Spatial Separation of Molecular Conformers and Clusters
January 9th, 2014
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.
The overall goal of the following experiment is to spatially separate different species such as conformers clusters or quantum states in the gas phase, facilitating further experiments on these samples. This is achieved by first producing a rotationally cold supersonic molecular beam containing the species of interest. As a second step, the different species present in the beam need to be spatially separated, which is achieved using strong in homogenous electric fields, separating species by their effective dipole moments induced by the stark effect.
Next, the spatial distributions of species are probed using resonance enhanced multiphoton ionization in order to identify areas where only a single species is present. Results are obtained that show the spatial separation of CYS and trans isomers of three fluoro ethanol, as well as the separation of water indu clusters from pure indu based on the fully species selective resident enhanced multi photon ionization yield recorded as a function of spatial position in the molecular beam. The main advantage of this technique over existing techniques like hpo, focuser or iron mobility drift tube, that the electric defactor much easier to implement and more generally applicable.
The implications Of this technique extend towards applications in molecular frame imaging as well as electron and x-ray diffraction experiments, as these require pure and homogeneous samples In the gas phase, A schematic of the gas phase molecular beam setup and deflector is shown here and it consists of the following components. The first component is a pulsed Evan Levy valve containing the molecular sample. In the experiments presented here, the valve is operated at a 20 hertz repetition rate with about 50 bar helium backing pressure and expanded into a vacuum chamber, evacuated to less than 10 to the negative six to mbar.
A two millimeter diameter molecular beam skimmer is placed 22 centimeters downstream from the valve coating the molecular beam and leading to differential pumping conditions between the pulsed valve and the rest of the vacuum system. Immediately after the skimmer, the molecules enter the electrostatic deflection device. This consists of a three millimeter radius rod and a trough with 3.2 millimeters radius of curvature each 24 centimeters long.
The vertical gap between the electrodes in the center of the device is 2.3 millimeters. A potential difference between zero and 26 kilovolts is applied between the rod and the trough, producing a strong in homogenous electric field with a nearly constant field gradient as indicated in the inset directly after the deflector molecules entered the interaction region through a second skimmer providing a further differential pumping stage. The interaction region evacuated to pressures less than 10 to the negative ninth millibar contains a standard Wiley McLaren time of flight set up molecules are ionized by focused laser pulses in the center of the extraction region between the repeller and extractor electrodes.
Produced ions are accelerated towards a multichannel plate or MCP detector where a mass spectrum is recorded. Laser pulses are derived from a neodymium YAG pumped frequency doubled pulsed dye laser, providing typical output wavelengths around 283 nanometers for the end O experiments, or 272 nanometers for the three fluoro phenol experiments and pulse energies of a few millijoules. Pulse durations are on the order of 10 nanoseconds and pulses are focused with the 750 millimeter focal length lens to a spot size of about 100 microns in the interaction region.
The timing sequence is controlled by a digital delay generator providing the master clock. This triggers the neo DMAC laser, the pulse valve, and the digitizer card used to record mass spectra. The digitizer card is triggered at the same time as the laser cue switch.
Molecular beam densities are extracted from appropriate mass gates in the recorded time of flight spectra. First place a few drops of three fluoro phenol on a small piece of filter paper, then load the sample reservoir of the pulsed valve with the chemical sample, produce the supersonic expansion using a high purity, high pressure backing gas, adjust the temperature of the sample reservoir within the valve such that the partial pressure of the sample is approximately 10 millibar. To characterize the produced molecular beam, set the ionization laser to a known wavelength for resonance enhanced multi photon ionization of a particular conformer of the sample record a temporal profile of the molecular beam pulse by monitoring the total parent ion yield on the MCP detector as a function of valve laser delay.
A typical temporal profile with the electrostatic deflector turned off is shown here for two different carrier gases using helium. A temporal width of approximately 12 microseconds full width at half maximum is observed typical for an expansion from an Evan levy valve under these operating conditions. For comparison, a temporal profile of a neon seated beam is also shown.
Next, fix the valve laser delay at the position of maximum intensity for all subsequent measurements. Record a transverse spatial profile of the molecular beam, moving the focusing lens perpendicular to the laser propagation direction such that the focus moves in the Y direction relative to the molecular beam. Then repeat the temporal and spatial profiling for all conformers of interest in the beam.
Finally, turn on the high voltage supply to the deflector and record spatial profiles for all isomers, which should now be deflected. According to the mast to dipole moment ratio, three, fluoro ethanol conformers were separated in a molecular beam from the supersonic expansion of 50 bars of helium. The insets showed the molecular structures of the two conformers.
The individual species were probed by other distinctive resonance enhanced multiphoton ionization resonances around 272 nanometers. The trans species exhibits a significantly larger stark effect than the cis conformer. This leads to a larger, effective dipole moment, which is given by the negative slope of the stark energies.
As a result, the transcon conformer experiences a larger deflection following passage through the deflector and is spatially separated from the cyst conformer and the carrier gas of the beam. The spatial distribution of the molecular beam is monitored by translation of the resonance enhanced multi photon ionization laser relative to the molecular beam direction and spatial profiles are shown here. Field free profiles are shown by the magenta for cys and cyan for trans curves.
These yield a spatial width of the molecular beam of about two millimeters and show that without the deflector, both species are mixed within the beam. Applying a deflection voltage of 14 kilovolts leads to a spatial separation of the conformers Separation increases when higher voltages are applied, such as 28 kilovolts as shown on the right in the presence of a deflection field. The transcon conformer undergoes a significantly larger deflection than the cis conformer and can effectively be separated from the other species present in the beam, such that at a position of y equals three millimeters, a pure trans sample is created and can be utilized for further experiments.
For the preparation of beams of molecular clusters, such as indu water, one coex expands indu and water from the molecular beam valve. This creates a mixture of species, including the respective monomers as well as clusters of varying compositions. Here we demonstrate the generation of a pure sample of the one indu.
One water dimer. Spatial profiles for a molecular beam of indu. Co expanded in the presence of water are shown here.
The detection of these profiles via resonance enhanced multi photon ionization is fully species selective for Indo Indu water one and indu water. Two profiles shown here have been recorded with a potential difference of 26 kilovolts between the rod and trough electrode. The lines indicate simulated values.
Details of numerical simulation methods can be found in the literature. For comparison, a field free or deflector grounded spatial profile is shown by the black curve as expected, the one-to-one cluster of indu and water experiences the largest deflection, and at a position of y equals two to three millimeters of pure beam of indu water. One is created to highlight the effect of the deflector on the spatial molecular beam profile, the inset shows the molecular beam density of indu water, one, as a function of potential difference applied across the deflector.
It indicates that as the field strength is increased, the coldest part of the molecular beam experiences an increasing deflection, while the warmer constituents experience a significantly smaller spatial separation and some density remains at the original position. This furthermore highlights the selection of the coldest part of the molecular beam. Following this procedure.
Other methods like molecular frame imaging and alignment can be significantly approved upon allowing the extraction of molecular frame data from state Selected samples. And don't forget that working with lasers is extremely hazardous, so precursion such as wearing preventive eyewear should always be taken.
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Overview
This study presents a technique for the spatial separation of different conformers or clusters in a molecular beam. By utilizing an electrostatic deflector, species are separated based on their mass-to-dipole moment ratio, enabling the production of gas-phase ensembles with a single conformer or cluster stoichiometry.
Key Study Components
Area of Science
- Physical Chemistry
- Molecular Physics
- Gas Phase Chemistry
Background
- Spatial separation of molecular species is crucial for various experimental applications.
- Rotationally cold supersonic molecular beams are effective for producing distinct species.
- Existing techniques for separation have limitations in implementation and applicability.
- The stark effect can be utilized to induce dipole moments for separation.
Purpose of Study
- To develop a method for the effective spatial separation of molecular conformers and clusters.
- To facilitate further experiments on isolated species.
- To demonstrate the advantages of the electrostatic deflector over traditional methods.
Methods Used
- Production of a rotationally cold supersonic molecular beam.
- Use of strong inhomogeneous electric fields for spatial separation.
- Probing spatial distributions using resonance enhanced multiphoton ionization.
- Recording species-selective ionization yields as a function of spatial position.
Main Results
- Successful spatial separation of CYS and trans isomers of three fluoroethanol.
- Separation of water-induced clusters from pure indu species.
- Demonstration of the technique's ease of implementation compared to existing methods.
- Identification of areas with single species presence in the molecular beam.
Conclusions
- The electrostatic deflector provides a versatile and efficient means of molecular separation.
- This method enhances the ability to study individual molecular species in the gas phase.
- Future applications could expand to various fields requiring precise molecular manipulation.
Frequently Asked Questions
Executive Industry Relevance
In biopharma R&D, isolating pure molecular species is critical for de-risking target validation and enabling reproducible assay development. Spatial separation of conformers and clusters via electrostatic deflection provides a mechanism to obtain conformationally pure samples, reducing mechanistic ambiguity in early discovery. This capability supports predictive confidence in lead identification by ensuring that functional readouts derive from a single, well-defined species.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Scientific Value: Enables interrogation of individual conformers to clarify structure-function relationships and reduce false positives in target screening.
- Operational Value: Produces conformationally pure samples that improve reproducibility in downstream binding and functional assays.
- Strategic Value: Supports go/no-go decisions by isolating bioactive conformers, thereby increasing confidence in target validation outcomes.
Screening & Assay Development
- Scientific Value: Generates homogeneous molecular beams that yield quantitative, species-specific signals for assay standardization.
- Operational Value: Facilitates reliable compound evaluation by eliminating signal contamination from mixed conformers or clusters.
- Strategic Value: Enhances assay robustness and scalability, supporting high-throughput screening campaigns with reduced variability.
Translational & Preclinical Research
- Scientific Value: Enables systematic study of solvation effects by selecting specific cluster stoichiometries, informing ligand design and binding thermodynamics.
- Operational Value: Provides pure samples for mechanistic de-risking, allowing clear attribution of observed effects to defined molecular species.
- Strategic Value: Supports translational continuity from discovery to preclinical by ensuring consistent species input across experimental stages.
Pipeline & Workflow Integration
The method fits within the discovery continuum, enabling pure sample generation for hypothesis testing in early discovery, assay readiness in screening, and mechanistic clarity in translational research.
- Discovery Biology: Supports hypothesis testing by isolating individual conformers to clarify target engagement mechanisms.
- Screening: Delivers assay-ready, homogeneous samples that improve reproducibility and quantitative readout reliability.
- Analytics: Provides species-selective ionization yields as a function of spatial position, enabling precise quantification and comparison of molecular variants.
- Translational Research: Connects to preclinical continuity by allowing selection of specific cluster structures to study solvation effects relevant to biological environments.
- Enterprise Reuse: Functions as a reusable platform for generating pure samples across multiple targets and projects, reducing redundant method development.
Operational & Enterprise Impact
- Scientific Value: Predictive confidence through reduction of mechanistic ambiguity and improved target validation.
- Operational Value: Standardization and reproducibility via spatially separated, pure molecular samples.
- Strategic Value: Better go/no-go decisions, capital efficiency, and reduced late-stage biological risk from early de-risking.
- Portfolio Impact: Risk-adjusted prioritization and advancement decisions based on unambiguous species-specific data.
Implementation Considerations
- Requires expertise in molecular beam techniques, electrostatic deflection, and laser-based ionization detection.
- Needs instrumentation including pulsed valves, high-voltage deflection rods and troughs, skimmers, and time-of-flight mass spectrometry detection.
- Demands cross-team standardization for spatial profiling and species-specific ionization setup to ensure reproducible separation.
- Involves adaptation considerations for different molecular systems based on mass-to-dipole moment ratios and conformational flexibility.
- Practical limitations include dependency on sufficient dipole moment differences for separation and accessibility to high-voltage vacuum infrastructure.
