl substituents. Some magenta shades of

neg: Pyridoxine 5'-phosphate oxidase electron acceptor in these enzymes’ reactions, they are unique because oxygen does not appear in the oxidized product. Pyridoxine 5’-phosphate oxidase is a homodimer, or a molecule consisting of two identical polypeptide subunits. It is hypothesized that the two monomers are held together via disulfide bonds. There are also salt-bridge interactions between the two monomers. Each subunit tightly binds one molecule of pyridoxal 5'-phosphate tightly on each subunit. Both alpha-helices and beta-sheets are present in the protein motif, which is best described as a split-barrel structure. This structure is due, in part, to the disulfide bonds present in the secondary

neg: Amino acid and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the

neg: Glycosidic bond Glycosidic bond In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide (or a molecule derived from a saccharide) and the hydroxyl group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside. The term 'glycoside' is now extended to also cover compounds with bonds formed between hemiacetal (or hemiketal) groups of sugars and several chemical groups other than

neg: Bifunctional Bifunctional In organic chemistry, when a single organic molecule has two different functional groups, it is called a bifunctional molecule . A bifunctional molecule has the properties of two different types of functional groups, such as an alcohol (-OH), amide (CONH), aldehyde (-CHO), nitrile (-CN) or carboxylic acid (-COOH). Many bifunctional molecules are used to produce medicines and catalysts, while others are used in condensation polymerization like polyester and polyamide. In organic molecules, functional groups are atoms or molecules that are responsible for the characteristic properties of that molecule, with the exceptions of double and triple bonds, which are also

neg: Molecule atoms is "sufficiently stable" to be considered a molecule is inherently an operational definition. Philosophically, therefore, a molecule is not a fundamental entity (in contrast, for instance, to an elementary particle); rather, the concept of a molecule is the chemist's way of making a useful statement about the strengths of atomic-scale interactions in the world that we observe. Molecule A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge. However, in quantum physics, organic chemistry, and biochemistry, the term "molecule" is often

neg: Nitrite reductase and bound by one Histidine from another monomer; the Cys-His bridge to the type 1 Cu. This gives the molecule a distorted tetrahedral geometry. In the resting state, the Cu is also binding a water molecule that is displaced by nitrite. As nitrite displaces water, Cu is bound by both oxygens in a bidentate fashion. A nearby Aspartic acid residue hydrogen bonds to one of the newly formed oxygen ligands. An incoming electron reduces the Cu from oxidation state (II) to (I). This change facilitates a shift in nitrite binding so that the nitrogen is bound to Cu, and one

neg: Avgas helps ensure that for those eligible aircraft, 91 AKI fuel provides sufficient detonation margin under normal conditions. Automotive gasoline is not a fully viable replacement for avgas in many aircraft, because many high-performance and/or turbocharged airplane engines require 100 octane fuel and modifications are necessary in order to use lower-octane fuel. Many general aviation aircraft engines were designed to run on 80/87 octane, roughly the standard (as unleaded fuel only, with the "{R+M}/2" 87 octane rating) is for North American automobiles today. Direct conversions to run on automotive fuel are fairly common and applied via the supplemental type certificate (STC)

neg: Molecular orbital these molecular orbitals involve low-energy d atomic orbitals, they are seen in transition-metal complexes. A δ bonding orbital has two nodal planes containing the internuclear axis, and a δ* antibonding orbital also has a third nodal plane between the nuclei. Theoretical chemists have conjectured that higher-order bonds, such as phi bonds corresponding to overlap of f atomic orbitals, are possible. There is as of 2005 only one known example of a molecule purported to contain a phi bond (a U−U bond, in the molecule U). For molecules that possess a center of inversion (centrosymmetric molecules) there are additional labels of

neg: Localized molecular orbitals and acceptor orbitals between two molecules or different regions within the same molecule, and molecular orbitals must be considered. Because proper (symmetry-adapted) molecular orbitals are fully delocalized and do not admit a ready correspondence with the "bonds" of the molecule, as visualized by the practicing chemist, the most common approach is to instead consider the interaction between filled and unfilled localized molecular orbitals that correspond to σ bonds, π bonds, lone pairs, and their unoccupied counterparts. These orbitals and typically given the notation σ (sigma bonding), π (pi bonding), "n" (occupied nonbonding orbital, "lone pair"), "p" (unoccupied nonbonding orbital, "empty

neg: Ring strain Ring strain In organic chemistry, ring strain is a type of instability that exists when bonds in a molecule form angles that are abnormal. Strain is most commonly discussed for small rings such as cyclopropanes and cyclobutanes, whose internal angles are substantially smaller than the idealized value of approximately 109°. Because of their high strain, the heat of combustion for these small rings is elevated. Ring strain results from a combination of angle strain, conformational strain or Pitzer strain (torsional eclipsing interactions), and transannular strain, also known as van der Waals strain or Prelog strain. The simplest examples of angle

neg: Lewis structure molecule should be equal to zero. For some molecules and ions, it is difficult to determine which lone pairs should be moved to form double or triple bonds, and two or more different "resonance" structures may be written for the same molecule or ion. In such cases it is usual to write all of them with two-way arrows in between (see Example below). This is sometimes the case when multiple atoms of the same type surround the central atom, and is especially common for polyatomic ions. When this situation occurs, the molecule's Lewis structure is said to be a resonance