"Such biogenic oxygens have ... contaminated the lunar surface," Kentaro Terada, an astrophysicist at Osaka University, tells The Verge.
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The oxygen atoms form a cubic lattice, but the hydrogen atoms spill free, flowing like a liquid through the rigid cage of oxygens.
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"The chlorine grabs the electrons from the hydrocarbons, the oxygens and chlorides get bonded to the carbons, and this makes your food stains water soluble, but just enough to unstick them from the dishware," Dr. Nyman said.
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2-deoxystrept-amine, 2D representation, oxygens, nitrogens (with attached hydrogens) in red, blue.
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All the lead (Pb) atoms in the carbonate sheets are surrounded by 9 oxygens from carbonate groups and by one hydroxyl from an adjacent sulfate sheet. The Pb atoms in the sulfate sheets are bonded to 9 or 10 oxygens.
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Each croconate is bound to the preceding metal by one oxygen atom, and to the next metal through its two opposite oxygens, leaving two oxygens unbound. Each metal is bound to three croconate oxygens and to one water molecule. Calcium also forms a compound with the same formula (yellow) but the structure appears to be different. The croconate anion also forms compounds with trivalent cations such as aluminium (yellow), chromium (brown), and iron (purple).
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In some cases, this leads to alternative formulae that differ in bond orders (the full set of which is called the resonance formulas). Consider the sulfate anion ( with 32 valence electrons; 24 from oxygens, 6 from sulfur, 2 of the anion charge obtained from the implied cation). The bond orders to the terminal oxygens have no effect on the oxidation state so long as the oxygens have octets. Already the skeletal structure, top left, yields the correct oxidation states, as does the Lewis structure, top right (one of the resonance formulas): :450px The bond-order formula at bottom is closest to the reality of four equivalent oxygens each having a total bond order of 2.
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The structure is rather different from that of potassium molybdenum purple bronze , except that both are organized in layers. The difference may be explained by the relative sizes of the and ions. The unit cell contains six crystallographically independent molybdenum sites. One-third of the molybdenum atoms are surrounded by four oxygens, two thirds are surrounded by six oxygens.
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Schellman loop. Nitrogen atoms, blue; oxygens, red; carbons, grey. The purple and yellow lines are hydrogen bonds. Side chain and hydrogen atoms omitted.
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Bacteria, dissolved organics and oxygens consumption in salinity stratified Chesapeake Bay, an anoxia paradigm. Am. Zool. 37, 612-620.Officer, C.B., Smayda, T.J. and Mann, R., 1982.
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Several real crystals with hydrogen bonds satisfy the ice model, including ice and potassium dihydrogen phosphate (KDP). Indeed, such crystals motivated the study of ice-type models. In ice, each oxygen atom is connected by a bond to four other oxygens, and each bond contains one hydrogen atom between the terminal oxygens. The hydrogen occupies one of two symmetrically located positions, neither of which is in the middle of the bond.
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There are three ways of synthesizing Demeton-S-methyl. It can be made by a reaction between Thiodiglycol and dimethyl thiophosphate. Here the sulfur in dimethyl thiophosphate attacks on one of the oxygens of thiodiglycol. One of the oxygens of dimethyl thiophosphate in turn forms a double bond with the phosphate and losing its hydrogen which forms water with the hydroxyl on the other side of the thiodiglycol.
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Each of the different possibilities is superimposed on the others, and the molecule is considered to have a Lewis structure equivalent to some combination of these states. The nitrate ion (NO3−), for instance, must form a double bond between nitrogen and one of the oxygens to satisfy the octet rule for nitrogen. However, because the molecule is symmetrical, it does not matter which of the oxygens forms the double bond. In this case, there are three possible resonance structures.
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Therefore, the induction of a minor metabolic pathway leads to the formation of toxic metabolites in considerable amounts. The toxic metabolites may bind to vital intracellular macromolecules and may generate reactive oxygens by redox cycling if quinone is formed. This could also lead to a depletion of protective glutathione which is responsible for the detoxification of reactive oxygens. The observed skin phototoxicity of patients treated with benoxaprofen can be explained with a look at the structure of the compound.
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561 This rule tends to increase the distance between highly charged cations, so as to reduce the electrostatic repulsion between them. One of Pauling's examples is olivine, M2SiO4, where M is a mixture of Mg2+ at some sites and Fe2+ at others. The structure contains distinct SiO4 tetrahedra which do not share any oxygens (at corners, edges or faces) with each other. The lower- valence Mg2+ and Fe2+ cations are surrounded by polyhedra which do share oxygens.
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Determination of oxidation states from a bond graph can be illustrated on ilmenite, FeTiO3. We may ask whether the mineral contains Fe2+ and Ti4+, or Fe3+ and Ti3+. Its crystal structure has each metal atom bonded to six oxygens and each of the equivalent oxygens to two irons and two titaniums, as in the bond graph below. Experimental data show that three metal–oxygen bonds in the octahedron are short and three are long (the metals are off-center).
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Its structure would not readily allow thiol-disulfide interchange or acyl transfer to cysteine. Instead, NV038 is believed to react with the zinc using its two carbonyl oxygens found in the esters.
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GNC zinc 50 mg tablets. The amount exceeds what is deemed the safe upper limit in the United States (40 mg) and European Union (25 mg) alt=Skeletal chemical formula of a planar compound featuring a Zn atom in the center, symmetrically bonded to four oxygens. Those oxygens are further connected to linear COH chains. In most single-tablet, over-the-counter, daily vitamin and mineral supplements, zinc is included in such forms as zinc oxide, zinc acetate, or zinc gluconate.
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Benzofurans are similar in structure to MD(M)A but differ in that the methylenedioxy groups have been modified, removing one of the two oxygens in the methylenedioxy ring to render a benzofuran ring.
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Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: and PDBeMotif: . Type 1 beta bulge loop. Main chain atoms only of hexapeptide; no hydrogen atoms. Carbons grey, oxygens red and nitrogens blue.
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The resorcinarene is also the basic structural unit for other molecular recognition scaffolds, typically formed by bridging the phenolic oxygens with alkyl or aromatic spacers. A number of molecular structures are based on this macrocycle, namely cavitands and carcerands.
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The molybdopterin cofactor has a Mo(VI) center, which is bonded to a sulfur from cysteine, an ene-dithiolate from pyranopterin, and two terminal oxygens. It is at this molybdenum center that the catalytic oxidation of sulfite takes place.
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Proline residues lack NH groups so are rare in nests. About one in 12 of amino acid residues in proteins, on average, belongs to a nest. RL nest bound to an egg oxygen. carbons grey, oxygens red and nitrogens blue.
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With the same central atom X, acid strength increases as the number of oxygens attached to X increases. With the same number of oxygens around E, acid strength increases with the electronegativity of X. Compared to salt of their deprotonated forms, the oxyanions, oxyacids are generally less stable, and many of them only exist formally as hypothetical species, or exist only in solution and cannot be isolated in pure form. There are several general reasons for this: (1) they may condense to form oligomers (e.g., H2CrO4 to H2Cr2O7), or dehydrate all the way to form the anhydride (e.g.
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Dissolved in water, it forms carbonic acid (), but as most compounds with multiple single-bonded oxygens on a single carbon it is unstable. Through this intermediate, though, resonance-stabilized carbonate ions are produced. Some important minerals are carbonates, notably calcite. Carbon disulfide () is similar.
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Uranium hexoxide is predicted to have octahedral symmetry; however, other forms have been studied. In the 1Oh the oxygen atoms are oxide ions (O2−). In the 1D3 form there are three peroxide ions (). The 3D2h form has two oxo oxygens and two pairs of superoxide ().
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The crystals formed during drawing are held together by hydrogen bonds between the amide hydrogens of one chain and the carbonyl oxygens of another chain. Polyethylene terephthalate (PET) sheet is drawn in two dimensions to make BoPET (biaxially- oriented polyethylene terephthalate) with improved mechanical properties.
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The Lys219 on the enzyme guides the phosphate group to the substrate. PGK proceeds through a charge-stabilized transition state that is favored over the arrangement of the bound substrate in the closed enzyme because in the transition state, all three phosphate oxygens are stabilized by ligands, as opposed to only two stabilized oxygens in the initial bound state. In the glycolytic pathway, 1,3-BPG is the phosphate donor and has a high phosphoryl- transfer potential. The PGK-catalyzed transfer of the phosphate group from 1,3-BPG to ADP to yield ATP can power the carbon-oxidation reaction of the previous glycolytic step (converting glyceraldehyde 3-phosphate to 3-phosphoglycerate).
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The Mg2+ ion on the right (Figure 3) interacts with negatively charged oxygens of the alpha(α), beta(β) and gamma(γ) phosphates to align the scissile bond for the primer to attack. Even if there is no general base within the active site to deprotonate the primer hydroxyl, the lowered pka of the metal-bound hydroxyl favors the formation of the 3’-hydroxide nucleophile. Metal ions and Lys522 contact non- bridging oxygens on the α-phosphate to stabilize the negative charge developing on the α-phosphorus during bond formation with the nucleophile. Moreover, the Lys522 sidechain also moves to neutralize the negatively charged pyrophosphate group.
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Residues are represented by black filled circles. Mainchain-mainchain hydrogen bonds are shown as dashed lines. The grey shading indicates the three nest residues. Consideration of the hydrogen bonding in the nests of Schellman loops bound to mainchain oxygens reveals two main types of arrangement: 1,3-bridged or not.
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Distortion involves the warping of polyhedra due to nonuniform bonding lengths, often due to differing electrostatic attraction between heteroatoms. For instance, a titanium center will likely bond evenly to six oxygens in an octahedra, but distortion would occur if one of the oxygens were replaced with a more electronegative fluorine. Distortions will not change the inherent geometry of the polyhedra—a distorted octahedron is still classified as an octahedron, but strong enough distortions can have an effect on the centrosymmetry of a compound. Disorder involves a split occupancy over two or more sites, in which an atom will occupy one crystallographic position in a certain percentage of polyhedra and the other in the remaining positions.
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The apical oxygens of one tetahedral sheet face the apical oxygens of the other tetrahedral sheet, forming octahedral sites between the sheets, and this is the octahedral "o" layer. The octahedral sites may be fully occupied by divalent cations, producing trioctahedral layers, where each O or OH ion is surrounded by 3 divalent cations. Alternatively the octahedral sites may be 2/3 occupied by trivalent cations, producing dioctahedral layers, where each O or OH ion is surrounded by 2 trivalent cations. There is one formula unit per unit cell (Z = 1), and the unit cell parameters are a = 5.256 Å and c = 14.822 Å. When treated with glycol the cell expands to 17.35 Å.
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The occupation of the LUMO decreases the strength of the N-O bond. A second electronic effect is the hydrogen bonding of both oxygens to nearby amino acids. These acids are often arginine and Histidine. The interactions lengthen the N-O bonds and facilitate cleavage of an oxygen from nitrogen.
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Anatase to Rutile Transition ART, in J. Mat. Sci. They also exhibit different melting points, solubilities, and X-ray diffraction patterns. One good example of this is the quartz form of silicon dioxide, or SiO2. In the vast majority of silicates, the Si atom shows tetrahedral coordination by 4 oxygens.
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In some compounds, borane replaces of one of the oxygens of a triphosphate or diphosphate functional group. Phosphorus remains tetrahedral, but the BH3-appended phosphorus center is trivalent. Boranophosphates have been incorporated into nucleotides and studied as potential therapeutic and diagnostic agents. They are one of several covalent modifications of phosphodi- and triesters.
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This signature sequence is highly conserved, with the exception that a valine residue in prokaryotic potassium channels is often substituted with an isoleucine residue in eukaryotic channels. This sequence adopts a unique main chain structure, structurally analogous to a nest protein structural motif. The four sets of electronegative carbonyl oxygen atoms are aligned toward the center of the filter pore and form a square anti-prism similar to a water-solvating shell around each potassium binding site. The distance between the carbonyl oxygens and potassium ions in the binding sites of the selectivity filter is the same as between water oxygens in the first hydration shell and a potassium ion in water solution, providing an energetically-favorable route for de-solvation of the ions.
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A computational study, combined with the available experimental data, suggests the following atomic-resolution mechanism for glyoxalase I. In the active site, the catalytic metal adopts an octahedral coordination geometry and, in the absence of substrate, binds two waters, two opposite glutamates, a histidine and one other sidechain, usually another histidine or glutamates. When the substrate enters the active site, the two waters are shed and the two carbonyl oxygens of the substrate are bound directly to the metal ion. The two opposing glutamates add and subtract protons from C1 and C2 and their respective oxygens, O1 and O2. The first half of the reaction transfers a proton from C1 to O2, whereas the second half transfers a proton from O1 to C2.
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Cuticular hydrocarbons are waxy coatings on S. postica bodies that signal the hierarchy and original colony of any bee. They are also important anti-desiccants. Workers have cuticular hydrocarbons lacking oxygens while the drones have more oxygenated compounds. Hydrocarbons also provide social dominance and fertility cues that are important when determining the queen during colonization.
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Top and side views of graphene (left) and HBS structures (right). Red atoms are oxygens. TEM images of defects in HBS (middle) and graphene (bottom row): Stone-Wales (a), flower (b), divacancy (c) and a more complex, interstitial defect (d). TEM images of amorphous HBS Two-dimensional silica (2D silica) is a layered polymorph of silicon dioxide.
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The IUPAC nomenclature uses dihydronaphthalenedione instead of "naphthoquinone", with the necessary prefixes to indicate the positions of the carbonyl oxygens (=O) — as in 5,8-dihydroxy-1a,8a-dihydronaphthalene-1,4-dione (= 5,8-dihydroxy-1,4-naphthoquinone). The hydroxynaphtoquinones (in the particular or the general sense) include many biologically and industrially important compounds, and are a building-block of many medicinal drugs.
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Images generated in PyMOL. FPPS adopts a 3-layered α-helical fold characteristic of many prenyltransferases with 11 helices and flexible loops in between. The centrally located helices (α4 and α8) contain conserved aspartate motifs (DDXXD) that participate in substrate binding and catalysis. Motif aspartate residues, water oxygens, and pyrophosphate coordinate three Mg2+in an octahedral manner.
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Dioptase is a cyclosilicate mineral consisting of Si6O18 rings which are linked together by Jahn–Teller distorted octahedral d9 Cu(II) ions. Each copper ion is coordinated by four cyclosilicate oxygens and two water molecules. Although the copper ions are six-coordinate, they can be viewed as square planar. The copper centers have approximately C4V symmetry.
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Two polymorphs are known, referred to as the α- and β-forms, but in each case the structures are similar. The Mn(III) centres occupy distorted octahedral sites, being surrounded by six oxygens provided by the pyrophosphate ligands.Yasmin Begum, Adrian J. Wright "Relating highly distorted Jahn–Teller MnO6 to colouration in manganese violet pigments" J. Mater. Chem., 2012, vol.
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The anions and cations are arranged in alternate planes. Within each plane, the anions are arranged in a hexagonal grid. Each potassium ion is arranged so that it connects symmetrically to eight oxygens of four anions, two from each adjacent plane. The anions are slightly twisted in the "boat" shape (with 0.108 Å of rms deviation from mean plane).
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However, the oxygens are always bridges between the zirconium and phosphate and one oxygen is never shared between two the same groups and half of the oxygens are also shared with K groups. The pattern of Two zirconium polyhedron, one potassium polyhedron, two zirconium polyhedron, and the oxygen and phosphate groups filling in the gaps creates kosnarite's unique crystal structure. Depending on the impurities present in the sample, the color of kosnarite can range from pale blue to blue-green depending on the amount of iron, manganese, or other impurities, and kosnarite can sometimes appear to be nearly colorless. Other physical properties of kosnarite include its vitreous lust, non-fluorescence, a hardness of 4.5 on the mohs scale of mineral hardness, conchoidal fracturing, and perfect cleavage in the {102} direction.
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Its cell parameters are approximately a = 5.7 Å, b = 11.71 Å and c = 8.24 Å. Wadsleyite is found to be stable in the upper part of the Transition Zone of the Earth's mantle between in depth. Because of oxygens not bound to silicon in the Si2O7 groups of wadsleyite, it leaves some oxygen atoms underbonded, and as a result, these oxygens are hydrated easily, allowing for high concentrations of hydrogen atoms in the mineral. Hydrous wadsleyite is considered a potential site for water storage in the Earth's mantle due to the low electrostatic potential of the underbonded oxygen atoms. Although wadsleyite does not contain H in its chemical formula, it may contain more than 3 percent by weight H2O, and may coexist with a hydrous melt at transition zone pressure- temperature conditions.
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The ozone (three oxygens) has very strong oxidation characteristics. It can form hydroxyl radicals (OH) when it decomposes, which will react with the organic matter to shut down the problem of biofouling.Cho, Min, Hyenmi Chung, and Jeyong Yoon, "Disinfection of Water Containing Natural Organic Matter by Using Ozone-Initiated Radical Reactions," Abstract, Applied and Environmental Microbiology Vol. 69 No.4 (2003): 2284-2291.
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A dihydroxyanthraquinone is any of several isomeric organic compounds with formula , formally derived from 9,10-anthraquinone by replacing two hydrogen atoms by hydroxyl groups. Dihyroxyantraquinones have been studied since the early 1900s, and include some compounds of historical and current importance. The isomers differ in the position of the hydroxyl groups, and of the carbonyl oxygens (=O) of the underlying anthraquinone.
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21- and 18-membered diazacrown ether derivatives exhibit excellent calcium and magnesium selectivities and are widely used in ion-selective electrodes. Some or all of the oxygen atoms in crown ethers can be replaced by nitrogens to form cryptands. A well-known tetrazacrown is cyclen in which there are no oxygens. Lariat crown ethers have sidearms that can augment complexation of cation.
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The proposed catalytic Cycle for MMO. From the MMOHred, the diiron centers react with the O2 to form intermediate P. This intermediate is a peroxide species where the oxygens are bound symmetrically, suggested by spectroscopic studies. However, the structure is not known. Intermediate P then converts to intermediate Q, which was proposed to contain two antiferromagnetically coupled high-spin FeIV centers.
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The rigid structure of each layer is built around 2− groups coordinating three crystallographically distinct aluminium centres, each of which has coordination number six. Near the middle of each layer, an aluminium ion octahedrally coordinates six HPO42−. Two other oxygens in each hydrogen phosphate group coordinate the other distinct aluminium centres, which in turn are coordinated octahedral to three hydrogen phosphate groups and three water molecules.
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The sulfate ion can act as a ligand attaching either by one oxygen (monodentate) or by two oxygens as either a chelate or a bridge. An example is the complex [Co(en)2(SO4)]+Br− or the neutral metal complex PtSO4(P(C6H5)3)2 where the sulfate ion is acting as a bidentate ligand. The metal–oxygen bonds in sulfate complexes can have significant covalent character.
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The active site of the mouse MIOX enzyme highlighting the di-iron active site along with the coordinated amino acids. The Fe atom binds to the oxygens of the C1 and C6 of myo-inositol. Lys 127 helps to promote the abstraction of the hydrogen atom from the C1 carbon. Myo-inositol oxygenase is a monomeric 33 kDa protein in both solution and crystal.
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The IUPAC nomenclature uses dihydrobenzenedione instead of "benzoquinone", with the necessary prefixes to indicate the positions of the carbonyl oxygens (=O) — as in 2,3-dihydroxy-1a,4a-dihydrobenzene-1,4-dione (= 2,3-dihydroxy-1,4-benzoquinone). The hydroxybenzoquinones (in the particular or the general sense) include many biologically and industrially important compounds, and are a building block of many medicinal drugs. Thomson R.H. Naturally Occurring Quinones.
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Orthoperiodic acid forms monoclinic crystals (space group P21/n) consisting of a slightly deformed IO6 octahedron interlinked via bridging hydrogens. Five I–O bond distances are in the range 1.87–1.91 Å and one I–O bond is 1.78 Å. The structure of metaperiodic acid also includes IO6 octahedra, however these are connected via cis-edge-sharing with bridging oxygens to form one-dimensional infinite chains.
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The molecular structure has three nitrate groups in bidentate coordination with the cobalt atom, which is thus bonded to six oxygen atoms in a distorted octahedral arrangement. The nitrates are approximately planar, and lie on three mutually perpendicular planes, resulting in a chiral molecule. The Co-O bonds are about 190 pm long. The O-Co-O angles for the two oxygens in the same nitrate is about 68 degrees.
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Pectin is most stable at a pH of 3.5, so the more basic pH within ketchup will protonate the hydroxyl side chains and therefore create a less viscous gel. Acetic acid within vinegar also has hydroxyl groups that will have a dispersed amount of negative and neutral charges along each molecule. The acetic acid and pectin will display repulsive interactions between the negatively charged oxygens on each molecule.
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The Weinreb ketone synthesis can also be used to convert acid halides to ketones. In this reaction, the acid halide is first converted to an N–methoxy–N–methylamide, known as a Weinreb amide. When a carbon nucleophile – such as a Grignard or organolithium reagent – adds to a Weinreb amide, the metal is chelated by the carbonyl and N–methoxy oxygens, preventing further nucleophilic additions.Kürti and Czakó 2005, p. 478.
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Sialoadhesin's variable immunoglobulin domain in complex with a sialylated glycan. Glycan carbons are in purple, protein carbons in green, oxygens in red, nitrogens in blue and hydrogens in white. Siglecs are Type I transmembrane proteins where the NH3+-terminus is in the extracellular space and the COO−-terminus is cytosolic. Each Siglec contains an N-terminal V-type immunoglobulin domain (Ig domain) which acts as the binding receptor for sialic acid.
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For example, a shared step in the biosynthesis of trichothecenes is controlled by the gene TRI4. This enzyme product controls the addition of either three or four oxygens to trichodiene to form either isotrichodiol or isotrichotriol respectively. A variety of trichothecenes can then be synthesized from either of these intermediates and they could therefore be classified as either t-type if synthesized from isotrichotriol or d-type if synthesized from isotrichodiol.
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A video describing the mechanism of action for poison ivy and other such plants containing urushiol To cause an allergic dermatitis reaction, the urushiol is first oxidized to create two double bonded oxygens on the chemical. It then reacts with a protein nucleophile to trigger a reaction within the skin. Dermatitis is mediated by an induced immune response. Urushiol is too small a molecule to directly activate an immune response.
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Propanephosphonic acid anhydride (PPAA, T3P) is an anhydride of propanephosphonic acid. Its structure is a cyclic trimer, with a phosphorus–oxygen core and propyl groups and additional oxygens attached. The chemical is a useful reagent for peptide synthesis reactions, where it activates the carboxylic acid partner for subsequent reaction with amines. It is commercially available as 50 % solution in DMF or ethyl acetate as a slightly yellow mixture.
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The calculated geometry of molecular uranium trioxide has C2v symmetry. Calculations predict that the point group of molecular UO3 is C2v, with an axial bond length of 1.75 Å, an equatorial bond length of 1.83 Å and an angle of 161° between the axial oxygens. The more symmetrical D3h species is a saddle point, 49 kJ/mol above the C2v minimum. The authors invoke a second-order Jahn–Teller effect as explanation.
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The crystal structure of a uranium trioxide phase of composition UO2·82 has been determined by X-ray powder diffraction techniques using a Guinier-type focusing camera. The unit cell is cubic with a = 4·138 ± 0·005 kX. A uranium atom is located at (000) and oxygens at (View the MathML source), (View the MathML source), and (View the MathML source) with some anion vacancies. The compound is isostructural with ReO3.
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They are normally handled as solutions in solvents such as diethyl ether or tetrahydrofuran; which are relatively stable as long as water is excluded. In such a medium, a Grignard reagent is invariably present as a complex with the magnesium atom connected to the two ether oxygens by coordination bonds. The discovery of the Grignard reaction in 1900 was awarded with the Nobel prize in 1912. For more details on the history see Victor Grignard.
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It is common for the Si4+ to be substituted by Al3+ because of similarity in ionic radius and charge; in those cases, the [AlO4]5− tetrahedra form the same structures as do the unsubstituted tetrahedra, but their charge-balancing requirements are different., pp. 104–20 The degree of polymerization can be described by both the structure formed and how many tetrahedral corners (or coordinating oxygens) are shared (for aluminium and silicon in tetrahedral sites)., p.
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Dickite is composed of regular sequences of one, two and six kaolin layers. Analysis of the dickite structure reveals the space group to be C4s-Cc. The a and c axis both lie on the glide plane of symmetry. Dickite's structure is made up of a shared layer of corner-sharing tetrahedra filled by a plane of oxygens and hydroxyls along with a sheet of edge-sharing octahedra with every third site left empty.
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The mechanism of potassium channel selectivity remains under continued debate. The carbonyl oxygens are strongly electro-negative and cation-attractive. The filter can accommodate potassium ions at 4 sites usually labelled S1 to S4 starting at the extracellular side. In addition, one ion can bind in the cavity at a site called SC or one or more ions at the extracellular side at more or less well- defined sites called S0 or Sext.
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Shorter oligos have lower hybridization energies, resulting in decreased stability of the oligo to the chromosomal target. Of this sequence, at least 15 base pairs should be homologous to the target sequence at both the 5’ and 3’ ends to provide sufficient oligo annealing. Another consideration is the inclusion of phosphorothioate bonds. In a phosphorothioate bond, one of the non-bridging oxygens between nucleotide bases is replaced with a sulfur atom, changing the chemical properties.
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Room-temperature structure of Ho2O3 viewed along a cubic axis. Red atoms are oxygens Electron micrograph of lamellar particles and aggregates of holmium oxide. Scale bar at bottom shows 10 μm. Holmium oxide has a cubic, yet rather complex structure, with many atoms per unit cell and a large lattice constant of 1.06 nm. This structure is characteristic of oxides of heavy rare-earth elements, such as Tb2O3, Dy2O3, Er2O3, Tm2O3, Yb2O3 and Lu2O3.
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Nicknamed the "GAS belt", all three carbonyl oxygens line the pore, producing a negative potential that contributes to the conductance of cations. The specific amino acid residue of aspartate on the extracellular side lumen of TMD2 in ASIC1 has been linked to the channel's low Ca2+ conductance. Additionally, The n-termini residues of the transmembrane region has also shown selectivity for Na+, since mutations within this region has altered function and of Na+ conductance.
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Substitutions in the outermost layers are more effective than for the innermost layers, as the electric charge strength drops off as the square of the distance. The net result is oxygen atoms with net negative charge and the ability to attract cations. # Edge-of-clay oxygen atoms are not in balance ionically as the tetrahedral and octahedral structures are incomplete. # Hydroxyls may substitute for oxygens of the silica layers, a process called hydroxylation.
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In the secondary structure of proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. When the spacing of the amino acid residues participating in a hydrogen bond occurs regularly between positions i and i + 4, an alpha helix is formed. When the spacing is less, between positions i and i + 3, then a 310 helix is formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a beta sheet is formed.
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Crystal structure of zemannite. Zemannite crystallizes in the hexagonal crystal system, space group P63m with the lattice parameters a = 941 pm and c = 764 pm and two formula units per unit cell. The Te4+ bind with three oxygen atoms forming [TeO3]2− anions, where oxygens form trigonal pyramids around the tellurium ion. The Zn2+ and Fe3+ cations share the same cite with typical respective probabilities of 40% and 60%; those values can vary from crystal to crystal.
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General chemical structure of a dithioketal In chemistry, a thioketal is the sulfur analogue of a ketal, with one of the oxygen replaced by sulfur. A dithioketal has both oxygens replaced by sulfur. Thioketals can be obtained by reacting ketones or aldehydes with thiols. Ketones can be reduced at neutral pH via conversion to thioketals; the thioketal prepared from the ketone can be easily reduced by catalytic hydrogenation using Raney nickel in a reaction known as the Mozingo reduction.
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In the lattice, the MoO42− anions are slightly distorted, though the bond lengths remain equal and the oxygens are linked through Pb-O bonds. Each lead atom has an 8-coordination with oxygen and two slightly different Pb-O bond distances. This structure closely resembles that of pure wulfenite. The structure of wulfenite-I4 is also very similar to that of wulfenite-I41/a but has an unequal distribution of tungsten and molybdenum which may explain the observed hemihedrism.
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Aside from being bound to a lysine residue, PLP is fixed within the substrate binding site of the enzyme through various interactions with catalytic residues. Amine- and hydroxyl-containing residues are located in hydrogen bonding distance to the four phosphate oxygens. This phosphate group is considered to be the main contributor to securing PLP in the active site. Additionally, residues neighboring the pyridine nitrogen in PLP help stabilize its positive charge, thereby increasing its electrophilic character.
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105 Orthosilicates (or nesosilicates) have no linking of polyhedra, thus tetrahedra share no corners. Disilicates (or sorosilicates) have two tetrahedra sharing one oxygen atom. Inosilicates are chain silicates; single- chain silicates have two shared corners, whereas double-chain silicates have two or three shared corners. In phyllosilicates, a sheet structure is formed which requires three shared oxygens; in the case of double-chain silicates, some tetrahedra must share two corners instead of three as otherwise a sheet structure would result.
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Anhydrous nickel(II) acetylacetonate exists as molecules of Ni3(acac)6. The three nickel atoms are approximately collinear and each pair of them is bridged by two μ2 oxygen atoms. Each nickel atom has tetragonally distorted octahedral geometry, caused by the difference in the length of the Ni-O bonds between the bridging and non-bridging oxygens. Ni3(acac)6 molecules are almost centrosymmetric, despite the non-centrosymmetric point group of the cis-Ni(acac)2 "monomers," which is uncommon.
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The oxygens of the carbonyl and the hydroxyl group chelate the indium of the organoindium intermediate as illustrated below on the left by the two green bonds. The incipient C-C bond, illustrated in red, creates a six-member ring in a chair conformation. Under chelation control, the allyl group attacks the carbonyl carbon from the less hindered side opposite to that of the R group. Once the C-C bond is fully formed, the indium is released, producing the syn diol.
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Acetic anhydride in a glass bottle Acetic anhydride, like most acid anhydrides, is a flexible molecule with a nonplanar structure. The pi system linkage through the central oxygen offers very weak resonance stabilization compared to the dipole-dipole repulsion between the two carbonyl oxygens. The energy barriers to bond rotation between each of the optimal aplanar conformations are quite low. Like most acid anhydrides, the carbonyl carbon atom of acetic anhydride has electrophilic character, as the leaving group is carboxylate.
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Adenosine 5′-(γ-thiotriphosphate) is an extremely common ATP analog in which one of the gamma-phosphate oxygens is replaced by a sulfur atom; this anion is hydrolyzed at a dramatically slower rate than ATP itself and functions as an inhibitor of ATP-dependent processes. In crystallographic studies, hydrolysis transition states are modeled by the bound vanadate ion. Caution is warranted in interpreting the results of experiments using ATP analogs, since some enzymes can hydrolyze them at appreciable rates at high concentration.
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Montroydite structure (red atoms are oxygens) Cinnabar structure The red form of HgO can be made by heating Hg in oxygen at roughly 350 °C, or by pyrolysis of Hg(NO3)2. The yellow form can be obtained by precipitation of aqueous Hg2+ with alkali. The difference in color is due to particle size, both forms have the same structure consisting of near linear O-Hg-O units linked in zigzag chains with an Hg-O-Hg angle of 108°.
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In the image, note the corner-touching between octahedra and tetrahedra; these are the location of the shared oxygen. The vertices of the tetrahedra and octahedra represent the oxygen, which are spread about the central zirconium and tungsten. Geometrically, the two shapes can "pivot" around these corner-sharing oxygens, without a distortion of the polyhedra themselves. This pivoting is what is thought to lead to the negative thermal expansion, as in certain low frequency normal modes this leads to the contracting 'RUMs' mentioned above.
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Sulf1 and Sulf2 are new members of a superfamily of arylsulfatases, being closely related to arylsulfatase A, B (ARSA; ARSB) and glucosamine 6-sulfatase (G6S). The x-ray crystal structure of neither Sulf1 or Sulf2 has been attempted, but ARSA active site crystal structure was deciphered. In ARSA, the conserved cysteine, which is posttranslationally modified to a C alpha formylglycine (FG) is critical for catalytic activity. In the first step, one of the two oxygens of the aldehyde hydrate attacks the sulfur of the sulfate ester.
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The type 2 copper center of a copper nitrite reductase is the active site of the enzyme. The Cu is bound by nitrogens of two Histidines from one monomer, 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.
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Gallucci and Gerkin (1988) analyzed the structure of the hydrate isomer barium perchlorate trihydrate (Ba(ClO4)2•3H2O) by X-ray crystallography. The barium ions are coordinated by six water oxygen atoms at 2.919Å and six perchlorate oxygens at 3.026Å in a distorted icosahedral arrangement. The perchlorate fails by a narrow margin to have regular tetrahedral geometry, and has an average Cl-O bond length of 1.433Å. The space-group assignment of the structure was resolved, with the centrosymmetric assignment of P63/m confirmed.
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Using X-ray diffraction data and atomic model computations a likely structure of the channel consists of a number of protein alpha-helixes forming an hourglass shaped pore with the narrowest point halfway through the membrane's lipid bilayer. To move through the channel the potassium ions must shed their aqueous matrix and enter a selectivity filter composed of carbonyl oxygens. The potassium ions pass through one atom at a time along five different cation (positively charged ion) binding sites.Roux, B., and Schulten, K. (2004).
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In this aza crown-type, macrocyclic compound, a proton sits between two amide carbonyl oxygens separated by a distance of 2.45 Å. Standard hydrogen bonds are longer (e.g. 2.8 Å for an O···O h-bond), and the hydrogen ion clearly belongs to one of the heteroatoms. When pKa of the heteroatoms is closely matched, a LBHB becomes possible at a shorter distance (~2.55 Å). When the distance further decreases (< 2.29 Å) the bond is characterized as a single-well or short-strong hydrogen bond.
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The n-terminal fragment of the TIMP binds in the active site cleft much like the peptide substrate would bind. The Cys1 residue of the TIMP chelates to the catalytic zinc and forms hydrogen bonds with one of the carboxylate oxygens of the catalytic glutamate residue (Glu202, see mechanism below). These interactions force the zinc-bound water molecule that is essential to the enzyme's function to leave the enzyme. The loss of the water molecule and the blocking of the active site by TIMP disable the enzyme.
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The RLuc mediated chemical reaction involves the catalytic degradation of coelenterazine, and proceeds through a 1,2-dioxetane (also called dioxetanone or cyclic peroxide) intermediate. Based on studies using radioactively labelled oxygen species within the RLuc complex, it has been determined that the luciferin carbonyl oxygen is exchanged rapidly with oxygen from water prior to incorporation of an oxygen atom from O2 via a dioxetane intermediate. The resultant CO2 also rapidly exchanges its oxygens with those from the surrounding water. The general mechanism is depicted below.
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It belongs to the hexagonal crystal system, but the crystal class is unknown. As with all phyllosilicates, the basic structural element is a triple layer, called a t-o-t layer, where "t" stands for a tetrahedral sheet and "o" stands for an octahedral sheet. The tetrahedral sheets comprise (Si,Al)O4 tetrahedra, linked together in nearly hexagonal rings. Three of the oxygens in each tetrahedron form links to other tetrahedra in the sheet, and the fourth oxygen, the apical oxygen, points away from the sheet.
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The acidity of these zeolites was determined by infrared spectroscopic studies and comparing the vibrational frequencies of the hydroxyl groups since their Brønsted acidity comes from the hydroxyl groups attached to it. The hydroxyl groups that are more accessible exhibit more acidic properties while the oxygens in the hexagonal prism are less acidic. Copper zeolites also act as oxidizing agents as seen in their ability to ionize anthracene, the electron transfer was proven to happen at the cupric ion.Naccache, C. J. Cat 1971, 22, 171–181.
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Its summary formula, HNO3, corresponds to two structural isomers; the peroxynitrous acid in the above figure and the more stable nitric acid. With the formula HNO3, the simple approach without bonding considerations yields −2 for all three oxygens and +5 for nitrogen, which is correct for nitric acid. For the peroxynitrous acid, however, the two oxygens in the O–O bond each have OS = −1 and the nitrogen has OS = +3, which requires a structure to understand. Organic compounds are treated in a similar manner; exemplified here on functional groups occurring in between CH4 and CO2: :500px Analogously for transition-metal compounds; CrO(O2)2 on the left has a total of 36 valence electrons (18 pairs to be distributed), and Cr(CO)6 on the right has 66 valence electrons (33 pairs): :380px A key step is drawing the Lewis structure of the molecule (neutral, cationic, anionic): atom symbols are arranged so that pairs of atoms can be joined by single two-electron bonds as in the molecule (a sort of "skeletal" structure), and the remaining valence electrons are distributed such that sp atoms obtain an octet (duet for hydrogen) with priority that increases with electronegativity.
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Every hydrogen is bonded to two oxygens, strongly to one and weakly to the other. The resulting configuration is geometrically a periodic lattice. The distribution of bonds on this lattice is represented by a directed-graph (arrows) and can be either ordered or disordered. In 1935, Linus Pauling used the ice rules to calculate the residual entropy (zero temperature entropy) of ice Ih. For this (and other) reasons the rules are sometimes mis-attributed and referred to as "Pauling's ice rules" (not to be confused with Pauling's rules for ionic crystals).
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Around each silicon there is one OH group and there are three oxygens that neighbor them. The silicon tetrahedra are arranged so that they share an edge with calcium(1), and silicon(2) shares edges with the calcium(2) and calcium(3) polyhedral. The silicon tetrahedra are held together by the OH group and hydrogen bonding occurs between the hydrogen in the OH and the silicon tetrahedra. Hydrogen bonding is caused because the positive ion, hydrogen, is attracted to negatively charge ions which, in this case, are the silicon tetrahedra.
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Two alternative positions of sodium observed, and sodium can only interacts with four rather than eight oxygens. The tertiary structure of TBA is an anti-parallel G-quadruplex. This chair-like structure is folded through the stacking of two guanine (G)-tetrads, and four guanines interacts with one another through non Watson-Crick-like hydrogen bonds (more likely Hoogsteen-like hydrogen bonds). In the structure of TBA, G1, G6, G10 and G15 form the top layer of G-tetrad; G2, G5, G11 and G14 form the second layer.
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The presence of two activating groups also make the benzene ring highly reactive toward electrophilic aromatic substitution. As the substituents are ortho, para-directing and para with respect to each other, all positions on the ring are more or less equally activated. The conjugation also greatly reduces the basicity of the oxygens and the nitrogen, while making the hydroxyl acidic through delocalisation of charge developed on the phenoxide anion. Paracetamol is part of the class of drugs known as "aniline analgesics"; it is the only such drug still in use today.
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Schellman loops incorporate a three amino acid residue RL nest (protein structural motif), in which three mainchain NH groups (from Schellman loop residues i+3 to i+5) form a concavity for hydrogen bonding to carbonyl oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins: ; or PDBeMotif: . The majority of Schellman loops (82%) occur at the C-terminus of an alpha-helix such that residues i, i+1, i+2 and i+3 are part of the helix.
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If one of the R groups has an oxygen as the first atom (that is, there are more than two oxygens single-bonded to the central carbon), the functional group is instead an orthoester. In contrast to variations of R, both R' groups are organic fragments. If one R' is a hydrogen, the functional group is instead a hemiacetal, while if both are H, the functional group is a ketone hydrate or aldehyde hydrate. Formation of an acetal occurs when the hydroxyl group of a hemiacetal becomes protonated and is lost as water.
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PCBs undergo xenobiotic biotransformation, a mechanism used to make lipophilic toxins more polar and more easily excreted from the body. The biotransformation is dependent on the number of chlorine atoms present, along with their position on the rings. Phase I reactions occur by adding an oxygen to either of the benzene rings by Cytochrome P450. The type of P450 present also determines where the oxygen will be added; phenobarbital (PB)-induced P450s catalyze oxygenation to the meta-para positions of PCBs while 3-methylcholanthrene (3MC)-induced P450s add oxygens to the ortho–meta positions.
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Fraser-Reid, B.; Wu, Z.; Andrews, C.W.; Skowronski, E.; Bowen, J.P. J. Am. Chem. Soc. 1991, 113, 1434-1435. These groups can be easily removed following glycosylation, effectively “arming” the sugar, and allowing for control of the glycosylation. 600px Further work has shown that the effect of 1,3-dioxanes and 1,3-dioxolanes on disarming sugars can be attributed to the electronics of the systems as well as torsional strain. When a 1,3-dioxane is formed between O-4 and O-6, the oxygens adapt an anti-periplanar geometry with O-5.
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Sodium ions, however, are too small to fill the space between the carbonyl oxygen atoms. Thus, it is energetically favorable for sodium ions to remain bound with water molecules in the extracellular space, rather than to pass through the potassium-selective ion pore. This width appears to be maintained by hydrogen bonding and van der Waals forces within a sheet of aromatic amino acid residues surrounding the selectivity filter. The selectivity filter opens towards the extracellular solution, exposing four carbonyl oxygens in a glycine residue (Gly79 in KcsA).
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The nitrate ion with the partial charges shown The anion is the conjugate base of nitric acid, consisting of one central nitrogen atom surrounded by three identically bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a formal charge of −1. This charge results from a combination formal charge in which each of the three oxygens carries a − charge, whereas the nitrogen carries a +1 charge, all these adding up to formal charge of the polyatomic nitrate ion. This arrangement is commonly used as an example of resonance.
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This primary structure leads to folding of the protein into the secondary structure, formed by hydrogen bonding between the carbonyl oxygens and amine hydrogens in the backbone. Further interactions between residues of the individual amino acids form the protein's tertiary structure. For this reason, the primary structure of the amino acids in the polypeptide backbone is the map of the final structure of a protein, and it therefore indicates its biological function. Spatial positions of backbone atoms can be reconstructed from the positions of alpha carbons using computational tools for the backbone reconstruction.
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A range of tripodal phosphines such as HC(CH2PR2)3, N(CH2CH2PPh2)3 and P(CH2CH2PMe2)3 have been reviewed.Cotton and Wilkinson (, 5th Ed) on page 436 The tetra amine (tris-(2-aminoethyl) amine) can be reacted with salicylaldehyde to form a ligand which can bind with three oxygens and three nitrogens to a metal. Trispyrazolylmethane (Tpm) is another class of scorpionate ligands, notable for having identical geometry and very similar coordination chemistry to Tp with only a difference in charge between them. Another variation is the Trisoxazolinylborate ligand.
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However, the U-O bond length varies from 167 pm, which is similar to the bond length of the uranyl ion, up to about 208 pm in the related compound α-UO3, so it is debatable as to whether these compounds all contain the uranyl ion. There are two principal types of uranate which are defined by the number of nearest-neighbour oxygen atoms in addition to the "uranyl" oxygens. In one group, including M2UO4 (M=Li, Na, K) and MUO4 (M=Ca, Sr) there are six additional oxygen atoms.
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The structure of the brackebuschite group minerals is composed of B-(O,OH)6 octahedra, two non- equivalent TO4 tetrahedra, TO4(1) and TO4(2), and two different irregular polyhedra of large cations. B and T represent different elements in different members of the group. Chains formed from the B octahedra link through the oxygens of TO4(2) tetrahedra, while the large cation polyhedra form double chains parallel to the b crystal axis through edge sharing with TO4(1) tetrahedra. The result is a tight three-dimensional structure.
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Uranium oxide is amphoteric and reacts as acid and as a base, depending on the conditions. ;As an acid: :UO3 \+ H2O → + 2 H+ Dissolving uranium oxide in a strong base like sodium hydroxide forms the doubly negatively charged uranate anion (). Uranates tend to concatenate, forming diuranate, , or other poly-uranates. Important diuranates include ammonium diuranate ((NH4)2U2O7), sodium diuranate (Na2U2O7) and magnesium diuranate (MgU2O7), which forms part of some yellowcakes. It is worth noting that uranates of the form M2UO4 do not contain ions, but rather flattened UO6 octahedra, containing a uranyl group and bridging oxygens.
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The ZrO6 octahedra are only slightly distorted from a regular conformation, and all oxygen sites in a given octahedron are related by symmetry. The W2O8 unit is made up of two crystallographically distinct WO4 tetrahedra, which are not formally bonded to each other. These two types of tetrahedra differ with respect to the W-O bond lengths and angles. The WO4 tetrahedra are distorted from a regular shape since one oxygen is unconstrained (an atom that is bonded only to the central tungsten (W) atom), and the three other oxygens are each bonded to a zirconium atom (i.e.
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C-2 in D-fructose). In aldohexoses the anomeric reference atom is the stereocenter that is farthest from anomeric carbon in the ring (the configurational atom, defining the sugar as D or L). For example, in α-D- glucopyranose the reference atom is C-5. If in the cyclic Fischer projection the exocyclic oxygen atom at the anomeric centre is cis (on the same side) to the exocyclic oxygen attached to the anomeric reference atom (in the OH group) the anomer is α. If the two oxygens are trans (on different sides) the anomer is β.
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Magnesium is predominantly coordinated by six oxygen atoms from the side chains of oxygen-containing residues, main chain carbonyl groups in proteins, or water molecules. D99 at the C-terminus of the S0-S1 loop and N172 in the S2-S3 loop contain side chain oxygens in the voltage sensor domain that are essential for Mg²⁺ binding. Much like the Ca²⁺-dependent activation model, Mg²⁺-dependent activation can also be described by an allosteric MCW gating model. While calcium activates the channel largely independent of the voltage sensor, magnesium activates the channel by channel by an electrostatic interaction with the voltage sensor.
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The C·C+ bond has three hydrogen bonds: two between the hydrogen of the amines and the double bonded oxygens of the opposite cytosine, and one between the nitrogen and the hydrogen bound to the N+. These base pairs cross-link two loops of DNA. Given the hemi-protonated nature of the nitrogens in cytosine participating in C·C+ bonding, this base pairing traditionally is most stable in the range of pH=5–6, significantly lower than physiological pH (7.3). However, recent work has found evidence of i-motif structures at near-neutral pH at room temperature. Wright et al.
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These provide an even larger space for the guest molecule to bind. This linear structure can have some rotation around the phi and psi angles, but for the most part bound glucose ring oxygens lie on one side of the structure. The α(1→4) structure promotes the formation of a helix structure, making it possible for hydrogen bonds to form between the oxygen atoms bound at the 2-carbon of one glucose molecule and the 3-carbon of the next glucose molecule. Fiber X-ray diffraction analysis coupled with computer- based structure refinement has found A-, B-, and C- polymorphs of amylose.
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The modifiers (calcium, lead, lithium, sodium, potassium) alter the network structure; they are usually present as ions, compensated by nearby non- bridging oxygen atoms, bound by one covalent bond to the glass network and holding one negative charge to compensate for the positive ion nearby. Some elements can play multiple roles; e.g. lead can act both as a network former (Pb4+ replacing Si4+), or as a modifier. The presence of non-bridging oxygens lowers the relative number of strong bonds in the material and disrupts the network, decreasing the viscosity of the melt and lowering the melting temperature.
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In chemistry, ice rules are basic principles that govern arrangement of atoms in water ice. They are also known as Bernal–Fowler rules, after British physicists John Desmond Bernal and Ralph H. Fowler who first described them in 1933. The rules state each oxygen is covalently bonded to two hydrogen atoms, and that the oxygen atom in each water molecule forms two hydrogen bonds with other oxygens, so that there is precisely one hydrogen between each pair of oxygen atoms.cf. In other words, in ordinary Ih ice, every oxygen is bonded to the total of four hydrogens, two of these bonds are strong and two of them are much weaker.
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The clusters sizes are between 5 and 10 nanometers.' For geopolymer material chemistsPimraksaa, K.; Chindaprasirt, P.; Rungchet, A.; Sagoe-Crentsil, K. and Sato, T. (2011) (Department of Industrial Chemistry, Chiang Mai University, Thailand; CSIRO, Melbourne, Australia; Tohoku University, Sendai, Japan), Lightweight geopolymer made of highly porous siliceous materials with various Na2O/Al2O3 and SiO2/Al2O3 ratios, Materials Science and Engineering A, 528, 6616–6623. :'...The reaction produces SiO4 and AlO4, tetrahedral frameworks linked by shared oxygens as poly(sialates) or poly(sialate–siloxo) or poly(sialate–disiloxo) depending on the SiO2/Al2O3 ratio in the system. The connection of the tetrahedral frameworks is occurred via long-range covalent bonds.
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The bicarbonate ion (hydrogencarbonate ion) is an anion with the empirical formula and a molecular mass of 61.01 daltons; it consists of one central carbon atom surrounded by three oxygen atoms in a trigonal planar arrangement, with a hydrogen atom attached to one of the oxygens. It is isoelectronic with nitric acid . The bicarbonate ion carries a negative one formal charge and is an amphiprotic species which has both acidic and basic properties. It is both the conjugate base of carbonic acid ; and the conjugate acid of , the carbonate ion, as shown by these equilibrium reactions: : + 2 H2O + H2O + OH− H2CO3 \+ 2 OH− :H2CO3 \+ 2 H2O + H3O+ \+ H2O + 2 H3O+.
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When finely divided, it is attacked slowly by hot concentrated hydrogen peroxide, hot concentrated nitric acid, hot sulfuric acid or hot mixture of sulfuric and chromic acids. The rate of oxidation of boron depends on the crystallinity, particle size, purity and temperature. Boron does not react with air at room temperature, but at higher temperatures it burns to form boron trioxide: :4 B + 3 O2 → 2 B2O3 Ball-and-stick model of tetraborate anion, [B4O5(OH)4]2−, as it occurs in crystalline borax, Na2[B4O5(OH)4]·8H2O. Boron atoms are pink, with bridging oxygens in red, and four hydroxyl hydrogens in white.
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Since the α-helix is defined by its hydrogen bonds and backbone conformation, the most detailed experimental evidence for α-helical structure comes from atomic-resolution X-ray crystallography such as the example shown at right. It is clear that all the backbone carbonyl oxygens point downward (toward the C-terminus) but splay out slightly, and the H-bonds are approximately parallel to the helix axis. Protein structures from NMR spectroscopy also show helices well, with characteristic observations of nuclear Overhauser effect (NOE) couplings between atoms on adjacent helical turns. In some cases, the individual hydrogen bonds can be observed directly as a small scalar coupling in NMR.
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Introductory chemistry uses postulates: the oxidation state for an element in a chemical formula is calculated from the overall charge and postulated oxidation states for all the other atoms. A simple example is based on two postulates, #OS = +1 for hydrogen #OS = −2 for oxygen where OS stands for oxidation state. This approach yields correct oxidation states in oxides and hydroxides of any single element, and in acids such as H2SO4 or H2Cr2O7. Its coverage can be extended either by a list of exceptions or by assigning priority to the postulates. The latter works for H2O2 where the priority of rule 1 leaves both oxygens with oxidation state −1.
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The N-terminus also has two extracellular loops in the pore, which are thought to aid in the signal transduction between ligand-binding and TonB-mediated transport, though the precise mechanism is not clear. Residues 12 to 18 of the N-terminus domain of FepA comprise a region called the TonB box, which includes at least a proline and glycine residue. Enterobactin is a cyclic tri-ester of 2,3-dihydroxybenzoylserine with a molecular mass of 719 Da. It binds ferric ions using six oxygens from three catechol groups, giving an overall charge of −3. Like the binding catechol, enterobactin is thought to also have a three-fold symmetry dissecting the metal center.
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Open-chain form as an intermediate product between α and β anomer Open-chain form of D-galactose Though the cyclic forms of sugars are usually heavily favoured, hemiacetals in aqueous solution are in equilibrium with their open-chain forms. In aldohexoses this equilibrium is established as the hemiacetal bond between C-1 (the carbon bound to two oxygens) and C-5 oxygen is cleaved (forming the open- chain compound) and reformed (forming the cyclic compound). When the hemiacetal group is reformed, the OH group on C-5 may attack either of the two stereochemically distinct sides of the aldehyde group on C-1. Which side it attacks on determines whether the α- or β-anomer is formed.
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Ammonium polyphosphate commercially produced by Clariant, (former business area of Hoechst AG), Budenheim and other sources is an inorganic salt of polyphosphoric acid and ammonia containing both chains and possibly branching. Its chemical formula is [NH4 PO3]n(OH)2 showing that each monomer consists of an orthophosphate radical of a phosphorus atom with three oxygens and one negative charge neutralized by an ammonium cation leaving two bonds free to polymerize. In the branched cases some monomers are missing the ammonium anion and instead link to three other monomers. The properties of ammonium polyphosphate depend on the number of monomers in each molecule and to a degree on how often it branches.
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GTPgammaS (GTPγS, guanosine 5'-O-[gamma-thio]triphosphate) is a non- hydrolyzable or slowly hydrolyzable G-protein-activating analog of guanosine triphosphate (GTP). Many GTP binding proteins demonstrate activity when bound to GTP, and are inactivated via the hydrolysis of the phosphodiester bond that links the γ-phosphate to the remainder of the nucleotide, leaving a bound guanosine diphosphate (GDP) and releasing an inorganic phosphate. This usually occurs rapidly, and the GTP binding protein can then only be activated by exchanging the GDP for a new GTP molecule. The substitution of sulfur for one of the oxygens of the γ-phosphate of GTP creates a nucleotide that either cannot be hydrolyzed or is only slowly hydrolyzed.
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BgK competes with I-α- dendrotoxin, a known probe used to indicate the presence of certain potassium channels, over binding to synaptic membranes within rat brains. The binding sites of the toxin between Kv1.1, Kv1.2, and Kv1.3 were found to include three common amino acid residues: Lys-25, Tyr-26, and Ser-23. This combination appear to form the core residues that are the site of binding of all Kv1 channel blockers from sea anemones. In particular with Kv1.1, the major reason for BgK's affinity towards binding to this specific channel stems from an electrostatic connections between the side chain of Lys-25 and the carbonyl oxygens of the amino acids found within the channel's molecular filter.
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A chromate ester is a chemical structure that contains a chromium atom (symbol Cr) in a +6 oxidation state that is connected via an oxygen (O) linkage to a carbon (C) atom. The Cr itself is in its chromate form, with several oxygens attached, and the Cr–O–C attachment makes this chemical group structurally similar to other ester functional groups. They can be synthesized from various chromium(VI) metal compounds, such as CrO3, chromium chloride complexes, and aqueous chromate ions, and tend to react via redox reactions to liberate chromium(IV). Chromate esters are the key reactive intermediates in the Jones oxidation, the mechanistically related oxidations using pyridinium dichromate or pyridinium chlorochromate.
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Enantiomers of Pillar[5]arene The orientation of the hydroquinone oxygens on both rims of the pillararene allow the macrocycle to exhibit planar chirality. When the substituent on the hydroquinone oxygen is small enough to fit through the cavity of the pillararene, allowing for oxygen-through-the- annulus rotation to occur, racemization occurs. If this substituent is large enough to prevent rotation, optically active pillararene macrocycles can be isolated.Ogoshi, T.; Masaki, K.; Shiga, R.; Kitajima, K.; Yamagishi, T.-a. Org. Lett. 2011, 13, 1264Strutt, N. L., Fairen-Jimenez, D.; Iehl, J.; Lalonde, M. B.; Snurr, R. Q.; Farha, O. K.; Hupp, J. T.; Stoddart, J. F. J. Am. Chem. Soc. 2012, 134, 17436.
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Urea is a very poor chelating ligand due to low Lewis base character of its NH2 groups. However the carbonyl oxygens of Alaα170 and Alaα366 enhance the basicity of the NH2 groups and allow for binding to Ni2. Therefore, in this proposed mechanism, the positioning of urea in the active site is induced by the structural features of the active site residues which are positioned to act as hydrogen-bond donors in the vicinity of Ni1 and as acceptors in the vicinity of Ni2. The main structural difference between the Ciurli/Mangani mechanism and the other two is that it incorporates a nitrogen, oxygen bridging urea that is attacked by a bridging hydroxide.
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Normally, carbon is tetravalent, while oxygen is divalent, and in most oxocarbons (as in most other carbon compounds) each carbon atom may be bound to four other atoms, while oxygen may be bound to at most two. Moreover, while carbon can connect to other carbons to form arbitrarily large chains or networks, chains of three or more oxygens are rarely if ever observed. Thus the known electrically neutral oxocarbons generally consist of one or more carbon skeletons (including cyclic and aromatic structures) connected and terminated by oxide (-O-, =O) or peroxide (-O-O-) groups. Carbon atoms with unsatisfied bonds are found in some oxides, such as the diradical C2O or :C=C=O; but these compounds are generally too reactive to be isolated in bulk.
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Nylon 66 can have multiple parallel strands aligned with their neighboring peptide bonds at coordinated separations of exactly 6 and 4 carbons for considerable lengths, so the carbonyl oxygens and amide hydrogens can line up to form interchain hydrogen bonds repeatedly, without interruption (see the figure opposite). Nylon 510 can have coordinated runs of 5 and 8 carbons. Thus parallel (but not antiparallel) strands can participate in extended, unbroken, multi-chain β-pleated sheets, a strong and tough supermolecular structure similar to that found in natural silk fibroin and the β-keratins in feathers. (Proteins have only an amino acid α-carbon separating sequential -CO-NH- groups.) Nylon 6 will form uninterrupted H-bonded sheets with mixed directionalities, but the β-sheet wrinkling is somewhat different.
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K+ ion permeation occurs at the upper selectivity filter region of the pore, while pH gating rises from the protonation of transmembrane helices at the end of the pore. At low pH, the M2 helix is protonated, shifting the ion channel from closed to open conformation. As ions flow through the channel, voltage gating mechanisms are thought to induce interactions between Glu71 and Asp80 in the selectivity filter, which destabilize the conductive conformation and facilitate entry into a long-lived nonconducting state that resembles the C-type–inactivation of voltage- dependent channels. In the nonconducting conformation of KcsA at pH 7, K+ is bound tightly to coordinating oxygens of the selectivity filter and the four TM2 helices converge near the cytoplasmic junction to block the passage of any potassium ions.
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The existence and mechanism for ion selectivity was first postulated in the late 1960s by Bertil Hille and Clay Armstrong. The idea of the ionic selectivity for potassium channels was that the carbonyl oxygens of the protein backbones of the "selectivity filter" (named by Bertil Hille) could efficiently replace the water molecules that normally shield potassium ions, but that sodium ions were smaller and cannot be completely dehydrated to allow such shielding, and therefore could not pass through. This mechanism was finally confirmed when the first structure of an ion channel was elucidated. A bacterial potassium channel KcsA, consisting of just the selectivity filter, "P" loop and two transmembrane helices was used as a model to study the permeability and the selectivity of ion channels in the Mackinnon lab.
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By analogy to the above, one can use an anion exchange (positively charged) column surface chemistry to reduce the influence on retention of cationic (positively charged) functional groups for a set of analytes, such as when selectively isolating phosphorylated peptides or sulfated polysaccharide molecules. Use of a pH between 1 and 2 pH units will reduce the polarity of two of the three ionizable oxygens of the phosphate group, and thus will allow easy desorption from the (oppositely charged) surface chemistry. It will also reduce the influence of negatively charged carboxyls in the analytes, since they will be protonated at this low a pH value, and thus contribute less overall polarity to the molecule. Any common, positively charged amino groups will be repelled from the column surface chemistry and thus these conditions enhance the role of the phosphate's polarity (as well as other neutral polar groups) in the separation.
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Taking calcium uranate, CaUO4, as an example, the six oxygen atoms are arranged as a flattened octahedron, flattened along the 3-fold symmetry axis of the octahedron which also runs through the O-U-O axis (local point group D3d at the uranium atom). Each of these oxygen atoms is shared between three uranium atoms, which accounts for the stoichiometry, U 2×O 6×1/3 O = UO4. The structure has been described as a hexagonal layer structure. It can also viewed as a distorted fluorite structure in which two U-O distances have decreased and the other six have increased. In the other group, exemplified by barium uranate, BaUO4, there are four additional oxygen atoms. These four oxygens lie in a plane and each is shared between two uranium atoms, which accounts for the stoichiometry, U 2×O 4×1/2 O = UO4.
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Other examples are the lipid A synthesis enzyme LpxA and insect antifreeze proteins with a regular array of Thr sidechains on one face that mimic the structure of ice. End-view of a 3-sided, right-handed β-helix () Righthanded β-helices, typified by the pectate lyase enzyme shown at left or P22 phage tailspike protein, have a less regular cross-section, longer and indented on one of the sides; of the three linker loops, one is consistently just two residues long and the others are variable, often elaborated to form a binding or active site. A two-sided β-helix (right-handed) is found in some bacterial metalloproteases; its two loops are each six residues long and bind stabilizing calcium ions to maintain the integrity of the structure, using the backbone and the Asp side chain oxygens of a GGXGXD sequence motif. This fold is called a β-roll in the SCOP classification.
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There are two different arrangements for the coordination of nitrate with aluminium in the complex. One nitrate is bonded with two oxygens to the aluminium (bidentate), and the other five oxygen atoms only link via one oxygen (monodentate). The bidentate nitrate has an O–Al length of 1.98 Å. Another two Al–O bonds roughly in the same plane have a length of 1.89 Å. The other two Al–O bonds complete a distorted octahedral arrangement and pop out the top and bottom of the aluminium with a length of 1.93 Å. The bidentate connected nitrate group is distorted so that the uncoordinated terminal oxygen bond is shorter than the coordinated oxygen–nitrogen distance (1.22 versus 1.31 Å). The angles are also warped, with coordinated oxygen angle subtended on the nitrogen of 109°, and angle of these oxygen atoms with the terminal atom of 126°. The whole nitrate is still planar along with the aluminium.
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Electron movements are represented by curly arrows. The cleavage reaction is a phosphodiester isomerization reaction that is initiated by abstraction of the cleavage-site ribose 2’-hydroxyl proton from the 2’-oxygen, which then becomes the attacking nucleophile in an “in-line” or SN2(P)-like reaction, although it is not known whether this proton is removed prior to or during the chemical step of the hammerhead cleavage reaction. (The cleavage reaction is technically not bimolecular, but behaves in the same way a genuine SN2(P) reaction does; it undergoes inversion of configuration subsequent to forming an associative transition-state consisting of a pentacoordinated oxyphosphrane.) The attacking and leaving group oxygens will both occupy the two axial positions in the trigonal bipyramidal transition-state structure as is required for an SN2-like reaction mechanism. The 5’-product, as a result of this cleavage reaction mechanism, possesses a 2’,3’-cyclic phosphate terminus, and the 3’-product possesses a 5’-OH terminus, as with nonenzymatic alkaline cleavage of RNA.
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