History

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2 History

The Sun symbol representing gold during Alchemy era

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3Chemical Symbols

Chemical nomenclature and symbols are two of the most important parts of the language of chemistry. Early nomenclature was completely empirical. As aresult, the confusion arose between substance names and their chemical properties. For example, “oil of vitriol” was the name of sulfuric acid, which is not an oil at all. By the mid-18th century, a large number of new substances were discovered thanks to the rapid development of chemistry. The old no-menclature could no longer meet the needs of chemist. Finally, at the end of 18th century, Antoine Lavoisier started chemical revolution, replacing the old empirical nomenclature with a new one based on chemical composition and properties.

The earliest use of chemical symbols could be traced back to ancient Egypt glyphs and Greek manuscripts. Experts think that a small number of chemical symbols could be evolved from Egypt glyphs; a few others came from Greek manuscripts. The majority symbols used by al-chemists from the 17th to 18th century were created by the alchemists themselves. Some of the alchemy symbols were pictorial representations of the chemical apparatuses, while others were just random graphical constructions. The main purpose of using symbols was to reduce texts and improve the reading speed of alchemy books. However, many alchemists believed that the secrets of philosopher’s stone were hidden within the symbols and worked endlessly to decipher them. Also, alchemy symbols could also cause confusion: some symbols with dif-ferent meanings looked very similar, and same symbols might be used to indicate different meanings by different alchemists. Because of the mystical and confusing nature of alchemy symbols, some scholars created new symbol systems to replace them. Lavoisier proposed that chemical information should also be encoded in symbols. In 1808, John Dalton published a new symbol system which was an important achievement. Dalton designed a circular symbol for each element known in his time. In his system, a compound was a graphic assembly of the element symbols based on their proportion. However, Dalton’s symbols were not easy to write and remember, just like old alchemy symbols. We should thank Jacob Berzelius for the chemical symbol system we are using today (e.g. Na stands for sodium, NaCl for salt, and H2O for water). Although Berzelius was not the first person who used the initial letters of element names as symbols, he was the first to apply this system to all the chemical substances known at his time.

Chemical Symbols–Part of Chemical Language

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4 History

Fire

EarthAir

Ether

Water

Kepler’s fifth element. The well-known concept of modern elements was proposed by Antoine Lavois-ier at the end of 18th century. Prior to this, the four-element theory, including “fire”, “water”, “air”, and “earth”, or the five-element theory with “ether” as the fifth element dominated the outlook of the world among western scholars. In Harmonice Mundi published in 1619, Kepler associated the five elements with five platonic polyhedra. According to Kepler’s point, as the most penetrating element, “fire” should correspond to tetrahedra because it is the sharpest in platonic polyhedra. “Ether” is different to all other elements. Because it doesn’t have essences such as “cold”, “hot”, “dry”, or “wet”, it should be related to icosahedra which is the closest to spheres. In the above figure, icons next to text are the corresponding symbols. [Figure reference: Kepler, J. Harmonice Mundi (1619)]

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5Chemical Symbols

S

GoldAu

SilverAg

CopperCu

IronFe

LeadPb

AntimonySb

SulfurS

MercuryHg

Hydrochloride acidHCl

Nitric acidHNO3

Sulfuric acidH2SO4

Calcium carbonateCaCO3

Potassium carbonateK2CO3

Ammonium hydroxideNH4OH

Acetic acidCH3COOH

AlcoholCH3CH2OH

Alchemy symbols.The above figure is the part of alchemy symbols published in “table of affinities” by Geoffroy in 1718. Similar symbols were widely adopted in the alchemy era after Renaissance. Geoffroy’s “table of affinities” prompted the popularity of alchemy symbols. Geoffroy believed that those symbols in the table could make a clear relationship of chemical reactions between each substance. However, more and more scholars rejected these symbols due to their shortcomings of mysticism, difficulty to re-member, and confusion. In 1813, Berzelius upgraded the chemical symbol system. (The only difference between his system and modern one is that he used superscripts instead of subscripts to represent the proportion of elements.) In contrast to alchemy symbols, modern chemical symbols are informative and much easier to write and remember, especially when it comes to represent the chemical composition and molecular structure of organics. [Figure reference:Geoffroy, É. F. Mémoirés de l’Academie Royale des Sciences (1718)].

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6 History

De Broglie's wave

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7Atomic Structure

The atomic theory has been around for a long time. However, from its inception by ancient Greek philosophers in the 5th century BC to its revival by scientists such as Boyle and Newton during the Renaissance, atomic theory seemed to be more relevant to philosophy and physics but not very useful to explain chemical properties of matter.

In the early 19th century, Lavoisier’s theory of chemical elements and Proust’s law of constant proportion of chemical compounds set a foundation for Dalton’s atomic theory. In 1803, Dal-ton described his theory clearly in his notebook: 1) Chemical elements are composed of very small, indivisible atoms. 2) All atoms of an element are the same, atoms of different elements are different, and the difference is in the weight of atom. 3) The ratios of different atoms in compounds are simple numerical ratios, such 1 : 2 or 2 : 3. Dalton’s theory provided a clear microscopic explanation to Proust’s law of constant proportion, and it was quickly accepted by chemists. Later with the development of analytical chemistry, all atomic weight and chemical formula of compounds were determined.

The discovery of the electron at the end of the 19th century invalidated the indivisibility of Dalton’s atom. In the early 20th century, many models of the internal atomic structure were proposed. In 1913, Bohr presented a revolutionary quantum atom based on Rutherford’s nucleus model and Planck’s quantum theory. With Bohr’s model, the emission spectrum of atomic hydrogen could be beautifully explained with very simple mathematical equations. Bohr’s model was a triumph of quantum theory in the early 20th century. Later, the estab-lishment of quantum mechanics completely changed our understanding of the atomic world. Today scientists are continuing the research on the atomic structure. Nuclear physicists are working on problems such as how protons and neutrons arrange inside a nucleus and what is the ultimate size of a nucleus. We now know that protons and neutrons are made of even smaller basic particles (quarks). By conducting high-energy experiments inside magnificent particle accelerators, particle physicists are now searching for the basic particles of matter and radiation (such as visible light), to answer the ultimate question: where does matter come from.

Atomic Structure–From Atomic Theory toQuantum Mechanics

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8 History

I Z C L S P G

HydrogenH

CarbonC

OxygenO

PhosphorusP

SulfurS

IronFe

ZincZn

NitrogenN

CopperCu

LeadPb

SilverAg

PlatinumPt

GoldAu

MercuryHg

Carbon monoxideCO

Carbon dioxideCO2

Nitric oxideNO

Nitrous oxideN2O

Dalton’s atomic theory. Greek philosophers first introduced a primitive atomic theory in the 5th century BCE. After Renaissance, Scientists such as Boyle and Hooke picked up atomic theory or p-what again and used it to explain natural phenomena. Dalton first detailed his atomic theory in 1803. Two major differences between his theory and the previous ones are: 1) different elements are composed of different atoms, 2) different atoms have different weight. In the early 19th century, Dalton’s theory was widely accepted by chemists, advancing the development of chemistry at the theoretical level. In his book A New System of Chemical Philosophy published in 1808, Dalton designed a circular symbol for each element known in his time and used combination of these symbols to represent compounds (above). Because it was difficult to determine accurate atomic weights, Dalton’s atom ratios of many compounds were wrong. Here we only show a few of his compound representations with correct atom ratios.[Figure reference:Dalton, J. A New System of Chemical Philosophy (1808)].

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9Atomic Structure

Dynamid Model

Plum Pudding Model Nuclear Model

Saturn Model

Early models of atomic structure. Dalton’s atoms are indivisible hard spheres. Since Thomson discov-ered the electron in 1897, however, new experiment evidence made scientists realize that atoms might have sophisticated inner structures. In the early 20th century, many atomic models emerged. Four of them are presented in the above figure, with red and blue colors representing positive and negative charges, respectively. In Dynamid Model, proposed by Lenard in 1903, the atom is an empty shell with dynamids in the center. A dynamid is made of a single positive charge and a single negative charge con-nected together. In Saturn Model, proposed by HantaroNagooka in 1904, the atom is similar as Saturn, with electrons orbiting a positively charged sphere in the center. In Plum Pudding Model, proposed by J. J. Thomson in 1904, the atom is composed of a positively charged shell and electrons imbedded in the shell. In Nucleus Model, proposed by Rutherford in 1911, the atom consists a positively charged nucleus in the center and electrons moving around it. The nucleus is very small but contains nearly all of the mass of the atom.[Figure reference:Ihde, A. J. The Development of Modern Chemistry (1964)]

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10 History

Bohr’s quantum atom. In 1913, Bohr proposed a new quantum atomic model, which was one of the most revolutionary theoretical models in the history of science. Bohr’s quantum atom is similar to a microscopic solar system, with a series of electron orbitals circulating the positively charged nucleus in the center. Every orbital is characterized by a specific energy, with lower-energy orbitals closer to the nucleus and higher-energy orbitals further away from the nucleus. An electron must belong to a certain orbital, with its energy the same as the orbital’s. An electron can transfer from one orbital to another only if it absorbs (for low-energy orbital to high-energy one) or emits (from high-energy orbital to low-energy one) a photon and the photon’s energy is the same as the energy difference of the two orbit-als. Bohr’s model provided perfect explanation to the hydrogen atomic spectrum (above we showed the corresponding electron transition of Lyman, Balmer and Paschen series of hydrogen spectrum), and set a foundation for Lewis’ chemical bond theory. In 1922, Bohr was awarded the Nobel Prize in physics for his contribution in quantum atomic model.[Figure reference: Bohr, N. Phil. Mag. 26, 1 (1913)]

1

2

3

4

5

6

Nuclear

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11Atomic Structure

Atomic orbitals of quantum mechanics. Although Bohr’s quantum model successfully explained some properties of hydrogen atoms and other single electron ion such as He ion, it was very limited for multi-electron atoms. From 1920 to 1930, de Broglie, W. Heisenberg, I. Schrodinger, and other phys-icists established quantum mechanics, which became the fundamental theory for understanding the atomic and molecular world. In quantum mechanics, an atomic orbital is interpreted as the possibility of finding an electron around a nucleus, which can be calculated using the elegant Schrodinger equation. To make these abstract mathematical concepts more intuitive, chemists usually use graphics to represent atomic orbitals. For the orbitals above, the 3D surfaces are selected based on isosurfaces, inside which the possibility of electron occurrence is 90%. (Figure reference: the three-dimensional atomic orbit mod-els by Dr. S. Immel from Darmstadt Applied Science and Technology University)

2p Orbital 3d Orbital 3d Orbital

4f Orbital 4f Orbital 4f Orbital

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12 History

Electron distribution inside hydrogen molecule.

London, F. Zeitschrift für Physik 46, 455 (1928)

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13Chemical Bonds

Chemical bond is a very important concept in chemistry. Atoms join together via covalent bonds to form molecules. Positive and negative ions form ionic crystals through ionic bonds, and metal atoms form crystals by metallic bonds. All chemical bonds involve electrons. How-ever, before the discovery of the electron, there were a few primitive theories of chemical bonds. For example, In Opticks, Newton wrote “particles attract one another by some forces, which, in immediate contact is exceedingly strong, at small distances performs the chemical operations above mentioned, and reaches not far from the particles with any sensible effect.”

After Bohr’s quantum atomic model, the most influential chemical bond theory is the one based on the octet rule proposed by Lewis in 1916. Using the octet rule, Lewis successfully ex-plained the formation of ionic bonds inside ionic crystals. In addition, he introduced the con-cept of electron pair and covalent bond. Even today, we are still using electron pairs and Lewis structure to teach the basic concepts of chemical bonds. In addition, valence shell electron pair repulsion (VSEPR) theory developed based on Lewis theory can be used to intuitively pre-dict the 3D molecular structure of simple compounds.

The establishment of quantum mechanics accelerated the development of chemical bond the-ories. Valence bond theory, molecular orbital theory, hybrid orbital theory, and density func-tional theory are important theoretical methods to study chemical bonds based on quantum mechanics. As computers are becoming more and more powerful, software applications based on these theories are used routinely by chemists to study molecular structures. For example, chemists could use computer to simulate the breaking and formation of chemical bonds, pro-viding theoretical explanation and reference to experiments.

Chemical Bonds–Foundation of All Chemical Structures

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14 History

Li Be B C N O

O

F

F F O OC

H

H H

H

N

H

H H

H

H

Lewis’s chemical bonding theory. In 1916, Lewis proposed a chemical bonding theory based on Bohr’s atomic model. In order to facilitate understanding, he placed all outmost shell electrons on each vertex of a cube. A stable atomic structure is obtained when all vertices are occupied or unoccupied. A Li atom with only one electron on the outmost shell prefers to donate it to a F atom that has seven elec-trons on the outmost shell. Then the Li atom become Li+ion while F atom changes to F-ion with com-pletely filled outmost shell. These two types of ions form a stable compound, LiF. Similarly, an O atom with 6 outmost shell electrons need to combine with two Li atoms, each of which should transfer one electron to the O atom and form the ionic compound of Li2O. In covalent compounds, atoms will share one edge of the cube, e.g. two F atoms forming a single bond, or share one face of the cube, e.g. two O atoms forming a double bond. By doing this, all atoms reach its stable configuration. In one of his pa-pers published in 1916, Lewis also gave a representation of electron configuration that used black dots surround element symbols to manifest the outmost shell electrons (blue dots in the above figure). This configuration was called “Lewis structure”, which has been widely used as an effective tool to explain chemical bonding in many chemistry textbooks. [Figure reference: Lewis, G. N. J. Am. Chem. Soc. 38, 762 (1916)]

Lithium Carbon Nitrogen Oxygen Fluorine

Fluorine molecule Oxygen molecule Methane molecule Ammonia molecule Water molecule

Beryllium Boron

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15Chemical Bonds

AB2

AB5

AB3

AB6

AB4

AB6

Valence-shell electron-pair repulsion (VSEPR) model. Based on Lewis’s chemical bonding theory, Nevil Sidgwick et al.developed a valence-shell electron-pair repulsion theory, which is able to predict the 3D structure of simple molecules by considering the repulsion of electron pairs. For instance, the repulsion among four electron pairs inside methane molecules results in the most stable tetrahedral structure. The carbon atom sits at the center of the tetrahedron while four hydrogen atoms are at four vertices. The above image includes some of the simple three-dimensional structures according to the VSEPR theory. [Figure reference:Sidgwick, N. V. and Powell, H. M. Proc. R. Soc. Lond. A 176, 153 (1940)]

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16 History

Silicon crystal structure

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17Crystal Structure

Early study of crystallography mainly focused on the external shape and symmetry of macro-scopic crystals. By carefully measuring the angles between different crystal surfaces, the sym-metry, which is an important basis for crystal classification at that time, can be determined.

At the end of the 18th century, Rene Just Haüy mathematically related the macroscopic shape of crystal to its microscopic periodicity for the first time. In 1781, Haüy accidentally broke a piece of calcium carbonate crystal. Surprisingly, he discovered unexpected tiny rhombohedra from shattered crystal pieces. From this accident and proceeding systematic research of crys-tal cutting, Haüy concluded that “crystal” is the ordered arrangement of micro constituent molecules and developed the mathematical theory to relate them. The Haüy’s “constituent molecules” has a different notion to the modern molecules. The constituent molecules are actually micro geometrical shapes, such as parallelepipeds. Different crystals are composed of different constituent molecules.

Laue’s X-Ray diffraction experiment in 1902 is a great breakthrough in crystallography. Be-fore this experiment,scientists could only guess what the structure inside a crystal was. Sir William Henry Bragg and Sir William Henry Bragg established the accurate analysis of the arrangement of atoms in crystal shortly after Laue’s work. The determination of structure is a prerequisite to understand physical and chemical properties of materials. For instance, un-derstanding the crystal structure of semiconductors is the foundation to study their electrical properties. The theory of semiconductors as well as the accurate control of semiconductor processing directly lead to the birth of computer and information revolution. In addition, the structural analysis of small organic molecules and biomacromolecules by X-Ray diffraction promotes our understanding to the 3D structure of molecules. Particularly, the structural de-termination of biomacromolecules, such as proteins, by X-Ray diffraction technology paves a possible way for scientists to explore the secret of life.

Crystal Structure–From Macroscopic Geometry to Atomic Arrangement

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18 History

Corpuscular theory of crystals.After Robert Hooke observed tiny crystals with regular-shaped faces under his microscope, he postulated that crystals were composed of identical spherical corpuscles. The ordered arrangement of these spheres gave rise to regular crystal faces. For example, three spheres can form equilateral triangles, while four can form rhombuses, and five can form isosceles trapezoids. Hooke also claimed that four spheres can form a tetrahedron, but he did not describe other possible three-di-mensional structures. Wollaston further developed Hooke’s theory (upright figure). In a paper published in 1897, he analyzed the packing of spherical,ellipsoidal corpuscles, and corpuscles with different sizes. [Figure reference:Hooke, R. Micrographia (1665). Wollaston, W. H. Philos. Trans. R. Soc. Lond. 8, 527 (1897)]

3 4 5 6

7 12 4

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19Crystal Structure

Haüy’s theory of crystals.Haüy is recognized as the father of modern crystallography. He believes that crystals are made up of orderly arranged “integrant molecules” and different crystals should have different “integrant molecules”. Haüy’s integrant molecule is similar to the concept of unit cell in crys-tallography. Using his laws of decrement, he explained why the same crystal could occur in different geometries. For example, a cube-shaped crystal with cubic integrant molecules (green color in the above figure) can be transformed to a dodecahedral crystal with rhombic faces. To do this, we can add new lay-ers of integrant molecules on each surface of the cubic crystal (gray color in the above figure) but each time diminish one line of molecules from each side. If we just diminish one molecule for two opposite sides and diminish two molecules for the other two sides when each time we overlay a layer of integrant molecules, the cubic crystal will be transformed to a dodecahedral crystal with pentagonal faces (not an orthogonal dodecahedron). In fact, Haüy’s laws were very advanced at that time and tightly connected to the lattice planes in modern crystallography.[Figure reference:Haüy, R. J. Traité de Minéralogie (1801)]

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20 History

Crystal structure similar as sodium chloride Crystal structure similar as cesium chloride

Barlow’s prediction of crystal structures. Scientists predicted some possible crystal structures before the invention of X-ray diffraction method. One good example is a series of crystal structures pub-lished by Barlow in 1897. For a crystal that only consisted of one type of atoms,he regarded all atoms as solid spheres. As a result, the crystal structure was equivalent to the closest packing of such solid spheres. (There are actually two types of closest packing but only one of them is shown in the above figure.) Barlow further analyzed the closest packing of two types of spheres and correctly predicted the structures similar asNaCl and CsCl. [Figure reference:Barlow, W. Sci. Proc. R. Dublin Soc.103, 51 (1897)]

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