JoVE Chemistry surveys a broad scope of chemical disciplines. This collection includes fundamental and applied research that investigates molecular interactions, properties, and structure spanning in the following core divisions: analytical, organic, organometallic, inorganic, bioinorganic, and biochemistry. This section also includes the design and preparation of materials and small molecules for advanced or unique applications.
1Focal Area Infection Biology, Biozentrum of the University of Basel, 2Proteomics Core Facility, Biozentrum of the University of Basel
The ubiquitous second messenger c-di-GMP controls growth and behavior of many bacteria. We have developed a novel Capture Compound Mass Spectrometry based technology to biochemically identify and characterize c-di-GMP binding proteins in virtually any bacterial species.
Published March 29, 2015. Keywords: Chemistry, Capture compound, photoactivable crosslinker, mass spectrometry, c-di-GMP effector, EAL, GGDEF, PilZ, Pseudomonas aeruginosa
1Department of Chemistry, Texas Christian University
The synthesis of asymmetric species of ferrocene is challenging using solution techniques. This report focuses on the methods carried out to produce a ferrocene-biotin bioconjugate using facile and clean reactions accomplished via solid-phase synthesis. Incorporation of a thiolate moiety is shown to impart the ability for immobilization on gold surfaces.
Published March 12, 2015. Keywords: Chemistry, Ferrocene, biotin, bio-conjugate, solid phase peptide synthesis, resin, asymmetric, peptide, amino-acid, gold
1X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 2Department of Physics and Astronomy, Northwestern University
Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.
Published March 12, 2015. Keywords: Chemistry, X-ray, fluorescence, imaging, metals, chemical biology, microscopy, synchrotron
1Faculty of Science, University of Ontario Institute of Technology
The goal of this manuscript is to demonstrate a straightforward method for the preparation of ynones from acyl chloride and potassium alkynyltrifluoroborate salt starting materials. The one-pot reaction proceeds rapidly in the presence of boron trichloride without exclusion of air and moisture.
Published February 24, 2015. Keywords: Chemistry, Organic synthesis, trifluoroborates, ketones, ynones, Lewis acid, boron, acyl chlorides
1Department of Radiology, Memorial Sloan Kettering Cancer Center
Due to its multi-day radioactive half-life and favorable decay properties, the positron-emitting radiometal 89Zr is extremely well-suited for use in antibody-based radiopharmaceuticals for PET imaging. In this protocol, the bioconjugation, radiosynthesis, and preclinical application of 89Zr-labeled antibodies will be described.
Published February 12, 2015. Keywords: Chemistry, Positron Emission Tomography, Antibody, Bioconjugation, Immunoconjugates, Desferrioxamine, 89Zr
1Department of Chemistry, Virginia Military Institute
A procedure for performing reductive electropolymerization of vinyl-containing compounds onto glassy carbon and fluorine doped tin-oxide coated electrodes is presented. Recommendations on electrochemical cell configurations and troubleshooting procedures are included. Although not explicitly described here, oxidative electropolymerization of pyrrole-containing compounds follows similar procedures to vinyl-based reductive electropolymerization.
Published January 30, 2015. Keywords: Chemistry, electrochemistry, electropolymerization, electrodeposition, fluorine doped tin oxide, glassy carbon, cyclic voltammetry, potentiostat, vinyl, pyrrole, ruthenium, controlled potential electrolysis, 3-compartment cell
1Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, 2Department of Environmental Sciences, Rutgers University
We demonstrate the extraction of ammonium from an ammonium-rich stream using an electrochemical and a bioelectrochemical system. The reactor setup, operation and data analysis are discussed.
Published January 22, 2015. Keywords: Chemistry, Electrochemical extraction, bioelectrochemical system, bioanode, ammonium recovery, microbial electrocatalysis, nutrient recovery, electrolysis cell
1Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 2Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care, Boston Children's Hospital
The objective of this protocol is to incorporate SDF-1α, a stem cell homing factor, into dextran sulfate-chitosan nanoparticles. The resultant particles are measured for their size and zeta potential, as well as the content, activity, and in vitro release rate of SDF-1α from the nanoparticles.
Published January 22, 2015. Keywords: Chemistry, Dextran sulfate, chitosan, glycan, SDF-1α, nanoparticle, polyelectrolyte complex
1MESA+ Institute for Nanotechnology, University of Twente
Various procedures are outlined to prepare atomically defined templates for epitaxial growth of complex oxide thin films. Chemical treatments of single crystalline SrTiO3 (001) and DyScO3 (110) substrates were performed to obtain atomically smooth, single terminated surfaces. Ca2 Nb3 O10- nanosheets were used to create atomically defined templates on arbitrary substrates.
Published December 4, 2014. Keywords: Chemistry, Substrates, oxides, perovskites, epitaxy, thin films, single termination, surface treatment, nanosheets, Langmuir-Blodgett
1Cancer Immunology Program, Peter MacCallum Cancer Centre
We describe a simple, quantitative colorimetric assay that specifically measures the proteolytic activity of human, mouse or rat Granzyme B (GzmB). This protocol can be easily adapted for determining protease activity of other granule serine proteases by the hydrolysis of other synthetic peptide substrates with an appropriate recognition sequence.
Published November 28, 2014. Keywords: Chemistry, Granzyme B, serine protease, peptide thioesters, BOC-Ala-Ala-Asp-S-Bzl, colorimetric substrate, hydrolysis, asp-ase activity