We thank Robert Berger (Philipps-Universit&#228;t Marburg, Germany) for inspiring discussions about the interpretation of our data and molecular chirality in general. We are grateful to Julia Kiedrowski, Alexander Schie&#223;er and Michael Reggelin from TU Darmstadt (Germany), as well as Benjamin Spenger, Manuel Mazenauer and J&#252;rgen Stohner from ZHAW W&#228;denswil (Switzerland) for providing the sample.
The project was supported by the Hessen State Initiative for Scientific and Economic Excellence under the focus ELCH (Electron dynamics of chiral systems) and the Federal Ministry of Education and Research (BMBF). MS acknowledges financial support by the Adolf Messer foundation.

<ol>
	<li>G&#252;bitz, G., Schmid, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chiral+Separation+by+Chromatographic+and+Electromigration+Techniques.+A+Review.">Chiral Separation by Chromatographic and Electromigration Techniques. A Review.</a> Biopharm. Drug Disposition. 22, 291-336 (2001).</li><li>Berova, N., Polaravapu, P. L., Nakanishi, K., Woody, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Comprehensive Chiroptical Spectroscopy. , (2012).</li><li>Bijvoet, J. M., Peerdeman, A. F., van Bommel, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+the+Absolute+Configuration+of+Optically+Active+Compounds+by+means+of+X-rays.">Determination of the Absolute Configuration of Optically Active Compounds by means of X-rays.</a> Nature. 168 (4268), 271-272 (1951).</li><li>Pitzer, M., 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=Direct+Determination+of+Absolute+Molecular+Stereochemistry+in+Gas+Phase+by+Coulomb+Explosion+Imaging.">Direct Determination of Absolute Molecular Stereochemistry in Gas Phase by Coulomb Explosion Imaging.</a> Science. 341 (6150), 1096-1100 (2013).</li><li>Pitzer, M., 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=Absolute+Configuration+from+Different+Multifragmentation+Pathways+in+Light-Induced+Coulomb+Explosion+Imaging.">Absolute Configuration from Different Multifragmentation Pathways in Light-Induced Coulomb Explosion Imaging.</a> Chem Phys Chem. 17 (16), 2465-2472 (2016).</li><li>Vager, Z., Naaman, R., Kanter, E. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coulomb+Explosion+Imaging+of+small+molecules.">Coulomb Explosion Imaging of small molecules.</a> Science. 244 (4903), 426-431 (1989).</li><li>Herwig, P. H., 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=Imaging+the+Absolute+Configuration+of+a+Chiral+Epoxide+in+the+Gas+Phase.">Imaging the Absolute Configuration of a Chiral Epoxide in the Gas Phase.</a> Science. 342 (6162), 1084-1186 (2013).</li><li>D&#246;rner, R., 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=Cold+Target+Recoil+Ion+Momentum+Spectroscopy:+a+'momentum+microscope'+to+view+atomic+collision+dynamics.">Cold Target Recoil Ion Momentum Spectroscopy: a 'momentum microscope' to view atomic collision dynamics.</a> Physics Reports. 330, 95-192 (2000).</li><li>Ullrich, J., 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=Recoil-ion+and+electron+momentum+spectroscopy:+reaction-microscopes.">Recoil-ion and electron momentum spectroscopy: reaction-microscopes.</a> Rep. Prog. Phys. 66 (9), 1463-1545 (2003).</li><li>Jagutzki, O., 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=Multiple+Hit+Readout+of+a+Microchannel+Plate+Detector+With+a+Three-Layer+Delay-Line+Anode.">Multiple Hit Readout of a Microchannel Plate Detector With a Three-Layer Delay-Line Anode.</a> IEEE Trans Nucl Sci. 49 (5), 2477-2483 (2002).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> RoentDek GmbH MCP Delay Line Detector Manual. , (2017).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> RoentDek GmbH The RoentDek Constant Fraction Discriminators CFD8c, CFD7x, CFD4c, CFD1c and CFD1x. , (2017).</li><li>Zeller, S., 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=Imaging+the+He2+quantum+halo+state+using+a+free+electron+laser.">Imaging the He2 quantum halo state using a free electron laser.</a> PNAS. 113 (51), 14651-14655 (2016).</li><li>Pitzer, M., 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=Stereochemical+configuration+and+selective+excitation+of+the+chiral+molecule+halothane.">Stereochemical configuration and selective excitation of the chiral molecule halothane.</a> J. Phys. B.: At. Mol. Opt. Phys. 49 (23), 234001 (2016).</li><li>Hine, J., Dowell, A. M., Singley, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Carbon+Dihalides+as+Intermediates+in+the+Basic+Hydrolysis+of+Haloforms:+IV+Relative+Reactivities+of+Haloforms.">Carbon Dihalides as Intermediates in the Basic Hydrolysis of Haloforms: IV Relative Reactivities of Haloforms.</a> J. Am. Soc. Chem. 78, 479-482 (1956).</li><li>Wales, B., 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=A+coincidence+detection+algorithm+for+improving+detection+rates+in+coulomb+explosion+imaging.">A coincidence detection algorithm for improving detection rates in coulomb explosion imaging.</a> Nucl. Instr. Meth. in Phys. Res. A. 667, 11-15 (2012).</li><li>Kastirke, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Konstruktion und Aufbau einer UHV-tauglichen COLTRIMS-Kammer. , (2014).</li><li>Calegari, 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=Charge+migration+induced+by+attosecond+pulses+in+bio-relevant+molecules.">Charge migration induced by attosecond pulses in bio-relevant molecules.</a> J. Phys. B.: At. Mol. Opt. Phys. 49 (14), 142001 (2016).</li><li>Gaie-Levrel, F., Garcia, G. A., Schwell, M., Nahon, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=VUV+state-selected+photoionization+of+thermally-desorbed+biomolecules+by+coupling+an+aerosol+source+to+an+imaging+photoelectron/photoion+coincidence+spectrometer:+case+of+the+amino+acids+tryptophan+and+phenylalanine.">VUV state-selected photoionization of thermally-desorbed biomolecules by coupling an aerosol source to an imaging photoelectron/photoion coincidence spectrometer: case of the amino acids tryptophan and phenylalanine.</a> Phys. Chem. Chem. Phys. 13, 7024-7036 (2010).</li><li>Ablikim, U., 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=Identification+of+absolute+geometries+of+cis+and+trans+molecular+isomers+by+Coulomb+Explosion+Imaging.">Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging.</a> Sci. Rep. 6, 38202 (2016).</li></ol>

The authors declare no competing interests.

Due to the variety of components, a COLTRIMS setup requires a rather high level of technical expertise, especially in the areas of vacuum technique, particle detection, fast electronics and data analysis. Before turning to the investigation of complex species, it should thus be thoroughly checked if the setup is running properly, e.g. by performing and analyzing a measurement on a diatomic or triatomic species.
Optimizing the intensity and duration of the laser pulses and the overlap ...

Chirality is a feature of our nature that has been fascinating researchers for more than 150 years. In the 19th century, Pasteur, van&#39;t Hoff and others discovered that molecules can occur in two mirror image structures that are not super-imposable - like our left and right hands. This property was termed &#39;chiral&#39;, from the Greek word for &#39;hand&#39;.
So far, no difference in thermodynamic properties or in energy levels of left- and right-handed forms (the two &#39;enantiomers&#39;) has been found. In order to analyze the handedness of a given sample and to separate the enantiomers, interaction with other chiral molecules can be used, as is for example done in various chromatographical approaches.1 Chiroptical methods such as (vibrational) circular dichroism, (V)CD, and optical rotatory dispersion, ORD, are routinely employed to distinguish between enantiomers.2
When it comes to the determination of the microscopic structure, these techniques require additional information, e.g. from quantum-chemical calculations. The only technique that is widely accepted to directly determine the absolute configuration is anomalous X-ray diffraction.3
It has recently been shown that the absolute configuration of simple chiral species can be determined by Coulomb Explosion Imaging.4,5 In this approach, molecules in the gas phase are multiply ionized so that the remaining cores strongly repel each other. This repulsion leads to fast fragmentation (&#39;explosion&#39;) of the molecules. The direction and the magnitude of the fragment momenta correlate to the structure of the molecule &#8211; for small molecules, the momentum directions correspond surprisingly well to the bond axes. Coulomb Explosion for molecular structure determination has been pioneered using molecular ion beams from an accelerator.6 This beam foil technique has recently also been applied for chiral recognition.7
Contrary to anomalous X-ray diffraction, the sample must not be crystalline but provided in the gas phase. This makes the Coulomb Explosion approach ideal for volatile species and thus complementary to X-ray diffraction. In certain cases, the handedness can even be determined for individual molecules.
In practice, the exact reconstruction of the molecular structure has proven difficult even for methane derivatives, e.g. molecules with a central carbon and different substituents. This is attributed to the fact that the interaction between the fragments is not exactly Coulombic and that not all bonds break simultaneously. In order to obtain stereochemical information, especially to distinguish between enantiomers, this reconstruction is fortunately not necessary. Instead, the momentum vectors of different fragments can be correlated to yield a quantity that is distinct for the left- and right-handed molecules. To get reliable results, at least four fragment momenta have to be recorded.
In order to measure this momentum information, the fragments from one &#8211; and only one &#8211; molecular break-up have to be detected in a single measurement step. This condition is usually referred to as &#39;coincident detection&#39;. In addition, the emission directions have to be analyzed, which amounts in practice to record the time and the position of the fragment impact in a list-mode data format.
In atomic and molecular physics, techniques have been developed that implement this approach of measurement by employing electrostatic spectrometers for mass separation and time- and position-sensitive multi-hit detectors. The most prominent example is the COLTRIMS (Cold Target Recoil Ion Momentum Spectroscopy) setup &#8211; also known as Reaction Microscope.8,9 A sketch for this kind of experiment is given in Figure 1. Contrary to a standard COLTRIMS that can record electrons as well, Coulomb Explosion Imaging requires only the ion detector.
Spectrometer and detector are mounted under ultra-high vacuum (&#60;1 x 10-9 hPa) to avoid creation of ions from residual gas. Single molecules of the sample are provided via a gaseous free molecular jet created by supersonic expansion: By virtue of the vapor pressure, the molecules expand through a small nozzle (around 50 &#181;m diameter) into the vacuum. This part of the experiment, the source chamber, is separated from the interaction region by usually two skimmers and differentially pumped stages. An additional differentially pumped section is located behind the interaction region to dump the gas jet and thus avoid background gas in the interaction region.
The ionizing radiation intersects with the molecular jet under 90&#176;. Most laboratories nowadays use femtosecond laser pulses, although synchrotron radiation, fast ions or electron impact are possible &#39;projectiles&#39; to induce Coulomb Explosion.
The following protocol makes the assumption that a running setup for coincident imaging of ions and a femtosecond laser are available in the lab. The peak intensity needed to induce Coulomb Explosion into four or even five fragments must be on the order of 6 x 1014 W/cm2. To avoid exceedingly long measurements, the repetition rate of the laser should be 10 kHz or more. This is crucial because, on the one hand, coincident detection can only be ascertained if the probability for fragmentation in the laser focus is significantly below 1 per laser pulse (ideally not more than 10%). The total fragmentation rate, on the other hand, should not be lower than a few kHz because the share of relevant multifragmentation pathways is usually less than 10-4. As encouraging fact, it should be mentioned that in principle already a single fragmentation event is sufficient to identify the configuration of an enantiopure sample, and that detection of a few hundred allows to determine the abundance of the enantiomers in a sample of unknown enantiomeric composition.

<table><tbody><tr><td>CHBrCl2</td><td>SigmaAldrich</td><td>139181-10G</td><td>or other suitable sample</td></tr><tr><td>femtosecond laser system</td><td>KMLabs</td><td>Wyvern500</td><td></td></tr><tr><td>High-reflective mirrors</td><td>EKSMA</td><td>042-0800</td><td></td></tr><tr><td>mirror mounts</td><td>Newport</td><td>U100-A-LH-2K&amp;nbsp;&amp;nbsp;</td><td></td></tr><tr><td>focusing mirror (protected silver, f = 75 mm)</td><td>Thorlabs&amp;nbsp;</td><td>CM254-075-P01</td><td>(if available: f = 60 mm)</td></tr><tr><td>COLTRIMS spectrometer, including electronics and data acquisition system</td><td>RoentDek</td><td>custom</td><td>contrary to the standard COLTRIMS, only one detector is needed</td></tr></tbody></table>

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.

In this part, we show results obtained for halomethanes. These species are ideal for proof-of-principle experiments due to their simplicity and high vapor pressure. In the meantime, the more complex species halothane has been investigated using single soft-x-ray photons from a synchrotron source to induce multiple ionization.14
CHBrClF
Bromochlo...

Watch this Scientific Journal Video about Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers at JoVE.com

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

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 ...

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Stereoisomerism

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9.0K Views.  Goethe-Universität Frankfurt am Main. For small chiral species, Coulomb Explosion Imaging provides a new approach to determine the handedness of individual molecules.

Video: Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

Spatial Separation of Molecular Conformers and Clusters

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.

We present a technique that allows the spatial separation of different conformers or clusters present in a molecular beam. An electrostatic deflector is used to separate species by their mass-to-dipole moment ratio, leading to the production of gas-phase ensembles of a single conformer or cluster stoichiometry.

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold ...

Engineering

Direct Imaging of Laser-driven Ultrafast Molecular Rotation

We present a method for visualizing laser-induced, ultrafast molecular rotational wave packet dynamics. We have developed a new 2-dimensional Coulomb explosion imaging setup in which a hitherto-impractical camera angle is realized. In our imaging technique, diatomic molecules are irradiated with a circularly polarized strong laser pulse. The ejected atomic ions are accelerated perpendicularly to the laser propagation. The ions lying in the laser polarization plane are selected through the use of a mechanical slit and imaged with a high-throughput, 2-dimensional detector installed parallel to the polarization plane. Because a circularly polarized (isotropic) Coulomb exploding pulse is used, the observed angular distribution of the ejected ions directly corresponds to the squared rotational wave function at the time of the pulse irradiation. To create a real-time movie of molecular rotation, the present imaging technique is combined with a femtosecond pump-probe optical setup in which the pump pulses create unidirectionally rotating molecular ensembles. Due to the high image throughput of our detection system, the pump-probe experimental condition can be easily optimized by monitoring a real-time snapshot. As a result, the quality of the observed movie is sufficiently high for visualizing the detailed wave nature of motion. We also note that the present technique can be implemented in existing standard ion imaging setups, offering a new camera angle or viewpoint for the molecular systems without the need for extensive modification.

We present a protocol for creating a real-time movie of a molecular rotational wave packet using a high-resolution Coulomb explosion imaging setup.

We present a method for visualizing laser-induced, ultrafast molecular rotational wave packet dynamics. We have developed a new 2-dimensional Coulomb ...

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F&#8722;

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound electrons with neutral molecules/atoms. State-of-the-art in vacuo anion generation techniques allow application to a broad range of atomic, molecular, and cluster anion systems. These are separated and selected using time-of-flight mass spectrometry. Electrons are removed by linearly polarized photons (photo detachment) using table-top laser sources which provide ready access to excitation energies from the infra-red to the near ultraviolet. Detecting the photoelectrons with a velocity mapped imaging lens and position sensitive detector means that, in principle, every photoelectron reaches the detector and the detection efficiency is uniform for all kinetic energies. Photoelectron spectra extracted from the images via mathematical reconstruction using an inverse Abel transformation reveal details of the anion internal energy state distribution and the resultant neutral energy states. At low electron kinetic energy, typical resolution is sufficient to reveal energy level differences on the order of a few millielectron-volts, i.e., different vibrational levels for molecular species or spin-orbit splitting in atoms. Photoelectron angular distributions extracted from the inverse Abel transformation represent the signatures of the bound electron orbital, allowing more detailed probing of electronic structure. The spectra and angular distributions also encode details of the interactions between the outgoing electron and the residual neutral species subsequent to excitation. The technique is illustrated by the application to an atomic anion (F&#8722;), but it can also be applied to the measurement of molecular anion spectroscopy, the study of low lying anion resonances (as an alternative to scattering experiments) and femtosecond (fs) time resolved studies of the dynamic evolution of anions.

Here, we present a protocol for photoelectron imaging of anionic species. Anions generated in vacuo and separated by mass spectrometry are probed using velocity mapped photoelectron imaging, providing details of anion and neutral energy levels, anion and neutral structure and the nature of the anion electronic state.

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound ...

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Accurate characterization of chemical structures is important to understand their underlying biological mechanisms and functional properties. Mass spectrometry (MS) is a popular tool but is not always sufficient to completely unveil all structural features. For example, although carbohydrates are biologically relevant, their characterization is complicated by numerous levels of isomerism. Ion mobility spectrometry (IMS) is an interesting complement because it is sensitive to ion conformations and, thus, to isomerism. 
Furthermore, recent advances have significantly improved the technique: the last generation of Cyclic IMS instruments offers additional capabilities compared to linear IMS instruments, such as an increased resolving power or the possibility to perform tandem ion mobility (IMS/IMS) experiments. During IMS/IMS, an ion is selected based on its ion mobility, fragmented, and reanalyzed to obtain ion mobility information about its fragments. Recent work showed that the mobility profiles of the fragments contained in such IMS/IMS data can act as a fingerprint of a particular glycan and can be used in a molecular networking strategy to organize glycomics datasets in a structurally relevant way. 
The goal of this protocol is thus to describe how to generate IMS/IMS data, from sample preparation to the final Collision Cross Section (CCS) calibration of the ion mobility dimension that yields reproducible spectra. Taking the example of one representative glycan, this protocol will show how to build an IMS/IMS control sequence on a Cyclic IMS instrument, how to account for this control sequence to translate IMS arrival time into drift time (i.e., the effective separation time applied to the ions), and how to extract the relevant mobility information from the raw data. This protocol is designed to clearly explain the critical points of an IMS/IMS experiment and thus help new Cyclic IMS users perform straightforward and reproducible acquisitions.

Ion mobility spectrometry (IMS) is an interesting complement to mass spectrometry for the characterization of biomolecules, notably because it is sensitive to isomerism. This protocol describes a tandem IMS (IMS/IMS) experiment, which allows the isolation of a molecule and the generation of the mobility profiles of its fragments.

Accurate characterization of chemical structures is important to understand their underlying biological mechanisms and functional properties. Mass ...

Direct Comparison of Hyperspectral Stimulated Raman Scattering and Coherent Anti-Stokes Raman Scattering Microscopy for Chemical Imaging

Stimulated Raman scattering (SRS) and coherent anti-Stokes Raman scattering (CARS) microscopy are the most widely used coherent Raman scattering imaging technologies. Hyperspectral SRS and CARS imaging offer Raman spectral information at every pixel, which enables better separation of different chemical compositions. Although both techniques require two excitation lasers, their signal detection schemes and spectral properties are quite different. The goal of this protocol is to perform both hyperspectral SRS and CARS imaging on a single platform and compare the two microscopy techniques for imaging different biological samples. The spectral focusing method is employed to acquire spectral information using femtosecond lasers. By using standard chemical samples, the sensitivity, spatial resolution, and spectral resolution of SRS and CARS in the same excitation conditions (i.e., power at the sample, pixel dwell time, objective lens, pulse energy) are compared. The imaging contrasts of CARS and SRS for biological samples are juxtaposed and compared. The direct comparison of CARS and SRS performances would allow for optimal selection of the modality for chemical imaging.

This paper directly compares the resolution, sensitivity, and imaging contrasts of stimulated Raman scattering (SRS) and coherent anti-Stokes Raman scattering (CARS) integrated into the same microscope platform. The results show that CARS has a better spatial resolution, SRS gives better contrasts and spectral resolution, and both methods have similar sensitivity.

Stimulated Raman scattering (SRS) and coherent anti-Stokes Raman scattering (CARS) microscopy are the most widely used coherent Raman scattering imaging ...

Differential Imaging of Biological Structures with Doubly-resonant Coherent Anti-stokes Raman Scattering (CARS)

Coherent Raman imaging techniques have seen a dramatic increase in activity over the past decade due to their promise to enable label-free optical imaging with high molecular specificity 1. The sensitivity of these techniques, however, is many orders of magnitude weaker than fluorescence, requiring milli-molar molecular concentrations 1,2. Here, we describe a technique that can enable the detection of weak or low concentrations of Raman-active molecules by amplifying their signal with that obtained from strong or abundant Raman scatterers. The interaction of short pulsed lasers in a biological sample generates a variety of coherent Raman scattering signals, each of which carry unique chemical information about the sample. Typically, only one of these signals, e.g. Coherent Anti-stokes Raman scattering (CARS), is used to generate an image while the others are discarded. However, when these other signals, including 3-color CARS and four-wave mixing (FWM), are collected and compared to the CARS signal, otherwise difficult to detect information can be extracted 3. For example, doubly-resonant CARS (DR-CARS) is the result of the constructive interference between two resonant signals 4. We demonstrate how tuning of the three lasers required to produce DR-CARS signals to the 2845 cm-1 CH stretch vibration in lipids and the 2120 cm-1 CD stretching vibration of a deuterated molecule (e.g. deuterated sugars, fatty acids, etc.) can be utilized to probe both Raman resonances simultaneously. Under these conditions, in addition to CARS signals from each resonance, a combined DR-CARS signal probing both is also generated. We demonstrate how detecting the difference between the DR-CARS signal and the amplifying signal from an abundant molecule's vibration can be used to enhance the sensitivity for the weaker signal. We further demonstrate that this approach even extends to applications where both signals are generated from different molecules, such that e.g. using the strong Raman signal of a solvent can enhance the weak Raman signal of a dilute solute.

Differential Imaging of Biological Structures with Doubly-resonant Coherent Anti-stokes Raman Scattering CARS

A combination of three single wavelength short-pulsed lasers is used to generate coherent anti-Stokes Raman scattering (CARS) and doubly-resonant CARS (DR-CARS). The difference between these signals provides enhanced sensitivity for otherwise difficult to detect coherent Raman signals, enabling imaging of weak Raman scatterers.

Coherent Raman imaging techniques have seen a dramatic increase in activity over the past decade due to their promise to enable label-free optical imaging ...

Biology

Using a VSFG Microscope for Multimodal, Rapid, Hyperspectral Chemical Analysis

Multimodal Nonlinear Hyperspectral Chemical Imaging Using Line-Scanning Vibrational Sum-Frequency Generation Microscopy

Vibrational sum-frequency generation (VSFG), a second-order nonlinear optical signal, has traditionally been used to study molecules at interfaces as a spectroscopy technique with a spatial resolution of ~100 &#181;m. However, the spectroscopy is not sensitive to the heterogeneity of a sample. To study mesoscopically heterogeneous samples, we, along with others, pushed the resolution limit of VSFG spectroscopy down to ~1 &#181;m level and constructed the VSFG microscope. This imaging technique not only can resolve sample morphologies through imaging, but also record a broadband VSFG spectrum at every pixel of the images. Being a second-order nonlinear optical technique, its selection rule enables the visualization of non-centrosymmetric or chiral self-assembled structures commonly found in biology, materials science, and bioengineering, among others. In this article, the audience will be guided through an inverted transmission design that allows for imaging unfixed samples. This work also showcases that VSFG microscopy can resolve chemical-specific geometric information of individual self-assembled sheets by combining it with a neural network function solver. Lastly, the images obtained under brightfield, SHG, and VSFG configurations of various samples briefly discuss the unique information revealed by VSFG imaging.

Author Spotlight: Unveiling the Potential of VSFG Microscopy in Studying Mesoscopically Heterogeneous Self-Assembled Structures 

A multimodal, rapid hyperspectral imaging framework was developed to obtain broadband vibrational sum-frequency generation (VSFG) images, along with brightfield, second harmonic generation (SHG) imaging modalities. Due to the infrared frequency being resonant with molecular vibrations, microscopic structural and mesoscopic morphology knowledge is revealed of symmetry-allowed samples.

Vibrational sum-frequency generation (VSFG), a second-order nonlinear optical signal, has traditionally been used to study molecules at interfaces as a ...

Stereoisomers

On the basis of mirror symmetry, stereoisomers of an organic molecule can be further classified into diastereomers and enantiomers. Diastereomers are stereoisomers that are not mirror images of each other. Substituted alkenes, such as the cis and trans isomers of 2-butene, are diastereomers, as these molecules exhibit different spatial orientations of their constituent atoms, are not mirror images of each other,&#160;and do not interconvert. Here, the interconversion is suppressed due to restricted rotation around the &#960; bond. Another class of diastereomers &#8212; those without &#960; bonds &#8212; are molecules that have non-superposable spatial orientations and exhibit different configurations of their substituent groups at some, but not all, stereocenters. For example, cis-1,2-dimethylcyclohexane and trans-1,2-dimethylcyclohexane are diastereomers, as these molecules are not superposable and have a different configuration of the methyl and hydrogen groups at only one out of their two stereocenters.
Enantiomers are stereoisomers that are mirror images of each other. As only chiral molecules can have non-superposable mirror images, enantiomers are chiral molecules. For example, the chiral molecule 2-butanol and its mirror image are enantiomers, as these molecules exhibit non-superposable spatial orientations of their constituent atoms and are mirror images of each other. A chiral molecule and its mirror image are collectively referred to as an enantiomeric pair, or a pair of enantiomers. The enantiomer of a chiral molecule can be drawn by taking its mirror image from any position or&#160;exchanging the positions of two of the substituents at each stereocenter of the molecule.

Stereoisomers: Diastereomers and Enantiomers

On the basis of mirror symmetry, stereoisomers of an organic molecule can be further classified into diastereomers and enantiomers. Diastereomers are ...

KEY TERMS AND CONCEPTS

<h3>Isomerism in Complexes</h3>
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric isomers, in which the same atoms are connected through the same types of bonds but with differences in their orientation in space. Coordination complexes with two different ligands in the cis and trans positions from a ligand of interest form isomers. For example, the octahedral [Co(NH3)4Cl2]+ ion has two isomers (Figure 1) In the cis configuration, the two chloride ligands are adjacent to each other. The other isomer, the trans configuration, has the two chloride ligands directly across from one another.
<img alt="Image1" src="/files/ftp_upload/11459/11459_Image1.svg" style="text-align: center; height: 200px;" />
Figure 1. The cis and trans isomers of [Co(H2O)4Cl2]+ contain the same ligands attached to the same metal ion, but the spatial arrangement causes these two compounds to have very different properties.
Different geometric isomers of a substance are different chemical compounds. They exhibit different properties, even though they have the same formula. For example, the two isomers of [Co(NH3)4Cl2]NO3 differ in color; the cis form is violet, and the trans form is green. Furthermore, these isomers have different dipole moments, solubilities, and reactivities. As an example of how the arrangement in space can influence the molecular properties, consider the polarity of the two [Co(NH3)4Cl2]NO3 isomers. Remember that the polarity of a molecule or ion is determined by the bond dipoles (which are due to the difference in electronegativity of the bonding atoms) and their arrangement in space. In one isomer, cis chloride ligands cause more electron density on one side of the molecule than on the other, making it polar. For the trans isomer, each ligand is directly across from an identical ligand, so the bond dipoles cancel out, and the molecule is nonpolar.
Another important type of isomers are optical isomers, or enantiomers, in which two objects are exact mirror images of each other but cannot be lined up so that all parts match. This means that optical isomers are non-superposable mirror images. A classic example of this is a pair of hands, in which the right and left hand are mirror images of one another but cannot be superposed. Optical isomers are very important in organic and biochemistry because living systems often incorporate one specific optical isomer and not the other. Unlike geometric isomers, pairs of optical isomers have nearly identical properties (boiling point, polarity, solubility, etc.). Optical isomers differ only in the way they affect polarized light and how they react with other optical isomers. For coordination complexes, many coordination compounds such as [M(en)3]n+ [in which Mn+ is a central metal ion such as iron(III) or cobalt(II)] form enantiomers, as shown in Figure 2. These two isomers will react differently with other optical isomers. For example, DNA helices are optical isomers, and the form that occurs in nature (right-handed DNA) will bind to only one isomer of [M(en)3]n+ and not the other.
<img alt="Image2" src="/files/ftp_upload/11459/11459_Image_2.svg" style="text-align: center; height: 200px;" />
Figure 2. The complex [M(en)3]n+ (Mn+ = a metal ion, en = ethylenediamine) has a non-superposable mirror image.
The [Co(en)2Cl2]+ ion exhibits geometric isomerism (cis/trans), and its cis isomer exists as a pair of optical isomers (Figure 3).
<img alt="Image3" src="/files/ftp_upload/11459/11459_Image_3.svg" style="text-align: center; height: 200px;" />
Figure 3. Three isomeric forms of [Co(en)2Cl2]+ exist. The trans isomer, formed when the chlorines are positioned at a 180&#176; angle, has very different properties from the cis isomers. The mirror images of the cis isomer form a pair of optical isomers, which have identical behavior except when reacting with other enantiomers.
This text is adapted from <a href="https://openstax.org/books/chemistry-2e/pages/19-2-coordination-chemistry-of-transition-metals">Openstax, Chemistry 2e, Chapter 19.2 Coordination Chemistry of Transition Metals.</a>

Stereoisomerism: Geometric &amp; Optical Isomers

Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric ...

&sup1;H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of diastereomers. Such protons are called diastereotopic, and they perceive different environments in all conformations. They cannot be interchanged by rotation or reflection and have slightly different chemical shifts.

1H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral ...

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

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