-
Journal of the American Society For... Feb 2021Improving the mobile phase of electrospray oligonucleotides has been a major focus in the field of oligonucleotides. These improved mobile phases should reduce the...
Improving the mobile phase of electrospray oligonucleotides has been a major focus in the field of oligonucleotides. These improved mobile phases should reduce the charge state envelope of oligonucleotides coupled with electrospray ionization, which is key to reducing spectral complexity and increasing sensitivity. Traditional mobile phase compositions with fluorinated alcohol and alkylamine, like hexafluoroisopropanol (HFIP) and triethylamine (TEA), have a large amount of cationic adduction and many charge states. Utilizing different fluorinated alcohol and alkylamine combinations, like nonafluoro--butyl alcohol (NFTB) and octylamine (OA), can selectively reduce the charge states analyzed. Other classes of biomolecules have been analyzed with anionic salts to stabilize complexes, increase the molecular peak detection, and even provide unique structural information about these molecules; however, there have been no studies using anionic salts with oligonucleotides. Our experiments systematically study the stability and binding of ammonium anionic salt. We show that anions selectively bind low charge states of these oligonucleotides. Ion-mobility measurements are made to determine the collision cross section (CCS) of these oligonucleotides with anion adduction. We utilize both a nucleic acid exact hard sphere simulation (EHSS) calibration and a protein calibration. We are able to show that NFTB/OA is a good choice for the study of oligonucleotides with reduced charge states for the binding of anionic salts and the determination of CCS using ion mobility.
Topics: Amines; Anions; Aptamers, Nucleotide; Gases; Oligonucleotides; Phosphorothioate Oligonucleotides; Solvents; Spectrometry, Mass, Electrospray Ionization; Sulfates; tert-Butyl Alcohol
PubMed: 33476148
DOI: 10.1021/jasms.0c00380 -
Chemical Communications (Cambridge,... Aug 2016Perfluoroaryl-substituted tellurophenes act as anion receptors through noncovalent chalcogen bonding interactions. Linking two tellurophenes through an ethynylene group...
Perfluoroaryl-substituted tellurophenes act as anion receptors through noncovalent chalcogen bonding interactions. Linking two tellurophenes through an ethynylene group results in a significant level of chelate cooperativity, thus demonstrating that chalcogen bonding can be used to achieve multidentate anion recognition.
Topics: Anions; Chalcogens; Hydrogen Bonding
PubMed: 27376877
DOI: 10.1039/c6cc04818h -
The Journal of Physical Chemistry... Apr 2022The influence of incremental hydration (≤4) on the electronic resonances of the pyrene anion is studied using two-dimensional photoelectron spectroscopy. The...
The influence of incremental hydration (≤4) on the electronic resonances of the pyrene anion is studied using two-dimensional photoelectron spectroscopy. The photoexcitation energies of the resonances do not change; therefore, from the anion's perspective, the resonances remain the same, but from the neutral's perspective of the electron-molecule reaction, the resonances decrease in energy by the binding energy of the water molecules. The autodetachment of the resonances shows that hydration has very little effect, showing that even the dynamics of most of the resonances are not impacted by hydration. Two specific resonances do show changes that are explained by the closing of specific autodetachment channels. The lowest-energy resonance leads to efficient electron capture as observed through thermionic emission and evaporation of water molecules (dissociative electron attachment). The implications of low-energy electron capture in dense molecular interstellar clouds are discussed.
Topics: Anions; Electrons; Photoelectron Spectroscopy; Pyrenes; Water
PubMed: 35420036
DOI: 10.1021/acs.jpclett.2c00523 -
Journal of Inorganic Biochemistry Mar 2012When the iron core of equine spleen ferritin is reduced, anions in solution cross the protein shell and enter the ferritin interior as part of a charge balancing...
When the iron core of equine spleen ferritin is reduced, anions in solution cross the protein shell and enter the ferritin interior as part of a charge balancing reaction. Anion sequestration inside ferritin during iron core reduction was monitored using ion selective electrodes, inductively coupled plasma emission, and energy-dispersive X-ray spectroscopy. The requirement for anion translocation to the ferritin interior occurs because upon iron core reduction, two OH(-) ions per iron are released or neutralized inside ferritin leaving a net positive charge. Halides and oxoanions were tested as anionic substrates for this reaction. A general trend for the halides showed that the smaller halides accumulated inside ferritin in greater abundance than larger halides, presumably because the protein channels restrict the transfer of the larger anionic species. In contrast, oxoanion accumulation inside ferritin did not show selectivity based on size or charge. Vanadate and molybdate accumulated to the highest concentrations and nitrate, phosphate and tungstate showed poor accumulation inside ferritin. Fe(II) remains stably sequestered inside ferritin, as shown by electron microscopy and by column chromatography. Upon oxidation of the iron core, the anions are expelled from ferritin, and OH(-) ions coordinate to the Fe(III) to form the original Fe(O)OH mineral. Anion transport across the ferritin protein shell represents an important mechanism by which ferritin maintains proper charge balance inside the protein cavity.
Topics: Anions; Ferritins; Hydroxides; Iron; Models, Chemical; Molybdenum; Nitrates; Phosphates; Tungsten Compounds; Vanadates
PubMed: 22265833
DOI: 10.1016/j.jinorgbio.2011.12.004 -
Molecules (Basel, Switzerland) May 2022In this article, we present fluorescent guanidiniocarbonyl-indoles as versatile oxo-anion binders. Herein, the guanidiniocarbonyl-indole (GCI) and...
In this article, we present fluorescent guanidiniocarbonyl-indoles as versatile oxo-anion binders. Herein, the guanidiniocarbonyl-indole (GCI) and methoxy-guanidiniocarbonyl-indole (MGCI) were investigated as ethylamides and compared with the well-known guanidiniocarbonyl-pyrrole (GCP) concerning their photophysical properties as well as their binding behavior towards oxo-anions. Hence, a variety of anionic species, such as carboxylates, phosphonates and sulfonates, have been studied regarding their binding properties with GCP, GCI and MGCI using UV-Vis titrations, in combination with the determination of the complex stoichiometry using the Job method. The emission properties were studied in relation to the pH value using fluorescence spectroscopy as well as the determination of the photoluminescence quantum yields (PLQY). Density functional theory (DFT) calculations were undertaken to obtain a better understanding of the ground-lying electronic properties of the investigated oxo-anion binders. Additionally, X-ray diffraction of GCP and GCI was conducted. We found that GCI and MGCI efficiently bind carboxylates, phosphonates and sulfonates in buffered aqueous solution and in a similar range as GCP (K ≈ 1000-18,000 M, in bis-tris buffer, pH = 6); thus, they could be regarded as promising emissive oxo-anion binders. They also exhibit a visible fluorescence with a sufficient PLQY. Additionally, the excitation and emission wavelength of MGCI was successfully shifted closer to the visible region of the electromagnetic spectrum by introducing a methoxy-group into the core structure, which makes them interesting for biological applications.
Topics: Anions; Arginine; Carboxylic Acids; Fluorescent Dyes; Indoles; Organophosphonates; Pyrroles
PubMed: 35566361
DOI: 10.3390/molecules27093005 -
Molecular and Cellular Biochemistry Jul 1979The functions of a number of amino acid residues in proteins have been studied by chemical modification techniques and much useful information has been obtained. Methods... (Review)
Review
The functions of a number of amino acid residues in proteins have been studied by chemical modification techniques and much useful information has been obtained. Methods using dicarbonyl compounds for the modification of arginine residues are the most recent to have been developed. Since their introduction about 10 years ago, they have led to the identification of a large number of enzymes and other proteins that contain arginine residues critical to biological function. These reagents are discussed in terms of their chemical reactivity and mechanisms of action and in relation to the unique chemical properties of the guanidinium group. Butanedione, phenylglyoxal and cyclohexanedione are the most commonly employed arginyl reagents, and their relative advantages are examined. A survey of the functional role of arginine residues in enzymes and other proteins is presented in which nearly 100 examples are cited. The prediction that arginine residues would be found to serve a general role as anionic binding sites in protein has obviously been validated. The genetic and physiological implications of the selection of arginine for this important function are discussed.
Topics: Anions; Arginine; Binding Sites; Biological Evolution; Chemical Phenomena; Chemistry; Cyclohexanones; Diacetyl; Guanidines; Phenylglyoxal; Phosphates; Proteins
PubMed: 388184
DOI: 10.1007/BF00232886 -
The Journal of General Physiology Dec 2000Ca(2+)-activated Cl channels (Cl(Ca)Cs) are an important class of anion channels that are opened by increases in cytosolic [Ca(2+)]. Here, we examine the mechanisms of...
Ca(2+)-activated Cl channels (Cl(Ca)Cs) are an important class of anion channels that are opened by increases in cytosolic [Ca(2+)]. Here, we examine the mechanisms of anion permeation through Cl(Ca)Cs from Xenopus oocytes in excised inside-out and outside-out patches. Cl(Ca)Cs exhibited moderate selectivity for Cl over Na: P(Na)/P(Cl) = 0.1. The apparent affinity of Cl(Ca)Cs for Cl was low: K(d) = 73 mM. The channel had an estimated pore diameter >0.6 nm. The relative permeabilities measured under bi-ionic conditions by changes in E(rev) were as follows: C(CN)(3) > SCN > N(CN)(2) > ClO(4) > I > N(3) > Br > Cl > formate > HCO(3) > acetate = F > gluconate. The conductance sequence was as follows: N(3) > Br > Cl > N(CN)(2) > I > SCN > COOH > ClO(4) > acetate > HCO(3) = C(CN)(3) > gluconate. Permeant anions block in a voltage-dependent manner with the following affinities: C(CN)(3) > SCN = ClO(4) > N(CN)(2) > I > N(3) > Br > HCO(3) > Cl > gluconate > formate > acetate. Although these data suggest that anionic selectivity is determined by ionic hydration energy, other factors contribute, because the energy barrier for permeation is exponentially related to anion hydration energy. Cl(Ca)Cs exhibit weak anomalous mole fraction behavior, implying that the channel may be a multi-ion pore, but that ions interact weakly in the pore. The affinity of the channel for Ca(2+) depended on the permeant anion at low [Ca(2+)] (100-500 nM). Apparently, occupancy of the pore by a permeant anion increased the affinity of the channel for Ca(2+). The current was strongly dependent on pH. Increasing pH on the cytoplasmic side decreased the inward current, whereas increasing pH on the external side decreased the outward current. In both cases, the apparent pKa was voltage-dependent with apparent pKa at 0 mV = approximately 9.2. The channel may be blocked by OH(-) ions, or protons may titrate a site in the pore necessary for ion permeation. These data demonstrate that the permeation properties of Cl(Ca)Cs are different from those of CFTR or ClC-1, and provide insights into the nature of the Cl(Ca)C pore.
Topics: Animals; Anions; Binding, Competitive; Calcium; Chloride Channels; Chlorides; Hydrogen-Ion Concentration; Oocytes; Osmolar Concentration; Permeability; Sodium; Xenopus laevis
PubMed: 11099350
DOI: 10.1085/jgp.116.6.825 -
Reviews of Physiology, Biochemistry and... 1994
Review
Topics: Amino Acids; Animals; Anions; Base Sequence; Bile Acids and Salts; Carboxylic Acids; Fatty Acids; Humans; Ion Transport; Liver; Molecular Sequence Data
PubMed: 8209137
DOI: 10.1007/BFb0030903 -
Journal of the American Chemical Society Sep 2022A molecular capsule () consisting of two calix[4]pyrroles connected via ethylene diamide linkers has been prepared as an anion receptor. H NMR spectroscopic studies...
A molecular capsule () consisting of two calix[4]pyrroles connected via ethylene diamide linkers has been prepared as an anion receptor. H NMR spectroscopic studies carried out in CDCl revealed that receptor recognizes a variety of anions with different binding modes and stoichiometries. For instance, receptor binds fluoride and acetate with 1:2 receptor/anion stoichiometry and other test anions with 1:1 stoichiometry in solution when their respective tetrabutylammonium (TBA) salts were used. In contrast, with tetraethylammnium (TEA) salts, receptor forms 1:2 complexes with chloride and bromide in addition to fluoride, overcoming expected Columbic repulsions between the anions co-bound in close proximity. Receptor is also able to bind oxoanions, such as oxalate (CO), dihydrogen phosphate (HPO), sulfate (SO), and hydrogen pyrophosphate (HPO), in the form of 1:1 complexes as the result of presumed cooperation between the two calix[4]pyrrole subunits. The selectivity of receptor for fluoride versus dihydrogen phosphate varies depending on their relative concentrations. For instance, in the presence of less than 1.0 equiv of an equimolar mixture of fluoride and dihydrogen phosphate, receptor shows high selectivity for dihydrogen phosphate. In contrast, in the presence of ≥2.0 anion equiv, receptor binds fluoride preferentially, forming a 1:2 complex. Moreover, when treated with F, the preformed 1:1 HPO complex of receptor is converted to the corresponding 1:2 receptor/fluoride complex with the release of the prebound dihydrogen phosphate anion. As inferred from gas-phase computations, this seemingly counterintuitive behavior is rationalized in terms of the precomplexed dihydrogen phosphate serving to reduce the reorganization energy required to bind two fluoride anions. The presence of a water molecule in addition to the bound fluoride anions may also favor the formation of the 1:2 F complex. The present study provides a new approach for fine-tuning the binding selectivity of polytopic anion receptors.
Topics: Anions; Bromides; Calixarenes; Chlorides; Diamide; Diphosphates; Ethylenes; Fluorides; Hydrogen; Oxalates; Phosphates; Pyrroles; Salts; Sulfates; Water
PubMed: 36074582
DOI: 10.1021/jacs.2c06284 -
Chemical Society Reviews Apr 2009The present critical review outlines the close relationship and mutual interplay between molecular recognition, active site considerations in enzyme catalysis involving... (Review)
Review
The present critical review outlines the close relationship and mutual interplay between molecular recognition, active site considerations in enzyme catalysis involving anions, and organocatalysis utilizing explicit hydrogen bonding. These interconnections are generally not made although, as we demonstrate, they are quite apparent as exemplified with pertinent examples in the field of (thio)urea organocatalysis. Indeed, the concepts of anion binding or binding with negatively (partially) charged heteroatoms is key for designing new organocatalytic transformations. Utilizing anions through recognition with hydrogen-bonding organocatalysts is still in its infancy but bears great potential. In turn, the discovery and mechanistic elucidation of such reactions is likely to improve the understanding of enzyme active sites (108 references).
Topics: Anions; Catalysis; Enzymes; Hydrogen Bonding; Thiourea; Urea
PubMed: 19421588
DOI: 10.1039/b801793j