Name: hyperspectral imaging as a tool to study optical anisotropy in lanthanide-based molecular single crystals
Uploaded: 2020-04-14T14:00:00
Description: Watch this Scientific Journal Video about Hyperspectral Imaging as a Tool to Study Optical Anisotropy in Lanthanide-Based Molecular Single Crystals at JoVE.com

The authors thank Mr. Dylan Errulat and Prof. Muralee Murugesu from the Department of Chemistry and Biomolecular Sciences of the University of Ottawa for the provision of [TbEu(bpm)(tfaa)6] single crystals. E.M.R, N.R., and E.H. gratefully acknowledge the financial support provided by the University of Ottawa, the Canadian Foundation for Innovation (CFI), and the Natural Sciences and Engineering Research Council Canada (NSERC).

CAUTION: It is recommended to use safety goggles specific for the excitation wavelength being used at all times when operating the imager.
1. Configuration of the hyperspectral microscope
NOTE: An overview of the hyperspectral imaging system is given in Figure 2a, with the main components of the imager being described. The imaging system can be used for the detection of the visible or the near-infrared (NIR) emission from a sample. Depend...

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F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tunable+Metal-Organic+Framework+Materials+Platform+for+Bioimaging+Applications.">Tunable Metal-Organic Framework Materials Platform for Bioimaging Applications.</a> ACS Applied Materials and Interfaces. 9 (27), 22268-22277 (2017).</li><li>Varghese, S., Das, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+molecular+packing+in+determining+solid-state+optical+properties+of+&#960;-conjugated+materials.">Role of molecular packing in determining solid-state optical properties of &#960;-conjugated materials.</a> Journal of Physical Chemistry Letters. 2 (8), 863-873 (2011).</li><li>Yan, D., Evans, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+crystalline+materials+with+tunable+luminescent+properties:+From+polymorphs+to+multi-component+solids.">Molecular crystalline materials with tunable luminescent properties: From polymorphs to multi-component solids.</a> Materials Horizons. 1 (1), 46-57 (2014).</li><li>Mu, S., Oniwa, K., Jin, T., Asao, N., Yamashita, M., Takaishi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+highly+emissive+distyrylthieno[3,2-b]thiophene+based+red+luminescent+organic+single+crystal:+Aggregation+induced+emission,+optical+waveguide+edge+emission,+and+balanced+ambipolar+carrier+transport.">A highly emissive distyrylthieno[3,2-b]thiophene based red luminescent organic single crystal: Aggregation induced emission, optical waveguide edge emission, and balanced ambipolar carrier transport.</a> Organic Electronics: Physics, Materials, Applications. 34, 23-27 (2016).</li><li>Binnemans, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interpretation+of+europium(III)+spectra.">Interpretation of europium(III) spectra.</a> Coordination Chemistry Reviews. 295, 1-45 (2015).</li><li>Koyama, H., Fauchet, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anisotropic+polarization+memory+in+thermally+oxidized+porous+silicon.">Anisotropic polarization memory in thermally oxidized porous silicon.</a> Applied Physics Letters. 77 (15), 2316-2318 (2000).</li><li>Kushida, T., Takushi, E., Oka, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Memories+of+photon+energy,+polarization+and+phase+in+luminescence+of+rare+earth+ions+under+resonant+light+excitation.">Memories of photon energy, polarization and phase in luminescence of rare earth ions under resonant light excitation.</a> Journal of Luminescence. 12-13, 723-727 (1976).</li><li>Onuma, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectroscopic+ellipsometry+studies+on+&#946;-Ga2O3+films+and+single+crystal.">Spectroscopic ellipsometry studies on &#946;-Ga2O3 films and single crystal.</a> Japanese Journal of Applied Physics. 55 (12), (2016).</li><li>Favreau, P. 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The hyperspectral imaging protocol here described provides a straightforward approach that allows to obtain spectroscopic information at precise locations of the sample. Using the described setup, the spatial resolution (x and y mapping) can reach down to 0.5 &#181;m while the spectral resolution can be of 0.2 nm for the mapping at the visible range and 0.6 nm for the NIR range.
In order to conduct hyperspectral mapping on a single crystal, sample preparation follows an easy ...

Hyperspectral Imaging (HSI) is a technique that generates a spatial map where each x-y coordinate contains a spectral information that could be based on any kind of spectroscopy, namely photoluminescence, absorption and scattering spectroscopies1,2,3. As a result, a 3-dimensional set of data (also called &#8220;hyperspectral cube&#8221;) is obtained, where the x-y coordinates are the spatial axes and the z coordinate is the spectral information from the analyzed sample. Therefore, the hyperspectral cube contains both spatial and spectral information, providing a more detailed spectroscopic investigation of the sample than traditional spectroscopy. While HSI has been known for years in the field of remote sensing (e.g., geology, food industries4), it recently emerged as an innovative technique for the characterization of nanomaterials2,5 or probes for biomedical applications3,6,7,8. Generally speaking, it is not limited to the UV/visible/near-infrared (NIR) domain, but can also be extended using other radiation sources, such as X-rays &#8211; for instance in order to characterize elemental distribution in different materials9 &#8211; or Terahertz radiation, where HSI was used to perform thermal sensing in biological tissues8. Further, photoluminescence mapping has been combined with Raman mapping to probe the optical properties of monolayer MoS210. Yet, amongst the reported applications of optical HSI, there are still only a few examples on HSI of lanthanide-based materials11,12,13,14,15,16,17. For instance, we can cite: detection of cancer in tissues6, analysis of the light penetration depth in biological tissues7, multiplexed biological imaging3, analysis of multicomponent energy transfer in hybrid systems11, and investigation of aggregation-induced changes in spectroscopic properties of upconverting nanoparticles12. Clearly, the attractiveness of HSI arises from its suitability for generating knowledge about environment-specific luminescence, providing simultaneous spatial and spectral information about the probe.
Taking advantage of this powerful technique we herein describe a protocol to investigate the optical anisotropy of the heterodinuclear Tb3+-Eu3+ single crystal [TbEu(bpm)(tfaa)6] (Figure 1a)13. The optical anisotropy observed resulted from the different molecular packing of the Ln3+ ions in the different crystallographic directions (Figure 1b), resulting in some crystal faces showing brighter, others showing dimmer photoluminescence. It was suggested that the increased luminescence intensity at specific faces of the crystal was correlated with more efficient energy transfer along those crystallographic directions where the Ln3+&#183;&#183;&#183;Ln3+ ion distances were the shortest13.
Motivated by these results, we propose the establishment of a detailed methodology to analyze optical anisotropy through HSI, opening the path for better understanding of ion-ion energy transfer processes and tunable luminescent properties stemming from specific molecular arrangement18,19. These structure-properties relationships have been recognized as important aspects for innovative optical materials design including, but not limited to waveguide systems and opto-magnetic storage devices at nano and microscale &#8211; addressing the demand for more efficient and miniaturized optic systems20.

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			<td height="21" style="height:21px;width:216px;">Microscope glass slides</td>
			<td style="width:123px;">FisherBrand</td>
			<td style="width:161px;">12-550-15</td>
			<td style="width:167px;">Glass slides used for sample preparation</td>
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			<td height="42" style="height:42px;width:216px;">Visible and Near Infrared Hyperspectral Confocal Imager</td>
			<td style="width:123px;">PhotonETC</td>
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			<td>Microscope used for the analysis, builted according to the user needs, therefore it is no catalog number</td>
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hyperspectral imaging as a tool to study optical anisotropy in lanthanide-based molecular single crystals

In this work, we describe a protocol for a novel application of hyperspectral imaging (HSI) in the analysis of luminescent lanthanide (Ln3+)-based molecular single crystals. As representative example, we chose a single crystal of the heterodinuclear Ln-based complex [TbEu(bpm)(tfaa)6] (bpm=2,2&#8217;-bipyrimidine, tfaa&#8211; =1,1,1-trifluoroacetylacetonate) exhibiting bright visible emission under UV excitation. HSI is an emerging technique that combines 2-dimensional spatial imaging of a luminescent structure with spectral information from each pixel of the obtained image. Specifically, HSI on single crystals of the [Tb-Eu] complex provided local spectral information unveiling variation of the luminescence intensity at different points along the studied crystals. These changes were attributed to the optical anisotropy present in the crystal, which results from the different molecular packing of Ln3+ ions in each one of the directions of the crystal structure. The HSI herein described is an example of the suitability of such technique for spectro-spatial investigations of molecular materials. Yet, importantly, this protocol can be easily extended for other types of luminescent materials (such as micron-sized molecular crystals, inorganic microparticles, nanoparticles in biological tissues, or labelled cells, among others), opening many possibilities for deeper investigation of structure-property relationships. Ultimately, such investigations will provide knowledge to be leveraged into the engineering of advanced materials for a wide range of applications from bioimaging to technological applications, such as waveguides or optoelectronic devices.

To illustrate the configuration of the hyperspectral microscope for the data acquisition on a Ln-based, molecular single crystal (i.e., [TbEu(bpm)(tfaa)6], Figure 1a), Figure 2 shows an overview of the system as well as the right placement of the optical cubes in the setup. Figure 3 shows a screen shot of the PHySpec software containing the menus used during the HSI acquisition. Figure 4 and ...

Watch this Scientific Journal Video about Hyperspectral Imaging as a Tool to Study Optical Anisotropy in Lanthanide-Based Molecular Single Crystals at JoVE.com

Hyperspectral Imaging as a Tool to Study Optical Anisotropy in Lanthanide-Based Molecular Single Crystals

Here, we present a protocol to obtain luminescent hyperspectral imaging data and to analyze optical anisotropy features of lanthanide-based single crystals using a Hyperspectral Imaging System.

In this work, we describe a protocol for a novel application of hyperspectral imaging (HSI) in the analysis of luminescent lanthanide (Ln3+)-based ...

Hyperspectral imaging allows for the acquisition of spectroscopic information at precise locations within a sample. For example, for the unveiling of optical anisotropy at a single crystal level. The generation of both spectral and spatial data of a sample allows for a more detailed investigation of the sample than is possible by either spectroscopy or fluorescence microscopy alone.A large number of adjustable parameters which affect the resolution can seem overwhelming at first. However, making a checklist may help with familiarizing yourself with the system. This technique requires manual tuning of the imaging hardware as well as software manipulation.It is essential to illustrate both aspects visually to showcase how both methods complement each other. Demonstrating the procedure with Nelson Rutajoga will be Emily Rodrigues, post-doctorate fellow at my laboratory. To set up the imager configuration for hyperspectral imaging mapping, starting from the microscope stage and following the emission beam pathway toward the detectors, leave the position for an optical cube right next to the optical microscope vacant and place the confocal microscope optical cube in that position that directs the emission from the sample through the visible light path.Looking along the optical path toward the detector, place the visible optical cube containing the dichroic mirror and filters for directing the visible emission to the detection path in its position. Continuing the path toward the detector, place the confocal pinhole optical cube in the right position to direct the light through the visible light detection path and following this path, place the confocal spectrometer optical cube in the appropriate position so that the emitted light reaches the detector. When all of the cubes are in place, manually adjust the detector's slit opening to match the size of the pinhole selected.Then, in the PHySpec software, select the aperture of the pinhole. For hyperspectral imaging mapping of terbium europium bi-pyrimidine trifluoroacetylacetonate single crystal, manually position the 20 times objective of the optical microscope under the sample and press the white button on the left side of the microscope to turn on the white light. Turn the knob under the button to adjust the brightness.Set the forward knob on the right side of the microscope to R to send 20%of the signal to the camera and 80%of the signal to the detector. Press play in the color camera window at the PHySpec software to initiate a live scan. If the color camera window shows a too dark or black image, increase the exposure time and/or the gain value under the color camera tab.If the image is too bright, decrease the exposure time and/or gain value. To focus on the sample, turn the knobs of the microscope to adjust the distance between the objective in the stage and open the broadband lamp shutter to allow UV excitation of the sample. Then turn the intensity knob to the desired position to control the intensity of the broadband lamp excitation.Click Show/Hide scale bar to add a scale bar to the bright-field optical microscopy image of the crystal and observe an image of the crystal under UV full or confined illumination. To select between the confined illumination or a wide field illumination, use the stick and knobs to adjust the size of the UV lamp field aperture. Under the SpectraPro SP 2300 tab, select a wavelength to observe the sample emission and adjust the exposure time of the detector.To obtain the hyperspectral cube in the sequencer, click plus to add a new node and click Confocal Imager. Click Multi-Spectrum Acquisition and input the desired X and Y position counts, as well as the desired step size. Select the hardware option for the camera sync and for visible emission mapping, and click okay.In the sequencer, click the newly added multi-spectrum acquisition line to highlight the node and click Play to run the selected node. For analysis of the captured hyperspectral imaging data, for example, for a spectral distribution of an image, in the Processing menu, select Data and Crop and Bend to increase the signal to noise ratio of the image. For an emission intensity profile, right-click on the cube image and select Create X-Profile for the analysis of one line.Drag to select the area and right-click on the region of interest. To select Add to Graph. To display the emission intensity as a function of the physical position of the target.The intensity profile will appear in the new graph. To obtain an emission spectrum of a specific area of the sample, hover the cursor over the cube image, right click, and click Rectangle Selection. Drag and click to draw the selection shape over the desired region.Then right click on the region of interest and select Add Selection to Graph. In the Add to Graph window, select Create a New Graph to display the emission spectra of the target, and click okay. Then save the acquired spectrum before selecting a new region.Here, a bright-field image of a crystal recorded after adjusting the sample in the proper focus is shown. The needle-like morphology of the crystal can be clearly observed. Here, images of the same crystal under UV excitation with either full illumination or locally confined illumination can be observed.The confined illumination can be used to investigate the effects of energy or light transfer within the crystal that may trigger wave guide-like behavior. For example, in this image, a strong emission is detected in a point not directly under excitation, suggesting that efficient energy migration takes place through the crystal. From the acquired hyperspectral cube, it is also possible to obtain the spectral distribution in the form of an image, representing a specific wavelength.The intensity profile of a specific emission wavelength and the emission spectra at any pixel or area of the acquired hyperspectral cube. For example, the emission spectra for this analysis shows the most characteristic emission bands of the europium ion. Moreover, the spatial profile along the different crystal faces indicates a brighter emission at the tip and side faces and can be correlated with the lanthanide/lanthanide ion distances in the three spatial directions.To obtain a good signal in a reasonable recording time of the hyperspectral cube, it is important to adjust the microscope configurations, focus, and detector exposure time. Emissions UV excitation and visible emission, this technique can be performed using near infrared excitation and near infrared emission detection. This allows it to be applicable for a large array of luminescent materials.Correlation of optical signals with an array of dependent features makes this technique very interesting for the investigation of structure/property relationships, including in-vitro assessment of nano-bio interactions.

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Chemistry

Synthesis and Exfoliation of Discotic Zirconium Phosphates to Obtain Colloidal Liquid Crystals

Due to their abundance in natural clay and potential applications in advanced materials, discotic nanoparticles are of interest to scientists and engineers. Growth of such anisotropic nanocrystals through a simple chemical method is a challenging task. In this study, we fabricate discotic nanodisks of zirconium phosphate [Zr(HPO4)2&#183;H2O] as a model material using hydrothermal, reflux and microwave-assisted methods. Growth of crystals is controlled by duration time, temperature, and concentration of reacting species. The novelty of the adopted methods is that discotic crystals of size ranging from hundred nanometers to few micrometers can be obtained while keeping the polydispersity well within control. The layered discotic crystals are converted to monolayers by exfoliation with tetra-(n)-butyl ammonium hydroxide [(C4H9)4NOH, TBAOH]. Exfoliated disks show isotropic and nematic liquid crystal phases. Size and polydispersity of disk suspensions is highly important in deciding their phase behavior.

A two dimensional model material of discotic zirconium phosphate was developed. The inorganic crystal with lamellar structure was synthesized by hydrothermal, reflux, and microwave-assisted methods. On exfoliation with organic molecules, layered crystals can be converted to monolayers, and nematic liquid crystal phase was formed at sufficient concentration of monolayers.

Due to their abundance in natural clay and potential applications in advanced materials, discotic nanoparticles are of interest to scientists and ...

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

This article shows how the COLTRIMS (Cold Target Recoil Ion Momentum Spectroscopy) or the "reaction microscope" technique can be used to distinguish between enantiomers (stereoisomers) of simple chiral species on the level of individual molecules. In this approach, a gaseous molecular jet of the sample expands into a vacuum chamber and intersects with femtosecond (fs) laser pulses. The high intensity of the pulses leads to fast multiple ionization, igniting a so-called Coulomb Explosion that produces several cationic (positively charged) fragments. An electrostatic field guides these cations onto time- and position-sensitive detectors. Similar to a time-of-flight mass spectrometer, the arrival time of each ion yields information on its mass. As a surplus, the electrostatic field is adjusted in a way that the emission direction and the kinetic energy after fragmentation lead to variations in the time-of-flight and in the impact position on the detector.
Each ion impact creates an electronic signal in the detector; this signal is treated by high-frequency electronics and recorded event by event by a computer. The registered data correspond to the impact times and positions. With these data, the energy and the emission direction of each fragment can be calculated. These values are related to structural properties of the molecule under investigation, i.e. to the bond lengths and relative positions of the atoms, allowing to determine molecule by molecule the handedness of simple chiral species and other isomeric features.

For small chiral species, Coulomb Explosion Imaging provides a new approach to determine the handedness of individual molecules.

This article shows how the COLTRIMS (Cold Target Recoil Ion Momentum Spectroscopy) or the "reaction microscope" technique can be used to distinguish ...

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation

Electrochemical impedance spectroscopy (EIS) was used for advanced characterization of organic electroactive compounds along with cyclic voltammetry (CV). In the case of fast reversible electrochemical processes, current is predominantly affected by the rate of diffusion, which is the slowest and limiting stage. EIS is a powerful technique that allows separate analysis of stages of charge transfer that have different AC frequency response. The capability of the method was used to extract the value of charge transfer resistance, which characterizes the rate of charge exchange on the electrode-solution interface. The application of this technique is broad, from biochemistry up to organic electronics. In this work, we are presenting the method of analysis of organic compounds for optoelectronic applications.

Electrochemical impedance spectroscopy (EIS) of species that undergo reversible oxidation or reduction in solution was used for determination of rate constants of oxidation or reduction.

Electrochemical impedance spectroscopy (EIS) was used for advanced characterization of organic electroactive compounds along with cyclic voltammetry (CV). ...

Color Spot Test As a Presumptive Tool for the Rapid Detection of Synthetic Cathinones

Synthetic cathinones are a large class of new psychoactive substances (NPS) that are increasingly prevalent in drug seizures made by law enforcement and other border protection agencies globally. Color testing is a presumptive identification technique indicating the presence or absence of a particular drug class using rapid and uncomplicated chemical methods. Owing to their relatively recent emergence, a color test for the specific identification of synthetic cathinones is not currently available. In this study, we introduce a protocol for the presumptive identification of synthetic cathinones, employing three aqueous reagent solutions: copper(II) nitrate, 2,9-dimethyl-1,10-phenanthroline (neocuproine) and sodium acetate. Small pin-head sized amounts (approximately 0.1-0.2 mg) of the suspected drugs are added to the wells of a porcelain spot plate, and each reagent is then added dropwise sequentially before heating on a hotplate. A color change from very light blue to yellow-orange after 10 min indicates the likely presence of synthetic cathinones. The highly stable and specific test reagent has the potential for use in the presumptive screening of unknown samples for synthetic cathinones in a forensic laboratory. However, the nuisance of an added heating step for the color change result limits the test to laboratory application and decreases the likelihood of an easy translation to field testing.

Here we present a simple, inexpensive, and selective chemical spot test protocol for the detection of synthetic cathinones, a class of new psychoactive substances. The protocol is suitable for use in various areas of law enforcement that encounter illicit material.

Synthetic cathinones are a large class of new psychoactive substances (NPS) that are increasingly prevalent in drug seizures made by law enforcement and ...

Light-driven Molecular Motors on Surfaces for Single Molecular Imaging

The design and synthesis of a synthetic system that aims for the direct visualization of a synthetic rotary motor at the single molecule level on surfaces are demonstrated. This work requires careful design, considerable synthetic effort, and proper analysis. The rotary motion of the molecular motor in solution is shown by 1H NMR and UV-vis absorption spectroscopy techniques. In addition, the method to graft the motor onto an amine-coated quartz is described. This method helps to gain more insight into molecular machines.

The manuscript describes how to synthesize and graft a molecular motor on surfaces for single molecular imaging.

The design and synthesis of a synthetic system that aims for the direct visualization of a synthetic rotary motor at the single molecule level on surfaces ...

In situ FTIR Spectroscopy as a Tool for Investigation of Gas/Solid Interaction: Water-Enhanced CO2 Adsorption in UiO-66 Metal-Organic Framework

In situ infrared spectroscopy is an inexpensive, highly sensitive, and selective valuable tool to investigate the interaction of polycrystalline solids with adsorbates. Vibrational spectra provide information on the chemical nature of adsorbed species and their structure. Thus, they are very useful for obtaining molecular level understanding of surface species. The IR spectrum of the sample itself gives some direct information about the material. General conclusions can be drawn concerning hydroxyl groups, some stable surface species and impurities. However, the spectrum of the sample is &#34;blind&#34; with respect to the presence of coordinatively unsaturated ions and gives rather poor information about the acidity of surface hydroxyls, species decisive for the adsorption and catalytic properties of the materials. Furthermore, no discrimination between bulk and surface species can be made. These problems are solved by the use of probe molecules, substances that interact specifically with the surface; the alteration of some spectral features of these molecules as a result of adsorption provides valuable information about the nature, properties, location, concentration, etc., of the surface sites.
The experimental protocol for in-situ IR studies of gas/sample interaction includes preparation of a sample pellet, activation of the material, initial spectral characterization through the analysis of the background spectra, characterization by probe molecules, and study of the interaction with a particular set of gas mixtures. In this paper we investigate a zirconium terephthalate metal organic framework, Zr6O4(OH)4(BDC)6 (BDC = benzene-1,4-dicarboxylate), namely UiO-66 (UiO refers to University of Oslo). The acid sites of the UiO-66 sample are determined by using CO and CD3CN as molecular probes. Furthermore, we have demonstrated that CO2 is adsorbed on basic sites exposed on dehydroxylated UiO-66. Introduction of water to the system produces hydroxyl groups acting as additional CO2 adsorption sites. As a result, CO2 adsorption capacity of the sample is strongly enhanced.

In situ FTIR Spectroscopy as a Tool for Investigation of Gas/Solid Interaction: Water-Enhanced CO2 Adsorption in UiO-66 Metal-Organic Framework

The use of FTIR spectroscopy for investigation of the surface properties of polycrystalline solids is described. Preparation of sample pellets, activation procedures, characterization with probe molecules and model studies of CO2 adsorption are discussed.

In situ infrared spectroscopy is an inexpensive, highly sensitive, and selective valuable tool to investigate the interaction of polycrystalline solids ...

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Rational design of disordered molecular aggregates and solids for optoelectronic applications relies on our ability to predict the properties of such materials using theoretical and computational methods. However, large molecular systems where disorder is too significant to be considered in the perturbative limit cannot be described using either first principles quantum chemistry or band theory. Multiscale modeling is a promising approach to understanding and optimizing the optoelectronic properties of such systems. It uses first-principles quantum chemical methods to calculate the properties of individual molecules, then constructs model Hamiltonians of molecular aggregates or bulk materials based on these calculations. In this paper, we present a protocol for constructing a tight-binding Hamiltonian that represents the excited states of a molecular material in the basis of Frenckel excitons: electron-hole pairs that are localized on individual molecules that make up the material. The Hamiltonian parametrization proposed here accounts for excitonic couplings between molecules, as well as for electrostatic polarization of the electron density on a molecule by the charge distribution on surrounding molecules. Such model Hamiltonians can be used to calculate optical absorption spectra and other optoelectronic properties of molecular aggregates and solids.

Here, we present a protocol for parametrizing a tight-binding excitonic Hamiltonian for calculating optical absorption spectra and optoelectronic properties of molecular materials from first-principles quantum chemical calculations.

Rational design of disordered molecular aggregates and solids for optoelectronic applications relies on our ability to predict the properties of such ...

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

The chemical space covered by natural products is immense and widely unrecognized. Therefore, convenient methodologies to perform wide-ranging evaluation of their functions in nature and potential human benefits (e.g., for drug discovery applications) are desired. This protocol describes the combination of genome mining (GM) and molecular networking (MN), two contemporary approaches that match gene cluster-encoded annotations in whole genome sequencing with chemical structure signatures from crude metabolic extracts. This is the first step towards the discovery of new natural entities. These concepts, when applied together, are defined here as MS-guided genome mining. In this method, the main components are previously designated (using MN), and structurally related new candidates are associated with genome sequence annotations (using GM). Combining GM and MN is a profitable strategy to target new molecule backbones or harvest metabolic profiles in order to identify analogues from already known compounds.

A mass spectrometry-guided genome mining protocol is established and described here. It is based on genome sequence information and LC-MS/MS analysis and aims to facilitate identification of molecules from complex microbial and plant extracts.

The chemical space covered by natural products is immense and widely unrecognized. Therefore, convenient methodologies to perform wide-ranging evaluation ...

Atomic Force Microscopy Combined with Infrared Spectroscopy as a Tool to Probe Single Bacterium Chemistry

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) is a novel combinatory technique, enabling simultaneous characterization of physical properties and chemical composition of sample with nanoscale resolution. By combining AFM with IR, the spatial resolution limitation of conventional IR is overcome, enabling a resolution of 20&#8211;100 nm to be achieved. This opens the door for a broad array of new applications of IR toward probing samples smaller than several micrometers, previously unachievable by means of conventional IR microscopy. AFM-IR is eminently suited for bacterial research, providing both spectral and spatial information at the single cell and intracellular level. The increasing global health concerns and unfavorable future prediction regarding bacterial infections, and especially, rapid development of antimicrobial resistance, has created an urgent need for a research tool capable of phenotypic probing at the single cell and subcellular level. AFM-IR offers the potential to address this need, by enabling detail characterization of chemical composition of a single bacterium. Here, we provide a complete protocol for sample preparation and data acquisition of single spectra and mapping modality, for the application of AFM-IR toward bacterial studies.

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) provides a powerful platform for bacterial studies, enabling to achieve nanoscale resolution. Both, mapping of subcellular changes (e.g., upon cell division) as well as comparative studies of chemical composition (e.g., arising from drug resistance) can be conducted at a single cell level in bacteria.

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) is a novel combinatory technique, enabling simultaneous characterization of physical properties and ...

Gas Chromatography-Mass Spectrometry Paired with Total Vaporization Solid-Phase Microextraction as a Forensic Tool

Gas Chromatography &#8211; Mass Spectrometry (GC-MS) is a frequently used technique for the analysis of numerous analytes of forensic interest, including controlled substances, ignitable liquids, and explosives. GC-MS can be coupled with Solid-Phase Microextraction (SPME), in which a fiber with a sorptive coating is placed into the headspace above a sample or immersed in a liquid sample. Analytes are sorbed onto the fiber which is then placed inside the heated GC inlet for desorption. Total Vaporization Solid-Phase Microextraction (TV-SPME) utilizes the same technique as immersion SPME but immerses the fiber into a completely vaporized sample extract. This complete vaporization results in a partition between only the vapor phase and the SPME fiber without interference from a liquid phase or any insoluble materials. Depending upon the boiling point of the solvent used, TV-SPME allows for large sample volumes (e.g., up to hundreds of microliters). On-fiber derivatization may also be performed using TV-SPME. TV-SPME has been used to analyze drugs and their metabolites in hair, urine, and saliva. This simple technique has also been applied to street drugs, lipids, fuel samples, post-blast explosive residues, and pollutants in water. This paper highlights the use of TV-SPME to identify illegal adulterants in very small samples (microliter quantities) of alcoholic beverages. Both gamma-hydroxybutyrate (GHB) and gamma-butyrolactone (GBL) were identified at levels that would be found in spiked drinks. Derivatization by a trimethylsilyl agent allowed for conversion of the aqueous matrix and GHB into their TMS derivatives. Overall, TV-SPME is quick, easy, and requires no sample preparation aside from placing the sample into a headspace vial.

Total Vaporization Solid Phase Microextraction (TV-SPME) completely vaporizes a liquid sample whilst analytes are sorbed onto a SPME fiber. This allows for partitioning of the analyte between only the solvent vapor and the SPME fiber coating.

Gas Chromatography &#8211; Mass Spectrometry (GC-MS) is a frequently used technique for the analysis of numerous analytes of forensic interest, including ...