Macs in Chemistry

Insanely Great Science

Mnova 14 is released

 

Mnova 14 has just been released this includes new features in most plugins: NMR, MS, NMRPredict, Screen, DB, Structure Elucidation, and also some new features.

We have added a new module, Mnova ElViS, for Electronic and Vibrational Spectroscopies, as we continue to add new analytical data that can be read, processed, archived and reported using Mnova. For those working on regulated markets and having to comply with 21 CFR Part 11 or GxP rules, Mnova 14 includes brand new Audit Trail and Digital signatures features


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An automated framework for NMR chemical shift calculations of small organic molecules

 

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:

cxcalc (license required from ChemAxon, Marvin)
NWChem http://www.nwchem-sw.org/index.php/Download.

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.


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Updated INSENSITIVE

 

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.

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Mnova 12.0.3 (minor release)

 

Update

IUPAC Name

  • 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

MS

  • 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


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A Review of MNova NMR

 

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

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NMR solvent peaks

 

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 is also a web-based version and a twitter feed for submitting bugs and finding out about updates.

There are a number of other NMR apps available


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Xplor-NIH for molecular structure determination from NMR

 

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/.


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ARIA2 (Ambiguous Restraints for Iterative Assignment)

 

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.


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Mnova updated

 

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.


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Mnova 11 released

 

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


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iNMR test release

 

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.

fig_01

See also the spectroscopy page.


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Orange NMR Updated

 

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.


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Topspin for NMR

 

I've added Topspin to the Spectroscopy page, this is an NMR processing package from Bruker. Looks to be free for academics.

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.


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Orange NMR Updated

 

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.

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ImageVis3D and Orange NMR updates

 

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

imagevis1

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.

orangenmr

There are now an increasing number of mobile spectroscopy apps available.

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Topspin

 

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.

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Mnova 9.1.0 released

 

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


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iNMR has been updated

 

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:

http://nmr-analysis.blogspot.it/2008/10/introduction-to-covariance-nmr.html

This link leads to the pioneer of the method:

https://research.chemistry.ohio-state.edu/bruschweiler/web-servers/370-2/

There are more spectroscopy applications for Mac OSX here

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iNMR 5.3.6 released

 

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

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rNMR added to spectroscopy page

 

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.

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Learn NMR FID

 

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.

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ACCEPT-NMR

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.