What's New in ACD/NMR Workbook Suite

Previous Software Versions

• Version 2018.1

  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

  Known Structure Identification Add-On

  Simplify unknown compound identification/dereplication by determining whether the compounds' experimental ¹³C resonances match the predicted signals of known structures. Uses ACD/Labs leading, proprietary NMR prediction neural network algorithms.

  • Uses a database of ~98 million known structures collected from open chemistry databases (e.g.  PubChem) with predicted ¹³C NMR signals
  • Rapid search using any combination of ¹³C, HSQC and HMBC NMR spectra in a project
  • Conveniently view results ranked in terms of the average chemical shift deviation between experimental and predicted spectrum, and their structure and database ID
  Search results for the ¹³C NMR spectrum of Retrorsine. The query spectrum is green and offset vertically from the hit spectrum, which is shown in red. The list of hits is shown in the window below the spectra.

  Data Analysis

  Multiple tools and improvements have been added to version 2018.1. The highlights include:

  • Improved peak picking and multiplet assignment accuracy in ¹³C NMR spectra of fluorinated compounds
  • 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

  NMR Workbook Suite 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
  Zoom Applied
  • 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
  Peak integration options available for chromatographic data analysis

  • 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
  • Added Clean Spectra view 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

• Version 2017.1

  Click to Expand

  Enhanced capabilities for handling biomolecules

  • Support for standard one-letter and three-letter peptide sequence codes
  • Manage peptide and amino acid nomenclature
  • Easily switch between single and three letter notation, and full structure of amino acids
  • Assign amino acid resonances from single or three letter notation, with suggestions for your convenience
  • Added convenient NMR spectral assignments of peptides
  • Software assisted assignment of entire peptide residues when they are drawn in either expanded or compact form
  

  Table of assignments with peptide notation

  • Assignments can be done when peptide is in the compact form
  

  Chemical structure with the peptide in a compact form

  Data Import/Export

  • Support of FASTA and HELM file formats for biomolecules
  • Full support of new Bruker TopSpin 4.0 and Avance Neo data format
  • Improved support for JEOL standard, JEOL NUS and benchtop (Magritek, Nanalysis) datasets
  • We continue to improve and support all major instrument vendor data formats. This version includes enhancements to the following:
  • Shimadzu LC-IT-TOF; Waters MassLynx MS^E, Empower (and UNIFI); Samsung GC-MS data; Bruker Compass; Thermo Xcalibur; SCIEX Analyst and Triple TOF; JEOL K9; and netCDF
  • Ability to export spectra series data in ASCII format
  • Improved support for MS^E/All Ions Fragmentation acquisition

  Data Analysis

  Click to Expand

  New Molecule Verification tool within Projects—Unbiased Verification (UBV)

  • For additional confidence in your structure verification by NMR, NMR WBS now provides the unique ability to interrogate your proposed compound entirely on data, thus eliminating user bias.
  • If alternative candidates have better data fit than your proposed structure, the software will display the alternatives for further evaluation. This capability is unique to NMR WBS and is based on ACD/Lab's CASE technology.
  • Unbiased verifications are limited to datasets that contain ¹H, ¹³C, HSQC, and HMBC experiments for molecules that are less than 400 Da, or contain less than 20 carbons or 22 carbon and nitrogen atoms.
  • When running UBV, confirmed fragments from their peak interpretation of the proposed molecule may be used.
  

  UBV options, and ability to select fragments to use for the generated molecules

  
  • Once completed, generated structures are ranked according to mean deviation of predicted ¹H and 13C chemical shifts from the experimental values
  

  Table of Structures containing the Proposed Structure (a requirement for UBV), and generated molecules sorted by Match Factor and the predicted vs. experimental chemical shift mean deviation score

  Expansion of Mixture Analysis Tools

  • Use 2D spectra to identify, compare and characterize mixtures and mixture components more efficiently
  • Identify mixture components more easily by searching your 1D database
  • Predicting mixtures of components can now be performed within the Spectrus Processor Interface
  • 1. Available from table of components for a mixture; this is also supported within an NMR Project:
  
  • 2. The second method is to import 2 molecules within the structure drawing widget in order to generate the corresponding spectrum of the mixture
  

  Mixture prediction functionality with mol ratios is available in NMR Workbook Suite

  

  Components of the mixture are colored within the ¹H NMR spectrum

  • Simulate a pure component spectrum from any mixture spectra
  • When working with a spectrum containing overlapping peaks from different components, the software provides the ability to simulate a pure component spectrum, thereby allowing clearer assignments and the ability to generate a spectral database of pure component spectra.
  • Mixture Searching has been extended to include 2D NMR
  • Identifying components within a mixture by doing a spectral search is difficult due to overlapping components—an inherent limitation with 1D NMR Spectra. The software now has the unique capability to search spectral databases based on either a single 2D NMR spectra or one that is part of a project.
  

  General Improvements

  NMR

  • Calculate Pure Shift ¹H NMR spectra to help assignments in overlapping, complex spectra
  
  • Filter between strong, medium, and weak NOESY correlations
  • Improved Non Uniform Sampling (NUS) processing with optimization of NUS reconstruction algorithm
  • Calculate T1 and T1? (rho) for solid state NMR saturation recovery experiments
  • Interpret inverted 1,n ADEQUATE experiments
  • Detect solvent signals in HMBC in the presence of satellite peaks
  Click to Expand
  • New algorithm that uses 2D peaks to select right 1D signal for solvent
  • Retain user/existing assignments during autoassignment and verification
  • Option to have wider automatic multiplet range for quantitation
  • Hide NOE correlation within a CH2 group

  MS/Chrom

  • Select an area of a chromatogram for processing and analysis to ignore early and late eluting artifacts
  

  Deconvolution of a representative LC/MS mixture using IntelliXtract 2.0—white section has been selected for further data analysis

  Databasing

  • Improved NMR spectral search options—support for 'Approximate Mode' and 'Search Empty Regions'
  • Search for spectra with no peaks in a specified region
  • Intelligent replication of search results for NMR COSY and TOCSY spectra
  • Improved search for stereo-structures
  • Sequential reaction schemes (drawn in several lines in ChemSketch) may be combined to an overall scheme in a record
  • Redundant reaction arrows in multi-line schemes are recognized correctly
  • The 'SDfile Field with Record ID' field is available in the Export/Import dialog box
  • The term 'project' is replaced with 'record set' for remote Spectrus DB databases
  • Sort values, specific to the root-level structure, in Table view mode
  • Screen and dialog forms
  • Display data from a user table into individual boxes in user-defined screen forms
  • Define the number of decimal places and the scientific format for numeric data in the 'Edit Column Settings' dialog box
  • Server side
  • Capability to implement more than one LDAP server
  • Addition of the 'Roles' panel to the Console

  Reporting

  • Disable/enable the assignment quality for a spectrum in standard report and templates
  • Add the Nucleus, Solvent, Frequency and number of nuclei as default to Header Information for NMR
  

  Additional Header Information labels now available to more easily discern key parameters

  • Added the ability to reorder columns in the Table Options dialog box

  Ease of Use

  • Many ease of use improvements have been made to this product, some of which are listed below:
  • Retention of atom numbering when a structure is duplicated
  • Modify atom numbering in a duplicated structure
  • Display data from a user table into individual boxes in user-defined screen forms
  • Define the number of decimal places and the scientific format for numeric data in the 'Edit Column Settings' dialog box
  • NMR record sets are labelled by 2D technique in the Record Tree subwindow
  • Specify table row height in tables (through the 'Setup Table' dialog box)
  • Improved support for high resolution program icons on 4K monitors