ChemRef Advanced - Online Help


Introduction
Shareware Registration
Periodic Table
Molecular Weight Calculator
Solution Concentration Calculator
Mol to Mass Converter
Physical Constants
Organic Classes
Organic Functional Groups Screen
Periodic Trend Analysis
Unit Converter
3D Model Viewer
Changing Backgrounds


Introduction

Thank you for downloading ChemRef Advanced. This software was created to provide a convenient set of chemistry reference tools for anyone who needs to have access to this information on the go.  We will continue to upgrade and add as many useful features into this application as we possibly can.  Thanks again for downloading!

This software was intended to be run on all Pocket PC's.  (2000,2002,2003 - ARM, MIPS, SH3)

Pocket PC 2000 and 2002 users will have to install the .NET Compact Framework from Microsoft.  This is a free download and can be found here.

Shareware Registration
This software is distributed as shareware and will operate in demo mode until it is registered. You don't need to install a new version once you register, simple enter your code into the 'About' screen and you will have full access to the program.

In demo mode the following limitations apply:

Periodic Table Limited to information on elements 1 to 36 only.
Molecular Weight Calculator Limited to 6 characters of input.
Solution Conc. Calculator Limited to 6 characters of input.
Unit Converter Limited to 6 characters of input.
Physical Constants Only the General Constants are available.
Periodic Trend Analysis Only Radius information can be plotted.
3D Molecular Viewer Only some of the molecules are viewable and file input is disabled.

Periodic Table
The periodic table is the first view presented after the program loads and shows a complete view of all the elements.  To view information on a particular element simply click on its symbol in the table.  Additionally the two tabs to the right of the large atomic symbol display allow selection alphabetized by symbol or proper name.

An explanation of each to the information types is as follows:

Name Name of the element.
Atomic # Atomic number of the element.
Mass Mass of the element in grams per mol.
State State of the element under standard conditions.
Family Family of the periodic table to which the element belongs.
Elec neg. Electronegativity of the element.
Ox states Oxidation states of the element.
Elec Config Electron configuration of the element at ground state.
Crystal Type of crystal structure the element has.
Density Density of the element in grams per milliliter.
Radius Atomic radius of the element in picometers.
IE 1st ionization energy of the element in KJ per mol.
MP Melting Point of the element in Kelvin.
BP Boiling Point of the element in Kelvin.

Molecular Weight Calculator

The molecular weight calculator is used to automatically calculate molecular weights.  Simply enter the formula and click calculate.  A status bar will show the progress until the weight has been calculated.  

Options have been added for rounding values to significant digits and for removing case sensitivity.  Support for brackets has also now been added.

In some cases, you may need to use case sensitive analysis.  For example, if you enter hf, the software has no idea whether you intend Hf , or HF.  For most calculations, using the case insensitive option works as expected.  Always check the recognized textbox to ensure the algorithm recognized everything in the input string correctly.

Example valid formula types:

c6h6

br(ch)6ch3

CH3(NaOH)6

Solution Concentration Calculator
The solution calculator is used to calculate the mass of a chemical to add to solution in order to create a desired concentration with known volume.  For example, you would need to add 0.0584 grams of NaCl  to 10 cc's of solution to yield a concentration of 0.100 mol/L NaCl solution.
Mol to Mass Converter
The mol - mass converter is a simple tool to convert between moles and grams based on an input molar mass.  Clicking the button below the entry field will grab a recent (if still in memory) molecular weight calculation result.
Physical Constants
The physical constants reference provides common constants and their values.  Select a type of constant and then a specific constant to display the symbol, value and unit for the constant.
Organic Classes
The common organic classes reference displays common simple organic classes.
Organic Functional Groups
The organic functional groups reference displays some common organic functional groups.  Use the scroll bar to scroll up and down the page.
Periodic Trend Analysis
The Periodic Trend Analysis allows any periodic table property to be plotted over a specified range.  Once a property is selected and a range specified, clicking the 'Plot' button plots the data to the screen.  Clicking on a plotted point causes its information to be displayed in the pink area under the display.  A label toggle is also provided.
Unit Converter
The unit converter provides a convenient way to convert the following types of units:

Angle
Energy
Force
Length
Mass
Power
Pressure
Temperature
Volume

Simply select the "To:" and "From:" units, then enter a value to convert. Click on calculate to convert the value.

3D Model Viewer
A powerful 3D model viewer has been added as of version 3.2.  This tool can be used to view many built-in structures as well as load a custom structure from a file.  The 3D viewer supports model rotations and translations.  Please note that none of the structures have been precisely calculated, and are suitable for orientation viewing purposes only.

The built-in structures can be accessed under the 'View' menu.  To view a structure simply select it from the menu entry and the molecule will be loaded to the screen.  The view types include:

Crystal Stuctures
VSEPR Models
Alkanes

Alkenes 
Alkynes
Alchohols
Caffeine

Once a molecule is loaded, it can be rotated by moving the stylus on the screen, or by using the axis rotation icons on the bottom right of the screen.  

The toolbar buttons provide additional functionality.  The first button is used to toggle atomic labels on and off.  The second button toggles between rotation and translation mode.  When in translation mode, the molecule can be moved around the screen with the stylus or with the movement icons.  The third toolbar button toggles the auto-rotate view.  This will rotate the molecule about the y-axis by 10 degrees every 500 ms.  A fourth button has been added as of version 3.3. This button allows angle measurements to be taken between any three atoms. Simply toggle the feature on, then click any 3 atoms and the contained angle will be displayed in the bottom left of the screen. Please note that the rotation is locked during angle measure mode.

A custom model can be loaded with the file menu.  Supported formats include standard *.pdb (Protein Data Bank) files and simple custom *.txt files.  Files must be located in the "\My Documents" directory.

It is recommended that only small *.pdb files be loaded as large ones take a very long time to load and redraw.  Also please note that bonds are only shown if the file contains connection data for the atoms, otherwise only the atoms are visible.

The format expected for a *.txt file is shown below.  Each atom in the molecule is represented by one line in the file. See the line format expected and the sample for Methane.  Please note this was not calculated precisely and is an example only.

Line Format
Atom Number,Element Symbol,x-position,y-position,z-position,bonded to#1,bonded to#2  ... etc

Example for Methane
1,C,0.000,0.000,0.000,2,3,4,5
2,H,0.000,1.090,0.000
3,H,1.031,-0.364,0.000
4,H,-0.516,-0.364,-0.893
5,H,-0.516,-0.364,0.893

Changing Backgrounds
The background image can be changed from the main periodic table screen.  There built-in default backgrounds to choose from, or a different image can be loaded from a file.  To use a custom image, it should be placed in the "My Documents" folder of your device.  Supported formats are (*.bmp) and (*.jpg).  The image should be 240 pixels wide and 268 pixels high.  Large images will work but will not be scaled.  Smaller images may cause the forms to not display correctly.