Name: qualitative identification of carboxylic acids, boronic acids, and amines using cruciform fluorophores
Uploaded: 2013-08-19T13:00:00
Description: Watch this Scientific Journal Video about Qualitative Identification of Carboxylic Acids, Boronic Acids, and Amines Using Cruciform Fluorophores at JoVE.com

Work in Bunz's laboratory at the Georgia Institute of Technology was supported in part by the National Science Foundation (NSF-CHE 07502753) and the work at Ruprecht-Karls-Universit&auml;t Heidelberg was funded by the "Struktur und Innovationsfond des Landes Baden-W&uuml;rttemberg". Work in Miljani&#263;'s laboratory at the University of Houston was funded by the National Science Foundation CAREER program (CHE-1151292), the Welch Foundation (grant no. E-1768), the University of Houston (UH) and its Small Grant program, and the Texas Center for Superconductivity at UH.

1. Detection of Carboxylic Acids Using Distyrylbis(arylethynyl)benzene Cruciforms
<ol>
	<li>Prepare a fresh stock solution of cruciforms 1-3 with a concentration of 1.0 x 10-3 mol/L in DCM. It is not necessary to use spectroscopic quality solvents; ACS reagent grade purity is sufficient.</li>
	<li>Using the stock solutions from 1.1 prepare 100 ml each of 2.0 x 10-6 M solution of 1-3 in dichloromethane (DCM), ethyl acetate (EtOAc), acetonitrile (AN), N,N-dimethylformamide (DMF), isopropyl ...

<ol>
	<li>Zucchero, A. J., McGrier, P. J., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cross-conjugated+cruciform+fluorophores.">Cross-conjugated cruciform fluorophores.</a> Acc. Chem. Res. 43 (3), 397-408 (2010).</li><li>Feldman, A. K., Steigerwald, M. L., Guo, X., Nuckolls, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+electronic+devices+based+on+single-walled+carbon+nanotube+electrodes.">Molecular electronic devices based on single-walled carbon nanotube electrodes.</a> Acc. Chem. Res. 41 (12), 1731-1741 (2008).</li><li>Galbrecht, F., B&#252;nnagel, T., Bilge, A., Scherf, T. J. J., M&#252;ller, U. H. F., Bunz, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Functional Organic Materials. , 83 (2007).</li><li>Marsden, J. A., Miller, J. J., Shirtcliff, L. D., Haley, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure-property+relationships+of+donor/acceptor-functionalized+tetrakis(phenylethynyl)benzenes+and+bis(dehydrobenzoannuleno)+benzenes.">Structure-property relationships of donor/acceptor-functionalized tetrakis(phenylethynyl)benzenes and bis(dehydrobenzoannuleno) benzenes.</a> J. Am. Chem. Soc. 127 (8), 2464-2476 (2005).</li><li>Lim, J., Albright, T. A., Martin, B. R., Miljani&#263;, O. &. #. 3. 5. 2. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Benzobisoxazole+cruciforms:+heterocyclic+fluorophores+with+spatially+separated+frontier+molecular+orbitals.">Benzobisoxazole cruciforms: heterocyclic fluorophores with spatially separated frontier molecular orbitals.</a> J. Org. Chem. 76 (24), 10207-10219 (2011).</li><li>Lirag, R. C., Le, H. T. M., Miljani&#263;, O. &. #. 3. 5. 2. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=L-shaped+benzimidazole+fluorophores:+synthesis,+characterization+and+optical+response+to+bases,+acids+and+anions.">L-shaped benzimidazole fluorophores: synthesis, characterization and optical response to bases, acids and anions.</a> Chem. Commun. , (2013).</li><li>Hauck, M., Schoenhaber, J., Zucchero, A. J., Hardcastle, K. I., Mueller, T. J. J., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenothiazine+cruciforms:+synthesis+and+metallochromic+properties.">Phenothiazine cruciforms: synthesis and metallochromic properties.</a> J. Org. Chem. 72 (18), 6714-6725 (2007).</li><li>Zucchero, A. J., Wilson, J. N., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cruciforms+as+functional+fluorophores:+response+to+protons+and+selected+metal+ions.">Cruciforms as functional fluorophores: response to protons and selected metal ions.</a> J. Am. Chem. Soc. 128 (36), 11872-11881 (2006).</li><li>Wilson, J. N., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Switching+of+intramolecular+charge+transfer+in+cruciforms:+metal+ion+sensing.">Switching of intramolecular charge transfer in cruciforms: metal ion sensing.</a> J. Am. Chem. Soc. 127 (12), 4124-4125 (2005).</li><li>Davey, E. A., Zucchero, A. J., Trapp, O., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discrimination+of+organic+acids+using+a+three+molecule+array+based+upon+cruciform+fluorophores.">Discrimination of organic acids using a three molecule array based upon cruciform fluorophores.</a> J. Am. Chem. Soc. 133 (20), 7716-7718 (2011).</li><li>Lim, J., Nam, D., Miljani&#263;, O. &. #. 3. 5. 2. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+carboxylic+and+organoboronic+acids+and+phenols+with+a+single+benzobisoxazole+fluorophore.">Identification of carboxylic and organoboronic acids and phenols with a single benzobisoxazole fluorophore.</a> Chem. Sci. 3 (2), 559-563 (2012).</li><li>Lim, J., Miljani&#263;, O. &. #. 3. 5. 2. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Benzobisoxazole+fluorophore+vicariously+senses+amines,+ureas,+anions.">Benzobisoxazole fluorophore vicariously senses amines, ureas, anions.</a> Chem. Commun. 48 (83), 10301-10303 (2012).</li><li>Braga, D., Polito, M., Bracaccini, M., D'Addario, D., Tagliavini, E., Sturba, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+organometallic+building+blocks+for+molecular+crystal+engineering.+2.+Synthesis+and+characterization+of+pyridyl+and+pyrimidyl+derivatives+of+diboronic+acid,+Fe(&#951;5-C5H4+-+B(OH)2)2],+and+of+pyridyl+boronic+acid,+[Fe(&#951;5-C5H4-4-C5H4N)(&#951;5-C5H4+-+B(OH)2)].">Novel organometallic building blocks for molecular crystal engineering. 2. Synthesis and characterization of pyridyl and pyrimidyl derivatives of diboronic acid, Fe(&#951;5-C5H4 - B(OH)2)2], and of pyridyl boronic acid, [Fe(&#951;5-C5H4-4-C5H4N)(&#951;5-C5H4 - B(OH)2)].</a> Organometallics. 22 (10), 2142-2150 (2003).</li><li>Schwaebel, T., Trapp, O., Bunz, U. H. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Digital+photography+for+the+analysis+of+fluorescence+responses.">Digital photography for the analysis of fluorescence responses.</a> Chem. Sci. 4 (3), 273-281 (2013).</li></ol>

The protocols for qualitative discrimination described in this paper and video hold significant potential in routine quality analyses, where even a minimally trained operator could discern the differences in composition, or deviations from a well-defined formula. Practicality of this technique could be further enhanced by using simple cellphone cameras, which, in combination with pattern- and image-recognition software such as Google Goggles, could match the recorded emission colors to the database of known compositions....

Molecular cruciforms are defined as X-shaped cross-conjugated molecules in which two conjugation circuits intersect at a central core.1,2,3 With appropriate donor-acceptor substitution, these molecules can spatially localize their frontier molecular orbitals (FMOs), so that the highest occupied molecular orbital (HOMO) resides dominantly along the electron-rich axis of the molecule, while the lowest unoccupied molecular orbital (LUMO) has the bulk of its density positioned along the electron-poor arm of the molecule. Such spatial isolation of FMOs is essential in the applications of these cruciforms as sensors for small molecules, since analyte binding to the cruciform invariably changes its HOMO-LUMO gap and the associated optical properties. This behavior has been demonstrated in cruciforms based on 1,4-distyryl-2,5-bis(arylethynyl)benzene,1 1,2,4,5-tetrakisethynylbenzene,4 and benzobisoxazole5,6 structural motifs. Since all three classes of molecules are inherently fluorescent, this methodology allowed their use as small-molecule sensors. In all three examples, cruciforms were substituted with Lewis basic pyridine and dialkylaniline groups and were thus responsive to Lewis acidic analytes, such as protons and metal ions.1,4,5,7,8,9
In 2011, Bunz and coworkers have shown10 that the fluorescence responses of 1,4-distyryl-2,5-bis(arylethynyl)benzene cruciforms 1 - 3 (Figure 1) dramatically varied depending on the structure of the carboxylic acid used to induce protonation of the cruciform. Subsequently, Miljani&#263; et al. demonstrated that benzobisoxazole cruciforms such as 4 (Figure 1) also show highly specific fluorescence emission responses to structurally related carboxylic acids, and that similar distinction can be seen among very similar organoboronic acids, too.11 Origins of this highly selective emission color changes are at present unclear, and are most likely complex - as fluorescence quenching by electron poor analytes, residual analyte fluorescence, and protonation-induced shifting of cruciforms&#39; emission maxima all presumably play a role. Nevertheless, the ability to discriminate among structurally related analytes is significant, especially since statistically relevant distinction can be obtained without the need to perform exhaustive UV/Vis absorption or fluorescence characterization of the optical response of cruciforms to analytes. Instead, simple photographs of emission color are sufficiently distinct to allow the discrimination among structurally closely related analytes, especially if the photographs are taken in different solvents or using more than one cruciform sensor. Using this quick methodology, dozens of analytes can be quickly analyzed in an afternoon (see panels in Figures 3-5), whereas the same analysis would require weeks if rigorous spectroscopy was employed. Furthermore, since boronic acids are dynamic species that can coordinate nucleophiles through boron&#39;s empty p-orbital, Miljani&#263; used this feature to develop hybrid sensors composed of benzobisoxazole cruciform 4 and simple non-fluorescent boronic acid additives B1 and B5 (Figure 4).11,12 This methodology operates as follows: cruciform 4 and boronic acids complex into a transient complex 4&#183;nB1 (or 4&#183;nB5); the precise structure of this complex is at present unknown, but its fluorescence differs from that of the pure cruciform. If this solution is exposed to Lewis basic analytes, they can replace one or both -OH groups on the boronic acid,13 thus significantly altering the electronic properties of boron and, in turn, the fluorescence of the entire complex. Using this &#34;vicarious sensing&#34; methodology, sensing of phenols, organic amines and ureas, as well as of small organic and inorganic anions, could be achieved.
In this paper, we present a tutorial on the use of both direct and vicarious sensing methodology to quickly qualitatively distinguish between structurally related (a) carboxylic acids (Figure 3), (b) boronic acids (Figure 4), and, vicariously, (c) organic amines (Figure 5). To illustrate the broad applicability of the reported protocols, Bunz&#39;s cruciforms were used to detect carboxylic acids, while Miljani&#263;&#39;s compounds were employed to detect boronic acids, and, through a hybrid sensor, small organic amines. We presume that these sensors could be readily interchanged without major consequences to the quality of analyte discrimination.

<table border="1">
		<tbody>
		 <tr>
			<td>Name of Material/ Equipment</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments/Description</td>
		 </tr>
		 <tr>
			<td>Cyclohexane (CH)</td>
			<td>Mallinckrodt</td>
			<td>4878-02</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Chlorobenzene (CB)</td>
			<td>JT Baker</td>
			<td>9179-1</td>
			<td></td>
		 </tr>
		 <tr>
			<td>1,2,4-Trichlorobenzene (TCB)</td>
			<td>Alfa Aesar</td>
			<td>19390</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Dichloromethane (DCM) - Miljani&#263;</td>
			<td>Mallinckrodt</td>
			<td>4879-06</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Acetonitrile (AN)</td>
			<td>Mallinckrodt</td>
			<td>2856-10</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Chloroform (CF)</td>
			<td>Mallinckrodt</td>
			<td>4440-19</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Dichloromethane (DCM) - Bunz</td>
			<td>Sigma Aldrich</td>
			<td>24233</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Ethyl Acetate (EtOAc)</td>
			<td>Brenntag</td>
			<td>10010447</td>
			<td>Additional distillation</td>
		 </tr>
		 <tr>
			<td>Acetonitrile (AN)</td>
			<td>Sigma Aldrich</td>
			<td>34851</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Dimethylformamide (DMF)</td>
			<td>Sigma Aldrich</td>
			<td>38840</td>
			<td></td>
		 </tr>
		 <tr>
			<td>2-Propanol (iPrOH)</td>
			<td>Ruprecht-Karls Universit&auml;t Heidelberg, Zentralbereich Neuenheimer Feld</td>
			<td>69595</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Methanol (MeOH)</td>
			<td>VWR</td>
			<td>20847.295</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Hydroxybenzoic Acid (A1)</td>
			<td>Fluka</td>
			<td>54630</td>
			<td></td>
		 </tr>
		 <tr>
			<td>(4-Hydroxyphenyl)acetic Acid (A2)</td>
			<td>Sigma Aldrich</td>
			<td>H50004</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Ibuprofen (A3)</td>
			<td>ABCR</td>
			<td>AB125950</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Aspirine (A4)</td>
			<td>Sigma Aldrich</td>
			<td>A5376</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Phenylacetic Acid (A5)</td>
			<td>Sigma Aldrich</td>
			<td>P16621</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Chlorophenylacetic Acid (A6)</td>
			<td>Sigma Aldrich</td>
			<td>139262</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Benzoic Acid (A7)</td>
			<td>Merck</td>
			<td>8222571000</td>
			<td></td>
		 </tr>
		 <tr>
			<td>3,5-Dihydroxybenzoic Acid (A8)</td>
			<td>Sigma Aldrich</td>
			<td>D110000</td>
			<td></td>
		 </tr>
		 <tr>
			<td>2,4-Dichlorobenzoic Acid (A9)</td>
			<td>Sigma Aldrich</td>
			<td>139572</td>
			<td></td>
		 </tr>
		 <tr>
			<td>2-Hydroxy-5-iodobenzoic Acid (A10)</td>
			<td>Sigma Aldrich</td>
			<td>I10600</td>
			<td></td>
		 </tr>
		 <tr>
			<td>2,6-Dichlorophenylboronic Acid (B1)</td>
			<td>TCI</td>
			<td>D3357</td>
			<td></td>
		 </tr>
		 <tr>
			<td>3,5-Bis(trifluoromethyl)phenylboronic Acid (B2)</td>
			<td>Sigma Aldrich</td>
			<td>471070</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Mercaptophenylboronic Acid (B3)</td>
			<td>Sigma Aldrich</td>
			<td>524018</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Methoxyphenylboronic Acid (B4)</td>
			<td>TCI</td>
			<td>M1126</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Benzeneboronic Acid (B5)</td>
			<td>Alfa Aesar</td>
			<td>A14257</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Cyclohexylboronic Acid (B6)</td>
			<td>Sigma Aldrich</td>
			<td>556580</td>
			<td></td>
		 </tr>
		 <tr>
			<td>3-Pyridylboronic Acid (B7)</td>
			<td>Sigma Aldrich</td>
			<td>512125</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Nitrophenylboronic Acid (B8)</td>
			<td>Sigma Aldrich</td>
			<td>673854</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Pentafluorophenylboronic Acid (B9)</td>
			<td>Sigma Aldrich</td>
			<td>465097</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Triethylamine (N1)</td>
			<td>Alfa Aesar</td>
			<td>A12646</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Piperidine (N2)</td>
			<td>JT Baker</td>
			<td>2895-05</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Piperazine (N3)</td>
			<td>Aldrich</td>
			<td>P45907</td>
			<td></td>
		 </tr>
		 <tr>
			<td>1,4-Diaminobenzene (N4)</td>
			<td>Alfa Aesar</td>
			<td>A15680</td>
			<td></td>
		 </tr>
		 <tr>
			<td>1,3-Diaminobenzene (N5)</td>
			<td>Eastman</td>
			<td></td>
			<td></td>
		 </tr>
		 <tr>
			<td>1,2-Diaminobenzene (N6)</td>
			<td>TCI</td>
			<td>P0168</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Methoxyaniline (N7)</td>
			<td>Alfa Aesar</td>
			<td>A10946</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Aniline (N8)</td>
			<td>Acros</td>
			<td>22173-2500</td>
			<td></td>
		 </tr>
		 <tr>
			<td>4-Nitroaniline (N9)</td>
			<td>Alfa Aesar</td>
			<td>A10369</td>
			<td></td>
		 </tr>
		 <tr>
			<td>N,N-Diphenylurea (N10)</td>
			<td>Alfa Aesar</td>
			<td>A18720</td>
			<td></td>
		 </tr>
		 <tr>
			<td>N,N-Dimethylurea (N11)</td>
			<td>Alfa Aesar</td>
			<td>B21329</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Urea (N12)</td>
			<td>Mallinckrodt</td>
			<td>8648-04</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Canon EOS 30D (objective EFS 18-55 mm zoom lens)</td>
			<td>Canon</td>
			<td></td>
			<td></td>
		 </tr>
		 <tr>
			<td>Canon EOS Rebel T3i (objective EFS 18-55 mm zoom lens)</td>
			<td>Canon</td>
			<td></td>
			<td></td>
		 </tr>
		 <tr>
			<td>FujiFilm FinePix S9000</td>
			<td>Fuji</td>
			<td></td>
			<td></td>
		 </tr>
		</tbody>
 </table>

qualitative identification of carboxylic acids, boronic acids, and amines using cruciform fluorophores

Molecular cruciforms are X-shaped systems in which two conjugation axes intersect at a central core. If one axis of these molecules is substituted with electron-donors, and the other with electron-acceptors, cruciforms&#39; HOMO will localize along the electron-rich and LUMO along the electron-poor axis. This spatial isolation of cruciforms&#39; frontier molecular orbitals (FMOs) is essential to their use as sensors, since analyte binding to the cruciform invariably changes its HOMO-LUMO gap and the associated optical properties. Using this principle, Bunz and Miljani&#263; groups developed 1,4-distyryl-2,5-bis(arylethynyl)benzene and benzobisoxazole cruciforms, respectively, which act as fluorescent sensors for metal ions, carboxylic acids, boronic acids, phenols, amines, and anions. The emission colors observed when these cruciform are mixed with analytes are highly sensitive to the details of analyte&#39;s structure and - because of cruciforms&#39; charge-separated excited states - to the solvent in which emission is observed. Structurally closely related species can be qualitatively distinguished within several analyte classes: (a) carboxylic acids; (b) boronic acids, and (c) metals. Using a hybrid sensing system composed from benzobisoxazole cruciforms and boronic acid additives, we were also able to discern among structurally similar: (d) small organic and inorganic anions, (e) amines, and (f) phenols. The method used for this qualitative distinction is exceedingly simple. Dilute solutions (typically 10-6 M) of cruciforms in several off-the-shelf solvents are placed in UV/Vis vials. Then, analytes of interest are added, either directly as solids or in concentrated solution. Fluorescence changes occur virtually instantaneously and can be recorded through standard digital photography using a semi-professional digital camera in a dark room. With minimal graphic manipulation, representative cut-outs of emission color photographs can be arranged into panels which permit quick naked-eye distinction among analytes. For quantification purposes, Red/Green/Blue values can be extracted from these photographs and the obtained numeric data can be statistically processed.

To illustrate the potential of cruciform fluorophores in sensing and discriminating closely related analytes, three classes of results are presented. First, 1,4-distyryl-2,5-bis(arylethynyl)benzene cruciforms 1-3 (Figure 1) are used to discriminate among structurally related carboxylic acids A1-A10 shown in Figure 3. Then, benzobisoxazole-based cruciform 4 (Figure 1) has been used to analyze boronic acids B1-B9 (Figure 4). Finally, cruciform 4 is used in...

Watch this Scientific Journal Video about Qualitative Identification of Carboxylic Acids, Boronic Acids, and Amines Using Cruciform Fluorophores at JoVE.com

Qualitative Identification of Carboxylic Acids, Boronic Acids, and Amines Using Cruciform Fluorophores

Cross-conjugated cruciform fluorophores based on 1,4-distyryl-2,5-bis(arylethynyl)benzene and benzobisoxazole nuclei can be used to qualitatively identify diverse Lewis acidic and Lewis basic analytes. This method relies on the differences in emission colors of the cruciforms that are observed upon analyte addition. Structurally closely related species can be distinguished from each other.

Molecular cruciforms are X-shaped systems in which two conjugation axes intersect at a central core. If one axis of these molecules is substituted with ...

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Gas chromatography (GC) is a highly sensitive method used to identify and quantify the fatty acid content of lipids from tissues, cells, and plasma/serum, ...

Quantitative and Qualitative Examination of Particle-particle Interactions Using Colloidal Probe Nanoscopy

Colloidal Probe Nanoscopy (CPN), the study of the nano-scale interactive forces between a specifically prepared colloidal probe and any chosen substrate using the Atomic Force Microscope (AFM), can provide key insights into physical interactions present within colloidal systems. Colloidal systems are widely existent in several applications including, pharmaceuticals, foods, paints, paper, soil and minerals, detergents, printing and much more.1-3 Furthermore, colloids can exist in many states such as emulsions, foams and suspensions. Using colloidal probe nanoscopy one can obtain key information on the adhesive properties, binding energies and even gain insight into the physical stability and coagulation kinetics of the colloids present within. Additionally, colloidal probe nanoscopy can be used with biological cells to aid in drug discovery and formulation development. In this paper we describe a method for conducting colloidal probe nanoscopy, discuss key factors that are important to consider during the measurement, and show that both quantitative and qualitative data that can be obtained from such measurements.

Colloidal probe nanoscopy can be used within a variety of fields to gain insight into the physical stability and coagulation kinetics of colloidal systems and aid in drug discovery and formulation sciences using biological systems. The method described within provides a quantitative and qualitative means to study such systems.

Colloidal Probe Nanoscopy (CPN), the study of the nano-scale interactive forces between a specifically prepared colloidal probe and any chosen substrate ...

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA)

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as char and soot. PyC is ubiquitous in the environment due to its long persistence, and its abundance might even increase with the projected increase in global wildfire activity and the continued burning of fossil fuel. PyC is also increasingly produced from the industrial pyrolysis of organic wastes, which yields charred soil amendments (biochar). Moreover, the emergence of nanotechnology may also result in the release of PyC-like compounds to the environment. It is thus a high priority to reliably detect, characterize and quantify these charred materials in order to investigate their environmental properties and to understand their role in the carbon cycle.
Here, we present the benzene polycarboxylic acid (BPCA) method, which allows the simultaneous assessment of PyC&#39;s characteristics, quantity and isotopic composition (13C and 14C) on a molecular level. The method is applicable to a very wide range of environmental sample materials and detects PyC over a broad range of the combustion continuum, i.e., it is sensitive to slightly charred biomass as well as high temperature chars and soot. The BPCA protocol presented here is simple to employ, highly reproducible, as well as easily extendable and modifiable to specific requirements. It thus provides a versatile tool for the investigation of PyC in various disciplines, ranging from archeology and environmental forensics to biochar and carbon cycling research.

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids BPCA

We present the benzene polycarboxylic acid (BPCA) method for assessing pyrogenic carbon (PyC) in the environment. The compound-specific approach uniquely provides simultaneous information about the characteristics, quantity and isotopic composition (13C and 14C) of PyC.

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as ...

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic acids containing three to six carbons), such as malate and citrate, are critical to the proper functioning of many biological systems, where they function in cellular respiration and can serve as indicators of cell health. In foods, organic acid content can have significant impact on taste, with increased SCCA levels resulting in a sour or &#34;acid&#34; taste. Because of this, methods for the rapid analysis of organic acid levels are of particular interest to the food and beverage industries. Unfortunately, however, most methods used for SCCA quantification are dependent on time-consuming protocols requiring the derivatization of samples with hazardous reagents, followed by costly chromatographic and/or mass spectrometric analyses. This method details an alternate method for the detection and quantification of organic acids from plant material and food samples using free zonal capillary electrophoresis (CZE), sometimes simply referred to as capillary electrophoresis (CE). CZE provides a cost-effective method for measuring SCCAs with a low limit of detection (0.005 mg/ml). This article details the extraction and quantification of SCCAs from plant samples. While the method provided focuses on measurement of SCCAs from coffee beans, the method provided can be applied to multiple plant-based food materials.

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

This article presents a method for the detection and quantification of organic acids from plant material using free zonal capillary electrophoresis. An example of the potential application of this method, determining the effects of a secondary fermentation on organic acid levels in coffee seeds, is provided.

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic ...

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Here we present a protocol to measure the force of interactions between a well-defined inorganic surface and either peptides or amino acids by single-molecule force spectroscopy measurements using an atomic force microscope (AFM). The information obtained from the measurement is important to better understand the peptide-inorganic material interphase.

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals ...

Green and Low-cost Production of Thermally Stable and Carboxylated Cellulose Nanocrystals and Nanofibrils Using Highly Recyclable Dicarboxylic Acids

Here we demonstrate potentially low cost and green productions of high thermally stable and carboxylated cellulose nanocrystals (CNCs) and nanofibrils (CNF) from bleached eucalyptus pulp (BEP) and unbleached mixed hardwood kraft pulp (UMHP) fibers using highly recyclable dicarboxylic solid acids. Typical operating conditions were acid concentrations of 50 - 70 wt% at 100 &#176;C for 60 min and 120 &#176;C (no boiling at atmospheric pressure) for 120 min, for BEP and UMHP, respectively. The resultant CNCs have a higher thermal degradation temperature than their corresponding feed fibers and carboxylic acid group content from 0.2 - 0.4 mmol/g. The low strength (high pKa of 1.0 - 3.0) of organic acids also resulted in CNCs with both longer lengths of approximately 239 - 336 nm and higher crystallinity than CNCs produced using mineral acids. Cellulose loss to sugar was minimal. Fibrous cellulosic solid residue (FCSR) from the dicarboxylic acid hydrolysis was used to produce carboxylated CNFs through subsequent mechanical fibrillation with low energy input.

Here we demonstrate a novel method for green and sustainable productions of highly thermally stable and carboxylated cellulose nanocrystals (CNC) and nanofibrils (CNF) using highly recyclable solid dicarboxylic acids.

Here we demonstrate potentially low cost and green productions of high thermally stable and carboxylated cellulose nanocrystals (CNCs) and nanofibrils ...

Regioselective O-Glycosylation of Nucleosides via the Temporary 2',3'-Diol Protection by a Boronic Ester for the Synthesis of Disaccharide Nucleosides

Disaccharide nucleosides, which consist of disaccharide and nucleobase moieties, have been known as a valuable group of natural products having multifarious bioactivities. Although chemical O-glycosylation is a commonly beneficial strategy to synthesize disaccharide nucleosides, the preparation of substrates such as glycosyl donors and acceptors requires&#160;tedious protecting&#160;group manipulations and a purification at each synthetic step. Meanwhile, several research groups have reported that boronic and borinic esters serve as a protecting or activating group of carbohydrate derivatives to achieve the regio- and/or stereoselective acylation, alkylation, silylation, and glycosylation. In this article, we demonstrate the procedure for the regioselective O-glycosylation of unprotected ribonucleosides utilizing boronic acid. The esterification of 2&#39;,3&#39;-diol of ribonucleosides with boronic acid makes the temporary protection of diol, and, following O-glycosylation with a glycosyl donor in the presence of p-toluenesulfenyl chloride and silver triflate, permits the regioselective reaction of the 5&#39;-hydroxyl group to afford the disaccharide nucleosides. This method could be applied to various nucleosides, such as guanosine, adenosine, cytidine, uridine, 5-metyluridine, and 5-fluorouridine. This article and the accompanying video represent&#160;useful (visual) information for the O-glycosylation of unprotected nucleosides and their analogs for the synthesis of not only disaccharide nucleosides, but also a variety of biologically relevant derivatives.

Regioselective O-Glycosylation of Nucleosides via the Temporary 2&#039;,3&#039;-Diol Protection by a Boronic Ester for the Synthesis of Disaccharide Nucleosides

Here, we present protocols for the synthesis of disaccharide nucleosides by the regioselective O-glycosylation of ribonucleosides via a temporary protection of their 2&#39;,3&#39;-diol moieties utilizing a cyclic boronic ester. This method applies to several unprotected nucleosides such as adenosine, guanosine, cytidine, uridine, 5-methyluridine, and 5-fluorouridine to give corresponding disaccharide nucleosides.

Disaccharide nucleosides, which consist of disaccharide and nucleobase moieties, have been known as a valuable group of natural products having ...

Enzymatic Synthesis of Epoxidized Metabolites of Docosahexaenoic, Eicosapentaenoic, and Arachidonic Acids

The epoxidized metabolites of various polyunsaturated fatty acids (PUFAs), termed epoxy fatty acids, have a wide range of roles in human physiology. These metabolites are produced endogenously by the cytochrome P450 class of enzymes. Because of their diverse and potent biological effects, there is considerable interest in studying these metabolites. Determining the unique roles of these metabolites in the body is a difficult task, as the epoxy fatty acids must first be obtained in significant amounts and with high purity. Obtaining compounds from natural sources is often labor intensive, and soluble epoxide hydrolases (sEH) rapidly hydrolyze the metabolites. On the other hand, obtaining these metabolites via chemical reactions is very inefficient, due to the difficulty of obtaining pure regioisomers and enantiomers, low yields, and extensive (and expensive) purification. Here, we present an efficient enzymatic synthesis of 19(S),20(R)- and 16(S),17(R)-epoxydocosapentaenoic acids (EDPs) from DHA via epoxidation with BM3, a bacterial CYP450 enzyme isolated originally from Bacillus megaterium (that is readily expressed in Escherichia coli). Characterization and determination of purity is performed with nuclear magnetic resonance spectroscopy (NMR), high-performance liquid chromatography (HPLC), and mass spectrometry (MS). This procedure illustrates the benefits of enzymatic synthesis of PUFA epoxy metabolites, and is applicable to the epoxidation of other fatty acids, including arachidonic acid (AA) and eicosapentaenoic acid (EPA) to produce the analogous epoxyeicosatrienoic acids (EETs) and epoxyeicosatetraenoic acids (EEQs), respectively.

We present a method useful for large-scale enzymatic synthesis and purification of specific enantiomers and regioisomers of epoxides of arachidonic acid (AA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA) with the use of a bacterial cytochrome P450 enzyme (BM3).

The epoxidized metabolites of various polyunsaturated fatty acids (PUFAs), termed epoxy fatty acids, have a wide range of roles in human physiology. These ...

Microwave-Assisted Preparation of 1-Aryl-1H-pyrazole-5-amines

A synthetic process for the preparation of a variety of 1-aryl-1H-pyrazole-5-amines was developed. The microwave-mediated nature of this method makes it efficient in both time and resources and utilizes water as the solvent. 3-Aminocrotononitrile or an appropriate &#945;-cyanoketone is combined with an aryl hydrazine and dissolved in 1 M HCl. The mixture is then heated in a microwave reactor at 150 &#176;C, typically for 10-15 min. The product can be readily obtained by basifying the solution with 10% NaOH and isolating the desired compound with a simple vacuum filtration. The use of water as a solvent in this reaction lends to its ease and utility in production, and this method is easily reproducible with a variety of functional groups. Typical isolated yields range from 70-90%, and reactions can be performed on the milligram to gram scale with little to no change in observed yields. Some of the applications of these molecules and their derivatives include pesticides, anti-malarials, and chemotherapeutics, among many others.

Microwave-Assisted Preparation of 1-Aryl-1H-pyrazole-5-amines

1-Aryl-1H-pyrazole-5-amines are prepared from aryl hydrazines combined with either 3-aminocrotononitrile or an &#945;-cyanoketone in a 1 M HCl solution using a microwave reactor. Most reactions are done in 10-15 minutes and pure product can be obtained via vacuum filtration with typical isolated yields of 70-90%.

A synthetic process for the preparation of a variety of 1-aryl-1H-pyrazole-5-amines was developed. The microwave-mediated nature of this method makes it ...

Synthesis of pH Dependent Pyrazole, Imidazole, and Isoindolone Dipyrrinone Fluorophores using a Claisen-Schmidt Condensation Approach

Methine-bridged conjugated bicyclic aromatic compounds are common constituents of a range of biologically relevant molecules such as porphyrins, dipyrrinones, and pharmaceuticals. Additionally, restricted rotation of these systems often results in highly to moderately fluorescent systems as observed in 3H,5H-dipyrrolo[1,2-c:2',1'-f]pyrimidin-3-ones, xanthoglows, pyrroloindolizinedione analogs, BODIPY analogs, and the phenolic and imidazolinone ring systems of Green Fluorescent Protein (GFP). This manuscript describes an inexpensive and operationally simple method of performing a Claisen-Schmidt condensation to generate a series of fluorescent pH dependent pyrazole/imidazole/isoindolone dipyrrinone analogs. While the methodology illustrates the synthesis of dipyrrinone analogs, it can be translated to produce a wide range of conjugated bicyclic aromatic compounds. The Claisen-Schmidt condensation reaction utilized in this method is limited in scope to nucleophiles and electrophiles that are enolizable under basic conditions (nucleophile component) and non-enolizable aldehydes (electrophile component). Additionally, both the nucleophilic and electrophilic reactants must contain functional groups that will not inadvertently react with hydroxide. Despite these limitations, this methodology offers access to completely novel systems that can be employed as biological or molecular probes.

The Claisen-Schmidt condensation reaction is an important methodology for the generation of methine-bridged conjugated bicyclic aromatic compounds. Through utilizing a base-mediated variant of the aldol reaction, a range of fluorescent and/or biologically relevant molecules can be accessed through a generally inexpensive and operationally simple synthetic approach.