Elucidate Unknown Structures | What's New in ACD/Structure Elucidator Suite

Version 2020

Data Analysis

Save time with real-time generation and ranking of structures during elucidation and identify the best structure at any time, even before the generation process is complete

Conveniently follow the ranking and generation of structures in real-time

More efficiently determine the best structure using DP4 metrics. This approach calculates the Match Factor based on the normalized multiplication of probabilities of each assigned atom (¹³C or ¹H). This enables much better structural candidates' discrimination compared to averaged-based approaches.

Confidently identify the best structure using DP4A and DP4N metrics with distinctively higher values — Confidently identify the best structure using DP4_A and DP4_N metrics with distinctively higher values

Conformer optimization and analysis using NOESY/ROESY spectra

Export the generated conformers and analysis results as SDFiles (*.sdf) to allow processing in third-party software
Import conformers generated by third-party programs as SDFiles. This option will allow conformer analysis and matching of these imported conformers with NOESY and ROESY spectra

Swap assignments of diastereotopic CH₂ groups in 3D conformers to potentially obtain better fit for inter-proton distances

Improve the best fit by switching the assignments of diastereotopic CH2 groups in 3D conformers. — Improve the best fit by switching the assignments of diastereotopic CH₂ groups in 3D conformers. The swap is reflected with "*" near the atom numbers and in this case results in lower distance error.

Perform Unbiased Verification (UBV) without full carbon assignment—partial structure assignment (25% assignment of carbons) is sufficient
Several enhancements and performance improvements in Mixture Analysis workflow as follows:

Intelligent automatic assignment of components in 2D spectra
View the different components corresponding to the same peak in the Table of Spectral Data

Improved Match Factor calculation for nitrogen containing compounds
"TMS aware" analysis— only the smallest peak closest to 0 ppm is automatically identified as TMS if the proposed structure contains a Si-CH₃ group
Improved peak picking of small signals in overlapped regions of 2D spectra for more accurate data analysis
Correctly identify NOESY peaks corresponding to negative NOE

Ease of Use

Visualize peak assignments on the spectra of matched fragments/structures
Choose to display the distance error between observed and best fit distance values over NOE arrows for convenient data analysis

View the calculated NOE distance errors on each structure

Automatic adjustment of nitrogen valence based on the manually defined charge
Delete 2D annotations and dark regions directly in the spectrum with a single click
Higher integral maximum (>32,000) to accommodate the larger dynamic range in modern high field NMR instruments
Flag critical correlations on the structure and related peak(s) for quick review

Mark and view the critical correlations on the structure and related peak(s).

Improvements in Prediction Capabilities

Predict spectra of whole polymers—both the end groups and the main chain

View the predicted chemical shifts for the terminal groups of polymers and the main chain

Predict APT and DEPT ¹³C spectra directly in the prediction interface (initial prediction of ¹³C NMR not necessary)

Reporting

Added option to include chemical shifts for ¹⁹F, ³¹P, and other X nuclei in reports

Databasing

Database Client

Attach files to lines in tables (Word, PDF, Excel, JPEG, etc.)
Connect record sets by User Data to display linked meta data
Consistency in the handling of "dates"—computer default date setting may be enforced; user may select the date format of imported fields

SpectrusDB Server

PostgreSQL database server 12.2 included in installation package
Improved performance for remote databases through mirroring of record sets between two Spectrus DB Enterprise servers (read only)
Manage Database groups and Users when LDAP or Custom Authentication is active
Update of audit trail upon change of record ownership

Technique-Specific Features

Structure Elucidator Suite contains spectral processing capabilities for a variety of other analytical techniques.

Processing and Analysis of LC/MS Data with Structure Elucidator
Data Import
- A new "Connect To" plug-in allows data import from Agilent™ OpenLab™
- Data import from Waters™ MassLynx™ version 4.2
- Upgraded data import from Thermo Scientific™ Xcalibur™
- Import additional information from Shimadzu® LabSolutions™ including component spectra, information about components and peaks, XIC curves, and peaks detected in SIM and MRM traces
Data Analysis

IXCR (Structure ID by Database Search)
- Conveniently match components identified by database search to the reference database and record of the candidate structure
- Search databases with MS2 spectra that do not contain a parent m/z ion (e.g., spectra acquired with Data Independent Acquisition)
- Easily compare the retention time of a component to that of its candidate structure and view the retention time difference in the Table of Components
Quantitation
- Quantitatively analyze chromatographic data
A calibration curve is automatically generated from chromatograms of calibration standards.

Peak Integration
- Choose how to calculate XIC area %—either by using a single ion (Single mode) or by summing together all fragment, adduct, and component ions (Summed mode)
Retention Time
- Calculate relative retention time for GC-FID data
- Import retention time from *.SDF files into the Table of Components
Manage Data from Multiple Instruments

Keep track of settings for each instrument by setting up instrument profiles
- Make profiles for single chromatogram data using the new Chrom Profile Manager—set and save chromatogram parameters for each profile
- New features for LC/UV/MS profiles
Data Display
- Easily see which scans are averaged to produce a component mass spectrum
- View InChI and SMILES structural descriptors in the Table of Components
- Customize the number of decimal places displayed for assigned and XIC m/z values in the LC/UV/MS legend
- Lock x-axis display range for spectra in LC/UV/MS datasets
Reporting
- Report LC/MS and LC/UV traces with or without baseline subtraction
- Toggle on/off the "Ion Mode" label on mass spectra
- Toggle on/off the labels of MS curves

Many other improvements have also been made to the software. Contact us below to learn more and to discuss updating your software installation.

Previous Software Versions

Version 2019
As of v2019 ACD/Spectrus is compiled in a 64-bit architecture allowing the software to take greater advantage of system resources.

Data Import

We continue to improve and support all major instrument vendor data formats. This version includes enhancements to the following:
- Support for JEOL Delta™ DOSY data
- Improved support for MAGRITEK® data
- Support for Q.OneTec data
- Improved import/export options for JCAMP files
- Full support for 1D NOESY and ROESY datasets and improved import defaults for 2D NOESY and ROESY spectra
- Basic support for NOAH experiments
- Improved support of Shimadzu data
- Read 'Extended Statistics' metadata for Waters™ MassLynx™
- Improved support for processed data from Empower™ (Waters), Chromeleon™ and Atlas™ (Thermo Scientific™) CDSs
- Import processed data from Chromeleon chromatography data systems (CDS) via a new add-on
Data Analysis
- Full support of 1D or 2D NOESY and ROESY spectra for 3D structure elucidation
- Automatically generate stereoisomers from a flat structure and rank them using data from NOESY/ROESY spectra
- New multi-thread processing algorithm provides 1.3-10 times faster structure generation and filtering speed
- Full support for proposed structures containing stereochemistry information
- Automatically distinguish CH₃ from CH groups if edited HSQC or DEPT information is provided
- Unbiased Verification may now be performed using only 1D ¹H, HMBC, and HSQC spectra (1D ¹³C spectrum is no longer required)
- Easily identify possible erroneous data using the diagnostic orange colored cells in the Table of Spectral Data
- Improved options for automatic alignment of ¹⁵N spectra
- Automatic alignment can now be performed using 1D NOESY or 1D ROESY
- Improved support for synchronization of APT and HSQC spectra
- Streamline the analysis of mixtures by applying Targeted Profiling to 1D spectra of samples with known composition and variable concentrations of components
- Structure Aware Analysis now supports automatic peak picking in ¹³C spectra of compounds containing ³¹P, as well as ¹⁹F atoms
- Easily import and use corresponding *.spectrus files as 1D projections for your 2D spectra
- Display a larger dynamic range to accommodate newer instruments
- 'Known Structures Search' results from PubChem databases now display IUPAC names
- Achieve faster, more accurate predictions with the improved Neural Network algorithm
- Access an extended Predictors training database
Databasing
- Improved default options for updating the ¹⁵N prediction databases
Reporting
- Improved structure display for mixture components
- Expended options for reporting peak assignments
Ease of Use
- 'Proposed Structure' has been replaced by 'Proposed Molecule' for better consistency across the product portfolio
- Improved performance of the interface when re-opening projects
- Ability to display all the assignments in the corresponding 1D curves of the 2D spectra
- Optional assignment of the existing NH₂ and OH peaks
- Automatically synchronize the 1D and 2D spectra processing modes
- Option to save the solvent tables, as well as the processing and the analysis parameters, for Automated Batch Verification
- Apply filters to only display the correlations representing the –H and –CH₃ groups attached to stereocenters in the NOE spectra
- Choose to display/hide the axis label for 1D spectra
- Directly calculate the HSQC-DEPT from the structural window
- Accommodation of large datasets (limited only by the user's Windows OS version)
Technique-Specific Features

Structure Elucidator Suite contains spectral processing capabilities for a variety of spectroscopic techniques.
- Processing and Analysis of LC/MS data with Structure Elucidator Suite
  Data Analysis
  - Independent control of chromatograms in hyphenated (LC/MS) datasets
  - Greater flexibility in data analysis and annotation of MSn spectra through independent control of individual spectral panes (undock MSn spectra as individual panes)
  - MSn component spectra are created automatically when a chemical structure is manually assigned to a component
  - Automatically calculate relative retention times
  Data Display
  - Undock MSn spectral panes for flexible visualization and review
Version 2018
Data Import/Export

We continue to improve and support all major instrument vendor data formats. This version includes enhancements to the following: [+]
- Export assigned NMR project data in NMReData format using a dedicated script
- Improved support of data import from Thermo Fisher Scientific's Atlas (v.14.07) and Waters' UNIFI software environments
- Relative retention time (RRT) values can now be imported from Atlas and Chromeleon (Thermo Fisher Scientific), plus Empower (Waters)
- Support of the new Agilent DAD data format, through import of *.sqlite files from instrument *.D folders
- Improved support for XCalibur (Thermo Fisher Scientific), NetCDF, Agilent LC/MS 6000 (*.bin), Agilent LC/MS TOF (*.wiff), and Shimadzu LC/MS-IT-TOF (*.lcd) files
Data Analysis

The following tools have been added to enhance the structure elucidation capabilities:
- Verify whether elucidation results are more likely to be in their cis/trans isomeric form
  - Generated isomers are ranked according to the mean deviation between predicted and experimental chemical shifts
- Automatic identification of charged species. The software identifies charged N or P atoms and creates a salt from the neutral structure
Further improvements have been made to the processing and analysis tools. Click here to expand the highlights [+]
- Unbiased Verification improvements:
  - The capability to define 2 or more fragments from the proposed structure. This was increased from 1 defined fragment. This could increase the calculation speed.
  - Now can accommodate molecules up to 800 Da in size
  - The "Best Structure" is now cis/trans isomer specific
- Automatically assign homonuclear coupling partners, in some cases potentially eliminating the need for a COSY spectrum
  - Easily view the connected ¹H assignments and their coupling constants on the proposed structure
  - Include homonuclear coupling data in the user database to increase the NMR prediction accuracy
Comparison of observed and calculated spectra when full prediction training is used with connected multiplet assignments.
- Enhanced 1D NMR Mixture Analysis Tools:
  - Conveniently compare spectra with automatic peak height and chemical shift offset scaling
  - Automatically rank hits within a spectral search region
  - Easily control the offset between a query spectrum and its respective hits
The new "Optimize Hit" feature can be seen in the spectra comparison menu on the left-hand side of the figure. The query spectrum is shown in green, the original hit is shown in red, and the blue line is the optimized hit curve.
- Additional tools have been added to improve spectral processing, 1D and 2D NMR structure assignments, automated structure verification, data visualization, and software usability
Ease of Use
- Easily share custom solvent information
- Save structure data files (*.sdf) to a predefined folder
- Option to manually set the spectrum type
- Option to set the display order according to the Bruker Expno parameter
Structure Elucidator contains spectral processing capabilities for a variety of spectroscopic techniques.

Click on each technique to read about what has been added.

MS [+]
Data Display
- Visualize multiple MSn spectra simultaneously through improved MS Tree control
  - All spectra, or only selected spectra, can be displayed
- Easily interpret MSn spectra by grouping display panels and performing collective zoom
- Track peaks more efficiently by transferring unique entity names from the Table of Peaks to the Table of Components
Chromatography [+]
Data Analysis

Improvements to peak detection algorithm for more comprehensive processing of chromatographic data
- Complete automated detection of peak riders and shoulders based on user-defined 'signal to noise ratio' thresholds.
- Greater flexibility in data processing through a variety of peak integration methods
- Achieve greater accuracy in peak area calculations through the capability to manually adjust the baseline
Refined processing options deliver the most relevant information from chromatographic data
- Define selected areas of a chromatogram for analysis by excluding 'dark regions'
- Refine processing routines with flexible settings based on time intervals
  - Define integration method
  - Fine-tune peak detection thresholds
  - Inclusion of negative peaks
Optical/Curve [+]
Data Analysis
- Simplify analyses by breaking a single curve into several curves with respect to temperature sweeps
- Analyze curves with ill-defined temperature gradients and plateaus
Reporting
- Improved control of the structure sizes in the Report Templates
- The 2D NMR Mixture Reporting is upgraded to use the Table of Components
- Clean Spectra view added for standard report templates
Databasing

A number of enhancements have been made to improve the security, integration, and performance of the databasing functionality, including faster indexing and searching by NMR and mass spectra. Further improvements include: [+]
General
- Electronic signatures supporting GxP validated workflows—easily build multi-level hierarchy using the 'Required Existing Signatures'
- UTF8 CSV formatting for export from database records
Security and Performance Metrics
- The Spectrus DB client and server now supports IPv6 protocol
- Improved security between the Spectrus DB client and Spectrus DB Enterprise server-connection from clients is denied in the absence of traffic encryption
- Capability to define Open Database Connectivity (ODBC) connection string for PostgreSQL DB server
- Integrated benchmark tool for monitoring of Spectrus DB client-server communication performance
Integration and Scripting
- Easily access Spectrus DB functionality via pop-up forms from within third-party applications, using a command line parameter