Macs in Chemistry

Insanely Great Science

Chemistry

Learning Carbons VR

 

Virtual reality apps for the iPhone are becoming more common and the latest is Learning Carbons VR. This is an educational virtual reality (VR) app where students can learn about the various forms of carbon.

screen520x924

For many of these types of apps you will need a VR Google Cardboard headset with head straps and a Bluetooth gamepad (MFi certified - made for iPhone).


Comments

iScienceSearch

 

iScienceSearch is an internet search portal for scientists that allows you to perform a search across multiple data sources with a single query. I wrote a review a while back but it has undergone several updates since then and has been significantly expanded.

iScienceSearch allows both text and structure based searches, but the really interesting thing is that when you do a search using a single query item it automatically searchs in the background for other synonyms, structure, CAS Registry Number, InChI etc.

The screenshot below (click to enlarge) was generated using a structure-based query, as you can see the search results also include the results from text-based queries using synonyms. The filters on the left-hand side allow you to sort and filter the results to allow you to focus on the most relevant information.

isearch

The searching is free and requires no registration.


Comments

GPView Wave Function Analysis and Visualization

 

The GPView program is a C++ package for wave function analysis and visualization.

It is developed and maintained by Tian Shi and Ping Wang Ref](http://arxiv.org/abs/1602.07302)

In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density. The visualization module of GPView can display molecular and electronic (iso-surfaces) structures. It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files. There are also other utilities help to extract and process the output of quantum chemistry calculations. The GPView provides full graphic user interface (GUI) which makes it very easy to use.

22


Comments

Chemistry Dictionary

 

I had the SSD fail on my MacPro and so I needed to reinstall a variety of programs etc. and I took the opportunity to update a number of things. One thing I thought I'd mention is the custom chemistry dictionary, once installed it is available for all Mac OSX applications.

Comments

Chemistry related LaTeX packages

 

LaTeX is used for the markup and publication of scientific documents, it is particularly popular in mathematics, physics, computer science. I know some chemists use it so I thought I'd mention this resource of Chemistry LaTeX packages. It includes packages for most of the major Chemistry journals.

Comments

ChemSpider website update

 

The ChemSpider Website has been updated.

ChemSpider is a free chemical structure database providing fast text and structure search access to over 34 million structures from hundreds of data sources.

The new website has a much cleaner look and perhaps more importantly is now viewable on the smaller screens of mobile devices. This is achieved by collapsing the individual page record into a tabbed view to reduce scrolling on long records and by eliminating the java based plugins and replacing them with javascript versions.

Comments

Chemical Names Spell Checker

 

The secret of a good iOS app is often finding a niche that is both useful but does not require lots of functionality or screen real estate. Chemical Names Spell Checker ticks both boxes nicely.

The Chemical Names Spell Checker provides chemical name spell checking and chemical name synonym look-up. Data are provided by the ChemSpell service that contains more than 1.3 million chemical names related to organic, inorganic, pharmaceutical, toxicological, and environmental health topics.

Once checked the name can be copied to the clipboard for use in another application.

The ChemSpell Web Service API is free of charge. Neither registration or licensing is required. This app nicely underlines the power of chemistry web services.

Well worth all chemists having on their iPhone or iPad.

photo

Comments

Molecule database framework

 

I thought I would highlight a recent publication I read in Journal of Cheminformatics “Molecule database framework: a framework for creating database applications with chemical structure search capability” Journal of Cheminformatics 2013, 5:48 DOI.

From the abstract

Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:Chemical structure searches combined with property searches. Support for multi-component compounds (mixtures) mport and export of SD-files. Optional security (authorization). For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.

While not a drag and drop solution it provides a means to create your own personal chemically searchable database.

Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

Comments

Teaching chemistry Apps

I was recently sent a link to an educational chemistry app Chemistry By Design: Learning by Using the Graphical Language of Organic Chemistry by University of Arizona. I had a quick look at it and it seems quite an interesting way to learn organic synthesis. There around a thousand synthetic routes to explore and it seems to cover a wide range of synthetic organic chemistry, the synthetic targets include natural products and pharmaceuticals. I was particularly delighted to see that Woodward’s 1954 synthesis of strychnine is included.

photo

Whilst looking it up I noticed several other educational chemistry apps, Organic Chemistry Essentials, Organic Chemistry FlashCards. What is clear is it would be very useful to have a science category to help find these sort of applications.

There is a list of mobile science apps here.



Comments

ChemSpider and spectral information

There was an interesting entry on the ChemSpider blog this week, apparently they are starting to capture spectral information

The RSC now encourages authors for several of our journals to supply extra information, structures and spectra in their original file formats – which are attached to the article as supplementary information. Already we’ve seen several submissions of data that we have incorporated into ChemSpider records, both enriching the ChemSpider database and also showcasing the research of these authors through their publications. In this way, the RSC hopes to encourage the addition of reusable data files to the research paper as the start of its efforts to promote increased data sharing within chemical science research. In a few short weeks we’ve received a number of submissions from authors that include key chemical structures as mol files and in some cases extra data including 1H and 13C NMR spectra as well as UV and IR spectra.

As you can see from this entry ChemSpider ID: 28945607 there are spectra associated with this record. unfortunately at the moment you can’t view them in Safari because the javascript looks for Internet Explorer and Firefox. Fortunately you can get around this by changing the user agent from the “Develop” menu in Safari.

temp1

Once you have done that you can see the spectra displayed using a Java applet.

chemspiderSpec



Comments

Software from Open Chemistry

The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.

It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for more details “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform” DOI.

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

The second component of the suite is MoleQueue, a new tool to manage and execute computational tools either locally or on a remote machine or cluster. The messages transmitted between the client and server are formatted use the increasingly popular JavaScript Object Notation (JSON) format and adhere to the JSON-RPC 2.0 specification.

The final element of this first beta release is a chemically aware database MongoChem built on MongoDB intended to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It uses Open Babel to provide the cheminformatics input

There is a slide presentation describing the project in more detail here/



Comments

Green Solvents updated

The latest version of Green Solvents (1.1) is now available on the AppStore. Worth noting is the fact that the app is now sponsored by the Royal Society of Chemistry.

There is a page of mobile science applications here.



Comments

Displaying structures using JSmol and GLMol

I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.



Comments

SPRESImobile updated

With SPRESImobile, a wealth of chemical reaction information is readily available at your fingertips from a mobile device (iPhone, iPad). You can search the entire ChemReact database easily with this highly intuitive app

There is a page of mobile science applications here.



Comments

Review of iScienceSearch

I’ve just published a review of iScienceSearch (iSS) an Internet search engine for chemists, it supports both chemical structure and text-based searches.

In addition to searching a wide range of databases it provides access to Chemicalize.org which gives access to chemical properties, and PASS (Prediction of Activity Spectra for Substances) to evaluate chemical structures.

There is a growing collection of software reviews here.



Comments

Added ChemEquate to alphabetical listing

ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.

FEATURES:

  • Create clear and professional looking chemical equations
  • Powerful tool for balancing chemical equations instantly
  • Export beautifully formatted equations to other applications
  • Quickly calculate the molecular weight of any compound
  • Save equations to Favorites list for future use


Comments

Chem+ is a chemical reference for your iPad

Chem+ is a chemical reference for your iPad. Databases Include: * NIOSH Pocket Guide (NPG) * Immediately Dangerous to Life and Health (IDLH) * Toxicity (TOX) * the Emergency Response Guidebook (ERG)

Comments

SPRESImobile added

SPRESImobile provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. SPRESImobile allows searching by name and structure queries, exact, substructure and All-in-one (Flex) search. There is a list of iOS applications on the mobile science page.

Comments

OLN Chemistry LabNotebook

Chemistry LabNotebook Read More...
Comments

Reaction101

Reaction App for iPhone/iPad etc. Read More...
Comments

iPhone Apps for Chemistry

Updated list of Chemistry application for the iPhone (and I assume iPad?). Read More...
Comments

iPhone Apps

A collection of iPhone apps that might be of interest. Read More...
Comments

Distillation Designer

Distillation Designer provides the simple McCabe-Thiele method for designing binary distillation systems. Read More...
Comments

Chemistry Dictionary

Chemistry dictionary in iWork format. Read More...
Comments

3D Animations of Organic Reactions

Visualisation of a number of organic chemistry reactions. Read More...
Comments

ChemAxon

I had a message from ChemAxon saying they had updated some of their products and I thought it might be worth a summary of their wares. Whilst Java based everything works fine on a Mac and note:-
  1. Instant JChem Personal (an new OS independent desktop application for working with chemical and non chemical data) and Marvin, a chemical editor and viewer suite are free for all users
  2. All products are free for academic teachers and researchers - including the enterprise edition of Instant JChem
  3. Most products are free for freely accessible, non commercial websites
Read More...
Comments

GSAS

Latest version of GSAS is now available for Intel Macs. Read More...
Comments

Support for Quicklook and coverflow for ChemDraw files

I sent in a request to Cambridgesoft asking them if it would be possible to support Quicklook and coverflow visualization of Chemdraw files

Read More...
Comments

Substructure searchable database

Creating a sub-structure searchable chemical database. Read More...
Comments

PyMOL and Plugins

Using PyMOL Plugins under Mac OS X

Read More...
Comments