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What’s New in Structure Elucidator Suite Version 2021

Version 2021 of Structure Elucidator Suite adds new features, including stereochemistry determination using residual dipolar couplings and new parameters to help with structure verification. It also improves existing functions. Read below for details, and contact us for help upgrading your software.

Use Residual Dipolar Couplings (RDCs) for Stereochemistry Determination

  • You can now measure RDCs from 2D spectra. You can fit these couplings to the 3D structures of conformers to help with stereochemistry determination.
    • The fit of the RDC to a given conformer is quantified by the Cornilescu Quality Factor (Q). A lower Q indicates a better fit.
      Pick peaks and measure RDCs from 2D spectra recorded in isotropic and anisotropic media
      After RDCs are measured, the Table of Spectral Data gains 3 new columns (J, T, and D) containing the isotropic and anisotropic coupling constants and the residual dipolar couplings

      The software fits the RDCs to all generated or imported conformers’ structures, and calculates the Q value. A Q below 0.1 indicates that a conformer structure has a high probability of being the correct one.

Identify the Best Structure During Structure Verification with New Metrics and Parameters

  • You can now use the NMR Purity parameter to evaluate structural candidates with similar match factors (MFs)
    • NMR Purity is defined as the ratio between the summed integrals of the assigned protons and the summed integrals of the entire spectrum

      Peaks corresponding to both Catechin and one of its subfragments can be found in an experimental spectrum. Since MF only looks for peaks in the spectrum appropriate for each structure and ignores extraneous peaks, both structures have high MFs. However, catechin has a much higher calculated NMR Purity, indicating that it is more likely the correct structure.
  • You can now use DP4 metrics in CCV and UBV to better rank generated candidates with similar MFs
    • This parameter is calculated using the predicted chemical shifts and their corresponding error distribution. It is a multiplicatively calculated statistical value and gives the probability that a structure from a set is the correct one.

      The software fits the RDCs to all generated or imported conformers’ structures, and calculates the Q value. A Q below 0.1 indicates that a conformer structure has a high probability of being the correct one.

Define Co-existing Rotamers in NMR Spectra

  • You can now define and report co-existing rotamers. Select the rotamer peaks in your spectrum and identify them as rotamers. You can then adjust the proton ratios with 0.1H accuracy.
1H NMR (DMSO-d6) δ: 8.47 (d, J=7.0 Hz, 0.4H rotamer), 8.18 (d, J=7.0 Hz, 0.6H rotamer)

Report multiplet results for samples containing rotamers in US patent format, or create customized reports in most other formats.

Unfold Folded 2D Spectra to Get the True Position of Peaks

  • You can now unfold folded 2D spectra along the F1 axis to reveal the correct positions of peaks

    Left: overlaid HMBC (red) and HSQC (green) spectra of azithromycin. The signals from HMBC appearing at ~0 ppm in 13C belong to folded peaks. Their true position is greater than the HMBC upper F1 range. Apply process-correct aliased frequencies to adjust the spectrum along F1 range. After unfolding, the signals appear at their correct position around 220ppm (right).

Automated Evaluation of Singly Charged Nitrogen Salts

  • On structures with multiple nonequivalent nitrogen atoms, you can automatically explore the possibilities of a positive charge on each nitrogen.
    • Previously, the software automatically detected the possibility of a positively charged nitrogen. But if there were several nonequivalent nitrogens, you had to consider all possibilities manually. Now, the software creates several MCDs by placing the charge on each nitrogen, and runs them in parallel to get the correct structure.
    • Enable this feature by selecting Enumerate Possible Charge of N Atoms in the Generator Options section of the Check MCDs Options dialog box

      Enable the automated consideration of singly charged nitrogen salts by selecting the Enumerate Possible Charge of N atoms checkbox

AutoMCDs Include 2-Bond C-F Connections

  • The software can now create C-F connections in the autoMCD based on 13C-19F 2J values taken from 13C spectra

    C-F connections are made in autoMCDs

Structure Aware Analysis in 2D Spectra of P- and F-Containing Compounds

  • You can now use the structure aware analysis algorithm to automatically recognize 19F-1H and 19F-13C multiplets in HMBC or HSQC spectra without a 1D 13C NMR spectrum

Control of Alignment Options of Spectra in Batch ASV

  • You now have control of alignment options of 2D spectra and corresponding 1D curves in Batch ASV

Integrate All Peaks in Series of NMR Data

  • In Group mode, view peak integral values for all spectra in a series

    A series of 1D 1H NMR spectra for ethylindanone. In group mode, you can display and selectively position the integral values for all peaks in the series.

More Data Types Can Be Included in Database Records

  • You can now represent large/complex molecules using graphical objects with defined formulas and modify them by attaching traditional chemical structures. The entire structure may be used in calculations and searches.

    Include multiple plots and charts to visualize datasets in records
  • Include multiple plots and charts to visualize datasets in records

    Include multiple plots and charts to visualize datasets in records

Improved Search for Data Range Values and Molecules with Chiral Centers

  • Improved definition of ranged values. Search results of ranged values are more reproducible (e.g., when searching for compounds with a melting point of 65°C, record sets with the following in the melting point field will now be returned: 50-100°C, <100°C, >50°C)
  • Improved search for structures that contain chiral atoms with “&” and “or” enhanced stereo labels (where “&” denotes a racemic center and “or” denotes relative configuration). Previously the labels provided incomplete/incorrect search results.

    Improved search for structures that contain chiral atoms with “&” and “or” enhanced stereo labels

In the search query, “or” labels indicate a search for the same relative chiral center configuration.

An exact search returns C and D as results. A and B are not returned since they have absolute stereo configuration, not relative. E is not returned because the centers have different relative configurations.

In a substructure search, only F–I are returned as results because those structures (can) have the same relative configuration as the query. J is not returned because it has a different relative configuration.

  • We improved data import from:
    • Shimadzu LabSolutions CDS—you can now import data via the Connect to External Application dialog box or the ACD/Labs/Shimadzu LabSolutions CDS Add-on
    • Agilent OpenLab CDS—you can now select a whole folder or several files to import at once, via the Connect to External Application dialog box or the Add-on
    • Thermo Chromeleon—you can now import LC/MS data, via the Connect to External Application dialog box or the Add-on

More Data Types Can Be Included in Database Records

  • You can now represent large/complex molecules using graphical objects with defined formulas and modify them by attaching traditional chemical structures. The entire structure may be used in calculations and searches.

    Represent complex molecules with graphical objects, e.g., proteins, antibody-drug conjugates, nanoparticles on surfaces, etc.
  • Include multiple plots and charts to visualize datasets in records

    Include multiple plots and charts to visualize datasets in records

Improved Search for Data Range Values and Molecules with Chiral Centers

  • Improved definition of ranged values. Search results of ranged values are more reproducible (e.g., when searching for compounds with a melting point of 65°C, record sets with the following in the melting point field will now be returned: 50-100°C, <100°C, >50°C)
  • Improved search for structures that contain chiral atoms with “&” and “or” enhanced stereo labels (where “&” denotes a racemic center and “or” denotes relative configuration). Previously the labels provided incomplete/incorrect search results.

    Improved search for structures that contain chiral atoms with “&” and “or” enhanced stereo labels

In the search query, “or” labels indicate a search for the same relative chiral center configuration.

An exact search returns C and D as results. A and B are not returned since they have absolute stereo configuration, not relative. E is not returned because the centers have different relative configurations.

In a substructure search, only F–I are returned as results because those structures (can) have the same relative configuration as the query. J is not returned because it has a different relative configuration.

Server Side Improvements

  • We added new capabilities to mirrored databases:
    • Read/write access
    • Ability to select records for mirroring
  • Improved logging of transactions to the database, e.g., view all successful and failed user logins
  • You can provide administrative privileges (to create, edit, and/or delete record sets) to LDAP users or groups

You can process data from other analytical techniques in Structure Elucidator Suite. We’ve improved features for these techniques as well:

Analysis of MS & Chrom Data with Structure Elucidator Suite

Display Fragment Structures as Peak Annotations

  • You can now annotate peaks with their associated fragment structures. This works with fragment structures assigned manually or via Auto Assignment.
    • Find this option, and adjust structure size and style, in the MS Preferences or LC/UV/MS Preferences dialog box

      Fragment structures appear above the corresponding peaks in the mass spectrum

Record and Automate Frequent Actions

  • Record automatic and manual processing actions for LC/UV/MS data in the Recording Log. Stop and start recording by clicking Recording in the toolbar or by using the Recording Log dialog box.
  • Automate actions by generating a script from actions saved in the Recording Log

Access More Features by Converting Flat Chromatograms into Hyphenated Data

  • Turn flat (single-channel) chromatograms into hyphenated data to access Projects and the Table of Components. Now single-channel and multi-dimensional datasets will have a consistent look.
    • This option automatically appears during data import. It can also be activated manually under Tools > Convert to Hyphenated Data.
    • Previously, single-channel chromatograms could only be imported as flat chromatograms, which don’t support features like the Table of Components

Get Better Results from Automatic Processing with IntelliXtract 2.0 and IXCR 2.0

  • You can now set an Abundance Threshold for components to be identified via spectral search
  • Auto Interpret Component Spectrum now gives more accurate adduct labels. We added checks for adduct pairs like [M+NH3+H]+. We also improved annotation of multiply charged ions and multimers.
  • You can now see the retention time difference (tR Difference) between experimental and reference chromatograms in the Table of Components
  • We made spectral search faster

Improve Processing with More Tools and Options

  • You can now match peaks between chromatograms in an LC/MS series. Both manual and automatic matching are available. Previously, peak matching was only available between datasets opened in separate windows (not in series mode).
  • Subtract one DAD (diode array detector, LC/UV) dataset from another, e.g., you can correct a sample chromatogram and spectrum by blank subtraction
  • We improved the peak detection algorithm, and added the Baseline Liftoff and Baseline Touchdown options, so you can refine the integration by moving the start and end points of the peak

    Peak integration results before and after improving the integration algorithm
  • Generate formulae for multiple m/z values within a mass spectrum, while setting individual parameters for each mass range
    • Select m/z values for formula generation by specifying the Abundance Threshold (%)
    • Define mass ranges, and set the types and numbers of atoms for each range
  • You can now annotate spectra with fragment losses (e.g., loss of HCl)

Filter MS Searches by Polarity

  • When searching databases by spectra, the search now returns only reference spectra with the same polarity as the query