Interactive Computer Models for Analytical Chemistry Instruction

Interactive Computer Models for Analytical Chemistry Instruction

Chemistry online Resources

Link - http://terpconnect.umd.edu/~toh/models/

"This is a collection of free, downloadable, interactive computer models and simulations of common analytical instruments and techniques. Most have a point-and-click interface; you click buttons and drag sliders to control variables and the model responds dynamically, often much faster than real time. I originally designed these models for students in my courses in Instrumental Analysis (an upper-division undergraduate laboratory course) and Spectrochemical Methods (a graduate lecture course). They were designed to be used by individual students either as homework assignments, for in-class use in a computer lab environment, in the laboratory for the analysis of student-generated data, or as a temporary replacement for unavailable laboratory equipment. They can also be used by the instructor in lecture-demonstration environments. Student assignment handouts and suggested experiments are attached to most of them. The mathematical basis for each model is described, including all cell definitions and equations. These spreadsheets make extensive use of named cells (variables), which makes the equations easier to understand (as compared to row-colunm references)'[1].
1.http://terpconnect.umd.edu/~toh/models/

Analytical Inorganic Organic Physical

World Best Free Online Courses, Visit and Learn

Free online Chemistry Courses

XRayView

XRayView - Chemistry Software

Chemistry online Resources

XRayView, G. N. Phillips Lab, supported by W. M. Keck Foundation. a Teaching Aid for X-ray Crystallography

XRayView : A Virtual X-Ray Crystallography Laboratory

Link - http://phillips-lab.biochem.wisc.edu/software.html

"This software uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.

XRayView is designed with "user-friendliness" in mind, using Motif style, pull-down menus to control the program. Many of the experiences of using real X-ray diffraction equipment to examine crystalline diffraction can be simulated. Exercises are available on-line to guide the users through typical X-ray diffraction experiments"[1].
1.http://phillips-lab.biochem.wisc.edu/software.html

XRayPlot

Link - http://phillips-lab.biochem.wisc.edu/software.html

"XRayPlot allows plots of arbitrary planes of diffraction data given the space group symmetry, the unit cell dimensions, and a list of intensities or structure factor amplitudes with their associated hkl indices"[1].
1.http://phillips-lab.biochem.wisc.edu/software.html

Analytical Inorganic Organic Physical

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Free online Chemistry Courses

Mathematical techniques in Powder diffraction

Mathematical techniques in Powder diffraction

Chemistry online Resources

Pepinsky's Machine, N. M. Glykos. A teaching aid to illustrate the principles and the application of the Fourier series in crystallography

Link - http://utopia.duth.gr/~glykos/pepinsky.html

• "Pepinsky's Machine is free software and you are encouraged to use, copy, modify, and distribute both the program and its documentation (PDF, 1.1 MBytes).


• If you ever need to reference this program in your publications (but note that you are not required -at least by me- to do so), please use the following citation : Glykos, N.M. (1999), "Pepinsky's Machine : an interactive, graphics-based Fourier synthesis program with applications in teaching and research.", J. Appl. Crystallogr., 32, 821-823.
  Electronic reprint (660 KBytes) : Local copy, or directly from J. Appl. Cryst. 32, 821-823, FREE ITEM, Copyright © International Union of Crystallography"[1].
  

1.http://utopia.duth.gr/~glykos/pepinsky.html

Statistical Descriptors in Crystallography, D. Schwarzenbach et al. Reports of a working group appointed by the IUCr Nomenclature Committee

Link - http://ww1.iucr.org/comm/cnom/statdes/preface.html

This document provides an authoratitive statement of the use of statistics in crystallography. The document contains a Glossary of statistical terms and sections on the following topics:

• Basic notions
• Uncertainty of measurement
• Refinement
• Refinement on I, |F|² or |F|?
• Defects in the model
• Weighting schemes
• Recommendations

Analytical Inorganic Organic Physical

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Free online Chemistry Courses

Symmetry

Symmetry

Chemistry online Resources

Escher Web Sketch, W. Hardecker and G. Chapuis. A program for drawing 2D periodic patterns with a web browser.

Link - http://www.iucr.org/education/resources/edu_2008_2

Escher Web Sketch allows you to draw repeating patterns. You can select the symmetry of the patterns by clicking on one of the icons in the bar above the drawing area. The drawing tools are selected from the icon bar under the drawing area. You can also change the pattern size and placement with the Modify cell button. The right hand side of the drawing area is reserved for each drawing tool's usage. Typically it changes the pen size and color.

An Interactive Course on Symmetry and Analysis of Crystal Structure by Diffraction, G. Chapuis and W. Hardecker.
Link - http://escher.epfl.ch/eCrystallography/1.html

An interactive course, freely available on Internet for the presentation of basic crystallography concepts

Discovering Symmetry, Nicolas Schoeni and Gervais Chapuis. An applet to discover the point group symmetry of platonic and other polyhedra

Link - http://www.iucr.org/education/resources/edu_2008_54

Point groups and Bravais Lattices, Marc De Graef.

Link - http://www.iucr.org/education/resources/edu_2008_55

Symmetry and Space Group Tutorial, Jerry P. Jasinski and Bruce M. Foxman.

Link - http://www.iucr.org/education/resources/edu_2008_57

Symmetry Tutorial, Dean H. Johnston, Otterbein College. Includes a symmetry challenge and symmetry gallery

Link - http://symmetry.otterbein.edu/

Welcome to the world of symmetry! The resources contained within this web site are designed to help students learn concepts of molecular symmetry and to help faculty teach concepts of molecular symmetry. The materials are designed for a variety of levels, so look around and see what we have to offer. Choose from the following pages:


Analytical Inorganic Organic Physical

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Free online Chemistry Courses

Bio-Rad -FREE and fully functional software

Bio-Rad -FREE and fully functional software

Chemistry online Resources

Link - http://www.knowitall.com/academic/welcome.asp

'Bio-Rad offers either free single-user copies or site licenses for your entire department or school if you meet our eligibility requirements outlined in our Terms & Conditions of Use Agreement.

To download your free copy of the KnowItAll Informatics System, Academic Edition, you will need to make a selection above (in the download the software now section), fill out a registration form, and download the software (unless you have already done so). After that, an e-mail with product registration code(s) will be sent to you. You will then need to use this code to activate your software.

What applications and features are included in the KnowItAll® Academic Edition?
DrawIt™ for chemical structure drawing
• Draw 2D & 3D structures
• Automatically assign stereochemical designators for R/S centers and E/Z bonds
• Automatically assign stereochemical designators for R/S centers in Fischer projections of sugars
ReportIt™ to generate high-quality lab reports
• Import IR, NMR, MS, and Raman spectra, & chromatograms in common native file formats
• Create reports complete with structures, spectra, tables, & more
• Access lab glassware and engineering symbol clip art with the click of the mouse
AnalyzeIt™ IR & Raman to interpret spectra
• Interpret the bands in an experimental infrared or Raman spectrum
• Correlate the expected group frequencies from a structure with a spectrum
RefineIt™ IR & Raman and ProcessIt™ NMR
• Import and process spectra from various instrument sources.
Sadtler Spectroscopy Handbooks – Internet Edition
• Review spectroscopy handbooks, starting with the Sadtler Handbook of IR Spectroscopy
• Access key spectroscopic insights by functional group
SymApps™ for molecular symmetry analysis
• Calculate, display, & animate the symmetry for a molecule
• Create movies for three basic rotations
• Calculate point groups, bond lengths, angles, & dihedral angles for all atoms in the structure
General laboratory calculations
• Convert from mole to mass or mass to mole
• Calculate molecular weight from structure
• Access MS fragmentation & MS documentation tools Analytical Inorganic Organic Physical"[1].

Virtual Computational Chemistry Laboratory

Virtual Computational Chemistry Laboratory

on-line software

Chemistry online Resources

Link - http://www.vcclab.org


"This site provides free on-line tools, which we hope you will find helpful in performing computational chemistry, ADME/T and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties and the analysis of relationships between chemical structure and properties. All these tools are developed, provided and supported by the VCCLAB partners.

Please feel free to browse our site and take advantage of the various on-line cheminformatics services provided. However, the calculation algorithms are running on remote servers, communicating via the Internet, so we are unable to control the speed of access to these services. An overview of on-line WWW resources for Phys-Prop calculations is also available"[1].
1.http://www.vcclab.org/



Analytical Inorganic Organic Physical

The CCP1GUI - free, extensible Graphical User Interface

The CCP1GUI - free, extensible Graphical User Interface

Chemistry online Resources

Link - http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/

"The CCP1GUI project has arisen as a result of demand within the UK academic community (principally through CCP1) for a free, extensible Graphical User Interface (GUI) for community codes, particularly for teaching purposes. There is also a long-standing requirement for a graphical interface for the GAMESS-UK quantum chemistry programme, which we plan to satisfy using the CCP1 developments.

The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit, both of which have been ported to all the major operating system platforms. The GUI is therefore capable of running on all of these systems. Distributions of the GUI have already been successfully tested on Windows, and Suse and Redhat Linux distributions, and packages for these distributions are freely available from our ftp site.

The CCP1GUI has been released under the GNU GPL licence and is freely available to download. Downloads are available from the CCP1GUI pages on sourceforge or from the ftp site of the Computational Chemistry Group at STFC Daresbury Laboratory.

The design of the GUI makes the most of Python's high degree of object-orientation, including advanced features such as multiple inheritance. The strong reliance on object orientation means that it is quick and easy to create interfaces to new computational chemistry codes as the need arises. The GUI already has a highly-featured interface for the GAMESS-UK program, and there are working interfaces for Dalton, Molpro, ChemShell and MOPAC"[1].
1.http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/

Analytical Inorganic Organic Physical

SmiLib - free, platform indepentend software

SmiLib - free, platform indepentend software

Chemistry online Resources

Link - http://gecco.org.chemie.uni-frankfurt.de/smilib/

"SmiLib is a free, platform indepentend software tool for rapid combinatorial library enumeration in the flexible and portable SMILES notation. SmiLib enumerates combinatorial libraries at rates of approximately 9,000,000 molecules per minute on fast computers"[1].
1.http://gecco.org.chemie.uni-frankfurt.de/smilib/

Analytical Inorganic Organic Physical

RasMol - free molecular viewer

RasMol - free molecular viewer

Chemistry online Resources

Link - http://www.openrasmol.org

"RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces"[1].
1.http://www.openrasmol.org/

Analytical Inorganic Organic Physical

Perl Modules for Molecular Chemistry

PerlMol - Perl Modules for Molecular Chemistry

Chemistry online Resources

Link - http://www.perlmol.org/

"PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging". The PerlMol toolkit provides objects and methods for representing molecules, atoms, and bonds in Perl; doing substructure matching; and reading and writing files in various formats"[1].
1.http://www.perlmol.org/

Analytical Inorganic Organic Physical

Open Babel: The Open Source Chemistry Toolbox

Open Babel: The Open Source Chemistry Toolbox

Chemistry online Resources

Link - http://openbabel.sourceforge.net/wiki/Main_Page

"Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

* Ready-to-use programs, and complete programmer's toolkit
* Read, write and convert over 90 chemical file formats
* Filter and search molecular files using SMARTS and other methods
* Supports molecular modeling, cheminformatics, bioinformatics
* Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry"[1]
1. http://openbabel.org/wiki/Main_Page

Analytical Inorganic Organic Physical

Molinspiration Cheminformatic

Molinspiration Cheminformatic

Chemistry online Resources

Link - http://www.molinspiration.com/

"Molinspiration Galaxy 3D Structure Generator Galaxy generates reliable 3D molecular structures from molecular connectivity (2D information) such Daylight SMILES or MDL Molfile. Galaxy is fast, what allows generation of 3D molecular structures for large chemical databases easily. It is written in Java, therefore can be used practically on any computer or operating system. Galaxy comes with a built-in 3D molecule viewer GalaxyVisualizer which allows also generation of molecular images in various formats.
Molinspiration offers a free web service which allows generation of 3D structures, display of various 3D molecular properties (molecular hydrophobicity potential or polar surface area) and download of generated 3D geometries"[1].
1.http://www.molinspiration.com/

Analytical Inorganic Organic Physical

Linux For Chemistry

Linux For Chemistry - More than 200 freewares

Chemistry online Resources

Link - http://www.redbrick.dcu.ie/~noel/linux4chemistry/

The most up-to-date Linux software (over 250) for chemistry including molecular modeling, graphics, visualization, molecular and quantum mechanic, dynamic, computational chemistry and some drug discovery, biochemistry and genetics related software.more than 200 software are free.

Analytical Inorganic Organic Physical

Jmol - open-source Java viewer

Jmol - open-source Java viewer

Chemistry online Resources

Link - http://jmol.sourceforge.net

"Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

* The JmolApplet is a web browser applet that can be integrated into web pages.
* The Jmol application is a standalone Java application that runs on the desktop.
* The JmolViewer is a development tool kit that can be integrated into other Java applications"[1].
1.http://jmol.sourceforge.net/

Analytical Inorganic Organic Physical

Hyleos: Free Chemistry Software

Hyleos: Free Chemistry Software

Chemistry online Resources

Link - http://www.hyleos.net/index.php

Free Windows software for working with MDL SDF files and molfiles. Includes descriptors calculation like TPSA, molecular weight, HBd and HBa.

Analytical Inorganic Organic Physical

CambridgeSoft

CambridgeSoft

Chemistry online Resources

Link - http://www.cambridgesoft.com/

"Success begins at the desktop, where scientists use ChemDraw, ChemOffice, and BioOffice to pursue ideas and communicate with the natural language of chemical structures, biological pathways, and models.

Scientists organize information and manage data with E-Notebook and Inventory. Chem3D provides modeling, ChemFinder aids searching, while BioOffice adds BioAssay, BioViz and BioDraw. Integrated with Microsoft Office to speed research tasks"[1].
http://www.cambridgesoft.com/software/



Analytical Inorganic Organic Physical

CACTVS Chemoinformatics Toolkit - free academic versions

CACTVS Chemoinformatics Toolkit - free academic versions

Chemistry Freeware

Link - http://www.xemistry.com/academic

"This page links to free academic versions of the Cactvs Chemoinformatics Toolkit. The packages found here are for evaluation and use in research and education only. They are not legal for use in any commercial environment. No redistribution in any format, but feel of course free to link to this page.

Commercial toolkit versions with enhanced functionality are available for licensing.

Not all releases are updated with the same frequency"[1].
1.http://www.xemistry.com/academic

Analytical Inorganic Organic Physical

ACD/ChemSketch 11.0 Freeware - Chemistry Freeware

Chemistry Freeware

ACD/ChemSketch 11.0 Freeware

"Visualize a chemically intelligent drawing interface that provides a portal to an entire range of analytical tools, and facilitates the transformation of structural or analytical data into professional, easy-to-decipher reports or presentations.

Advanced Chemistry Development, Inc., (ACD/Labs) has developed such an interface, and has integrated it with every desktop software module they produce. To date, over 800,000 chemists have incorporated ACD/Labs' chemical drawing and graphics package, ACD/ChemSketch, into their daily routines. Academic institutions worldwide have adopted this software as an interactive teaching tool to simplify and convey chemistry concepts to their students, and publishing bodies such as Thieme, the publisher of Science of Synthesis, consider it to be "...supportive of the organic chemistry publisher's role, both in the construction of compounds and their basic analysis."

ACD/ChemSketch is an advanced chemical drawing tool and is the accepted interface for the industry's best NMR and molecular property predictions, nomenclature, and analytical data handling software.

ACD/ChemSketch is also available as freeware, with functionalities that are highly competitive with other popular commercial software packages. The freeware contains tools for 2D structure cleaning, 3D optimization and viewing, InChI generation and conversion, drawing of polymers, organometallics, and Markush structures—capabilities that are not even included in some of the commercial packages from other software producers. Also included is an IUPAC systematic naming capability for molecules with fewer than 50 atoms and 3 rings. The capabilities of ACD/ChemSketch can be further extended and customized by programming.

The commercial version of ACD/ChemSketch offers additional capabilities above and beyond the freeware offering. It includes a number of advanced features including a dictionary of more than 158,000 trivial, common, and trade names with their corresponding structures. It allows the user to view SDfiles, and search Microsoft Word or Adobe PDF reports, SDfiles, molfiles, and CambridgeSoft ChemDraw files by chemical structure, substructure, or structure similarity.."*

* Ref - http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/

Download Page - http://www.freechemsketch.com/

Note: ChemSketch 11.0 freeware is not compatible with other versions of free and commercial ACD/Labs software and should be installed separately.

Analytical Inorganic Organic Physical