invisibleV i s u a l i z i n g t h e

t o u r t h e i n n o v a t i v e i d e a s t h a t s h a p e m o d e r n c h e m i s t r y

14oos

Cosmology of an alchemist

Basil Valentine

This traditional image illustrated

17th- and 18th-century editions of an

explanation by a legendary alchemist

of man’s integral relationship with the

universe. Reading inward from the

perimeter of the circle are a statement

of God’s creative activity; the signs

of the zodiac; the three alchemical

elements of salt, sulfur, and mercury;

the four classical elements of earth,

air, fire, and water; and, located on

and around the human figure, the

symbols for the seven planets and

their associated metals.

From ancient times to the present, investigators of the natural world

have created symbols to represent matter and its transformations. These

symbols allow researchers to communicate a level of reality invisible

to the naked eye.

Here you see a selection of such visualizations in two dimensions. The

series begins with an alchemical cosmology and ends with an example

of a substance composed of atoms—depicted in schematic fashion and

photographed with the aid of a scanning tunneling microscope.

invisibleV i s u a l i z i n g t h e

1619

Platonic solids

Johannes Kepler

Kepler presented the connections

that various ancients made between

the regular geometric solids and the

four classical elements, plus a fifth

element added by Plato. In this system

the tetrahedron represents fire; the

cube, earth; the octahedron, air; the

icosahedron, water; and the dodecahe-

dron, the material of the heavens. But

Kepler found another use for these

solids in determining the distances

of the planets from the sun.

1763

Table of affinities

Guillaume-François Rouelle

Columns from a table presenting the

reactive powers of substances display

symbols, many—like the crescent moon,

which represents silver—dating from

ancient times. Each column is headed

by a substance—here nitric acid, sulfuric

acid, and absorbent earth (a weak

alkali)––that will react with the sub-

stances listed below it. The strongest

reactions occur with the substances

closest to the top of a column.

1787

Compound nature of water

Antoine-Laurent Lavoisier, Pierre AugusteAdet, and Jean-Henri Hassenfratz

Because Lavoisier and his colleagues

were reforming chemical nomenclature,

they needed an appropriate chemical

shorthand. Adet and Hassenfratz

accordingly created a new system of

symbols. The symbols shown here

representing water as solid, liquid, and

gas are constructed from that system’s

symbols for oxygen, hydrogen, and heat.

Because it was so abstract, this system

never caught on among chemists.

1853

Crystals of a tartrate

Louis Pasteur

Early in his career Pasteur discovered

that tartaric acid crystals occur in

mirror-image pairs. When he separated

them, he found that in solution one

form rotated plane-polarized light

clockwise, while the other form rotated

it counterclockwise. This course of

research led him to speculate that these

differences must be due to differences

in the spatial arrangement of atoms.

1808

Atoms and molecules

John Dalton

The atomic theory, as advanced by Dalton,

states that substances are composed of

extremely small particles that differ in

number and weight. Dalton proceeded

to calculate the relative weights of these

atoms using assumed molecular struc-

tures and experimental data on what

percentage of a compound is made up

of a given element. To represent such

structures, Dalton created his own sym-

bols. Here nitrogen (2) and oxygen (4)

combine into a number of compounds.

1902

Electronic structure

of atoms

Gilbert Newton Lewis

Cubic atoms, as drawn by Lewis in his

lecture notes early in his career, had

spaces for electrons at each corner of

the cubes––some filled and some vacant.

These atomic models represent the

beginning of the theory Lewis devel-

oped to explain chemical bonding.

As has occurred in the one compound

shown here, NaCl, bonds form between

atoms to make a complete “octet.”

1875

Tetrahedral arrangements

of atoms

Jacobus Henricus van’t Hoff

In a pamphlet published before his

doctoral thesis, van’t Hoff developed

three-dimensional structural formulas

for a variety of carbon compounds.

In these illustrations he envisaged a

carbon atom in the center of each tetra-

hedron with bonds extending to atoms

forming its vertices.

1861

Benzene ring

August Kekulé

Kekulé, one of the founders of struc-

tural organic chemistry, represented

the ring structure of benzene this way.

He drew the carbons with radiating

lines to represent their combining

powers, or valences. The structural

formula that became known as

Kekulé’s––the hexagon with alternat-

ing single and double bonds––was

originally suggested by others, and

Kekulé himself continued to have

reservations about it.

1869

Early table of the elements

Dmitri Mendeleev

This section of Mendeleev’s first

published periodic table shows the

use of the alphabetic element symbols,

which were introduced in the early

19th century by Jöns Jakob Berzelius.

The handwritten notes alongside are

reproduced from the back of a letter

on which Mendeleev had begun to

formulate his famous arrangement

of the elements.

1967

Defect in a crystal matrix

N. Bruce Hannay

Modern solid-state chemistry focuses

on the interesting and important prop-

erties of solids that result from their

defects and imperfections. In this

diagram the repeating cubic arrange-

ments of atoms (or “unit cells”) in one

part of a crystal are displaced relative to

the rest of the crystal. This “dislocation”

can affect the electronic, mechanical,

or other properties of the crystal.

1964

Heme molecule

Linus Pauling

The atoms of the heme shown here

are drawn in space-filling notation

to indicate the amount of space they

occupy––in contrast to the accompany-

ing diagram that implies big gaps

between atoms, which are indicated as

alphabetic element symbols connected

by lines for bonds. Four heme groups

are present in hemoglobin and are

responsible for its ability to distribute

oxygen to the body.

1953

Orbitals for a carbon atom

Linus Pauling

Orbitals delineate regions of space

where electrons are likely to be found

and therefore places where bonds can

form between atoms. The diagram on

the left shows carbon’s lowest-energy

(nonbonding) orbital, which contains

two electrons. The diagram on the right

shows the tetrahedral bonding sites of

molecular carbon made possible by the

promotion of an unpaired electron to a

higher energy state.

1962

Structure of DNA

Maurice Wilkins

The double-helical structure of DNA

proposed by James Watson and Francis

Crick in 1953 is represented here in

much greater detail, with balls for atoms

and sticks for bonds. Wilkins used this

diagram to illustrate his Nobel Prize

lecture when the prize in physiology

or medicine was presented to the three

men. The refinements in this depiction

derived from Wilkins’s further study

of DNA by X-ray crystallography.

1985

Silicon

Jene A. Golovchenko

This image taken by a scanning

tunneling microscope makes visible

the individual atoms on the surface

of a silicon crystal––a feat not possible

with earlier instrumental techniques.

The new understanding of this surface

is diagrammed in perspective ball-

and-stick notation.

1981

Triose phosphate isomerase

Jane Richardson

The ribbon diagram was developed to

represent the secondary structures––

carbon-atom chains and sheets––within

the overall structures of proteins.

Although this diagram was hand drawn,

such “Richardson diagrams” are now

usually computer drawn. They have

become the standard method of

visualizing proteins in order to study

their form and function.

1985

Part of a buckyball

Robert Curl, Jr., Harold Kroto, and Richard Smalley

Buckminsterfullerene is a form of

carbon that was discovered in 1985 by

Curl, Kroto, and Smalley. The buckyball

structure shown here was drawn in

perspective using a computer program

developed well after the molecule’s

discovery. Physical models of buckyballs

sag like aging pumpkins, but computer

models of it or other large molecules

can be ever renewed and manipulated.

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