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Posts Tagged ‘families of elements’

Visualizing electronegativity of the elements in 3D

Visualizing electronegativity of the elements in 3D

While teaching the history and patterns of the periodic table of the elements to my chemistry students, I wanted them to get a better feel for the concept of periodicity – that some elemental properties repeat periodically as you increase atomic numbers.

Melting points of the elements visualized in 3D

Melting points of the elements visualized in 3D

For example, at the left of each period (row) is an element that is a soft metal that will react with water to produce a strong base. As a family they are called the alkali metals, and consist of lithium, sodium, potassium, rubidium, cesium, and francium. We now know they have a similar electron configuration, with a single electron in an s-type orbital. This electron is easily ionized away and accounts for the alkali metals’ high reactivity. Other families of elements (usually found in columns in the table) include the noble gases, the halogens, and the royal metals (copper, silver, and gold). It was the relationships of similar properties that led Mendelyev (and de Chancourtois, Newlands, Oddling, and Meyer) to develop the periodic table in the first place.

Melting points with a golden texture

Melting points with a golden texture

In an effort to visualize these patterns more clearly, I have devised a technique for taking the numerical values of a property, such as electronegativity, atomic radius, or melting point and turning them into three-dimensional models.

Chart for recording the numerical values of a periodic property

Chart for recording the numerical values of a periodic property

I start with a chart that is divided into squares in the shape of the periodic table, with white squares representing elements and black squares the spaces between and around the sections of the table (you can download this diagram here).

Periodic Properties Chart: 3D periodic properties table

Pairs of students look up one of the periodic properties, then write the numbers down for each element on the chart.

In a text editing program such as Text Edit or Microsoft Word, my students then type in the numbers for each row of the chart, separating them by commas and hitting return or enter to make the next row. For the black squares, they type in a zero. They have to be careful not to leave any element or blank square out. They will have 12 rows of 20 numbers each.

Electronegativity values typed in as comma-separated rows. Blank spaces on the chart are given zeros. The final grid is 12 rows of 20 values each.

Electronegativity values typed in as comma-separated rows. Blank spaces on the chart are given zeros. The final grid is 12 rows of 20 values each.

Once the comma-separated rows of numbers are done and checked, the students save the array as a raw text file (.txt) so that all formatting is erased. They then load the file up into a program called Image J. This program is freeware developed by the National Institute of Health and is very useful for analyzing images. To load in the number array .txt file, students need to go to the file menu and choose “File-Import-Text Image” and select their .txt file. This will create a grayscale image based on the .txt values: the lowest values (the zeros around the edges of the periodic table) are black and the highest value is made white. It will be a small image since the entire array is 20 by 12 pixels. You can save the image created or zoom in on it as close as it will with Command-+ and save a screen shot of it.

Importing the .txt file as a Text Image into Image J software

Importing the .txt file as a Text Image into Image J software

The original grayscale heightmap is only 20 x 12 pixels. You will need to zoom in and save a screen shot of the image.

The original grayscale heightmap is only 20 x 12 pixels. You will need to zoom in and save a screen shot of the image.

In Adobe Photoshop or GIMP, students load in the screen shot and cut it so only the grayscale area remains, then increase the resolution. You will need to blur it slightly (2-3 pixel Gaussian blur) to get rid of artifacts around the edges of the squares. Then make the canvas square by adding a black background using the “Image-Canvas Size” feature in Photoshop. You can do a similar function in GIMP. Save it as an RGB or 8-bit grayscale PSD or PNG file. This prevents the grayscale heightmap from getting distorted in the 3-D terrain editor.

The grayscale heightmap in Image J after zooming in.

The grayscale heightmap in Image J after zooming in.

Now open up your favorite 3-D modeling software. I use Daz3D Bryce because it makes excellent terrains. Most other 3-D software can do terrains out of grayscale heightmaps. Some free or low cost options are Blender and Autodesk Maya (you can find a free PLE version of it). You will then need to load in the square grayscale file you just made using the “Load” buttons in the Picture tab of the Terrain Editor, smooth it, and put a texture on it.

Electronegativity heightmap after adding black edges to make it a square. This avoids distortion in the 3D modeler.

Electronegativity heightmap after adding black edges to make it a square. This avoids distortion in the 3D modeler.

At this point you have a 3-D terrain showing the strength of a periodic property for each element. I am including several examples here. The models can be animated or have a camera fly around it. You can add lights and render out images, then put together a class powerpoint using all the student’s images to demonstrate periodicity and the Periodic Law.

The Terrain Editor in Daz3D Bryce. The model may need additional smoothing to round off artifacts.

The Terrain Editor in Daz3D Bryce. The model may need additional smoothing to round off artifacts.

I’ve also put together a video that describes the history of the periodic table as narrated by Dr. Eric Scerri of UCLA. You can find it on the video page of this blog.

Electronegativity model in Daz3D Bryce. An altitude sensitive texture has been applied.

Electronegativity model in Daz3D Bryce. An altitude sensitive texture has been applied.

Give it this activity a try and let me know how it turns out. I’d love to see examples of what your students come up with.

Electronegativity model in Daz3D Carrara with a little mood lighting

Electronegativity model in Daz3D Carrara with a little mood lighting

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Periodic Table of Elements

Periodic Table of Elements

I had hoped to have the two episodes on the history of the periodic table ready to upload by yesterday but the editing is progressing slower than planned, mostly because my “day” job has picked up and I am editing Business Profile Videos for three clients at the same time. Work on the Elements Unearthed podcasts has had to take a back seat to actually earning money. It has also taken more time to create the animations for the episodes than expected. I added an extra section to my original script, explaining what elements were known at the time Mendeleev built his table, and since this will be done by narration there must be some sort of visual material to show while the narrator (me) is talking, and I have devised several animations that go along with the script.

I’ve put these animations and a few still renders into a compilation clip that I am attaching to this blog here:

To explain the animations, the first two animations (after four stills) are of A. E. Béguyer de Chancourtois’ Telluric Screw, which was the first table to recognize the periodic law. He envisioned a cylinder with a spiral sequence of the elements, listed by order of atomic weights from the top down. He divided the elements into periods of 16 columns each, so that every 16 positions the pattern repeats, although not every position is occupied (atomic weights often increase by several units from element to element). It works quite well for the first few turns of the screw, but by the time it gets past titanium into the transition metals, the pattern of periodicity starts to break down because, as we now know, the periods of the periodic table aren’t the same length. The second animation shows the alignment of the elements into groups. Here are two still images rendered from the animation that show this alignment of elements by properties.

The Telluric Screw 1

Alignment of Li, Na, and K

Telluric Screw 2

Telluric Screw: Alignment of B & Al, C & Si

The next animation is simply a list of the elements by date of discovery, divided into periods of 25 years. 63 elements were known by 1869. The next animation shows all of the elements arranged in order by atomic number into six columns (there’s no reason for the six; it was just the number that I picked to set up the animation). They are also given colors by elemental families: red for the alkali metals, orange for the alkaline earths, green and blue for the transition metals, indigo for the metalloids, purple for the non-metals, bright purple for the halogens, magenta for the noble gases, and yellow and brown for the rare earths. The next animation shows the same list, but now takes away the elements that were unknown to Mendeleev, leaving only those that he was able to work with when building his table. Only a few rare earths were known, there were significant gaps, and an entire group of elements, the noble gases, was unknown. So trying to organize these elements into some sort of table was a difficult task.

Elements by atomic number

The elements listed by atomic number

The next animation shows this list of known elements moving into position to form Mendeleev’s first periodic table of Feb., 1869. One can see that he made some mistakes – beryllium and magnesium should be moved down to a position underneath lithium and sodium, and he has the rare earths out of place (mostly the trouble was that their atomic weights hadn’t been accurately measured yet). He has gold and mercury reversed, and a few groups shifted. His table is also organized vertically by periods instead of horizontally as is our usual medium format table today. If you were to take his table and rotate it clockwise 90 degrees, then flip the whole table horizontally, it would be oriented as our standard table is today and quite recognizable. This was quite an achievement given the limitations he worked with. His main insight was realizing that the periods didn’t have the same lengths; all his competitors had tried to force the elements into periods of equal lengths and it just wouldn’t work. Another insight was that he realized there were gaps in the table –  jumps of atomic weights and properties, and Mendeleev put himself out on a limb predicting that those elements were yet to be discovered; he even predicted their properties with high accuracy. The three most famous cases were gallium (discovered about five years later), scandium, and germanium.

Mendeleev's first table

Mendeleev's First Periodic Table, 1869

I am still working on several animations and one is rendering right now showing the medium format table opening up to become a long format table; I’ll do another one where the medium format table rearranges itself into a left-step table, and even try a few 3D tables as well. To build these tables, I created each element as a separate, moving tile which can be arranged in any position. The software used is Daz3D Bryce. The music playing in the animations is a simple loop I created using Garageband on my Mac. As for the sample images I’m showing here, feel free to download them and use them however you like as long as you give me credit. I’m trying to provide accurate scientific information but do so with visual appeal and artistic merit.

Meanwhile, editing on the video itself is progressing and I will have these two episodes posted along with the Rationale episode ASAP. I’ll then follow with the beryllium episodes and one on Greek matter theories, then move on to blown glass, cement making, stained glass, synthetic diamonds, and the Tintic mining district in Utah. I hope to have all of these done and posted before March 17, as I will be traveling back to Philadelphia then to attend and present at the National Science Teachers Association annual conference. My proposal to present was accepted by NSTA, and I will need to have several episodes posted by then to use in the presentation, one way or another, even if I have to put some client projects on hold.

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