# The &kalzium; Handbook

Carsten
Niehaus

    &Carsten.Niehaus.mail;

2001
2002
2004
2005
2006
2007
2008
&Carsten.Niehaus;
2005
&Anne-Marie.Mahfouf;
&FDLNotice;
2012-09-04
2.4.00 (&kde; 4.9)

&kalzium; is a program which shows you the Periodic Table of Elements. You can use &kalzium; to search for information about the elements or to learn facts about the periodic table.

KDE
education
elements
chemistry
education
kalzium

## Introduction

&kalzium; provides you with all kinds of information about the Periodic Table of the Elements. You can lookup lots of information about the elements and also use visualizations to show them. It is free and licensed under the &GNU; Public License.

You can visualize the Periodic Table of the Elements by groups, blocks, and families. You can plot data for a range of elements for properties like the boiling point or the atomic mass. You can go back in time and see what elements were known at a given date. You can also calculate the molecular mass of molecules.

## &kalzium; quick start guide

Here is &kalzium; the first time you run it, either by selecting Applications Edutainment Science&kalzium; from the &kmenu; or with &Alt;F2 and entering `kalzium` into the field.

&kalzium; main window
&kalzium; main window

&kalzium; is divided in an information panel on the left (in red), the table view (in blue) which shows the elements of the periodic table, and a legend panel at the bottom (in green). The standard menubar allows you to choose what you want to display and the status bar reports facts. The table view and the panels can be hidden using the corresponding items in View menu. For example, you can hide the information panel with View Information .

When you move the mouse cursor on an element of the table, an overview of the current element is displayed in the Overview tab of the information panel.

You can choose several views for the table: classic periodic table, short periodic table, long periodic table, &etc;. It is also possible to change numeration scheme or display the elements per families, per groups, per crystal structure, depending on their acidic behavior, &etc;. You can change all that in the View menu.

If you want to know facts about a precise element, click on it in the table and the information dialog will be displayed.

Information dialog
Information dialog

You can plot data using the Tools Plot Data... menu item. You choose what you want to plot on the y-axis and a range of elements to plot that for on the x-axis. The screenshot below shows the mass of the elements 1 to 10.

The Plot Data dialog
The Plot Data dialog

The Glossary ( Tools Glossary... ) explains the most important chemical words and shows you pictures of the most common tools along with an explanation.

The Glossary
The Glossary

## Using &kalzium;

### Overview of &kalzium; usage

&kalzium; is very easy to use. It is specially designed for students of all ages to use as a small and quick database.

Here is a screenshot of &kalzium; in action:

&kalzium; main screen, immediately after the first start
&kalzium; main screen

### The information dialog

The information dialog is accessed by clicking with the &LMB; on any element. This is the place to get information about an element. With the buttons at the bottom of the dialog you can change the element which is displayed without closing the dialog.

#### Data Overview

The Data Overview page tells you about different facts related to the element.

Depending on the data available in &kalzium; you will see different radii of the element. The covalent radius is the radius of a non charged atom of the element in a molecule. The could for example be the O-H-distance in Water. The atomic radius is the radius of an elemental atom, &eg; not bound to anything. The van der Waals-radius is defined as the distance of two atoms of the same sort in two equal molecules, for example two carbon-atoms in propane. The last possible radius is the ionic radius including its charge.

The mass of an element is the average mass of all isotopes in relation to their percentage.

&kalzium; information dialog
&kalzium; information dialog

#### Bohr Orbitals

The Atom Model page displays the atomic shells. Every orbit stands for a atomic shell and every yellow circle represents an electron.

&kalzium; information dialog
&kalzium; information dialog

#### Isotopes

The Isotopes page presents information about the isotopes of an element.

Mass

  The mass of this isotope.

Neutrons

  The number of neutrons this isotope has.

Percentage

  The percentage of atoms occurring that are of this isotope type. Also called abundance.

Half-life period

  Only unstable isotopes have a half-life period. It is defined as the time in which half the isotopes decay.

Energy and Mode of Decay

  Some isotopes are known to emit particle radiation under the process of radioactive decay. Each decay transformation has a typical energy release, which is listed along with the mode of decay.

Spin and Parity

  The spin of the nucleus and its parity.

Magnetic Moment

  The magnetic dipole moment of the nucleus. Measured in units of the nuclear magneton.

&kalzium; information dialog
&kalzium; information dialog

#### Miscellaneous

The Miscellaneous page tells you other information about the current element, including when it was discovered and the origin of the name.

&kalzium; information dialog
&kalzium; information dialog

#### Spectrum

The Spectrum page shows you elements spectrum. You can choose the range of the wavelengths, units and type of the spectrum. The intensity table can be seen at the right bottom part of the page.

&kalzium; information dialog
&kalzium; information dialog

#### Extra Information

The Extra information page gives you the links to the element pages on Wikipedia, Jefferson Lab, and WebElements.

&kalzium; information dialog
&kalzium; information dialog

### Tables

The periodic table can be presented in various ways. You can switch the table view from View menu or toolbar drop-down list.

The following options in the View Tables menu can be used to change the table shown:

Classic Periodic Table

  Display the classic periodic table with all elements.

Short Periodic Table

  Display a periodic table without transition elements.

Long Periodic Table

  Display a periodic table with inner transition elements (f-elements) embedded.

Transition Elements

  Display a periodic table only with transition elements.

DZ Periodic Table

  This item represents the table the DZ Deutscher Zentralausschuss "German Central Committee" suggests.

### Numeration

The numeration is the way of numbering the 18 groups of the periodic table. You can change the numeration to IUPAC, old IUPAC or CAS, or you can switch it off entirely.

The following options in the View Numeration menu can be used to change the numeration shown:

- No Numeration: if this option is active, no period-numeration will be in effect.

- IUPAC (default) is the International Union of Pure and Applied Chemistry. This is an organization which defines most of the standards for chemical concerns. The new IUPAC system numbers each column with Arabic numbers from 1 (one) through 18 (eighteen).

- CAS is the Chemical Abstracts Service. In the CAS system the letters A and B were designated to main group elements (A) and transition elements (B). Though the IUPAC numeration is the official, the CAS numeration is what is still used in classrooms and laboratories.

- The Old IUPAC system labeled columns with Roman numerals followed by either the letter A or B. Columns were numbered such that columns one through seven were numbered IA through VIIA, columns 8 through 10 were labeled VIIIA, columns 11 through 17 were numbered IB through VIIB and column 18 was numbered VIII. Because of the confusion the old IUPAC and the CAS system created, the IUPAC adopted their new system.

### Color schemes

&kalzium; can show you which elements are where with regard to their Periodic block and group, their behavior with acid and which state of matter (&ie; solid/liquid/vapor) they are in at a given temperature.

Color schemes can be changed in the View Scheme menu, toolbar drop-down list, or View tab of the Sidebar.

- Monochrome: all the elements have the same color. You can change the default color by choosing Settings Configure &kalzium;... and going to the Schemes page.

- Blocks: displays a color for each block.

- Iconic: displays icons for each element.

- Family: represents each of the nine families with a color.

- Groups: displays a color for each group. A group is a vertical column in the periodic table of the elements. There are 18 groups in the standard periodic table. Elements in a group have similar configurations of their valence shell electrons, which gives them similar properties.

### Gradients

The gradient views displays the elements according to a property you can select below and with a gradient colored scheme. The elements for which the data is not available are displayed in gray.

Gradients can be changed in the View Gradients menu, toolbar drop-down list, or View tab of the Sidebar.

Gradient for Covalent Radius
Gradient for Covalent Radius

Implemented are the following gradients

- None: Do not use gradients.

- State of matter

- Covalent Radius

- van der Waals: gradient by van der Waals radius.

- Atomic Mass

- Boiling Point

- Melting Point

- Electronegativity (Pauling)

- Electronaffinity

- Discovery date

- First Ionization

### Tools

#### Molecular Editor

The Molecular Editor allows you to view and edit molecules using Avogadro libraries.

Using control panel on the left you can change the view parameters, edit molecule, or measure molecules. There are three tabs on this panel: Display, Edit, and Measure. The buttons along the bottom of the window can be used to Save molecule, Download New Molecules, Load Molecule, and Close the window.

Statistics pane shows name (if available), formula, and weight of the molecule.

The Display tab can be used to change Quality of the image (Low, Medium, or High, can be useful on low-end system), Style (can be Balls and sticks, Sticks, Van der Waals, or Wireframe), 2nd Style (can be None, Ribbon, Ring, or Molecular Orbital), and Labels (can be None, Atom Numbers, Element Names, or Element Symbols).

The Edit tab allows you to edit the molecule. You can add elements by choosing them in the Element drop-down list then clicking with the &LMB; on the view panel on the right. The molecule can be optimized by clicking Optimize button.

The Measure tab can be used to measure distances and angles in the molecule. To make the measurement use the instructions shown on the tab.

On the right of the Molecular Editor window the molecule will be shown. Use &LMB; to rotate molecule, &RMB; to move it, and &MMB; to zoom.

the Molecular Editor

#### Isotope Table

The Isotope Table... shows you the isotopes of the elements.

There are different kinds of isotopes, some are stable, some are not. The unstable isotopes can decay as alpha-rays are two different beta-rays. These differences are encoded by using different colors.

the Isotope Table window

&kalzium; can display the isotopes of a range of elements

#### Plot Data

The Plot Data... dialog allows you to plot some information about elements. The X-axis represents a range of elements (from one number to a higher number). You set this range using the First Element and Last Element fields on the dialog.

the Plot Data Dialog

&kalzium; can plot some data about a range of elements.

#### Perform Calculation

The Perform Calculation is the &kalzium; calculator. This calculator contains a variety of calculators for different tasks performing different calculations.

You can find the following calculators in &kalzium;

Molecular mass calculator

  This calculator helps you calculate the molecular masses of different molecules.

  You can specify short form of the molecule names add more such aliases.

  the Molecular mass calculator dialog

  &kalzium; calculates molecular mass of phenol.

Concentrations calculator

  You can calculate quantities which include

  - Amount of substance

  - Volume of solvent

  - Concentration of substance

  There are a wide range of units to choose from and different methods to specify quantities.

  the Concentrations calculator dialog

  &kalzium; calculates solution parameters.

Nuclear calculator

  This calculator makes use of the nuclear data available in &kalzium; to predict the expected masses of a material after time.

  the Nuclear calculator dialog

  &kalzium; calculates parameters of uranium decay.

Gas calculator

  This calculator can calculate the values of Temperature, pressure, volume, amount of gas etc. for various ideal as well as non-ideal gases.

  the Gas calculator dialog

  &kalzium; calculates gas parameters.

Titration calculator

  This calculator tries to find out the equivalence point of a pH-meter followed titration best fitting it with an hyperbolic tangent. You can also let it solve an equilibrium system of equations and see how the concentration of a species changes in function of another one.

  There are two tabs on the calculator page, namely:

  Experimental Values

    You can use this calculator to draw the plot of your experimental data obtained during a titration and find out the volume of equivalence. It's strongly recommended to insert a even number of points, because of the best fit algorithm, sorted by volume (the X axis value).

  Theoretical Equations

    Here you can fill the table with the equations you have previously obtained for the chemical equilibrium.

    For example, if you have this reaction A + B -> C + D then you will have the equation K=(C*D)/(A*B) so you must write `K` in the Parameter column and `(C*D)/(A*B)` in the Value column. If you want to assign a known value to a parameter you can simply write the numeric value in the Value field.

    For example, you can use the system

    `A=(C*D)/(B*K)`

    `K=10^-3`

    `C=OH`

    `OH=(10^-14)/H`

    `H=10^-4`

    `B=6*(10^-2)`

    Then you have to write `D` as X axis and `A` as Y axis: so you will find out how the concentration of A changes as a function of D concentration.

    Please don't use parenthesis for exponents: `10^-3` is correct, while `10^(-3)` is wrong.

  The results can be visualized by pressing Draw Plot button. The plot shows in red the curve that comes from theoretical equations, in blue the experimental points, and in green the approximated curve for experimental points. You can save the plot as SVG image.

  the Titration calculator dialog

  Predefined example of titration results.

Equation Balancer

  The Equation Balancer enables the user to solve chemical equations. This is an example:

  > aH2O + bCO2 -> cH2CO3

  The computed equation will be displayed on the top of the window. As you can see in the first example you can also define the value of one or more coefficients. The other coefficients will be adjusted. Furthermore, it is possible to use brackets around elements or electronic charges as shown in the last two examples.

  the Equation Balancer dialog

  &kalzium; calculates equation balance.

#### Risk/Security Phrases

The R/S Phrases, also known as Risk and Safety Statements, R/S statements, R/S numbers, and R/S sentences, is a system of hazard codes and phrases for labeling dangerous chemicals and compounds. The R/S phrase of a compound consists of a risk part (R) and a safety part (S), each followed by a combination of numbers. Each number corresponds to a phrase. The phrase corresponding to the letter/number combination has the same meaning in different languages.

the R/S Phrases window

&kalzium; can display Risk/Security Phrases

#### Glossary

The Glossary gives you definitions of the most used tools in chemistry as well as some knowledge data. On the left side of the windows you can see the tree of items. On top, there are chemical terms, below that there is a second tree of laboratory-tools.

On the top of the widget you can see a searchbar. If you type in the bar the trees will be adjusted immediately. The small button in the right end of the searchbar will clear it.

the Glossary

#### Tables

The Tables shows you the tables for Greek alphabet which is used to denote some chemical and physical entities, and for Latin prefixes and Roman numbers which correspond to common Arabic numbers.

the Tables window

#### Sidebar

##### Overview

Overview

The Overview tab is the first one and it shows you an overview of the element the mouse is over.

##### View

The View tab is the second in the navigation panel.

You are first presented with the following icons and text:

the State of Matter Dialog

&kalzium; can show you which elements are solid/liquid/vaporous at a given temperature.

The View tab can be used to filter PSE. For example, this feature allows you to explore the elements of the set time period. This is great for getting a feel for how the PSE evolved over time, as more and more elements were discovered. Choose Discovery date from Gradient list. If you move the slider you will notice that color of some elements disappear if you move it to the left and reappear if you move it to the right. Furthermore the number will change constantly.

The number represents the date you are looking at. If you move the slider to &eg; 1856 you will only see the elements which where known in the year 1856.

the Discovery date gradient

The PSE back in time (elements known in 1856)

##### Calculate

The Calculate tab is the last in the sidebar. It allows you to calculate molecules weights.

You are first presented with the following icons and text:

Calculate

Calculate

## Configuring &kalzium;

&kalzium; has many configuration options, which you can access by opening the configuration dialog by selecting Settings Configure &kalzium;... from the menu.

Configure &kalzium; Dialog
Schemes

In the Schemes tab, you can change the different colors for each scheme.

Configure &kalzium; Dialog
Gradients

Instead of using a linear gradient to display the given property of an element in the periodic table, &kalzium; can also use a logarithmic gradient.

In the Gradients tab, you can check the properties you want to have displayed with a logarithmic gradient.

You can also choose Maximal Value Color and Minimal Value Color for the gradient.

Configure &kalzium; Dialog
Units

In the Units tab, you can choose the units for temperature and energy. You can select if you prefer kJ/mol by default or you can choose eV. The Temperature is in Kelvin by default but you can change to degrees Celsius or degrees Fahrenheit.

Configure &kalzium; Dialog
Calculator

Using the Calculator page, you can configure &kalzium; calculators.

## Command Reference

### Menus and shortcut keys

#### The File Menu

File Save As...

  Save &kalzium;'s table as image.

File Export Data...

  Open a dialog where you can select Elements and their Properties to export them to a &HTML;, &XML;, or CSV file.

File Convert chemical files...

  Open a dialog to import and export a wide range of chemical file formats and data types with the Open Babel library.

&Ctrl;Q File Quit

  Quits &kalzium;.

#### The View Menu

View Tables Classic Periodic Table

  Display the classic periodic table with all elements.

View Tables Short Periodic Table

  Display a periodic table without transition elements.

View Tables Long Periodic Table

  Display a periodic table with inner transition elements (f-elements) embedded.

View Tables Transition Elements

  Display a periodic table only with transition elements.

View Tables DZ Periodic Table

  This item represents the table the DZ Deutscher Zentralausschuss "German Central Committee" suggests.

View Numeration No Numeration

  Display no numeration scheme.

View Numeration IUPAC

  Display the IUPAC numeration.

View Numeration CAS

  Display the CAS numeration.

View Numeration Old IUPAC

  Display the Old IUPAC numeration.

View Scheme Monochrome

  Display all elements with one background color.

View Scheme Blocks

  Display the four blocks of elements.

View Scheme Iconic

  Display icons for each element.

View Scheme Family

  Display the families of elements.

View Scheme Groups

  Display the groups of elements.

View Gradients None

  Disable any gradient for the table.

View Gradients State of matter

  Display the elements' state of matter.

View Gradients Covalent Radius

  Display the elements' covalent radius.

View Gradients van der Waals

  Display the elements' van der Waals radius.

View Gradients Atomic Mass

  Display the elements' atomic mass.

View Gradients Boiling Point

  Display the elements' boiling point.

View Gradients Melting Point

  Display the elements' melting point.

View Gradients Electronegativity (Pauling)

  Display the elements' electronegativity.

View Gradients Electronaffinity

  Display the elements' electron affinity.

View Gradients Discovery date

  Display the discovery date of each element with different background colors for each century.

View Gradients First Ionization

  Display the elements' energy of first ionization.

View Legend

  Toggle the legend view. Allows you to display the legend for the scheme you are in (Groups, Family, Blocks). The legend is displayed by default but if you hide it, it will stay hidden until you choose to show it. &kalzium; will keep this setting in its configuration file, so that the next time you run it, the setting will be as you left it.

View Information

  Toggle the Sidebar.

View Table Information

  Toggle the Table Information view.

#### The Tools Menu

Tools Molecular Editor...

  Open the Molecular Editor dialog.

Tools Isotope Table...

  Open the Isotope Table window.

Tools Plot Data...

  Open the Plot Data dialog.

Tools Perform Calculation...

  Open the Perform Calculation dialog.

Tools R/S Phrases

  Open the Risk/Security Phrases dialog.

Tools Glossary...

  Open the Glossary.

Tools Tables...

  Display a dialog with the Greek alphabet and Numeric Prefixes and Roman Numerals.

#### The Settings Menu

Settings Show Toolbar

  Toggle the Main Toolbar.

Settings Show Statusbar

  Toggle the Status bar.

Settings Configure Shortcuts...

  Configure the keyboard keys you use to access the different actions.

Settings Configure Toolbars...

  Configure the items you want to put in the toolbar.

Settings Configure &kalzium;...

  Display the &kalzium; settings dialog.

#### The Help Menu

&help.menu.documentation;

## Questions and Answers

Will I ever have to pay for &kalzium;?

No, never. But the author always welcomes a nice mail or a DVD as a Thank You. &kalzium; is licensed under the GPL, so you will never have to pay for this program.

## How can I contribute?

Support me with data.

In the world of science, the progress is quite fast. If you ever find an incorrect or missing value, please drop me an email.

Find some bugs or give some suggestions

If you find any bugs in the program, or have a few suggestions for improvements, please let me know at &Carsten.Niehaus.mail;.

## Credits and License

&kalzium;

Program Copyright, 2001-2005 &Carsten.Niehaus; &Carsten.Niehaus.mail;

Contributors:

- Pino Toscano toscano.pino@tiscali.it

&underFDL; &underGPL;

## Installation

### How to obtain &kalzium;

&install.intro.documentation;

### Web Presence

&kalzium; itself can be found on The &kalzium; home page and is part of the &kde;-Edu project

### Compilation and Installation

&install.compile.documentation;

&documentation.index;