What's New in ACD/NMR Workbook Suite

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 [+]

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 [+]

Chromatography [+]

Optical/Curve [+]

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: [+]

• 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
• Version 2016.1

  Mixture Analysis Tools

  • Advanced mixture analysis search tools for 1D NMR spectra
  

  The layout above displays a process to support the rapid identification of multiple components from a relevant database, or set of databases, in the NMR spectrum of a mixture. Here, the user can select any number of spectral hits from the DB, adjust their positions relative to the query spectrum, adjust individual scales, and change peak widths until as many hits as possible are identified, and the residual is as low as possible. When the cursor is hovering on "more info" on the Spectra Comparison dialog box, the software displays a tool-tip with a list of capabilities to manage spectra display in the search result series.

  

  Note that at any time it is possible to create Sum and Residual curves as separate 1D spectra for further inspection.

  When the user sees that the hit spectra displayed in the search result series explains all desired peaks in the query spectrum (for example, the residual curve for that component approaches zero) it is possible to transfer all multiplets, structures and assignments from the displayed hit (considered to be pure component spectra) to the query spectrum (press "Replicate and Close" button). Note that there is an option to tell the software how the components in query or mixture spectrum should be named (Replication Parameters).

  

  Shown above is a typical layout after replication. The query spectrum is active and contains multiplets with assignments from all transferred structures. The assignment to components is encoded by colors (adjustable in the table of components) of multiplet labels and integrals. The colors of "pure component" spectra which are original DB hits are the same as component colors in the Table of Components. The first component is always named as "Query" (user-editable) to account for possible unexplained signals.

  • Improvements in mixture analysis workflows for 1D NMR spectra
  • When a user has a spectrum of a mixture and knows which signals in it came from which compounds, the software enables the user to set signals and assign them to various components, along with structures
  
  • A "Pure Component Spectrum" can be created, including only those signals which belong to multiplets assigned to the appropriate component. By looking at the difference between the original spectrum and the sum of all pure component spectra, unexplained signals in mixtures can be quickly tracked.
  

  Data Analysis

  • Reference Deconvolution—use experimental peak shape to determine proper parameters for peak-fitting.
  • "Staggering" integration—Define an integral range on spectrum, then define sub-ranges within original range
  • Users can monitor relative concentrations of several isomers or rotamers while keeping total signal normalized to the required number of protons
  • "Autoscale Zoomed Region" for spectral similarity searches, which prevents oversized peaks outside the search region from obscuring the search results
  • Improvements to DOSY analysis:
  • Calculate the diffusion coefficient over a spectrum range using the Brush tool, and evaluate DOSY profile. Quickly see the D values for signals of interest and evaluate the diffusion profile.
  • This profile is deemed "not optimal" due to a low dynamic range in the measurements
  
  • Calculate average slice over a user-selected region in the DOSY spectrum
  • Seamless workflow for DOSY experiments that were not automatically recognized
  • For cases when DOSY data was imported as a 1D series, the conversion is simplified
  
  • User-editable little delta (d) and big delta (D) values for Bruker data in DOSY options dialog
  • Updated solvent, water and impurity detection
  • A new "water range" column for 1D spectra, Residuals columns for all spectra, and the ability to export/import the whole table to share its content with other users
  • The solvent detection options have been expanded:
  • The "Create New Component" option works for 1D spectra and assigns a signal for each detected solvent or impurity to new component
  • If "Create Dark Region" has been checked, the same compound signals in 2D spectra get Darkregioned
  • "Apply to Project" directs the software to act on all spectra included in the project
  • Clearer visualization of calculated chemical shifts calculated by HOSE-code or Neural Net methods
  • Option to detect solvent signals in multiplet detection options
  • Improved calculation algorithms for the automated threshold detection of phase-sensitive 2D spectra
  • Separation of overlapped multiplets in ¹H 1D NMR spectrum when all components are clearly separated in HSQC
  • The decimal places for chemical shift and coupling constant in the table of multiplets are now remembered separately for ¹H, ¹³C, ¹⁹F, ³¹P and ¹⁵N nuclei
  • The Verify macro command (applicable to ¹H or ¹³C data) has been replaced by Verify1DNMR (¹H, ¹³C, ¹⁹F, ³¹P and ¹⁵N) for 1D spectra, which ensures that results are identical between scripting and the graphical user interface (GUI)
  • Reverse the order of spectra in a series
  • Display multiplets in the Table of Spectral Data using the chemical shift range instead of just standard multiplet format
  • Ignore dark regions in database/query spectra for Sum and difference curves
  • Custom coloring of correlation arrows for different 2D NMR experiments
  • Improved calculation and display of ¹H decoupled ¹⁵N, ¹⁹F or ³¹P spectra
  
  • Assignment from NMR projects can be updated in C+H and XNMR user databases simultaneously

  Data Import/Export

  • Integral ranges can now be read from vendor files (Bruker TopSpin and Agilent/Varian only)
  • Support for the benchtop Oxford Instruments data format
  • Support for ThermoFisher picoSpin 1D format—import single spectra and collecting in series, taking date stamp into account.
  • Forward Linear Prediction for raw TOPSPIN 2D data is automatically applied—This doubles the number of data points to make these files appear more as they would when processed in TopSpin
  • Data initialization and settings for phase-sensitive HMBC are handled and remembered properly, with F2=Magnitude, F1=Phase.
  • Export assigned NMR spectral and project data to an SDfile, including structure and assigned chemical shifts in multiple formats

  Reporting

  • Interactive zoom for insets in 2D spectra reports (previously only for 1D data)
  • Additional control options for tuning the 1D-curve appearance in visualization and reporting of 2D NMR spectra
  
  • Export and report only the assigned shifts in Spectral Data Table, if desired.
  • Load Multiplet Report Journal Templates from a user defined folder
  • Control the level of detail in the multiplet report, showing the detailed coupling pattern either for all multiplets, or only those with explicitly defined coupling patterns.
  • Custom correlation arrow coloration legend in the reporting template

  Databasing

  Visualization

  • View error bars on graph plots

  For record/components data, data from tables (including data from spectra tables)

  
  • The selected spectrum table remains selected when navigating between spectra and/or records.
  • Display all spectra and chromatograms from a record in overlay mode
  
  • Display spectra and chromatogram chemical structures in Tile mode using custom or default screen forms.
  • Pictures from tables and documents in linked records can be displayed using Object Linking and Embedding (OLE) control.

  Ease of Use

  • Export chemical structures to Percepta
  • Export all chemical structures from a record, with option to include their respective data fields. Can be used for current record, or for all records in a search result list
  • Notes from the record root level can remain displayed while selecting different structures

  Utilizes the option "Show Data from the Record Root Only"

  
  • Options to Expand record tree by levels, and show spectra names in record tree control context menu

  Reporting

  • Create templated reports for either the selected record component, or the whole database record
  • New template objects and options for reporting data of record root, Spectrus project (NMR and LC/MS/Metabolites), sample and parent components of a record

  Screen Form Editor

  • Scrollbars added for large form-editing windows
  • Define controls for record root, Spectrus project, and sample components in popup form controls
  
  • Manage record tree nodes by embedding scripts into screen forms
  • By attaching a script to the record tree control, it will run when a user clicks on the tree node. It is possible to enumerate nodes of control, hide/show, expand/collapse any node, change auto labeling options, switch on/off nodes with details through the script
  • Utilize *MOLECULE control within popup forms, with a variety of context-based options

  User can copy/paste existing chemical structures, or create new components in a record with or without chemical structures

  

  New Features for Other Techniques

  ACD/NMR Workbook Suite includes multi-technique processing and analysis capabilities; the latest version also includes new features for other techniques such as LC-MS.

  Data Analysis

  • Subtract Baseline option, with a dedicated button, which is displayed in Peak Picking mode
  • A consistent peak detection/integration algorithm for flat chromatograms and hyphenated (i.e., LC/MS, GC/MS, LC/DAD) data
  • "All tRs" column in the Table of Components, showing the retention times of peaks from all traces corresponding to the current component.
  
  • Peak Picking macro with additional parameters.
  
  • Peak areas are displayed and editable in extracted ion chromatogram (XIC)
  
  • Edit Markush structures within the Structure Window
  • Select atoms and groups by shift-click, or using the lasso tool. Easily add/delete or modify Markush fragments
  
  • Edits to names within Table of Components and Table of Peaks are synchronized—an edit in one location will be automatically updated everywhere else
  • Manual Peak Detection is synchronized across all chromatograms inside a data set

  Improved Reporting

  • Define custom color schemes for report templates
  • Edit the order of appearance of components in an LC-MS report
  • Create LC-MS reports using the Zoom Region around the mass value corresponding to the molecular ion in the Table of Components
  
  • Option to report a component mass spectrum as a Raw Spectrum, if spectrum combining was not completed
  

  Data Import/Export

  Click to Expand

  • Instrument-dependent profiles available for xC/UV/MS data import.
  • Import tR Window values from *.sd files to Target Ions or Ion Presence lists
  • Improvements to import of XCalibur data (Thermo Fisher Scientific)
  • Import all relevant information for HPLC instrument and method setup (Sample Name, Operator ID, Injection Volume, and Instrument Name)
  • Import Injection Volume and Sample ID to Chromatogram Parameters
  • Import metadata from Bruker LC-MS sampleinfo.xml into Spectrum Parameters

  General Features

  • Support of Thermo Scientific's Chromeleon 7 software via 'connect-to' functionality
  • Improved and simplified export of data from Dionex Chromeleon (Thermo Fisher Scientific) into ACD/Labs environment with the ACD/Labs Chromleon add-on
  • Improved visualization of series
  • Choose to view peak areas for either selected, or all chromatograms in a series
• View What's New in the previous version

  Software Update: Version 2015, Pack 2

  Click to Expand

  Non-Uniform Sampling (NUS)

  • Process raw NMR data acquired with non-uniform sampling (NUS support for Bruker and Agilent data)

  DOSY Analysis*

  • Capability to display and report processed DOSY spectra in logarithm scale
  • Use of peak area of the common signals for DOSY calculations to better discriminate overlapping signals
  

  Standard threshold-based processed DOSY spectrum. Two overlapped signals with different D-values show a merged peak in the DOSY spectrum

  

  DOSY spectrum based on fitted peak areas of signals shows 3 distinct signals

  

  The original DOSY set as a series of 1D NMR with fitted peaks in blue and the residual in red

  • Ignore "dark region" signals for DOSY calculation

  Click to Expand

  *Developments partially funded by the PharmaSea project www.pharma-sea.eu.

  NMR Spectrum Assignment and Visualization

  • Use advanced slice management for 2D display (2D NMR and DOSY) to streamline reporting
  • The slices setup is now possible in the standard report setup dialog box, as well as in report templates under the Slices tab for 2D NMR spectrum
  • Quickly Merge multiplets in ¹³C NMR spectra into a single multiplet with couplings
  • Automatic identification of ambiguous structural assignments when working only with 1D NMR
  • Simulate ¹H NMR spectra from a multiplet report to compare experimental and published data
  

  Experimental ¹H NMR spectrum

  

  Recreated ¹H NMR spectrum from a multiplet report

  • Obtain simulated ¹³C-like spectra as a Merged Stick Projection from 2D data
  • Synchronize the workflow of active tools (e.g., apply the action of phasing on the current spectrum to all other open 1D and 2D NMR spectra)
  • Looseness factor for peak search in Spectrus DB is now nucleus-dependent—default values are 0.05 ppm for ¹H-spectra, 1 ppm for ¹³C, and 5ppm for all other nuclei
  • Display complete assignment notation (e.g., ', '', ax, eq, etc.) in the H Atom# or H Label columns of the Spectral Data table
  • Phase only zoomed-in regions of 1D spectrum
  • Select either HOSE Code or Neural Network algorithm for the ³¹P, ¹⁹F, and ¹⁵N NMR prediction calculations, as previously possible for ¹H and ¹³C NMR spectra
  • Automatic storage of Varian/Agilent "text" and Bruker "title" files in User Notes
  • Display uncompleted correlations on structures to review a project for peaks which have only been partially assigned
  • Display nucleus information on 2D NMR spectra
  
  • Improvements to the Clustering Add-On
  

  Click to Expand

  Reporting Template Options

  • Auto-scale 1D NMR spectra along the vertical axis
  • There are advanced sorting options for the tables in the report

  Databasing & Knowledge Management

  • Automatic recognition of textual data associated with molecular structures/schemes when adding/updating the structures, reactions, and reaction schemes from the ChemSketch window
  • Extended capabilities for stoichiometric calculations for reactions
  • Merge spectral data on import
  • Add/Update molecular structures with ambiguous atoms and/or bonds
  • Improve speed performance and reduce disk space by compressing spectral data in the database
  • Capability to implement different data input forms for different spectral data types when adding/updating database
  • Support for the Unicode Standard (text and characters from all major writing systems)
  • Support for export of spectral data and parameters into SDF, TXT, and CSV file
  • Improved data visualization
  • Set up a template to view custom regions of spectra
  • Autofit column width in User Tables and Spectrum/Chromatogram Tables Screen and data input forms
  • New Default (One Record) screen form for visualization of records in the database
  • Improvements to search functionality
  • Implementation of calendar functionality for date queries
  • Global metadata searching across all levels in the database
  
  • Expanded capabilities when using Screen Forms
  • Select spectra for display based on spectral parameters
  • Specify field label background colors
  • Capability to enforce validation of data in text fields—ability to modify the warning message

  Version 2014 to Version 2015

  Quantitation and Reaction Monitoring

  A number of improvements and new features are added to aid phasing, baseline correction and quantitative measurements.

  • Apply various signal threshold options to DOSY calculations and report easily
  • Use existing reference signals to calibrate calculations—reaction rate may be based on absolute signal
  values
  • Calculate pKa based on NMR titration series
  • Improvements to tools for working with series of spectra
  • Align Spectra in a series based on peaks of interest
  
  • Better visualization of data with adjustable fading of inactive spectra
  
  • Perform peak-fitting on series of spectra
  
  • Group peaks to calculate the sum of their areas. This is useful for peak quantitation, to track signals that overlap, for fitting any complex peak shape by several analytical functions, etc.
  

  NMR Spectrum Assignment

  • Assign multiple atoms to a multiplet (e.g., to include rotamers)
  • Enhanced Peak Picking:
  • Set one shared peak in HMQC/HSQC for multiple signals in the F1 dimension
  • Select linked peaks when the corresponding 1D NMR high resolution spectrum is present in the project
  • Projects perform a Solvent Consistency check and automatically provide a flag to the user if inconsistencies are found
  
  • Synchronized Peak Picking (SyncPP) includes more flexibility for datasets with especially strong overlap in 1D NMR spectra
  

  Three options now exist: on for all spectra in a project (default), on just for 1D and HSQC NMR spectra, and turned off completely. The 1D & HSQC NMR option is recommended when users create and assign signals serially primarily in 1D NMR spectra. After completing PP and assignment it is enough to perform automatic PP in each remaining spectrum.

  Improvements to Databasing Capabilities

  • 1D NMR Mixture search added to local and remote Spectrus databases
  
  • Improvements to creating/updating records to the database
  • Copy metadata from previous record when adding NMR projects
  • All chemical structures attached to a spectrum are stored in the database (e.g., assignment of multiple proposed structures can be stored in the database record)—particularly beneficial for structure verification/mixture analysis
  • Expanded search capabilities—search by screenform and search spectrum user data directly from the interface
  • Improved handling of records in the database
  • Specify where data is linked (record level, spectral data or structures) when entering meta data via pop-up forms
  • Select node for attachment of NMR projects in ACD/NMR Workbook Suite
  • Database Permissions
  • Option to restrict users from switching to Update Mode
  • Improved protection controls for local databases