ACD/Structure Elucidator Suite What's New

Version 2017.1

General Enhancements

• After structure elucidation, the software may now generate and evaluate all possible stereoisomers
• Stereoisomer ranking is based on HOSE code predictions of the atom chemical shifts and comparison with experimental
• New, m/z indexed, databases of PubChem structures with predicted ¹³C shift (Neural Network) for more rapid searching of over 90 million structures. Together with an enhanced ChemSpider ¹³C database with 48 million structures, allowing for faster dereplication and unique fragment discovery

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

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New Molecular 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:


Molecules from the Table of Components can be synced with other datasets

• 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.

Technique-Specific Processing & Analysis

NMR

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• Calculate Pure Shift ¹H NMR spectra to help assignments in overlapping, complex spectra


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 T1ρ (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
• 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

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
• Added Hybridization and Heteroatom columns to the merged ¹³C table

Databasing

• New databases of PubChem structures with predicted ¹³C shift (Neural Network) for more rapid indexed searching of over 90 million structures allowing for faster dereplication and unique fragment discovery
• 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

Ease of Use

• 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

• Version 2015 to Version 2016.1

  Structure ELucidation Features

  • Errors preventing the Structure Elucidation process are now displayed in the spectral data tree, such as no MF (molecular formula), no peaks in data. Improper phase inversion for multiplicity-edited HSQC is recognized and flagged.
  
  • Merged ¹H, ¹³C, etc., spectra are now placed in the "NMR summary" section of spectral data tree.
  • During structure generation, the software immediately reports when any proposed structure(s) is generated rather than waiting until the procedure is completed
  • The list of proposed structure list from an elucidation can be saved to a user database.
  • The current structure list and/or user database can be used to generate structural fragments, and the result saved to another user database.

  NMR Analysis

  • 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.
  
  • 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 ¹⁵ 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

  LC-MS Analysis

  • A consistent peak detection/integration algorithm for flat chromatograms and hyphenated (i.e., LC/MS, GC/MS, LC/DAD) data
  • New Subtract Baseline option—with a dedicated button displayed in Peak Picking mode
  • Retention times of peaks from all traces corresponding to the current component can be displayed in the Table of Components
  • New Peak Picking macro with additional parameters
  • 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
  • Merge single chromatograms into an existing LC/UV/MS project using drag-and-drop functionality
  • 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

  
  • Improved visualization of series
  • Choose to view peak areas for either selected, or all chromatograms in a series

  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
  • Instrument-dependent profiles available for LC/UV/MS data import
  • Import tR Window values from *.sd files to Target Ions or Ion Presence lists
  • 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
  • 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
  • Improvements to Empower Add-on—all channels/results corresponding to the same injection are combined into a single LC/UV/MS dataset

  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.
  • Define custom color schemes for report templates, including correlation arrow coloration
  • 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
  

  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
  
• View What's New in the previous version

  With the release of ACD/Structure Elucidator Suite version 2014, the software has been fully integrated with ACD/Structure Elucidator Suite, enabling drastically streamlined elucidation workflows. Data preparation is enhanced by the assignment and interpretation algorithms of NMR Workbook Suite, and there is no need to change software applications to initiate de novo structure elucidation, spectral dereplication, or advanced structure verification.

  Click to view a sample elucidation workflow