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Organic Pigments – the inside (the cell) story

Last time on the blog we discussed inorganic natural pigments: natural colors from mineral, geological sources. This time we will talk about natural organic (meaning, containing tetrahedral carbon, as opposed to inorganic carbonates or graphite or diamond) pigments, of plant and animal origin.


But first, some breaking news: An organic pigment, thought to be lost to history, has been rediscovered in its plant source, and has been for the first time chemically characterized. Portuguese scientist Paula Nabais, from the Universidade NOVA de Lisboa, and her colleagues reported last week in Science Advances (a publication of the American Association for the Advancement of Science) the results of a thorough historical and chemical investigation into folium, a stable blue pigment used in the Middle Ages for manuscript illumination, but unfamiliar and unavailable to artists in the modern era. Dr. Nabais and her colleagues read primary sources from the Middle Ages up to the 19th century CE to learn how medieval artists identified the plant (Chrozophora tinctoria) and extracted its water-soluble blue color (including some tricks and tips that may have stymied modern researchers trying to recreate the historical pigment). They then used state-of-the-art spectroscopic techniques and computer modeling to elucidate the exact chemical structure of the pigment extracted from the plants and to confirm its absorption spectrum. The pigment thus described was new to science, and was given the name chrozophoridin by Dr. Nabais and her coauthors. This is very exciting, and may lead to this ancient color returning to modern works of art.

The fruits of Chrozophora tinctoria, examples of the water-soluble folium pigment solution adsorbed into linen clothlets, and the chemical structures of hermidin (a precursor) and the newly described chrozophoridin. Figure 1 from P. Nabais, J. Oliveira, F. Pina, N. Teixeira, V. de Freitas, N. F. Brás, A. Clemente, M. Rangel, A. M. S. Silva, M. J. Melo, Science Advances 17 Apr 2020 : eaaz7772.

Organic (and organometallic) pigments differ from the inorganic pigments because of the presence of organic carbon. Carbon has several chemical forms: carbonate, graphite, diamond, and organic. Organic carbon’s particular chemical properties and reactivity have made it the basis for all biochemicals (at least on this planet). Carbon becomes organic by way of photosynthesis, in which carbon dioxide (a non-ionic inorganic form of carbon) is reduced (meaning, electrons are added), and incorporated into (at first) simple sugars, which then go on in metabolism to make carbohydrates, proteins, lipids, nucleic acids – all the useful biochemicals. Most biochemicals are, however, largely colorless, particularly in solution; think of egg whites (proteins) or sugar syrup (carbohydrates). They absorb ultraviolet light, but we can’t see this (sometimes, if the absorption spectrum is strong enough, these look somewhat yellow, as the absorption peak spills over into visible light). However, some biochemicals, including some that are in coordination with metal ions, have chemical structures that result in absorption peaks in the visible wavelength range, which means they have color. These compounds, or the portions of the compounds that are responsible for light absorption (if it’s a large compound) are frequently called chromophores.

The chemical structure of beta-carotene. Double bonds are shown as parallel lines: single bonds as single lines. Each “corner” or end of a line segment represents a carbon atom. In this kind of diagram hydrogen atoms are not shown, and you just know that there are sufficient hydrogens at each corner or end to add up to 4 bonds coming from each carbon atom. Other elements are shown by their abbreviations, but beta carotene contains nothing but carbon and hydrogen.
The alternating single and double bonds give rise to its familiar orange color.

What gives chromophores their optical properties is a particular chemical structure: alternating single and double bonds (often called conjugated bonds) between carbon atoms. This structure creates a ‘cloud’ of electrons with energy levels that can be similar to visible light photons (and thus result in absorption of the photon). The location and shape of the resulting absorption peaks depends on the number of conjugated bonds, and the shape of the structure itself. Orange and yellow carotenes, for example, are long lines of conjugated bonds, with some stuff at either end. Rings are frequently found in these structures. In The Science of Pigments we talked about the porphyrin rings that bind up metal ions to make chlorophyll or heme (found in hemoglobin or cytochromes). Open up this ring, remove the metal ion, and you get a bilin, which is a chromophore found in blue-green algae or, yes, bile. Eww.

An important chemical structure that is often part of chromophores is a ring of six carbon atoms, with alternating single and double bonds that make what is called an aromatic structure. Aromatic structures are very important biochemicals because they not only occur in strong-smelling compounds (thus the name), but they are also very chemically and physically stable. They resist chemical and physical attack quite well. Hold that thought, because one of the main factors that regulate whether a biological pigment is useful for making artistic pigment is its stability. We don’t use chlorophyll a as a painting pigment in part because if you expose it to acidic conditions or even just look at it funny the chromophore will give up its magnesium ion and turn from a lush blue-green color to a dispiriting gray in an instant. And the brilliant colors of anthocyanins of flowers (and purple carrots) can fade quickly (how disappointing it is to cook a purple carrot and see that color lost – in this case the orange or yellow carotenes are far more stable than the purple anthocyanins).

But for a moment let’s consider the role of pigments in organisms. In some cases, but not necessarily all, the color of the pigment plays some sort of crucial role in the life of the organism; sometimes the color is incidental. But, the electronic arrangements that make them able to absorb light makes them uniquely useful as biochemicals. Pigments, such as chlorophylls, absorb light energy for the purpose of photosynthesis; also, pigments can block excess light from damaging cells, like the yellow lutein or flavonoids found in land plants, or melanin in some mammals. Pigments, such as cytochromes (heme containing) are involved in electron transport chains in everything from bacteria on up, used in photosynthesis and respiration to generate chemical energy for cells. Lots of vitamins contain chromophores – and in fact the important role of translating light flux into nerve impules in the eye is played by a carotenoid derivative, retinol. Red colored heme is also found in hemoglobin, where it is used to transport oxygen through blood in many organisms. And, importantly, organisms use pigments as color for recognition purposes (colors and patterns so members of the same species can recognize each other so as to avoid mating … accidents, warning coloration for poisonous organisms), and for stealth. The bright colors of flowers, often from a diverse group of organic compounds called anthocyanins, help their pollinators recognize them (many bees can see into the ultraviolet so some flower pigments have features invisible to our eyes but stand out quite obviously to the right bee). Unfortunately, despite the wide range of colors all across the spectrum that can be produced by organic pigments, not all are suitable for making paints or dyes. The main reason for this is stability. Many of these biochemicals are evolved to be reactive: biochemical processes in the cells transform them into something else, but they can subsequently be recycled by other biochemical processes. Away from the cellular machinery that maintains them, organic pigments can break down, fall into disrepute, become fugitive.

The chemical structure of indigo. Black balls are carbon, blue are nitrogen, red are oxygen. The dotted lines indicate the aromatic structures. Via Wikipedia, by Jynto.
This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication.

One example of a reputable, upright, good citizen amongst organic pigments is the familiar blue of indigo. Indigo has a chemical structure that contains not one but two of those aromatic rings, in part leading to its resistance to degradation by enzymes and ultraviolet radiation. The exact role of indigo and its precursors in the cell is obscure, but it is derived from the amino acid tryptophan (which does not make you sleepy, and isn’t particularly abundant in turkey, but contains an aromatic ring, and is a component of most proteins and enzymes in all cells). Indigo is also widely distributed, occurring in multiple plant species around the world. The same pigment is found in ‘true indigo’ in the Indian subcontinent, woad in Europe, anil in America, and dyer’s knotweed in Asia. Amazingly enough the important historical color Tyrian purple contains essentially the same chemical compound as does indigo and woad, but its source is the shell of a marine snail.

Indigo requires some chemical gymnastics to properly implement as a dye or pigment (the topic of a future article?) but once extracted and properly prepared, provides a stable and beautiful color.

Yarn dyed with madder, Colonial Williamsburg (modern era). This illustrates the range of colors that can be realized from the same plant material. Photo: Madison60, licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

Another important historical color that is known to be less of a good pigment citizen is madder. Madder is a medium sized (up to 4′) plant whose roots contain a couple different closely related anthoquinones (not terribly different from the quinine in your gin and tonic, cheers), alizarin and purpurin. These can function as antioxidants and antimicrobials in the plant, and incidentally happen to have crimson and purple colors that were much prized in the middle ages for dyeing. Madder is known to be rather fugitive as a pigment for paints (mean it breaks down over time as a result of oxidation by oxygen or sunlight), and has been largely replaced by synthetic dyes. However, madder gives us a good transition to the end of this article, as madder is one of the earliest examples of pigments that were known to have been chemically altered by people to make their properties more useful. Next time we’ll talk about ancient and modern methods of altering natural products to better suit our purposes.

Thank you for joining us as we do Pandemic Projects, meant to keep you energized, curious and learning!

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Pigments in the Landscape

Last time we talked about the physics and chemistry of pigments, both natural and synthetic, and how they come to have the colors that we value. This time we’re going to discuss natural earth and mineral pigments, their origins, and their mineral and chemical composition.

The Altamira cave bison paintings date from 20,000 years BCE. The ancient artists used ochre and hematite-containing clays for the red, yellow and brown tones, and charcoal for the black lines. Reproductions at the Museo del Mamut, Barcelona 2011. Photo by Thomas Quine. This file is licensed under the Creative Commons Attribution-Share Alike 2.0 Generic license.

Natural earth pigments are, according to archaeologists, some of the earliest pigments used for art by humans. The earliest paintings known included paints made from earth pigments, and charcoal. Earth pigments are, in their simplest form, soil that lacks organic matter, composed of mixtures of minerals, some of which confer color to the mixture. Soil can be classified by its mineral composition and its particle size, with clay being much smaller than (for example) sand particles. Clays are generally formed in river beds, with the action of flowing water grinding the mineral particles down to tiny sizes. But massive clay deposits, relics of ancient water bodies, are found in rocks on dry land as well. The earliest artists used naturally occuring clay of varying colors as the basis for their pigments, as the fine grains of clay are best for making smooth, regular pigment powders that can be mixed with binders or dispersants to make paints.

The clay deposits found in Roussilon, France, were a major source of ocher pigments in the 18th and 19th centuries.
Photo by “BlueBreezeWiki.” This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

The bulk of the material in earth pigments is not the actual mineral that confers the color. The deposits of colorful clay that ancient and modern artists use come from the erosion of rocks into tiny particles, and reflect the origin and chemical composition of the original rocks. For the most part, these are mostly varying degrees of black or white or even crystalline and clear. Take a look at your beach sand. If your beach sand comes from the erosion of mixed continental rocks, you will see individual bits of clear quartz, or black or gray bits of other kinds of rock, mixed in with a few brightly colored grains of minerals. If your beach sand comes from fresh(ish) lava deposits, it could be very black. If your sand comes from coral reefs or limestone, it may be bright white. The famous pink sand beaches in Bermuda are mostly pure white grains of calcium carbonate from coral reefs, with a few bright red shells of a particular foraminiferan (a microorganism that makes a red calcium carbonate shell). If you were to clean and dry and grind Bermuda sand to the consistency of clay, you would have a pale pink pigment powder. Most of the naturally occurring earth pigments are similar sorts of mixtures; a ground of silicate-containing mineral rocks of no particular color, with bright mineral additives. Some synthetic pigments are made this way; a colorless natural earth is doped with a brightly colored synthetic mineral, so that it behaves similarly to a natural earth when used in pigments.

The most common and robust colors in natural earths are of course the reds and yellows and browns. These colors almost all come from various forms of iron oxide, complexed with water and oxygen in various ways that result in different shades, and mixed of course with the background material. Iron is quite abundant in the universe, as it is the heaviest element that can be made by the nuclear reactions of a normal star. To make larger elements requires a supernova explosion, and those are rather rare. So it is no surprise to see the familiar colors of rust and earth pigments in the canyons of Mars, the ice sheets of Europa, and the craggy surface of distant Pluto. Metallic iron, combined with water, leads to the familiar rust, which is one kind of iron oxide. Other iron oxides are formed through geological processes, involving heat or pressure or exposure to oxidixing chemicals other than water.

Purple sand at Pfeiffer Beach, Big Sur, also contains a black magnetic ferrous mineral. Fun stuff!

The mineral that gives yellow ocher its color is called limonite (not surprisingly). It is a hydrated iron oxide, which means the iron oxide (plain old rust) is complexed with water in a more or less permanent way that changes the electronic structure of the metal to change its absorption spectrum. The red in natural pigments often comes from hematite, which is an anhydrous (lacking water) iron oxide. Some hematites look purple (as in the sand at Pfeiffer Beach, in Big Sur), but it is the same mineral, and a feature of the grain size causes the red to have a purplish tone. Grinding the sand down to clay size may, sadly, eliminate the purple. Green colors in some natural earths come from iron in a different oxidation state, complexed with magnesium and aluminum, in minerals like celedonite (also, not surprisingly named).

Historically, natural clays found in the landscape were used by artists for pigments, giving each their local flavor. When trade began moving materials long distances across the Earth, pigments went with them. Desirable colors found in deposits in particular locations the world have become standards. For example, clay deposits found near the city of Siena or the region of Umbria in Italy have given their names to the colors that derive from their pigment powders. Sienna and Umber pigments have more manganese oxides than ocher pigments, leading to darker colors. Heating sienna and umber pigments causes some of the iron oxides to dehydrate, further darkening their color and leading to burnt sienna or burnt umber.

Naturally occuring colored clay is not the only way to obtain a natural mineral pigment, however. Certain minerals that occur in interesting colors and in large enough deposits can be ground finely to make a pigment directly. These minerals generally originate from infrequent and inconveniently located geological processes, deep in the earth. Making them available for use on the surface requires uplift of the regions where they occurred, and erosion to expose them, and perhaps even mining into the earth to find them. Frequently these situations occur in the high mountains of the world, where uplift and erosion can be ongoing processes in the present.

The most precious pigment used in Europe in the ancient world and the middle ages – more expensive than gold! – was ultramarine, made from finely-ground bits of the semiprecious stone lapis lazuli. Lapis lazuli is a metamorphic rock (meaning, transformed by temperatures or pressures deep in the earth) found in several places around the world, but most importantly in the mountains of Afghanistan. Lapis lazuli from Afghanistan traveled very far in the ancient and prehistoric world, with ancient examples of lapis beads found in west Africa, and famously on the coffin of the pharoah Tutankhamen. The mineral that gives lapis lazuli its lovely blue color is called lazurite. The rock itself is often found with inclusions of pyrite (a shiny, gold or brassy iron mineral). The blue itself comes from a particular ionic state of sulfur. Burning sulfur in an oxygen atmosphere can produce blue flames (don’t do this). Another place you can see blue sulfur is erupting from the famous sulfur volcanoes of Jupiter’s moon Io. Iozurite, a blue pigment similar to lapis lazuli, may be a very precious AEP product of the far future.

Green malachite and blue azurite are found in this rock from Arizona.
Photo by Robert Lavinsky. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

As you can imagine, from ancient times people have ground up interesting colored rocks and minerals to try and make pigments (at this point I should caution you not to grind up the gorgeous blue-green serpentine rocks of central California as this could be hazardous; the fibrous minerals are similar to asbestos). The ancients were familiar with the bright green mineral malachite as a copper ore: heating malachite over a hot fire causes it to break down and release the copper metal. But they also ground malachite to make a green pigment. Malachite is found in the deposits of ancient limestone caves, where mineral rich water ran over the calcium carbonate, producing reactions that precipitated the mineral into a solid. Deposits of malachite in the Fertile Crescent supplied the ancient world with copper for making bronze, but malachite is found in many places around the world. Malachite sometimes occurs alongside azurite, also a copper mineral, which is a bright blue. Azurite was also used as a pigment (like ultramarine, it is rare and expensive). Turquoise is another mineral rock whose blue color comes from copper, and whose formation involves the weathering of rocks (igneous, rather than carbonate). Deposits of turquoise are found in many places and it is one of the most important gemstones worldwide. Turquoise can be ground to make pigment, but it is more precious than malachite so this was rare.

Of course, artists have never been limited in the colors they use by what they can dig up from the ground. Next time we’ll talk more about organic pigments, derived from biological materials, and their origins.

Thank you for joining us as we do Pandemic Projects, meant to keep you energized, curious and learning!

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Urban Raptor

One of our artists lives by the Los Angeles River. This week some wildlife (unrestrained by quarantine travel restrictions) came to visit. Here is her account of the Cooper’s Hawk (Accipiter cooperii) that lives on her street.


A few weeks ago I was FaceTiming with friends while walking to the mailbox, when something big and silent flew right over my head. My jaw dropped. It had a long narrow tail like a falcon– I knew it wasn’t a Red Tailed Hawk. I decided to do some Birding from Home and see if I could catch sight of this elusive newcomer again.

In the morning, I sat on the porch with my coffee and kept a keen eye out. I noticed a huge crowd of little birds. Aside from a noisy pair of mockingbirds, there are Cedar Waxwings, mourning doves, fighty little hummingbirds, bright yellow Western Tanagers, phoebes, sparrows, and even blackbirds. I kept coming back at 7:45, but no hawk.

One morning, I slept in a little bit, and came outside to an eerily quiet street. Aside from the constantly noisy mockingbirds, the other little birds were being veryyyyy quiet. Interesting. Someone must be hunting… I took a seat and waited.

..and finally spotted a Cooper’s Hawk!

Over the next few weeks I kept coming out to check on my new neighbor, but she was too good at social distancing!

Finally I got my chance.

I couldn’t believe she was perched so close by.

Then I tried to get closer by taking pictures *through* the binoculars, with interesting results!

Looks like I shot it with a Holga! 

Here you can see how the head shape is so different from a Buteo (Red tails and Red-shouldered). Tiny little beak! Long, narrow tail. Amazing flat top hair style!

These pictures don’t do justice to her deep amber eyes, which have a fierce red gleam in the sunlight.

Accipiters are known for their agile hunting style. Unlike Red Tails who drop down suddenly on their prey from above, Accipiters often hunt in wooded areas, turning tightly around trees to pursue small birds.

My neighbor was perched with one foot lifted, looking around and listening carefully. Suddenly she launched herself from the branch and wheeled around to silently dispatch some unlucky squawking thing in the next tree over, which sadly I couldn’t see!

Stay tuned for updates on this fascinating neighbor. And remember–be like the Cooper’s Hawk and practice social distancing!

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OGRs in the Garden

Ogres are fairy tale creatures, meant to scare the listener or reader with their fearsome looks or behavior. A charming exception to this image are the movie characters, Shrek and Fiona.

To a rose lover and history buff an OGR is an Old Garden Rose! Generally, these are roses that were known to cultivation prior to 1867, at which point the first Hybrid Tea rose, “La France” was introduced. This was the beginning of modern Hybrid Teas, Floribundas, Grandifloras, Miniatures and Shrub roses.

Old roses existed in Europe long before but were generally once-blooming per year. These include the Alba, Centifolia, Damask, Gallica and Moss roses. The famous “Apothecary’s Rose” or “Red Rose of Lancaster” is a Gallica.

In the late 1700’s there was fierce competition by explorers, collectors and botanists (plant scientists) to bring back the newest and rarest of botanical “finds” from their distant travels. In the mid 1790’s several China roses made it to Europe causing a sensation with their ability to be ever-blooming. One of the botanists active during 1843- 1861 was named Robert Fortune. He worked in China, Japan and Taiwan collecting some 250 plant species.

Fortune’s Five Colored Rose (before 1844) also known as Smith’s Parish (red), rediscovered in Bermuda in the 1960’s.

Once China Roses (and “Tea-scented China Roses”) were introduced, their ability to bloom multiple times per year brought them into breeding programs resulting in the Bourbon, Hybrid Perpetual, Noisette and Hybrid Tea roses.

Rosette Delizy a charming Hybrid Tea Rose with tea fragrance. Nabonnand, 1922
Monsieur Tillier, lovely multicolored Hybrid Tea rose of salmon, pale pink and purple. Berniax, 1891

Bermuda Mystery: Priscilla’s Rose, found in the garden of Priscilla Brewer

Lovers of OGR’s and Antique Roses know that rare or varieties thought to be extinct can be found in surprising places like old homesteads, very old church grounds, towns and countries with a long, sea-faring history such as Bermuda. Bermuda Mystery Roses include candidates for “Hume’s Blush”, locally known as “Spice”, “Slater’s Crimson China”, locally known as “Belfield” and five others.

Bermuda Kathleen (a sport of Mutabilis) on left; Mrs. B. R. Cant and Mons. Tillier at center; Bermuda Trinity at right.

Older roses have a soft charm to them, are scented, and are remarkably care-free; requiring little pruning, are hardy and remarkably disease-resistant. Organic rose gardening is a balancing act, allowing beneficial insects, using compost tea, mulching with compost, amending the soil to feed the plants and the beneficial soil microbes.

My thanks to Antique Rose Emporium, helpmefind.com (rose search), Dave’s Garden, Wikipedia, Monticello.org, Smithsonian.org and the Bermuda Rose Society for their websites and published works. Any omissions or mistakes are my own.

Thank you for joining us as we do Pandemic Projects, meant to keep you energized, curious and learning!