Abstruse

Since atoms are smaller than the wavelength of visible lite, information technology is theoretically impossible to "encounter" an atom, fifty-fifty with the most powerful microscope. Notwithstanding, we recognize that atoms consist of "shells" of electrons buzzing around a cardinal nucleus. Therefore, it'south common to depict an atom as a uncomplicated sphere, its diameter proportional to the size of its outermost electron shell. Furthermore, scientists take adult experimental methods, such as x-ray crystallography and NMR spectroscopy, to determine the geometric arrangement of atoms within a molecule. These data tin can exist used to construct three-dimensional models of molecules, but the illustrator must be enlightened that such a model is an abstract representation and is not meant to show what the molecule really "looks like".

Cantlet Colors

Considering an atom is smaller than the wavelength of visible low-cal, information technology cannot reflect lite and, therefore, has no colour. The colorful atoms you see in chemical science textbooks are based on conventions that have been adopted by chemists over several centuries. The alchemists of the Middle Ages and the Renaissance used iconic symbols to draw the different elements (Figure 1). They also associated certain colors with each chemical element based on its physical properties, although these colors never appeared in print considering of the rarity of color press prior to the late 19th Century.

By the mid-1800s, it was recognized that atoms bonded to ane another to course molecules. In 1865, the pharmacist August Hoffman gave a Fri Evening Discourse at London's Royal Institution on the "Combining Power of Atoms." In order to demonstrate the chemic bonding of atoms, he drilled holes in croquet assurance and continued them with metal pipes (Figure 2). His choices were limited past the available colors of croquet assurance and he relied on many of the same color conventions that had been adopted centuries earlier:

  • Carbon is colored blackness considering information technology's the color of charcoal.
  • Oxygen is ruddy because information technology's necessary for combustion.
  • Nitrogen is blue because it'south the near arable element in the Earth's atmosphere and the sky appears blue.
  • Hydrogen is white because it forms a colorless gas.
  • Chlorine is green considering it forms a greenish gas.
  • Sulfur is yellow because that'due south its color in mineral form.
  • Phosphorus is orange because information technology glows orange in a flame.
  • Iron is cherry brown considering it rusts.

With small-scale variations, these color conventions are yet in employ today. In the 1950s, Robert Corey and Linus Pauling at CalTech developed a set of wooden atomic models for constructing molecular models. Soon thereafter, plastic molecular model kits became popular in chemical science classes. The Corey-Pauling models were further refined by Walter Koltun at NIH in the early 1960s. The color scheme used in these models is now known as "CPK" after Corey, Pauling, and Koltun. See Wikipedia for a complete listing of CPK colors of the elements: http://en.wikipedia.org/wiki/CPK_coloring

Atom Sizes

In 1945, Linus Pauling described the van der Waal's radius, a measure out of the size of an atom. Strictly speaking, it represents "ane-half the distance between two equivalent nonbonded atoms in their almost stable arrangement." Put another manner, it is the closest that ii unbonded atoms can go earlier they begin to repel one some other. However, nearly people think of it just as the size of the atom's outermost electron trounce.

Many molecular models employ the van der Waal's radius to distinguish the relative size of different atoms and to requite a sense of the overall size and shape of the molecule. Figure 3 shows the van der Waal's radii of the elements bundled in a simplified periodic table (information technology likewise shows the CPK colors of common elements). Note that hydrogen and helium in the acme row are tiny because they take just a single shell with only one or two electrons. As y'all go down the table, from top-to-lesser, the elements in each row are larger because each row adds an additional electron beat. Equally y'all become from left-to-correct across the table, the elements in each column become somewhat smaller. This is surprising considering each column represents the addition of 1 more proton to the nucleus and one more electron to the outermost shell. You lot might presume that this would brand the elements on the right side larger than those on the left. Still, the atoms on the correct are smaller because there is a greater attraction betwixt the positively charged nucleus and negative electrons, causing the electrons to orbit closer to the nucleus.

Representing Molecules

In 1858, the English language chemist Archibald Couper published the offset drawing of a molecule, using simple lines to connect atoms to i another. In the same twelvemonth, Freidrich August Kekulé von Stradonitz published what would later be known equally the theory of valence, that atoms of each element class a specific number of bonds (e.thousand., carbon always forms 4 bonds, nitrogen forms three, oxygen forms two, etc.). In 1874, Jacobus van 't Hoff, a former student in Kekulé's lab, demonstrated that these bonds are bundled in specific geometric configurations. For case, the four bonds of a carbon cantlet are arranged in a tetrahedron, spaced autonomously at equal 109.5° angles. Since then, it has been possible to construct 3D models of simple molecules only past knowing which atoms are bonded to one another. (In larger molecules, such equally proteins and Dna, there are other forces at work and the shape cannot be predicted from bond angles alone.)

Molecular visualization software now makes it easy to create accurate 3D models of any molecule. Figure 4 shows iii mutual methods for representing simple molecules. A stick model shows just the bonds and does not prove the atoms themselves. A ball-and-stick model adds small-scale spheres to represent the center of each atom. A space-filling model uses much larger spheres proportionate in size to each atom's van der Waal's radius. Space-filling models were first developed by Robert Corey and Linus Pauling and later refined by Walter Koltun. Therefore, the acronym "CPK" may exist used to depict either the space-filling mode or the colour scheme used for the private atoms. Figure 5 shows an additional instance of space-filling models.

I am oftentimes asked which type of representation is the best for illustrating molecules. As is often the case in scientific illustration, the answer depends on what you are trying to show. Many illustrators prefer space-filling models because the big spheres lend themselves to dramatic lighting effects (see Figure vi). Withal, one must realize that these effects are purely creative since an atom is incapable of producing a highlight, a core shadow, or reflections. More importantly, a space-filling model completely obscures the bonds between atoms, making information technology nearly impossible to tell which atom is connected to which. Therefore, space-filling models are ideal for editorial illustration simply may not be suitable for a chemistry textbook where it's necessary to see the bonding between atoms.

Illustrating Deoxyribonucleic acid

Because of its central importance to biological science, scientific illustrators are oftentimes called upon to illustrate the Deoxyribonucleic acid molecule. Unfortunately, many illustrations of DNA, even those in scientific discipline textbooks and scientific websites, are inaccurate. In fact, entire websites have been created to catalog inaccurate Deoxyribonucleic acid images, e.1000., the Left-Handed Deoxyribonucleic acid Hall of Fame: http://users.fred.net/tds//leftdna/

All nucleic acids, including DNA and RNA, are formed from subunits called nucleotides. Each nucleotide consists of a base, plus a sugar molecule, plus a phosphate. In DNA, the bases are adenine, guanine, cytosine, and thymine (see Figure 7). Uracil is substituted for thymine in RNA. After improver of a sugar molecule, each base is called a nucleoside (Figure 8). In RNA, the carbohydrate is called ribose. In Dna, it is deoxyribose. Calculation a phosphate to the v' carbon of the sugar molecule creates a nucleotide.

Nucleotides, in turn, are linked into long strands past creating bonds between the phosphate and 3' carbon of the sugar molecule (Figure nine). In Dna, two complementary strands are joined by hydrogen bonds betwixt the bases. The two strands resemble a ladder with the saccharide-phosphates forming the sides of the ladder (or "courage") and the bases facing in to form the "rungs" of the ladder.

The DNA "ladder" is twisted to form the distinctive double helix. Figure 10 is a schematic but highly accurate representation of the double helix, showing the precise measurements (in Angstroms) of each part of the helix. Annotation that there are ten pairs of bases for each consummate plow (wavelength or "pitch") of the helix. Because of the way the ladder twists, information technology forms singled-out major and minor grooves. The major groove is exactly twice the width of the small groove.

Failing to distinguish the two grooves is 1 of the nearly mutual errors in illustrating DNA. Yet, by far the well-nigh mutual error is reversing the handedness of the helix. Every spiral can be described every bit either left-handed or right-handed (Figure 11). For unknown reasons, right-handed spirals are much more common in nature, as well as in man-made spirals such equally threads on a screw. Although a left-handed course of DNA does exist (zDNA), the naturally occurring form found in the nucleus of living organisms (called bDNA) is always a right-handed helix.

Left- and right-handed spirals are mirror images of one some other. Because computer graphics software makes it so easy to flip an image, information technology is very like shooting fish in a barrel to inadvertently opposite the handedness of a Dna helix. I doubtable ane reason for the prevalence of left-handed Deoxyribonucleic acid images is that art directors unwittingly flip the art for purely aesthetic reasons without realizing that it affects the scientific content of the illustration.

DNA tin be represented using whatever of the styles described above (stick, brawl-and-stick, infinite-filling). Figure 12 shows a space-filling model with CPK colors rendered in Cinema 4D. In addition, DNA is often represented as a ladder (as in Fig. 10) or using icons to correspond the nucleotide bases. Figure 12 shows a 3D model of Dna with such icons. This effigy also uses a colour scheme to differentiate the bases. Although non equally universal equally the CPK color scheme, this system is used past some molecular visualization software and by the online Nucleic Acid Database. The arrangement uses the first letter of each base name to determine its colour:

  • Adenine (A) = azure (bluish)
  • Guanine (Chiliad) = dark-green
  • Cytosine (C) = crimson (red)
  • Thymine (T) = "Tweety Bird" (yellow)
  • Uracil (U) = umber (brown)

Well-nigh the Author

Jim Perkins is Professor of Medical Illustration in the College of Health Sciences and Technology at Rochester Institute of Technology. Prof. Perkins is a Board Certified Medical Illustrator (CMI), Fellow of the Clan of Medical Illustrators (FAMI), and currently serves equally President of the Vesalius Trust for Visual Advice in the Health Sciences. An adept in the visual communication of complex biomedical subject field matter, particularly in the areas of prison cell biological science, molecular biological science, physiology, and pathology, he has illustrated over xl medical textbooks and serves as a consultant to major medical publishers.

Prof. Perkins received his Bachelor's degree in Biology and Geology from Cornell University (1985), and studied paleontology and anatomy at the University of Texas, Austin and University of Rochester, completing his PhD coursework (1989). He received an MA in Medical Illustration from RIT (1992), and following work in medical publishing and the medical legal exhibit field, he joined the RIT kinesthesia in 1998.

Figures

> Fig. 01 – Before color printing was widely available, elementary geometric symbols were used to designate the different elements. from Dalton, James. 1808. A new theory of chemic philosophy. 1=hydrogen, 2=nitrogen, 3=carbon, 4=oxygen.

> Fig. two – Pharmacist August Hoffman used colored croquet balls and metal pipes to demonstrate the bonding of atoms to class molecules. From Hoffmann, August. 1865. On the combining power of atoms. Proceedings of the Royal Institution 4: 401-430.

> Fig. 3 – A simplified periodic table showing the Van der Waal'southward radii and CPK colors of the elements. Annotation that the atoms become larger going from top to bottom and slightly smaller going from left to right.

Fig. 4 – Vitamin A (all-trans-retinol) depicted using three mutual representations. A tick model emphasizes the bonds and hides the atoms themselves. A ball-and-stick model adds small spheres to represent the atoms. A space-filling or CPK model represents each cantlet past its Van der Waal's radius.

Fig. 5 — A infinite-filling model of the chemotherapy drug gemcitabine used on the cover of a cancer periodical.

> Fig. half-dozen — Computer-generated representations of the cancer drug doxorubicin (pinnacle) and vitamin E. These illustrations use a great deal of artistic license since atoms are smaller than the wavelength of visible light and, therefore, cannot take highlights, shadows, or reflections.

> Fig. 7 – The bases adenine, guanine, cytosine, thymine, and uracil.

> Fig. 8 – After adding a sugar molecule, each base of operations is called a nucleoside. The sugar can exist either ribose (in RNA) or deoxyribose (in Deoxyribonucleic acid). Addition of a phosphate grouping creates the 5 nucleotides.

> Fig. 9 – Bonding between the phosphate of one nucleotide and the carbohydrate of some other can create long strands of nucleotides. In DNA, two strands are joined together past hydrogen bonds connecting the bases. The sugar and phosphate groups form the courage or sides of a "ladder' while the bases confront one another to form the rungs.

> Fig. x – A schematic illustration of bDNA with accurate proportions and features. at that place are x base pairs for each complete turn (pitch) of the helix. the double helix has singled-out major and minor grooves, the major groove being twice the width of the minor.

> Fig. 11 – Comparison of left- and right-handed spirals. In a left-handed spiral, if you wrap the fingers of your left hand around the spiral, it "moves" in the direction of your left thumb. In a correct-handed spiral, wrap the fingers of the correct hand around the spiral and it moves in the direction of the right pollex. These spirals are mirror images of i another, so flipping such an image in the computer changes the handedness of the spiral.

> Fig. 12— Three-dimensional infinite-filling model of bDNA rendered in Movie house 4D.

Fig. xiii — Schematic representation of DNA using the nucleotide color scheme generated using UCSF Chimera molecular visualization software.

Notes

This article appears in the 2011 Journal of Natural Science Analogy.