A recent paper in Journal of Cheminformatics describes An automated framework for NMR chemical shift calculations of small organic molecules DOI.
As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem.
Isicle is available from GitHub https://github.com/pnnl/isicle or can be installed using Conda (with required dependencies
conda create -n isicle -c bioconda -c openbabel -c rdkit -c ambermd python=3.6.1 openbabel rdkit ambertools snakemake numpy pandas yaml statsmodels
In addition, ensure the following third-party software is installed and added to your PATH:
ISiCLE is implemented using the Snakemake workflow management system, enabling scalability, portability, provenance, fault tolerance, and automatic job restarting. Snakemake provides a readable Python-based workflow definition language and execution environment that scales, without modification, from single-core workstations to compute clusters through as-available job queuing based on a task dependency graph.
There is more details on Snakemake here.
I've added Isicle to the Spectroscopy Page.
Insensitive (Incredible Nuclear Spin EvolutioN Simulation Tool Intended for Visual Education) is an application to simulate the NMR experiment based on the quantum mechanical density matrix formalism.
It is available for Mac OS X 10.6 and above and iOS 5.1.1 and above. Full details can be found in Concepts In Magnetic Resonance, 2011, 38A (2), 17-24 DOI.
The NMR experiment is usually described by a choice of three models that operate on different levels of abstraction: the vector model, the product operator formalism and the density matrix approach. The transition between these models poses a didactic challenge for teacher and student alike. A new computer program is presented, which simulates a spin system on the textbook level and compares the three approaches, with the possibility to manipulate the system at every step. It closes a gap between NMR education and professional simulation tools. Some algorithms are explained, which are used in the simulation to extract information from the density matrix.
- Able to name molecules with atoms in non-standard valence
- Implement skeletal replacement (“a”) nomenclature for heteropolycyclic ring systems
- Naming of branched ring assemblies
- Correct names of several suffix groups
- Able to name ring assemblies of 3-6 identical cyclic systems
- Precursors m/z values displayed in the MSn extracted spectra title
Full details here http://resources.mestrelab.com/whats-new-mnova-12-0-3/
There is a review of Mnova here
MNova NMR is Mestrelab Research’s NMR analysis program that can be used to quickly view, process and analyse both 1D and 2D spectra, as well as to easily produce publication quality assignments and images. The software can be downloaded from Mestrelab’s website (45-day free trial licences are available).
You can read the review here
I just noticed this mentioned on Twitter and so I've added it to the Mobile Science site.
NMR Solvent peaks is a conveniently-searchable version of the ungainly table of NMR data most organic chemists keep a copy of nearby. Instead of searching through the table for a peak near your unidentified peak, just enter your solvent and the peak's multiplicity and location and you'll have a short list of candidate impurities
There are a number of other NMR apps available
A discussion on the new developments of Xplor-NIH DOI. Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources.
Most of Xplor-NIH's code is now being developed directly in the Python language, and thus is directly accessible for modification by the end-user without recompilation, while code paths which require high performance, such as those executed at every timestep of molecular dynamics, are coded in C++. The Python interface to Xplor-NIH provides an extensible toolbox for developing further functionality. Precompiled packages for most popular Unix and Unix-like operating systems (such as Linux and Mac OS X), as well as documentation and support are available directly from http://nmr.cit.nih.gov/xplor-nih/.
I just came across a publication DOI describing ARIA2 (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation.
ARIA comes as a software library written in the object-oriented programming language Python. The modular design makes it easy for the user to extend and modify the program. The GUI is based on the graphics libraries Tcl/Tk and Tix, interfaced by Python.
ARIA runs on Linux, SGI machines and Mac OS X.
More details can be found on the website http://aria.pasteur.fr.
I've added ARIA2 to the spectroscopy page.
Mnova 11.0.4 (April 2017) has been released, this is another minor release with some bug fixes such as:
- Improved NUS processing algorithm: some 2D experiments that showed unexpected noise artefacts are now processed properly by the improved NUS processing algorithm.
- HSQC stripped transformed in Topspin files loads spectra correctly referenced.
- All shortcuts (Mac version) are now fully functional.
- Agilent LCMS files with negative ion traces are now detected appropriately.
Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for various plugins.
A new update to the popular spectroscopy application Mnova has been announced.
This is a major release that incorporates many new features in NMR, MS, Molecule Editor, Database, Verify and NMRPredict plugins. We have integrated a new PhysChem properties module as well as important enhancements in our Scripting Engine. This version has fixed several bugs.
There is also a page of spectroscopy applications here
The latest update to iNMR version 6.0.0 is available for testing.
Version 6.0.0 requires Mac OS X El Capitan. Today only 60% of Mac users have it. This doesn’t seem the right moment for replacing version 5. In conclusion, version 6 is currently available for a few selected testers only. Anybody can apply. Testers will receive a key that is going to expire in December. The keys for version 5 are not valid for version 6.
iNMR is a high performance NMR analysis program.
See also the spectroscopy page.
Orange NMR has been updated, with more accurate 4J HH couplings prediction and improvements to the peaks table.
Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly).
There are an increasing number of spectroscopy application available for mobile devices.
In order to provide students, researchers and teachers with unlimited access to the best tools for off-line NMR processing, Bruker is making their market leading NMR processing software TopSpin available free of charge for all academic users.
There are also an increasing number of spectroscopy application available for mobile devices.
Orange NMR the iOS app to predict 13C and 1H NMR spectra has been updated, just draw a structure to see its spectrum.
What's New in Version 2.2
iOS 9 multitasking supported.
Optional calculation of MF, MW, Monoisotopic Mass and Elemental Composition added.
Ability to show terminal and all carbons on structure added.
Some minor bugs fixed.
I've just got details of a couple of updates to mobile science apps.
ImageVis3D Mobile is a mobile visualization application one to visualize and share volume and surface data while you are on the go. With ImageVis3D (available for free at www.imagevis3d.com) and ImageVis3D mobile you can transfer your own data directly from the desktop to your mobile device.
What's New in Version 5.1 - new iOS 9 compatible UI (support for Slide Over and Split View) - numerous improvements in the rendering engine - slice viewer visualizes geometry in addition to volume data
Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly). The number of heavy atoms in structure to predict for free is restricted to 12 atoms. This restriction can be removed by purchasing additional licenses.
What's New in Version 2.1. Table of peaks added. Structure drawing enhanced: Touch and drag from bond to draw ring. Double click inside ring to make it aromatic. P and I elements added. Help added.
There are now an increasing number of mobile spectroscopy apps available.
I just added Topspin from Bruker to the list of spectroscopy applications.
Topspin is capable of data processing of 1D and higher dimensional NMR datasets including Fourier transform, window functions, baseline and phase correction, peak picking, integration, line shape analysis (Gauss/Lorentz, dynamic NMR, solids), relaxation and multiplet analysis, spectrum and Fid simulation, printing/plotting, quantification, AU/Python/Macro programming. Optionally NUS processing and small molecule structure elucidation (demo licenses available). For Mac systems the CPU must be capable of executing 64bit-instructions according to “Intel Core 2 Duo” processor type or newer.
Mestrelab Research have just announced the release of the NMR application Mnova 9.1.0. This release fixes several bugs and incorporates many new features on NMR, MS, the Molecule Editor and the GUI.
This new version also includes the release of the Mnova Screen plugin, an automatic tool for the analysis of ligand screening NMR data.
It also includes a long list of bug fixes
The very popular NMR processing tool iNMR has been updated
The new versions 5.3.7 (for Mac) and 2.3.7 (for Windows), both available since June 20, add Covariance NMR to the processing toolbox. This technique creates a symmetric square matrix, starting from any 2-D matrix. The result can look completely different from the starting spectrum, though the information contained is necessarily the same. An example is hsqc-tocy (a kind of hetero-correlation experiment). After normal processing, it has two different axes: a 1-H axis and a 13-C axes. Starting from here you can apply two different kinds of Covariance. The so-called Direct Covariance creates a symmetric H-H matrix. The so-called Indirect Covariance creates a symmetric C-C matrix. Both are homo-correlation plots.
A more detailed description is available here:
This link leads to the pioneer of the method:
There are more spectroscopy applications for Mac OSX here
The very popular NMR application iNMR was updated recently to version 5.3.6. This is a minor update:
When the slider for the first-order phase correction reaches the end-of-the-run, a message appears at the center of the same dialog: "Move This!", meaning that, if you want to go further, it's enough to touch the "fine-coarse" selector.
I’ve updated the spectroscopy page to reflect this
rNMR is an add-on for R.
rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.
I’ve added it to the spectroscopy page.
Learn NMR FID is a great teaching tool to learn the basics of NMR data collection and processing. Use simulated free induction decays (FIDs) and spectra to see apodization, noise and relaxation effects. Move peaks and see how the FID changes. Real and imaginary FIDs prior to and after processing are displayed as is the resultant spectrum after the Fourier transform.
There are more science apps for iOS on the mobilescience site.
I also thought I’d mention this framework that was brought to my attention recently. There is a trend to move massively parallel tasks to the GPU, GPU Image is a framework (BSD license) that simplifies the creation of GPU filters. This framework is built around OpenGL ES 2.0, so it will only work on devices that support this API. This means that this framework will not work on the original iPhone, iPhone 3G, and 1st and 2nd generation iPod touches. All other iOS devices are supported.
Accept-NMR uses an input PDB file, generate symmetry-related copies of a biological molecule of interest, and predict specific user-defined classes of intermolecular contacts between these (using a user-defined distance cutoff). Sort and analyze the resulting contacts, and visualize the results using several visualization schemes in PyMOL. Predict NMR spectra, and specifically the positions of intermolecular contact cross-peaks, based on the contacts predicted and chemical shift table. It is written in Perl, utilizing Gtk2-Perl bindings to provide a cross-platform compatible graphical user interface,
Added to the Spectroscopy page.
Mnova 8.1.1 is a minor release that fixes several bugs in Mnova NMR, MS and the installation process.
Capability to update gamma value of a DOSY spectrum depending on the detected nucleus
- Withewashed view looked wrong in 2D spectra
- Peaks integrated using Peaks method did not get deleted
- Problem copy/pasting a spectrum from Mnova to MS Word as OLE
- Wrong order on assignments reported by Assignments script
- Problems opening a document with deleted molecules and with the compounds table linked to the Page Navigator
There is a page of spectroscopy applications for the Mac here.
I noticed this in the iNMR newsletter.
FREE FOR EVERYBODY Only today 22nd Feb, anybody can ask for a free key for iNMR reader 5. No questions asked. iNMR reader 5 is a 64-bit application that requires Snow Leopard (or a later OS).
A new iNMR reader is available after many months. Instead of restarting from the old version, I have started from the full edition(which includes CPM, DOSY, relaxation times and many other things missing in the old reader), from which I have removed just three commands: Save, Export and Console. In practice it's the iNMR you have appreciated in the past year at a much lower price. Another thing that changes is the key: the old key isn't good. If you already have a license, please wait until March to install this new version and ask for the key. There is no upgrade fee to pay, but remember that a disposable license can't be moved to another computer. You will receive the key valid for your old computer. To ask for a new key, please send the old one back.
The Collaborative Computing Project for NMR was updated last night. No details are available.
The Collaborative Computing Project for NMR (CCPN) is a project that aims to bring together computational aspects of the scientific community involved in NMR spectroscopy of biological molecules, especially those who work in the field of protein NMR. The CcpNmr software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model. Between programs written by the CCPN, external contributions, and ‘outside’ programs integrated with the data model, it is the intention to provide one suite of programs to carry out all tasks needed in macromolecular NMR spectroscopy. The nature of the data model guarantees that any other program or suite that interfaces with the data model can be used alongside or instead of the CcpNmr suite.
CCPN will be giving a demonstration at the EUROMAR conference during the first week of July (see http://www.euromar.org/). They will also be handing out CDs with the latest release.
There is a page of spectroscopy applications for Mac OS X here.
The latest Mac version of iNMR is 5.2.4, released today. Due to popular demand it restores the slider for zero-order phase correction, which reappears side-by-side with the knob that has been in its place for a whole year. Their function is equivalent. This seems to be a case where it's better to have redundant controls.
Just got this message I thought I’d pass on.
The iNMR reader will remain at €39 for another 5 days only. Staring from Tuesday, it will return to its old (historical) price of € 50. The same applies for the student promo and the laptop extensions, everything that now costs €39 will cost €50 starting from next Tuesday.
iNMR is the only NMR software expressly written for Mac OS X, it uses Mac technologies and is tightly integrated with Mac OS X.
There is a listing of spectroscopy applications here.
After many months of beta testing the latest version of the popular Mac dedicated NMR spectroscopy application iNMR5 has been released. The key new features are tabulated below.
- Version 5 requires a 64-bit Intel chip and Snow Leopard. Version 4 is 32-bit Universal Binary and requires Tiger.
- real-time dragging
- When you drag the margins of the plot, or the integrals, or most of the objects, the plot is continuously updated. Overlay manager
- The Overlay Manager becomes non-modal and can be enlarged to show the full path of the individual documents. Sorting the overlays is simpler and more transparent.
- Manual phase correction
- The zero-order correction is controlled by a knob that never reaches the end of the run. The fine-coarse selector has many more stops. The phase panel is more compact.
- Other dialogs
- “Units and Scales” and “Colors and Levels” change the corresponding plots as soon as you click into a control. The Preferences dialog includes a “Preview” button. The color panel is no more modal. When the open dialog is open, the corresponding menu item isn't dimmed anymore. The console is more compact than in the past, but can be enlarged at will.
- Fit to overlay
- Fitting a simulated spin system is visibly faster.
- The new cursors are more specific. The horizontal palette has a single row of buttons.
- Info tool
- The interpolator is faster, more predictable and more reliable.
- The visual effect of the command ”New Page” is realistic.
- The printed area is no more centered and no more clipped.
- Shows an estimate of the T1.
Depending on your existing license you may be eligible for a free upgrade, for other users there is a small upgrade fee.
There is a list of spectroscopy applications for the Mac here